A B C D E F G H I J K L M N O P Q R S T U V W X _

## A

abortOnFirstJobFailure() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a boolean indicating whether seqexec trips on the first job failure.
abortOnFristJobFailure() - Method in class edu.isi.pegasus.planner.cluster.aggregator.MPIExec
  Returns a boolean indicating whether to fail the aggregated job on detecting the first failure during execution of constituent jobs.
abortOnFristJobFailure() - Method in class edu.isi.pegasus.planner.cluster.aggregator.SeqExec
  Returns a boolean indicating whether to fail the aggregated job on detecting the first failure during execution of constituent jobs.
abortOnFristJobFailure() - Method in interface edu.isi.pegasus.planner.cluster.JobAggregator
  Returns a boolean indicating whether to fail the aggregated job on detecting the first failure during execution of constituent jobs.
Abstract - Class in edu.isi.pegasus.common.credential.impl
  An abstract base class to be used by other CredentialHandler implementations.
Abstract() - Constructor for class edu.isi.pegasus.common.credential.impl.Abstract
  The default constructor.
Abstract - Class in edu.isi.pegasus.planner.catalog.site.impl.old
  An abstract implementation of the PoolInfoProvider.
Abstract() - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.old.Abstract
Abstract - Class in edu.isi.pegasus.planner.catalog.transformation.impl
  An abstract base class that provides useful methods for all the TransformationCatalog Implementations to use.
Abstract() - Constructor for class edu.isi.pegasus.planner.catalog.transformation.impl.Abstract
Abstract - Class in edu.isi.pegasus.planner.cluster
  An abstract clusterer that the other clusterers can extend.
Abstract() - Constructor for class edu.isi.pegasus.planner.cluster.Abstract
  The Abstract constructor.
Abstract - Class in edu.isi.pegasus.planner.cluster.aggregator
  An abstract implementation of the JobAggregator interface, which the other implementations can choose to extend.
Abstract() - Constructor for class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  The default constructor.
Abstract - Class in edu.isi.pegasus.planner.code.generator
  An Abstract Base class implementing the CodeGenerator interface.
Abstract() - Constructor for class edu.isi.pegasus.planner.code.generator.Abstract
Abstract - Class in edu.isi.pegasus.planner.code.generator.condor.style
  An abstract implementation of the CondorStyle interface.
Abstract() - Constructor for class edu.isi.pegasus.planner.code.generator.condor.style.Abstract
  The default constructor.
Abstract - Class in edu.isi.pegasus.planner.namespace.aggregator
  An abstract implementation of the Profile Aggregators.
Abstract() - Constructor for class edu.isi.pegasus.planner.namespace.aggregator.Abstract
Abstract - Class in edu.isi.pegasus.planner.selector.site
  The Abstract Site selector.
Abstract() - Constructor for class edu.isi.pegasus.planner.selector.site.Abstract
Abstract - Class in edu.isi.pegasus.planner.transfer.implementation
  An abstract implementation that implements some of the common functions in the Implementation Interface that are required by all the implementations.
Abstract(PegasusBag) - Constructor for class edu.isi.pegasus.planner.transfer.implementation.Abstract
  The overloaded constructor, that is called by the Factory to load the class.
AbstractFileFactoryBasedMapper - Class in edu.isi.pegasus.planner.transfer.mapper.impl
  The abstract class that serves as the base class for the File Factory based mappers.
AbstractFileFactoryBasedMapper() - Constructor for class edu.isi.pegasus.planner.transfer.mapper.impl.AbstractFileFactoryBasedMapper
  The default constructor.
AbstractJob - Class in edu.isi.pegasus.planner.dax
AbstractJob() - Constructor for class edu.isi.pegasus.planner.dax.AbstractJob
AbstractJob(AbstractJob) - Constructor for class edu.isi.pegasus.planner.dax.AbstractJob
  Copy constructor
AbstractLogFormatter - Class in edu.isi.pegasus.common.logging.format
  The abstract formatter that implements all of the functions except the addEvent function
AbstractLogFormatter() - Constructor for class edu.isi.pegasus.common.logging.format.AbstractLogFormatter
  The default constructor.
AbstractMultipleFTPerXFERJob - Class in edu.isi.pegasus.planner.transfer.implementation
  An abstract implementation for implementations that can handle multiple file transfers in a single file transfer job.
AbstractMultipleFTPerXFERJob(PegasusBag) - Constructor for class edu.isi.pegasus.planner.transfer.implementation.AbstractMultipleFTPerXFERJob
  The overloaded constructor, that is called by the Factory to load the class.
AbstractPerJob - Class in edu.isi.pegasus.planner.selector.site
  The base class for the site selectors that want to map one job at a time.
AbstractPerJob() - Constructor for class edu.isi.pegasus.planner.selector.site.AbstractPerJob
AbstractRefiner - Class in edu.isi.pegasus.planner.transfer
  An abstract implementation that implements some of the common functions in the Refiner Interface and member variables that are required by all the refiners.
AbstractRefiner(ADag, PegasusBag) - Constructor for class edu.isi.pegasus.planner.transfer.AbstractRefiner
  The overloaded constructor.
AbstractSingleFTPerXFERJob - Class in edu.isi.pegasus.planner.transfer.implementation
  An abstract implementation for implementations that can handle only a single file transfer in a single file transfer job.
AbstractSingleFTPerXFERJob(PegasusBag) - Constructor for class edu.isi.pegasus.planner.transfer.implementation.AbstractSingleFTPerXFERJob
  The overloaded constructor, that is called by the Factory to load the class.
AbstractSiteData - Class in edu.isi.pegasus.planner.catalog.site.classes
  The abstract data class for Site classes.
AbstractSiteData() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.AbstractSiteData
AbstractStrategy - Class in edu.isi.pegasus.planner.refiner.createdir
  The interface that defines how the cleanup job is invoked and created.
AbstractStrategy() - Constructor for class edu.isi.pegasus.planner.refiner.createdir.AbstractStrategy
AbstractXMLPrintVisitor - Class in edu.isi.pegasus.planner.catalog.site.classes
  The base class to be used by the various visitor implementors for displaying the Site Catalog in different XML formats
AbstractXMLPrintVisitor() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.AbstractXMLPrintVisitor
accept(SiteDataVisitor) - Method in class edu.isi.pegasus.planner.catalog.site.classes.AbstractSiteData
  Accept method for the SiteData classes that accepts a visitor
accept(SiteDataVisitor) - Method in class edu.isi.pegasus.planner.catalog.site.classes.Connection
accept(SiteDataVisitor) - Method in class edu.isi.pegasus.planner.catalog.site.classes.Directory
  Accept method for the SiteData classes that accepts a visitor
accept(SiteDataVisitor) - Method in class edu.isi.pegasus.planner.catalog.site.classes.FileServer
accept(SiteDataVisitor) - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Accepts a Site Data Visitor
accept(SiteDataVisitor) - Method in class edu.isi.pegasus.planner.catalog.site.classes.HeadNodeFS
  Accepts the visitor and calls visit method on the visitor accordingly
accept(SiteDataVisitor) - Method in class edu.isi.pegasus.planner.catalog.site.classes.InternalMountPoint
accept(SiteDataVisitor) - Method in class edu.isi.pegasus.planner.catalog.site.classes.LocalDirectory
  Accepts the visitor and calls visit method on the visitor accordingly
accept(SiteDataVisitor) - Method in class edu.isi.pegasus.planner.catalog.site.classes.ReplicaCatalog
  Accept the visitor
accept(SiteDataVisitor) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SharedDirectory
  Accepts the visitor and calls visit method on the visitor accordingly
accept(SiteDataVisitor) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Accept method for the visitor interface
accept(SiteDataVisitor) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Accept method for the visitor interface
accept(SiteDataVisitor) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  Accept method for the SiteStore object
accept(SiteDataVisitor) - Method in class edu.isi.pegasus.planner.catalog.site.classes.StorageType
accept(SiteDataVisitor) - Method in class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeFS
  Accepts the visitor and calls visit method on the visitor accordingly
accept(SiteDataVisitor) - Method in class edu.isi.pegasus.planner.catalog.site.classes.WorkerSharedDirectory
accept(File, String) - Method in class edu.isi.pegasus.planner.client.SubmitDirectoryFilenameFilter
  Tests if a specified file should be included in a file list.
accept(File, String) - Method in class edu.isi.pegasus.planner.common.RunDirectoryFilenameFilter
  Tests if a specified file should be included in a file list.
accept(File, String) - Method in class edu.isi.pegasus.planner.parser.pdax.RunDirectoryFilenameFilter
  Tests if a specified file should be included in a file list.
acceptRequest(Object) - Method in class edu.isi.pegasus.planner.refiner.ThreadPool
  Accepts an authentication request, that has to be serviced.
actionmap - Static variable in class edu.isi.pegasus.common.util.Separator
  Maps the action associated with a state and a character class.
actionmap2 - Static variable in class edu.isi.pegasus.common.util.Separator
  Maps the action associated with a state and char class.
ACTUAL_FINISH_TIME - Static variable in class edu.isi.pegasus.planner.selector.site.heft.HeftBag
  The constant to be passed to the accessor functions to get or set the actual end time for a job.
ACTUAL_START_TIME - Static variable in class edu.isi.pegasus.planner.selector.site.heft.HeftBag
  The constant to be passed to the accessor functions to get or set the actual start time for a job.
ADag - Class in edu.isi.pegasus.planner.classes
  This class object contains the info about a Dag.
ADag() - Constructor for class edu.isi.pegasus.planner.classes.ADag
  Initialises the class member variables.
ADAG - Class in edu.isi.pegasus.planner.dax
  This class provides the Java API to create DAX files. The DAX XML SCHEMA is available at http://pegasus.isi.edu/schema/dax-3.3.xsd and documentation available at http://pegasus.isi.edu/wms/docs/schemas/dax-3.3/dax-3.3.html The DAX consists of 6 parts the first 4 are optional and the last is optional.
ADAG(String) - Constructor for class edu.isi.pegasus.planner.dax.ADAG
  The Simple constructor for the DAX object
ADAG(String, int, int) - Constructor for class edu.isi.pegasus.planner.dax.ADAG
  DAX Constructor
Adapter - Class in edu.isi.pegasus.planner.catalog.site.classes
  An adapter class that converts the SiteCatalogEntry class to older supported formats and vice-versa
Adapter() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.Adapter
add(String, String) - Method in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
  Add a string.
add(String, int) - Method in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
  Add an int.
add(String, long) - Method in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
  Add a long.
add(String, float) - Method in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
  Add a float.
add(String, double) - Method in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
  Add a double.
add(String, String) - Method in interface edu.isi.pegasus.common.logging.Event
  Add to the log message.
add(String) - Method in class edu.isi.pegasus.common.logging.format.AbstractLogFormatter
  Add to the log message with just a value.
add(String, String) - Method in class edu.isi.pegasus.common.logging.format.AbstractLogFormatter
  Add to the log message for the event on the top.
add(String, String) - Method in class edu.isi.pegasus.common.logging.format.NetloggerEvent
  Add to the log message.
add(String) - Method in class edu.isi.pegasus.common.logging.format.Simple
  Add to the log message with just a value.
add(String, String) - Method in class edu.isi.pegasus.common.logging.format.SimpleEvent
  Add to the log message.
add(String) - Method in interface edu.isi.pegasus.common.logging.LogFormatter
  Add to the log message with just a value.
add(String, String) - Method in interface edu.isi.pegasus.common.logging.LogFormatter
  Add to the log message.
add(String) - Method in class edu.isi.pegasus.common.logging.LogManager
  Add to the internal log buffer message a value with the default key.
add(String, String) - Method in class edu.isi.pegasus.common.logging.LogManager
  Add to the internal log buffer message a value with the key oassed The buffer is logged later when the log() method is called.
add(String, SiteInfo) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.PoolConfig
  Adds a SiteInfo object to the container.
add(PoolConfig) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.PoolConfig
  Adds all the sites in a controlled fashion, to the existing map containing information about the sites.
add(PoolConfig, boolean) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.PoolConfig
  Adds all the sites in a controlled fashion, to the existing map containing information about the sites.
add(Job) - Method in class edu.isi.pegasus.planner.classes.ADag
  This adds a new job to the ADAG object.
add(Job) - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Adds a job to the aggregated job.
add(Invoke) - Method in class edu.isi.pegasus.planner.classes.Notifications
  Adds a Invoke object correpsonding to a notification.
add(Object, Object) - Method in class edu.isi.pegasus.planner.classes.PegasusBag
  Adds an object to the underlying bag corresponding to a particular key.
add(Map) - Method in class edu.isi.pegasus.planner.classes.ReplicaStore
  Adds ReplicaCatalogEntries into the store.
add(String, Collection) - Method in class edu.isi.pegasus.planner.classes.ReplicaStore
  Adds replica catalog entries into the store.
add(ReplicaLocation) - Method in class edu.isi.pegasus.planner.classes.ReplicaStore
  Adds replica catalog entries into the store.
add - Variable in class edu.isi.pegasus.planner.client.TCClient
add(Object, Object) - Method in interface edu.isi.pegasus.planner.partitioner.graph.Bag
  Adds an object to the underlying bag corresponding to a particular key.
add(Object, Object) - Method in class edu.isi.pegasus.planner.partitioner.graph.LabelBag
  Adds an object to the underlying bag corresponding to a particular key.
add(String) - Method in class edu.isi.pegasus.planner.provenance.pasoa.producer.InMemory
  Adds to the internal XML representation.
add(String) - Method in interface edu.isi.pegasus.planner.provenance.pasoa.XMLProducer
  Adds an XML fragment to the internal XML store
add(Node) - Method in class edu.isi.pegasus.planner.provisioner.OccupationDiagram
  Add tasks into the occupation diagram.
add(Object, Object) - Method in class edu.isi.pegasus.planner.refiner.DataReuseEngine.BooleanBag
  Ignores the key and only adds the value .
add(boolean) - Method in class edu.isi.pegasus.planner.refiner.DataReuseEngine.BooleanBag
  Adds a boolean value to the bag
add(Object, Object) - Method in class edu.isi.pegasus.planner.selector.site.heft.HeftBag
  Adds an object to the underlying bag corresponding to a particular key.
add(String) - Method in class edu.isi.pegasus.planner.transfer.refiner.Chain.TransferChain
  Adds to the end of the chain.
addAbstractJob(AbstractJob) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add AbstractJob to the DAX
addAbstractJobs(List<AbstractJob>) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add AbstractJobs to the DAX
addAlias(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.ReplicaCatalog
  Adds an alias site handle.
addAll(Notifications) - Method in class edu.isi.pegasus.planner.classes.Notifications
  Adds all the notifications passed to the underlying container.
addAll(Invoke.WHEN, Collection<Invoke>) - Method in class edu.isi.pegasus.planner.classes.Notifications
  Convenience method at add all the notifications corresponding to a particular event
addArgument(String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add a string argument to the argument List.
addArgument(File) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add a file object to the argument List.
addArgument(File[]) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add a Array of `File` objects to the argument list.
addArgument(List<File>) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add a List of `File` objects to the argument list.
addArgument(File[], String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add a Array of `File` objects to the argument list.
addArgument(List<File>, String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add a List of `File` objects to the argument list.
addArgument(String, String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add a argument key and value to the argument List.
addArgument(String, String, String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add a argument key and value to the argument List.
  The argkey and argvalue are seperated by argdelimiter.
  Example addArgument("-p","0","=") will result in the argument being added as -p=0
  Multiple calls to addArgument results in the arguments being separated by space.
addArgument(String, File) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add a argument key and File value to the argument List.
  The argkey and argvalue are seperated by space.
  Example addArgument("-i",new File("f.a")) will result in the argument being added as -i <file name="f.a">
  Multiple calls to addArgument results in the arguments being separated by space.
addArgument(String, File, String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add a argument key and File value to the argument List.
  The argkey and argvalue are separated by the argdelimiter.
  Example addArgument("-i",new File("f.a"),"=") will result in the argument being added as -i=<file name="f.a">
  Multiple calls to addArgument results in the arguments being separated by space.
addArgument(String, File[]) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add a argument key and an array of Files to the argument List.
  The argkey and argvalue are separated space.
  The files are separated by a space
  Example:
  File[] files = {new File("f.a1"), new File("f.a2")};
  job.addArgument("-i",files)
  will result in the argument being added as -i <file name="f.a1"> <file name="f.a2">
  Multiple calls to addArgument results in the arguments being separated by space.
addArgument(String, List<File>) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add a argument key and a List of Files to the argument List.
  The argkey and argvalue are separated space.
  The files are separated by a space
  Example:
  List<File> files = new LinkedList<File>();
  files.add(new File("f.a1"));
  files.add(new File("f.a2"));
  job.addArgument("-i",files)
  will result in the argument being added as -i <file name="f.a1"> <file name="f.a2">
  Multiple calls to addArgument results in the arguments being separated by space.
addArgument(String, File[], String, String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add a argument key and an array of Files to the argument List.
  The argkey and argvalue are separated by the argdelimiter.
  The files are separated by a filedelimiter
  Example:
  File[] files = {new File("f.a1"), new File("f.a2")};
  job.addArgument("-i",files,"=",",")
  will result in the argument being added as -i=<file name="f.a1">,<file name="f.a2">
  Multiple calls to addArgument results in the arguments being separated by space.
addArgument(String, List<File>, String, String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add a argument key and a List of Files to the argument List.
  The argkey and argvalue are separated by the argdelimiter.
  The files are separated by a filedelimter
  Example:
  List<File> files = new LinkedList<File>();
  files.add(new File("f.a1"));
  files.add(new File("f.a2"));
  job.addArgument("-i",files,"=",",")
  will result in the argument being added as -i=<file name="f.a1">,<file name="f.a2">
  Multiple calls to addArgument results in the arguments being separated by space.
addArgument(String) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser3.Arguments
  Adds text to the arguments string
addArgument(ReplicaLocation) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser3.Arguments
  Adds filename to the arguments
addArgument(File) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser3.Arguments
  Adds a file name to the argument string
addAttribute(String, Object) - Method in class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  Adds an attribute to the set of attributes.
addAttribute(Map) - Method in class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  Adds attributes to the existing attributes.
addAttribute(String, String) - Method in class edu.isi.pegasus.planner.invocation.MachineInfo
  Adds an attribute.
addAttributes(List, List) - Method in class edu.isi.pegasus.planner.invocation.MachineInfo
  Add multiple attributes to the machine info element.
addBulk() - Method in class edu.isi.pegasus.planner.catalog.transformation.client.TCAdd
  Adds multiple entries into the TC.
addChild(GraphNode) - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  Adds a child to end of the child list.
addCleanupJobs(Graph) - Method in interface edu.isi.pegasus.planner.refiner.cleanup.CleanupStrategy
  Adds cleanup jobs to the workflow.
addCleanupJobs(Graph) - Method in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  Adds cleanup jobs to the workflow.
addCleanUpJobs(String, Set, Graph) - Method in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  Adds cleanup jobs for the workflow scheduled to a particular site a breadth first search strategy is implemented based on the depth of the job in the workflow
addCleanupJobs(ADag) - Method in class edu.isi.pegasus.planner.refiner.CleanupEngine
  Adds the cleanup jobs in the workflow that removes the files staged to the remote site.
addCleanupNodesForWorkerPackage(ADag) - Method in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Adds cleanup nodes in the workflow for sites specified.
addCleanupPostScript(Job, List) - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Adds a /bin/rm post constituentJob to kickstart that removes the files passed.
addConnection(Connection) - Method in class edu.isi.pegasus.planner.catalog.site.classes.ReplicaCatalog
  Adds a connection parameter
addCreateDirectoryNodes(ADag) - Method in class edu.isi.pegasus.planner.refiner.createdir.HourGlass
  It modifies the concrete dag passed in the constructor and adds the create random directory nodes to it at the root level.
addCreateDirectoryNodes(ADag) - Method in class edu.isi.pegasus.planner.refiner.createdir.Minimal
  Modifies the workflow to add create directory nodes.
addCreateDirectoryNodes(ADag, Set<String>) - Method in class edu.isi.pegasus.planner.refiner.createdir.Minimal
  Adds create dir nodes to the workflow.
addCreateDirectoryNodes(ADag) - Method in interface edu.isi.pegasus.planner.refiner.createdir.Strategy
  Modifies the workflow to add create directory nodes.
addCreateDirectoryNodes(ADag) - Method in class edu.isi.pegasus.planner.refiner.createdir.Tentacles
  Modifies the workflow to add create directory nodes.
addCreateDirectoryNodes(ADag) - Method in class edu.isi.pegasus.planner.refiner.CreateDirectory
  It modifies the concrete dag passed in the constructor and adds the create random directory nodes to it at the root level.
addCredentialType(String, String) - Method in class edu.isi.pegasus.planner.classes.Job
  Looks at a URL to determine whether a credential should be associated with a job or not.
addCredentialType(String, CredentialHandler.TYPE) - Method in class edu.isi.pegasus.planner.classes.Job
  Adds a type of credential that will be required by a job.
addDAG(DAG) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add a DAG job to the DAX
addDAGs(List<DAG>) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add multiple DAG jobs to the DAX
addDataDependencies() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a boolean indicating whether to automatically add edges as a result of underlying data dependecnies between jobs.
addDataDependencies() - Method in class edu.isi.pegasus.planner.parser.dax.DAX2CDAG
  Goes through the ADag and computes any data dependencies.
addDAX(DAX) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add a DAX job to the DAX
addDAXs(List<DAX>) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add multiple DAX jobs to the DAX
addDefaultTCEntry(String, String, SysInfo, boolean, String, String) - Method in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Returns a default TC entry to be used in case entry is not found in the transformation catalog.
addDefaultTCEntryForPegasusWebsite(String, String) - Method in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Returns a default TC entry for the pegasus site.
addDependantFile(PegasusFile) - Method in class edu.isi.pegasus.planner.classes.CompoundTransformation
  Adds a dependant file.
addDependency(String, String) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add a parent child dependency between two jobs,dax,dag
addDependency(AbstractJob, AbstractJob) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add a parent child dependency between two jobs,dax,dag
addDependency(String, String, String) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add a parent child dependency with a dependency label
addDependency(AbstractJob, AbstractJob, String) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add a parent child dependency with a dependency label
addDependency(Job) - Method in class edu.isi.pegasus.planner.refiner.createdir.Minimal
addDestination(NameValue) - Method in class edu.isi.pegasus.planner.classes.FileTransfer
  Adds a destination URL for the transfer.
addDestination(String, String) - Method in class edu.isi.pegasus.planner.classes.FileTransfer
  Adds a destination URL for the transfer.
addDirectory(SiteCatalogEntry3, Directory) - Static method in class edu.isi.pegasus.planner.catalog.site.classes.Adapter
  Adds a directory to the site catalog entry object.
addDirectory(Directory) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Adds a directory internally.
addEdge(String, String) - Method in class edu.isi.pegasus.planner.classes.ADag
  Adds an edge between two already existing nodes in the graph.
addEdge(GraphNode, GraphNode) - Method in class edu.isi.pegasus.planner.classes.ADag
  Adds an edge between two already existing nodes in the graph.
addEdge(String, String) - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Adds an edge between two already existing nodes in the graph.
addEdge(GraphNode, GraphNode) - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Adds an edge between two already existing nodes in the graph.
addEdge(String, String) - Method in interface edu.isi.pegasus.planner.partitioner.graph.Graph
  Adds an edge between two already existing nodes in the graph.
addEdge(GraphNode, GraphNode) - Method in interface edu.isi.pegasus.planner.partitioner.graph.Graph
  Adds an edge between two already existing nodes in the graph.
addEdge(String, String) - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph
  Adds an edge between two already existing nodes in the graph.
addEdge(GraphNode, GraphNode) - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph
  Adds an edge between two already existing nodes in the graph.
addEdges(String, List<String>) - Method in class edu.isi.pegasus.planner.classes.ADag
  A convenience method that allows for bulk addition of edges between already existing nodes in the graph.
addEdges(String, List) - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  A convenience method that allows for bulk addition of edges between already existing nodes in the graph.
addEdges(String, List<String>) - Method in interface edu.isi.pegasus.planner.partitioner.graph.Graph
  A convenience method that allows for bulk addition of edges between already existing nodes in the graph.
addEdges(String, List) - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph
  A convenience method that allows for bulk addition of edges between already existing nodes in the graph.
addEntry(SiteCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  Adds a site catalog entry to the store.
addEntry(TransformationCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.TransformationStore
  Adds an entry into the store.
addEntry() - Method in class edu.isi.pegasus.planner.catalog.transformation.client.TCAdd
  Adds a single entry into the TC.
addEntry(EnvEntry) - Method in class edu.isi.pegasus.planner.invocation.Environment
  Adds an environment entry, effectively a key value pair, to the current environment settings.
addEntry(String, String) - Method in class edu.isi.pegasus.planner.invocation.Environment
  Adds an environment entry, effectively a key value pair, to the current environment settings.
addEvent(String, String, String) - Method in class edu.isi.pegasus.common.logging.format.AbstractLogFormatter
  Adds the event that is to be associated with the log messages onto an internal stack
addEvent(String, String, String) - Method in class edu.isi.pegasus.common.logging.format.Netlogger
  Adds the event that is to be associated with the log messages onto an internal stack
addEvent(String, Map<String, String>) - Method in class edu.isi.pegasus.common.logging.format.Netlogger
  Adds the event that is to be associated with the log messages onto an internal stack
addEvent(String, String, String) - Method in class edu.isi.pegasus.common.logging.format.Simple
  Adds the event that is to be associated with the log messages onto an internal stack
addEvent(String, Map<String, String>) - Method in class edu.isi.pegasus.common.logging.format.Simple
  Adds the event that is to be associated with the log messages onto an internal stack
addEvent(String, String, String) - Method in interface edu.isi.pegasus.common.logging.LogFormatter
  Adds the event that is to be associated with the log messages onto an internal stack
addEvent(String, Map<String, String>) - Method in interface edu.isi.pegasus.common.logging.LogFormatter
  Adds the event that is to be associated with the log messages onto an internal stack
addExecutable(Executable) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add Executable to the DAX
addExecutables(List<Executable>) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add Multiple Executable objects to the DAX
addFile(File) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add a RC File object to the top of the DAX.
addFiles(List<File>) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add Files to the RC Section on top of the DAX
addFileServer(FileServer) - Method in class edu.isi.pegasus.planner.catalog.site.classes.DirectoryLayout
  Adds a FileServer that can access this directory.
addFilesForTransfer(Collection<String>, String) - Method in class edu.isi.pegasus.planner.namespace.Condor
  Adds multiple files that are to be transferred from the submit host via the Condor File Transfer Mechanism.
addFilesForTransfer(String, String) - Method in class edu.isi.pegasus.planner.namespace.Condor
  Adds an input file that is to be transferred from the submit host via the Condor File Transfer Mechanism.
addGridGateway(GridGateway) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Add a GridGateway to the site.
addGridGateway(GridGateway) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Add a GridGateway to the site.
addIn(Edge) - Method in class edu.isi.pegasus.planner.provisioner.Node
  add a data dependency edge to this task
addInputFile(PegasusFile) - Method in class edu.isi.pegasus.planner.classes.Job
  Adds an input file to the underlying collection of input files associated with the job.
addInterSiteTXNodes(Job, Collection, boolean) - Method in interface edu.isi.pegasus.planner.transfer.Refiner
  Adds the inter pool transfer nodes that are required for transferring the output files of the parents to the jobs execution site.
addInterSiteTXNodes(Job, Collection, boolean) - Method in class edu.isi.pegasus.planner.transfer.refiner.Basic
  Adds the inter pool transfer nodes that are required for transferring the output files of the parents to the jobs execution site.
addInterSiteTXNodes(Job, Collection, boolean) - Method in class edu.isi.pegasus.planner.transfer.refiner.Empty
  Adds the inter pool transfer nodes that are required for transferring the output files of the parents to the jobs execution site.
addInvoke(Invoke.WHEN, String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add Notification to the job
addInvoke(Invoke) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add notification to the job
addInvoke(Invoke.WHEN, String) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add a Notification for this Workflow
addInvoke(Invoke) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add a Notification for this Workflow
addInvoke(Invoke.WHEN, String) - Method in class edu.isi.pegasus.planner.dax.Executable
  Add a Notification for this Executable same as addNotification
addInvoke(Invoke) - Method in class edu.isi.pegasus.planner.dax.Executable
  Add a Notification for this Executable Same as add Notification
addInvoke(Invoke.WHEN, String) - Method in class edu.isi.pegasus.planner.dax.Transformation
  Add a Notification for this Transformation
addInvoke(Invoke) - Method in class edu.isi.pegasus.planner.dax.Transformation
  Add a Notification for this Transformation
addInvokes(List<Invoke>) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add Notifications to the job
addInvokes(List<Invoke>) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add a List of Notifications for this Workflow
addInvokes(List<Invoke>) - Method in class edu.isi.pegasus.planner.dax.Executable
  Add a List of Notifications for this Executable Same as addNotifications
addInvokes(List<Invoke>) - Method in class edu.isi.pegasus.planner.dax.Transformation
  Add a List of Notifications for this Transformation
addIPFileForTransfer(Collection<String>) - Method in class edu.isi.pegasus.planner.namespace.Condor
  Adds multiple files that are to be transferred from the submit host via the Condor File Transfer Mechanism.
addIPFileForTransfer(String) - Method in class edu.isi.pegasus.planner.namespace.Condor
  Adds an input file that is to be transferred from the submit host via the Condor File Transfer Mechanism.
addItem(Object, String, boolean) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Helper function to assemble various pieces.
addJob(Job) - Method in class edu.isi.pegasus.planner.cluster.Abstract
  Adds jobs to the internal map of jobs that is maintained by the clusterer.
addJob(Job) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add Job to the DAX
addJob(Job) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor: Appends a job to the list of jobs.
addJob(int, Job) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor: Inserts a Job into a specific position of the job list.
addJob(Job) - Method in interface edu.isi.pegasus.planner.transfer.Refiner
  Add a new job to the workflow being refined.
addJob(Job) - Method in class edu.isi.pegasus.planner.transfer.refiner.Basic
  Add a new job to the workflow being refined.
addJob(Job) - Method in class edu.isi.pegasus.planner.transfer.refiner.Empty
  Add a new job to the workflow being refined.
addJobs(List<Job>) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add multiple Jobs to the DAX
addLFNProfile(String, String, String, List) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Add additional profile to a logical transformation .
addLFNProfile(String, String, String, List) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Add additional profile to a logical transformation .
addLFNProfile(String, String, String, List) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Add additional profile to a logical transformation .
addLFNProfile(String, String, String, List) - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Add additional profile to a logical transformation .
addLineToText(StringBuffer, String, String, String, String) - Static method in class edu.isi.pegasus.planner.catalog.transformation.client.TCFormatUtility
  Convenience method to add a line to the internal textual representation.
addList(String, List) - Method in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
addLogicalTr(String, String, String) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Adds a logical entry to the logicaltx table
addMachineInfo(MachineInfo) - Method in class edu.isi.pegasus.planner.invocation.MachineSpecific
  Add a `MachineInfo` element.
addMap(String, Map) - Method in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
  Add a Map to the buffer.
addMetaData(String, String, String) - Method in class edu.isi.pegasus.planner.dax.CatalogType
  Add a Metadata entry for the Catalog object
addMetaData(MetaData) - Method in class edu.isi.pegasus.planner.dax.CatalogType
  Add a `MetaData` object for the Catalog object
addMetaData(List<MetaData>) - Method in class edu.isi.pegasus.planner.dax.CatalogType
  Add a List of `MetaData` objects to the Catalog entry object
addMsg(String) - Method in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
  Add an natural language message to the log message.
addNewRelation(String, String) - Method in class edu.isi.pegasus.planner.classes.ADag
  Adds a new PCRelation pair to the Vector of `PCRelation` pairs.
addNode(GraphNode) - Method in class edu.isi.pegasus.planner.classes.ADag
  Adds a node to the Graph.
addNode(GraphNode) - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Adds a node to the Graph.
addNode(GraphNode) - Method in interface edu.isi.pegasus.planner.partitioner.graph.Graph
  Adds a node to the Graph.
addNode(GraphNode) - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph
  Adds a node to the Graph.
addNode(GraphNode) - Method in class edu.isi.pegasus.planner.partitioner.Partition
  Adds a node to the partition.
addNotification(Invoke) - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Adds a Invoke object correpsonding to a notification.
addNotification(Invoke) - Method in class edu.isi.pegasus.planner.classes.ADag
  Adds a Invoke object corresponding to a notification.
addNotification(Invoke) - Method in class edu.isi.pegasus.planner.classes.CompoundTransformation
  Adds a Invoke object correpsonding to a notification.
addNotification(Invoke) - Method in class edu.isi.pegasus.planner.classes.Job
  Adds a Invoke object correpsonding to a notification.
addNotification(Invoke.WHEN, String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add Notification to the job
addNotification(Invoke) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add notification to the job
addNotification(Invoke.WHEN, String) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add a Notification for this Workflow
addNotification(Invoke) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add a Notification for this Workflow
addNotification(Invoke.WHEN, String) - Method in class edu.isi.pegasus.planner.dax.Executable
  Add a Notification for this Executable same as addInvoke
addNotification(Invoke) - Method in class edu.isi.pegasus.planner.dax.Executable
  Add a Notification for this Executable Same as addInvoke
addNotification(Invoke.WHEN, String) - Method in class edu.isi.pegasus.planner.dax.Transformation
  Add a Notification for this Transformation same as addInvoke()
addNotifications(Notifications) - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Adds all the notifications passed to the underlying container.
addNotifications(Notifications) - Method in class edu.isi.pegasus.planner.classes.ADag
  Adds all the notifications passed to the underlying container.
addNotifications(Notifications) - Method in class edu.isi.pegasus.planner.classes.CompoundTransformation
  Adds all the notifications passed to the underlying container.
addNotifications(TransformationCatalogEntry) - Method in class edu.isi.pegasus.planner.classes.Job
  Adds all the notifications specfied in the TransformationCatalogEntry to the underlying job notifications.
addNotifications(Notifications) - Method in class edu.isi.pegasus.planner.classes.Job
  Adds all the notifications passed to the underlying container.
addNotifications(List<Invoke>) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add Notifications to the job
addNotifications(List<Invoke>) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add a List of Notifications for this Workflow
addNotifications(List<Invoke>) - Method in class edu.isi.pegasus.planner.dax.Executable
  Add a List of Notifications for this Executable.
addNotifications(List<Invoke>) - Method in class edu.isi.pegasus.planner.dax.Transformation
  Add a List of Notifications for this Transformation.
addOPFileForTransfer(Collection<String>) - Method in class edu.isi.pegasus.planner.namespace.Condor
  Adds multiple output files that are to be transferred from the submit host via the Condor File Transfer Mechanism.
addOPFileForTransfer(String) - Method in class edu.isi.pegasus.planner.namespace.Condor
  Adds an output file that is to be transferred from the submit host via the Condor File Transfer Mechanism.
addOut(Edge) - Method in class edu.isi.pegasus.planner.provisioner.Node
  add a data dependency edge from this task
addOutputFile(PegasusFile) - Method in class edu.isi.pegasus.planner.classes.Job
  Adds an output file to the underlying collection of output files associated with the job.
addPair(String, String, String) - Method in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
  Add a key,value pair The result looks like: key = (pairKey, pairValue)
addParent(GraphNode) - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  Adds a parent to end of the parent list.
addParents(String, List) - Method in class edu.isi.pegasus.planner.partitioner.Partition
  Ends up assigning the parents to a particular node.
addPFN(PFN) - Method in class edu.isi.pegasus.planner.classes.ReplicaLocation
  Adds a PFN specified in the DAX to the object
addPFN(ReplicaCatalogEntry) - Method in class edu.isi.pegasus.planner.classes.ReplicaLocation
  Add a PFN and it's attributes.
addPFNProfile(String, TCType, String, List) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Add additional profile to a physical transformation.
addPFNProfile(String, TCType, String, List) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Add additional profile to a physical transformation.
addPFNProfile(String, TCType, String, List) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Add additional profile to a physical transformation.
addPFNProfile(String, TCType, String, List) - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Add additional profile to a physical transformation.
addPFNs(List) - Method in class edu.isi.pegasus.planner.classes.ReplicaLocation
  Add a PFN and it's attributes.
addPhysicalFile(String) - Method in class edu.isi.pegasus.planner.dax.CatalogType
  Add a pfn url to the Catalog
addPhysicalFile(String, String) - Method in class edu.isi.pegasus.planner.dax.CatalogType
  Add a PFN url and a site id to the Catalog
addPhysicalFile(PFN) - Method in class edu.isi.pegasus.planner.dax.CatalogType
  Add a PFN object to the Catalog
addPhysicalFiles(List<PFN>) - Method in class edu.isi.pegasus.planner.dax.CatalogType
  Add a list of PFN objects to the Catalog
addPhysicalTr(String, String, TCType, long) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Adds a physical entry to the physicaltxtable
addProfile(Profile) - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Adds a profile.
addProfile(Profiles.NAMESPACES, String, String) - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Add a profile.
addProfile(String, String, String) - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Add a profile.
addProfile(Profile) - Method in class edu.isi.pegasus.planner.catalog.site.classes.FileServerType
  Adds a profile.
addProfile(Profile) - Method in class edu.isi.pegasus.planner.catalog.site.classes.HeadNodeFS
  Adds a profile.
addProfile(Profile) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Adds a profile.
addProfile(Profile) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Adds a profile.
addProfile(Profile) - Method in class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeFS
  Adds a profile.
addProfile(Profile, long, boolean) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Add a lfn or pfn profile to the TC
addProfile(Profile) - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Allows you to add one profile at a time to the transformation.
addProfile(Profile) - Method in class edu.isi.pegasus.planner.classes.Job
  Adds a profile to the job object
addProfile(String, String, String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add a profile to the job
addProfile(Profile.NAMESPACE, String, String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add a profile to the job
addProfile(Profile) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add a Profile object
addProfile(String, String, String) - Method in class edu.isi.pegasus.planner.dax.CatalogType
  Add a profile to the catalog entry
addProfile(Profile.NAMESPACE, String, String) - Method in class edu.isi.pegasus.planner.dax.CatalogType
  Add a profile to the catalog entry
addProfile(String, String, String) - Method in class edu.isi.pegasus.planner.dax.PFN
addProfile(Profile.NAMESPACE, String, String) - Method in class edu.isi.pegasus.planner.dax.PFN
addProfileDirectly(Profile) - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Adds a profile directly to namespace bypassing any underlying namespace specific checks.
addProfileDirectly(Profiles.NAMESPACES, String, String) - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Add a profile.
addProfileDirectly(String, String, String) - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Add a profile.
addProfiles(Profiles) - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Adds multiple profiles.
addProfiles(List<Profile>) - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Adds multiple profiles.
addProfiles(Profiles) - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Allows you to add one profile at a time to the transformation.
addProfiles(List) - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Allows you to add multiple profiles to the transformation.
addProfiles(List<Profile>) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Add a list of Profile objects
addProfiles(List<Profile>) - Method in class edu.isi.pegasus.planner.dax.CatalogType
  Add a List of profile objects to this Catalog entry
addProfiles(Profile) - Method in class edu.isi.pegasus.planner.dax.CatalogType
  Add a Profile object to this Catalog entry
addProfiles(List<Profile>) - Method in class edu.isi.pegasus.planner.dax.PFN
addProfiles(Profile) - Method in class edu.isi.pegasus.planner.dax.PFN
addProfilesDirectly(Profiles) - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Adds multiple profiles .
addProfilesDirectly(List<Profile>) - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Adds multiple profiles to namespace bypassing any underlying namespace specific checks.
addProperties(Properties, Properties) - Static method in class edu.isi.pegasus.common.util.CommonProperties
  Adds new properties to an existing set of properties while substituting variables.
addRegistrationFiles(FileTransfer) - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.TransferContainer
  Adds a single file for registration.
addRegistrationFiles(Collection) - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.TransferContainer
  Adds a Collection of File transfer to the underlying collection of files to be registered.
addRegistrationFiles(Collection) - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle.TransferContainer
  Adds a Collection of File transfer to the underlying collection of files to be registered.
addRelation(String, String) - Method in interface edu.isi.pegasus.planner.transfer.Refiner
  Adds a new relation to the workflow being refiner.
addRelation(String, String, String, boolean) - Method in interface edu.isi.pegasus.planner.transfer.Refiner
  Adds a new relation to the workflow.
addRelation(String, String) - Method in class edu.isi.pegasus.planner.transfer.refiner.Basic
  Adds a new relation to the workflow being refiner.
addRelation(String, String, String, boolean) - Method in class edu.isi.pegasus.planner.transfer.refiner.Basic
  Adds a new relation to the workflow.
addRelation(String, String, String, boolean) - Method in class edu.isi.pegasus.planner.transfer.refiner.Chain
  Adds a new relation to the workflow.
addRelation(String, String) - Method in class edu.isi.pegasus.planner.transfer.refiner.Empty
  Adds a new relation to the workflow being refiner.
addRelation(String, String, String, boolean) - Method in class edu.isi.pegasus.planner.transfer.refiner.Empty
  Adds a new relation to the workflow.
addRemoveDirectoryNodes(ADag) - Method in class edu.isi.pegasus.planner.refiner.RemoveDirectory
  Modifies the workflow to add remove directory nodes.
addRemoveDirectoryNodes(ADag, Set<String>) - Method in class edu.isi.pegasus.planner.refiner.RemoveDirectory
  Adds create dir nodes to the workflow.
addReplicaCatalog(ReplicaCatalog) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Add a Replica Catalog to the site.
addReplicaCatalog(ReplicaCatalog) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Add a Replica Catalog to the site.
addRoot(GraphNode) - Method in class edu.isi.pegasus.planner.classes.ADag
  Adds a single root node to the Graph.
addRoot(GraphNode) - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Adds a single root node to the Graph.
addRoot(GraphNode) - Method in interface edu.isi.pegasus.planner.partitioner.graph.Graph
  Adds a single root node to the Graph.
addRoot(GraphNode) - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph
  Adds a single root node to the Graph.
addSetupNodes(ADag) - Method in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Adds a setup node per execution site in the workflow that will stage the worker node executables to the workdirectory on the sites the workflow has been scheduled to.
addSetupNodesWithoutUntarNodes(ADag, Set<String>) - Method in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Adds only the stage worker nodes to the workflow.
addSetupNodesWithUntarNodes(ADag, Set<String>) - Method in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Adds untar nodes to the workflow, in addition to the stage worker nodes
addSetXBitJobs(Job, Job, Collection) - Method in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  Adds the dirmanager to the workflow, that do a chmod on the files being staged.
addSetXBitJobs(Job, String, Collection, int) - Method in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  Adds the dirmanager job to the workflow, that do a chmod on the files being staged.
addSetXBitJobs(Job, String, Collection, int, int) - Method in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  Adds the dirmanager job to the workflow, that do a chmod on the files being staged.
addSetXBitJobs(Job, String, Collection, int, int) - Method in interface edu.isi.pegasus.planner.transfer.Implementation
  Adds the dirmanager job to the workflow, that do a chmod on the files being staged.
addSource(NameValue) - Method in class edu.isi.pegasus.planner.classes.FileTransfer
  Adds a source URL for the transfer.
addSource(String, String) - Method in class edu.isi.pegasus.planner.classes.FileTransfer
  Adds a source URL for the transfer.
addStageInXFERNodes(Job, Collection<FileTransfer>, Collection<FileTransfer>) - Method in class edu.isi.pegasus.planner.transfer.AbstractRefiner
  Default behaviour to preserve backward compatibility when the stage in and symbolic link jobs were not separated.
addStageInXFERNodes(Job, Collection<FileTransfer>) - Method in class edu.isi.pegasus.planner.transfer.AbstractRefiner
  Default behaviour to preserve backward compatibility when the stage in and symbolic link jobs were not separated.
addStageInXFERNodes(Job, Collection<FileTransfer>, Collection<FileTransfer>) - Method in interface edu.isi.pegasus.planner.transfer.Refiner
  Adds the stage in transfer nodes which transfer the input files for a job, from the location returned from the replica catalog to the job's execution pool.
addStageInXFERNodes(Job, Collection<FileTransfer>, Collection<FileTransfer>) - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  Adds the stage in transfer nodes which transfer the input files for a job, from the location returned from the replica catalog to the job's execution pool.
addStageInXFERNodes(Job, boolean, Collection, int, Map<String, BalancedCluster.PoolTransfer>, BalancedCluster.BundleValue, Implementation) - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  Adds the stage in transfer nodes which transfer the input files for a job, from the location returned from the replica catalog to the job's execution pool.
addStageInXFERNodes(Job, Collection<FileTransfer>, Collection<FileTransfer>) - Method in class edu.isi.pegasus.planner.transfer.refiner.Basic
  Adds the stage in transfer nodes which transfer the input files for a job, from the location returned from the replica catalog to the job's execution pool.
addStageInXFERNodes(Job, Collection<FileTransfer>, String, Implementation) - Method in class edu.isi.pegasus.planner.transfer.refiner.Basic
  Adds the stage in transfer nodes which transfer the input files for a job, from the location returned from the replica catalog to the job's execution pool.
addStageInXFERNodes(Job, Collection<FileTransfer>, Collection<FileTransfer>) - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  Adds the stage in transfer nodes which transfer the input files for a job, from the location returned from the replica catalog to the job's execution pool.
addStageInXFERNodes(Job, boolean, Collection, int, Map<String, Bundle.PoolTransfer>, Bundle.BundleValue, Implementation) - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  Adds the stage in transfer nodes which transfer the input files for a job, from the location returned from the replica catalog to the job's execution pool.
addStageInXFERNodes(Job, Collection<FileTransfer>, Collection<FileTransfer>) - Method in class edu.isi.pegasus.planner.transfer.refiner.Cluster
  Adds the stage in transfer nodes which transfer the input files for a job, from the location returned from the replica catalog to the job's execution pool.
addStageInXFERNodes(Job, boolean, Collection, int, Map<String, Bundle.PoolTransfer>, Bundle.BundleValue, Implementation) - Method in class edu.isi.pegasus.planner.transfer.refiner.Cluster
  Adds the stage in transfer nodes which transfer the input files for a job, from the location returned from the replica catalog to the job's execution pool.
addStageInXFERNodes(Job, Collection<FileTransfer>, Collection<FileTransfer>) - Method in class edu.isi.pegasus.planner.transfer.refiner.Empty
  Adds the stage in transfer nodes which transfer the input files for a job, from the location returned from the replica catalog to the job's execution pool.
addStageInXFERNodes(Job, Collection<FileTransfer>, String, Implementation) - Method in class edu.isi.pegasus.planner.transfer.refiner.Empty
  Adds the stage in transfer nodes which transfer the input files for a job, from the location returned from the replica catalog to the job's execution pool.
addStageOutXFERNodes(Job, Collection, ReplicaCatalogBridge, boolean) - Method in interface edu.isi.pegasus.planner.transfer.Refiner
  Adds the stageout transfer nodes, that stage data to an output site specified by the user.
addStageOutXFERNodes(Job, Collection, ReplicaCatalogBridge, boolean, boolean) - Method in interface edu.isi.pegasus.planner.transfer.Refiner
  Adds the stageout transfer nodes, that stage data to an output site specified by the user.
addStageOutXFERNodes(Job, Collection, ReplicaCatalogBridge, boolean, boolean) - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  Adds the stageout transfer nodes, that stage data to an output site specified by the user.
addStageOutXFERNodes(Job, Collection, ReplicaCatalogBridge, boolean) - Method in class edu.isi.pegasus.planner.transfer.refiner.Basic
  Adds the stageout transfer nodes, that stage data to an output site specified by the user.
addStageOutXFERNodes(Job, Collection, ReplicaCatalogBridge, boolean, boolean) - Method in class edu.isi.pegasus.planner.transfer.refiner.Basic
  Adds the stageout transfer nodes, that stage data to an output site specified by the user.
addStageOutXFERNodes(Job, Collection, ReplicaCatalogBridge, boolean, boolean) - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  Adds the stageout transfer nodes, that stage data to an output site specified by the user.
addStageOutXFERNodes(Job, Collection, ReplicaCatalogBridge, boolean) - Method in class edu.isi.pegasus.planner.transfer.refiner.Empty
  Adds the stageout transfer nodes, that stage data to an output site specified by the user.
addStageOutXFERNodes(Job, Collection, ReplicaCatalogBridge, boolean, boolean) - Method in class edu.isi.pegasus.planner.transfer.refiner.Empty
  Adds the stageout transfer nodes, that stage data to an output site specified by the user.
addStatCall(StatCall) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor: Appends a stat to the list of stats.
addStatCall(int, StatCall) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor: Inserts a StatCall into a specific position of the stat list.
addSubExpression(StringBuffer, String, String) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.GLite
  Adds a sub expression to a string buffer
addSubExpression(StringBuffer, String, Integer) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.GLite
  Adds a sub expression to a string buffer
addSysInfo(VDSSysInfo) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Adds a system information entry into the TC.
addTCEntry(String, String, String, String, TCType, String, List, List, SysInfo, Notifications, boolean) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Add an single entry into the transformation catalog.
addTCEntry(String, String, String, String, TCType, String, List, List, SysInfo, Notifications, boolean) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Add an single entry into the transformation catalog.
addTCEntry(String, String, String, String, TCType, String, List, List, SysInfo, Notifications, boolean) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Add an single entry into the transformation catalog.
addTime(String, long) - Method in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
addTimeStamp() - Method in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
  Add a timestamp to the message.
addToFile(File, OutputStream) - Method in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  Adds contents to an output stream.
addToForwardOptions(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Parses the argument in form of option=[value] and adds to the options that are to be passed ahead to pegasus-run.
addToNonStandardJavaOptions(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Adds to the Set of non standard JAVA options that need to be passed to the JVM.
addToStagingSitesMappings(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Adds to the staging sites
addToStagingSitesMappings(String, String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Adds to the staging sites
addTransfer(Collection<FileTransfer>, int, int) - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.PoolTransfer
  Adds a a collection of `FileTransfer` objects to the appropriate TransferContainer.
addTransfer(FileTransfer, int, int) - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.PoolTransfer
  Adds a single `FileTransfer` objects to the appropriate TransferContainer.
addTransfer(FileTransfer) - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.TransferContainer
  Adds a file transfer to the underlying collection.
addTransfer(Collection) - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.TransferContainer
  Adds a file transfer to the underlying collection.
addTransfer(Collection, int, int) - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle.PoolTransfer
  Adds a a collection of `FileTransfer` objects to the appropriate TransferContainer.
addTransfer(FileTransfer, int) - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle.PoolTransfer
  Adds a file transfer to the appropriate TransferContainer.
addTransfer(FileTransfer) - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle.TransferContainer
  Adds a file transfer to the underlying collection.
addTransfer(Collection) - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle.TransferContainer
  Adds a file transfer to the underlying collection.
addTransfer(String) - Method in class edu.isi.pegasus.planner.transfer.refiner.Chain.SiteTransfer
  Adds a file transfer to the appropriate TransferChain.
addTransferNodes(ReplicaCatalogBridge, PlannerCache) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  Adds the transfer nodes to the workflow.
addTransformation(Transformation) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add Transformation to the DAX
addTransformations(List<Transformation>) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Add Multiple Transformation to the DAX
addVector(Vector, Vector) - Method in class edu.isi.pegasus.planner.refiner.Engine
  Adds elements (PegasusFile type) in a Vector to another Vector and returns the new Vector.
addWQ(String, String) - Method in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
  Add a string.
AggregatedJob - Class in edu.isi.pegasus.planner.classes
  This class holds all the specifics of an aggregated job.
AggregatedJob() - Constructor for class edu.isi.pegasus.planner.classes.AggregatedJob
  The default constructor.
AggregatedJob(int) - Constructor for class edu.isi.pegasus.planner.classes.AggregatedJob
  The overloaded constructor.
AggregatedJob(Job, int) - Constructor for class edu.isi.pegasus.planner.classes.AggregatedJob
  The overloaded constructor.
aggregatedJobArguments(AggregatedJob) - Method in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  Returns the arguments with which the `AggregatedJob` needs to be invoked with.
aggregatedJobArguments(AggregatedJob) - Method in class edu.isi.pegasus.planner.cluster.aggregator.MPIExec
  Returns the arguments with which the `AggregatedJob` needs to be invoked with.
aggregatedJobArguments(AggregatedJob) - Method in class edu.isi.pegasus.planner.cluster.aggregator.SeqExec
  Returns the arguments with which the `AggregatedJob` needs to be invoked with.
Aggregator - Interface in edu.isi.pegasus.planner.namespace.aggregator
  An internal interface, that allows us to perform aggregation functions on profiles during merging of profiles.
aggregator(String) - Method in class edu.isi.pegasus.planner.namespace.Globus
  Returns the aggregator to be used for the profile key while merging.
AIX - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Os
Algorithm - Class in edu.isi.pegasus.planner.selector.site.heft
  The HEFT based site selector.
Algorithm(PegasusBag) - Constructor for class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  The default constructor.
All - Class in edu.isi.pegasus.planner.catalog.transformation.mapper
  This implementation of the mapper generates maps for sites with installed as well as stageable transformations.
All(PegasusBag) - Constructor for class edu.isi.pegasus.planner.catalog.transformation.mapper.All
  The private constructor.
ALL_POST_SCRIPT_SCOPE - Static variable in class edu.isi.pegasus.planner.code.GridStartFactory
  The postscript mode in which post scripts are added only for all jobs.
ALL_REMOTE_TYPE - Static variable in class edu.isi.pegasus.planner.transfer.RemoteTransfer.TransferState
  The constant to denote that all transfers are to be exectuted remotely
ALL_SITES - Static variable in class edu.isi.pegasus.planner.transfer.RemoteTransfer
  The constant to apply to all sites.
ALL_SITES - Static variable in class edu.isi.pegasus.planner.transfer.TPT
  The constant to apply to all sites.
ALL_TPT_PROPERTY - Static variable in class edu.isi.pegasus.planner.transfer.TPT
  The property name to get the sites for which all transfers need to be TPT.
ALL_TPT_REMOTE - Static variable in class edu.isi.pegasus.planner.transfer.TPT.TPTState
  The constant to denote that all transfers are to be executed on the remote site.
ALL_TPT_REMOTE_PROPERTY - Static variable in class edu.isi.pegasus.planner.transfer.TPT
  The property name to get the sites for which all TPT transfers need to be executed on the remote site.
ALL_TPT_TYPE - Static variable in class edu.isi.pegasus.planner.transfer.TPT.TPTState
  The constant to denote that all transfers are to be third party.
ALL_TRANSFER_PRIORITY_PROPERTY_KEY - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
  Default properties that applies priorities to all kinds of transfer jobs.
ALL_TRANSFERS_REMOTE_PROPERTY - Static variable in class edu.isi.pegasus.planner.transfer.RemoteTransfer
  The property name to get the sites for which all transfers need to be executed remotely.
allowExists - Variable in class edu.isi.pegasus.gridftp.MakeDirectoryCommand
AMD64 - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Arch
ancestors - Variable in class edu.isi.pegasus.planner.provisioner.Node
ancET - Variable in class edu.isi.pegasus.planner.provisioner.Node
append(StringBuffer, String, Object, String) - Method in class edu.isi.pegasus.planner.classes.Job
  Appends a key value mapping to the StringBuffer.
append(StringBuffer, String, String) - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Appends a key=value pair to the StringBuffer.
append(StringBuffer, String, String) - Method in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  Appends a key=value pair to the StringBuffer.
append(StringBuffer, String, int) - Method in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  Appends a key=value pair to the StringBuffer.
append(StringBuffer, String, String, String) - Method in class edu.isi.pegasus.planner.namespace.Dagman
appendArrayList(ArrayList, ArrayList) - Method in class edu.isi.pegasus.planner.refiner.Engine
  It appends the source list at the end of the destination list.
appendAttribute(StringBuffer, String, String) - Method in class edu.isi.pegasus.planner.cluster.Horizontal
  Appends an xml attribute to the xml feed.
appendAttribute(StringBuffer, String, String) - Method in class edu.isi.pegasus.planner.transfer.refiner.Basic
  Appends an xml attribute to the xml feed.
APPENDER - Static variable in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
appendProperty(StringBuffer, String, String) - Method in class edu.isi.pegasus.planner.code.gridstart.NetloggerPostScript
  Appends a property to the StringBuffer, in the java command line format.
appendProperty(StringBuffer, String, String) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusExitCode
  Appends a property to the StringBuffer, in the java command line format.
appendProperty(StringBuffer, String, String) - Method in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  Appends a property to the StringBuffer, in the java command line format.
appendValue(String) - Method in class edu.isi.pegasus.planner.invocation.Architecture
  Appends a piece of text to the existing text.
appendValue(String) - Method in class edu.isi.pegasus.planner.invocation.ArgEntry
  Appends a piece of text to the existing text.
appendValue(String) - Method in class edu.isi.pegasus.planner.invocation.ArgString
  Appends a piece of text to the existing text.
appendValue(String) - Method in class edu.isi.pegasus.planner.invocation.Boot
  Appends a piece of text to the existing text.
appendValue(String) - Method in class edu.isi.pegasus.planner.invocation.CommandLine
  Appends a piece of text to the existing text.
appendValue(String) - Method in class edu.isi.pegasus.planner.invocation.CPU
  Appends a piece of text to the existing text.
appendValue(String) - Method in class edu.isi.pegasus.planner.invocation.Data
  Appends a piece of text to the existing text.
appendValue(String) - Method in class edu.isi.pegasus.planner.invocation.EnvEntry
  Appends a piece of text to the existing text.
appendValue(String) - Method in class edu.isi.pegasus.planner.invocation.File
  Appends a piece of text to the existing text.
appendValue(String) - Method in interface edu.isi.pegasus.planner.invocation.HasText
  Appends a piece of text to the existing text.
appendValue(String) - Method in class edu.isi.pegasus.planner.invocation.Ignore
  Appends a piece of text to the existing text.
appendValue(String) - Method in class edu.isi.pegasus.planner.invocation.JobStatusFailure
  Appends a piece of text to the existing text.
appendValue(String) - Method in class edu.isi.pegasus.planner.invocation.JobStatusSignal
  Appends a piece of text to the existing text.
appendValue(String) - Method in class edu.isi.pegasus.planner.invocation.JobStatusSuspend
  Appends a piece of text to the existing text.
appendValue(String) - Method in class edu.isi.pegasus.planner.invocation.Stamp
  Appends a piece of text to the existing text.
appendValue(String) - Method in class edu.isi.pegasus.planner.invocation.Uname
  Appends a piece of text to the existing text.
appendValue(String) - Method in class edu.isi.pegasus.planner.invocation.WorkingDir
  Appends a piece of text to the existing text.
apply(Job) - Method in interface edu.isi.pegasus.planner.code.generator.condor.CondorStyle
  Apply a style to a job.
apply(AggregatedJob) - Method in interface edu.isi.pegasus.planner.code.generator.condor.CondorStyle
  Apply a style to an AggregatedJob
apply(AggregatedJob) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.Abstract
  Apply a style to an AggregatedJob
apply(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.Condor
  Applies the condor style to the job.
apply(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.CondorC
  Applies the CondorC style to the job.
apply(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.CondorG
  Applies the globus style to the job.
apply(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.CondorGlideIN
  Applies the style to the job to be run in a condor glide in environment.
apply(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.CondorGlideinWMS
apply(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.CreamCE
  Applies the CREAM CE style to the job.
apply(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.GLite
  Applies the gLite style to the job.
apply(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.SSH
  Applies the CREAM CE style to the job.
applyCredentialsForJobSubmission(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.Abstract
  Associates credentials required for job submission.
applyCredentialsForLocalExec(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.Abstract
  Examines the credential requirements for a job and adds appropiate transfer and environment directives for the credentials to be picked up for the local job
applyCredentialsForRemoteExec(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.Abstract
  Examines the credential requirements for a job and adds appropiate transfer and environment directives for the credentials to be staged and picked up by the job.
applyJobPriorities(Graph) - Method in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  Adds job priorities to the jobs in the workflow on the basis of the levels in the traversal order given by the iterator.
applyPriority(TransferJob) - Method in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  Applies priorities to the transfer jobs if a priority is specified in the properties file.
applyPriority(TransferJob) - Method in interface edu.isi.pegasus.planner.transfer.Implementation
  Applies priorities to the transfer jobs if a priority is specified in the properties file.
applyStyle(Job, PrintWriter) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Applies a submit file style to the job, according to the fact whether the job has to be submitted directly to condor or to a remote jobmanager via CondorG and GRAM.
Arch - Class in edu.isi.pegasus.planner.catalog.transformation.classes
Arch(String) - Constructor for class edu.isi.pegasus.planner.catalog.transformation.classes.Arch
arch - Variable in class edu.isi.pegasus.planner.catalog.transformation.classes.VDSSysInfo
  Architecture of the system.
ARCH() - Constructor for enum edu.isi.pegasus.planner.dax.Executable.ARCH
ARCH - Static variable in class edu.isi.pegasus.planner.parser.tokens.TransformationCatalogReservedWord
  token value for the reserved word "arch".
ARCH_TYPE - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The constant to be passed to the accessor functions to get or set the architecture type of the remote machines to which the jobmanager talks to.
Architecture() - Constructor for enum edu.isi.pegasus.planner.catalog.classes.SysInfo.Architecture
Architecture - Class in edu.isi.pegasus.planner.invocation
  This class is transient for XML parsing.
Architecture() - Constructor for class edu.isi.pegasus.planner.invocation.Architecture
  Default c'tor: Construct a hollow shell and allow further information to be added later.
ARCHMODE_ATTRIBUTE_KEY - Static variable in class edu.isi.pegasus.planner.invocation.Uname
  The archmode attribute for the uname
ARG_DELIMITER - Static variable in class edu.isi.pegasus.planner.dax.AbstractJob
ArgEntry - Class in edu.isi.pegasus.planner.invocation
  This class carries an argument vector entry for the argument vector.
ArgEntry() - Constructor for class edu.isi.pegasus.planner.invocation.ArgEntry
  Default c'tor: Construct a hollow shell and allow further information to be added later.
ArgEntry(int) - Constructor for class edu.isi.pegasus.planner.invocation.ArgEntry
  C'tor: Prepares a given key for accepting a value later on.
ArgEntry(int, String) - Constructor for class edu.isi.pegasus.planner.invocation.ArgEntry
  C'tor: Fully initializes the class
argsmap - Variable in class edu.isi.pegasus.planner.client.TCClient
ArgString - Class in edu.isi.pegasus.planner.invocation
  This class maintains the application that was run, and the arguments to the commandline that were actually passed on to the application.
ArgString() - Constructor for class edu.isi.pegasus.planner.invocation.ArgString
  Default c'tor: Construct a hollow shell and allow further information to be added later.
ArgString(String) - Constructor for class edu.isi.pegasus.planner.invocation.ArgString
  Constructs an applications without arguments.
ArgString(String, String) - Constructor for class edu.isi.pegasus.planner.invocation.ArgString
  Constructs an applications with arguments.
Arguments - Class in edu.isi.pegasus.planner.invocation
  This class maintains the application that was run, and the arguments to the commandline that were actually passed on to the application.
Arguments() - Constructor for class edu.isi.pegasus.planner.invocation.Arguments
  Default c'tor: Construct a hollow shell and allow further information to be added later.
Arguments(String) - Constructor for class edu.isi.pegasus.planner.invocation.Arguments
  Constructs an applications without arguments.
Arguments() - Constructor for class edu.isi.pegasus.planner.parser.dax.DAXParser3.Arguments
  The default constructor
ARGUMENTS_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The attribute key for task arguments.
ARGUMENTS_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The name of the key that denotes the arguments of the job.
ArgVector - Class in edu.isi.pegasus.planner.invocation
  This class maintains the application that was run, and the arguments to the commandline that were actually passed on to the application.
ArgVector() - Constructor for class edu.isi.pegasus.planner.invocation.ArgVector
  Default c'tor: Construct a hollow shell and allow further information to be added later.
ArgVector(String) - Constructor for class edu.isi.pegasus.planner.invocation.ArgVector
  Constructs an applications without arguments.
assignDefaultJobPriorities() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a boolean indicating whether we assign job priorities or not to the jobs Referred to by the "pegasus.job.priority.assign" property.
assignLevels(Graph, GraphNode) - Method in class edu.isi.pegasus.planner.refiner.ReduceEdges
  Prunes redundant edges from the workflow.
assimilate(PegasusProperties, Profiles.NAMESPACES) - Method in class edu.isi.pegasus.planner.namespace.Dagman
  Assimilate the profiles in the namespace in a controlled manner.
assimilate(PegasusProperties, Profiles.NAMESPACES) - Method in class edu.isi.pegasus.planner.namespace.Namespace
  Assimilate the profiles in the namespace in a controlled manner.
assimilateJobs() - Method in class edu.isi.pegasus.planner.cluster.Horizontal
  Puts the jobs in the abstract workflow into the job that is index by the logical name of the jobs.
associate(String, String) - Static method in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  Associates a VDS property with the new pegasus property.
associate(Partition, Job) - Method in class edu.isi.pegasus.planner.cluster.Abstract
  Maps the partition to the corresponding clustered job.
associate(POSTScript) - Static method in class edu.isi.pegasus.planner.code.GridStartFactory
  Associates a shortname with the classname.
associate(String, String) - Static method in class edu.isi.pegasus.planner.code.GridStartFactory
  Associates a shortname with the classname.
associateCredentials(Job, Collection<FileTransfer>) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Associates credentials with the job corresponding to the files that are being transferred.
attributeNotSupported(String, String, String) - Method in class edu.isi.pegasus.planner.parser.StackBasedXMLParser
  This is called when an attribute is encountered for an element that is valid in the schema context but not supported right now.
attributes(String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Slurps all attributes from related to a mapping into a map.
Authenticate - Class in edu.isi.pegasus.planner.refiner
  It takes in a authenticate request and authenticates against the resource on the basis of the type of the resource against which authentication is required.
Authenticate(PegasusProperties, PoolInfoProvider) - Constructor for class edu.isi.pegasus.planner.refiner.Authenticate
  The overloaded constructor.
authenticate(AuthenticateRequest) - Method in class edu.isi.pegasus.planner.refiner.Authenticate
  Authenticates against a resource referred to in the authenticate request object.
authenticate() - Method in class edu.isi.pegasus.planner.refiner.AuthenticateEngine
  It returns a set of pools against which the user can authenticate to.
Authenticate.HostPort - Class in edu.isi.pegasus.planner.refiner
  A convenience inner class that stores the host and the port associated with a server.
AuthenticateEngine - Class in edu.isi.pegasus.planner.refiner
  It authenticates the user with the sites, that the user specifies at the execution time.
AuthenticateEngine(PegasusBag, Set) - Constructor for class edu.isi.pegasus.planner.refiner.AuthenticateEngine
  The overloaded constructor.
authenticateJobManager(String) - Method in class edu.isi.pegasus.planner.refiner.Authenticate
  It authenticates against the jobmanager specifyied.
AuthenticateRequest - Class in edu.isi.pegasus.planner.classes
  The object that describes the authenticate request.
AuthenticateRequest() - Constructor for class edu.isi.pegasus.planner.classes.AuthenticateRequest
  Default Constructor.
AuthenticateRequest(char, String, String) - Constructor for class edu.isi.pegasus.planner.classes.AuthenticateRequest
  Overloaded Constructor.
AuthenticateThread(int) - Constructor for class edu.isi.pegasus.planner.refiner.ThreadPool.AuthenticateThread
  The overloaded constructor.
authenticationSet() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the authenticate option for the planner.
AVERAGE_BANDWIDTH - Static variable in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  The average bandwidth between the sites.
AVERAGE_DATA_SIZE_BETWEEN_JOBS - Static variable in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  The average data that is transferred in between 2 jobs in the workflow.
avg_bandwidth - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPBandwidth
Avg_Bandwidth - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
avg_bandwidth_range1 - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPBandwidth
Avg_Bandwidth_range1 - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
avg_bandwidth_range2 - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPBandwidth
Avg_Bandwidth_range2 - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
avg_bandwidth_range3 - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPBandwidth
Avg_Bandwidth_range3 - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
avg_bandwidth_range4 - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPBandwidth
Avg_Bandwidth_range4 - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
AVG_BW - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPBandwidth
AVG_BW_RANGE1 - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPBandwidth
AVG_BW_RANGE2 - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPBandwidth
AVG_BW_RANGE3 - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPBandwidth
AVG_BW_RANGE4 - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPBandwidth
AVG_COMPUTE_TIME - Static variable in class edu.isi.pegasus.planner.selector.site.heft.HeftBag
  The constant to be passed to the accessor functions to get or set the average compute time for the node.

## B

Bag - Interface in edu.isi.pegasus.planner.partitioner.graph
  An interface to define a BAG of objects.
balance(int, boolean) - Method in class edu.isi.pegasus.planner.provisioner.OccupationDiagram
  Run Task redistribution phase of BTS algorithm
BalancedCluster - Class in edu.isi.pegasus.planner.transfer.refiner
  An extension of the default refiner, that allows the user to specify the number of transfer nodes per execution site for stagein and stageout.
BalancedCluster(ADag, PegasusBag) - Constructor for class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  The overloaded constructor.
BalancedCluster.BundleValue - Class in edu.isi.pegasus.planner.transfer.refiner
BalancedCluster.PoolTransfer - Class in edu.isi.pegasus.planner.transfer.refiner
  A container to store the transfers that need to be done per staging site The transfers are stored over a collection of Transfer Containers with each transfer container responsible for one transfer job.
BalancedCluster.TransferContainer - Class in edu.isi.pegasus.planner.transfer.refiner
  A container class for storing the name of the transfer job, the list of file transfers that the job is responsible for.
BASE_BUILD_DIRECTORY_URL - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The base directory URL for the builds.
Basic - Class in edu.isi.pegasus.planner.transfer.refiner
  The default transfer refiner, that implements the multiple refiner.
Basic(ADag, PegasusBag) - Constructor for class edu.isi.pegasus.planner.transfer.refiner.Basic
  The overloaded constructor.
BATCH_KEY - Static variable in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  The suffix for the property that if set, specifies the size of the chunk in which the implementations handle multiple queries.
BATCH_QUEUE_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The queue to be used when using batch gahp.
beginWorkflowRefinementStep(Refiner, String, boolean) - Method in interface edu.isi.pegasus.planner.provenance.pasoa.PPS
beginWorkflowRefinementStep(Refiner, String, boolean) - Method in class edu.isi.pegasus.planner.provenance.pasoa.pps.Empty
bestFitBinPack(List<Job>, double) - Method in class edu.isi.pegasus.planner.cluster.Horizontal
  Perform best fit bin packing.
bestFitBinPack(List<Job>, int) - Method in class edu.isi.pegasus.planner.cluster.Horizontal
  Perform best fit bin packing.
BFS - Class in edu.isi.pegasus.planner.partitioner
  This does a modified breadth first search of the graph to identify the levels.
BFS(GraphNode, Map, PegasusProperties) - Constructor for class edu.isi.pegasus.planner.partitioner.BFS
  The overloaded constructor.
BLACK_COLOR - Static variable in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
Boolean - Class in edu.isi.pegasus.common.util
  This class converts a boolean property specification (string) in various representations into a booelan value.
Boolean() - Constructor for class edu.isi.pegasus.common.util.Boolean
BooleanBag() - Constructor for class edu.isi.pegasus.planner.refiner.DataReuseEngine.BooleanBag
  The default constructor.
booleanToInt(boolean) - Method in class edu.isi.pegasus.planner.code.generator.Stampede
  Returns boolean as an integer
Boot - Class in edu.isi.pegasus.planner.invocation
  The boot element.
Boot() - Constructor for class edu.isi.pegasus.planner.invocation.Boot
  The default constructor
Boot(String) - Constructor for class edu.isi.pegasus.planner.invocation.Boot
  Constructs a piece of data.
bottomNode - Variable in class edu.isi.pegasus.planner.provisioner.Estimator
bottomUpIterator() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns an iterator that traverses the graph bottom up from the leaves.
bottomUpIterator() - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Returns an iterator that traverses the graph bottom up from the leaves.
bottomUpIterator() - Method in interface edu.isi.pegasus.planner.partitioner.graph.Graph
  Returns an iterator that traverses the graph bottom up from the leaves.
bottomUpIterator() - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph
  Returns an iterator that traverses the graph bottom up from the leaves.
BottomUpIterator() - Constructor for class edu.isi.pegasus.planner.partitioner.graph.MapGraph.BottomUpIterator
  The default constructor.
Braindump - Class in edu.isi.pegasus.planner.code.generator
  Braindump file code generator that generates a Braindump file for the executable workflow in the submit directory.
Braindump() - Constructor for class edu.isi.pegasus.planner.code.generator.Braindump
BRAINDUMP_FILE - Static variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The basename of the braindump file.
BTS() - Method in class edu.isi.pegasus.planner.provisioner.Estimator
buf - Variable in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
BUILD_AD_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.ClassADSGenerator
  The classad key for the pegasus build.
BUILD_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The Key for the pegasus build.
buildAncestors() - Method in class edu.isi.pegasus.planner.provisioner.Node
  build the list of ancestor tasks
buildDescendants() - Method in class edu.isi.pegasus.planner.provisioner.Node
  build the list of descendant tasks
builder - Variable in class edu.isi.pegasus.gridftp.GridFTPConnection.StringBuilderDataSink
buildState() - Method in class edu.isi.pegasus.planner.transfer.RemoteTransfer
  Builds up the remote transfers state for all the sites.
buildState(int) - Method in class edu.isi.pegasus.planner.transfer.RemoteTransfer
  Adds to the existing state table, state information for a particular type of transfers.
buildState() - Method in class edu.isi.pegasus.planner.transfer.TPT
  Builds up the third party state for all the sites.
buildState(int) - Method in class edu.isi.pegasus.planner.transfer.TPT
  Adds to the existing state table, state information for a particular type of transfers.
bulk - Variable in class edu.isi.pegasus.planner.client.TCClient
Bundle - Class in edu.isi.pegasus.planner.transfer.refiner
  An extension of the default refiner, that allows the user to specify the number of transfer nodes per execution site for stagein and stageout.
Bundle(ADag, PegasusBag) - Constructor for class edu.isi.pegasus.planner.transfer.refiner.Bundle
  The overloaded constructor.
Bundle.BundleValue - Class in edu.isi.pegasus.planner.transfer.refiner
Bundle.PoolTransfer - Class in edu.isi.pegasus.planner.transfer.refiner
  A container to store the transfers that need to be done on a single pool.
Bundle.TransferContainer - Class in edu.isi.pegasus.planner.transfer.refiner
  A container class for storing the name of the transfer job, the list of file transfers that the job is responsible for.
BUNDLE_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the key that if set, determines the number of super jobs that are made corresponding to a logical transformation and an execution pool.
BUNDLE_LOCAL_STAGE_IN_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the key that determines the bundling parameter for the local stagein transfer node.
BUNDLE_LOCAL_STAGE_OUT_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the key that determines the bundling parameter for the local stagein transfer node.
BUNDLE_REMOTE_STAGE_IN_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the key that determines the bundling parameter for the remote stagein transfer node.
BUNDLE_REMOTE_STAGE_OUT_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the key that determines the bundling parameter for the remote stagein transfer node.
BUNDLE_STAGE_IN_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the key that determines the bundling parameter for the stagein transfer node.
BUNDLE_STAGE_OUT_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the key that determines the bundling parameter for the stageout transfer node.
BundleValue() - Constructor for class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.BundleValue
  The default constructor.
BundleValue() - Constructor for class edu.isi.pegasus.planner.transfer.refiner.Bundle.BundleValue
  The default constructor.
bypassFirstLevelStagingForInputs() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a boolean indicating whether to bypass first level staging of inputs.
bypassStagingForInputFile(ReplicaCatalogEntry, PegasusFile, String) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  Returns a boolean indicating whether to bypass first level staging for a file or not

## C

c_action - Static variable in class edu.isi.pegasus.common.util.ProfileParser
  There are six identified actions.
c_action - Static variable in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Contains the actions to perform upon each state transition including transition into self state.
c_action - Static variable in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Contains the actions to perform upon each state transition including transition into self state.
c_cdone - Static variable in class edu.isi.pegasus.planner.invocation.SimpleServerThread
c_count - Static variable in class edu.isi.pegasus.planner.invocation.SimpleServerThread
c_error - Static variable in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  This message is sent whenever one of the member function is executed which relies on an established database context.
c_expression - Static variable in class edu.isi.pegasus.common.util.Currently
  Store the regular expressions necessary to parse ISO timestamps.
c_final - Static variable in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Provides the final states and associated messages.
c_final - Static variable in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Provides the final states and associated messages.
c_logger - Static variable in class edu.isi.pegasus.planner.invocation.SimpleServer
c_logger - Static variable in class edu.isi.pegasus.planner.invocation.SimpleServerThread
c_pattern - Static variable in class edu.isi.pegasus.common.util.Currently
  Stores compiled patterns at first use, quasi-Singleton.
c_prefix - Static variable in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Prefix for the property subset to use with this catalog.
c_prefix - Static variable in interface edu.isi.pegasus.planner.catalog.SiteCatalog
  Prefix for the property subset to use with this catalog.
c_prefix - Static variable in interface edu.isi.pegasus.planner.catalog.WorkCatalog
  Prefix for the property subset to use with this catalog.
c_prefix - Static variable in class edu.isi.pegasus.planner.ranking.GetDAX
  Prefix for the property subset to use with this catalog.
c_state - Static variable in class edu.isi.pegasus.common.util.ProfileParser
  Table to contain the state transition diagram for the parser.
c_state - Static variable in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Contains the state transition tables.
c_state - Static variable in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Contains the state transition tables.
c_terminate - Static variable in class edu.isi.pegasus.planner.invocation.SimpleServer
CACHE_FILE_SUFFIX - Static variable in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Suffix to be applied for cache file generation.
CACHE_FILE_SUFFIX - Static variable in class edu.isi.pegasus.planner.code.generator.DAXReplicaStore
  Suffix to be applied for cache file generation.
CACHE_READ_ONLY_KEY - Static variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  The name of the key that disables writing back to the cache file.
CACHE_REPLICA_CATALOG_IMPLEMENTER - Static variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  The name of the Replica Catalog Implementer that serves as the source for cache files.
CACHE_REPLICA_CATALOG_KEY - Static variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  The name of the source key for Replica Catalog Implementer that serves as cache
cAction - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorQuoteParser
  There are five identified actions.
calculateAverageComputeTime(Job) - Method in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  Returns the average compute time in seconds for a job.
calculateEstimatedStartAndFinishTime(GraphNode, String) - Method in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  Estimates the start and finish time of a job on a site.
calculateSlotSize() - Method in class edu.isi.pegasus.planner.provisioner.Estimator
calendar - Static variable in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
call() - Method in class edu.isi.pegasus.planner.code.generator.SendMetrics
Callback - Interface in edu.isi.pegasus.planner.parser.dax
  This interfaces defines the callback calls from DAX parsing.
Callback - Interface in edu.isi.pegasus.planner.parser.pdax
  This interfaces defines the callback calls from PDAX parsing.
Callback - Interface in edu.isi.pegasus.planner.partitioner
  This interface defines the callback calls from the partitioners.
canBeCleanedup() - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Returns cleanup denoting whether the file can be cleaned up or not
canSetXBit() - Method in interface edu.isi.pegasus.planner.code.GridStart
  Indicates whether the enabling mechanism can set the X bit on the executable on the remote grid site, in addition to launching it on the remote grid stie
canSetXBit() - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Indicates whether the enabling mechanism can set the X bit on the executable on the remote grid site, in addition to launching it on the remote grid site.
canSetXBit() - Method in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  Indicates whether the enabling mechanism can set the X bit on the executable on the remote grid site, in addition to launching it on the remote grid stie
canSetXBit() - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Indicates whether the enabling mechanism can set the X bit on the executable on the remote grid site, in addition to launching it on the remote grid stie
cascadeDeletionUpwards(Graph, List<GraphNode>) - Method in class edu.isi.pegasus.planner.refiner.DataReuseEngine
  Cascade the deletion of the jobs upwards in the workflow.
Catalog - Interface in edu.isi.pegasus.planner.catalog
  This interface create a common ancestor for all cataloging interfaces.
CATALOG_URL - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
CatalogEntry - Interface in edu.isi.pegasus.planner.catalog.classes
  This interface create a common ancestor for all catalog entries.
CatalogException - Exception in edu.isi.pegasus.planner.catalog
  Class to notify of failures.
CatalogException() - Constructor for exception edu.isi.pegasus.planner.catalog.CatalogException
CatalogException(String) - Constructor for exception edu.isi.pegasus.planner.catalog.CatalogException
  Constructs a `CatalogException` with the specified detailed message.
CatalogException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.catalog.CatalogException
  Constructs a `CatalogException` with the specified detailed message and a cause.
CatalogException(Throwable) - Constructor for exception edu.isi.pegasus.planner.catalog.CatalogException
  Constructs a `CatalogException` with the specified just a cause.
CatalogType - Class in edu.isi.pegasus.planner.dax
  Abstract Type for RC and TC Sections of the DAX.
CatalogType() - Constructor for class edu.isi.pegasus.planner.dax.CatalogType
CatalogType(CatalogType) - Constructor for class edu.isi.pegasus.planner.dax.CatalogType
  Copy Constructor
CATEGORY_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The name of the key that determines the category to which the job belongs to.
categoryRelatedKey(String) - Static method in class edu.isi.pegasus.planner.namespace.Dagman
  Determines whether a key is category related or not.
cb_document(Map) - Method in class edu.isi.pegasus.planner.partitioner.MultipleLook.MyCallBackHandler
  Callback when the opening tag was parsed.
cb_document(Map) - Method in class edu.isi.pegasus.planner.partitioner.SingleLook.MyCallBackHandler
  Callback when the opening tag was parsed.
cb_done() - Method in class edu.isi.pegasus.planner.partitioner.MultipleLook.MyCallBackHandler
cb_done() - Method in class edu.isi.pegasus.planner.partitioner.SingleLook.MyCallBackHandler
  Callback when the parsing of the document is done.
cb_filename(Filename) - Method in class edu.isi.pegasus.planner.partitioner.MultipleLook.MyCallBackHandler
cb_filename(Filename) - Method in class edu.isi.pegasus.planner.partitioner.SingleLook.MyCallBackHandler
  Callback for the filename from section 1 filenames.
cb_job(Job) - Method in class edu.isi.pegasus.planner.partitioner.MultipleLook.MyCallBackHandler
cb_job(Job) - Method in class edu.isi.pegasus.planner.partitioner.SingleLook.MyCallBackHandler
  Callback for the job from section 2 jobs.
cb_parents(String, List) - Method in class edu.isi.pegasus.planner.partitioner.MultipleLook.MyCallBackHandler
cb_parents(String, List) - Method in class edu.isi.pegasus.planner.partitioner.SingleLook.MyCallBackHandler
  Callback for child and parent relationships from section 3.
cbCompoundTransformation(CompoundTransformation) - Method in interface edu.isi.pegasus.planner.parser.dax.Callback
  Callback when a compound transformation is encountered in the DAX from Section 3: that lists Transformations that Aggregate executables and Files
cbCompoundTransformation(CompoundTransformation) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2CDAG
  Callback when a compound transformation is encountered in the DAX
cbCompoundTransformation(CompoundTransformation) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2Graph
  Callback when a compound transformation is encountered in the DAX
cbCompoundTransformation(CompoundTransformation) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2Metadata
  Callback when a compound transformation is encountered in the DAX
cbCompoundTransformation(CompoundTransformation) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2NewGraph
  Callback when a compound transformation is encountered in the DAX
cbCompoundTransformation(CompoundTransformation) - Method in class edu.isi.pegasus.planner.parser.dax.ExampleDAXCallback
  Callback when a compound transformation is encountered in the DAX
cbDocument(Map) - Method in interface edu.isi.pegasus.planner.parser.dax.Callback
  Callback when the opening tag was parsed.
cbDocument(Map) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2CDAG
  Callback when the opening tag was parsed.
cbDocument(Map) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2Graph
  Callback when the opening tag was parsed.
cbDocument(Map) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2Metadata
  Callback when the opening tag was parsed.
cbDocument(Map) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2NewGraph
  Callback when the opening tag was parsed.
cbDocument(Map) - Method in class edu.isi.pegasus.planner.parser.dax.ExampleDAXCallback
  Callback when the opening tag was parsed.
cbDocument(Map) - Method in interface edu.isi.pegasus.planner.parser.pdax.Callback
  Callback when the opening tag was parsed.
cbDocument(Map) - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Callback when the opening tag was parsed.
cbDone() - Method in interface edu.isi.pegasus.planner.parser.dax.Callback
  Callback when the parsing of the document is done.
cbDone() - Method in class edu.isi.pegasus.planner.parser.dax.DAX2CDAG
  Callback when the parsing of the document is done.
cbDone() - Method in class edu.isi.pegasus.planner.parser.dax.DAX2Graph
  Callback to signal that traversal of the DAX is complete.
cbDone() - Method in class edu.isi.pegasus.planner.parser.dax.DAX2LabelGraph
  Callback to signal that traversal of the DAX is complete.
cbDone() - Method in class edu.isi.pegasus.planner.parser.dax.DAX2Metadata
  Callback when the parsing of the document is done.
cbDone() - Method in class edu.isi.pegasus.planner.parser.dax.DAX2NewGraph
  Callback to signal that traversal of the DAX is complete.
cbDone() - Method in class edu.isi.pegasus.planner.parser.dax.ExampleDAXCallback
  Callback when the parsing of the document is done.
cbDone() - Method in interface edu.isi.pegasus.planner.parser.pdax.Callback
  Callback when the parsing of the document is done.
cbDone() - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Callback when the parsing of the document is done.
cbDone() - Method in interface edu.isi.pegasus.planner.partitioner.Callback
  Callback for the partitioner to signal that it is done with the processing.
cbDone() - Method in class edu.isi.pegasus.planner.partitioner.ClustererCallback
  Callback for the partitioner to signal that it is done with the processing.
cbDone() - Method in class edu.isi.pegasus.planner.partitioner.WriterCallback
  Callback for the partitioner to signal that it is done with the processing.
cbExecutable(TransformationCatalogEntry) - Method in interface edu.isi.pegasus.planner.parser.dax.Callback
  Callback when a transformation catalog entry is encountered in the DAX from Section 2: Executables that list entries in a Transformaton Catalog
cbExecutable(TransformationCatalogEntry) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2CDAG
  Callback when a transformation catalog entry is encountered in the DAX
cbExecutable(TransformationCatalogEntry) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2Graph
  Callback when a transformation catalog entry is encountered in the DAX
cbExecutable(TransformationCatalogEntry) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2Metadata
  Callback when a transformation catalog entry is encountered in the DAX
cbExecutable(TransformationCatalogEntry) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2NewGraph
  Callback when a transformation catalog entry is encountered in the DAX
cbExecutable(TransformationCatalogEntry) - Method in class edu.isi.pegasus.planner.parser.dax.ExampleDAXCallback
  Callback when a transformation catalog entry is encountered in the DAX
cbFile(ReplicaLocation) - Method in interface edu.isi.pegasus.planner.parser.dax.Callback
  Callback when a replica catalog entry is encountered in the DAX from Section 1: Files that lists entries in a Replica Catalog
cbFile(ReplicaLocation) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2CDAG
  Callback when a replica catalog entry is encountered in the DAX
cbFile(ReplicaLocation) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2Graph
  Callback when a replica catalog entry is encountered in the DAX
cbFile(ReplicaLocation) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2Metadata
  Callback when a replica catalog entry is encountered in the DAX
cbFile(ReplicaLocation) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2NewGraph
  Callback when a replica catalog entry is encountered in the DAX
cbFile(ReplicaLocation) - Method in class edu.isi.pegasus.planner.parser.dax.ExampleDAXCallback
  Callback when a replica catalog entry is encountered in the DAX
cbJob(Job) - Method in interface edu.isi.pegasus.planner.parser.dax.Callback
  Callback for the job from section 4: Job's, DAX's or Dag's that list a JOB or DAX or DAG .
cbJob(Job) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2CDAG
  Callback for the job from section 2 jobs.
cbJob(Job) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2Graph
  This constructs a graph node for the job and ends up storing it in the internal map.
cbJob(Job) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2LabelGraph
  This constructs a graph node for the job and ends up storing it in the internal map.
cbJob(Job) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2Metadata
  Callback for the job from section 2 jobs.
cbJob(Job) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2NewGraph
  This constructs a graph node for the job and ends up storing it in the internal map.
cbJob(Job) - Method in class edu.isi.pegasus.planner.parser.dax.ExampleDAXCallback
  Callback for the job from section 2 jobs.
cbParents(String, List<PCRelation>) - Method in interface edu.isi.pegasus.planner.parser.dax.Callback
  Callback for child and parent relationships from Section 5: Dependencies that lists Parent Child relationships (can be empty)
cbParents(String, List<PCRelation>) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2CDAG
  Callback for child and parentID relationships from section 3.
cbParents(String, List) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2Graph
  This updates the internal graph nodes of child with references to it's parents referred to by the list of parents passed.
cbParents(String, List) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2Metadata
  Callback for child and parent relationships from section 3.
cbParents(String, List) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2NewGraph
  This updates the internal graph nodes of child with references to it's parents referred to by the list of parents passed.
cbParents(String, List) - Method in class edu.isi.pegasus.planner.parser.dax.ExampleDAXCallback
  Callback for child and parent relationships from section 3.
cbParents(String, List) - Method in interface edu.isi.pegasus.planner.parser.pdax.Callback
  Callback for child and parent relationships from section 3.
cbParents(String, List) - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Callback for child and parent relationships from section 3.
cbParents(String, List) - Method in interface edu.isi.pegasus.planner.partitioner.Callback
  Callback for when a partitioner determines the relations between partitions that it has previously constructed.
cbParents(String, List) - Method in class edu.isi.pegasus.planner.partitioner.ClustererCallback
  Callback for when a partitioner determines the relations between partitions that it has previously constructed.
cbParents(String, List) - Method in class edu.isi.pegasus.planner.partitioner.WriterCallback
  Callback for when a partitioner determines the relations between partitions that it has previously constructed.
cbPartition(Partition) - Method in interface edu.isi.pegasus.planner.parser.pdax.Callback
  Callback for the partition .
cbPartition(Partition) - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Callback for the partition .
cbPartition(Partition) - Method in interface edu.isi.pegasus.planner.partitioner.Callback
  Callback for when a partitioner determines that partition has been constructed.
cbPartition(Partition) - Method in class edu.isi.pegasus.planner.partitioner.ClustererCallback
  Callback for when a partitioner determines that partition has been constructed.
cbPartition(Partition) - Method in class edu.isi.pegasus.planner.partitioner.WriterCallback
  Callback for when a partitioner determines that partition has been constructed.
cbWfInvoke(Invoke) - Method in interface edu.isi.pegasus.planner.parser.dax.Callback
  Callback when a invoke is encountered in the DAX from the top level inside adag tag.
cbWfInvoke(Invoke) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2CDAG
  Callback when a invoke entry is encountered in the top level inside the adag element in DAX.
cbWfInvoke(Invoke) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2Graph
  Callback when a invoke entry is encountered in the top level inside the adag element in the DAX.
cbWfInvoke(Invoke) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2Metadata
  Callback when a invoke entry is encountered in the top level inside the adag element in the DAX.
cbWfInvoke(Invoke) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2NewGraph
  Callback when a invoke entry is encountered in the top level inside the adag element in the DAX.
cbWfInvoke(Invoke) - Method in class edu.isi.pegasus.planner.parser.dax.ExampleDAXCallback
  Callback when a invoke entry is encountered in the top level inside the adag element in the DAX.
Chain - Class in edu.isi.pegasus.planner.transfer.refiner
  This transfer refiner builds upon the Default Refiner.
Chain(ADag, PegasusBag) - Constructor for class edu.isi.pegasus.planner.transfer.refiner.Chain
  The overloaded constructor.
Chain.SiteTransfer - Class in edu.isi.pegasus.planner.transfer.refiner
  A container to manage the transfer jobs that are needed to be done on a single site.
Chain.TransferChain - Class in edu.isi.pegasus.planner.transfer.refiner
  A shallow container class, that contains the list of the names of the transfer jobs and can return the last job in the list.
CHAIN_STAGE_IN_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the key that determines the number of chains of stagein nodes that are to be created per site.
CHANGE_DIR_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the profile key that triggers the kickstart to change directory before launching an executable instead of launching the executable from the directory where kickstart is being run.
CHANGE_XBIT_TRANSFORMATION - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  The logical name of the transformation that creates directories on the remote execution pools.
characters(char[], int, int) - Method in class edu.isi.pegasus.planner.client.DAXValidator
characters(char[], int, int) - Method in class edu.isi.pegasus.planner.parser.InvocationParser
  This method is the callback function for characters in an element.
characters(char[], int, int) - Method in class edu.isi.pegasus.planner.parser.Parser
  This is used to store the character data that is in xml.
CHECK_DB_EXISTS_STMT - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.CreateTCDatabase
  MySQL statement for checking if DB exists
checkAndSetProperty(PegasusProperties, String, String) - Method in class edu.isi.pegasus.planner.common.PegasusConfiguration
  Checks for a property, if it does not exist then sets the property to the value passed
checkAndTransferIrodsEnvFile(TransferJob) - Method in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  Deprecated.
checkAndTransferProxy(TransferJob) - Method in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  Deprecated.
checkAndTransferProxy(TransferJob) - Method in interface edu.isi.pegasus.planner.transfer.Implementation
  Determines if there is a need to transfer proxy for the transfer job or not.
checkCompatibility(Implementation) - Method in class edu.isi.pegasus.planner.transfer.MultipleFTPerXFERJobRefiner
  Checks whether the implementation loaded is compatible with the refiner.
checkFile(String) - Method in class edu.isi.pegasus.planner.invocation.SimpleServer
  Reads the contents of the specified file, and returns with the remote exit code contained in the job chain.
checkForCorruption() - Method in class edu.isi.pegasus.planner.classes.ADag
  Checks the underlying graph structure for any corruption.
checkID(String) - Static method in class edu.isi.pegasus.planner.dax.AbstractJob
  Copy Constructor
checkIfDatabaseExists(String) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.CreateTCDatabase
  Checks if the given database exists
checkIn() - Method in class edu.isi.pegasus.planner.provisioner.Node
  check whether all parent tasks are finished.
checkIntegrity() - Method in class edu.isi.pegasus.planner.provisioner.Node
  check all child task's start time is scheduled after the finishtime of this task
checkKey(String, String) - Method in class edu.isi.pegasus.planner.namespace.Condor
  Additional method to handle the Condor namespace with convenience mappings.
checkKey(String, String) - Method in class edu.isi.pegasus.planner.namespace.Dagman
  This checks whether the key passed by the user is valid in the current namespace or not.
checkKey(String, String) - Method in class edu.isi.pegasus.planner.namespace.ENV
  This checks whether the key passed by the user is valid in the current namespace or not.
checkKey(String, String) - Method in class edu.isi.pegasus.planner.namespace.Globus
  Additional method to handle the globus namespace with convenience mappings.
checkKey(String, String) - Method in class edu.isi.pegasus.planner.namespace.Hints
  This checks whether the key passed by the user is valid in the current namespace or not.
checkKey(String, String) - Method in class edu.isi.pegasus.planner.namespace.Namespace
  This checks the whether a key value pair specified is valid in the current namespace or not, and whether it clashes with other key value pairs that might have been set by Pegasus internally.
checkKey(String, String) - Method in class edu.isi.pegasus.planner.namespace.Pegasus
  This checks whether the key passed by the user is valid in the current namespace or not.
checkKey(String, String) - Method in class edu.isi.pegasus.planner.namespace.Selector
  This checks whether the key passed by the user is valid in the current namespace or not.
checkKey(String, String) - Method in class edu.isi.pegasus.planner.namespace.Stat
  This checks whether the key passed by the user is valid in the current namespace or not.
checkKeyInNS(PegasusProperties, String) - Method in class edu.isi.pegasus.planner.namespace.Condor
  It puts in the namespace specific information specified in the properties file into the namespace.
checkKeyInNS(String, String) - Method in class edu.isi.pegasus.planner.namespace.Condor
  This checks the whether a key value pair specified is valid in the current namespace or not by calling the checkKey function and then on the basis of the values returned puts them into the associated map in the class.
checkKeyInNS(String, String) - Method in class edu.isi.pegasus.planner.namespace.Dagman
  This checks the whether a key value pair specified is valid in the current namespace or not by calling the checkKey function and then on the basis of the values returned puts them into the associated map in the class.
checkKeyInNS(PegasusProperties, String) - Method in class edu.isi.pegasus.planner.namespace.Dagman
  It puts in the namespace specific information specified in the properties file into the namespace.
checkKeyInNS(PegasusProperties, String) - Method in class edu.isi.pegasus.planner.namespace.ENV
  It puts in the namespace specific information specified in the properties file into the namespace.
checkKeyInNS(String) - Method in class edu.isi.pegasus.planner.namespace.ENV
  It takes in key=value pairs separated by a ; and puts them into the namespace after checking if they are valid or not.
checkKeyInNS(PegasusProperties, String) - Method in class edu.isi.pegasus.planner.namespace.Globus
  It puts in the namespace specific information specified in the properties file into the namespace.
checkKeyInNS(PegasusProperties, String) - Method in class edu.isi.pegasus.planner.namespace.Hints
  It puts in the namespace specific information specified in the properties file into the namespace.
checkKeyInNS(Namespace) - Method in class edu.isi.pegasus.planner.namespace.Namespace
  It puts in the namespaces keys from another namespace instance.
checkKeyInNS(TransformationCatalogEntry) - Method in class edu.isi.pegasus.planner.namespace.Namespace
  It puts in the namespace specific information from the Transformation Catalog into the namespace.
checkKeyInNS(Profile) - Method in class edu.isi.pegasus.planner.namespace.Namespace
  It takes in a Profiles object and puts them into the namespace after checking if the namespace in the Profile object is same as the namepsace implementation.
checkKeyInNS(List) - Method in class edu.isi.pegasus.planner.namespace.Namespace
  It takes in a list of profiles and puts them into the namespace after checking if they are valid or not.
checkKeyInNS(PegasusProperties, String) - Method in class edu.isi.pegasus.planner.namespace.Namespace
  It puts in the namespace specific information specified in the properties file into the namespace.
checkKeyInNS(String, String) - Method in class edu.isi.pegasus.planner.namespace.Namespace
  This checks the whether a key value pair specified is valid in the current namespace or not by calling the checkKey function and then on the basis of the values returned puts them into the associated map in the class.
checkKeyInNS(PegasusProperties, String) - Method in class edu.isi.pegasus.planner.namespace.Pegasus
  It puts in the namespace specific information specified in the properties file into the namespace.
checkKeyInNS(PegasusProperties, String) - Method in class edu.isi.pegasus.planner.namespace.Selector
  It puts in the namespace specific information specified in the properties file into the namespace.
checkKeyInNS(String) - Method in class edu.isi.pegasus.planner.namespace.Selector
  It takes in key=value pairs separated by a ; and puts them into the namespace after checking if they are valid or not.
checkKeyInNS(PegasusProperties, String) - Method in class edu.isi.pegasus.planner.namespace.Stat
  It puts in the namespace specific information specified in the properties file into the namespace.
checkKeyInNS(String) - Method in class edu.isi.pegasus.planner.namespace.Stat
  It takes in key=value pairs separated by a ; and puts them into the namespace after checking if they are valid or not.
checkLfnPfnMap(long, long) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Checks if a lfn,pfn exist in the map.
checkProfile(String, String, String, long, boolean) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Checks if a given profile exists
child - Variable in class edu.isi.pegasus.planner.classes.PCRelation
  the child making up the parent child relationship pair in a dag
CHILD_JOB_ID_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The atrribute key for child job id.
CHILD_TASK_ID_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The atrribute key for child task id.
childrenColored(int) - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  Returns if all the children of the node have the color that is specified.
childrenRepresentation() - Method in class edu.isi.pegasus.planner.partitioner.Topological
  Returns a map that is index by GraphNode ID's and each value is the list of ID's of children of that GraphNode.
childrenToString() - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  A convenience methods that generates a comma separated list of children as String
CHMOD_JOB - Static variable in class edu.isi.pegasus.planner.classes.Job
  Denotes a chmod job that sets the xbit on the remote end.
ClassADSGenerator - Class in edu.isi.pegasus.planner.code.generator.condor
  A helper class, that generates Pegasus specific classads for the jobs.
ClassADSGenerator() - Constructor for class edu.isi.pegasus.planner.code.generator.condor.ClassADSGenerator
classname - Variable in class edu.isi.pegasus.planner.client.TCClient
CLASSNAME - Static variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  The basename of the class that is implmenting this.
CLASSNAME - Static variable in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  The basename of the class that is implmenting this.
CLASSNAME - Static variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  The basename of the class that is implmenting this.
Cleanup - Class in edu.isi.pegasus.planner.refiner.cleanup
  Uses pegasus-cleanup to do removal of the files on the remote sites.
Cleanup() - Constructor for class edu.isi.pegasus.planner.refiner.cleanup.Cleanup
  The default constructor.
CLEANUP_BIT_FLAG - Static variable in class edu.isi.pegasus.planner.classes.PegasusFile
  If set, means can be considered for cleanup
CLEANUP_DAG_PREFIX - Static variable in class edu.isi.pegasus.planner.refiner.RemoveDirectory
  The prefix that is attached to the name of the dag for which the cleanup Dag is being generated, to generate the name of the cleanup Dag.
CLEANUP_DIR - Static variable in class edu.isi.pegasus.planner.client.CPlanner
  The basename of the directory that contains the submit files for the cleanup DAG that for the concrete dag generated for the workflow.
CLEANUP_DIR - Static variable in class edu.isi.pegasus.planner.refiner.MainEngine
  The basename of the directory that contains the submit files for the cleanup DAG that for the concrete dag generated for the workflow.
CLEANUP_JOB - Static variable in class edu.isi.pegasus.planner.classes.Job
  Denotes a cleanup job, that removes the files that from the remote working directories of the remote sites.
CLEANUP_JOB_PREFIX - Static variable in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  The prefix for CLEANUP_JOB ID i.e prefix+the parent compute_job ID becomes ID of the cleanup job.
CLEANUP_OPTIONS() - Constructor for enum edu.isi.pegasus.planner.classes.PlannerOptions.CLEANUP_OPTIONS
CLEANUP_PREFIX - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Constant suffix for the names of the deployment nodes.
CLEANUP_PREFIX - Static variable in class edu.isi.pegasus.planner.refiner.RemoveDirectory
  Constant suffix for the names of the deployment nodes.
CLEANUP_SCOPE() - Constructor for enum edu.isi.pegasus.planner.common.PegasusProperties.CLEANUP_SCOPE
CleanupEngine - Class in edu.isi.pegasus.planner.refiner
  The refiner that results in the creation of cleanup jobs within the workflow.
CleanupEngine(PegasusBag) - Constructor for class edu.isi.pegasus.planner.refiner.CleanupEngine
  The overloaded constructor.
CleanupFactory - Class in edu.isi.pegasus.planner.refiner.cleanup
  A factory class to load the appropriate type of Code Generator.
CleanupFactory() - Constructor for class edu.isi.pegasus.planner.refiner.cleanup.CleanupFactory
CleanupFactoryException - Exception in edu.isi.pegasus.planner.refiner.cleanup
  Class to notify of failures while instantiating Cleanup Strategy and Implementation classes.
CleanupFactoryException(String) - Constructor for exception edu.isi.pegasus.planner.refiner.cleanup.CleanupFactoryException
  Constructs a `CleanupFactoryException` with no detail message.
CleanupFactoryException(String, String) - Constructor for exception edu.isi.pegasus.planner.refiner.cleanup.CleanupFactoryException
  Constructs a `CleanupFactoryException` with the specified detailed message.
CleanupFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.refiner.cleanup.CleanupFactoryException
  Constructs a `CleanupFactoryException` with the specified detailed message and a cause.
CleanupFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.planner.refiner.cleanup.CleanupFactoryException
  Constructs a `CleanupFactoryException` with the specified detailed message and a cause.
CleanupImplementation - Interface in edu.isi.pegasus.planner.refiner.cleanup
  The interface that defines how the cleanup job is invoked and created.
CleanupJobContent - Class in edu.isi.pegasus.planner.refiner.cleanup
  A container class that is used to hold the contents for a cleanup job
CleanupJobContent(GraphNode, List<PegasusFile>) - Constructor for class edu.isi.pegasus.planner.refiner.cleanup.CleanupJobContent
CleanupStrategy - Interface in edu.isi.pegasus.planner.refiner.cleanup
  The interface that defines how the cleanup job is invoked and created.
clear() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Removes everything.
clear() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
clear() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Removes everything.
clear() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Removes everything from the catalogs.
clear() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Removes everything.
clear() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Removes everything.
clear() - Method in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Removes everything.
clear() - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.TransformationStore
  Clears all the entries in the store.
clear() - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Deletes the entire transformation catalog.
clear() - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Deletes the entire transformation catalog.
clear() - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Deletes the entire transformation catalog.
clear() - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Deletes the entire transformation catalog.
clear() - Method in class edu.isi.pegasus.planner.provenance.pasoa.producer.InMemory
  Clears the internal state.
clear() - Method in interface edu.isi.pegasus.planner.provenance.pasoa.XMLProducer
  Clears the internal state.
clearAliases() - Method in class edu.isi.pegasus.planner.catalog.site.classes.ReplicaCatalog
  Clears the aliases associates with the replica catalog.
client - Variable in class edu.isi.pegasus.gridftp.GridFTPConnection
Client - Class in edu.isi.pegasus.planner.catalog.transformation.client
Client() - Constructor for class edu.isi.pegasus.planner.catalog.transformation.client.Client
clone() - Method in class edu.isi.pegasus.common.util.CommonProperties
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.catalog.classes.SysInfo
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
clone() - Method in class edu.isi.pegasus.planner.catalog.site.classes.AbstractSiteData
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.catalog.site.classes.Connection
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.catalog.site.classes.Directory
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.catalog.site.classes.DirectoryLayout
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.catalog.site.classes.FileServerType
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.catalog.site.classes.FileSystemType
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.catalog.site.classes.HeadNodeFS
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.catalog.site.classes.ReplicaCatalog
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.catalog.site.classes.StorageType
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeFS
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeScratch
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.VDSSysInfo
  Return a copy of this Sysinfo object
clone() - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  creates a new instance of this object and returns you it.
clone() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns a new copy of the Object.
clone() - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Returns a new copy of the Object.
clone() - Method in class edu.isi.pegasus.planner.classes.AuthenticateRequest
  Returns a clone of the object.
clone() - Method in class edu.isi.pegasus.planner.classes.DagInfo
  Returns a new copy of the Object.
clone() - Method in class edu.isi.pegasus.planner.classes.DAGJob
  Returns a new copy of the Object.
clone() - Method in class edu.isi.pegasus.planner.classes.DAXJob
  Returns a new copy of the Object.
clone() - Method in class edu.isi.pegasus.planner.classes.FileTransfer
  Returns a clone of the object.
clone() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns a new copy of the Object.
clone() - Method in class edu.isi.pegasus.planner.classes.NameValue
  Returns a copy of this object
clone() - Method in class edu.isi.pegasus.planner.classes.Notifications
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.classes.PCRelation
  returns a new copy of the Object
clone() - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Returns a copy of the existing data object.
clone() - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns a new copy of the Object.
clone() - Method in class edu.isi.pegasus.planner.classes.Profile
  Returns a copy of the object.
clone() - Method in class edu.isi.pegasus.planner.classes.ReplicaLocation
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.classes.ReplicaStore
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.classes.TransferJob
  Returns a new copy of the Object.
clone() - Method in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.dax.Edge
clone() - Method in class edu.isi.pegasus.planner.dax.File
  Return a clone of this File
clone() - Method in class edu.isi.pegasus.planner.dax.Invoke
  Create a copy of this Invoke object
clone() - Method in class edu.isi.pegasus.planner.dax.MetaData
  Create a copy of this Metdata Object
clone() - Method in class edu.isi.pegasus.planner.dax.Profile
  Create a copy of this Profile
clone() - Method in class edu.isi.pegasus.planner.namespace.Condor
  Returns a copy of the current namespace object.
clone() - Method in class edu.isi.pegasus.planner.namespace.Dagman
  Returns a copy of the current namespace object.
clone() - Method in class edu.isi.pegasus.planner.namespace.ENV
  Returns a copy of the current namespace object.
clone() - Method in class edu.isi.pegasus.planner.namespace.Globus
  Returns a copy of the current namespace object
clone() - Method in class edu.isi.pegasus.planner.namespace.Hints
  Returns a copy of the current namespace object.
clone() - Method in class edu.isi.pegasus.planner.namespace.Namespace
  Returns the clone of the object.
clone() - Method in class edu.isi.pegasus.planner.namespace.Pegasus
  Returns a copy of the current namespace object
clone() - Method in class edu.isi.pegasus.planner.namespace.Selector
  Returns a copy of the current namespace object.
clone() - Method in class edu.isi.pegasus.planner.namespace.Stat
  Returns a copy of the current namespace object.
clone() - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  Returns a copy of the object.
clone() - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph
  Returns a copy of the object.
clone() - Method in class edu.isi.pegasus.planner.partitioner.Partition
  Returns a copy of the object
clone() - Method in class edu.isi.pegasus.planner.selector.site.RoundRobin.NameValue
  Returns a copy of this object.
cloneRCE(ReplicaCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
cloneSet(Set) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Clones a Set.
close() - Method in class edu.isi.pegasus.common.util.StreamGobbler
  Closes the underneath input and output stream that were opened.
close() - Method in class edu.isi.pegasus.common.util.XMLWriter
close() - Method in class edu.isi.pegasus.gridftp.GridFTPConnection
  Close the connection
close() - Method in class edu.isi.pegasus.gridftp.GridFTPConnection.StringBuilderDataSink
close() - Method in interface edu.isi.pegasus.planner.catalog.Catalog
  Explicitely free resources before the garbage collection hits.
close() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  This operation will dump the in-memory representation back onto disk.
close() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
  This operation will dump the in-memory representation back onto disk.
close() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Explicitely free resources before the garbage collection hits.
close() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Explicitely free resources before the garbage collection hits.
close() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  This operation will dump the in-memory representation back onto disk.
close() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  This operation will dump the in-memory representation back onto disk.
close() - Method in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  Closes the connection.
close() - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML
  Close the connection to backend file.
close() - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  Close the connection to backend file.
close() - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
close() - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
close() - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Closes the connection to the back end.
close() - Method in class edu.isi.pegasus.planner.catalog.work.Database
  Explicitely free resources before the garbage collection hits.
close() - Method in class edu.isi.pegasus.planner.classes.PlannerCache
  Explicitely free resources before the garbage collection hits.
close() - Method in class edu.isi.pegasus.planner.client.RCClient
  Frees resources taken by the instance of the replica catalog.
close() - Method in class edu.isi.pegasus.planner.partitioner.DAXWriter
  Close the write handle to the file that is written.
close() - Method in class edu.isi.pegasus.planner.partitioner.PDAXWriter
  Close the xml file that is written.
close() - Method in class edu.isi.pegasus.planner.ranking.GetDAX
  Explicitely free resources before the garbage collection hits.
CLOSE_COMMENT_TAG - Static variable in class edu.isi.pegasus.common.util.XMLWriter
CLOSE_ELEMENT_TAG - Static variable in class edu.isi.pegasus.common.util.XMLWriter
CLOSE_EMPTY_ELEMENT_TAG - Static variable in class edu.isi.pegasus.common.util.XMLWriter
CloseBrace - Class in edu.isi.pegasus.planner.parser.tokens
  Class to convey a closed brace, no token value necessary.
CloseBrace() - Constructor for class edu.isi.pegasus.planner.parser.tokens.CloseBrace
closeConnection() - Method in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  To close the connection to replica services.
closeElement() - Method in class edu.isi.pegasus.common.util.XMLWriter
  Close open elements start tag.
closeElement(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.AbstractXMLPrintVisitor
  Generates a closing tag for an element
CloseParanthesis - Class in edu.isi.pegasus.planner.parser.tokens
  Class to convey a closed paranthesis, no token value necessary.
CloseParanthesis() - Constructor for class edu.isi.pegasus.planner.parser.tokens.CloseParanthesis
  Default Constructor
cluster - Variable in class edu.isi.pegasus.planner.provisioner.Node
cluster(ADag) - Method in class edu.isi.pegasus.planner.refiner.NodeCollapser
  Clusters the jobs in the workflow.
cluster(ADag, String) - Method in class edu.isi.pegasus.planner.refiner.NodeCollapser
  Clusters the jobs in the workflow.
Cluster - Class in edu.isi.pegasus.planner.transfer.refiner
  A cluster refiner that builds upon the Bundle Refiner.
Cluster(ADag, PegasusBag) - Constructor for class edu.isi.pegasus.planner.transfer.refiner.Cluster
  The overloaded constructor.
CLUSTER_ARGUMENTS - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  Arguments that need to be passed to the clustering executable.
CLUSTER_LOCAL_STAGE_IN_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the key that determines the cluster parameter for the local stagein transfer node.
CLUSTER_LOCAL_STAGE_OUT_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the key that determines the cluster parameter for the local stagein transfer node.
CLUSTER_REMOTE_STAGE_IN_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the key that determines the clustering parameter for the stagein transfer node.
CLUSTER_REMOTE_STAGE_OUT_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the key that determines the bundling parameter for the remote stagein transfer node.
CLUSTER_STAGE_IN_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the key that determines the clustering parameter for the stagein transfer node.
CLUSTER_STAGE_OUT_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the key that determines the clustering parameter for the stageout transfer node.
clusterCleanupGraphNodes(List<GraphNode>, HashMap, String, int) - Method in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  Takes in a list of cleanup nodes ,one per cleanupNode(compute/stageout job) whose files need to be deleted) and clusters them into a smaller set of cleanup nodes.
CLUSTERED_JOB_PREFIX - Static variable in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  The prefix that is assigned to the jobname of the collapsed jobs to get the jobname for the fat job.
clusteredJob(Partition) - Method in class edu.isi.pegasus.planner.cluster.Abstract
  Returns the job corresponding to a partition.
clusteredJob(String) - Method in class edu.isi.pegasus.planner.cluster.Abstract
  Returns the job corresponding to a partition.
Clusterer - Interface in edu.isi.pegasus.planner.cluster
  The clustering API, that constructs clusters of jobs out of a single partition.
ClustererCallback - Class in edu.isi.pegasus.planner.partitioner
  A Callback implementation that passes the partitions detected during the partitioning of the worflow to a Clusterer for clustering.
ClustererCallback() - Constructor for class edu.isi.pegasus.planner.partitioner.ClustererCallback
  The default constructor.
ClustererException - Exception in edu.isi.pegasus.planner.cluster
  The baseclass of the exception that is thrown by all Clusterers.
ClustererException() - Constructor for exception edu.isi.pegasus.planner.cluster.ClustererException
  Constructs a `ClustererException` with no detail message.
ClustererException(String) - Constructor for exception edu.isi.pegasus.planner.cluster.ClustererException
  Constructs a `ClustererException` with the specified detailed message.
ClustererException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.cluster.ClustererException
  Constructs a `ClustererException` with the specified detailed message and a cause.
ClustererException(Throwable) - Constructor for exception edu.isi.pegasus.planner.cluster.ClustererException
  Constructs a `ClustererException` with the specified just a cause.
ClustererFactory - Class in edu.isi.pegasus.planner.cluster
  A factory class to load the appropriate Partitioner, and Clusterer Callback for clustering.
ClustererFactory() - Constructor for class edu.isi.pegasus.planner.cluster.ClustererFactory
ClustererFactoryException - Exception in edu.isi.pegasus.planner.cluster
  Class to notify of failures while instantiating Clusterer implementations.
ClustererFactoryException(String) - Constructor for exception edu.isi.pegasus.planner.cluster.ClustererFactoryException
  Constructs a `ClustererFactoryException` with no detail message.
ClustererFactoryException(String, String) - Constructor for exception edu.isi.pegasus.planner.cluster.ClustererFactoryException
  Constructs a `ClustererFactoryException` with the specified detailed message.
ClustererFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.cluster.ClustererFactoryException
  Constructs a `ClustererFactoryException` with the specified detailed message and a cause.
ClustererFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.planner.cluster.ClustererFactoryException
  Constructs a `ClustererFactoryException` with the specified detailed message and a cause.
clustererTable() - Static method in class edu.isi.pegasus.planner.cluster.ClustererFactory
  Returns a table that maps, the clustering technique to an appropriate class implementing that clustering technique.
clusteringOf(String, List) - Method in interface edu.isi.pegasus.planner.provenance.pasoa.PPS
clusteringOf(String, List) - Method in class edu.isi.pegasus.planner.provenance.pasoa.pps.Empty
  clusteringOf
CODE_GENERATOR_CLASS - Static variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The SubmitWriter that has to be loaded for now.
CodeGenerator - Interface in edu.isi.pegasus.planner.code
  The interface that allows us to plug in various code generators for writing out the concrete plan.
CodeGeneratorException - Exception in edu.isi.pegasus.planner.code
  The baseclass of the exception that is thrown by all Code Generators.
CodeGeneratorException() - Constructor for exception edu.isi.pegasus.planner.code.CodeGeneratorException
  Constructs a `CodeGeneratorException` with no detail message.
CodeGeneratorException(String) - Constructor for exception edu.isi.pegasus.planner.code.CodeGeneratorException
  Constructs a `CodeGeneratorException` with the specified detailed message.
CodeGeneratorException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.code.CodeGeneratorException
  Constructs a `CodeGeneratorException` with the specified detailed message and a cause.
CodeGeneratorException(Throwable) - Constructor for exception edu.isi.pegasus.planner.code.CodeGeneratorException
  Constructs a `CodeGeneratorException` with the specified just a cause.
CodeGeneratorFactory - Class in edu.isi.pegasus.planner.code
  A factory class to load the appropriate type of Code Generator.
CodeGeneratorFactory() - Constructor for class edu.isi.pegasus.planner.code.CodeGeneratorFactory
CodeGeneratorFactoryException - Exception in edu.isi.pegasus.planner.code
  Class to notify of failures while instantiating Code Generator implementations.
CodeGeneratorFactoryException(String) - Constructor for exception edu.isi.pegasus.planner.code.CodeGeneratorFactoryException
  Constructs a `CodeGeneratorFactoryException` with no detail message.
CodeGeneratorFactoryException(String, String) - Constructor for exception edu.isi.pegasus.planner.code.CodeGeneratorFactoryException
  Constructs a `CodeGeneratorFactoryException` with the specified detailed message.
CodeGeneratorFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.code.CodeGeneratorFactoryException
  Constructs a `CodeGeneratorFactoryException` with the specified detailed message and a cause.
CodeGeneratorFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.planner.code.CodeGeneratorFactoryException
  Constructs a `CodeGeneratorFactoryException` with the specified detailed message and a cause.
COLLAPSE_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the key that if set in the Pegasus namespace determines the number of jobs that are collapsed into the super job.
COLLAPSE_LOGICAL_NAME - Static variable in class edu.isi.pegasus.planner.cluster.aggregator.MPIExec
  The logical name of the transformation that is able to run multiple jobs via mpi.
COLLAPSE_LOGICAL_NAME - Static variable in class edu.isi.pegasus.planner.cluster.aggregator.SeqExec
  The logical name of the transformation that is able to run multiple jobs sequentially.
collapseJobs(String, List, String) - Method in class edu.isi.pegasus.planner.cluster.Horizontal
  Collapses the jobs having the same logical name according to the sites where they are scheduled.
COLLAPSER_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  Deprecated.
COLLECT_METRICS_ENV_VARIABLE - Static variable in class edu.isi.pegasus.planner.code.generator.Metrics
  The name of the environment variable that sets whether to collect metrics or not
COLLECTOR_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.CondorC
  The key that designates the collector associated with the job
COLLECTOR_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The key that designates the collector associated with the job.
columnLength(String[], int[]) - Static method in class edu.isi.pegasus.planner.catalog.transformation.client.TCQuery
  Computes the maximum column lenght for pretty printing.
columnLength(String[], int[]) - Static method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Computes the maximum column lenght for pretty printing.
combine(Profiles) - Static method in class edu.isi.pegasus.common.util.ProfileParser
  Creates a profile string from the internal representation.
combine(List) - Static method in class edu.isi.pegasus.common.util.ProfileParser
  Creates a profile string from the internal representation.
combine(String, String, String) - Static method in class edu.isi.pegasus.common.util.Separator
  Combines the three components that constitute a fully-qualified definition identifier into a single string.
combine(String, String, String, String) - Static method in class edu.isi.pegasus.common.util.Separator
  Combines the four components that reference a fully-qualified definition identifier into a single string.
combine(String, String, String) - Static method in class edu.isi.pegasus.planner.classes.Job
  Combines the three components together into a single string as namespace-name-version.
combine(String, int) - Method in class edu.isi.pegasus.planner.refiner.Authenticate
  A small helper method that returns the standard host and port combination to be used for logging purposes.
Command - Class in edu.isi.pegasus.gridftp
Command() - Constructor for class edu.isi.pegasus.gridftp.Command
CommandLine - Class in edu.isi.pegasus.planner.invocation
  This class maintains the application that was run, and the arguments to the commandline that were actually passed on to the application.
CommandLine() - Constructor for class edu.isi.pegasus.planner.invocation.CommandLine
  Default c'tor: Construct a hollow shell and allow further information to be added later.
CommandLine(String) - Constructor for class edu.isi.pegasus.planner.invocation.CommandLine
  Constructs an applications without arguments.
CommandLine(String, String) - Constructor for class edu.isi.pegasus.planner.invocation.CommandLine
  Constructs an applications with arguments.
commandLineOpts - Variable in class edu.isi.pegasus.planner.client.Executable
  The command line options passed to the executable
CommonProperties - Class in edu.isi.pegasus.common.util
  This class creates a common interface to handle package properties.
CommonProperties(String) - Constructor for class edu.isi.pegasus.common.util.CommonProperties
  ctor.
compare(Object, Object) - Method in class edu.isi.pegasus.planner.catalog.transformation.client.TCQuery.LFNComparator
  Compares this object with the specified object for order.
compare(Object, Object) - Method in class edu.isi.pegasus.planner.cluster.Horizontal.JobComparator
  Compares this object with the specified object for order.
compare(Object, Object) - Method in class edu.isi.pegasus.planner.partitioner.Horizontal.GraphNodeComparator
  Compares this object with the specified object for order.
compare(Node, Node) - Method in class edu.isi.pegasus.planner.provisioner.OccupationDiagram.NodeComp
compare(Object, Object) - Method in class edu.isi.pegasus.planner.selector.site.heft.HeftGraphNodeComparator
  Implementation of the `Comparable` interface.
compareTo(FileInfo) - Method in class edu.isi.pegasus.gridftp.FileInfo
compareTo(Object) - Method in class edu.isi.pegasus.planner.classes.NameValue
  Implementation of the `Comparable` interface.
compareTo(Object) - Method in class edu.isi.pegasus.planner.classes.PCRelation
compareTo(Object) - Method in class edu.isi.pegasus.planner.ranking.Ranking
  Implementation of the `Comparable` interface.
compareTo(Object) - Method in class edu.isi.pegasus.planner.selector.replica.Regex.Rank
  Compares the Rank object with another rank object.
complain(Directory.TYPE) - Method in class edu.isi.pegasus.planner.catalog.site.classes.StorageType
  Throws a Runtime Exception
complain(String, GraphNode, GraphNode) - Method in class edu.isi.pegasus.planner.classes.ADag
  Convenience method to complain for a linked node from a node that does not exist in the DAG
complain(String, String, String) - Method in class edu.isi.pegasus.planner.cluster.aggregator.MPIExec
  Complains for invalid values passed in profiles
complain(String, String, String) - Method in class edu.isi.pegasus.planner.parser.InvocationParser
  Small helper method to bundle repetitive complaints in a template for reporting progress.
complain(String, String, String) - Method in class edu.isi.pegasus.planner.parser.StackBasedXMLParser
  This is called when an attribute is encountered for an element that is invalid from the schema context and is not supported.
complainForCredential(Job, String, String) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.Abstract
  Complain if a particular credential key is not found for a site
complainForHeadNodeFileServer(String, String) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Complains for a missing head node file server on a site for a job
complainForHeadNodeURLPrefix(String, String, FileServerType.OPERATION) - Method in class edu.isi.pegasus.planner.refiner.Engine
  Complains for head node url prefix not specified
complainForHeadNodeURLPrefix(String, String, FileServerType.OPERATION, Job) - Method in class edu.isi.pegasus.planner.refiner.Engine
  Complains for head node url prefix not specified
complainForHeadNodeURLPrefix(String) - Method in class edu.isi.pegasus.planner.transfer.sls.Transfer
  Complains for head node url prefix not specified
complainForHeadNodeURLPrefix(Job, String) - Method in class edu.isi.pegasus.planner.transfer.sls.Transfer
  Complains for head node url prefix not specified
complainForScratchFileServer(Job, FileServerType.OPERATION, String) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  Complains for a missing head node file server on a site for a job
complainForScratchFileServer(String, FileServerType.OPERATION, String) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  Complains for a missing head node file server on a site for a job
complainForStorageFileServer(FileServerType.OPERATION, String) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.AbstractFileFactoryBasedMapper
  Complains for a missing head node storage file server on a site for a job
complete - Variable in class edu.isi.pegasus.planner.provisioner.Edge
COMPLETE_TRANSFORMATION_NAME - Static variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  The complete TC name for kickstart.
COMPLETE_TRANSFORMATION_NAME - Static variable in class edu.isi.pegasus.planner.refiner.createdir.DefaultImplementation
  The complete TC name for kickstart.
COMPLETE_TRANSFORMATION_NAME - Static variable in class edu.isi.pegasus.planner.refiner.createdir.HourGlass
  The complete TC name for dirmanager.
COMPLETE_TRANSFORMATION_NAME - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The complete TC name for pegasus worker package.
COMPLETE_UNTAR_TRANSFORMATION_NAME - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The complete TC name for untar.
CompoundTransformation - Class in edu.isi.pegasus.planner.classes
  A data class to contain compound transformations.
CompoundTransformation(String) - Constructor for class edu.isi.pegasus.planner.classes.CompoundTransformation
  Constructor
CompoundTransformation(String, String, String) - Constructor for class edu.isi.pegasus.planner.classes.CompoundTransformation
  Overloaded Constructor
compTime - Variable in class edu.isi.pegasus.planner.provisioner.Edge
compute(String, String, String) - Method in interface edu.isi.pegasus.planner.namespace.aggregator.Aggregator
  Do the aggregation function on the profile values.
compute(String, String, String) - Method in class edu.isi.pegasus.planner.namespace.aggregator.MAX
  Returns the maximum of two values.
compute(String, String, String) - Method in class edu.isi.pegasus.planner.namespace.aggregator.MIN
  Returns the minimum of two values.
compute(String, String, String) - Method in class edu.isi.pegasus.planner.namespace.aggregator.Sum
  Sums up the values.
compute(String, String, String) - Method in class edu.isi.pegasus.planner.namespace.aggregator.UniqueMerge
  Sums up the values.
compute(String, String, String) - Method in class edu.isi.pegasus.planner.namespace.aggregator.Update
  Returns the minimum of two values.
COMPUTE_JOB - Static variable in class edu.isi.pegasus.planner.classes.Job
  Denotes a compute job.
computeDownwardRank(GraphNode) - Method in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  Computes the downward rank of a node.
computeRuntime() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the runtime associated with the job.
concreteDagEmpty(String, ADag) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  A callout method that dictates what needs to be done in case the concrete plan that is generated is empty.
ConditionVariable() - Constructor for class edu.isi.pegasus.planner.refiner.ThreadPool.ConditionVariable
  The default constructor.
CONDOR - Static variable in class edu.isi.pegasus.planner.classes.Profile
Condor - Class in edu.isi.pegasus.planner.code.generator.condor.style
  Enables a job to be directly submitted to the condor pool of which the submit host is a part of.
Condor() - Constructor for class edu.isi.pegasus.planner.code.generator.condor.style.Condor
  The default constructor.
Condor - Class in edu.isi.pegasus.planner.namespace
  This helper class helps in handling the arguments specified in the Condor namespace by the user either through dax or through profiles in pool.
Condor() - Constructor for class edu.isi.pegasus.planner.namespace.Condor
  The default constructor.
Condor(Map) - Constructor for class edu.isi.pegasus.planner.namespace.Condor
  The overloaded constructor
Condor - Class in edu.isi.pegasus.planner.transfer.sls
  This uses the Condor File Transfer mechanism for the second level staging.
Condor() - Constructor for class edu.isi.pegasus.planner.transfer.sls.Condor
  The default constructor.
CONDOR_CODE_GENERATOR_CLASS - Static variable in class edu.isi.pegasus.planner.code.CodeGeneratorFactory
  The name of the class implementing the condor code generator.
CONDOR_CONFIGURATION_VALUE - Static variable in class edu.isi.pegasus.planner.common.PegasusConfiguration
  The value for the condor configuration.
CONDOR_DAGMAN_LOGICAL_NAME - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  The logical name with which to query the transformation catalog for the condor_dagman executable, that ends up running the mini dag as one job.
CONDOR_DAGMAN_LOGICAL_NAME - Static variable in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  The logical name with which to query the transformation catalog for the condor_dagman executable, that ends up running the mini dag as one job.
CONDOR_DAGMAN_LOGICAL_NAME - Static variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The logical name with which to query the transformation catalog for the condor_dagman executable, that ends up running the mini dag as one job.
CONDOR_DAGMAN_NAMESPACE - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  The namespace to use for condor dagman.
CONDOR_DAGMAN_NAMESPACE - Static variable in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  The namespace to use for condor dagman.
CONDOR_DAGMAN_NAMESPACE - Static variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The namespace to use for condor dagman.
CONDOR_KICKSTART - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
CONDOR_REMOTE_DIRECTORY_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.GLite
  The Condor remote directory classad key to be used with Glite
CONDOR_STYLE - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The style indicating that the submit files are to be generated for a vanilla condor execution.
CONDOR_STYLE_IMPLEMENTING_CLASS - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactory
  The name of the class implementing the Condor Style.
CONDOR_VERSION_COMMAND - Static variable in class edu.isi.pegasus.common.util.CondorVersion
  The condor version command to be executed.
CondorC - Class in edu.isi.pegasus.planner.code.generator.condor.style
  Enables a job to be directly submitted to the condor pool of which the submit host is a part of.
CondorC() - Constructor for class edu.isi.pegasus.planner.code.generator.condor.style.CondorC
  The default constructor.
CONDORC_STYLE - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The style indicating that the submit files are to be generated for a CondorC submission to remote schedds.
CONDORC_STYLE_IMPLEMENTING_CLASS - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactory
  The name of the class implementing the CondorC Style.
CondorG - Class in edu.isi.pegasus.planner.code.generator.condor.style
  This implementation enables a job to be submitted via CondorG to remote grid sites.
CondorG() - Constructor for class edu.isi.pegasus.planner.code.generator.condor.style.CondorG
  The default Constructor.
CondorGenerator - Class in edu.isi.pegasus.planner.code.generator.condor
  This class generates the condor submit files for the DAG which has to be submitted to the Condor DagMan.
CondorGenerator() - Constructor for class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  The default constructor.
CondorGlideIN - Class in edu.isi.pegasus.planner.code.generator.condor.style
  Enables a job to be submitted to nodes that are logically part of the local pool, but physically are not.
CondorGlideIN() - Constructor for class edu.isi.pegasus.planner.code.generator.condor.style.CondorGlideIN
  The default constructor.
CondorGlideinWMS - Class in edu.isi.pegasus.planner.code.generator.condor.style
  Jobs targeting glidinWMS pools.
CondorGlideinWMS() - Constructor for class edu.isi.pegasus.planner.code.generator.condor.style.CondorGlideinWMS
  The default constructor.
CondorQuoteParser - Class in edu.isi.pegasus.planner.code.generator.condor
  A utility class to correctly quote arguments strings before handing over to Condor.
CondorQuoteParser() - Constructor for class edu.isi.pegasus.planner.code.generator.condor.CondorQuoteParser
CondorQuoteParserException - Exception in edu.isi.pegasus.planner.code.generator.condor
  This class is used to signal errors while parsing argument strings for Condor Quoting.
CondorQuoteParserException(String, int) - Constructor for exception edu.isi.pegasus.planner.code.generator.condor.CondorQuoteParserException
  The overloaded constructor
CondorQuoteParserException(String, int, Throwable) - Constructor for exception edu.isi.pegasus.planner.code.generator.condor.CondorQuoteParserException
  The overloaded constructor
CondorStyle - Interface in edu.isi.pegasus.planner.code.generator.condor
  An interface to allow us to apply different execution styles to a job via Condor DAGMAN.
CondorStyleException - Exception in edu.isi.pegasus.planner.code.generator.condor
  A specific exception for the Condor Style generators.
CondorStyleException() - Constructor for exception edu.isi.pegasus.planner.code.generator.condor.CondorStyleException
  Constructs a `CondorStyleException` with no detail message.
CondorStyleException(String) - Constructor for exception edu.isi.pegasus.planner.code.generator.condor.CondorStyleException
  Constructs a `CondorStyleException` with the specified detailed message.
CondorStyleException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.code.generator.condor.CondorStyleException
  Constructs a `CondorStyleException` with the specified detailed message and a cause.
CondorStyleException(Throwable) - Constructor for exception edu.isi.pegasus.planner.code.generator.condor.CondorStyleException
  Constructs a `CondorStyleException` with the specified just a cause.
CondorStyleFactory - Class in edu.isi.pegasus.planner.code.generator.condor
  A factory class to load the appropriate type of Condor Style impelementations.
CondorStyleFactory() - Constructor for class edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactory
  The default constructor.
CondorStyleFactoryException - Exception in edu.isi.pegasus.planner.code.generator.condor
  Class to notify of failures while instantiating Condor Style implementations.
CondorStyleFactoryException(String) - Constructor for exception edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactoryException
  Constructs a `CondorStyleFactoryException` with no detail message.
CondorStyleFactoryException(String, String) - Constructor for exception edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactoryException
  Constructs a `CondorStyleFactoryException` with the specified detailed message.
CondorStyleFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactoryException
  Constructs a `CondorStyleFactoryException` with the specified detailed message and a cause.
CondorStyleFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactoryException
  Constructs a `CondorStyleFactoryException` with the specified detailed message and a cause.
condorUniverse - Variable in class edu.isi.pegasus.planner.classes.Job
  The universe in which the job has to be executed.
condorVariables - Variable in class edu.isi.pegasus.planner.classes.Job
  For Condor Namespace.
CondorVersion - Class in edu.isi.pegasus.common.util
  A utility class that allows us to determine condor version.
CondorVersion(LogManager) - Constructor for class edu.isi.pegasus.common.util.CondorVersion
  The default constructor.
CondorVersion.CondorVersionCallback - Class in edu.isi.pegasus.common.util
  An inner class, that implements the StreamGobblerCallback to determine the version of Condor being used.
CondorVersionCallback() - Constructor for class edu.isi.pegasus.common.util.CondorVersion.CondorVersionCallback
  The Default Constructor
CONFIG_MESSAGE_LEVEL - Static variable in class edu.isi.pegasus.common.logging.LogManager
  The level value, to indicate a CONFIG message.
CONFIG_MESSAGE_TYPE - Static variable in class edu.isi.pegasus.common.logging.logger.Default
  The type value to indicate a CONFIG message.
CONFIGURED_TEMPLATES_Q - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
ConfigXmlParser - Class in edu.isi.pegasus.planner.parser
  This is the parsing class, used to parse the pool config file in xml format.
ConfigXmlParser(PegasusProperties) - Constructor for class edu.isi.pegasus.planner.parser.ConfigXmlParser
  Default Class Constructor.
ConfigXmlParser(String, PegasusProperties) - Constructor for class edu.isi.pegasus.planner.parser.ConfigXmlParser
  Class Constructor intializes the parser and turns on validation.
connect(GridFTPURL) - Method in class edu.isi.pegasus.gridftp.Command
connect(Properties) - Method in interface edu.isi.pegasus.planner.catalog.Catalog
  Establishes a link between the implementation and the thing the implementation is build upon.
connect(Properties) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Establishes a connection to the database from the properties.
connect(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Does the file listing on the directory to create the mappings in memory.
connect(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
  Opens the file for writing.
connect(Properties) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
  Establishes a connection to the database from the properties.
connect(String, String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Connects to the database.
connect(Properties) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Establishes a connection to the database from the properties.
connect(Properties) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Establishes a link between the implementation and the thing the implementation is build upon.
connect(String, Properties) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Connects to an individual replica catalog.
connect(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Reads the on-disk map file into memory.
connect(Properties) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Establishes a connection to the database from the properties.
connect(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Reads the on-disk map file into memory.
connect(Properties) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Establishes a connection to the database from the properties.
connect(Properties) - Method in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  Issues the condor status command, and stores the results retrieved back into a List.
connect(Properties) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML
  Establishes a connection to the file from the properties.
connect(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML
  Initializes the Site Catalog Parser instance for the file.
connect(Properties) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  Establishes a connection to the file from the properties.
connect(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  Initializes the Site Catalog Parser instance for the file.
connect(Properties) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
connect(Properties) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
connect(Properties) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Empty for the time being.
connect(String, String, String) - Method in class edu.isi.pegasus.planner.catalog.work.Database
  Connects to the database.
connect(Properties) - Method in class edu.isi.pegasus.planner.catalog.work.Database
  Establishes a connection to the database from the properties.
connect(PegasusProperties) - Method in class edu.isi.pegasus.planner.client.RCClient
  Connects the interface with the replica catalog implementation.
connect(PegasusProperties) - Method in class edu.isi.pegasus.planner.ranking.GetDAX
  A convenience method to connect on the basis of PegasusProperties.
connect(Properties) - Method in class edu.isi.pegasus.planner.ranking.GetDAX
  Establishes a connection to the database from the properties.
Connection - Class in edu.isi.pegasus.planner.catalog.site.classes
  This data class describes a connection property for replica catalog.
Connection() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.Connection
  The default constructor.
Connection(String, String) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.Connection
  The overloaded constructor.
connectionCache - Variable in class edu.isi.pegasus.gridftp.Command
connectMds() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
  Create and return a MDS LdapContext.
CONSOLE_MESSAGE_LEVEL - Static variable in class edu.isi.pegasus.common.logging.LogManager
  The level value, to indicate a CONSOLE error message.
CONSOLE_MESSAGE_TYPE - Static variable in class edu.isi.pegasus.common.logging.logger.Default
  The type value to indicate a CONSOLE message.
constituentJobsIterator() - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Returns an iterator to the constituent jobs of the AggregatedJob.
construct(Job, String, String) - Method in class edu.isi.pegasus.planner.client.CPlanner
  Constructs a condor variable in the condor profile namespace associated with the job.
construct(Job, String, String) - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Constructs a condor variable in the condor profile namespace associated with the constituentJob.
construct(Job, String) - Method in class edu.isi.pegasus.planner.code.gridstart.NetloggerPostScript
  Constructs the postscript that has to be invoked on the submit host after the job has executed on the remote end.
construct(Job, String, String) - Method in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  Constructs a condor variable in the condor profile namespace associated with the job.
construct(Job, String) - Method in class edu.isi.pegasus.planner.code.gridstart.NoPOSTScript
  Constructs the postscript that has to be invoked on the submit host after the job has executed on the remote end.
construct(Job, String) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusExitCode
  Constructs the postscript that has to be invoked on the submit host after the job has executed on the remote end.
construct(Job, String, String) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Constructs a condor variable in the condor profile namespace associated with the job.
construct(Job, String) - Method in class edu.isi.pegasus.planner.code.gridstart.UserPOSTScript
  Constructs the postscript that has to be invoked on the submit host after the job has executed on the remote end.
construct(Job, String) - Method in interface edu.isi.pegasus.planner.code.POSTScript
  Constructs the postscript that has to be invoked on the submit host after the job has executed on the remote end.
construct(String, String) - Method in class edu.isi.pegasus.planner.namespace.Condor
  Constructs a new element of the format (key=value).
construct(String, String) - Method in class edu.isi.pegasus.planner.namespace.Dagman
  Constructs a new element of the format (key=value).
construct(String, String) - Method in class edu.isi.pegasus.planner.namespace.ENV
  Constructs a new element of the format (key=value).
construct(String, String) - Method in class edu.isi.pegasus.planner.namespace.Globus
  Constructs a new element of the format (key=value).
construct(String, String) - Method in class edu.isi.pegasus.planner.namespace.Hints
  Constructs a new element of the format (key=value).
construct(String, String) - Method in class edu.isi.pegasus.planner.namespace.Namespace
  Constructs a new element of the format (key=value).
construct(String, String) - Method in class edu.isi.pegasus.planner.namespace.Pegasus
  Constructs a new element of the format (key=value).
construct(String, String) - Method in class edu.isi.pegasus.planner.namespace.Selector
  Constructs a new element of the format (key=value).
construct(String, String) - Method in class edu.isi.pegasus.planner.namespace.Stat
  Constructs a new element of the format (key=value).
construct(Job, String, String) - Method in class edu.isi.pegasus.planner.refiner.createdir.HourGlass
  Constructs a condor variable in the condor profile namespace associated with the job.
construct(Job, String, String) - Method in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  Constructs a condor variable in the condor profile namespace associated with the job.
constructAbstractAggregatedJob(List, String, String) - Method in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  Constructs a new aggregated job that contains all the jobs passed to it.
constructAbstractAggregatedJob(List, String, String, String) - Method in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  Constructs an abstract aggregated job that has a handle to the appropriate JobAggregator that will be used to aggregate the jobs.
constructAbstractAggregatedJob(List, String, String) - Method in interface edu.isi.pegasus.planner.cluster.JobAggregator
  Constructs an abstract aggregated job that has a handle to the appropriate JobAggregator that will be used to aggregate the jobs.
constructCleanupJob(Job, String) - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Constructs a kickstart setup constituentJob
constructClusteredJobID(Partition) - Method in class edu.isi.pegasus.planner.cluster.Abstract
  Returns the ID for the clustered job corresponding to a partition.
constructClusteredJobID(Partition) - Method in class edu.isi.pegasus.planner.cluster.Vertical
  Returns the ID for the clustered job corresponding to a partition.
constructCondorKey(Job, String, String) - Method in class edu.isi.pegasus.planner.transfer.refiner.Cluster
  Constructs a condor variable in the condor profile namespace associated with the job.
constructDAGJob(String, String, String) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Constructs a job that plans and submits the partitioned workflow, referred to by a Partition.
constructDAGJob(Job, File, File, String) - Method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Constructs a job that plans and submits the partitioned workflow, referred to by a Partition.
constructDAGJob(Partition, File, String) - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Constructs a job that plans and submits the partitioned workflow, referred to by a Partition.
constructDAGManKnobs(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Constructs Any extra arguments that need to be passed to dagman, as determined from the properties file.
constructDAGManKnobs(PegasusProperties) - Static method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Constructs Any extra arguments that need to be passed to dagman, as determined from the properties file.
constructDefaultURLToPegasusWorkerPackage(String, SysInfo) - Method in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Constructs the default URL's for the pegasus worker package.
constructFileKey(String, String) - Method in class edu.isi.pegasus.planner.transfer.refiner.Basic
  Constructs the key for an entry to the file table.
constructFileTX(PegasusFile, Job, String, String, boolean) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  Constructs the FileTransfer object on the basis of the transiency information.
constructGridResource(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.CondorC
  Constructs the grid_resource entry for the job.
constructGridResource(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.CreamCE
  Constructs the grid_resource entry for the job.
constructGridResource(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.SSH
  Constructs the grid_resource entry for the job.
constructID(String, int) - Method in class edu.isi.pegasus.planner.cluster.Horizontal
  Given an integer id, returns a string id that is used for the clustered job.
constructJobID(Job) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser3
  Returns the id for a job
constructLevelRelations(Callback, int, int) - Method in class edu.isi.pegasus.planner.partitioner.BFS
  Calls out to the callback with appropriate relations between the partitions constructed for the levels.
constructLevelRelations(Callback, int, int) - Method in class edu.isi.pegasus.planner.partitioner.Horizontal
  Calls out to the callback with appropriate relations between the partitions constructed for the levels.
constructMap(String) - Method in class edu.isi.pegasus.planner.cluster.Horizontal
  Constructs a map with the numbers/values for the collapsing factors to collapse the nodes of same type.
constructMap(String) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Constructs a map with the numbers/values to be passed in the RSL handle for certain pools.
constructPartition() - Method in class edu.isi.pegasus.planner.partitioner.Partition
  It while looking at the node list constructs the relations between the jobs in the partition, that can be gotten through getRelationsInPartition().
constructPartitionName(String, boolean) - Static method in class edu.isi.pegasus.planner.partitioner.DAXWriter
  It constructs the partition name given the daxName.
constructPartitions(Callback, List, int) - Method in class edu.isi.pegasus.planner.partitioner.BFS
  Given a list of jobs, constructs (one or more) partitions out of it.
constructPartitions(Callback, List, int) - Method in class edu.isi.pegasus.planner.partitioner.Horizontal
  Given a list of jobs, constructs (one or more) partitions out of it.
constructPartitions(Callback, List, int, String) - Method in class edu.isi.pegasus.planner.partitioner.Horizontal
  Given a list of jobs, constructs (one or more) partitions out of it.
constructPegasusPlanPrescript(Job, PlannerOptions, String, String, String) - Method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Constructs the pegasus plan prescript for the subdax
constructPlannerPrescriptWrapper(Job, File, String, String) - Method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Construct a pegasus plan wrapper script that changes the directory in which pegasus-plan is launched.
constructPREJob(Job, String, String, String, String) - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Constructs the prejob that fetches sls file, and then invokes transfer again.
constructRegistrationURL(String, String) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  Constructs a Registration URL for a LFN
constructSetupJob(Job, String) - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Constructs a kickstart setup constituentJob
constructSiteCatalog(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.CreateSampleSiteCatalog
  Generates a sample site catalog.
constructSiteToSRMServerMap(PegasusProperties) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  Constructs a Properties objects by parsing the relevant SRM pegasus properties.
constructTCEntryFromEnvironment() - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Returns a tranformation catalog entry object constructed from the environment An entry is constructed if either of the following environment variables are defined 1) CONDOR_HOME 2) CONDOR_LOCATION CONDOR_HOME takes precedence over CONDOR_LOCATION
constructTCEntryFromEnvironment() - Method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Returns a transformation catalog entry object constructed from the environment An entry is constructed if either of the following environment variables are defined 1) CONDOR_HOME 2) CONDOR_LOCATION CONDOR_HOME takes precedence over CONDOR_LOCATION
constructTCEntryFromEnvironment() - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Returns a tranformation catalog entry object constructed from the environment An entry is constructed if either of the following environment variables are defined 1) CONDOR_HOME 2) CONDOR_LOCATION CONDOR_HOME takes precedence over CONDOR_LOCATION
constructTCEntryFromEnvProfiles(ENV) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Returns a tranformation catalog entry object constructed from the environment An entry is constructed if either of the following environment variables are defined 1) CONDOR_HOME 2) CONDOR_LOCATION CONDOR_HOME takes precedence over CONDOR_LOCATION
constructTCEntryFromEnvProfiles(ENV) - Method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Returns a tranformation catalog entry object constructed from the environment An entry is constructed if either of the following environment variables are defined 1) CONDOR_HOME 2) CONDOR_LOCATION CONDOR_HOME takes precedence over CONDOR_LOCATION
constructTCEntryFromEnvProfiles(ENV) - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Returns a tranformation catalog entry object constructed from the environment An entry is constructed if either of the following environment variables are defined 1) CONDOR_HOME 2) CONDOR_LOCATION CONDOR_HOME takes precedence over CONDOR_LOCATION
constructTCEntryFromJobHints(Job) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Constructs a TC entry object from the contents of a job.
constructTCEntryFromPath() - Method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Returns a tranformation catalog entry object constructed from the path environment variable
constructTransformationCatalogEntryForDAGMan(String) - Method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Constructs TransformationCatalogEntry for DAGMan.
constructURL(FileServer, String) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.AbstractFileFactoryBasedMapper
  Returns the full path on remote output site, where the lfn will reside, using the FileServer passed.
contains(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  Returns boolean indicating whether the store has a SiteCatalogEntry matching a handle.
contains(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.PoolConfig
  Returns a boolean indicating if an entry for a Site with a particular id exists or not.
containsAbstractJob(AbstractJob) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Check if an abstractjob exists in the DAX
containsAbstractJobId(String) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Check if a jobid exists in the DAX
containsDAG(DAG) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Check if a DAG job exists in the DAX
containsDAGId(String) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Check if a DAG job id exists in the DAX
containsDAX(DAX) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Check if a DAX job exists in the DAX
containsDAXId(String) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Check if a DAX job id exists in the DAX
containsExecutable(Executable) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Checks if a given executable exists in the DAX based Transformation Catalog
containsJob(Job) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Check if a job exists in the DAX
containsJobId(String) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Check if a jobid exists in the DAX
containsKey(Object) - Method in class edu.isi.pegasus.planner.classes.PegasusBag
  Returns true if the namespace contains a mapping for the specified key.
containsKey(Object) - Method in class edu.isi.pegasus.planner.namespace.Hints
  Returns true if the namespace contains a mapping for the specified key.
containsKey(Object) - Method in class edu.isi.pegasus.planner.namespace.Namespace
  Returns true if the namespace contains a mapping for the specified key.
containsKey(Object) - Method in class edu.isi.pegasus.planner.namespace.Pegasus
  Returns true if the namespace contains a mapping for the specified key.
containsKey(Object) - Method in interface edu.isi.pegasus.planner.partitioner.graph.Bag
  Returns true if the namespace contains a mapping for the specified key.
containsKey(Object) - Method in class edu.isi.pegasus.planner.partitioner.graph.LabelBag
  Returns true if the namespace contains a mapping for the specified key.
containsKey(Object) - Method in class edu.isi.pegasus.planner.refiner.DataReuseEngine.BooleanBag
  Returns false.
containsKey(Object) - Method in class edu.isi.pegasus.planner.selector.site.heft.HeftBag
  Returns true if the namespace contains a mapping for the specified key.
containsKey(String) - Method in class edu.isi.pegasus.planner.transfer.RemoteTransfer
  Returns whether there is an entry for a particular site or not.
containsKey(String) - Method in class edu.isi.pegasus.planner.transfer.TPT
  Returns whether there is an entry for a particular site or not.
containsLFN(String) - Method in class edu.isi.pegasus.planner.classes.ReplicaStore
  Returns a boolean indicating whether the store has a mapping for a particular LFN or not.
containsTransformation(String, String, String) - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.TransformationStore
  Returns a boolean indicating whether the store contains an entry corresponding to a particular transformation or not.
containsTransformation(String) - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.TransformationStore
  Returns a boolean indicating whether the store contains an entry corresponding to a particular transformation or not.
containsTransformation(Transformation) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Checks if a given Transformation exists in the DAX based Transformation Catalog
convert(SiteCatalogEntry3) - Static method in class edu.isi.pegasus.planner.catalog.site.classes.Adapter
  An adapter method that converts the `SiteCatalogEntry3` object to `SiteCatalogEntry` object.
convert(SiteCatalogEntry) - Static method in class edu.isi.pegasus.planner.catalog.site.classes.Adapter
  An adapter method that converts the `SiteCatalogEntry` object to `SiteCatalogEntry3` object.
convert(SiteInfo) - Static method in class edu.isi.pegasus.planner.catalog.site.classes.SiteInfo2SiteCatalogEntry
  An adapter method that converts the `SiteInfo` object to `SiteCatalogEntry` object.
convert(SiteInfo, LogManager) - Static method in class edu.isi.pegasus.planner.catalog.site.classes.SiteInfo2SiteCatalogEntry
  An adapter method that converts the `SiteInfo` object to `SiteCatalogEntry` object.
convert(String, String) - Method in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  Convert a VDS Properties file to Pegasus properties.
convert(Map) - Method in class edu.isi.pegasus.planner.namespace.Globus
  Converts a map with RSL kv-pairs into an RSL string.
convertException(String, Exception) - Static method in class edu.isi.pegasus.common.util.DynamicLoader
  Converts an exception from the class loader into an error message.
convertException(Exception) - Method in class edu.isi.pegasus.common.util.DynamicLoader
  Converts an exception from the class loader into an error message.
convertException() - Method in exception edu.isi.pegasus.common.util.FactoryException
  Converts most of the common instantiation exceptions from the class loader into an error message.
convertException(int) - Method in exception edu.isi.pegasus.common.util.FactoryException
  Converts most of the common instantiation exceptions from the class loader into an error message.
convertException(String, Throwable, int) - Static method in exception edu.isi.pegasus.common.util.FactoryException
  Converts most of the common instantiation exceptions from the class loader into an error message.
convertException(Exception, int) - Static method in class edu.isi.pegasus.planner.catalog.transformation.client.Client
  Returns an error message that chains all the lower order error messages that might have been thrown.
convertException(Exception) - Static method in class edu.isi.pegasus.planner.client.Executable
  Returns an error message that chains all the lower order error messages that might have been thrown.
convertException(Exception, int) - Static method in class edu.isi.pegasus.planner.client.Executable
  Returns an error message that chains all the lower order error messages that might have been thrown.
convertExceptionToString(String, Throwable) - Static method in class edu.isi.pegasus.common.util.DynamicLoader
  Converts an exception from the class loader into an error message.
convertExecutableToTCE(Executable) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser3
  Converts the executable into transformation catalog entries
convertTC() - Method in class edu.isi.pegasus.planner.client.TCConverter
  Converts transformation catalog from one format to another
convertTCEntryFrom(List<String>, String) - Method in class edu.isi.pegasus.planner.client.TCConverter
  Parses the input files in the input format and returns the output as a TransformationStore instance
convertTCEntryTo(TransformationStore, String, String) - Method in class edu.isi.pegasus.planner.client.TCConverter
  Converts Transformation store to the given output format.
convertToList(Vector) - Method in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  Converts a Vector to a List.
convertToList(Set) - Method in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  Converts a Set to a List.
convertToSiteInfo(SiteCatalogGenerator.Site) - Static method in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  An adapter method that converts the Site object to the SiteInfo object corresponding to the site catalog schema version 2.
convertToTransferInputFormat(Collection<FileTransfer>) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Convers the collection of files into an input format suitable for the transfer executable
CORES_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.ClassADSGenerator
  The key for the number of cores for the multiplier factor in stampede.
CORES_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The number of cores that are associated with the job.
cost - Variable in class edu.isi.pegasus.planner.provisioner.Edge
CPlanner - Class in edu.isi.pegasus.planner.client
  This is the main program for the Pegasus.
CPlanner() - Constructor for class edu.isi.pegasus.planner.client.CPlanner
  Default constructor.
CPlanner(LogManager) - Constructor for class edu.isi.pegasus.planner.client.CPlanner
  The overload constructor.
CPLANNER_LOGICAL_NAME - Static variable in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  The logical name with which to query the transformation catalog for cPlanner executable.
CPLANNER_LOGICAL_NAME - Static variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The logical name with which to query the transformation catalog for cPlanner executable.
CPU - Class in edu.isi.pegasus.planner.invocation
  The CPU element.
CPU() - Constructor for class edu.isi.pegasus.planner.invocation.CPU
  The default constructor
CPU(String) - Constructor for class edu.isi.pegasus.planner.invocation.CPU
  Constructs a piece of data.
CreamCE - Class in edu.isi.pegasus.planner.code.generator.condor.style
  Enables a job to be directly submitted to a remote CREAM CE front end The CREAM CE support in Condor is documented at the following link
CreamCE() - Constructor for class edu.isi.pegasus.planner.code.generator.condor.style.CreamCE
  The default constructor.
CREAMCE_STYLE - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The style indicating that the submit files are to be generated for a creamce submission
CREAMCE_STYLE_IMPLEMENTING_CLASS - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactory
  The name of the class implementing the CREAMCE Style.
CREATE_AND_CHANGE_DIR_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the profile key that triggers the kickstart to create and then the working directory to it before launching an executable.
CREATE_DATABASE_STMT - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.CreateTCDatabase
  MySQL statement for checking for creating database
CREATE_DIR_JOB - Static variable in class edu.isi.pegasus.planner.classes.Job
  Denotes a job that creates directories at the remote pools.
CREATE_DIR_PREFIX - Static variable in class edu.isi.pegasus.planner.refiner.createdir.AbstractStrategy
  Constant prefix for the names of the create directory nodes.
CREATE_DIR_SUFFIX - Static variable in class edu.isi.pegasus.planner.refiner.createdir.AbstractStrategy
  Constant suffix for the names of the create directory nodes.
createAndGetAddOn(String, String, boolean) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.AbstractFileFactoryBasedMapper
  Returns the addOn part that is retrieved from the File Factory.
createAndGetAddOn(String, String, boolean) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Flat
  Returns the addOn part that is retrieved from the File Factory.
createAndGetAddOn(String, String, boolean) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Hashed
  Returns the addOn part that is retrieved from the File Factory.
createCleanupJob(String, List, Job) - Method in class edu.isi.pegasus.planner.refiner.cleanup.Cleanup
  Creates a cleanup job that removes the files from remote working directory.
createCleanupJob(String, List, Job) - Method in interface edu.isi.pegasus.planner.refiner.cleanup.CleanupImplementation
  Creates a cleanup job that removes the files from remote working directory.
createCleanupJob(String, List, Job) - Method in class edu.isi.pegasus.planner.refiner.cleanup.RM
  Creates a cleanup job that removes the files from remote working directory.
createClusteredCleanupGraphNode(List<GraphNode>, HashMap, String, int, int) - Method in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  Creates a clustered cleanup graph node that aggregates multiple cleanup nodes into one node
createDatabase(String) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.CreateTCDatabase
  Creates data base
CreateDirectory - Class in edu.isi.pegasus.planner.refiner
  This common interface that identifies the basic functions that need to be implemented to introduce random directories in which the jobs are executed on the remote execution pools.
CreateDirectory(PegasusBag) - Constructor for class edu.isi.pegasus.planner.refiner.CreateDirectory
  A pratically nothing constructor !
createEndLogMsg() - Method in class edu.isi.ikcap.workflows.util.logging.LogEvent
createEntityHierarchyMessage(String, String, String, Collection<String>) - Method in interface edu.isi.pegasus.common.logging.Event
  Creates a log message that connects the parent entities with the children.
createEntityHierarchyMessage(String, String, String, Collection<String>) - Method in class edu.isi.pegasus.common.logging.format.AbstractLogFormatter
  Creates a log message that connects the parent entities with the children.
createEntityHierarchyMessage(String, String, String, Collection<String>) - Method in class edu.isi.pegasus.common.logging.format.NetloggerEvent
  Creates a log message that connects the parent entities with the children.
createEntityHierarchyMessage(String, String, String, Collection<String>) - Method in class edu.isi.pegasus.common.logging.format.SimpleEvent
  Creates a log message that connects the parent entities with the children.
createEntityHierarchyMessage(String, String, String, Collection<String>) - Method in interface edu.isi.pegasus.common.logging.LogFormatter
  Creates a log message that connects the parent entities with the children.
createHeadNodeFS() - Method in class edu.isi.pegasus.planner.catalog.site.classes.CreateSampleSiteCatalog
  Creates an object describing the head node filesystem.
createIdHierarchyLogMsg(String, String, String, Iterator<String>) - Static method in class edu.isi.ikcap.workflows.util.logging.LogEvent
createLogMessage() - Method in interface edu.isi.pegasus.common.logging.Event
  Creates a log message with the contents of the internal log buffer.
createLogMessage() - Method in class edu.isi.pegasus.common.logging.format.AbstractLogFormatter
  Creates a log message with the contents of the internal log buffer.
createLogMessage() - Method in class edu.isi.pegasus.common.logging.format.NetloggerEvent
  Creates a log message with the contents of the internal log buffer.
createLogMessage() - Method in class edu.isi.pegasus.common.logging.format.SimpleEvent
  Creates a log message with the contents of the internal log buffer.
createLogMessage() - Method in interface edu.isi.pegasus.common.logging.LogFormatter
  Creates a log message with the contents of the internal log buffer.
createLogMessageAndReset() - Method in interface edu.isi.pegasus.common.logging.Event
  Creates a log message with the contents of the internal log buffer.
createLogMessageAndReset() - Method in class edu.isi.pegasus.common.logging.format.AbstractLogFormatter
  Creates a log message with the contents of the internal log buffer.
createLogMessageAndReset() - Method in class edu.isi.pegasus.common.logging.format.NetloggerEvent
  Creates a log message with the contents of the internal log buffer.
createLogMessageAndReset() - Method in class edu.isi.pegasus.common.logging.format.SimpleEvent
  Creates a log message with the contents of the internal log buffer.
createLogMessageAndReset() - Method in interface edu.isi.pegasus.common.logging.LogFormatter
  Creates a log message with the contents of the internal log buffer.
createLogMsg() - Method in class edu.isi.ikcap.workflows.util.logging.LogEvent
createNoOPJob(String) - Method in class edu.isi.pegasus.planner.client.CPlanner
  It creates a NoOP job that runs on the submit host.
createNoOPJob(String) - Method in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  It creates a NoOP job that runs on the submit host.
createObject(String, List, List) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser3
  Composes the `SiteData` object corresponding to the element name in the XML document.
createObject(Invocation, String, List, List) - Method in class edu.isi.pegasus.planner.parser.InvocationParser
  This method determines the actively parsed element, creates the Java object that corresponds to the element, and sets the member variables with the values of the attributes of the element.
createObject(String, List, List) - Method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser3
  Composes the `SiteData` object corresponding to the element name in the XML document.
createObject(String, List, List) - Method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser4
  Composes the `SiteData` object corresponding to the element name in the XML document.
createObject(String, List, List) - Method in class edu.isi.pegasus.planner.parser.StackBasedXMLParser
  Composes the `SiteData` object corresponding to the element name in the XML document.
createParserInstance() - Method in class edu.isi.pegasus.planner.parser.Parser
  Creates an instance of the parser, and sets the various options to it.
createPartition(List) - Method in class edu.isi.pegasus.planner.partitioner.Horizontal
  Creates a partition out of a list of nodes.
createPropertyKey(String, String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  Creates the property key
createRegistrationJob(String, Job, Collection, ReplicaCatalogBridge) - Method in class edu.isi.pegasus.planner.transfer.refiner.Basic
  Creates the registration jobs, which registers the materialized files on the output site in the Replica Catalog.
createRegistrationJob(String, Job, Collection, ReplicaCatalogBridge) - Method in class edu.isi.pegasus.planner.transfer.refiner.Empty
  Creates the registration jobs, which registers the materialized files on the output site in the Replica Catalog.
createRegistrationJobs() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a boolean indicating whether we create registration jobs or not.
CreateSampleSiteCatalog - Class in edu.isi.pegasus.planner.catalog.site.classes
  Generates a sample site catalog in XML.
CreateSampleSiteCatalog() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.CreateSampleSiteCatalog
createSetXBitJob(Job, Collection<FileTransfer>, int, int) - Method in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  Adds the dirmanager job to the workflow, that do a chmod on the files being staged.
createSetXBitJob(Collection<FileTransfer>, String, String) - Method in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  Creates a dirmanager job, that does a chmod on the file being staged.
createSetXBitJob(FileTransfer, String) - Method in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  Creates a dirmanager job, that does a chmod on the file being staged.
createSetXBitJob(Job, Collection<FileTransfer>, int, int) - Method in interface edu.isi.pegasus.planner.transfer.Implementation
  Adds the dirmanager job to the workflow, that do a chmod on the files being staged.
createStartLogMsg() - Method in class edu.isi.ikcap.workflows.util.logging.LogEvent
createSubmitDirectory(ADag, String, String, String, boolean) - Method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Creates the submit directory for the workflow.
createSubmitDirectory(String, String, String, String, boolean) - Method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Creates the submit directory for the workflow.
createSubmitDirectory(String, String, String, String, boolean) - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Creates the submit directory for the workflow.
createSymbolicLink(String, String, File, boolean) - Method in class edu.isi.pegasus.planner.client.CPlanner
  This method generates a symlink between two files
createSymbolicLink(String, String) - Method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  This method generates a symlink between two files
createSymbolicLink(String, String, boolean) - Method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  This method generates a symlink between two files
createSymbolicLinktoCacheFile(PlannerOptions, String, String) - Method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Creates a symbolic link to the DAX file in a dax sub directory in the submit directory
createSymbolicLinktoDAX(String, String) - Method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Creates a symbolic link to the DAX file in a dax sub directory in the submit directory
createSymlink(String, File) - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Returns the number of partitions referred to in the PDAX file.
createSyncJobBetweenLevels(String) - Method in class edu.isi.pegasus.planner.transfer.refiner.Cluster
  It creates a NoOP synch job that runs on the submit host.
CreateTCDatabase - Class in edu.isi.pegasus.planner.catalog.transformation.impl
  This class provides a bridge for creating and initializing transformation catalog on database .
CreateTCDatabase(String, String, String, String, String) - Constructor for class edu.isi.pegasus.planner.catalog.transformation.impl.CreateTCDatabase
  Creates a JDBCTC instance .
createTest1() - Method in class edu.isi.pegasus.planner.refiner.TestReduceEdges
createTest2() - Method in class edu.isi.pegasus.planner.refiner.TestReduceEdges
createTransferJob(Job, String, Collection, Collection, String, int) - Method in class edu.isi.pegasus.planner.transfer.implementation.AbstractMultipleFTPerXFERJob
  Constructs a general transfer job that handles multiple transfers per transfer job.
createTransferJob(Job, String, Collection, Collection, String, int) - Method in class edu.isi.pegasus.planner.transfer.implementation.AbstractSingleFTPerXFERJob
  Constructs a general transfer job that handles single transfers per transfer job.
createTransferJob(Job, String, FileTransfer, Collection, String, int) - Method in class edu.isi.pegasus.planner.transfer.implementation.AbstractSingleFTPerXFERJob
  Constructs a general transfer job that handles single transfers per transfer job.
createTransferJob(Job, String, Collection, Collection, String, int) - Method in interface edu.isi.pegasus.planner.transfer.Implementation
  This constructs the Job object for the transfer node.
createTransferJob(Job, FileTransfer, Collection, String, int) - Method in class edu.isi.pegasus.planner.transfer.implementation.Stork
  Constructs a general transfer job that handles single transfers per transfer job.
createWorkerNodeFS() - Method in class edu.isi.pegasus.planner.catalog.site.classes.CreateSampleSiteCatalog
  Creates an object describing the worker node filesystem.
credential - Variable in class edu.isi.pegasus.gridftp.Command
credential - Variable in class edu.isi.pegasus.gridftp.GridFTPConnection
CredentialHandler - Interface in edu.isi.pegasus.common.credential
  The credential interface that defines the credentials that can be associated with jobs.
CredentialHandler.TYPE - Enum in edu.isi.pegasus.common.credential
  An enumeration of valid types of credentials that are supported.
CredentialHandlerFactory - Class in edu.isi.pegasus.common.credential
  A factory class to load the appropriate type of Condor Style impelementations.
CredentialHandlerFactory() - Constructor for class edu.isi.pegasus.common.credential.CredentialHandlerFactory
  The default constructor.
CredentialHandlerFactoryException - Exception in edu.isi.pegasus.common.credential
  Class to notify of failures while instantiating Condor Style implementations.
CredentialHandlerFactoryException(String) - Constructor for exception edu.isi.pegasus.common.credential.CredentialHandlerFactoryException
  Constructs a `CondorStyleFactoryException` with no detail message.
CredentialHandlerFactoryException(String, String) - Constructor for exception edu.isi.pegasus.common.credential.CredentialHandlerFactoryException
  Constructs a `CondorStyleFactoryException` with the specified detailed message.
CredentialHandlerFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.common.credential.CredentialHandlerFactoryException
  Constructs a `CondorStyleFactoryException` with the specified detailed message and a cause.
CredentialHandlerFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.common.credential.CredentialHandlerFactoryException
  Constructs a `CondorStyleFactoryException` with the specified detailed message and a cause.
critEdge - Variable in class edu.isi.pegasus.planner.provisioner.Node
cState - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorQuoteParser
  Table to contain the state transition diagram for the parser.
Currently - Class in edu.isi.pegasus.common.util
  Create a common interface to handle obtaining string timestamps.
Currently() - Constructor for class edu.isi.pegasus.common.util.Currently
  Default ctor: Create a new instance with a default formatting string for timestamps.
Currently(String) - Constructor for class edu.isi.pegasus.common.util.Currently
  Ctor: Create a new instance with a formatting string for time stamps.
Currently(SimpleDateFormat) - Constructor for class edu.isi.pegasus.common.util.Currently
  Ctor: Create a new instance with a formatting string for time stamps.

## D

DAG - Class in edu.isi.pegasus.planner.dax
  DAG Class to hold the DAG job object.
DAG(String, String) - Constructor for class edu.isi.pegasus.planner.dax.DAG
  Create a DAG object
DAG(DAG) - Constructor for class edu.isi.pegasus.planner.dax.DAG
  Copy Constructor
DAG(String, String, String) - Constructor for class edu.isi.pegasus.planner.dax.DAG
  Create a DAG object
DAG_ID - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
DAG_ID - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
DAG_JOB - Static variable in class edu.isi.pegasus.planner.classes.Job
  Denotes a chmod job that sets the xbit on the remote end.
DAG_JOB - Static variable in class edu.isi.pegasus.planner.code.generator.MonitordNotify
  The constant string to write for dag job notifications.
DAG_JOB_ID_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.ClassADSGenerator
  The class ad for the jobId.
DagInfo - Class in edu.isi.pegasus.planner.classes
  Holds the information needed to make one dag file corresponding to a Abstract Dag.
DagInfo() - Constructor for class edu.isi.pegasus.planner.classes.DagInfo
  The default constructor.
DAGJob - Class in edu.isi.pegasus.planner.classes
  This is a data class that stores the contents of the DAG job in a DAX conforming to schema 3.0 or higher.
DAGJob() - Constructor for class edu.isi.pegasus.planner.classes.DAGJob
  The default constructor.
DAGJob(Job) - Constructor for class edu.isi.pegasus.planner.classes.DAGJob
  The overloaded construct that constructs a DAG job by wrapping around the `Job` job.
DAGMAN - Static variable in class edu.isi.pegasus.planner.classes.Profile
Dagman - Class in edu.isi.pegasus.planner.namespace
  This profile namespace is the placeholder for the keys that go into the .dag file .
Dagman() - Constructor for class edu.isi.pegasus.planner.namespace.Dagman
  The default constructor.
Dagman(Map) - Constructor for class edu.isi.pegasus.planner.namespace.Dagman
  The overloaded constructor.
Dagman(Map, String) - Constructor for class edu.isi.pegasus.planner.namespace.Dagman
  The overloaded constructor.
DAGMAN_KNOBS - Static variable in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  The dagman knobs controlled through property.
DAGMAN_KNOBS - Static variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The dagman knobs controlled through property.
DAGMAN_PROPERTIES_PREFIX - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  The prefix for DAGMan specific properties
dagmanVariables - Variable in class edu.isi.pegasus.planner.classes.Job
  The DAGMAN namespace profile variable holding the dagman profiles.
Data - Class in edu.isi.pegasus.planner.classes
  This is the container for all the Data classes.
Data() - Constructor for class edu.isi.pegasus.planner.classes.Data
  The default constructor.
Data - Class in edu.isi.pegasus.planner.invocation
  This class is transient for XML parsing.
Data() - Constructor for class edu.isi.pegasus.planner.invocation.Data
  Default c'tor: Construct a hollow shell and allow further information to be added later.
Data(String) - Constructor for class edu.isi.pegasus.planner.invocation.Data
  Constructs a piece of data.
Data(String, boolean) - Constructor for class edu.isi.pegasus.planner.invocation.Data
  Constructs a piece of data.
DATA_CHARACTERIZATION_PROGRAM - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
DATA_FILE - Static variable in class edu.isi.pegasus.planner.classes.PegasusFile
  The type denoting that a logical file is a data file.
DATA_TYPE - Static variable in class edu.isi.pegasus.planner.classes.PegasusFile
  The string value of a file that is of type data.
Database - Class in edu.isi.pegasus.planner.catalog.transformation.impl
Database() - Constructor for class edu.isi.pegasus.planner.catalog.transformation.impl.Database
Database - Class in edu.isi.pegasus.planner.catalog.work
  This class implements a work catalog on top of a simple table in a JDBC database.
Database(String, String, String, String) - Constructor for class edu.isi.pegasus.planner.catalog.work.Database
  Convenience c'tor: Establishes the connection to the work catalog database.
Database() - Constructor for class edu.isi.pegasus.planner.catalog.work.Database
  Default empty constructor creates an object that is not yet connected to any database.
DATABASE_FORMAT - Static variable in class edu.isi.pegasus.planner.client.TCConverter
  The database format.
DataReuseEngine - Class in edu.isi.pegasus.planner.refiner
  The data reuse engine reduces the workflow on the basis of existing output files of the workflow found in the Replica Catalog.
DataReuseEngine(ADag, PegasusBag) - Constructor for class edu.isi.pegasus.planner.refiner.DataReuseEngine
  The constructor
DataReuseEngine.BooleanBag - Class in edu.isi.pegasus.planner.refiner
  A bag implementation that cam be used to hold a boolean value associated with the graph node
DATE_KW - Static variable in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
dateEnd - Variable in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
dateStart - Variable in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
DAX - Class in edu.isi.pegasus.planner.dax
  Creates a DAX job object
DAX(String, String) - Constructor for class edu.isi.pegasus.planner.dax.DAX
  Create a DAX job object
DAX(DAX) - Constructor for class edu.isi.pegasus.planner.dax.DAX
  Copy Constructor
DAX(String, String, String) - Constructor for class edu.isi.pegasus.planner.dax.DAX
  Create a DAX job object
DAX2CDAG - Class in edu.isi.pegasus.planner.parser.dax
  This creates a dag corresponding to one particular partition of the whole abstract plan.
DAX2CDAG() - Constructor for class edu.isi.pegasus.planner.parser.dax.DAX2CDAG
DAX2Graph - Class in edu.isi.pegasus.planner.parser.dax
  This callback implementation ends up building a detailed structure of the graph referred to by the abstract plan in dax, that should make the graph traversals easier.
DAX2Graph() - Constructor for class edu.isi.pegasus.planner.parser.dax.DAX2Graph
DAX2LabelGraph - Class in edu.isi.pegasus.planner.parser.dax
  The callback, that ends up building a label graph.
DAX2LabelGraph() - Constructor for class edu.isi.pegasus.planner.parser.dax.DAX2LabelGraph
DAX2Metadata - Class in edu.isi.pegasus.planner.parser.dax
  A callback that causes the parser to exit after the metadata about the DAX has been parsed.
DAX2Metadata() - Constructor for class edu.isi.pegasus.planner.parser.dax.DAX2Metadata
DAX2NewGraph - Class in edu.isi.pegasus.planner.parser.dax
  An exploratory implementation that builds on the DAX2Graph.
DAX2NewGraph() - Constructor for class edu.isi.pegasus.planner.parser.dax.DAX2NewGraph
DAX_ID - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
DAX_ID - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
DAX_INDEX_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The dax index
DAX_JOB - Static variable in class edu.isi.pegasus.planner.classes.Job
  Denotes a chmod job that sets the xbit on the remote end.
DAX_JOB - Static variable in class edu.isi.pegasus.planner.code.generator.MonitordNotify
  The constant string to write for dax job notifications.
DAX_JOB_ID_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.ClassADSGenerator
  The classad for generating the DAX ID
DAX_LABEL_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The DAX label.
DAX_PARSER2_CLASS - Static variable in class edu.isi.pegasus.planner.parser.DAXParserFactory
  The DAXParser3 classname
DAX_PARSER3_CLASS - Static variable in class edu.isi.pegasus.planner.parser.DAXParserFactory
  The DAXParser3 classname
DAX_REPLICA_STORE_CATALOG_IMPLEMENTER - Static variable in class edu.isi.pegasus.planner.code.generator.DAXReplicaStore
  The name of the Replica Catalog Implementer that serves as the source for cache files.
DAX_REPLICA_STORE_CATALOG_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.DAXReplicaStore
  The name of the source key for Replica Catalog Implementer that serves as the repository for DAX Replica Store
DAX_REPLICA_STORE_SUFFIX - Static variable in class edu.isi.pegasus.planner.code.generator.DAXReplicaStore
  Suffix to be applied for the DAX Replica Store.
DAX_VERRSION_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The DAX version.
DAX_VERSION_3_2_0 - Static variable in class edu.isi.pegasus.planner.parser.dax.DAXParser3
DAX_VERSION_3_2_0 - Static variable in class edu.isi.pegasus.planner.parser.DAXParserFactory
DAX_VERSION_3_3_0 - Static variable in class edu.isi.pegasus.planner.parser.dax.DAXParser3
DAX_VERSION_WITHOUT_DOUBLE_NEGATIVE - Static variable in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  The constant designating the version when the double negative transfer and registration flags were removed.
DAXJob - Class in edu.isi.pegasus.planner.classes
  This is a data class that stores the contents of the DAX job in a DAX conforming to schema 3.0 or higher.
DAXJob() - Constructor for class edu.isi.pegasus.planner.classes.DAXJob
  The default constructor.
DAXJob(Job) - Constructor for class edu.isi.pegasus.planner.classes.DAXJob
  The overloaded construct that constructs a DAX job by wrapping around the `Job` job.
DAXParser - Interface in edu.isi.pegasus.planner.parser.dax
  An interface for all the DAX Parsers
DAXParser2 - Class in edu.isi.pegasus.planner.parser.dax
  This class parses the XML file whichis generated by Abstract Planner and ends up making an ADag object which contains theinformation to make the Condor submit files.
DAXParser2(PegasusBag) - Constructor for class edu.isi.pegasus.planner.parser.dax.DAXParser2
  The default constructor
DAXParser3 - Class in edu.isi.pegasus.planner.parser.dax
  This class uses the Xerces SAX2 parser to validate and parse an XML document conforming to the DAX Schema 3.2
DAXParser3(PegasusBag) - Constructor for class edu.isi.pegasus.planner.parser.dax.DAXParser3
  The overloaded constructor.
DAXParser3.Arguments - Class in edu.isi.pegasus.planner.parser.dax
  Private class to handle mix data content for arguments tags.
DAXParserFactory - Class in edu.isi.pegasus.planner.parser
  A factory class to load the appropriate DAX Parser and Callback implementations that need to be passed to the DAX Parser.
DAXParserFactory() - Constructor for class edu.isi.pegasus.planner.parser.DAXParserFactory
DAXParserFactoryException - Exception in edu.isi.pegasus.planner.parser
  Class to notify of failures while instantiating DAXCallback implementations.
DAXParserFactoryException(String) - Constructor for exception edu.isi.pegasus.planner.parser.DAXParserFactoryException
  Constructs a `DAXParserFactoryException` with no detail message.
DAXParserFactoryException(String, String) - Constructor for exception edu.isi.pegasus.planner.parser.DAXParserFactoryException
  Constructs a `DAXParserFactoryException` with the specified detailed message.
DAXParserFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.parser.DAXParserFactoryException
  Constructs a `DAXParserFactoryException` with the specified detailed message and a cause.
DAXParserFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.planner.parser.DAXParserFactoryException
  Constructs a `DAXParserFactoryException` with the specified detailed message and a cause.
DAXReplicaStore - Class in edu.isi.pegasus.planner.code.generator
  A generator that writes out the replica store containing a file based replica catalog that has the file locations mentioned in the DAX.
DAXReplicaStore() - Constructor for class edu.isi.pegasus.planner.code.generator.DAXReplicaStore
DAXValidator - Class in edu.isi.pegasus.planner.client
  This class reads to validate a DAX document.
DAXValidator(boolean) - Constructor for class edu.isi.pegasus.planner.client.DAXValidator
  default c'tor
DAXWriter - Class in edu.isi.pegasus.planner.partitioner
  The abstract class that identifies the interface for writing out a dax corresponding to a partition.
DAXWriter() - Constructor for class edu.isi.pegasus.planner.partitioner.DAXWriter
  The default constructor
DAXWriter(String, String) - Constructor for class edu.isi.pegasus.planner.partitioner.DAXWriter
  The overloaded constructor.
DB_ALL_PREFIX - Static variable in interface edu.isi.pegasus.planner.catalog.Catalog
  The default DB Driver properties prefix.
DB_PREFIX - Static variable in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  The DB Driver properties prefix.
DB_PREFIX - Static variable in interface edu.isi.pegasus.planner.catalog.WorkCatalog
  The DB Driver properties prefix.
DB_PREFIX - Static variable in class edu.isi.pegasus.planner.ranking.GetDAX
  The DB Driver properties prefix.
DEBUG_MESSAGE_LEVEL - Static variable in class edu.isi.pegasus.common.logging.LogManager
  The level value, to indicate a DEBUG message.
DEBUG_MESSAGE_TYPE - Static variable in class edu.isi.pegasus.common.logging.logger.Default
  The type value to indicate a DEBUG message.
decide(LoggingEvent) - Method in class edu.isi.ikcap.workflows.util.logging.EventLogMessage.Log4jFilter
decode(String) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusExitCodeEncode
  Transforms a given string by decoding all characters and unescaping where required.
decrement(Job) - Method in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  Decrement the metrics when on the basis of type of job being removed
decrementIndentIndex() - Method in class edu.isi.pegasus.planner.catalog.site.classes.AbstractXMLPrintVisitor
  Decrements the indent index
decrementJobMetrics(Job) - Method in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  Decrement the metrics when on the basis of type of job.
decrementLogging() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Deccrements the logging level by 1.
decrementLogging() - Method in class edu.isi.pegasus.planner.client.SCClient
  Decrements the logging level by 1.
decrementLogging() - Method in class edu.isi.pegasus.planner.client.TCConverter
  Decrements the logging level by 1.
decrementTaskMetrics(Job) - Method in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  Decrement the task metrics when on the basis of type of job.
Default - Class in edu.isi.pegasus.common.logging.logger
  The logging class that to log messages at different levels.
Default() - Constructor for class edu.isi.pegasus.common.logging.logger.Default
  The constructor.
DEFAULT - Static variable in class edu.isi.pegasus.common.util.Separator
  Deprecated.
  The default namespace is `null`.
Default - Class in edu.isi.pegasus.planner.selector.replica
  The default replica selector that is used if non is specifed by the user.
Default(PegasusProperties) - Constructor for class edu.isi.pegasus.planner.selector.replica.Default
  The overloaded constructor, that is called by load method.
DEFAULT_ADAG_COUNT_ATTRIBUTE - Static variable in class edu.isi.pegasus.planner.parser.dax.DAX2Metadata
  Default attribute value for the count attribute
DEFAULT_ADAG_INDEX_ATTRIBUTE - Static variable in class edu.isi.pegasus.planner.parser.dax.DAX2Metadata
  Default index value for the count attribute
DEFAULT_ARCHITECTURE - Static variable in class edu.isi.pegasus.planner.catalog.classes.SysInfo
  The default Architecture the entry is associated with if none is specified
DEFAULT_BPS - Static variable in class edu.isi.pegasus.planner.provisioner.Edge
DEFAULT_BUNDLE_FACTOR - Static variable in class edu.isi.pegasus.planner.transfer.refiner.Chain
  The default bundling factor that identifies the number of transfer jobs that are being created per execution pool for the workflow.
DEFAULT_CALLBACK_PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.parser.DAXParserFactory
  Package to prefix "just" class names with.
DEFAULT_CHMOD_PRIORITY_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  The default priority key associated with chmod jobs.
DEFAULT_CHUNK_FACTOR - Static variable in class edu.isi.pegasus.planner.client.RCClient
  The default chunk factor that is used for biting off chunks of large files.
DEFAULT_CLEANUP_CATEGORY_KEY - Static variable in interface edu.isi.pegasus.planner.refiner.cleanup.CleanupImplementation
  Default category for registration jobs
DEFAULT_CLEANUP_PRIORITY_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  The default priority key associated with the cleanup jobs.
DEFAULT_CLUSTERED_CLEANUP_JOBS_PER_LEVEL - Static variable in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  The default value for the number of clustered cleanup jobs created per level.
DEFAULT_COLLAPSE_FACTOR - Static variable in class edu.isi.pegasus.planner.cluster.Horizontal
  The default collapse factor for collapsing jobs with same logical name scheduled onto the same execution pool.
DEFAULT_COLLAPSE_FACTOR - Static variable in class edu.isi.pegasus.planner.partitioner.Horizontal
  The default collapse factor for collapsing jobs with same logical name scheduled onto the same execution pool.
DEFAULT_COMP_ERROR_PERCENTAGE - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_COMP_MULTIPLICATION_FACTOR - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_COMP_VARIANCE_PERCENTAGE - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_CONDOR_BIN_DIR - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_CONDOR_COLLECTOR - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  The default condor collector to query to for non LIGO VO's
DEFAULT_CONDOR_COLLECTOR_PROPERTY_KEY - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  The property key without the pegasus prefix'es to get the condor collector host.
DEFAULT_CONDOR_CONFIG_DIR - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_CREATE_DIR_PRIORITY_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  The default priority key associated with the create dir jobs.
DEFAULT_CTX - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
DEFAULT_DAGMAN_MAX_PRE_VALUE - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
  The default value to be assigned for dagman.maxpre .
DEFAULT_DATA_CONFIGURATION_VALUE - Static variable in class edu.isi.pegasus.planner.common.PegasusConfiguration
  The default data configuration value
DEFAULT_DATA_MULTIPLICATION_FACTOR - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_DATABASE - Static variable in class edu.isi.pegasus.planner.client.TCConverter
  The default database .
DEFAULT_DAX_CALLBACK - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
  The default DAXCallback that is loaded, if none is specified by the user.
DEFAULT_DAX_PARSER_CLASS - Static variable in class edu.isi.pegasus.planner.parser.DAXParserFactory
  The default DAXParser classname
DEFAULT_DELIMITER - Static variable in class edu.isi.pegasus.planner.namespace.aggregator.UniqueMerge
  Default delimiter
DEFAULT_EXEC_DIR - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_FORMAT - Static variable in class edu.isi.pegasus.common.util.Currently
  Default time format, which is compact and has a timezone
DEFAULT_GRID - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  The default Grid to retreive the sites for.
DEFAULT_GRID_PROPERTY_KEY - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  The property key without the pegasus prefix'es to get the grid.
DEFAULT_GRIDSTART_MODE - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_INTER_SITE_PRIORITY_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  The default priority key associated with the inter site transfer jobs.
DEFAULT_INVOKE_LENGTH - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_JOB_AGGREGATOR - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_KEY - Static variable in class edu.isi.pegasus.common.logging.format.AbstractLogFormatter
  The default key to use for logging messages
DEFAULT_LABEL_KEY - Static variable in class edu.isi.pegasus.planner.parser.dax.DAX2LabelGraph
  The default key for the VDS namespace profile, that is used in case none is specified by the user.
DEFAULT_LATENCY - Static variable in class edu.isi.pegasus.planner.provisioner.Edge
DEFAULT_LIGO_CONDOR_COLLECTOR - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  The default condor collector to query to for LIGO VO
DEFAULT_LOCAL_STAGE_IN_BUNDLE_FACTOR - Static variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  The default bundling factor that identifies the number of transfer jobs that are being created per execution pool for stageing in data for the workflow.
DEFAULT_LOCAL_STAGE_IN_CLUSTER_FACTOR - Static variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  The default bundling factor that identifies the number of transfer jobs that are being created per execution pool for stageing in data for the workflow.
DEFAULT_LOCAL_STAGE_IN_CLUSTER_FACTOR - Static variable in class edu.isi.pegasus.planner.transfer.refiner.Cluster
  The default clustering factor that identifies the number of transfer jobs that are being created per execution pool for stageing in data for the workflow.
DEFAULT_LOCAL_STAGE_OUT_BUNDLE_FACTOR - Static variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  The default bundling factor that identifies the number of transfer jobs that are being created per execution pool for stageing out data for the workflow.
DEFAULT_LOCAL_STAGE_OUT_CLUSTER_FACTOR - Static variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  The default bundling factor that identifies the number of transfer jobs that are being created per execution pool for stageing out data for the workflow.
DEFAULT_LOCAL_STAGE_OUT_CLUSTER_FACTOR - Static variable in class edu.isi.pegasus.planner.transfer.refiner.Cluster
  The default bundling factor that identifies the number of transfer jobs that are being created per execution pool for stageing out data for the workflow.
DEFAULT_LOGGER - Static variable in class edu.isi.pegasus.common.logging.LogManager
  The default Logger
DEFAULT_LOGGING_FILE - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_LOGGING_LEVEL - Static variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  The default logging level.
DEFAULT_LRC_IGNORE_URL - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_MAX_JOBS_FOR_CLEANUP_CATEGORY - Static variable in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  The default value for the maxjobs variable for the category of cleanup jobs.
DEFAULT_MEGADAG_MODE - Static variable in class edu.isi.pegasus.planner.client.CPlanner
  The default megadag mode that is used for generation of megadags in deferred planning.
DEFAULT_METADATA_TYPE - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser3
  Constant denoting default metadata type
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.common.credential.CredentialHandlerFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.common.logging.LogFormatterFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.common.logging.LogManagerFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.common.util.FactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.planner.catalog.site.impl.old.SiteFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.planner.catalog.site.SiteFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.planner.catalog.transformation.TransformationFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.planner.catalog.work.WorkFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in class edu.isi.pegasus.planner.classes.DagInfo
  The default name for the ADag object, if not supplied in the DAX.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.planner.cluster.aggregator.JobAggregatorFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.planner.cluster.ClustererFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.planner.code.CodeGeneratorFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.planner.code.GridStartFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.planner.parser.DAXParserFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.planner.parser.pdax.PDAXCallbackFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.planner.parser.SiteCatalogXMLParserFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.planner.partitioner.PartitionerFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.planner.provenance.pasoa.pps.PPSFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.planner.provenance.pasoa.producer.XMLProducerFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.planner.refiner.cleanup.CleanupFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.planner.selector.replica.ReplicaSelectorFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.planner.selector.site.SiteSelectorFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.planner.transfer.implementation.TransferImplementationFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.planner.transfer.mapper.OutputMapperFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.planner.transfer.refiner.TransferRefinerFactoryException
  The default classname that is associated with the exception.
DEFAULT_NAME - Static variable in exception edu.isi.pegasus.planner.transfer.sls.SLSFactoryException
  The default classname that is associated with the exception.
DEFAULT_NUMBER_OF_FREE_NODES - Static variable in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  The default number of nodes that are associated with a site if not found in the site catalog.
DEFAULT_NUMBER_OF_RESCUE_TRIES - Static variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  The value of number of rescue retries if no value is specified
DEFAULT_NUMBER_OF_THREADS - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Transfer
  The default number of threads pegasus-transfer uses
DEFAULT_NUMBER_OF_THREADS - Static variable in class edu.isi.pegasus.planner.transfer.sls.Transfer
  The default number of threads pegasus-transfer uses
DEFAULT_OS - Static variable in class edu.isi.pegasus.planner.catalog.classes.SysInfo
  The default OS the entry is associated with if none is specified
DEFAULT_OUTPUT_MAPPER_IMPLEMENTATION - Static variable in class edu.isi.pegasus.planner.transfer.mapper.OutputMapperFactory
  The default mapper implementation that is picked up.
DEFAULT_PACKAGE - Static variable in class edu.isi.pegasus.planner.catalog.replica.ReplicaFactory
  Package to prefix "just" class names with.
DEFAULT_PACKAGE - Static variable in class edu.isi.pegasus.planner.catalog.work.WorkFactory
  Package to prefix "just" class names with.
DEFAULT_PACKAGE_NAME - Static variable in class edu.isi.pegasus.common.credential.CredentialHandlerFactory
  The default package where the all the implementing classes are supposed to reside.
DEFAULT_PACKAGE_NAME - Static variable in class edu.isi.pegasus.common.logging.LogFormatterFactory
  The default package where all the implementations reside.
DEFAULT_PACKAGE_NAME - Static variable in class edu.isi.pegasus.common.logging.LogManagerFactory
  The default package where all the implementations reside.
DEFAULT_PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.SiteFactory
  The default package where all the implementations reside.
DEFAULT_PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.catalog.site.SiteFactory
  The default package where all the implementations reside.
DEFAULT_PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.catalog.transformation.TransformationFactory
  The default package where all the implementations reside.
DEFAULT_PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.cluster.aggregator.JobAggregatorFactory
  Package to prefix "just" class names with.
DEFAULT_PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.cluster.ClustererFactory
  The default package where all the implementations reside.
DEFAULT_PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.code.CodeGeneratorFactory
  The default package where the all the implementing classes are supposed to reside.
DEFAULT_PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactory
  The default package where the all the implementing classes are supposed to reside.
DEFAULT_PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.code.GridStartFactory
  The package name where the implementations of this interface reside by default.
DEFAULT_PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.parser.pdax.PDAXCallbackFactory
  Package to prefix "just" class names with.
DEFAULT_PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.partitioner.PartitionerFactory
  Package to prefix "just" class names with.
DEFAULT_PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.provenance.pasoa.pps.PPSFactory
  The default package where all the implementations reside.
DEFAULT_PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.provenance.pasoa.producer.XMLProducerFactory
  The default package where all the implementations reside.
DEFAULT_PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.refiner.cleanup.CleanupFactory
  The default package where the all the implementing classes are supposed to reside.
DEFAULT_PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.selector.replica.ReplicaSelectorFactory
  The default package where the all the implementing classes provided with the VDS reside.
DEFAULT_PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.selector.site.SiteSelectorFactory
  The default package where the all the implementing classes provided with the VDS reside.
DEFAULT_PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.transfer.implementation.ImplementationFactory
  The default package where the implementations reside, which this factory loads.
DEFAULT_PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.transfer.mapper.OutputMapperFactory
  The default package where the implementations reside, which this factory loads.
DEFAULT_PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.transfer.refiner.RefinerFactory
  The default package where the implementations reside, which this factory loads.
DEFAULT_PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.transfer.sls.SLSFactory
  The default package where the all the implementing classes are supposed to reside.
DEFAULT_PARSER_NAME - Variable in class edu.isi.pegasus.planner.parser.Parser
  Default parser name.
DEFAULT_PARSER_PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.parser.DAXParserFactory
  Package to prefix "just" class names with.
DEFAULT_PARSER_PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParserFactory
  Package to prefix "just" class names with.
DEFAULT_PARTITIONER_TYPE - Static variable in class edu.isi.pegasus.planner.client.PartitionDAX
  The name of the default partitioner that is loaded, if none is specified by the user.
DEFAULT_PARTITIONING_CLASS - Static variable in class edu.isi.pegasus.planner.partitioner.PartitionerFactory
  The name of the class that does level based partitioning.
DEFAULT_PERIODIC_RELEASE_VALUE - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Default value for the periodic_release for a job
DEFAULT_PERIODIC_REMOVE_VALUE - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Default value for the periodic_remove for a job
DEFAULT_POOL_MODE - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_POST_SCRIPT_ARGUMENTS_KEY_VALUE - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The default value for the arguments passed to postscript
DEFAULT_PPS_PROVIDER - Static variable in class edu.isi.pegasus.planner.provenance.pasoa.pps.PPSFactory
  The default PPS implementation to be used.
DEFAULT_PRE_SCRIPT_ARGUMENTS_KEY_VALUE - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The default value for the arguments passed to prescript
DEFAULT_PRIORITY_KEY - Static variable in class edu.isi.pegasus.planner.refiner.cleanup.RM
  The default priority key associated with the cleanup jobs.
DEFAULT_PROTOCOL - Static variable in class edu.isi.pegasus.common.util.PegasusURL
  The default protocol if none is determined from the PegasusURL or path
DEFAULT_RC_COLLECTION - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_REFINER - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The default transfer refiner name.
DEFAULT_REFINER_IMPLEMENTATION - Static variable in class edu.isi.pegasus.planner.transfer.refiner.RefinerFactory
  The default refiner implementation that is picked up.
DEFAULT_REGISTRATION_CATEGORY_KEY - Static variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  Default category for registration jobs
DEFAULT_REMOTE_STAGE_IN_BUNDLE_FACTOR - Static variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  The default bundling factor that identifies the number of transfer jobs that are being created per execution pool for stageing in data for the workflow.
DEFAULT_REMOTE_STAGE_IN_CLUSTER_FACTOR - Static variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  The default bundling factor that identifies the number of transfer jobs that are being created per execution pool for stageing in data for the workflow.
DEFAULT_REMOTE_STAGE_IN_CLUSTER_FACTOR - Static variable in class edu.isi.pegasus.planner.transfer.refiner.Cluster
  The default clustering factor that identifies the number of transfer jobs that are being created per execution pool for stageing in data for the workflow.
DEFAULT_REMOTE_STAGE_OUT_BUNDLE_FACTOR - Static variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  The default bundling factor that identifies the number of transfer jobs that are being created per execution pool for stageing out data for the workflow.
DEFAULT_REMOTE_STAGE_OUT_CLUSTER_FACTOR - Static variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  The default bundling factor that identifies the number of transfer jobs that are being created per execution pool for stageing out data for the workflow.
DEFAULT_REMOTE_STAGE_OUT_CLUSTER_FACTOR - Static variable in class edu.isi.pegasus.planner.transfer.refiner.Cluster
  The default bundling factor that identifies the number of transfer jobs that are being created per execution pool for stageing out data for the workflow.
DEFAULT_REPLICA_BACKEND - Variable in class edu.isi.pegasus.planner.transfer.mapper.impl.Replica
  The default replica catalog backend.
DEFAULT_REPLICA_REG_PRIORITY_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  The default priority key associated with the replica registration jobs.
DEFAULT_REPLICA_SELECTOR - Static variable in class edu.isi.pegasus.planner.selector.replica.ReplicaSelectorFactory
  The name of the class in the DEFAULT package, that corresponds to the default replica selector.
DEFAULT_RETRIEVE_VALIDATED_SITES - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  The default VO to use to query the condor collector.
DEFAULT_RETRIEVE_VALIDATED_SITES_PROPERTY_KEY - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  The property key without the pegasus prefix'es to get the VO.
DEFAULT_RETRY_VALUE - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The default value for the JOB Retries
DEFAULT_RLI_URL - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_RLS_EXIT_MODE - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_RLS_QUERY_ATTRIB - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_RLS_QUERY_MODE - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_RLS_TIMEOUT - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_RM_LOCATION - Static variable in class edu.isi.pegasus.planner.refiner.cleanup.RM
  The default path to rm executable.
DEFAULT_RM_LOGICAL_NAME - Static variable in class edu.isi.pegasus.planner.refiner.cleanup.RM
  The default logical name to rm executable.
DEFAULT_SC_PARSER_CLASS - Static variable in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParserFactory
  The default Site Catalog Parser
DEFAULT_SETUP_TRANSFER_IMPLEMENTATION - Static variable in class edu.isi.pegasus.planner.transfer.implementation.ImplementationFactory
DEFAULT_SITE_HANDLE - Static variable in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  The default site handle to use.
DEFAULT_SITE_SELECTOR - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_SITE_SELECTOR - Static variable in class edu.isi.pegasus.planner.selector.site.SiteSelectorFactory
  The name of the class in the DEFAULT package, that corresponds to the default site selector.
DEFAULT_SITE_SELECTOR_KEEP - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_SITE_SELECTOR_TIMEOUT - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_SIZE - Static variable in class edu.isi.pegasus.planner.provisioner.Edge
DEFAULT_SLS_IMPL_CLASS - Static variable in class edu.isi.pegasus.planner.transfer.sls.SLSFactory
  The name of the class implementing the condor code generator.
DEFAULT_STAGE_IN_PRIORITY_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  The default priority key associated with the stagein jobs.
DEFAULT_STAGE_OUT_PRIORITY_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  The default priority key associated with the stage out jobs.
DEFAULT_STAGING_DELIMITER - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_STORAGE_DIR - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_SUBDAG_CATEGORY_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  The default category for the sub dax jobs.
DEFAULT_SUBDAX_CATEGORY_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  The default category for the sub dax jobs.
DEFAULT_TC_CLASS - Static variable in class edu.isi.pegasus.planner.catalog.transformation.TCMode
DEFAULT_TC_CLASS - Static variable in class edu.isi.pegasus.planner.catalog.transformation.TransformationFactory
  Some Constants for backward compatibility.
DEFAULT_TC_MAPPER_MODE - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_TC_MODE - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_TRANSFER_IMPLEMENTATION - Static variable in class edu.isi.pegasus.planner.transfer.implementation.ImplementationFactory
DEFAULT_TRANSFER_PROCESSES - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_TRANSFER_STREAMS - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_TX_SELECTOR_MODE - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
DEFAULT_URL_PREFIX - Static variable in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  The default URL Prefix to use.
DEFAULT_VO - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  The default VO to use to query the condor collector.
DEFAULT_VO_PROPERTY_KEY - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  The property key without the pegasus prefix'es to get the VO.
DEFAULT_WEIGHT - Static variable in class edu.isi.pegasus.planner.provisioner.Node
DEFAULT_XML_PRODUCER - Static variable in class edu.isi.pegasus.planner.provenance.pasoa.producer.XMLProducerFactory
  The default XML producer implementation to be used.
defaultBrainDumpEntries(ADag) - Method in class edu.isi.pegasus.planner.code.generator.Braindump
  Returns default braindump entries.
DefaultImplementation - Class in edu.isi.pegasus.planner.refiner.createdir
  The default implementation for creating create dir jobs.
DefaultImplementation() - Constructor for class edu.isi.pegasus.planner.refiner.createdir.DefaultImplementation
defaultPOSTScript() - Method in interface edu.isi.pegasus.planner.code.GridStart
  Returns the SHORT_NAME for the POSTScript implementation that is used to be as default with this GridStart implementation.
defaultPOSTScript() - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Returns the SHORT_NAME for the POSTScript implementation that is used to be as default with this GridStart implementation.
defaultPOSTScript() - Method in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  Returns the SHORT_NAME for the POSTScript implementation that is used to be as default with this GridStart implementation.
defaultPOSTScript() - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Returns the SHORT_NAME for the POSTScript implementation that is used to be as default with this GridStart implementation.
defaultProps() - Static method in class edu.isi.pegasus.common.util.CommonProperties
  Set some defaults, should values be missing in the dataset.
DefaultStreamGobblerCallback - Class in edu.isi.pegasus.common.util
  The default callback for the stream gobbler, that logs all the messages to a particular logging level.
DefaultStreamGobblerCallback(int) - Constructor for class edu.isi.pegasus.common.util.DefaultStreamGobblerCallback
  The overloaded constructor.
defaultTCEntry(String, String, String) - Method in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  Returns a default TC entry to be used in case entry is not found in the transformation catalog.
defaultTCEntry(String) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Returns a default TC entry to be used in case entry is not found in the transformation catalog.
defaultTCEntry(String) - Method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Returns a default TC entry to be used in case entry is not found in the transformation catalog.
defaultTCEntry(String) - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Returns a default TC entry to be used in case entry is not found in the transformation catalog.
defaultTCEntry(String) - Method in class edu.isi.pegasus.planner.refiner.cleanup.Cleanup
  Returns a default TC entry to be used in case entry is not found in the transformation catalog.
defaultTCEntry() - Static method in class edu.isi.pegasus.planner.refiner.cleanup.RM
  Returns a default TransformationCatalogEntry object for the rm executable.
defaultTCEntry(String) - Method in class edu.isi.pegasus.planner.refiner.createdir.DefaultImplementation
  Returns a default TC entry to be used in case entry is not found in the transformation catalog.
defaultTCEntry(SiteCatalogEntry) - Method in class edu.isi.pegasus.planner.refiner.RemoveDirectory
  Returns a default TC entry to be used in case entry is not found in the transformation catalog.
defaultTCEntry(String, String, String, String, String) - Method in class edu.isi.pegasus.planner.transfer.implementation.AbstractMultipleFTPerXFERJob
  Returns a default TC entry to be used in case entry is not found in the transformation catalog.
defaultTCEntry(String, String, String, String) - Method in class edu.isi.pegasus.planner.transfer.implementation.GUC
  Returns a default TC entry to be used in case entry is not found in the transformation catalog.
defaultTCEntry(String, String, String, String, String) - Method in class edu.isi.pegasus.planner.transfer.sls.Transfer
  Returns a default TC entry to be used in case entry is not found in the transformation catalog.
defaultTCRCEntry() - Method in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  Returns a default TC entry to be used in case entry is not found in the transformation catalog.
defaultUntarTCEntry(SiteCatalogEntry) - Method in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Returns a default TC entry to be used in case entry is not found in the transformation catalog.
defaultXBitTCEntry(String) - Method in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  Returns a default TC entry to be used in case entry is not found in the transformation catalog.
delete(String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Deletes a specific mapping from the replica catalog.
delete(Map, boolean) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Deletes multiple mappings into the replica catalog.
delete(String, ReplicaCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Deletes a very specific mapping from the replica catalog.
delete(String, String, Object) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Deletes all PFN entries for a given LFN from the replica catalog where the PFN attribute is found, and matches exactly the object value.
delete(String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
delete(Map, boolean) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
delete(String, ReplicaCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
delete(String, String, Object) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
delete(Map, boolean) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Deletes multiple mappings into the replica catalog.
delete(String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Deletes a specific mapping from the replica catalog.
delete(String, ReplicaCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Deletes a very specific mapping from the replica catalog.
delete(String, String, Object) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Deletes all PFN entries for a given LFN from the replica catalog where the PFN attribute is found, and matches exactly the object value.
delete(String, String, Object) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Deletes all PFN entries for a given LFN from the replica catalog where the PFN attribute is found, and matches exactly the object value.
delete(String, ReplicaCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Deletes a very specific mapping from the replica catalog.
delete(Map, boolean) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Deletes multiple mappings into the replica catalog.
delete(String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Deletes a specific mapping from the replica catalog.
delete(String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Deletes a specific mapping from the replica catalog.
delete(Map, boolean) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Deletes multiple mappings into the replica catalog.
delete(String, ReplicaCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Deletes a very specific mapping from the replica catalog.
delete(String, String, Object) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Deletes all PFN entries for a given LFN from the replica catalog where the PFN attribute is found, and matches exactly the object value.
delete(String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Deletes a specific mapping from the replica catalog.
delete(Map, boolean) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Deletes multiple mappings into the replica catalog.
delete(String, ReplicaCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Deletes a very specific mapping from the replica catalog.
delete(String, String, Object) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Deletes all PFN entries for a given LFN from the replica catalog where the PFN attribute is found, and matches exactly the object value.
delete(Map, boolean) - Method in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Deletes multiple mappings into the replica catalog.
delete(String, String) - Method in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Deletes a specific mapping from the replica catalog.
delete(String, ReplicaCatalogEntry) - Method in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Deletes a very specific mapping from the replica catalog.
delete(String, String, Object) - Method in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Deletes all PFN entries for a given LFN from the replica catalog where the PFN attribute is found, and matches exactly the object value.
delete(String, String, String, String) - Method in class edu.isi.pegasus.planner.catalog.work.Database
  Deletes a mapping from the work catalog.
delete(String, String, String, String) - Method in interface edu.isi.pegasus.planner.catalog.WorkCatalog
  Deletes a mapping from the work catalog.
delete - Variable in class edu.isi.pegasus.planner.client.TCClient
deleteByResource(String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Deletes all PFN entries for a given LFN from the replica catalog where the resource handle is found.
deleteByResource(String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
deleteByResource(String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Deletes all PFN entries for a given LFN from the replica catalog where the resource handle is found.
deleteByResource(String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Deletes all PFN entries for a given LFN from the replica catalog where the resource handle is found.
deleteByResource(String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Deletes all PFN entries for a given LFN from the replica catalog where the resource handle is found.
deleteByResource(String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Deletes all PFN entries for a given LFN from the replica catalog where the resource handle is found.
deleteByResource(String, String) - Method in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Deletes all PFN entries for a given LFN from the replica catalog where the resource handle is found.
deleted - Variable in class edu.isi.pegasus.planner.provisioner.Edge
DELETED_JOBS_LEVEL - Static variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  The MAX level is assigned as the level for deleted jobs.
deleteDatabase(String) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.CreateTCDatabase
  Deletes the database
deleteLFNProfiles(String, String, String, List) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Delete a list of profiles or all the profiles associated with a logical transformation.
deleteLFNProfiles(String, String, String, List) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Delete a list of profiles or all the profiles associated with a logical transformation.
deleteLFNProfiles(String, String, String, List) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Delete a list of profiles or all the profiles associated with a logical transformation.
deleteLFNProfiles(String, String, String, List) - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Delete a list of profiles or all the profiles associated with a logical transformation.
deletePFNProfiles(String, TCType, String, List) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Delete a list of profiles or all the profiles associated with a pfn on a resource and of a type.
deletePFNProfiles(String, TCType, String, List) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Delete a list of profiles or all the profiles associated with a pfn on a resource and of a type.
deletePFNProfiles(String, TCType, String, List) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Delete a list of profiles or all the profiles associated with a pfn on a resource and of a type.
deletePFNProfiles(String, TCType, String, List) - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Delete a list of profiles or all the profiles associated with a pfn on a resource and of a type.
deleteProfile(Profile, long, boolean) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Delete a given lfn or pfn profile
DELIMITER - Static variable in class edu.isi.pegasus.planner.classes.Job
  The delimiter that has to be used to combine the name for the staged executable.
DELIMITER - Static variable in class edu.isi.pegasus.planner.code.generator.MonitordNotify
  The delimiter with which to separate different fields in the notifications file.
depart(SiteData) - Method in class edu.isi.pegasus.planner.catalog.site.classes.AbstractXMLPrintVisitor
depart(SiteStore) - Method in interface edu.isi.pegasus.planner.catalog.site.classes.SiteDataVisitor
  Depart the Site Store object.
depart(SiteCatalogEntry) - Method in interface edu.isi.pegasus.planner.catalog.site.classes.SiteDataVisitor
  Depart the Site Catalog Entry object.
depart(GridGateway) - Method in interface edu.isi.pegasus.planner.catalog.site.classes.SiteDataVisitor
  Depart the GridGateway object
depart(Directory) - Method in interface edu.isi.pegasus.planner.catalog.site.classes.SiteDataVisitor
  Depart the Directory object
depart(FileServer) - Method in interface edu.isi.pegasus.planner.catalog.site.classes.SiteDataVisitor
  Depart the Directory object
depart(ReplicaCatalog) - Method in interface edu.isi.pegasus.planner.catalog.site.classes.SiteDataVisitor
  Depart the ReplicaCatalog object
depart(Connection) - Method in interface edu.isi.pegasus.planner.catalog.site.classes.SiteDataVisitor
  Depart the connection object
depart(SiteData) - Method in interface edu.isi.pegasus.planner.catalog.site.classes.SiteDataVisitor
depart(SiteStore) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
  Depart the Site Store object.
depart(SiteCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
  Depart the Site Catalog Entry object.
depart(GridGateway) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
  Depart the GridGateway object
depart(Directory) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
  Depart the shared directory
depart(FileServer) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
  Depart the Directory object
depart(ReplicaCatalog) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
  Depart the ReplicaCatalog object
depart(Connection) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
  Depart the connection object
depart(SiteStore) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML4PrintVisitor
  Depart the Site Store object.
depart(SiteCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML4PrintVisitor
  Depart the Site Catalog Entry object.
depart(GridGateway) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML4PrintVisitor
  Depart the GridGateway object
depart(Directory) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML4PrintVisitor
  Depart the shared directory
depart(FileServer) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML4PrintVisitor
  Depart the Directory object
depart(ReplicaCatalog) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML4PrintVisitor
  Depart the ReplicaCatalog object
depart(Connection) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML4PrintVisitor
  Depart the connection object
DEPLOY_WORKER_PREFIX - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Constant suffix for the names of the deployment nodes.
DeployWorkerPackage - Class in edu.isi.pegasus.planner.refiner
  The refiner that is responsible for adding - setup nodes that deploy a worker package on each deployment site at start of workflow execution - cleanup nodes that undeploy a worker package on each deployment site at end workflow execution
DeployWorkerPackage(PegasusBag) - Constructor for class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  A pratically nothing constructor !
DEPRECATED_BUNDLE_STAGE_IN_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The deprecated bundle stagein key.
DEPRECATED_CHANGE_DIR_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The deprecated change dir key.
DEPRECATED_CONDOR_CONFIGURATION_VALUE - Static variable in class edu.isi.pegasus.planner.common.PegasusConfiguration
  The value for the condor configuration.
DEPRECATED_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Namespace
  The key is deprecated.
DEPRECATED_S3_CONFIGURATION_VALUE - Static variable in class edu.isi.pegasus.planner.common.PegasusConfiguration
  The value for the S3 configuration.
deprecatedKey(String, String) - Method in class edu.isi.pegasus.planner.namespace.Namespace
  Warns about a deprecated profile key.
deprecatedTable() - Method in class edu.isi.pegasus.planner.namespace.Namespace
  Singleton access to the deprecated table that holds the deprecated keys, and the keys that replace them.
deprecatedTable() - Method in class edu.isi.pegasus.planner.namespace.Pegasus
  Singleton access to the deprecated table that holds the deprecated keys, and the keys that replace them.
deprecatedValueMessage(String, String, String) - Method in class edu.isi.pegasus.planner.common.PegasusConfiguration
  Returns the deperecated value message
DERIVATION_NAME - Static variable in class edu.isi.pegasus.planner.refiner.cleanup.Cleanup
  The name of the underlying derivation.
DERIVATION_NAME - Static variable in class edu.isi.pegasus.planner.refiner.createdir.DefaultImplementation
  The logical name of the transformation that creates directories on the remote execution pools.
DERIVATION_NAME - Static variable in class edu.isi.pegasus.planner.refiner.createdir.HourGlass
  The logical name of the transformation that creates directories on the remote execution pools.
DERIVATION_NAME - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The logical name of the transformation for the worker package
DERIVATION_NAME - Static variable in class edu.isi.pegasus.planner.refiner.RemoveDirectory
  The logical name of the transformation that removes directories on the remote execution pools.
DERIVATION_NAME - Static variable in class edu.isi.pegasus.planner.transfer.implementation.GUC
  The name of the underlying derivation.
DERIVATION_NAME - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Stork
  The name of the underlying derivation.
DERIVATION_NAME - Static variable in class edu.isi.pegasus.planner.transfer.implementation.T2
  The name of the underlying derivation.
DERIVATION_NAME - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Transfer
  The name of the underlying derivation.
DERIVATION_NAME - Static variable in class edu.isi.pegasus.planner.transfer.sls.Transfer
  The name of the underlying derivation.
DERIVATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  The derivation namespace for the cluster jobs.
DERIVATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.refiner.cleanup.Cleanup
  The derivation namespace for the job.
DERIVATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.refiner.createdir.DefaultImplementation
  The derivation namespace for the create dir jobs.
DERIVATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.refiner.createdir.HourGlass
  The derivation namespace for the create dir jobs.
DERIVATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The derivation namespace for the worker package.
DERIVATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.refiner.RemoveDirectory
  The derivation namespace for the create dir jobs.
DERIVATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.transfer.implementation.GUC
  The derivation namespace for for the transfer job.
DERIVATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Stork
  The derivation namespace for for the transfer job.
DERIVATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.transfer.implementation.T2
  The derivation namespace for for the transfer job.
DERIVATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Transfer
  The derivation namespace for for the transfer job.
DERIVATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.transfer.sls.Transfer
  The derivation namespace for for the transfer job.
DERIVATION_VERSION - Static variable in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  The version number for the derivations for cluster jobs.
DERIVATION_VERSION - Static variable in class edu.isi.pegasus.planner.refiner.cleanup.Cleanup
  The derivation version number for the job.
DERIVATION_VERSION - Static variable in class edu.isi.pegasus.planner.refiner.createdir.DefaultImplementation
  The version number for the derivations for create dir jobs.
DERIVATION_VERSION - Static variable in class edu.isi.pegasus.planner.refiner.createdir.HourGlass
  The version number for the derivations for create dir jobs.
DERIVATION_VERSION - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The version number for the derivations for worker package.
DERIVATION_VERSION - Static variable in class edu.isi.pegasus.planner.refiner.RemoveDirectory
  The version number for the derivations for create dir jobs.
DERIVATION_VERSION - Static variable in class edu.isi.pegasus.planner.transfer.implementation.GUC
  The derivation version number for the transfer job.
DERIVATION_VERSION - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Stork
  The derivation version number for the transfer job.
DERIVATION_VERSION - Static variable in class edu.isi.pegasus.planner.transfer.implementation.T2
  The derivation version number for the transfer job.
DERIVATION_VERSION - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Transfer
  The derivation version number for the transfer job.
DERIVATION_VERSION - Static variable in class edu.isi.pegasus.planner.transfer.sls.Transfer
  The derivation version number for the transfer job.
descendants - Variable in class edu.isi.pegasus.planner.provisioner.Node
DESCRIPTION - Static variable in class edu.isi.pegasus.common.credential.impl.Irods
  The description.
DESCRIPTION - Static variable in class edu.isi.pegasus.common.credential.impl.Proxy
  The description.
DESCRIPTION - Static variable in class edu.isi.pegasus.common.credential.impl.S3CFG
  The description
DESCRIPTION - Static variable in class edu.isi.pegasus.common.credential.impl.Ssh
  The description
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Describes the transformation catalog mode.
description() - Method in interface edu.isi.pegasus.planner.cluster.Clusterer
  Returns a textual description of the transfer implementation.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.cluster.Horizontal
  A short description about the partitioner.
description() - Method in class edu.isi.pegasus.planner.cluster.Horizontal
  Returns a textual description of the transfer implementation.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.cluster.Vertical
  A short description about the partitioner.
description() - Method in class edu.isi.pegasus.planner.cluster.Vertical
  Returns a textual description of the transfer implementation.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.partitioner.BFS
  A short description about the partitioner.
description() - Method in class edu.isi.pegasus.planner.partitioner.BFS
  Returns a textual description of the transfer implementation.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.partitioner.Horizontal
  A short description about the partitioner.
description() - Method in class edu.isi.pegasus.planner.partitioner.Horizontal
  Returns a textual description of the partitioner implementation.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.partitioner.Label
  A short description about the partitioner.
description() - Method in class edu.isi.pegasus.planner.partitioner.Label
  Returns a textual description of the transfer implementation.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.partitioner.One2One
  A short description about the partitioner.
description() - Method in class edu.isi.pegasus.planner.partitioner.One2One
  Returns a textual description of the transfer implementation.
description() - Method in class edu.isi.pegasus.planner.partitioner.Partitioner
  Returns a textual description of the transfer implementation.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.partitioner.Whole
  A short description about the partitioner.
description() - Method in class edu.isi.pegasus.planner.partitioner.Whole
  Returns a textual description of the transfer implementation.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.refiner.cleanup.Cleanup
  A short description of the transfer implementation.
description() - Method in class edu.isi.pegasus.planner.selector.replica.Default
  Returns a short description of the replica selector.
description() - Method in class edu.isi.pegasus.planner.selector.replica.Local
  Returns a short description of the replica selector.
description() - Method in class edu.isi.pegasus.planner.selector.replica.Regex
  Returns a short description of the replica selector.
description() - Method in class edu.isi.pegasus.planner.selector.replica.Restricted
  Returns a short description of the replica selector.
description() - Method in interface edu.isi.pegasus.planner.selector.ReplicaSelector
  Returns a short description of the replica selector, that is being implemented by the implementing class.
description() - Method in class edu.isi.pegasus.planner.selector.site.Group
  Returns the description of the site selector.
description() - Method in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  This method returns a String describing the site selection technique that is being implemented by the implementing class.
description() - Method in class edu.isi.pegasus.planner.selector.site.Heft
  This method returns a String describing the site selection technique that is being implemented by the implementing class.
description() - Method in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  Returns a brief description of the site selection technique implemented by this class.
description() - Method in class edu.isi.pegasus.planner.selector.site.Random
  Returns a brief description of the site selection technique being used.
description() - Method in class edu.isi.pegasus.planner.selector.site.RoundRobin
  Returns a brief description of the site selection techinque implemented by this class.
description() - Method in interface edu.isi.pegasus.planner.selector.SiteSelector
  This method returns a String describing the site selection technique that is being implemented by the implementing class.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.transfer.implementation.GUC
  A short description of the transfer implementation.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Stork
  A short description of the transfer implementation.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.transfer.implementation.T2
  A short description of the transfer implementation.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Transfer
  A short description of the transfer implementation.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.transfer.mapper.impl.Fixed
  Short description.
description() - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Fixed
  Returns a short description of the mapper.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.transfer.mapper.impl.Flat
  Short description.
description() - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Flat
  Returns a short description of the mapper.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.transfer.mapper.impl.Hashed
  Short description.
description() - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Hashed
  Returns a short description of the mapper.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.transfer.mapper.impl.Replica
  Short description.
description() - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Replica
  Returns a short description of the mapper.
description() - Method in interface edu.isi.pegasus.planner.transfer.mapper.OutputMapper
  Returns a short description of the mapper.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  A short description of the transfer refinement.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.transfer.refiner.Basic
  A short description of the transfer refinement.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  A short description of the transfer refinement.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.transfer.refiner.Chain
  A short description of the transfer refinement.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.transfer.refiner.Cluster
  A short description of the transfer refinement.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.transfer.refiner.Empty
  A short description of the transfer refinement.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.transfer.sls.Condor
  A short description of the transfer implementation.
DESCRIPTION - Static variable in class edu.isi.pegasus.planner.transfer.sls.Transfer
  A short description of the transfer implementation.
Descriptor - Class in edu.isi.pegasus.planner.invocation
  This class is the container for a file descriptor object.
Descriptor() - Constructor for class edu.isi.pegasus.planner.invocation.Descriptor
  Default c'tor: Construct a hollow shell and allow further information to be added later.
Descriptor(int) - Constructor for class edu.isi.pegasus.planner.invocation.Descriptor
  Constructs a file descriptor.
desET - Variable in class edu.isi.pegasus.planner.provisioner.Node
DEST_ID - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPBandwidth
dest_subnet_id - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPBandwidth
Dest_Subnet_Id - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
determine(Implementation, Job) - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.BundleValue
  Determines the bundle factor for a particular site on the basis of the stage in bundle value associcated with the underlying transfer transformation in the transformation catalog.
determine(Implementation, Job) - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle.BundleValue
  Determines the bundle factor for a particular site on the basis of the stage in bundle value associcated with the underlying transfer transformation in the transformation catalog.
determineBuilt() - Method in class edu.isi.pegasus.common.util.Version
  Deprecated.
  Use getTimestamp() instead
determineChunkFactor() - Method in class edu.isi.pegasus.planner.client.RCClient
  Sets the chunk factor for chunking up large input files.
determineClusters(Partition) - Method in class edu.isi.pegasus.planner.cluster.Abstract
  It creates a single clustered job for the partition.
determineClusters(Partition) - Method in interface edu.isi.pegasus.planner.cluster.Clusterer
  Determine the clusters for a partition.
determineClusters(Partition) - Method in class edu.isi.pegasus.planner.cluster.Horizontal
  Determine the clusters for a partition.
determineDisabledChmodSites(String) - Method in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  Builds up a set of disabled chmod sites
determineExitStatus(InvocationRecord) - Method in class edu.isi.pegasus.planner.invocation.SimpleServer
  Determines the exit code of an invocation record.
determineInputOutputFiles(AggregatedJob, List<Job>) - Method in class edu.isi.pegasus.planner.cluster.Abstract
  Determine the input and output files of the job on the basis of the order of the constituent jobs in the AggregatedJob.
determineInputOutputFiles(AggregatedJob, List<Job>) - Method in class edu.isi.pegasus.planner.cluster.Vertical
  Determine the input and output files of the job on the basis of the order of the constituent jobs in the AggregatedJob.
determineInstalled() - Method in class edu.isi.pegasus.common.util.Version
  Determines the built and architecture of the installation.
determinePartitions(Callback) - Method in class edu.isi.pegasus.planner.partitioner.BFS
  Does a constrained breadth first search to identify the partitions, and calls out to write out the partition graph.
determinePartitions(Callback) - Method in class edu.isi.pegasus.planner.partitioner.Label
  Partitions the graph passed in the constructor, on the basis of the labels associated with the nodes in the graph.
determinePartitions(Callback) - Method in class edu.isi.pegasus.planner.partitioner.One2One
  This ends up writing out a partition for each job in the dax.
determinePartitions(Callback) - Method in class edu.isi.pegasus.planner.partitioner.Partitioner
  The main function that ends up traversing the graph structure corrsponding to the dax and creates the smaller dax files(one dax file per partition) and the .pdax file that illustrates the partition graph.
determinePartitions(Callback) - Method in class edu.isi.pegasus.planner.partitioner.Whole
  This ends up writing out a partition for each job in the dax.
determinePlatform() - Method in class edu.isi.pegasus.common.util.Version
  Deprecated.
  Used getPlatform() instead
determineRelativeSubmitDirectory(ADag, String, String, String, boolean) - Method in class edu.isi.pegasus.planner.client.CPlanner
  Creates the submit directory for the workflow.
determineRelativeSubmitDirectory(String, String, String, String, boolean) - Method in class edu.isi.pegasus.planner.client.CPlanner
  Creates the submit directory for the workflow.
determineRootWorkflowUUID(ADag, PlannerOptions, PegasusProperties) - Method in class edu.isi.pegasus.planner.client.CPlanner
  Determines the workflow uuid for a workflow
determineSites() - Method in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  This is where the callout to the Partitioner should take place, that partitions the workflow into clusters and sends to the site selector only those list of jobs that are ready to be scheduled.
determineSLSInputTransfers(Job, String, FileServer, String, String) - Method in class edu.isi.pegasus.planner.transfer.sls.Condor
  Generates a second level staging file of the input files to the worker node directory.
determineSLSInputTransfers(Job, String, FileServer, String, String) - Method in interface edu.isi.pegasus.planner.transfer.SLS
  Generates a second level staging file of the input files to the worker node directory.
determineSLSInputTransfers(Job, String, FileServer, String, String) - Method in class edu.isi.pegasus.planner.transfer.sls.Transfer
  Generates a second level staging file of the input files to the worker node directory.
determineSLSOutputTransfers(Job, String, FileServer, String, String) - Method in class edu.isi.pegasus.planner.transfer.sls.Condor
  Generates a second level staging file of the input files to the worker node directory.
determineSLSOutputTransfers(Job, String, FileServer, String, String) - Method in interface edu.isi.pegasus.planner.transfer.SLS
  Generates a second level staging file of the input files to the worker node directory.
determineSLSOutputTransfers(Job, String, FileServer, String, String) - Method in class edu.isi.pegasus.planner.transfer.sls.Transfer
  Generates a second level staging file of the input files to the worker node directory.
Diamond() - Static method in class edu.isi.pegasus.planner.dax.ADAG
Diamond - Class in edu.isi.pegasus.planner.dax.examples
  An example class to highlight how to use the JAVA DAX API to generate a diamond DAX.
Diamond() - Constructor for class edu.isi.pegasus.planner.dax.examples.Diamond
DIGIT - Static variable in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
Directory - Class in edu.isi.pegasus.planner.catalog.replica.impl
  This class implements a replica catalog on top of a directory.
Directory() - Constructor for class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Default empty constructor creates an object that is not yet connected to any database.
Directory - Class in edu.isi.pegasus.planner.catalog.site.classes
  The Directory class used for Site Catalog Schema version 4 onwards.
Directory() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.Directory
  Default constructor
Directory(DirectoryLayout, Directory.TYPE) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.Directory
  Convenience constructor for adapter class
Directory.TYPE - Enum in edu.isi.pegasus.planner.catalog.site.classes
  Enumerates the new directory types supported in this schema
DIRECTORY_EXTERNAL_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The name of the key that indicates the directory in which the DAG has to be execute
DIRECTORY_PROPERTY_KEY - Static variable in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  The name of the key that specifies the path to directory.
DIRECTORY_REPLICA_CATALOG_IMPLEMENTER - Static variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  The name of the Replica Catalog Implementer that serves as the source for cache files.
DIRECTORY_REPLICA_CATALOG_KEY - Static variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  The name of the source key for Replica Catalog Implementer that serves as cache
DirectoryLayout - Class in edu.isi.pegasus.planner.catalog.site.classes
  An abstract base class that creates a directory type.
DirectoryLayout() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.DirectoryLayout
  The default constructor.
DirectoryLayout(DirectoryLayout) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.DirectoryLayout
  The copy constructor
DirectoryLayout(Map<FileServerType.OPERATION, List<FileServer>>, InternalMountPoint) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.DirectoryLayout
  The overloaded constructor
DirectoryNotEmptyException - Exception in edu.isi.pegasus.gridftp
DirectoryNotEmptyException(String) - Constructor for exception edu.isi.pegasus.gridftp.DirectoryNotEmptyException
DirectoryNotEmptyException(String, Throwable) - Constructor for exception edu.isi.pegasus.gridftp.DirectoryNotEmptyException
DirectoryRemovalException - Exception in edu.isi.pegasus.gridftp
DirectoryRemovalException(String) - Constructor for exception edu.isi.pegasus.gridftp.DirectoryRemovalException
DirectoryRemovalException(String, Throwable) - Constructor for exception edu.isi.pegasus.gridftp.DirectoryRemovalException
DirectoryTypes() - Constructor for enum edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor.DirectoryTypes
DISABLE_INVOKE_PROPERTY - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
  the name of the property to disable invoke functionality
disableChmodJobCreation(String) - Method in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  Returns a boolean indicating whether to disable chmod job creation for a site or not.
disableInvokeInGridStart() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a boolean indicating whether to disable use of invoke or not.
displayResults(NamingEnumeration, String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
  Displays the result on stdout instead of putting it in data classes.
DO_NOT_REGISTER_BIT_FLAG - Static variable in class edu.isi.pegasus.planner.classes.PegasusFile
  The index of the flags field which when set indicates that the file is not to be registered in the RLS/ RC.
doAdds() - Method in class edu.isi.pegasus.planner.catalog.transformation.client.TCAdd
doBackupAndCreateSymbolicLinkForSubmitDirectory(String, String) - Method in class edu.isi.pegasus.planner.client.CPlanner
doDelete() - Method in class edu.isi.pegasus.planner.catalog.transformation.client.TCDelete
doesCondorModifications() - Method in class edu.isi.pegasus.planner.transfer.sls.Condor
  Returns a boolean whether the SLS implementation does a condor based modification or not.
doesCondorModifications() - Method in interface edu.isi.pegasus.planner.transfer.SLS
  Returns a boolean whether the SLS implementation does a condor based modification or not.
doesCondorModifications() - Method in class edu.isi.pegasus.planner.transfer.sls.Transfer
  Returns a boolean whether the SLS implementation does a condor based modification or not.
doesPreserveXBit() - Method in interface edu.isi.pegasus.planner.transfer.Implementation
  Returns a boolean indicating whether the transfer protocol being used by the implementation preserves the X Bit or not while staging.
doesPreserveXBit() - Method in class edu.isi.pegasus.planner.transfer.implementation.GUC
  Returns a boolean indicating whether the transfer protocol being used by the implementation preserves the X Bit or not while staging.
doesPreserveXBit() - Method in class edu.isi.pegasus.planner.transfer.implementation.Stork
  Returns a boolean indicating whether the transfer protocol being used by the implementation preserves the X Bit or not while staging.
doesPreserveXBit() - Method in class edu.isi.pegasus.planner.transfer.implementation.T2
  Returns a boolean indicating whether the transfer protocol being used by the implementation preserves the X Bit or not while staging.
doesPreserveXBit() - Method in class edu.isi.pegasus.planner.transfer.implementation.Transfer
  Returns a boolean indicating whether the transfer protocol being used by the implementation preserves the X Bit or not while staging.
DOMAIN - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
done(Callback) - Method in class edu.isi.pegasus.planner.partitioner.BFS
  Indicates that we are done with the partitioning.
done(Callback) - Method in class edu.isi.pegasus.planner.partitioner.Horizontal
  Indicates that we are done with the traversal of the graph.
done() - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  Signals that the traversal of the workflow is done.
done() - Method in class edu.isi.pegasus.planner.transfer.refiner.Basic
  Signals that the traversal of the workflow is done.
done() - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  Signals that the traversal of the workflow is done.
done() - Method in class edu.isi.pegasus.planner.transfer.refiner.Chain
  Prints out the bundles and chains that have been constructed.
done() - Method in class edu.isi.pegasus.planner.transfer.refiner.Cluster
  Signals that the traversal of the workflow is done.
done() - Method in interface edu.isi.pegasus.planner.transfer.Refiner
  Signals that the traversal of the workflow is done.
done() - Method in class edu.isi.pegasus.planner.transfer.refiner.Empty
  Signals that the traversal of the workflow is done.
doneStageIn(Map<String, Bundle.PoolTransfer>, Implementation, int, boolean) - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  Signals that the traversal of the workflow is done.
doQuery() - Method in class edu.isi.pegasus.planner.catalog.transformation.client.TCQuery
doSet(Level) - Method in class edu.isi.pegasus.planner.client.RCClient
doStatWithKickstart() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Return a boolean indicating whether to turn the stat option for kickstart on or not.
dotfiles - Variable in class edu.isi.pegasus.gridftp.ListCommand
downLen - Variable in class edu.isi.pegasus.planner.provisioner.Node
DOWNWARD_RANK - Static variable in class edu.isi.pegasus.planner.selector.site.heft.HeftBag
  The constant to be passed to the accessor functions to get or set the downward rank for a node.
DROP_DATABASE_STMT - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.CreateTCDatabase
  MySQL statement for checking for dropping database
DSC() - Method in class edu.isi.pegasus.planner.provisioner.Estimator
DUMMY_CONCAT_JOB - Static variable in class edu.isi.pegasus.planner.refiner.createdir.HourGlass
  The name concatenating dummy job that ensures that Condor does not start staging in before the directories are created.
DUMMY_CONCAT_JOB_PREFIX - Static variable in class edu.isi.pegasus.planner.refiner.createdir.HourGlass
  The prefix assigned to the concatenating dummy job that ensures that Condor does not start staging in before the directories are created.
DUMMY_NODE_ID - Static variable in class edu.isi.pegasus.planner.parser.dax.DAX2Graph
  The id of the dummy root node added on the top of the graph.
dvName - Variable in class edu.isi.pegasus.planner.classes.Job
  The name of the derivation in Chimera that generated the job.
dvNamespace - Variable in class edu.isi.pegasus.planner.classes.Job
  The namespace to which the derivation is bound.
dvVersion - Variable in class edu.isi.pegasus.planner.classes.Job
  The version of the derivation.
DynamicLoader - Class in edu.isi.pegasus.common.util
  This class provides a dynamic class loading facility.
DynamicLoader(String) - Constructor for class edu.isi.pegasus.common.util.DynamicLoader

## E

Edge - Class in edu.isi.pegasus.planner.dax
Edge(String, String) - Constructor for class edu.isi.pegasus.planner.dax.Edge
Edge(Edge) - Constructor for class edu.isi.pegasus.planner.dax.Edge
Edge(String, String, String) - Constructor for class edu.isi.pegasus.planner.dax.Edge
Edge - Class in edu.isi.pegasus.planner.provisioner
  An instance of this class represent an edge of workflow which is data dependencies between two tasks.
Edge(Node, Node, String, long) - Constructor for class edu.isi.pegasus.planner.provisioner.Edge
  Constructor
edgeList2Graph(ADag, Map) - Method in class edu.isi.pegasus.planner.refiner.NodeCollapser
  Returns an adjacency list representation of the graph referred to by the list of edges.
edgeList2Graph(Collection<PCRelation>, Map) - Method in class edu.isi.pegasus.planner.refiner.NodeCollapser
  Deprecated.
  as part of PM-747
edges - Variable in class edu.isi.pegasus.planner.provisioner.Estimator
edgeToDOT(Writer, String, String, String) - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the DOT description of the object.
edu.isi.ikcap.workflows.util.logging - package edu.isi.ikcap.workflows.util.logging
edu.isi.pegasus.common.credential - package edu.isi.pegasus.common.credential
edu.isi.pegasus.common.credential.impl - package edu.isi.pegasus.common.credential.impl
edu.isi.pegasus.common.logging - package edu.isi.pegasus.common.logging
edu.isi.pegasus.common.logging.format - package edu.isi.pegasus.common.logging.format
edu.isi.pegasus.common.logging.logger - package edu.isi.pegasus.common.logging.logger
edu.isi.pegasus.common.util - package edu.isi.pegasus.common.util
edu.isi.pegasus.gridftp - package edu.isi.pegasus.gridftp
edu.isi.pegasus.planner.catalog - package edu.isi.pegasus.planner.catalog
edu.isi.pegasus.planner.catalog.classes - package edu.isi.pegasus.planner.catalog.classes
edu.isi.pegasus.planner.catalog.replica - package edu.isi.pegasus.planner.catalog.replica
edu.isi.pegasus.planner.catalog.replica.impl - package edu.isi.pegasus.planner.catalog.replica.impl
edu.isi.pegasus.planner.catalog.site - package edu.isi.pegasus.planner.catalog.site
edu.isi.pegasus.planner.catalog.site.classes - package edu.isi.pegasus.planner.catalog.site.classes
edu.isi.pegasus.planner.catalog.site.impl - package edu.isi.pegasus.planner.catalog.site.impl
edu.isi.pegasus.planner.catalog.site.impl.old - package edu.isi.pegasus.planner.catalog.site.impl.old
edu.isi.pegasus.planner.catalog.site.impl.old.classes - package edu.isi.pegasus.planner.catalog.site.impl.old.classes
edu.isi.pegasus.planner.catalog.transformation - package edu.isi.pegasus.planner.catalog.transformation
edu.isi.pegasus.planner.catalog.transformation.classes - package edu.isi.pegasus.planner.catalog.transformation.classes
edu.isi.pegasus.planner.catalog.transformation.client - package edu.isi.pegasus.planner.catalog.transformation.client
edu.isi.pegasus.planner.catalog.transformation.impl - package edu.isi.pegasus.planner.catalog.transformation.impl
edu.isi.pegasus.planner.catalog.transformation.mapper - package edu.isi.pegasus.planner.catalog.transformation.mapper
edu.isi.pegasus.planner.catalog.work - package edu.isi.pegasus.planner.catalog.work
edu.isi.pegasus.planner.classes - package edu.isi.pegasus.planner.classes
edu.isi.pegasus.planner.client - package edu.isi.pegasus.planner.client
edu.isi.pegasus.planner.cluster - package edu.isi.pegasus.planner.cluster
edu.isi.pegasus.planner.cluster.aggregator - package edu.isi.pegasus.planner.cluster.aggregator
edu.isi.pegasus.planner.code - package edu.isi.pegasus.planner.code
edu.isi.pegasus.planner.code.generator - package edu.isi.pegasus.planner.code.generator
edu.isi.pegasus.planner.code.generator.condor - package edu.isi.pegasus.planner.code.generator.condor
edu.isi.pegasus.planner.code.generator.condor.style - package edu.isi.pegasus.planner.code.generator.condor.style
edu.isi.pegasus.planner.code.gridstart - package edu.isi.pegasus.planner.code.gridstart
edu.isi.pegasus.planner.common - package edu.isi.pegasus.planner.common
edu.isi.pegasus.planner.dax - package edu.isi.pegasus.planner.dax
edu.isi.pegasus.planner.dax.examples - package edu.isi.pegasus.planner.dax.examples
edu.isi.pegasus.planner.invocation - package edu.isi.pegasus.planner.invocation
edu.isi.pegasus.planner.namespace - package edu.isi.pegasus.planner.namespace
edu.isi.pegasus.planner.namespace.aggregator - package edu.isi.pegasus.planner.namespace.aggregator
edu.isi.pegasus.planner.parser - package edu.isi.pegasus.planner.parser
edu.isi.pegasus.planner.parser.dax - package edu.isi.pegasus.planner.parser.dax
edu.isi.pegasus.planner.parser.pdax - package edu.isi.pegasus.planner.parser.pdax
edu.isi.pegasus.planner.parser.tokens - package edu.isi.pegasus.planner.parser.tokens
edu.isi.pegasus.planner.partitioner - package edu.isi.pegasus.planner.partitioner
edu.isi.pegasus.planner.partitioner.graph - package edu.isi.pegasus.planner.partitioner.graph
edu.isi.pegasus.planner.provenance.pasoa - package edu.isi.pegasus.planner.provenance.pasoa
edu.isi.pegasus.planner.provenance.pasoa.pps - package edu.isi.pegasus.planner.provenance.pasoa.pps
edu.isi.pegasus.planner.provenance.pasoa.producer - package edu.isi.pegasus.planner.provenance.pasoa.producer
edu.isi.pegasus.planner.provisioner - package edu.isi.pegasus.planner.provisioner
edu.isi.pegasus.planner.ranking - package edu.isi.pegasus.planner.ranking
edu.isi.pegasus.planner.refiner - package edu.isi.pegasus.planner.refiner
edu.isi.pegasus.planner.refiner.cleanup - package edu.isi.pegasus.planner.refiner.cleanup
edu.isi.pegasus.planner.refiner.createdir - package edu.isi.pegasus.planner.refiner.createdir
edu.isi.pegasus.planner.selector - package edu.isi.pegasus.planner.selector
  Provides the interface and call-out to the site selector mechanism.
edu.isi.pegasus.planner.selector.replica - package edu.isi.pegasus.planner.selector.replica
edu.isi.pegasus.planner.selector.site - package edu.isi.pegasus.planner.selector.site
edu.isi.pegasus.planner.selector.site.heft - package edu.isi.pegasus.planner.selector.site.heft
edu.isi.pegasus.planner.selector.transformation - package edu.isi.pegasus.planner.selector.transformation
edu.isi.pegasus.planner.transfer - package edu.isi.pegasus.planner.transfer
edu.isi.pegasus.planner.transfer.implementation - package edu.isi.pegasus.planner.transfer.implementation
edu.isi.pegasus.planner.transfer.mapper - package edu.isi.pegasus.planner.transfer.mapper
edu.isi.pegasus.planner.transfer.mapper.impl - package edu.isi.pegasus.planner.transfer.mapper.impl
edu.isi.pegasus.planner.transfer.refiner - package edu.isi.pegasus.planner.transfer.refiner
edu.isi.pegasus.planner.transfer.sls - package edu.isi.pegasus.planner.transfer.sls
ELEMENT_NAME - Static variable in class edu.isi.pegasus.planner.invocation.Boot
  The element name
ELEMENT_NAME - Static variable in class edu.isi.pegasus.planner.invocation.CPU
  The element name
ELEMENT_NAME - Static variable in class edu.isi.pegasus.planner.invocation.Load
  The element name
ELEMENT_NAME - Static variable in class edu.isi.pegasus.planner.invocation.Machine
  element name
ELEMENT_NAME - Static variable in class edu.isi.pegasus.planner.invocation.Proc
  The element name
ELEMENT_NAME - Static variable in class edu.isi.pegasus.planner.invocation.RAM
  The element name
ELEMENT_NAME - Static variable in class edu.isi.pegasus.planner.invocation.Stamp
  The element name
ELEMENT_NAME - Static variable in class edu.isi.pegasus.planner.invocation.Swap
  The element name
ELEMENT_NAME - Static variable in class edu.isi.pegasus.planner.invocation.Task
  The element name
ELEMENT_NAME - Static variable in class edu.isi.pegasus.planner.invocation.Uname
  The element name
Empty - Class in edu.isi.pegasus.planner.provenance.pasoa.pps
  The default empty implementation to be used.
Empty() - Constructor for class edu.isi.pegasus.planner.provenance.pasoa.pps.Empty
Empty - Class in edu.isi.pegasus.planner.transfer.refiner
  An Empty implementation for performance evaluation purposes
Empty(ADag, PegasusBag) - Constructor for class edu.isi.pegasus.planner.transfer.refiner.Empty
  The overloaded constructor.
EMPTY_FINAL_WORKFLOW_MESSAGE - Static variable in class edu.isi.pegasus.planner.client.CPlanner
  The final successful message that is to be logged.
EMPTY_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Namespace
  The key value is empty .
EmptyIterator() - Constructor for class edu.isi.pegasus.planner.namespace.Namespace.EmptyIterator
emptyKey(String) - Method in class edu.isi.pegasus.planner.namespace.Namespace
  Deletes the key from the namespace.
enable(AggregatedJob, boolean) - Method in interface edu.isi.pegasus.planner.code.GridStart
  Enables a job to run on the grid.
enable(Job, boolean) - Method in interface edu.isi.pegasus.planner.code.GridStart
  Enables a job to run on the grid.
enable(AggregatedJob, boolean) - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Enables a constituentJob to run on the grid.
enable(Job, boolean) - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Enables a constituentJob to run on the grid by launching it through kickstart.
enable(Job, boolean, boolean, boolean, boolean) - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Enables a constituentJob to run on the grid by launching it through kickstart.
enable(AggregatedJob, Collection) - Method in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  Enables a collection of jobs and puts them into an AggregatedJob.
enable(AggregatedJob, boolean) - Method in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  Enables a job to run on the grid.
enable(Job, boolean) - Method in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  Enables a job to run on the grid by launching it directly.
enable(AggregatedJob, boolean) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Enables a job to run on the grid.
enable(Job, boolean) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Enables a job to run on the grid by launching it directly.
enableForWorkerNodeExecution(Job, boolean) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Enables jobs for worker node execution.
encode(String) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusExitCodeEncode
  Transforms a given string by encoding single whitespace with the escape character set ( defaults to + ), and escapes the escape itself
END_POSTFIX - Static variable in class edu.isi.ikcap.workflows.util.logging.LogEvent
endDocument() - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
endDocument() - Method in class edu.isi.pegasus.planner.client.DAXValidator
endDocument() - Method in class edu.isi.pegasus.planner.parser.ConfigXmlParser
endDocument() - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Here we have all the elements in our data structure.
endDocument() - Method in class edu.isi.pegasus.planner.parser.InvocationParser
  The parser comes to the end of the document.
endDocument() - Method in class edu.isi.pegasus.planner.parser.Parser
  This is called automatically when the end of the XML file is reached.
endDocument() - Method in class edu.isi.pegasus.planner.parser.PDAXParser
  This is called automatically when the end of the XML file is reached.
endDocument() - Method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLMetadataParser
  Sets the boolean indicating parsing is done
endDocument() - Method in class edu.isi.pegasus.planner.parser.StackBasedXMLParser
endElement() - Method in class edu.isi.pegasus.common.util.XMLWriter
endElement(int) - Method in class edu.isi.pegasus.common.util.XMLWriter
endElement(String, String, String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
endElement(String, String, String) - Method in class edu.isi.pegasus.planner.client.DAXValidator
endElement(String, String, String) - Method in class edu.isi.pegasus.planner.parser.ConfigXmlParser
endElement(String, String, String) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Overrides the default implementation when the elements end tag comes.
endElement(String, String, String) - Method in class edu.isi.pegasus.planner.parser.InvocationParser
  The parser is at the end of an element.
endElement(String, String, String) - Method in class edu.isi.pegasus.planner.parser.Parser
  An empty implementation is provided by DefaultHandler class.
endElement(String, String, String) - Method in class edu.isi.pegasus.planner.parser.PDAXParser
  An empty implementation is provided by DefaultHandler class.
endElement(String, String, String) - Method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLMetadataParser
  An empty implementation
endElement(String, String, String) - Method in class edu.isi.pegasus.planner.parser.StackBasedXMLParser
  The parser is at the end of an element.
endPrefixMapping(String) - Method in class edu.isi.pegasus.planner.parser.InvocationParser
  Out of the reach of the prefix, remove it from the HashMap.
endWorkflowRefinementStep(Refiner) - Method in class edu.isi.pegasus.planner.provenance.pasoa.pps.Empty
  endWorkflowRefinementStep
endWorkflowRefinementStep(Refiner) - Method in interface edu.isi.pegasus.planner.provenance.pasoa.PPS
ENGAGE_VO - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  The name of the ENGAGE VO
Engine - Class in edu.isi.pegasus.planner.refiner
  The class which is a superclass of all the various Engine classes.
Engine(PegasusBag) - Constructor for class edu.isi.pegasus.planner.refiner.Engine
  A pratically nothing constructor !
enter(String, String) - Method in class edu.isi.pegasus.planner.client.RCClient
  Adds a preference to the instance preferences settings.
entryIterator() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  Returns an iterator to SiteCatalogEntry objects in the store.
entryNotInTC(String, String, String, String, String) - Method in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  Determines whether there is NOT an entry in the transformation catalog for a particular transformation on a particular site.
entryNotInTC(String) - Method in class edu.isi.pegasus.planner.cluster.aggregator.MPIExec
  Determines whether there is NOT an entry in the transformation catalog for the job aggregator executable on a particular site.
entryNotInTC(String) - Method in class edu.isi.pegasus.planner.cluster.aggregator.SeqExec
  Determines whether there is NOT an entry in the transformation catalog for the job aggregator executable on a particular site.
entryNotInTC(String) - Method in interface edu.isi.pegasus.planner.cluster.JobAggregator
  Determines whether there is NOT an entry in the transformation catalog for the job aggregator executable on a particular site.
env - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
ENV - Static variable in class edu.isi.pegasus.planner.classes.Profile
ENV - Class in edu.isi.pegasus.planner.namespace
  The environment namespace, that puts in the environment variables for the transformation that is being run, through Condor.
ENV() - Constructor for class edu.isi.pegasus.planner.namespace.ENV
  The default constructor.
ENV(Map) - Constructor for class edu.isi.pegasus.planner.namespace.ENV
  The overloaded constructor.
EnvEntry - Class in edu.isi.pegasus.planner.invocation
  This class pushes an environmental entry into the environment map.
EnvEntry() - Constructor for class edu.isi.pegasus.planner.invocation.EnvEntry
  Default c'tor: Construct a hollow shell and allow further information to be added later.
EnvEntry(String) - Constructor for class edu.isi.pegasus.planner.invocation.EnvEntry
  C'tor: Prepares a given key for accepting a value later on.
EnvEntry(String, String) - Constructor for class edu.isi.pegasus.planner.invocation.EnvEntry
  C'tor: Fully initializes the class
Environment - Class in edu.isi.pegasus.planner.invocation
  This class maintains the application that was run, and the arguments to the commandline that were actually passed on to the application.
Environment() - Constructor for class edu.isi.pegasus.planner.invocation.Environment
  Default c'tor: Construct a hollow shell and allow further information to be added later.
envVariables - Variable in class edu.isi.pegasus.planner.classes.Job
  To accomodate the environment variables which might needed to be set.
equals(Object) - Method in class edu.isi.pegasus.planner.catalog.classes.SysInfo
  Check if the system information matches.
equals(Object) - Method in class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  Matches two ReplicaCatalogEntry objects.
equals(Object) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPServer
  Checks if an object is similar to the one referred to by this class.
equals(Object) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  Checks if an object is similar to the one referred to by this class.
equals(Object) - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.Arch
  Compares if a given Arch object is equal to this.
equals(Object) - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.Os
  Compares if a given Os object is equal to this.
equals(Object) - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.VDSSysInfo
  Check if the system information matches.
equals(TransformationCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Compares two catalog entries for equality.
equals(Object) - Method in class edu.isi.pegasus.planner.classes.CompoundTransformation
  Returns whether two objects are equal or not on the basis of the complete name of the transformation.
equals(Object) - Method in class edu.isi.pegasus.planner.classes.Job
  Checks if an object is similar to the one referred to by this class.
equals(Object) - Method in class edu.isi.pegasus.planner.classes.PCRelation
  Checks if an object is similar to the one referred to by this class.
equals(Object) - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Checks if an object is similar to the one referred to by this class.
equals(Object) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
equals(Object) - Method in class edu.isi.pegasus.planner.dax.Edge
equals(Object) - Method in class edu.isi.pegasus.planner.dax.Executable
equals(Object) - Method in class edu.isi.pegasus.planner.dax.File
  Check if this File is equal to Object o
equals(Object) - Method in class edu.isi.pegasus.planner.dax.Transformation
equals(Object) - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  Matches two GraphNode objects.
equals(Object) - Method in class edu.isi.pegasus.planner.provisioner.Node
equals(Object) - Method in class edu.isi.pegasus.planner.ranking.Ranking
err - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Arch
err - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Os
ERR_SUCCESS_MSG_DELIMITER - Static variable in class edu.isi.pegasus.planner.code.gridstart.PegasusExitCode
  The delimiter used for delimited error and success message internally
error(SAXParseException) - Method in class edu.isi.pegasus.planner.client.DAXValidator
error(SAXParseException) - Method in class edu.isi.pegasus.planner.parser.XMLErrorHandler
  Logs the error messages which SAX parser generates while validating the XML file against an XML Schema
ERROR_MESSAGE_AGGREGATOR - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  Static Handle to the delimiter aggregator.
ERROR_MESSAGE_LEVEL - Static variable in class edu.isi.pegasus.common.logging.LogManager
  The level value, to indicate an ERROR message.
ERROR_MESSAGE_TYPE - Static variable in class edu.isi.pegasus.common.logging.logger.Default
  The type value to indicate an ERROR message.
errorMessage(Job, String, String) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.Abstract
  Constructs an error message in case of style mismatch.
Escape - Class in edu.isi.ikcap.workflows.util.logging
  This class tries to define an interface to deal with quoting, escaping, and the way back.
Escape() - Constructor for class edu.isi.ikcap.workflows.util.logging.Escape
  Defines the default quoting and escaping rules, escaping the apostrophe, double quote and backslash.
Escape(String, char) - Constructor for class edu.isi.ikcap.workflows.util.logging.Escape
  Constructs arbitrary escaping rules.
Escape(String, char, boolean) - Constructor for class edu.isi.ikcap.workflows.util.logging.Escape
  Constructs arbitrary escaping rules.
escape(String) - Method in class edu.isi.ikcap.workflows.util.logging.Escape
  Transforms a given string by escaping all characters inside the quotable characters set with the escape character.
escape - Static variable in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
Escape - Class in edu.isi.pegasus.common.util
  This class tries to define an interface to deal with quoting, escaping, and the way back.
Escape() - Constructor for class edu.isi.pegasus.common.util.Escape
  Defines the default quoting and escaping rules, escaping the apostrophe, double quote and backslash.
Escape(String, char) - Constructor for class edu.isi.pegasus.common.util.Escape
  Constructs arbitrary escaping rules.
escape(String) - Method in class edu.isi.pegasus.common.util.Escape
  Transforms a given string by escaping all characters inside the quotable characters set with the escape character.
escape(String) - Static method in class edu.isi.pegasus.common.util.XMLOutput
  Escapes certain characters inappropriate for textual output.
escape(String) - Method in class edu.isi.pegasus.planner.client.RCClient
  Escapes quotes and backslashes by backslashing them.
escapeXML(String) - Static method in class edu.isi.pegasus.common.util.XMLWriter
ESSENTIAL_POST_SCRIPT_SCOPE - Static variable in class edu.isi.pegasus.planner.code.GridStartFactory
  The postscript mode in which post scripts are added only for essential jobs.
estimate() - Method in class edu.isi.pegasus.planner.provisioner.Estimator
  Estimate the number of processors and return the value.
Estimator - Class in edu.isi.pegasus.planner.provisioner
  This Estimator is used to find the near-optimal number of processors required to complete workflow within a given RFT(requested finish time).
Estimator(String, String, long, int) - Constructor for class edu.isi.pegasus.planner.provisioner.Estimator
  Constructor
evalWeight() - Method in class edu.isi.pegasus.planner.provisioner.Node
  return execution time of this task
Event - Interface in edu.isi.pegasus.common.logging
EVENT_DC_ADD_DATASOURCE_LOCATION - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_AUGMENT_DATASOURCE - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_CHARACTERIZE - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_CHARACTERIZE_STATUS - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_CHARACTERIZE_STATUSES - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_DATASOURCE_EXISTS - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_DISSEMINATE_DATASOURCE - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_GET_ALL_DATASOURCES - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_GET_ALL_METRICS - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_GET_AUGMENTED_TYPES - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_GET_DATASOURCE - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_GET_DATASOURCE_DESCRIPTION_FOR_UUID - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_GET_DATASOURCE_LOCATIONS - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_GET_DATASOURCE_UUID_FOR_DESCRIPTION - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_GET_DATASOURCES - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_GET_DMO_METRICS - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_GET_INGEST_STATUS - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_GET_INGEST_TIME - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_GET_SATURATED_TYPES - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_GET_UNCHARACTERIZED_DATASOURCES - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_INGEST_DATASOURCE - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_REGISTER_DATASOURCE - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_REMOVE_DATASOURCE - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_REMOVE_DATASOURCE_LOCATION - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_RICH_CHARACTERIZE - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_SATURATE_DATASOURCE - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_SET_DATASOURCE_DESCRIPTION_FOR_UUID - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_DC_UPDATE_INGEST_MAP - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_ENSEMBLE_EXECUTE - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_ENSEMBLE_PLANNING - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_ENSEMBLE_RANKING - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_ENSEMBLE_WG - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_ID_KEY - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_ID_KEY - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_INFER_TEMPLATE - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_KW - Static variable in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
EVENT_PEGASUS_ADD_DATA_DEPENDENCIES - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_PEGASUS_ADD_TRANSFER_NODES - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_PEGASUS_ADDCLEANUP - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_PEGASUS_ADDDATASTAGING - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_PEGASUS_ADDREGISTRATION - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_PEGASUS_AUTHENTICATION - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_PEGASUS_CLUSTER - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_PEGASUS_CLUSTER - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_PEGASUS_CODE_GENERATION - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_PEGASUS_GENERATE_CLEANUP - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_PEGASUS_GENERATE_CLEANUP_WF - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_PEGASUS_GENERATE_WORKDIR - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_PEGASUS_GENERATECLEANUP - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_PEGASUS_LOAD_DIRECTORY_CACHE - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_PEGASUS_LOAD_TRANSIENT_CACHE - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_PEGASUS_PARSE_DAX - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_PEGASUS_PARSE_PDAX - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_PEGASUS_PARSE_SITE_CATALOG - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_PEGASUS_PARTITION - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_PEGASUS_PLAN - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_PEGASUS_PLAN - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_PEGASUS_RANKING - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_PEGASUS_RANKING_RETRIEVE_DAX - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_PEGASUS_REDUCE - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_PEGASUS_REDUCE - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_PEGASUS_REFINEMENT - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_PEGASUS_SITESELECTION - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_PEGASUS_SITESELECTION - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_QUERY_DATACATALOG - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_QUERY_DATACATALOG - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_QUERY_PROCESSCATALOG - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_QUERY_PROCESSCATALOG - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENT_RANKING - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_WG - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_WG_BACKWARD_SWEEP - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_WG_CONFIGURE - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_WG_DATA_SELECTION - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_WG_FETCH_METRICS - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_WG_FORWARD_SWEEP - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_WG_GET_CANDIDATE_SEEDS - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_WG_GET_DAX - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_WG_INITIALIZE_DC - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_WG_INITIALIZE_PC - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_WG_LOAD_SEED - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_WG_SPECIALIZE - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
EVENT_WORKFLOW_JOB_STATUS - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EventLogMessage - Class in edu.isi.ikcap.workflows.util.logging
  This is a modification of gov.lbl.netlogger.LogMessage This class lets you easily construct a set of typed (name, value) pairs that formats itself as a CEDPS Best Practices log message.
EventLogMessage(String) - Constructor for class edu.isi.ikcap.workflows.util.logging.EventLogMessage
  Create a new LogMessage at the current time with a given event name.
EventLogMessage.Log4jFilter - Class in edu.isi.ikcap.workflows.util.logging
  In log4j, ignore all messages not specifically directed at this appender.
EVENTS_PEGASUS_CODE_GENERATION - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
EVENTS_PEGASUS_STAMPEDE_GENERATION - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
examined - Variable in class edu.isi.pegasus.planner.provisioner.Node
ExampleDAXCallback - Class in edu.isi.pegasus.planner.parser.dax
  An example callback that prints out the various elements in the DAX.
ExampleDAXCallback() - Constructor for class edu.isi.pegasus.planner.parser.dax.ExampleDAXCallback
executable - Variable in class edu.isi.pegasus.planner.classes.Job
  The path of the executable on the machine at which the job is executed.
Executable - Class in edu.isi.pegasus.planner.client
  The interface which defines all the methods , any executable should implement.
Executable() - Constructor for class edu.isi.pegasus.planner.client.Executable
  The default constructor.
Executable(LogManager) - Constructor for class edu.isi.pegasus.planner.client.Executable
  The constructor which ends up initialising the PegasusProperties object.
Executable - Class in edu.isi.pegasus.planner.dax
  The Transformation Catalog object the represent the entries in the DAX transformation section.
Executable(String) - Constructor for class edu.isi.pegasus.planner.dax.Executable
  Create a new executable
Executable(Executable) - Constructor for class edu.isi.pegasus.planner.dax.Executable
  Copy Constructor
Executable(String, String, String) - Constructor for class edu.isi.pegasus.planner.dax.Executable
  Create a new Executable
Executable.ARCH - Enum in edu.isi.pegasus.planner.dax
  ARCH Types
Executable.OS - Enum in edu.isi.pegasus.planner.dax
  OS Types
EXECUTABLE_BASENAME - Static variable in class edu.isi.pegasus.planner.cluster.aggregator.MPIExec
  The basename of the executable that is able to run multiple jobs via mpi.
EXECUTABLE_BASENAME - Static variable in class edu.isi.pegasus.planner.cluster.aggregator.SeqExec
  The basename of the pegasus cluster executable.
EXECUTABLE_BASENAME - Static variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  The basename of the kickstart executable.
EXECUTABLE_BASENAME - Static variable in class edu.isi.pegasus.planner.refiner.cleanup.Cleanup
  The basename of the pegasus cleanup executable.
EXECUTABLE_BASENAME - Static variable in class edu.isi.pegasus.planner.refiner.createdir.DefaultImplementation
  The basename of the pegasus cleanup executable.
EXECUTABLE_BASENAME - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Transfer
  The executable basename for the transfer executable.
EXECUTABLE_BASENAME - Static variable in class edu.isi.pegasus.planner.transfer.sls.Transfer
  The executable basename
EXECUTABLE_FILE - Static variable in class edu.isi.pegasus.planner.classes.PegasusFile
  The type denoting that a logical file is a executable file.
EXECUTABLE_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The name of the key that denotes the executable of the job.
EXECUTABLE_TYPE - Static variable in class edu.isi.pegasus.planner.classes.PegasusFile
  The string value of a file that is of type executable.
execute(List<GridFTPURL>) - Method in class edu.isi.pegasus.gridftp.Command
execute(String[]) - Static method in class edu.isi.pegasus.gridftp.PegasusGridFTP
executeCommand() - Method in class edu.isi.pegasus.planner.client.CPlanner
  Executes the command on the basis of the options specified.
executeCommand(PlannerOptions) - Method in class edu.isi.pegasus.planner.client.CPlanner
  Executes the command on the basis of the options specified.
executeCommand() - Method in class edu.isi.pegasus.planner.client.PartitionDAX
  Executes the partition dax on the basis of the options given by the user.
executeCommand() - Method in class edu.isi.pegasus.planner.client.PegasusGetSites
  Executes the command on the basis of the command line options passed.
executeCommand() - Method in class edu.isi.pegasus.planner.client.RankDAX
  Executes the command on the basis of the options specified.
executeCommand() - Method in class edu.isi.pegasus.planner.client.SCClient
  Call the correct commands depending on options.
executeCommand() - Method in class edu.isi.pegasus.planner.client.TCClient
  Call the correct commands depending on options.
executeCommand() - Method in class edu.isi.pegasus.planner.client.TCConverter
  Call the correct commands depending on options.
executeCommand() - Method in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  Executes the command on the basis of the options specified.
executeOnWorkerNode() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a boolean indicating whether to have jobs executing on worker node tmp or not.
EXECUTION_POOL_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Hints
  The execution pool key
executionPool - Variable in class edu.isi.pegasus.planner.classes.Job
  The pool on which this job has been decided to be executed by the Interpool Engine.
executionToHintsNamespace(String) - Static method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Maps the execution key to corresponding key in hints namespace.
exists(String) - Method in class edu.isi.pegasus.gridftp.GridFTPConnection
  Return true if path exists, false otherwise
ExitCode - Class in edu.isi.pegasus.planner.client
  This class gets the exit code of a job from invocation record.
ExitCode(String) - Constructor for class edu.isi.pegasus.planner.client.ExitCode
  ctor: Constructs a new instance object with the given application name.
EXITCODE_FAILURE_MESSAGE - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The message to look for while detecting failures condor job's stdout/stderr
EXITCODE_SUCCESS_MESSAGE - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  the message to look for while detecting success in condor job's stdout/stderr
extractToMemory(File) - Method in class edu.isi.pegasus.planner.invocation.SimpleServer
  Copy the content of the file into memory.
extractVersionFromSchema(String) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Determines the version of the DAX as specified in a schema string.

## F

FactoryException - Exception in edu.isi.pegasus.common.util
  The base exception class to notify of errors, while instantiating classes via any of the factories.
FactoryException(String) - Constructor for exception edu.isi.pegasus.common.util.FactoryException
  Constructs a `FactoryException` with no detail message.
FactoryException(String, String) - Constructor for exception edu.isi.pegasus.common.util.FactoryException
  Constructs a `FactoryException` with the specified detailed message.
FactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.common.util.FactoryException
  Constructs a `FactoryException` with the specified detailed message and a cause.
FactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.common.util.FactoryException
  Constructs a `FactoryException` with the specified detailed message and a cause.
FAKE_DATE - Static variable in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
FALSE - Static variable in class edu.isi.pegasus.common.util.Boolean
  The character representation of a `false` value.
FATAL_MESSAGE_LEVEL - Static variable in class edu.isi.pegasus.common.logging.LogManager
  The level value, to indicate a FATAL error message.
FATAL_MESSAGE_TYPE - Static variable in class edu.isi.pegasus.common.logging.logger.Default
  The type value to indicate a FATAL error message.
fatalError(SAXParseException) - Method in class edu.isi.pegasus.planner.client.DAXValidator
fatalError(SAXParseException) - Method in class edu.isi.pegasus.planner.parser.XMLErrorHandler
  Logs the the fatal messages which SAX parser generates while validating the XML file against an XML Schema
Fifo - Class in edu.isi.pegasus.planner.invocation
  This class is the container for a FIFO object.
Fifo() - Constructor for class edu.isi.pegasus.planner.invocation.Fifo
  Default c'tor: Construct a hollow shell and allow further information to be added later.
Fifo(String, int) - Constructor for class edu.isi.pegasus.planner.invocation.Fifo
  Constructs a FIFO object.
file - Variable in class edu.isi.pegasus.planner.catalog.transformation.client.Client
File - Class in edu.isi.pegasus.planner.catalog.transformation.impl
  This is the new file based TC implementation storing the contents of the file in memory.
File() - Constructor for class edu.isi.pegasus.planner.catalog.transformation.impl.File
File() - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  The default constructor.
file - Variable in class edu.isi.pegasus.planner.client.TCClient
File - Class in edu.isi.pegasus.planner.dax
  This class is the container for any File object, either the RC section, or uses
File(File) - Constructor for class edu.isi.pegasus.planner.dax.File
  Copy constructor
File(File, File.LINK) - Constructor for class edu.isi.pegasus.planner.dax.File
  Copy constructor, but change the linkage of the file.
File(String, String, String) - Constructor for class edu.isi.pegasus.planner.dax.File
  Create new File object
File(String) - Constructor for class edu.isi.pegasus.planner.dax.File
  Create new file object
File(String, File.LINK) - Constructor for class edu.isi.pegasus.planner.dax.File
  Create new file object
File(String, String, String, File.LINK) - Constructor for class edu.isi.pegasus.planner.dax.File
  Create a new file object
File - Class in edu.isi.pegasus.planner.invocation
  This class is the base class for a file object.
File() - Constructor for class edu.isi.pegasus.planner.invocation.File
  Default c'tor: Construct a hollow shell and allow further information to be added later.
File(String) - Constructor for class edu.isi.pegasus.planner.invocation.File
  C'tor: Constructs the value in the base class.
File.LINK - Enum in edu.isi.pegasus.planner.dax
  The linkages that a file can be of
File.TRANSFER - Enum in edu.isi.pegasus.planner.dax
  Three Transfer modes supported, Transfer this file, don't transfer or stageout as well as optional.
FILE_DELIMITER - Static variable in class edu.isi.pegasus.planner.dax.AbstractJob
FILE_FORMAT - Static variable in class edu.isi.pegasus.planner.client.TCConverter
  The File format.
FILE_OUTPUT_CONTENTS - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
FILE_OUTPUT_CONTENTS - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
FILE_OUTPUT_NAME - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
FILE_OUTPUT_NAME - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
FILE_PRIORTY - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
FILE_PRIORTY - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
FILE_SYSTEM_DOMAIN_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The name of the key that denotes the File System Domain.
FILE_TYPE - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
FILE_TYPE - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
FILE_URL_SCHEME - Static variable in class edu.isi.pegasus.common.util.PegasusURL
  The scheme name for file url.
FileExistsException - Exception in edu.isi.pegasus.gridftp
FileExistsException(String) - Constructor for exception edu.isi.pegasus.gridftp.FileExistsException
FileExistsException(String, Throwable) - Constructor for exception edu.isi.pegasus.gridftp.FileExistsException
FileInfo - Class in edu.isi.pegasus.gridftp
  Stores information about a file or directory, such as its name, size, type, etc.
FileInfo(String, String) - Constructor for class edu.isi.pegasus.gridftp.FileInfo
fileName - Variable in class edu.isi.pegasus.planner.provisioner.Edge
fileName - Variable in class edu.isi.pegasus.planner.provisioner.Estimator
fileOptional() - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Returns optional flag denoting the file to be optional or not.
FileServer - Class in edu.isi.pegasus.planner.catalog.site.classes
  This class describes a file server that can be used to stage data to and from a site.
FileServer() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.FileServer
  The default constructor.
FileServer(String, String, String) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.FileServer
  Overloaded constructor.
FileServerType - Class in edu.isi.pegasus.planner.catalog.site.classes
  An abstract class that describes a file server that can be used to stage data to and from a site.
FileServerType() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.FileServerType
  The default constructor.
FileServerType(String, String, String) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.FileServerType
  Overloaded constructor.
FileServerType.OPERATION - Enum in edu.isi.pegasus.planner.catalog.site.classes
  The operations supported by the file server
fileSize - Variable in class edu.isi.pegasus.planner.provisioner.Edge
FileSystemType - Class in edu.isi.pegasus.planner.catalog.site.classes
  An abstract class describing a filesystem type.
FileSystemType() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.FileSystemType
  The default constructor.
FileSystemType(String, String, String) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.FileSystemType
  The overloaded constructor.
FileTransfer - Class in edu.isi.pegasus.planner.classes
  This is a container for the storing the transfers that are required in between sites.
FileTransfer() - Constructor for class edu.isi.pegasus.planner.classes.FileTransfer
  Default constructor.
FileTransfer(PegasusFile) - Constructor for class edu.isi.pegasus.planner.classes.FileTransfer
  The overloaded constructor.
FileTransfer(String, String) - Constructor for class edu.isi.pegasus.planner.classes.FileTransfer
  The overloaded constructor.
FileTransfer(String, String, BitSet) - Constructor for class edu.isi.pegasus.planner.classes.FileTransfer
  The overloaded constructor.
fillArgs(Map) - Method in class edu.isi.pegasus.planner.catalog.transformation.client.Client
  Takes the arguments from the TCClient and stores it for acess to the other TC Client modules.
finalize() - Method in class edu.isi.pegasus.common.util.StreamGobbler
  Closes the open connections to the streams whenever this object is destroyed.
finalize() - Method in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  Closes the connection to the rli.
findExec(String) - Static method in class edu.isi.pegasus.common.util.FindExecutable
  Finds the path to an executable of a given name , based on the value of PATH environment variable.
FindExecutable - Class in edu.isi.pegasus.common.util
  A convenice class that allows us to determine the path to an executable
FindExecutable() - Constructor for class edu.isi.pegasus.common.util.FindExecutable
findLCA(GraphNode, GraphNode) - Method in class edu.isi.pegasus.planner.refiner.ReduceEdges
  We find LCA of from and to.
Fixed - Class in edu.isi.pegasus.planner.transfer.mapper.impl
  A convenience mapper implementation that stages output files to a fixed directory, specified using properties.
Fixed() - Constructor for class edu.isi.pegasus.planner.transfer.mapper.impl.Fixed
  The default constructor.
Flat - Class in edu.isi.pegasus.planner.transfer.mapper.impl
  Maps the output files to a flat directory on the output site.
Flat() - Constructor for class edu.isi.pegasus.planner.transfer.mapper.impl.Flat
  The default constructor.
FLAT_LFN_PROPERTY_KEY - Static variable in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  the name of the key that specifies whether we want flat lfns or not.
flush() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
  Check if the buffer is full i.e.
FlushedCache - Class in edu.isi.pegasus.planner.catalog.replica.impl
  This class implements a replica catalog which directly writes to the output file.
FlushedCache() - Constructor for class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
force - Variable in class edu.isi.pegasus.gridftp.RemoveCommand
FORK_JOBMANAGER_TYPE - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The jobmanager type associated with the transfer jobs.
format - Static variable in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
FREE_MEM - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The constant to be passed to the accessor functions to get or set the free memory .
FREE_SIZE - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPServer
  The constant to be passed to the accessor functions to get or set the free size.
FREE_SIZE - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.WorkDir
  The constant to be passed to the accessor functions to get or set the free space available.
fromArguments(List<String>) - Static method in class edu.isi.pegasus.gridftp.ListCommand
fromArguments(List<String>) - Static method in class edu.isi.pegasus.gridftp.MakeDirectoryCommand
fromArguments(List<String>) - Static method in class edu.isi.pegasus.gridftp.RemoveCommand
fromLongFormat(String) - Static method in class edu.isi.pegasus.gridftp.FileInfo
fromMlsxEntry(MlsxEntry) - Static method in class edu.isi.pegasus.gridftp.FileInfo
fromNode - Variable in class edu.isi.pegasus.planner.provisioner.Edge
fromShortFormat(String) - Static method in class edu.isi.pegasus.gridftp.FileInfo
fromString(String) - Static method in class edu.isi.pegasus.planner.catalog.transformation.classes.Arch
  Creates a new Arch object given a arch string.
fromString(String) - Static method in class edu.isi.pegasus.planner.catalog.transformation.classes.Os
  Creates a new Os object given an os string.
fromValue(String) - Static method in class edu.isi.pegasus.planner.catalog.transformation.classes.Arch
  Creates a new Arch Object givan a arch string.
fromValue(String) - Static method in class edu.isi.pegasus.planner.catalog.transformation.classes.Os
  Creates a new Os object given an os string.
ftToRC(FileTransfer) - Method in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  Converts a `FileTransfer` to a RC compatible string representation.
full_where() - Method in class edu.isi.pegasus.planner.client.DAXValidator
full_where() - Method in class edu.isi.pegasus.planner.parser.InvocationParser

## G

generate(PrintWriter, ADag) - Static method in class edu.isi.pegasus.planner.code.generator.condor.ClassADSGenerator
  Writes out the classads for a workflow to corresponding writer stream.
generate(PrintWriter, ADag, Job) - Static method in class edu.isi.pegasus.planner.code.generator.condor.ClassADSGenerator
  Writes out the classads for a job to corresponding writer stream.
generate(String, String) - Method in class edu.isi.pegasus.planner.dax.examples.Diamond
GENERATE_SUBDAG_KEYWORD - Static variable in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Whether to generate the SUBDAG keyword or not.
generateArgumentString(TransferJob) - Method in class edu.isi.pegasus.planner.transfer.implementation.AbstractMultipleFTPerXFERJob
  It constructs the arguments to the transfer executable that need to be passed to the executable referred to in this transfer mode.
generateArgumentString(TransferJob) - Method in class edu.isi.pegasus.planner.transfer.implementation.GUC
  It constructs the arguments to the transfer executable that need to be passed to the executable referred to in this transfer mode.
generateArgumentString(TransferJob) - Method in class edu.isi.pegasus.planner.transfer.implementation.T2
  It constructs the arguments to the transfer executable that need to be passed to the executable referred to in this transfer mode.
generateArgumentString(TransferJob) - Method in class edu.isi.pegasus.planner.transfer.implementation.TPTGUC
  It constructs the arguments to the transfer executable that need to be passed to the executable referred to in this transfer mode.
generateArgumentString(TransferJob) - Method in class edu.isi.pegasus.planner.transfer.implementation.Transfer
  It constructs the arguments to the transfer executable that need to be passed to the executable referred to in this transfer mode.
generateArgumentStringAndAssociateCredentials(TransferJob, FileTransfer) - Method in class edu.isi.pegasus.planner.transfer.implementation.AbstractSingleFTPerXFERJob
  It constructs the arguments to the transfer executable that need to be passed to the executable referred to in this transfer mode.
generateArgumentStringAndAssociateCredentials(TransferJob, FileTransfer) - Method in class edu.isi.pegasus.planner.transfer.implementation.Stork
  It constructs the arguments to the transfer executable that need to be passed to the executable referred to in this transfer mode.
generateCallToCheckExitcode(Job, String) - Method in class edu.isi.pegasus.planner.code.generator.Shell
  Generates a call to check_exitcode function that is used
generateCallToExecuteJob(Job, String, String) - Method in class edu.isi.pegasus.planner.code.generator.Shell
  Generates a call to execute_job function , that is used to launch a job from the shell script.
generateCallToExecutePostScript(Job, String) - Method in class edu.isi.pegasus.planner.code.generator.Shell
  Generates a call to execute_post_script function , that is used to launch a job from the shell script.
generateClassAdAttribute(String, String) - Static method in class edu.isi.pegasus.planner.code.generator.condor.ClassADSGenerator
  Generates a classad attribute given the name and the value.
generateClassAdAttribute(String, int) - Static method in class edu.isi.pegasus.planner.code.generator.condor.ClassADSGenerator
  Generates a classad attribute given the name and the value.
generateClassAdAttribute(String, String, boolean) - Static method in class edu.isi.pegasus.planner.code.generator.condor.ClassADSGenerator
  Generates a classad attribute given the name and the value.
generateCleanupID(Job) - Method in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  Returns the identifier that is to be assigned to cleanup job.
generateClusteredJobID(String, int, int) - Method in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  Generated an ID for a clustered cleanup job
generateCode(ADag) - Method in interface edu.isi.pegasus.planner.code.CodeGenerator
  Generates the code for the concrete workflow in the input format of the workflow executor being used.
generateCode(ADag, Job) - Method in interface edu.isi.pegasus.planner.code.CodeGenerator
  Generates the code for a single job in the input format of the workflow executor being used.
generateCode(ADag) - Method in class edu.isi.pegasus.planner.code.generator.Braindump
  Generates the code for the executable workflow in terms of a braindump file that contains workflow metadata useful for monitoring daemons etc.
generateCode(ADag, Map<String, String>) - Method in class edu.isi.pegasus.planner.code.generator.Braindump
  Generates the code for the executable workflow in terms of a braindump file that contains workflow metadata useful for monitoring daemons etc.
generateCode(ADag, Job) - Method in class edu.isi.pegasus.planner.code.generator.Braindump
  Method not implemented.
generateCode(ADag) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Generates the code for the concrete workflow in Condor DAGMAN and CondorG input format.
generateCode(ADag, Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Generates the code (condor submit file) for a single job.
generateCode(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Generates code for a job
generateCode(ADag) - Method in class edu.isi.pegasus.planner.code.generator.DAXReplicaStore
  Generates the notifications input file.
generateCode(ADag, Job) - Method in class edu.isi.pegasus.planner.code.generator.DAXReplicaStore
  Not implemented
generateCode(ADag) - Method in class edu.isi.pegasus.planner.code.generator.MonitordNotify
  Generates the notifications input file.
generateCode(ADag, Job) - Method in class edu.isi.pegasus.planner.code.generator.MonitordNotify
  Not implemented
generateCode(ADag) - Method in class edu.isi.pegasus.planner.code.generator.PBS
  Generates the code for the concrete workflow in the GRMS input format.
generateCode(ADag, Job) - Method in class edu.isi.pegasus.planner.code.generator.PBS
  Generates the code for a single job in the input format of the workflow executor being used.
generateCode(ADag) - Method in class edu.isi.pegasus.planner.code.generator.PMC
  Generates the code for the concrete workflow in the GRMS input format.
generateCode(ADag, Job) - Method in class edu.isi.pegasus.planner.code.generator.PMC
  Generates the code for a single job in the input format of the workflow executor being used.
generateCode(ADag) - Method in class edu.isi.pegasus.planner.code.generator.Shell
  Generates the code for the concrete workflow in the GRMS input format.
generateCode(ADag, Job) - Method in class edu.isi.pegasus.planner.code.generator.Shell
  Generates the code for a single job in the input format of the workflow executor being used.
generateCode(ADag) - Method in class edu.isi.pegasus.planner.code.generator.Stampede
  Generates the code for the executable workflow in terms of a braindump file that contains workflow metadata useful for monitoring daemons etc.
generateCode(ADag, Job) - Method in class edu.isi.pegasus.planner.code.generator.Stampede
  Method not implemented.
generateCode(ADag) - Method in class edu.isi.pegasus.planner.code.generator.Stork
  Generates the code for the concrete workflow in the input format of the workflow executor being used.
generateCode(ADag, Job) - Method in class edu.isi.pegasus.planner.code.generator.Stork
  Generates the code for a single job in the Stork format.
generateEventsForDAXTask(PrintWriter, ADag, Job) - Method in class edu.isi.pegasus.planner.code.generator.Stampede
  Generates stampede events corresponding to jobs/tasks in the DAX
generateEventsForExecutableJob(PrintWriter, ADag, Job) - Method in class edu.isi.pegasus.planner.code.generator.Stampede
  Generates stampede events corresponding to an executable job
generateFlowID() - Method in class edu.isi.pegasus.planner.classes.ADag
  Generates the flow id for this current run.
generateFlowID() - Method in class edu.isi.pegasus.planner.classes.DagInfo
  Generates the flow id for this current run.
generateFlowName() - Method in class edu.isi.pegasus.planner.classes.ADag
  Generates the name of the flow.
generateFlowName() - Method in class edu.isi.pegasus.planner.classes.DagInfo
  Generates the name of the flow.
generateKickstartExtraOptions() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a boolean indicating whehter to pass extra options to kickstart or not.
generateList(String) - Method in class edu.isi.pegasus.planner.client.RankDAX
  Generates a List by parsing a comma separated string.
generateListofFilenamesFile(Set, String) - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Writes out the list of filenames file for the constituentJob.
generateListofFilenamesFile(Set, String) - Method in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  Writes out the list of filenames file for the job.
generateListofFilenamesFile(Set, String) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Writes out the list of filenames file for the job.
generateLOFFiles() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Return a boolean indicating whether to generate the LOF files for the jobs or not.
generateLogEvent(Job, String) - Method in class edu.isi.pegasus.planner.code.generator.NetloggerJobMapper
  Generates a log event message in the netlogger format for a job
generateLogFileSymlink(String, String) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  This method generates a symlink to the actual log file written in the local temp directory.
generateMappingsFile(String, Collection) - Method in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  Generates the registration mappings in a text file that is generated in the dax directory (the directory where all the condor submit files are generated).
generateMask(int, boolean) - Method in class edu.isi.pegasus.common.logging.logger.Default
  Generates the appropriate mask value, corresponding to the level passed.
generateName(String) - Method in class edu.isi.pegasus.planner.classes.DAGJob
  Generates a name for the job that serves as the primary id for the job
generateName(String) - Method in class edu.isi.pegasus.planner.classes.DAXJob
  Generates a name for the job that serves as the primary id for the job
generatePMCInputFile(Graph, String, boolean) - Method in class edu.isi.pegasus.planner.cluster.aggregator.MPIExec
  Writes out the input file for the aggregated job
generateRandomDirectory() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns whether to generate a random directory or not.
generateRandomDirectory() - Method in class edu.isi.pegasus.planner.common.UserOptions
  Returns whether we want to create a Random Directory or not.
generateRepJobArgumentString(SiteCatalogEntry, String, Collection) - Method in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  Generates the argument string to be given to the replica registration job.
generateSet(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Generates a Set by parsing a comma separated string.
generateSRMProperties() - Method in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  Generates SRM properties that can be used by Pegasus to do SRM URL substitution for the case where all the data is accessible on the worker nodes locally.
generateSRMProperties(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  Generates SRM properties that can be used by Pegasus to do SRM URL substitution for the case where all the data is accessible on the worker nodes locally for a particular site.
generateStampedeEventsForAbstractWorkflow(ADag, PegasusBag) - Method in class edu.isi.pegasus.planner.client.CPlanner
  Generates events for the abstract workflow.
generateTaskMapEvents(PrintWriter, ADag, Job) - Method in class edu.isi.pegasus.planner.code.generator.Stampede
  Generates the task.map events that link the jobs in the DAX with the jobs in the executable workflow
generateValidOptions() - Method in class edu.isi.pegasus.planner.client.CPlanner
  Tt generates the LongOpt which contain the valid options that the command will accept.
generateValidOptions() - Method in class edu.isi.pegasus.planner.client.Executable
  Generates an array of valid `LongOpt` objects which contain all the valid options to the Executable.
generateValidOptions() - Method in class edu.isi.pegasus.planner.client.ExitCode
  Creates a set of options.
generateValidOptions() - Method in class edu.isi.pegasus.planner.client.PartitionDAX
  Tt generates the LongOpt which contain the valid options that the command will accept.
generateValidOptions() - Method in class edu.isi.pegasus.planner.client.PegasusGetSites
  Generates valid LongOpts.
generateValidOptions() - Method in class edu.isi.pegasus.planner.client.RankDAX
  It generates the LongOpt which contain the valid options that the command will accept.
generateValidOptions() - Method in class edu.isi.pegasus.planner.client.RCClient
  Creates a set of GNU long options.
generateValidOptions() - Method in class edu.isi.pegasus.planner.client.SCClient
generateValidOptions() - Method in class edu.isi.pegasus.planner.client.TCClient
generateValidOptions() - Method in class edu.isi.pegasus.planner.client.TCConverter
  Generates the list of valid options for the tc-converter client
generateValidOptions() - Method in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  Tt generates the LongOpt which contain the valid options that the command will accept.
generateValidOptions() - Method in class edu.isi.pegasus.planner.client.VersionNumber
  Creates a set of options.
generateWorkflowUUID() - Method in class edu.isi.pegasus.planner.classes.ADag
  Generates the UUID for the workflow
GENERATOR - Static variable in class edu.isi.pegasus.planner.code.generator.condor.ClassADSGenerator
  The name of the generator.
GENERATOR_AD_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.ClassADSGenerator
  The complete classad designating Pegasus as the generator.
GENERATOR_TYPE_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The Key designating type of Pegasus Code Generator.
get(CredentialHandler.TYPE) - Method in class edu.isi.pegasus.common.credential.CredentialHandlerFactory
  Returns the implementation from the implementing class table.
get(Profiles.NAMESPACES) - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Returns the namespace object corresponding to a namespace
get(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.PoolConfig
  Retrives the information about a site.
get(Object) - Method in class edu.isi.pegasus.planner.classes.PegasusBag
  Returns an objects corresponding to the key passed.
get(String) - Method in class edu.isi.pegasus.planner.classes.ReplicaStore
  Returns an entry corresponding to the LFN
get(String) - Method in class edu.isi.pegasus.planner.cluster.aggregator.JobAggregatorInstanceFactory
  Returns the implementation from the implementing class table.
get(String) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactory
  Returns the implementation from the implementing class table.
get(String) - Method in class edu.isi.pegasus.planner.invocation.Environment
  Retrieves the value for a given key
get(String) - Method in class edu.isi.pegasus.planner.invocation.MachineInfo
  Returns attribute value for a key
get(Object) - Method in class edu.isi.pegasus.planner.namespace.ENV
  Returns the value to which this namespace maps the specified key.
get(Object) - Method in class edu.isi.pegasus.planner.namespace.Namespace
  Returns the value to which this namespace maps the specified key.
get(Object) - Method in class edu.isi.pegasus.planner.namespace.Pegasus
  Returns the value to which this namespace maps the specified key.
get(Object) - Method in class edu.isi.pegasus.planner.namespace.Selector
  Returns the value to which this namespace maps the specified key.
get(Object) - Method in class edu.isi.pegasus.planner.namespace.Stat
  Returns the value to which this namespace maps the specified key.
get(Object) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2Graph
  It returns the value associated with the key in the map.
get(String) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2NewGraph
  Returns the `GraphNode` of the corresponding id.
get(Object) - Method in interface edu.isi.pegasus.planner.partitioner.graph.Bag
  Returns an objects corresponding to the key passed.
get(Object) - Method in class edu.isi.pegasus.planner.partitioner.graph.LabelBag
  Returns an objects corresponding to the key passed.
get(Object) - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph
  It returns the value associated with the key in the map.
get(String, String) - Method in class edu.isi.pegasus.planner.ranking.GetDAX
  Given a request ID it fetches the DAX's from the DB and writes out to the directory passed.
get(Object) - Method in class edu.isi.pegasus.planner.refiner.DataReuseEngine.BooleanBag
  For all keys returns the boolean value
get(Object) - Method in class edu.isi.pegasus.planner.selector.site.heft.HeftBag
  Returns an objects corresponding to the key passed.
get(String) - Method in class edu.isi.pegasus.planner.transfer.RemoteTransfer
  Returns the TPT state for a particular site.
get(int) - Method in class edu.isi.pegasus.planner.transfer.RemoteTransfer.TransferState
  Returns a boolean indicating whether the attribute passed is set in the transfer state or not.
get(String) - Method in class edu.isi.pegasus.planner.transfer.TPT
  Returns the TPT state for a particular site.
get(int) - Method in class edu.isi.pegasus.planner.transfer.TPT.TPTState
  Returns a boolean indicating whether the attribute passed is set in the transfer state or not.
GET_ENV_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The condor key for using the local environment
getAbsolutePath(Partition, String, String) - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Returns the absolute path to a dagman (usually) related file for a particular partition in the submit directory that is passed as an input parameter.
getAbstractChildID() - Method in class edu.isi.pegasus.planner.classes.PCRelation
  Returns the abstract child id associated with the edge.
getAbstractJob(String) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Returns an abstract Job with id ajobid if present otherwise null.
getAbstractParentID() - Method in class edu.isi.pegasus.planner.classes.PCRelation
  Returns the abstract parent id associated with the edge.
getAbstractWorkflowName() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the workflow id
getAccessTime() - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor
getAdditionalBraindumpEntries(ADag) - Method in class edu.isi.pegasus.planner.code.generator.Abstract
  Returns a Map containing additional metrics entries that are specific to a Code Generator
getAdditionalBraindumpEntries(ADag) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Returns a Map containing additional braindump entries that are specific to a Code Generator.
getAdditionalBraindumpEntries(ADag) - Method in class edu.isi.pegasus.planner.code.generator.PBS
  Returns a Map containing additional braindump entries that are specific to a Code Generator
getAdditionalBraindumpEntries(ADag) - Method in class edu.isi.pegasus.planner.code.generator.PMC
  Returns a Map containing additional braindump entries that are specific to a Code Generator.
getAdditionalBraindumpEntries(ADag) - Method in class edu.isi.pegasus.planner.code.generator.Shell
  Returns a Map containing additional braindump entries that are specific to a Code Generator
getAdditionalBraindumpEntries(ADag) - Method in class edu.isi.pegasus.planner.code.generator.Stork
  Returns an empty map
getAliasIterator() - Method in class edu.isi.pegasus.planner.catalog.site.classes.ReplicaCatalog
  Returns an iterator to aliases associated with the site.
getAllEntries() - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.TransformationStore
  Returns all the entries in the Transformation Store
getAllIgnoredSites() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a comma separated list of sites, from which to ignore data transfers for all sites.
getAllPreferredSites() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a comma separated list of sites, from which to prefer data transfers for all sites.
getAncET() - Method in class edu.isi.pegasus.planner.provisioner.Node
getAncSize() - Method in class edu.isi.pegasus.planner.provisioner.Node
getApplicationMetrics() - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Returns the application specific metrics that will be forwarded to the server
getArch() - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.VDSSysInfo
  Returns the architecture of the sytem.
getArchitecture() - Method in class edu.isi.pegasus.planner.catalog.classes.SysInfo
  Returns the architecture of the site.
getArchitecture() - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Returns the architecture of the nodes that this grid gateway talks to.
getArchitecture() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Returns the architecture of the site.
getArchitecture() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Returns the architecture of the site.
getArchitecture() - Method in class edu.isi.pegasus.planner.dax.Executable
  Get the architecture the Executable is compiled for
getArchitecture() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor
getArchMode() - Method in class edu.isi.pegasus.planner.invocation.Architecture
  Accessor
getArguments() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the argument string with which the job has to be invoked.
getArguments() - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Return the argument List.
getArguments() - Method in class edu.isi.pegasus.planner.invocation.Job
  Accessor
getAssociatedCreateDirSite(Job) - Method in class edu.isi.pegasus.planner.refiner.createdir.Minimal
  Returns the associated site that job is dependant on.
getAssociatedCreateDirSite(Job) - Method in class edu.isi.pegasus.planner.refiner.RemoveDirectory
  Returns the associated site that job is dependant on.
getAttribute(String) - Method in class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  Obtains the attribute value for a given key.
getAttributeCount() - Method in class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  Counts the number of attributes known for the PFN.
getAttributeIterator() - Method in class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  Provides an iterator to traverse the attributes by their keys.
getAttributeKeysIterator() - Method in class edu.isi.pegasus.planner.invocation.MachineInfo
  Returns Iterator for attribute keys.
getAuthenticateRequest() - Method in class edu.isi.pegasus.planner.refiner.ThreadPool.AuthenticateThread
  Returns an authentication request to the worker thread.
getAvailableProcessors() - Method in class edu.isi.pegasus.planner.selector.site.heft.Site
  Returns the number of available processors.
getAvailableTime(String, long) - Method in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  Returns the available time for a site.
getAvailableTime(long) - Method in class edu.isi.pegasus.planner.selector.site.heft.Processor
  Returns the earliest time the processor is available for scheduling a job.
getAvailableTime(long) - Method in class edu.isi.pegasus.planner.selector.site.heft.Site
  Returns the earliest time the site is available for scheduling a job.
getBag() - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  Returns the bag of objects associated with the node.
getBaseName(String) - Method in interface edu.isi.pegasus.common.credential.CredentialHandler
  returns the basename of the credential file name
getBaseName(String) - Method in class edu.isi.pegasus.common.credential.impl.Irods
  returns the basename of the path to the local credential
getBaseName(String) - Method in class edu.isi.pegasus.common.credential.impl.Proxy
  returns the basename of the path to the local credential
getBaseName(String) - Method in class edu.isi.pegasus.common.credential.impl.S3CFG
  returns the basename of the path to the local credential
getBaseName(String) - Method in class edu.isi.pegasus.common.credential.impl.Ssh
  returns the basename of the path to the local credential
getBasename(String, String) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  A covenience method to construct the basename.
getBasename(String, String) - Method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Returns the basename of a dagman (usually) related file for a particular partition.
getBaseName(Partition) - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Returns the base name of the submit directory in which the submit files for a particular partition reside.
getBasename(Partition, String) - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Returns the basename of a dagman (usually) related file for a particular partition.
getBasename(String) - Method in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Returns the basename of the URL using substring.
getBasenamePrefix() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the basename prefix for the per workflow files that are to be generated by the planner.
getBasenamePrefix(Job) - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Returns the basename prefix of a dagman (usually) related file for a a job that submits nested dagman.
getBaseSourceURLForSetupTransfers() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the base source URL where pointing to the directory where the worker package executables for pegasus releases are kept.
getBaseSubmitDirectory() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the root of submit directory hierarchy for the workflow.
getBaseSubmitDirectory() - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Returns the path to the base submit directory.
getBaseSubmitDirectory() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the base submit directory
getBinDir() - Method in class edu.isi.pegasus.common.util.CommonProperties
  Accessor pegasus bin directory
getBinDir() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Accessor to the bin directory of the Pegasus install
getBinPackingComparator() - Method in class edu.isi.pegasus.planner.cluster.Horizontal
  The comparator is used to sort a collection of jobs in decreasing order of their run times as specified by the Pegasus.JOB_RUN_TIME property.
getBlocks() - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor
getBlockSize() - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor
getBooleanValue(Object) - Method in class edu.isi.pegasus.planner.namespace.Condor
  Returns a boolean value, that a particular key is mapped to in this namespace.
getBooleanValue(Object) - Method in class edu.isi.pegasus.planner.namespace.Pegasus
  Returns a boolean value, that a particular key is mapped to in this namespace.
getBooleanValue() - Method in class edu.isi.pegasus.planner.refiner.DataReuseEngine.BooleanBag
  Returns the boolean value
getCacheFile(PlannerOptions, String, String) - Method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Returns the path to the cache file in a workflow's submit directory
getCacheFileName(ADag, FileServerType.OPERATION) - Method in class edu.isi.pegasus.planner.classes.PlannerCache
  Constructs the basename to the cache file that is to be used to log the transient files.
getCacheFileName(PlannerOptions, String, String) - Method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Constructs the basename to the cache file that is to be used to log the transient files.
getCacheFileName(ADag) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  Constructs the basename to the cache file that is to be used to log the transient files.
getCacheFilePath(Job) - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Returns the full path to a cache file that corresponds for one partition.
getCacheFiles() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the cache files.
getCacheFiles() - Method in class edu.isi.pegasus.planner.common.UserOptions
  It returns the set of cache files.
getCategoryDAGManKnobs(PegasusProperties) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Write out the DAGMan knobs for each category the user mentions in the properties.
getCERequirementsForJob(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.GLite
  Constructs the value for remote CE requirements expression for the job .
getChild() - Method in class edu.isi.pegasus.planner.classes.PCRelation
  Returns the child in the edge.
getChild() - Method in class edu.isi.pegasus.planner.dax.Edge
getChildren() - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  Returns a list of `GraphNode` objects that are children of the node.
getChmodDisabledSites() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the list of sites for which the chmod job creation has to be disabled for executable staging.
getClassName() - Method in class edu.isi.pegasus.common.util.DynamicLoader
  Obtains the fully-qualified class name that this instance works with.
getClassname() - Method in exception edu.isi.pegasus.common.util.FactoryException
  Returns the name of the class that was trying to be loaded when this error occured, or some other signifier like a module name.
getClassPath(String) - Method in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  Returns the classpath for the default rc-client entry.
getCleanup() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the option indicating whether to do cleanup or not.
getCleanupDAG() - Method in class edu.isi.pegasus.planner.refiner.MainEngine
  Returns the cleanup dag for the concrete dag.
getCleanupImplementation() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the name of the class that the user wants, to render the cleanup jobs.
getCleanupJobname(ADag, String) - Method in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  It returns the name of the untar job, that is to be assigned.
getCleanupScope() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the scope for file cleanup.
getCleanupStrategy() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the name of the Strategy class that the user wants, to insert the cleanup jobs in the graph.
getClusteredDAG() - Method in class edu.isi.pegasus.planner.cluster.Abstract
  Returns the clustered workflow.
getClusteredDAG() - Method in interface edu.isi.pegasus.planner.cluster.Clusterer
  Returns the clustered workflow.
getClusteredDAG() - Method in class edu.isi.pegasus.planner.cluster.Horizontal
  Returns the clustered workflow.
getClustererLabelKey() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the key that is to be used as a label key, for labelled clustering.
getClusterExecutableBasename() - Method in class edu.isi.pegasus.planner.cluster.aggregator.MPIExec
  Returns the executable basename of the clustering executable used.
getClusterExecutableBasename() - Method in class edu.isi.pegasus.planner.cluster.aggregator.SeqExec
  Returns the executable basename of the clustering executable used.
getClusterExecutableBasename() - Method in interface edu.isi.pegasus.planner.cluster.JobAggregator
  Returns the executable basename of the clustering executable used.
getClusterExecutableLFN() - Method in class edu.isi.pegasus.planner.cluster.aggregator.MPIExec
  Returns the logical name of the transformation that is used to collapse the jobs.
getClusterExecutableLFN() - Method in class edu.isi.pegasus.planner.cluster.aggregator.SeqExec
  Returns the logical name of the transformation that is used to collapse the jobs.
getClusterExecutableLFN() - Method in interface edu.isi.pegasus.planner.cluster.JobAggregator
  Returns the logical name of the transformation that is used to collapse the jobs.
getClusteringTechnique() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the clustering technique to be used for clustering.
getClusterSize(int) - Method in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  Returns the number of cleanup jobs clustered into one job per level.
getClusterSizeCleanupJobsPerLevel() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the fraction of cleanup jobs clustered into a single clustered cleanup job.
getCode() - Method in class edu.isi.pegasus.planner.code.generator.SendMetricsResult
getCollapseFactor(String, Job, int) - Method in class edu.isi.pegasus.planner.cluster.Horizontal
  Returns the collapse factor, that is used to chunk up the jobs of a particular type on a pool.
getCollapseFactor(String, int) - Method in class edu.isi.pegasus.planner.partitioner.Horizontal
  Returns the collapse factor, that is used to determine the number of nodes going in a partition.
getCollapseFactors() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a comma separated list for the node collapsing criteria for the execution pools.
getCommandLineOptions() - Method in class edu.isi.pegasus.planner.client.Executable
  Returns the command line arguments passed to the executable
getCommandLineProperties(PegasusProperties) - Method in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  Returns the properties that need to be passed to the the rc-client invocation on the command line .
getCommentString(Job, int) - Method in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  Generates the comment string for the job .
getCompleteDVName() - Method in class edu.isi.pegasus.planner.classes.Job
  Constructs the fully qualified name of the corresponding derivation used to generate this job in Chimera including the namespace and version.
getCompleteName() - Method in class edu.isi.pegasus.planner.classes.CompoundTransformation
  Returns the complete name for the transformation.
getCompleteOptions() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the complete options string that is used to invoke pegasus
getCompleteTCName() - Method in class edu.isi.pegasus.planner.classes.Job
  Constructs the fully qualified name of a transformation with which to query the TC, including the namespace and version.
getCompleteTCName() - Method in class edu.isi.pegasus.planner.transfer.implementation.AbstractMultipleFTPerXFERJob
  Returns the complete name for the transformation that the implementation is using..
getCompleteTCName() - Method in class edu.isi.pegasus.planner.transfer.implementation.AbstractSingleFTPerXFERJob
  Returns the complete name for the transformation that the implementation is using.
getCompleteTCName() - Method in class edu.isi.pegasus.planner.transfer.implementation.GUC
  Returns the complete name for the transformation.
getCompleteTCName() - Method in class edu.isi.pegasus.planner.transfer.implementation.Stork
  Returns the complete name for the transformation.
getCompleteTCName() - Method in class edu.isi.pegasus.planner.transfer.implementation.T2
  Returns the complete name for the transformation.
getCompleteTCName() - Method in class edu.isi.pegasus.planner.transfer.implementation.Transfer
  Returns the complete name for the transformation.
getCompleteTranformationName(String) - Static method in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  A convenience method to return the complete transformation name being used to construct jobs in this class.
getCompleteTranformationName() - Static method in class edu.isi.pegasus.planner.refiner.cleanup.Cleanup
  A convenience method to return the complete transformation name being used to construct jobs in this class.
getCompleteTranformationName() - Static method in class edu.isi.pegasus.planner.refiner.RemoveDirectory
  A convenience method to return the complete transformation name being used to construct jobs in this class.
getComputeJobBundleValue(Job) - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  Returns the bundle value associated with a compute job as a String.
getComputeJobBundleValue(Job) - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  Returns the bundle value associated with a compute job as a String.
getComputeJobBundleValue(Job) - Method in class edu.isi.pegasus.planner.transfer.refiner.Cluster
  Returns the bundle value associated with a compute job as a String.
getConcatJobname(ADag) - Method in class edu.isi.pegasus.planner.refiner.createdir.HourGlass
  Returns the name of the concat job
getCondorFileName(String, int, String) - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  A small utility method that constructs the name of the Condor files that are generated when a dag is submitted.
getCondorFileName(String, int, String, String) - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  A small utility method that constructs the name of the Condor files that are generated when a dag is submitted.
getCondorLogInSubmitDirectory() - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Returns the path to the condor log file in the submit directory.
getCondorLogInSubmitDirectory(ADag) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Returns the path to the condor log file in the submit directory.
getCondorLogInTmpDirectory() - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Returns the name of Condor log file in a tmp directory that is created if generation of symlink for condor logs is turned on.
getConfFile() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the property file pointed to by the --conf option passed to the planner
getConfigurationProperties(String) - Method in class edu.isi.pegasus.planner.common.PegasusConfiguration
  Returns Properties corresponding to a particular configuration.
getConnectionIterator() - Method in class edu.isi.pegasus.planner.catalog.site.classes.ReplicaCatalog
  Returns an iterator to connection params associated with the replica catalog.
getConstituentJob(int) - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Returns a job from a particular position in the list of constituent jobs
getConstructedObject() - Method in interface edu.isi.pegasus.planner.parser.dax.Callback
  Return a object that is constructed during the parsing of the object.
getConstructedObject() - Method in class edu.isi.pegasus.planner.parser.dax.DAX2CDAG
  Returns an ADag object corresponding to the abstract plan it has generated.
getConstructedObject() - Method in class edu.isi.pegasus.planner.parser.dax.DAX2Graph
  Returns a Map indexed by the logical ID of the jobs, and each value being a GraphNode object.
getConstructedObject() - Method in class edu.isi.pegasus.planner.parser.dax.DAX2Metadata
  Returns an ADag object corresponding to the abstract plan it has generated.
getConstructedObject() - Method in class edu.isi.pegasus.planner.parser.dax.DAX2NewGraph
  Returns the workflow represented in the `Graph` form.
getConstructedObject() - Method in class edu.isi.pegasus.planner.parser.dax.ExampleDAXCallback
  Returns an ADag object corresponding to the abstract plan it has generated.
getConstructedObject() - Method in interface edu.isi.pegasus.planner.parser.pdax.Callback
  Return a object that is constructed during the parsing of the object.
getConstructedObject() - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Returns the MEGADAG that is generated
getContact() - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Returns the contact string for the Grid gateway
getContent() - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  Returns the content associated with the node.
getContents() - Method in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM.ListCallback
  Returns the contents captured.
getContents() - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  List all the contents of the TC
getContents() - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  List all the contents of the TC
getContents() - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  List all the contents of the TC
getContents() - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  List all the contents of the TC
getCoreFlag() - Method in class edu.isi.pegasus.planner.invocation.JobStatusSignal
  Accessor
getCost(long, long) - Method in class edu.isi.pegasus.planner.provisioner.Edge
getCost() - Method in class edu.isi.pegasus.planner.provisioner.Edge
getCount() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the count of the workflow, that was specified in the DAX.
getCount() - Method in class edu.isi.pegasus.planner.classes.DagInfo
  Returns the count of the workflow, that was specified in the DAX.
getCount() - Method in class edu.isi.pegasus.planner.dax.ADAG
  Returns the total count of the dax collection.
getCount() - Method in class edu.isi.pegasus.planner.invocation.Fifo
  Accessor
getCount() - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG.GrepCallback
  Returns the number of words counted so far.
getCPURequirementsArgument(Job) - Method in class edu.isi.pegasus.planner.cluster.aggregator.MPIExec
  Looks at the profile keys associated with the job to generate the argument string fragment containing the cpu required for the job.
getCreateDirClass() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the name of the class that the user wants, to insert the create directory jobs in the graph in case of creating random directories.
getCreateDirImplementation() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the name of the class that the user wants, to render the directory creation jobs.
getCreateDirJobExecutionSite(String, String) - Method in class edu.isi.pegasus.planner.refiner.createdir.DefaultImplementation
  Determines the site where the create dir job should be run , looking at the directory URL passed.
getCreateDirJobName(ADag, String) - Method in class edu.isi.pegasus.planner.refiner.createdir.AbstractStrategy
  It returns the name of the create directory job, that is to be assigned.
getCreateDirSites(ADag) - Static method in class edu.isi.pegasus.planner.refiner.createdir.AbstractStrategy
  Retrieves the sites for which the create dir jobs need to be created.
getCreateDirSites(ADag) - Method in class edu.isi.pegasus.planner.refiner.RemoveDirectory
  Retrieves the sites for which the create dir jobs need to be created.
getCreationTime() - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor
getCredentialTypes() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the various credential types required by a job indexed by a site from which to pick up the credential
getCredName() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the credential name to be used for the stork transfer jobs.
getCurrentIndent() - Method in class edu.isi.pegasus.planner.catalog.site.classes.AbstractXMLPrintVisitor
  Returns the current indent to be used while writing out
getDAG(String) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Returns a DAG object with id dagid if present otherwise null.
getDAGFile() - Method in class edu.isi.pegasus.planner.classes.DAGJob
  Returns the DAGFile the job refers to.
getDAGFilename(ADag, PlannerOptions) - Method in class edu.isi.pegasus.planner.client.CPlanner
  Returns the basename of the dag file
getDAGFilename(ADag, String) - Method in class edu.isi.pegasus.planner.code.generator.Abstract
  Returns the name of the file on the basis of the metadata associated with the DAG.
getDAGFilename(PlannerOptions, String, String, String) - Static method in class edu.isi.pegasus.planner.code.generator.Abstract
  Returns the name of the file on the basis of the metadata associated with the DAG.
getDAGInfo() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the DAGInfo that stores the metadata about the DAX
getDAGLFN() - Method in class edu.isi.pegasus.planner.classes.DAGJob
  Returns the lfn for the DAGFile the job refers to.
getDAGMANOutFilename(ADag) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Returns the basename of the file, that contains the output of the dagman while running the dag generated for the workflow.
getDAGs() - Method in class edu.isi.pegasus.planner.dax.ADAG
  Get a list of all the DAG jobs.
getData() - Method in class edu.isi.pegasus.planner.invocation.StatCall
  Accessor
getDatabaseName(String) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.CreateTCDatabase
  Returns the database name from the database url string
getDataConfiguration() - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Returns the data configuration
getDateFormat() - Method in class edu.isi.pegasus.common.util.Currently
  Accessor: Obtains the default timestamp format for all queues.
getDateTime(boolean) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the time at which planning started in a ISO 8601 format.
getDAX() - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Sets the path to the DAX.
getDAX() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the path to the dax file being used by the planner.
getDAX(String) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Returns a DAX object with id daxid if present otherwise null.
GetDAX - Class in edu.isi.pegasus.planner.ranking
  This class is responsible for the fetching the DAX'es on the basis of the request ID's from the Windward Provenance Tracking Catalog.
GetDAX() - Constructor for class edu.isi.pegasus.planner.ranking.GetDAX
  The default constructor.
getDAXCallback() - Method in interface edu.isi.pegasus.planner.parser.dax.DAXParser
  Retuns the DAXCallback for the parser
getDAXCallback() - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Retuns the DAXCallback for the parser
getDAXCallback() - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser3
  Retuns the DAXCallback for the parser
getDAXFile() - Method in class edu.isi.pegasus.planner.classes.DAXJob
  Returns the DAXFile the job refers to.
getDaxFile() - Method in class edu.isi.pegasus.planner.common.UserOptions
  Returns the dax file, that was generated by Chimera containing the description of the Abstract plan.
getDAXID() - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Clustered jobs never originate in the DAX.
getDAXID() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the DAX ID for the job if it appeared in the DAX, else null
getDAXLFN() - Method in class edu.isi.pegasus.planner.classes.DAXJob
  Returns the lfn for the DAXFile the job refers to.
getDAXMetadata(PegasusBag, String) - Static method in class edu.isi.pegasus.planner.parser.DAXParserFactory
  Returns the metadata stored in the root adag element in the DAX
getDAXReplicaStoreFile(PlannerOptions, String, String) - Static method in class edu.isi.pegasus.planner.code.generator.DAXReplicaStore
  Returns the path to the DAX Replica Store File.
getDAXs() - Method in class edu.isi.pegasus.planner.dax.ADAG
  Get a list of all the DAX jobs.
getDAXSchemaLocation() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the location of the schema for the DAX.
getDAXSchemaLocation(String) - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the location of the schema for the DAX.
getDAXVersion() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the dax version
getDAXVersion() - Method in class edu.isi.pegasus.planner.classes.DagInfo
  Returns the dax version
getDefaultBundleValueFromProperties(String, String, String) - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  Returns the default value for the clustering/bundling of jobs to be used.
getDefaultCleanupMaxJobsPropertyKey() - Method in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  Returns the property key that can be used to set the max jobs for the default category associated with the registration jobs.
getDefaultClusterValueFromProperties(String, String, String) - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  Returns the default value for the clustering/bundling of jobs to be used.
getDefaultExitCodePath() - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusExitCode
  Returns the path to exitcode that is to be used on the kickstart output.
getDefaultPathToCondorKickstart() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the default path to the condor kickstart.
getDefaultPathToSC() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the default path to the site catalog file.
getDefaultPathToTC() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the default path to the transformation catalog.
getDefaultRegistrationMaxJobsPropertyKey() - Method in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  Returns the property key that can be used to set the max jobs for the default category associated with the registration jobs.
getDefaultThirdPartySites() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the default list of third party sites.
getDefaultTransferImplementation() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the default transfer implementation to be picked up for constructing transfer jobs.
getDefaultTransferPriority() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the default priority for the transfer jobs if specified in the properties file.
getDeletedFileTX(String, Job) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  This gets the file transfer objects corresponding to the location of files found in the replica mechanism, and transfers it to the output pool asked by the user.
getDeletedJobs() - Method in class edu.isi.pegasus.planner.refiner.DataReuseEngine
  This returns all the jobs deleted from the workflow after the reduction algorithm has run.
getDeletedLeafJobs() - Method in class edu.isi.pegasus.planner.refiner.DataReuseEngine
  This returns all the deleted jobs that happen to be leaf nodes.
getDependantFiles() - Method in class edu.isi.pegasus.planner.classes.CompoundTransformation
  Returns the List of dependant files
getDepET() - Method in class edu.isi.pegasus.planner.provisioner.Node
getDeployJobName(ADag, String, boolean) - Method in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  It returns the name of the deployment job, that is to be assigned.
getDeploymentSites(ADag) - Method in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Retrieves the sites for which the deployment jobs need to be created.
getDepSize() - Method in class edu.isi.pegasus.planner.provisioner.Node
getDepth() - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  Returns the depth of the node in the graph.
getDerivation() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor
getDerivationName() - Method in class edu.isi.pegasus.planner.transfer.implementation.AbstractMultipleFTPerXFERJob
  Returns the logical name of the derivation that this implementation refers to.
getDerivationName() - Method in class edu.isi.pegasus.planner.transfer.implementation.AbstractSingleFTPerXFERJob
  Returns the logical name of the derivation that this implementation refers to.
getDerivationName() - Method in class edu.isi.pegasus.planner.transfer.implementation.GUC
  Returns the logical name of the derivation that this implementation refers to.
getDerivationName() - Method in class edu.isi.pegasus.planner.transfer.implementation.Stork
  Returns the logical name of the derivation that this implementation refers to.
getDerivationName() - Method in class edu.isi.pegasus.planner.transfer.implementation.T2
  Returns the logical name of the derivation that this implementation refers to.
getDerivationName() - Method in class edu.isi.pegasus.planner.transfer.implementation.Transfer
  Returns the logical name of the derivation that this implementation refers to.
getDerivationNamespace() - Method in class edu.isi.pegasus.planner.transfer.implementation.AbstractMultipleFTPerXFERJob
  Returns the namespace of the derivation that this implementation refers to.
getDerivationNamespace() - Method in class edu.isi.pegasus.planner.transfer.implementation.AbstractSingleFTPerXFERJob
  Returns the namespace of the derivation that this implementation refers to.
getDerivationNamespace() - Method in class edu.isi.pegasus.planner.transfer.implementation.GUC
  Returns the namespace of the derivation that this implementation refers to.
getDerivationNamespace() - Method in class edu.isi.pegasus.planner.transfer.implementation.Stork
  Returns the namespace of the derivation that this implementation refers to.
getDerivationNamespace() - Method in class edu.isi.pegasus.planner.transfer.implementation.T2
  Returns the namespace of the derivation that this implementation refers to.
getDerivationNamespace() - Method in class edu.isi.pegasus.planner.transfer.implementation.Transfer
  Returns the namespace of the derivation that this implementation refers to.
getDerivationVersion() - Method in class edu.isi.pegasus.planner.transfer.implementation.AbstractMultipleFTPerXFERJob
  Returns the version of the derivation that this implementation refers to.
getDerivationVersion() - Method in class edu.isi.pegasus.planner.transfer.implementation.AbstractSingleFTPerXFERJob
  Returns the version of the derivation that this implementation refers to.
getDerivationVersion() - Method in class edu.isi.pegasus.planner.transfer.implementation.GUC
  Returns the version of the derivation that this implementation refers to.
getDerivationVersion() - Method in class edu.isi.pegasus.planner.transfer.implementation.Stork
  Returns the version of the derivation that this implementation refers to.
getDerivationVersion() - Method in class edu.isi.pegasus.planner.transfer.implementation.T2
  Returns the version of the derivation that this implementation refers to.
getDerivationVersion() - Method in class edu.isi.pegasus.planner.transfer.implementation.Transfer
  Returns the version of the derivation that this implementation refers to.
getDescription() - Method in interface edu.isi.pegasus.common.credential.CredentialHandler
  Returns the description for the implementing handler
getDescription() - Method in class edu.isi.pegasus.common.credential.impl.Irods
  Returns the description for the implementing handler
getDescription() - Method in class edu.isi.pegasus.common.credential.impl.Proxy
  Returns the description for the implementing handler
getDescription() - Method in class edu.isi.pegasus.common.credential.impl.S3CFG
  Returns the description for the implementing handler
getDescription() - Method in class edu.isi.pegasus.common.credential.impl.Ssh
  Returns the description for the implementing handler
getDescription() - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Returns the TC implementation being used
getDescription() - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Returns a textual description of the transformation mode.
getDescription() - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Returns a textual description of the transformation mode.
getDescription() - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Returns the TC implementation being used
getDescription() - Method in interface edu.isi.pegasus.planner.transfer.Implementation
  Returns a textual description of the transfer implementation.
getDescription() - Method in class edu.isi.pegasus.planner.transfer.implementation.GUC
  Returns a textual description of the transfer implementation.
getDescription() - Method in class edu.isi.pegasus.planner.transfer.implementation.Stork
  Returns a textual description of the transfer implementation.
getDescription() - Method in class edu.isi.pegasus.planner.transfer.implementation.T2
  Returns a textual description of the transfer implementation.
getDescription() - Method in class edu.isi.pegasus.planner.transfer.implementation.Transfer
  Returns a textual description of the transfer implementation.
getDescription() - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  Returns a textual description of the transfer mode.
getDescription() - Method in class edu.isi.pegasus.planner.transfer.refiner.Basic
  Returns a textual description of the transfer mode.
getDescription() - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  Returns a textual description of the transfer mode.
getDescription() - Method in class edu.isi.pegasus.planner.transfer.refiner.Chain
  Returns a textual description of the transfer mode.
getDescription() - Method in class edu.isi.pegasus.planner.transfer.refiner.Cluster
  Returns a textual description of the transfer mode.
getDescription() - Method in class edu.isi.pegasus.planner.transfer.refiner.Empty
  Returns a textual description of the transfer mode.
getDescription() - Method in interface edu.isi.pegasus.planner.transfer.Refiner
  Returns a textual description of the transfer mode.
getDescriptor() - Method in class edu.isi.pegasus.planner.invocation.Descriptor
  Accessor
getDescriptor() - Method in interface edu.isi.pegasus.planner.invocation.HasDescriptor
  Accessor: Obtains the descriptor of the file handle
getDescriptor() - Method in class edu.isi.pegasus.planner.invocation.Temporary
  Accessor
getDesET() - Method in class edu.isi.pegasus.planner.provisioner.Node
getDesSize() - Method in class edu.isi.pegasus.planner.provisioner.Node
getDestURL() - Method in class edu.isi.pegasus.planner.classes.FileTransfer
  Returns a single destination url associated with the transfer.
getDestURL(boolean) - Method in class edu.isi.pegasus.planner.classes.FileTransfer
  Returns a single destination url associated with the transfer.
getDirectory(Directory.TYPE) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Returns a directory corresponding to a particular type
getDirectory() - Method in class edu.isi.pegasus.planner.classes.DAGJob
  Returns the directory the job refers to.
getDirectory() - Method in class edu.isi.pegasus.planner.classes.DAXJob
  Returns the directory the job refers to.
getDirectory() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the directory where the job runs.
getDirectory(Job) - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Returns the directory in which the job should run.
getDirectory(Job) - Method in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  Returns the directory in which the job should run.
getDirectoryIterator() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Returns a directory corresponding to a particular type
getDirectoryKey(Job) - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Returns the exectionSiteDirectory that is associated with the constituentJob to specify the exectionSiteDirectory in which the constituentJob needs to run
getDirectoryKey(Job) - Method in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  Returns the directory that is associated with the job to specify the directory in which the job needs to run
getDirectoryKey(Job) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Returns the directory that is associated with the job to specify the directory in which the job needs to run
getDomainName() - Method in class edu.isi.pegasus.planner.invocation.Architecture
  Accessor
getDOTColor() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the color with which DOT should color the node representing the job.
getDownLen() - Method in class edu.isi.pegasus.planner.provisioner.Node
  return the DnLength of this task.
getDuration() - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Returns the duration for the planning
getDuration() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor
getDuration() - Method in class edu.isi.pegasus.planner.invocation.Job
  Accessor
getDVName() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the name of the underlying derivation.
getDVNamespace() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the namespace of the underlying derivation.
getDVVersion() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the version of the underlying derivation.
getEdges(String) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Returns a list of Edge objects for a child job/dax/dag id.
getEdges() - Method in class edu.isi.pegasus.planner.dax.ADAG
  Returns a Set of all the Edge objects for the DAX.
getElementName() - Method in class edu.isi.pegasus.planner.invocation.Boot
  Returns the name of the xml element corresponding to the object.
getElementName() - Method in class edu.isi.pegasus.planner.invocation.CPU
  Returns the name of the xml element corresponding to the object.
getElementName() - Method in class edu.isi.pegasus.planner.invocation.Load
  Returns the name of the xml element corresponding to the object.
getElementName() - Method in class edu.isi.pegasus.planner.invocation.Machine
  Returns the name of the xml element corresponding to the object.
getElementName() - Method in class edu.isi.pegasus.planner.invocation.MachineInfo
  Returns the name of the xml element corresponding to the object.
getElementName() - Method in class edu.isi.pegasus.planner.invocation.MachineSpecific
  Returns the name of the xml element corresponding to the object.
getElementName() - Method in class edu.isi.pegasus.planner.invocation.Proc
  Returns the name of the xml element corresponding to the object.
getElementName() - Method in class edu.isi.pegasus.planner.invocation.RAM
  Returns the name of the xml element corresponding to the object.
getElementName() - Method in class edu.isi.pegasus.planner.invocation.Stamp
  Returns the name of the xml element corresponding to the object.
getElementName() - Method in class edu.isi.pegasus.planner.invocation.Swap
  Returns the name of the xml element corresponding to the object.
getElementName() - Method in class edu.isi.pegasus.planner.invocation.Task
  Returns the name of the xml element corresponding to the object.
getElementName() - Method in class edu.isi.pegasus.planner.invocation.Uname
  Returns the name of the xml element corresponding to the object.
getElementName() - Method in class edu.isi.pegasus.planner.parser.ParserStackElement
  Returns the element name.
getElementObject() - Method in class edu.isi.pegasus.planner.parser.ParserStackElement
  Returns the object referred to by the element.
getEndEventMessage() - Method in interface edu.isi.pegasus.common.logging.Event
  Creates the end message for the event.
getEndEventMessage() - Method in class edu.isi.pegasus.common.logging.format.AbstractLogFormatter
  Creates the end message for the event on top of the stack.
getEndEventMessage() - Method in class edu.isi.pegasus.common.logging.format.NetloggerEvent
  Creates the end message for the event.
getEndEventMessage() - Method in class edu.isi.pegasus.common.logging.format.SimpleEvent
  Creates the end message for the event.
getEndEventMessage() - Method in interface edu.isi.pegasus.common.logging.LogFormatter
  Creates the end message for the event on top of the stack.
getEndTime() - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Returns the end time for the planning operation as epoch with millisecond precision
getEntries(String, String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.TransformationStore
  Returns List of TransformationCatalogEntry objects for a transformation on a particular site and a type.
getEntries(String, String) - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.TransformationStore
  Returns List of TransformationCatalogEntry objects for a transformation on a particular site.
getEntries(String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.TransformationStore
  Returns a list of TransformationCatalogEntry objects matching on a site and transformation type.
getEnvArrFromMap() - Method in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  Generates an array of environment variables.
getEnvironment() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor
getEnvironmentVariable(String) - Method in interface edu.isi.pegasus.common.credential.CredentialHandler
  Returns the name of the environment variable that needs to be set for the job associated with the credential.
getEnvironmentVariable(String) - Method in class edu.isi.pegasus.common.credential.impl.Irods
  Returns the name of the environment variable that needs to be set for the job associated with the credential.
getEnvironmentVariable(String) - Method in class edu.isi.pegasus.common.credential.impl.Proxy
  Returns the name of the environment variable that needs to be set for the job associated with the credential.
getEnvironmentVariable(String) - Method in class edu.isi.pegasus.common.credential.impl.S3CFG
  Returns the name of the environment variable that needs to be set for the job associated with the credential.
getEnvironmentVariable(String) - Method in class edu.isi.pegasus.common.credential.impl.Ssh
  Returns the name of the environment variable that needs to be set for the job associated with the credential.
getEnvironmentVariable(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Returns an environment variable associated with the site.
getEnvironmentVariable(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Returns an environment variable associated with the site.
getEnvironmentVariable(String, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  Returns an environment variable associated with the site.
getEnvironmentVariable(String, String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  Returns an environment variable for a particular site set in the Site Catalog.
getEnvironmentVariables(String) - Method in class edu.isi.pegasus.planner.transfer.implementation.AbstractMultipleFTPerXFERJob
  Returns the environment profiles that are required for the default entry to sensibly work.
getEnvironmentVariables(String) - Method in class edu.isi.pegasus.planner.transfer.implementation.GUC
  Returns the environment profiles that are required for the default entry to sensibly work.
getEnvironmentVariables(String) - Method in class edu.isi.pegasus.planner.transfer.implementation.T2
  Returns the environment profiles that are required for the default entry to sensibly work.
getEnvironmentVariables(String) - Method in class edu.isi.pegasus.planner.transfer.implementation.Transfer
  Returns the environment profiles that are required for the default entry to sensibly work.
getEnvironmentVariables(String) - Method in class edu.isi.pegasus.planner.transfer.sls.Transfer
  Returns the environment profiles that are required for the default entry to sensibly work.
getEnvValue(String) - Method in class edu.isi.pegasus.planner.client.Executable
  Get the value of the environment variable.
getError() - Method in class edu.isi.pegasus.planner.invocation.JobStatusFailure
  Accessor
getError() - Method in class edu.isi.pegasus.planner.invocation.StatCall
  Accessor
getErrorMessage() - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Returns the error message that we want to log
getErrorMessagePrefix() - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.AbstractFileFactoryBasedMapper
  Returns the prefix message to be attached to an error message
getErrorMessagePrefix() - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Fixed
  Returns the prefix message to be attached to an error message
getErrorMessagePrefix() - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Replica
  Returns the prefix message to be attached to an error message
getEventName() - Method in interface edu.isi.pegasus.common.logging.Event
  Returns the name of event that is currently associated with the log messages.
getEventName() - Method in class edu.isi.pegasus.common.logging.format.AbstractLogFormatter
  Returns the name of event that is currently associated with the log messages and is on the top of the stack
getEventName() - Method in class edu.isi.pegasus.common.logging.format.NetloggerEvent
  Returns the name of event that is currently associated with the log messages.
getEventName() - Method in class edu.isi.pegasus.common.logging.format.SimpleEvent
  Returns the name of event that is currently associated with the log messages.
getEventName() - Method in interface edu.isi.pegasus.common.logging.LogFormatter
  Returns the name of event that is currently associated with the log messages and is on the top of the stack
getExecDirectory() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the execution directory suffix or absolute specified that is appended/replaced to the exec-mount-point specified in the pool catalog for the various pools.
getExecMountPoint() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  A helper method that returns the execution mount point.
getExecPoolWorkDir(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  This determines the working directory on remote execution pool on the basis of whether an absolute path is specified in the pegasus.dir.exec directory or a relative path.
getExecPoolWorkDir(Job) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  This determines the working directory on remote execution pool for a particular job.
getExecPoolWorkDir(String, String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  This determines the working directory on remote execution pool on the basis of whether an absolute path is specified in the pegasus.dir.exec directory or a relative path.
getExecPoolWorkDir(String, String, int) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  This determines the working directory on remote execution pool on the basis of whether an absolute path is specified in the pegasus.dir.exec directory or a relative path.
getExecutable() - Method in class edu.isi.pegasus.planner.dax.File
  Check if the file is an executable
getExecutable() - Method in class edu.isi.pegasus.planner.invocation.Arguments
  Accessor
getExecutable() - Method in class edu.isi.pegasus.planner.invocation.CommandLine
  Accessor
getExecutable() - Method in class edu.isi.pegasus.planner.invocation.Job
  Accessor
getExecutableBasename() - Method in class edu.isi.pegasus.planner.transfer.sls.Transfer
  Return the executable basename for transfer executable used.
getExecutables() - Method in class edu.isi.pegasus.planner.dax.ADAG
  Returns a set of Executable Objects stored as part of the inDAX Transformation Catalog;
getExecutableWorkflowName() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the workflow id
getExecutionDirectory(Job) - Method in class edu.isi.pegasus.planner.code.generator.Shell
  Returns the directory in which a job should be executed.
getExecutionSites() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the names of the execution sites where the concrete workflow can be run.
getExecutionSites() - Method in class edu.isi.pegasus.planner.common.UserOptions
  Returns the list of execution pools where the user wants the data products to be computed.
getExitcode() - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Returns the exitcode for the planner
getExitCode() - Method in class edu.isi.pegasus.planner.invocation.JobStatusRegular
  Accessor
getExitCodePath() - Method in class edu.isi.pegasus.planner.code.gridstart.UserPOSTScript
  Returns the path to exitcode that is to be used on the kickstart output.
getExpectedRuntime(Job, TransformationCatalogEntry) - Method in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  Return expected runtime.
getExpectedRuntimeFromAC(Job, TransformationCatalogEntry) - Method in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  Return expected runtime from the AC only if the process catalog is initialized.
getExternalWorkDirectory(FileServer, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  Return the work directory as seen externally (including external mount point)
getExternalWorkDirectoryURL(String, FileServerType.OPERATION) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  Returns a URL to the work directory as seen externally ( including external mount point ).
getExternalWorkDirectoryURL(FileServer, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  Returns a URL to the work directory as seen externally ( including external mount point ).
getExtraArguments(Job) - Method in class edu.isi.pegasus.planner.cluster.aggregator.MPIExec
  Looks at the profile key for pegasus::pmc_task_arguments to determine if extra arguments are required for the task.
getFile() - Method in class edu.isi.pegasus.planner.invocation.StatCall
  Accessor
getFileBaseName(Job) - Method in class edu.isi.pegasus.planner.code.generator.Abstract
  Returns the basename of the file to which the job is written to.
getFileBaseName(Job) - Method in class edu.isi.pegasus.planner.code.generator.Stork
  Returns the basename of the file to which the job is written to.
getFileLocs(String) - Method in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  Returns all the locations as returned from the Replica Lookup Mechanism.
getFilename() - Method in interface edu.isi.pegasus.planner.invocation.HasFilename
  Accessor: Obtains the name of the file
getFilename() - Method in class edu.isi.pegasus.planner.invocation.Regular
  Accessor
getFilename() - Method in class edu.isi.pegasus.planner.invocation.Temporary
  Accessor
getFiles() - Method in class edu.isi.pegasus.planner.dax.ADAG
  Returns a list of File objects defined as the inDax Replica Catalog
getFileServerIterator() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Not implmented as yet.
getFileServerIterator() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Not implmented as yet.
getFileServers(FileServerType.OPERATION) - Method in class edu.isi.pegasus.planner.catalog.site.classes.DirectoryLayout
  Selects all file servers and returns it matching an operation type.
getFileServers() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Not implemented as yet.
getFileServers() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Not implemented as yet.
getFileServersIterator(FileServerType.OPERATION) - Method in class edu.isi.pegasus.planner.catalog.site.classes.DirectoryLayout
  Returns at iterator to the file servers.
getFilesFromRC(DAGJob, Collection) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  Special Handling for a DAGJob for retrieving files from the Replica Catalog.
getFilesFromRC(DAXJob, Collection) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  Special Handling for a DAXJob for retrieving files from the Replica Catalog.
getFilesFromRC(Job, Collection) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  It looks up the RCEngine Hashtable to lookup the locations for the files and add nodes to transfer them.
getFilesInReplica() - Method in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  This returns the files for which mappings exist in the Replica Catalog.
getFileTransfers() - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.TransferContainer
  Returns the collection of transfers associated with this transfer container.
getFileTransfers() - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle.TransferContainer
  Returns the collection of transfers associated with this transfer container.
getFileTX(String, Job, boolean) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  This gets the Vector of FileTransfer objects for the files which have to be transferred to an one destination pool.
getFlags() - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Returns the bit fields that contain the transient flags (dR and optional).
getFloatValue(Object) - Method in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  A convenience method to get the intValue for the object passed.
getFlowID() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the flow ID for the workflow.
getFlowID() - Method in class edu.isi.pegasus.planner.classes.DagInfo
  Returns the generated flow ID for the workflow.
getFlowName() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the flow name
getFlowName() - Method in class edu.isi.pegasus.planner.classes.DagInfo
  Returns the flow name
getFlowTimestamp() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the flow timestamp for the workflow.
getFlowTimestamp() - Method in class edu.isi.pegasus.planner.classes.DagInfo
  Returns the flow timestamp for the workflow.
getForce() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the force option set for the planner.
getForceOption() - Method in class edu.isi.pegasus.planner.common.UserOptions
  Returns true if the user had asked for the force option.
getForceReplan() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the force replan option
getForwardOptions() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the forward options set
getFreeNodesForSite(String) - Method in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  Returns the freenodes for a site.
getFreeSize() - Method in class edu.isi.pegasus.planner.catalog.site.classes.FileSystemType
  Sets the free directory size
getFrom() - Method in class edu.isi.pegasus.planner.provisioner.Edge
  return the 'from' task
getGID() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor
getGID() - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor
getGlibc() - Method in class edu.isi.pegasus.planner.catalog.classes.SysInfo
  Returns the glibc version of the site.
getGlibc() - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Returns the glibc version of the site.
getGlibc() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Returns the glibc version of the site.
getGlibc() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Returns the glibc version of the site.
getGlibc() - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.VDSSysInfo
  Retuns the glibc version of the system.
getGlibc() - Method in class edu.isi.pegasus.planner.dax.Executable
  Get the Glibc version if any set for this file.
getGlobusVersion(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GlobusVersion
  Returns the version corresponding to a particular version type.
getGlobusVersion() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GlobusVersion
  Returns the Globus version as a dot separated String.
getGridDN() - Method in class edu.isi.pegasus.planner.code.generator.Braindump
  Returns the distinguished name from the proxy
getGridFTPBandwidthInfo() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPServer
  Returns a list of `GridFTPBandwidth` objects that contain the bandwidths by which a site is connected to other sites.
getGridFTPServers(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.Abstract
  It returns all the gridftp servers corresponding to a specified pool.
getGridFTPServers(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  It returns all the gridftp servers corresponding to a specified pool.
getGridFTPTimeout() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the timeout value in seconds after which to timeout in case of opening sockets to grid ftp server.
getGridGateway(GridGateway.JOB_TYPE) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Returns a grid gateway object corresponding to a job type.
getGridGateway(GridGateway.JOB_TYPE) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Returns a grid gateway object corresponding to a job type.
getGridGatewayIterator() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Return an iterator to value set of the Map.
getGridGatewayIterator() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Return an iterator to value set of the Map.
getGridGatewayJobType() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the corresponding grid gateway job type
getGridGateways() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Not implemented as yet
getGridGateways() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Not implemented as yet
getGridStart() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the GRIDSTART that is to be used to launch the jobs on the grid.
getGridStartInvokeLength() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the trigger value for invoking an application through kickstart using kickstart.
getGroup() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor
getGroup() - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor
getGSSCredential(String) - Method in class edu.isi.pegasus.planner.refiner.ThreadPool
  Loads a GSSCredential from the proxy file residing at the path specified.
getGVDSVersion() - Method in class edu.isi.pegasus.planner.client.Executable
  Returns the version of the Griphyn Virtual Data System.
getHandle() - Method in class edu.isi.pegasus.planner.invocation.StatCall
  Accessor
getHandletoPDAXWriter(String, String, String) - Method in class edu.isi.pegasus.planner.partitioner.WriterCallback
  It returns the handle to the writer for writing out the pdax file that contains the relations amongst the partitions and the jobs making up the partitions.
getHandleToPlannerCache() - Method in class edu.isi.pegasus.planner.classes.PegasusBag
  A convenice method to get the handle to the planner cache
getHandleToSiteStore() - Method in class edu.isi.pegasus.planner.classes.PegasusBag
  A convenice method to get the handle to the site store
getHandleToTransformationCatalog() - Method in class edu.isi.pegasus.planner.classes.PegasusBag
  A convenice method to get the handle to the transformation catalog.
getHandleToTransformationMapper() - Method in class edu.isi.pegasus.planner.classes.PegasusBag
  A convenice method to get the handle to the transformation mapper.
getHeadNodeFS() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Returns the headnode filesystem.
getHeadNodeStorageDirectory() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Returns the local-storage directory.
getHelp() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns whether to display or not.
getHorizontalClusterPreference() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the users horizontal clustering preference.
getHorizontalPartitionerBundleValue(String) - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the bundle value for a particular transformation.
getHorizontalPartitionerCollapseValue(String) - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the collapse value for a particular transformation.
getHost() - Method in class edu.isi.pegasus.common.util.PegasusURL
  Returns the host asscoiated with the PegasusURL
getHost() - Method in class edu.isi.pegasus.gridftp.GridFTPURL
getHost() - Method in class edu.isi.pegasus.planner.refiner.Authenticate.HostPort
  Returns the host associated with this object.
getHostAddress() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor
getHostname() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor
getHostPort() - Method in class edu.isi.pegasus.gridftp.GridFTPURL
getHostPort(String) - Method in class edu.isi.pegasus.planner.refiner.Authenticate
  Determines the hostname from the urlPrefix string in the pool file.
getHttpLog4jURL() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the http url for log4j properties for windward project.
getID() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the ID associated with the job.
getId() - Method in class edu.isi.pegasus.planner.dax.AbstractJob
getID() - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  Returns the logical id of the graph node.
getID() - Method in class edu.isi.pegasus.planner.partitioner.Partition
  It returns the unique id that is associated with the partition.
getID() - Method in class edu.isi.pegasus.planner.provisioner.Edge
getID() - Method in class edu.isi.pegasus.planner.provisioner.Node
getIdleNodes() - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Returns the total number of nodes that this grid gateway talks to.
getImplementingClass(String) - Static method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolMode
  Given a string readMode returns the name of the class that implements that read mode.
getImplementingClass(String) - Static method in class edu.isi.pegasus.planner.catalog.transformation.TCMode
  This method just checks and gives the correct classname if a user provides the classname in a different case.
getIn() - Method in class edu.isi.pegasus.planner.provisioner.Node
  return the list of incoming edges.
getIndex(Profiles.NAMESPACES) - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Returns the index for the namespace.
getIndex() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the index of the workflow, that was specified in the DAX.
getIndex() - Method in class edu.isi.pegasus.planner.classes.DagInfo
getIndex() - Method in class edu.isi.pegasus.planner.dax.ADAG
getIndex() - Method in class edu.isi.pegasus.planner.partitioner.Partition
  It returns the index to number of the partition.
getInfo(int) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPBandwidth
  This method gets the info about gridftpbw based on the gridftpbwkey
getInfo(int) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPServer
  Returns the attribute value of a particular attribute of the server.
getInfo(int) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  Returns the attribute value of a particular attribute of the jobmanager.
getInfo(int) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  Returns an `Object` containing the attribute value corresponding to the key specified.
getInfo(int) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.WorkDir
  Returns the attribute value of a particular attribute of the work directory.
getInheritedRCFiles() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the inherited rc files.
getINode() - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor
getInputBlocks() - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor.
getInputDirectory() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the input directory.
getInputFiles() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the set of input files associated with the job.
getInputSize() - Method in class edu.isi.pegasus.planner.invocation.Fifo
  Accessor
getInstalled() - Method in class edu.isi.pegasus.planner.dax.Executable
  Check if the executable is of type installed.
getInstance(String, String) - Static method in class edu.isi.pegasus.common.logging.LogManager
  To get a reference to the the object.
getInstance() - Static method in class edu.isi.pegasus.common.util.CondorVersion
  Factory method to instantiate the class.
getInstance(LogManager) - Static method in class edu.isi.pegasus.common.util.CondorVersion
  Factory method to instantiate the class.
getInstance() - Static method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Deprecated.
getInstance() - Static method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Deprecated.
getInstance() - Static method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns an instance to this properties object.
getInstance(String) - Static method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns an instance to this properties object.
getInstance(PlannerOptions) - Static method in class edu.isi.pegasus.planner.common.UserOptions
  The method used to invoke the singleton instance the first time, from the CPlanner class.
getInstance() - Static method in class edu.isi.pegasus.planner.common.UserOptions
  The method used to invoke the singleton instance from the other classes.
getInteger(int) - Static method in class edu.isi.pegasus.planner.common.PegRandom
  This calls the next double function and returns an integer between the 0 and upper index.
getInteger(int, int) - Static method in class edu.isi.pegasus.planner.common.PegRandom
  This calls the next double function and returns an integer between the lower index and upper index.
getInterface() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
getInternalMountPoint() - Method in class edu.isi.pegasus.planner.catalog.site.classes.DirectoryLayout
  Returns the internal mount point for the directory.
getInternalMountPointOfWorkDirectory() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Returns the work directory for the compute jobs on a site.
getInternalMountPointOfWorkDirectory() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Returns the work directory for the compute jobs on a site.
getInternalWorkDirectory(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  This determines the working directory on remote execution pool on the basis of whether an absolute path is specified in the pegasus.dir.exec directory or a relative path.
getInternalWorkDirectory(Job) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  This determines the working directory on remote execution pool for a particular job.
getInternalWorkDirectory(Job, boolean) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  This determines the working directory on remote execution pool or a staging site for a particular job.
getInternalWorkDirectory(String, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  This determines the working directory on remote execution pool on the basis of whether an absolute path is specified in the pegasus.dir.exec directory or a relative path.
getInternalWorkDirectory(String, String, int) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  This determines the working directory on remote execution pool on the basis of whether an absolute path is specified in the pegasus.dir.exec directory or a relative path.
getInterpoolFileTX(Job, Collection<GraphNode>) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  This gets the Vector of FileTransfer objects for all the files which have to be transferred to the destination pool in case of Interpool transfers.
getIntValue(Object) - Method in class edu.isi.pegasus.planner.classes.PegasusBag
  A convenience method to get the intValue for the object passed.
getIntValue(Object) - Method in class edu.isi.pegasus.planner.selector.site.heft.HeftBag
  A convenience method to get the intValue for the object passed.
getInvoke() - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Returns list of Invoke objects
getInvoke() - Method in class edu.isi.pegasus.planner.dax.ADAG
  Returns a list of Invoke objects associated with the workflow
getInvoke() - Method in class edu.isi.pegasus.planner.dax.Executable
  Return the list of Notification objects
getInvoke() - Method in class edu.isi.pegasus.planner.dax.Transformation
  Return the list of Notification objects
getInvoluntarySwitches() - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor: Obtains the involuntary context switches.
getIPFilesForTransfer() - Method in class edu.isi.pegasus.planner.namespace.Condor
  Returns a comma separated list of files that are designated for transfer via condor file transfer mechanism for the job.
getJDBCURL(String, Properties) - Method in class edu.isi.pegasus.planner.ranking.GetDAX
  Constructs the jdbc url on the basis fo the driver and db properties.
getJob(String) - Method in class edu.isi.pegasus.planner.cluster.Abstract
  Returns the job object corresponding to the id of the job.
getJob(String) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Returns a Job object with id jobid if present otherwise null.
getJob(int) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor: Obtains a job at a certain position in the job list.
getJob(String) - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Returns the job that has been constructed for a particular partition.
getJobAggregator() - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Returns the JobAggregator that created this aggregated job.
getJobAggregator() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns what job aggregator is to be used to aggregate multiple compute jobs into a single condor job.
getJobCount() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor: Obtains the size of the job list.
getJobList() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor: Gets an array of all values that constitute the current content.
getJobManager() - Method in class edu.isi.pegasus.planner.classes.Job
  Returnss the remote jobmanager on which the job has to run.
getJobManager(String, String) - Method in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  It returns a jobmanager for the given pool.
getJobmanagers(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.Abstract
  It returns all the jobmanagers corresponding to a specified site.
getJobmanagers(String, String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.Abstract
  It returns all the jobmanagers corresponding to a specified pool and universe.
getJobmanagers() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  It returns all the jobmanagers corresponding to a specified pool.
getJobmanagers(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  It returns all the jobmanagers corresponding to a specified pool and universe.
getJobmanagers(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  It returns all the jobmanagers corresponding to a specified site.
getJobmanagers(String, String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  It returns all the jobmanagers corresponding to a specified pool and universe.
getJobName() - Method in class edu.isi.pegasus.planner.classes.FileTransfer
  It returns the name of the main/compute job making up the VDS supernode with which this transfer is related.
getJobnamePrefix() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the job prefix to be used while constructing the job names.
getJobPriority(Job, int) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Computes the priority for a job based on job type and depth in the workflow
getJobPriority(Job) - Method in class edu.isi.pegasus.planner.transfer.refiner.Basic
  Returns the priority associated with a job based on the condor profile key priority .
getJobs() - Method in class edu.isi.pegasus.planner.dax.ADAG
  Get a list of all the DAG jobs.
getJobsInRC(Graph, Set) - Method in class edu.isi.pegasus.planner.refiner.DataReuseEngine
  Returns all the jobs whose output files exist in the Replica Catalog.
getJobStatus() - Method in class edu.isi.pegasus.planner.invocation.Status
  Accessor
getJobType() - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Returns the type of jobs that run via this grid gateway.
getJobType() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the type of the job.
getJobTypeDescription() - Method in class edu.isi.pegasus.planner.classes.Job
  Gets the textual description of the type associated with the job.
getJobTypeDescription(int) - Method in class edu.isi.pegasus.planner.classes.Job
  Gets the textual description of the type that can be associated with a job.
getKeepTMPValue(String) - Method in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  Returns the int value corresponding to the string value passed.
getKey(String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Returns the key with the prefix stripped off.
getKey() - Method in class edu.isi.pegasus.planner.catalog.site.classes.Connection
  Returns the connection key.
getKey() - Method in class edu.isi.pegasus.planner.classes.NameValue
  Returns the key associated with this tuple.
getKey(String, String) - Method in class edu.isi.pegasus.planner.code.generator.NetloggerJobMapper
  Adds a prefix to the key and returns it.
getKey() - Method in class edu.isi.pegasus.planner.dax.MetaData
  Get the key of this metadata object
getKey() - Method in class edu.isi.pegasus.planner.dax.Profile
  Get the key of this Profile
getKey() - Method in class edu.isi.pegasus.planner.invocation.EnvEntry
  Accessor
getKickstartPath() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  A helper method that returns the path to gridlaunch on the site.
getKickstartPath(SiteCatalogEntry) - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Returns the default path to kickstart as constructed from the environment variable associated with a site in the site catalog
getLabel() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the label of the workflow, that was specified in the DAX.
getLabel() - Method in class edu.isi.pegasus.planner.classes.DagInfo
  Returns the label of the workflow, that was specified in the DAX.
getLabel() - Method in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  Returns the DAXlabel.
getLabel() - Method in class edu.isi.pegasus.planner.dax.Edge
getLabel(GraphNode) - Method in class edu.isi.pegasus.planner.partitioner.Label
  Returns the label for the node.
getLast() - Method in class edu.isi.pegasus.planner.transfer.refiner.Chain.TransferChain
  Returns the last element in the chain.
getLeaves() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the leaf nodes of the Graph.
getLeaves() - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Returns the leaf nodes of the Graph.
getLeaves() - Method in interface edu.isi.pegasus.planner.partitioner.graph.Graph
  Returns the leaf nodes of the Graph.
getLeaves() - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph
  Returns the leaf nodes of the Graph.
getLevel() - Method in class edu.isi.pegasus.common.logging.logger.Default
  Returns the debug level.
getLevel() - Method in class edu.isi.pegasus.common.logging.logger.Log4j
  Returns the debug level.
getLevel() - Method in class edu.isi.pegasus.common.logging.LogManager
  Returns the debug level.
getLevel() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the level associated with the job.
getLfn(String, String) - Method in class edu.isi.pegasus.planner.catalog.transformation.client.TCQuery
  Get logical transformations on a given resource and/or of a particular type.
getLFN() - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  It returns the lfn of the file that is associated with this transfer.
getLFN() - Method in class edu.isi.pegasus.planner.classes.ReplicaLocation
  Returns the associated LFN.
getLFN() - Method in class edu.isi.pegasus.planner.invocation.StatCall
  Accessor
getLFNCount() - Method in class edu.isi.pegasus.planner.classes.ReplicaStore
  Returns the number of LFN's for which the mappings are stored in the store.
getLfnProfile(String, String, String) - Method in class edu.isi.pegasus.planner.catalog.transformation.client.TCQuery
  Get the LFn profiles associated with a logical transformation
getLFNs() - Method in class edu.isi.pegasus.planner.classes.DagInfo
  It returns the list of lfns referred to by the DAG.
getLFNs(boolean) - Method in class edu.isi.pegasus.planner.classes.DagInfo
  Returns the list of lfns referred to by the DAG.
getLFNs() - Method in class edu.isi.pegasus.planner.classes.ReplicaStore
  Returns the set of LFN's for which the mappings are stored in the store.
getLFNs(Set) - Method in class edu.isi.pegasus.planner.classes.ReplicaStore
  Returns a `Set` of lfns for which the mappings are stored in the store, amongst the `Set` passed as input.
getLineNumber() - Method in exception edu.isi.pegasus.planner.parser.ScannerException
getLineNumber() - Method in class edu.isi.pegasus.planner.parser.SiteCatalogTextScanner
  Obtains the current line number in the input stream from the outside.
getLineNumber() - Method in class edu.isi.pegasus.planner.parser.TransformationCatalogTextScanner
  Obtains the current line number in the input stream from the outside.
getLink() - Method in class edu.isi.pegasus.planner.dax.File
  Get the linkage of the file.
getLinkage() - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Returns the linkage for the file during parsing.
getLinkCount() - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor
getListOfFilesToDelete() - Method in class edu.isi.pegasus.planner.refiner.cleanup.CleanupJobContent
  Returns the list of files to be deleted for a cleanupNode
getLocalDirectory() - Method in class edu.isi.pegasus.planner.catalog.site.classes.StorageType
  Returns the local directory.
getLocalPath() - Method in class edu.isi.pegasus.common.credential.impl.Irods
  Returns the path to user cred on the local site.
getLocalPath() - Method in class edu.isi.pegasus.common.credential.impl.Proxy
  Returns the path to user proxy on the local site.
getLocalPath() - Method in class edu.isi.pegasus.common.credential.impl.S3CFG
  Returns the path to user cred on the local site.
getLocalPath() - Method in class edu.isi.pegasus.common.credential.impl.Ssh
  Returns the path to user cred on the local site.
getLog4JLogFile() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the location of the local log file where you want the messages to be logged.
getLogFormatter() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the log formatter to use.
getLogger() - Method in class edu.isi.pegasus.planner.classes.PegasusBag
  A convenice method to get Logger/
getLoggingFile() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the file to which all the logging needs to be directed to.
getLoggingLevel() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the logging level.
getLoggingLevel() - Method in class edu.isi.pegasus.planner.client.SCClient
  Returns the logging level.
getLoggingLevel() - Method in class edu.isi.pegasus.planner.client.TCConverter
  Returns the logging level.
getLogicalId(String, String, String) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Returns the id associated with the logical transformation.
getLogicalID() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the logical id of the job.
getLogicalName() - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Returns the Name of the logical transformation.
getLogicalNameForJobs(List<Job>) - Method in class edu.isi.pegasus.planner.cluster.Abstract
  Returns the logical names for the jobs.
getLogicalNameForJobs(List<Job>) - Method in class edu.isi.pegasus.planner.cluster.Vertical
  Returns null as for label based clustering we dont want the transformation name to be considered for constructing the name of the clustered jobs
getLogicalNamespace() - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Returns the Namespace associated with the logical transformation.
getLogicalTransformation() - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Gets the Fully Qualified Transformation mName in the format NS::Name:Ver.
getLogicalVersion() - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Returns the mVersion of the logical transformation.
getLogManager() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the log manager to use.
getMachine() - Method in class edu.isi.pegasus.planner.invocation.Architecture
  Accessor
getMachine() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
getMachineInfoIterator() - Method in class edu.isi.pegasus.planner.invocation.MachineSpecific
  Returns an iterator for the machine info objects
getMachineSpecific() - Method in class edu.isi.pegasus.planner.invocation.Machine
  Obtains the machine-specific grouping element.
getMajor() - Method in class edu.isi.pegasus.common.util.Version
getMajorFaults() - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor: Obtains the major page faults.
getMakespan() - Method in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  Returns the makespan of the scheduled workflow.
getMatchingJMList(List, String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  Returns a list containing only those jobmanager entries that match a particular universe.
getMatchingProperties(String, boolean) - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the properties matching a particular prefix as a list of sorted name value pairs, where name is the full name of the matching property (including the prefix) and value is it's value in the properties file.
getMaximumCleanupJobsPerLevel() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the maximum number of clean up jobs created per level of the workflow in case of InPlace cleanup.
getMaximumRSS() - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor.
getMegaDAGMode() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the megadag generation option .
getMemoryRequirementsArgument(Job) - Method in class edu.isi.pegasus.planner.cluster.aggregator.MPIExec
  Looks at the profile keys associated with the job to generate the argument string fragment containing the memory required for the job.
getMetaData() - Method in class edu.isi.pegasus.planner.dax.CatalogType
  Returns the List of MetaData objects associated with this Catalog entry object
getMetadata() - Method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLMetadataParser
  Returns the metadata/attributes assoicated with the element that was parsed for.
getMetadata(PegasusBag, String) - Static method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParserFactory
  Returns the metadata stored in the root adag element in the DAX
getMethodName(int) - Static method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolMode
  Its returns the name of the method that needs to be invoked to get the object of the implementing pool class.
getMetricsFileLocationInSubmitDirectory() - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Sets the metrics file location in the submit directory
getMetricsLogFile() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the path to the file that is used to be logging metrics Referred to by the "pegasus.log.metrics.file" property.
getMetricsType() - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Returns the metric type
getMinor() - Method in class edu.isi.pegasus.common.util.Version
getMinorFaults() - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor: Obtains the minfor page faults.
getMode() - Method in class edu.isi.pegasus.planner.catalog.transformation.mapper.All
  Returns the mode description.
getMode() - Method in class edu.isi.pegasus.planner.catalog.transformation.Mapper
  Returns the TCMapper Mode.
getMode() - Method in class edu.isi.pegasus.planner.catalog.transformation.mapper.Installed
getMode() - Method in class edu.isi.pegasus.planner.catalog.transformation.mapper.Staged
getMode() - Method in class edu.isi.pegasus.planner.catalog.transformation.mapper.Submit
getMode() - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor
getModificationTime() - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor
getMountPoint() - Method in class edu.isi.pegasus.planner.catalog.site.classes.FileServerType
  Returns the mount point
getMountPoint() - Method in class edu.isi.pegasus.planner.catalog.site.classes.FileSystemType
  Returns the mount point for the file system type.
getMTime() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the last modified time for the file containing the workflow description.
getMTime() - Method in class edu.isi.pegasus.planner.classes.DagInfo
  Returns the last modified time for the file containing the workflow description.
getName() - Method in class edu.isi.pegasus.gridftp.FileInfo
getName(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Returns the name from the key.
getName() - Method in class edu.isi.pegasus.planner.classes.CompoundTransformation
  Returns name of compound transformation.
getName() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the name of the job.
getName() - Method in class edu.isi.pegasus.planner.dax.AbstractJob
getName() - Method in class edu.isi.pegasus.planner.dax.ADAG
  Return the name/label of the dax
getName() - Method in class edu.isi.pegasus.planner.dax.Executable
  Get the name of the executable
getName() - Method in class edu.isi.pegasus.planner.dax.File
  Get the name of the file
getName() - Method in class edu.isi.pegasus.planner.dax.Transformation
  Get the name of the transformation
getName() - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  Returns the logical name of the graph node.
getName() - Method in class edu.isi.pegasus.planner.partitioner.Partition
  It returns the name of the partition.
getName() - Method in class edu.isi.pegasus.planner.ranking.Ranking
  Returns the name of the dax.
getName() - Method in class edu.isi.pegasus.planner.selector.site.heft.Site
  Returns the name of the site.
getName() - Method in class edu.isi.pegasus.planner.selector.site.RoundRobin.NameValue
  Returns the key of this pair, i.e the left hand side of the mapping.
getNameOfDAX() - Method in class edu.isi.pegasus.planner.parser.dax.DAX2Graph
  Returns the name of the dax.
getNameOfDAX() - Method in class edu.isi.pegasus.planner.parser.dax.DAX2NewGraph
  Returns the name of the dax.
getNamespace() - Method in class edu.isi.pegasus.planner.classes.CompoundTransformation
  Returns the namespace
getNamespace() - Method in class edu.isi.pegasus.planner.dax.Executable
  Get the namespace of the executable
getNamespace() - Method in class edu.isi.pegasus.planner.dax.File
  Get the namespace of the file
getNamespace() - Method in class edu.isi.pegasus.planner.dax.Job
getNameSpace() - Method in class edu.isi.pegasus.planner.dax.Profile
  Get the namespace of this profile
getNamespace() - Method in class edu.isi.pegasus.planner.dax.Transformation
  Get the namespace of the transformation
getNetloggerExitCodePath() - Method in class edu.isi.pegasus.planner.code.gridstart.NetloggerPostScript
  Returns the path to exitcode that is to be used on the kickstart output.
getNextException() - Method in exception edu.isi.pegasus.planner.catalog.CatalogException
  Retrieves the exception chained to this `CatalogException` object.
getNextIndent() - Method in class edu.isi.pegasus.planner.catalog.site.classes.AbstractXMLPrintVisitor
  Returns the indent to be used for the nested element.
getNode(String) - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the node matching the id passed.
getNode(String) - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Returns the node matching the id passed.
getNode(String) - Method in interface edu.isi.pegasus.planner.partitioner.graph.Graph
  Returns the node matching the id passed.
getNode(String) - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph
  Returns the node matching the id passed.
getNode() - Method in class edu.isi.pegasus.planner.refiner.cleanup.CleanupJobContent
  Returns the associated cleanupNode for which the files are deleted.
getNodeIDs() - Method in class edu.isi.pegasus.planner.partitioner.Partition
  It returns the set of the job ids making up the partition.
getNodeLabel() - Method in class edu.isi.pegasus.planner.dax.AbstractJob
getNodeName() - Method in class edu.isi.pegasus.planner.invocation.Architecture
  Accessor
getNodes() - Method in class edu.isi.pegasus.planner.partitioner.Partition
  Returns a list of nodes making up the partition.
getNonStandardJavaOptions() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the Set of non standard java options.
getNonThirdPartySite() - Method in class edu.isi.pegasus.planner.classes.TransferJob
  Returns the site at which the job would have run if the transfer job was being run in non third party mode.
getNoOfJobs() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the number of jobs in the dag on the basis of number of elements in the `dagJobs` Vector.
getNOOPJobName(ADag) - Method in class edu.isi.pegasus.planner.client.CPlanner
  Returns the name of the noop job.
getNOOPJobName(String, int) - Method in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  Generates the name of the noop job , that is unique for the given workflow.
getNotification() - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Same as getInvoke().
getNotification() - Method in class edu.isi.pegasus.planner.dax.ADAG
  Returns a list of Invoke objects associated with the workflow.
getNotification() - Method in class edu.isi.pegasus.planner.dax.Executable
  Return the list of Notification objects (same as getInvoke)
getNotification() - Method in class edu.isi.pegasus.planner.dax.Transformation
  Return the list of Notification objects (same as getInvoke()
getNotifications(Invoke.WHEN) - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Returns a collection of all the notifications that need to be done for a particular condition
getNotifications() - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Returns all the notifications associated with the job.
getNotifications(Invoke.WHEN) - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns a collection of all the notifications that need to be done for a particular condition
getNotifications() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns all the notifications associated with the job.
getNotifications(Invoke.WHEN) - Method in class edu.isi.pegasus.planner.classes.CompoundTransformation
  Returns a collection of all the notifications that need to be done for a particular condition
getNotifications() - Method in class edu.isi.pegasus.planner.classes.CompoundTransformation
  Returns all the notifications associated with the job.
getNotifications(Invoke.WHEN) - Method in class edu.isi.pegasus.planner.classes.Job
  Returns a collection of all the notifications that need to be done for a particular condition
getNotifications() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns all the notifications associated with the job.
getNotifications(Invoke.WHEN) - Method in class edu.isi.pegasus.planner.classes.Notifications
  Returns a collection of all the notifications that need to be done for a particular condition
getNumberOfRescueTries() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the number of times to try for rescue dag submission.
getNumOfTransferProcesses() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  It returns the number of processes of g-u-c that the transfer script needs to spawn to do the transfers.
getNumOfTransferStreams() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  It returns the number of streams that each transfer process uses to do the ftp transfer.
getOptional() - Method in class edu.isi.pegasus.planner.dax.File
  Check the optional flag of the file
getOptions() - Method in class edu.isi.pegasus.planner.common.UserOptions
  Returns the options passed to the planner.
getOriginalArgString() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the argument string of how planner was invoked.
getOS() - Method in class edu.isi.pegasus.planner.catalog.classes.SysInfo
  Returns the OS of the site.
getOS() - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Returns the OS of the nodes that this grid gateway talks to.
getOS() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Returns the OS of the site.
getOS() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Returns the OS of the site.
getOs() - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.VDSSysInfo
  Returns the os type of the system.
getOS() - Method in class edu.isi.pegasus.planner.dax.Executable
  Get the OS the Executable is compiled for
getOSRelease() - Method in class edu.isi.pegasus.planner.catalog.classes.SysInfo
  Returns the OS release of the site.
getOSRelease() - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Returns the OS release of the site.
getOSRelease() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Returns the OS release of the site.
getOSRelease() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Returns the OS release of the site.
getOsRelease() - Method in class edu.isi.pegasus.planner.dax.Executable
  Get the OS release set for this executable.
getOSVersion() - Method in class edu.isi.pegasus.planner.catalog.classes.SysInfo
  Returns the OS version of the site.
getOSVersion() - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Returns the OS version of the site.
getOSVersion() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Returns the OS version of the site.
getOSVersion() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Returns the OS version of the site.
getOsversion() - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.VDSSysInfo
  Returns the os version of the system.
getOsVersion() - Method in class edu.isi.pegasus.planner.dax.Executable
  Get the OS version set for this executable.
getOut() - Method in class edu.isi.pegasus.planner.provisioner.Node
  return the list of outgoing edges.
getOutputBlocks() - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor.
getOutputDirectory() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the output directory
getOutputFiles() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the set of output files associated with the job.
getOutputFiles(Collection<GraphNode>) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  It gets the output files for all the nodes which are specified in the nodes passed.
getOutputFilesForTransfer() - Method in class edu.isi.pegasus.planner.namespace.Condor
  Returns a comma separated list of files that are designated for transfer via condor file transfer mechanism for the job.
getOutputPool() - Method in class edu.isi.pegasus.planner.common.UserOptions
  Returns output pool where the user wants the data products to be transferred to.
getOutputSite() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the output site where to stage the output .
getOutputSize() - Method in class edu.isi.pegasus.planner.invocation.Fifo
  Accessor
getPageSize() - Method in class edu.isi.pegasus.planner.invocation.Machine
  Obtains the page size information.
getParent() - Method in class edu.isi.pegasus.planner.classes.PCRelation
  Returns the parent in the edge.
getParent() - Method in class edu.isi.pegasus.planner.dax.Edge
getParents() - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  Returns a list of `GraphNode` objects that are parents of the node.
getParents(String) - Method in class edu.isi.pegasus.planner.partitioner.Partition
  Returns a list of id's of parents for a node in the partition.
getParentsTransientRC(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Returns a set containing the paths to the parent dax jobs transient replica catalogs.
getPartitionCount(String) - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Returns the number of partitions referred to in the PDAX file.
getPartitionerDAXCallback() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the DAXCallback that is to be used while parsing the DAX.
getPartitionerLabelKey() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the key that is to be used as a label key, for labelled partitioning.
getPartitionID(int) - Method in class edu.isi.pegasus.planner.partitioner.BFS
  Constructs the id for the partition.
getPartitionID(int) - Method in class edu.isi.pegasus.planner.partitioner.Horizontal
  Constructs the id for the partition.
getPartitionID(int) - Method in class edu.isi.pegasus.planner.partitioner.Label
  Constructs the id for the partition.
getPartitioningType() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the partitioning type in case of partition and plan.
getPartitionName() - Method in class edu.isi.pegasus.planner.partitioner.DAXWriter
  It returns the name of the partitioned dax, that the object is currently writing or initialized to write.
getPartitionName() - Method in class edu.isi.pegasus.planner.partitioner.WriterCallback
  Returns the name of the partition, that needs to be set while creating the Partition object corresponding to each partition.
getPartitionParsingMode() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the mode for parsing the dax while writing out the partitioned daxes.
getPatch() - Method in class edu.isi.pegasus.common.util.Version
getPath() - Method in interface edu.isi.pegasus.common.credential.CredentialHandler
  Returns the path to the credential on the submit host.
getPath(String) - Method in interface edu.isi.pegasus.common.credential.CredentialHandler
  Returns the path to the credential for a particular site handle
getPath() - Method in class edu.isi.pegasus.common.credential.impl.Abstract
  Returns the path to the credential on the submit host.
getPath(String) - Method in class edu.isi.pegasus.common.credential.impl.Irods
  Returns the path to irodsEnv.
getPath(String) - Method in class edu.isi.pegasus.common.credential.impl.Proxy
  Returns the path to user proxy.
getPath(String) - Method in class edu.isi.pegasus.common.credential.impl.S3CFG
  Returns the path to S3CFG .
getPath(String) - Method in class edu.isi.pegasus.common.credential.impl.Ssh
  Returns the path to SSH_PRIVATE_KEY .
getPath() - Method in class edu.isi.pegasus.common.util.PegasusURL
  Returns the path associated with the PegasusURL
getPath() - Method in class edu.isi.pegasus.gridftp.GridFTPURL
getPathToChmodExecutable(String) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Returns the path to the chmod executable for a particular execution site by looking up the transformation executable.
getPathToLocalProxy() - Method in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  Returns path to the local proxy
getPathtoPBSFile(ADag) - Method in class edu.isi.pegasus.planner.code.generator.PBS
  Returns the basename for the PBS script file for the dag
getPathtoPMCFile(ADag) - Method in class edu.isi.pegasus.planner.code.generator.PMC
  Returns the basename for the pmc file for the dag
getPathToShellScript(ADag) - Method in class edu.isi.pegasus.planner.code.generator.Shell
  Returns path to the shell script that is generated
getPDAX() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the path to the PDAX file being used by the planner.
getPDAX() - Method in class edu.isi.pegasus.planner.partitioner.WriterCallback
  Returns the name of the pdax file written out.
getPDAXFilename(String, int) - Static method in class edu.isi.pegasus.planner.partitioner.DAXWriter
  It constructs the name of the partitioned dax file that has to be written corresponding to a partition of the dax.
getPDAXFilename(String, int, boolean) - Static method in class edu.isi.pegasus.planner.partitioner.DAXWriter
  It constructs the name of the partitioned dax file that has to be written corresponding to a partition of the dax.
getPDAXSchemaLocation(String) - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the location of the schema for the PDAX.
getPegasusBag() - Method in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  Returns the bag of intialization objects.
getPegasusBag() - Method in class edu.isi.pegasus.planner.refiner.MainEngine
  Returns the bag of intialization objects.
getPegasusHome() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Deprecated.
getPegasusHome() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Deprecated.
getPegasusHome(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  Deprecated.
getPegasusHome(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  Returns the value of PEGASUS_HOME for a site.
getPegasusProperties() - Method in class edu.isi.pegasus.planner.classes.PegasusBag
  A convenice method to get PegasusProperties
getPegasusRunInvocation() - Method in class edu.isi.pegasus.planner.client.CPlanner
  Returns the pegasus-run invocation on the workflow planned.
getPFN() - Method in class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  Accessor: Obtains the PFN portion from this entry.
getPfn(String, String, String, String, String) - Method in class edu.isi.pegasus.planner.catalog.transformation.client.TCQuery
  Get physical transformation for a particular logical transformation and/or on a resource and/or of a particular type
getPFN(int) - Method in class edu.isi.pegasus.planner.classes.ReplicaLocation
  Return a PFN as a `ReplicaCatalogEntry`
getPFNCount() - Method in class edu.isi.pegasus.planner.classes.ReplicaLocation
  Returns the number of pfn's associated with the lfn.
getPFNList() - Method in class edu.isi.pegasus.planner.classes.ReplicaLocation
  Returns the list of pfn's as `ReplicaCatalogEntry` objects.
getPfnProfile(String, String, String) - Method in class edu.isi.pegasus.planner.catalog.transformation.client.TCQuery
  Get the profiles associated with a physical transformation.
getPhysicalFiles() - Method in class edu.isi.pegasus.planner.dax.CatalogType
  Returns a List of PFN objects associated with this Catalog entry
getPhysicalId(String, TCType, String) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Returns the id of the physical transformation
getPhysicalIds(String, TCType, String) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Returns a list of pfnid for a given pfn on any resource, and of any type.
getPhysicalMemory() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
getPhysicalTransformation() - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Returns the physical location of the transformation.
getPID() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor
getPID() - Method in class edu.isi.pegasus.planner.invocation.Job
  Accessor
getPlannerOptions() - Method in class edu.isi.pegasus.planner.classes.PegasusBag
  A convenice method to get PlannerOptions
getPlatform() - Method in class edu.isi.pegasus.common.util.Version
getPool() - Method in class edu.isi.pegasus.planner.classes.AuthenticateRequest
  Returns the pool id of the associated resource in this request.
getPoolConfig() - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  This class returns the reference to the `PooConfig` object containing information about all the pools.
getPoolConfig() - Method in class edu.isi.pegasus.planner.parser.ConfigXmlParser
  This class returns the reference to the `PooConfig` object containing information about all the pools.
getPoolEntry(String, String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.Abstract
  Gets the pool information from the pool.config file on the basis of the name of the pool, and the universe.
getPoolEntry(String, String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  Gets the pool information from the pool.config file on the basis of the name of the pool, and the universe.
getPoolFile() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the path to the pool file.
getPoolMode() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  Returns a textual description of the pool mode being used.
getPoolMode() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.Text
  Returns a textual description about the pool mode that is implemented by this class.
getPoolMode() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.XML
  Returns a textual description about the pool mode that is implemented by this class.
getPoolMode() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the mode to be used for accessing the pool information.
getPoolName() - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.PoolTransfer
  Return the pool for which the transfers are grouped
getPoolName() - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle.PoolTransfer
  Return the pool for which the transfers are grouped
getPoolProfile(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.Abstract
  It returns the profile information associated with a particular pool.
getPoolProfile(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  It returns the profile information associated with a particular pool.
getPoolProfile(String, String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  It returns profile information associated with a particular namespace and pool.
getPools() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.Abstract
  It returns all the pools available in the site catalog
getPools() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  It returns all the pools available in the site catalog
getPoolSchemaLocation() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the location of the schema for the DAX.
getPoolSchemaLocation(String) - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the location of the schema for the site catalog file.
getPort() - Method in class edu.isi.pegasus.gridftp.GridFTPURL
getPort() - Method in class edu.isi.pegasus.planner.refiner.Authenticate.HostPort
  Returns the port associated with this object.
getPosition() - Method in exception edu.isi.pegasus.common.util.ProfileParserException
  Obtains the position at which point the exception was thrown.
getPosition() - Method in exception edu.isi.pegasus.planner.code.generator.condor.CondorQuoteParserException
  Obtains the position at which point the exception was thrown.
getPosition() - Method in class edu.isi.pegasus.planner.invocation.ArgEntry
  Accessor
getPOSTScriptPath(String) - Method in class edu.isi.pegasus.planner.namespace.Dagman
  Returns the path to the postscript of a particular type
getPostScriptProperties(PegasusProperties) - Method in class edu.isi.pegasus.planner.code.gridstart.NetloggerPostScript
  Returns the properties that need to be passed to the the postscript invocation in the java format.
getPostScriptProperties(PegasusProperties) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusExitCode
  Returns the properties that need to be passed to the the postscript invocation in the java format.
getPrefix(int) - Method in class edu.isi.pegasus.common.logging.logger.Default
  Returns the prefix that needs to be logged corresponding to a particular message type, when a message is being logged.
getPreScriptArguments() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the arguments to the prescript for the job if set.
getPreScriptPath() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the path to the prescript for the job if set.
getPrintStream(String) - Method in class edu.isi.pegasus.common.logging.logger.Default
  Sets an internal writer to point to a particular stream.
getPrintStream(int) - Method in class edu.isi.pegasus.common.logging.logger.Default
  Returns a PrintWriter stream on which to log the message.
getPriority() - Method in class edu.isi.pegasus.planner.classes.FileTransfer
  Sets the priority for the File Transfer
getPriority(TransferJob) - Method in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  Returns the priority for the transfer job as specified in the properties file.
getPriorityArgument(Job) - Method in class edu.isi.pegasus.planner.cluster.aggregator.MPIExec
  Looks at the profile keys associated with the job to generate the argument string fragment containing the priority to be associated for the job.
getProfile() - Method in class edu.isi.pegasus.planner.classes.Profile
  Returns the Profile (namespace, value and key);
getProfile() - Method in class edu.isi.pegasus.planner.parser.TransformationCatalogTextParser
  Parses a single line and returns a profile.
getProfileKey() - Method in interface edu.isi.pegasus.common.credential.CredentialHandler
  Returns the env or pegasus profile key that needs to be associated for the credential.
getProfileKey() - Method in class edu.isi.pegasus.common.credential.impl.Irods
  Returns the env or pegasus profile key that needs to be associated for the credential.
getProfileKey() - Method in class edu.isi.pegasus.common.credential.impl.Proxy
  Returns the env or pegasus profile key that needs to be associated for the credential.
getProfileKey() - Method in class edu.isi.pegasus.common.credential.impl.S3CFG
  Returns the env or pegasus profile key that needs to be associated for the credential.
getProfileKey() - Method in class edu.isi.pegasus.common.credential.impl.Ssh
  Returns the env or pegasus profile key that needs to be associated for the credential.
getProfileKey() - Method in class edu.isi.pegasus.planner.classes.Profile
  Returns the Key of the Profile
getProfileKeyIterator(Profiles.NAMESPACES) - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Returns a iterator over the profile keys corresponding to a particular namespace.
getProfileKeyIterator() - Method in class edu.isi.pegasus.planner.namespace.Hints
  Provides an iterator to traverse the profiles by their keys.
getProfileKeyIterator() - Method in class edu.isi.pegasus.planner.namespace.Namespace
  Provides an iterator to traverse the profiles by their keys.
getProfileNamespace() - Method in class edu.isi.pegasus.planner.classes.Profile
  Returns the NameSpace of the Profile
getProfiles() - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Returns the list of profiles for all namespaces.
getProfiles(String) - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Returns the list of profiles corresponding to a single namespace
getProfiles(Profiles.NAMESPACES) - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Returns the list of profiles corresponding to a single namespace
getProfiles(Namespace) - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Returns the list of profiles corresponding to a single namespace
getProfiles() - Method in class edu.isi.pegasus.planner.catalog.site.classes.FileServer
  Returns the associated profiles
getProfiles() - Method in class edu.isi.pegasus.planner.catalog.site.classes.HeadNodeFS
  Returns the profiles associated with the file server.
getProfiles() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Returns the profiles associated with the site.
getProfiles() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Returns the profiles associated with the site.
getProfiles() - Method in class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeFS
  Returns the profiles associated with the file server.
getProfiles() - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Returns the list of profiles associated with the transformation.
getProfiles(String) - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Returns the profiles for a particular Namespace.
getProfiles(Profiles.NAMESPACES) - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns all the profiles relevant to a particular namespace
getProfiles() - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Return the profile List.
getProfiles() - Method in class edu.isi.pegasus.planner.dax.CatalogType
  Return the List of `Profile` objects associated with this Catalog entry
getProfiles() - Method in class edu.isi.pegasus.planner.dax.PFN
getProfilesForTransformation() - Method in class edu.isi.pegasus.planner.parser.TransformationCatalogTextParser
  Returns a list of profiles that have to be applied to the entries for all the sites corresponding to a transformation.
getProfileValue() - Method in class edu.isi.pegasus.planner.classes.Profile
  Returns the Value for the profile
getProgramName(String) - Method in interface edu.isi.pegasus.common.logging.Event
  Returns the program name for the software whose log statement are logged.
getProgramName(String) - Method in class edu.isi.pegasus.common.logging.format.AbstractLogFormatter
  Returns the program name for the software whose log statement are logged.
getProgramName(String) - Method in class edu.isi.pegasus.common.logging.format.NetloggerEvent
  Returns the program name for the software whose log statement are logged.
getProgramName(String) - Method in class edu.isi.pegasus.common.logging.format.SimpleEvent
  Returns the program name for the software whose log statement are logged.
getProgramName(String) - Method in interface edu.isi.pegasus.common.logging.LogFormatter
  Returns the program name for the software whose log statement are logged.
getProperties() - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Returns the path to the properties file for the run.
getPropertiesInSubmitDirectory() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the path to the property file that has been writting out in the submit directory.
getProperty(String) - Method in class edu.isi.pegasus.common.util.CommonProperties
  Accessor: access to the internal properties as read from file.
getProperty(String, String) - Method in class edu.isi.pegasus.common.util.CommonProperties
  Accessor: access to the internal properties as read from file An existing system property of the same key will have precedence over any project property.
getProperty(String) - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  It allows you to get any property from the property file without going through the corresponding accesor function in this class.
getProperty(String, String) - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  This function is used to check whether a deprecated property is used or not.
getProperty(String, String, String) - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  This function is used to check whether a deprecated property is used or not.
getProperty(String, String) - Method in class edu.isi.pegasus.planner.selector.replica.Restricted
  Returns the name of the property, for a particular site X.
getPropertyKey(String, String) - Method in class edu.isi.pegasus.planner.client.PegasusGetSites
  Returns the full name of the property key with the appropriate prefix
getPropertyKey(int) - Static method in class edu.isi.pegasus.planner.transfer.implementation.ImplementationFactory
  Returns the name of the property that needs to be loaded for a particular type.
getProtocol() - Method in class edu.isi.pegasus.common.util.PegasusURL
  Returns the protocol associated with the PegasusURL
getProtocol() - Method in class edu.isi.pegasus.planner.catalog.site.classes.FileServerType
  Returns protocol implemented by the file server.
getQuotedValue(String) - Method in class edu.isi.pegasus.planner.parser.TransformationCatalogTextParser
  Parses a quoted value and strips out the enclosing quotes.
getRandomDir() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the random directory option.
getRandomDirectory(ADag) - Method in class edu.isi.pegasus.planner.client.CPlanner
  Sets the basename of the random directory that is created on the remote sites per workflow.
getRandomDirName() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the name of the random directory, only if the generate Random Dir flag is set.
getRandomDirName() - Method in class edu.isi.pegasus.planner.common.UserOptions
  Returns the name of the random directory, only if the generate Random Dir flag is set.
getRank() - Method in class edu.isi.pegasus.planner.ranking.Ranking
  Returns the rank.
getRank() - Method in class edu.isi.pegasus.planner.selector.replica.Regex.Rank
  Returns the rank associated with it.
getReceived() - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor.
getRefinementProvenanceStore() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the provenance store to use to log the refiner actions.
getRegex() - Method in class edu.isi.pegasus.planner.selector.replica.Regex.Rank
  Returns the underlying regex pattern associated with the Rank object.
getRegexSet(Properties) - Method in class edu.isi.pegasus.planner.selector.replica.Regex
  Returns a sorted set containing the various Patterns pre-compiled.
getRegister() - Method in class edu.isi.pegasus.planner.dax.File
  Get the register flag of this file.
getRegisterFlag() - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Returns the value of the register flag
getRegistrationFiles() - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.TransferContainer
  Returns the collection of registration files associated with this transfer container.
getRegistrationFiles() - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle.TransferContainer
  Returns the collection of registration files associated with this transfer container.
getRegJobName(int, int) - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.PoolTransfer
  Generates the name of the transfer job, that is unique for the given workflow.
getRegJobName(int, int) - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle.PoolTransfer
  Generates the name of the transfer job, that is unique for the given workflow.
getRegName() - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.TransferContainer
  Returns the name of the registration job.
getRegName() - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle.TransferContainer
  Returns the name of the registration job.
getRelations() - Method in class edu.isi.pegasus.planner.partitioner.Partition
  A function to return the child-parent relations for the jobs making up the partition.
getRelativeDirectory() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the relative directory.
getRelativeStorageDirectoryAddon() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  Return the relative directory that needs to be appended to the storage directory for the workflow.
getRelativeSubmitDirectory() - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Returns the path to the relative submit directory.
getRelativeSubmitDirectory() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the relative submit directory.
getRelativeSubmitDirectoryOption() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the relative submit directory option.
getRelease() - Method in class edu.isi.pegasus.planner.invocation.Architecture
  Accessor
getReleaseVersion() - Method in class edu.isi.pegasus.planner.classes.ADag
  Return the release version
getReleaseVersion() - Method in class edu.isi.pegasus.planner.classes.DagInfo
  Return the release version
getRemoteExecutable() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the path of the underlying executable on the remote grid site.
getRemoveDirJobName(ADag, String) - Method in class edu.isi.pegasus.planner.refiner.RemoveDirectory
  It returns the name of the remove directory job, that is to be assigned.
getReplicaCatalogIterator() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Return an iterator to the replica catalog associated with the site.
getReplicaCatalogIterator() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Return an iterator to the replica catalog associated with the site.
getReplicaLocation(String) - Method in class edu.isi.pegasus.planner.classes.ReplicaStore
  Returns a `ReplicaLocation` corresponding to the LFN.
getReplicaMode() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the replica mode.
getReplicaSelector() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the name of the selector to be used for selection amongst the various replicas of a single lfn.
getReplicaStore() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the Replica Store
getReplicaStoreFromDirectory(String) - Method in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  Loads the mappings from the input directory
getReplicaStoreFromFiles(Set) - Method in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  Ends up loading a Replica Store from replica catalog files
getRequestID() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the request id.
getResource(String) - Method in class edu.isi.pegasus.planner.catalog.transformation.client.TCQuery
  Get and print the Resource entries for a given logical transformation and transformation type
getResource() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor
getResourceContact() - Method in class edu.isi.pegasus.planner.classes.AuthenticateRequest
  Returns the url of the resource to contact.
getResourceHandle() - Method in class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  Obtains the resource handle from the attributes map.
getResourceId() - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Returns the resource where the transformation is located.
getResourceType() - Method in class edu.isi.pegasus.planner.classes.AuthenticateRequest
  Returns the type of the request.
getResponseMessage() - Method in class edu.isi.pegasus.planner.code.generator.SendMetricsResult
getRLIURL() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the url to the RLI of the RLS.
getRLSTimeout() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  It returns the timeout value in seconds after which to timeout in case of no activity from the RLS.
getRootDirectoryNameForPegasus(String) - Method in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Does regex magic to figure out the version of pegasus from the url, and use it to construct the name of pegasus directory, when worker package is untarred.
getRootNodes() - Method in class edu.isi.pegasus.planner.partitioner.Partition
  Returns the root nodes in the partition.
getRoots() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the root nodes of the Graph.
getRoots() - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Returns the root nodes of the Graph.
getRoots() - Method in interface edu.isi.pegasus.planner.partitioner.graph.Graph
  Returns the root nodes of the Graph.
getRoots() - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph
  Returns the root nodes of the Graph.
getRootWorkflowUUID() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the UUID for the Root workflow
getRootWorkflowUUID() - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Returns the UUID for the Root workflow
getRootWorkflowUUID() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the root workflow UUID if defined in the properties, else null Referred to by the "pegasus.workflow.root.uuid" property.
getRuntime() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the expected runtime for the job that is set using the setRuntime method.
getRunTime(Job) - Method in class edu.isi.pegasus.planner.cluster.Horizontal
getRuntime() - Method in class edu.isi.pegasus.planner.ranking.Ranking
  Returns the runtime.
getScheduler() - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Returns the the underlying scheduler that gateway talks to.
getSchemaDir() - Method in class edu.isi.pegasus.common.util.CommonProperties
  Accessor to schema directory
getSchemaDir() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Accessor to the schema directory of the Pegasus install
getSchemaLocation() - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
getSchemaLocation() - Method in class edu.isi.pegasus.planner.parser.ConfigXmlParser
getSchemaLocation() - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Helps the load database to locate the DAX XML schema, if available.
getSchemaLocation() - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser3
  Returns the local path to the XML schema against which to validate.
getSchemaLocation() - Method in class edu.isi.pegasus.planner.parser.Parser
  Helps the load database to locate the XML schema, if available.
getSchemaLocation() - Method in class edu.isi.pegasus.planner.parser.PDAXParser
  Helps the load database to locate the PDAX XML schema, if available.
getSchemaLocation() - Method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLMetadataParser
  Not implemented as yet
getSchemaLocation() - Method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser3
  Returns the local path to the XML schema against which to validate.
getSchemaLocation() - Method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser4
  Returns the local path to the XML schema against which to validate.
getSchemaNamespace() - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  Returns the XML schema namespace that a document being parsed conforms to.
getSchemaNamespace() - Method in class edu.isi.pegasus.planner.parser.ConfigXmlParser
  Returns the XML schema namespace that a document being parsed conforms to.
getSchemaNamespace() - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Returns the XML schema namespace that a document being parsed conforms to.
getSchemaNamespace() - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser3
  Returns the XML schema namespace that a document being parsed conforms to.
getSchemaNamespace() - Method in class edu.isi.pegasus.planner.parser.Parser
  Returns the XML schema namespace that a document being parsed conforms to.
getSchemaNamespace() - Method in class edu.isi.pegasus.planner.parser.PDAXParser
  Returns the XML schema namespace that a document being parsed conforms to.
getSchemaNamespace() - Method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLMetadataParser
  Not implemented as yet
getSchemaNamespace() - Method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser3
  Returns the XML schema namespace that a document being parsed conforms to.
getSchemaNamespace() - Method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser4
  Returns the XML schema namespace that a document being parsed conforms to.
getSchemaOfDocument(String) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  A convenience method that tries to get the name of the schema the document refers to.
getScratch() - Method in class edu.isi.pegasus.planner.catalog.site.classes.HeadNodeFS
  Returns the scratch area on the head node.
getScratch() - Method in class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeFS
  Returns the scratch area on the head node.
getScriptFooter() - Method in class edu.isi.pegasus.planner.code.generator.Shell
  Returns the footer for the generated shell script.
getScriptHeader(String) - Method in class edu.isi.pegasus.planner.code.generator.Shell
  Returns the header for the generated shell script.
getSeMountPoint(SiteInfo) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  Return the storage mount point for a particular pool.
getSent() - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor.
getSetXBitJobName(String, int) - Method in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  Generates the name of the setXBitJob , that is unique for the given workflow.
getSetXBitJobName(String, int) - Method in interface edu.isi.pegasus.planner.transfer.Implementation
  Generates the name of the setXBitJob , that is unique for the given workflow.
getSharedDir() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Accessor to the bin directory of the Pegasus install
getSharedDirectory() - Method in class edu.isi.pegasus.planner.catalog.site.classes.StorageType
  Returns the shared directory.
getSharedRSS() - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor.
getSharedStateDir() - Method in class edu.isi.pegasus.common.util.CommonProperties
  Accessor to $PEGASUS_HOME/com.
getShiwaBundle() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the Shiwa Bundle set
getShortName() - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.AbstractFileFactoryBasedMapper
  Returns the short name for the implementation class.
getShortName() - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Fixed
getShortName() - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Flat
  Returns the short name for the implementation class.
getShortName() - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Hashed
  Returns the short name for the implementation class.
getShortName() - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Replica
getSignalNumber() - Method in class edu.isi.pegasus.planner.invocation.JobStatusSignal
  Accessor
getSignalNumber() - Method in class edu.isi.pegasus.planner.invocation.JobStatusSuspend
  Accessor
getSignals() - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor: Obtains the system signals sent.
getSISiteBundleValue(String, String) - Method in class edu.isi.pegasus.planner.transfer.refiner.Cluster
  Determines the bundle factor for a particular site on the basis of the stage in bundle value associcated with the underlying transfer transformation in the transformation catalog.
getSite() - Method in class edu.isi.pegasus.planner.dax.PFN
getSite() - Method in class edu.isi.pegasus.planner.parser.TransformationCatalogTextParser
  Returns the site transformation for a site, and moves the scanner to hold the next `TransformationCatalogReservedWord`.
getSiteBundleValue(String, String) - Method in class edu.isi.pegasus.planner.transfer.refiner.Chain
  Determines the bundle factor for a particular site on the basis of the key associcated with the underlying transfer transformation in the transformation catalog.
getSiteForCleanup(Job) - Method in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  Returns site to be used for the cleanup algorithm.
getSiteHandle() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Returns the site handle for the site
getSiteHandle() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Returns the site handle for the site
getSiteHandle() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the handle of the site where the job is scheduled.
getSiteHandle() - Method in class edu.isi.pegasus.planner.parser.SiteCatalogTextParser
  Returns the site handle for a site, and moves the scanner to hold the next `SiteCatalogReservedWord`.
getSiteList(String, String, String, List) - Method in class edu.isi.pegasus.planner.catalog.transformation.Mapper
  Returns a list of sites that are valid sites for a given lfn and a list of sites.
getSiteList(String) - Method in class edu.isi.pegasus.planner.classes.TCMap
  Returns a List of siteid's that are valid for a particular lfn.
getSiteList(String, List) - Method in class edu.isi.pegasus.planner.classes.TCMap
  Returns a list of siteid's that are valid for a particular lfn and among a list of input sites
getSiteMap(String, String, String, List) - Method in class edu.isi.pegasus.planner.catalog.transformation.mapper.All
  This method returns a Map of compute sites to List of TransformationCatalogEntry objects that are valid for that site.
getSiteMap(String, String, String, List) - Method in class edu.isi.pegasus.planner.catalog.transformation.Mapper
  This method returns a Map of compute sites to List of TransformationCatalogEntry objects that are valid for that site.
getSiteMap(String, String, String, List) - Method in class edu.isi.pegasus.planner.catalog.transformation.mapper.Installed
  This method returns a Map of compute sites to List of TransformationCatalogEntry objects that are valid for that site.
getSiteMap(String, String, String, List) - Method in class edu.isi.pegasus.planner.catalog.transformation.mapper.Staged
  This method returns a Map of compute sites to List of TransformationCatalogEntry objects that are valid for that site
getSiteMap(String, String, String, List) - Method in class edu.isi.pegasus.planner.catalog.transformation.mapper.Submit
  This method returns a Map of compute sites to List of TransformationCatalogEntry objects that are valid for that site
getSiteMap(String) - Method in class edu.isi.pegasus.planner.classes.TCMap
  Returns a HashMap of sites as keys and a List of TransformationCatalogEntry object as values.
getSiteNameForEnvironmentKey(String) - Method in class edu.isi.pegasus.common.credential.impl.Abstract
  Returns the site name sanitized for use in an environment variable.
getSites() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.PoolConfig
  Returns information about all the sites.
getSiteSelectorKeep() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a value designating whether we need to keep the temporary files that are passed to the external site selectors.
getSiteSelectorMode() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the class name of the site selector, that needs to be invoked to do the site selection.
getSiteSelectorPath() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the path to the external site selector that needs to be called out to make the decision of site selection.
getSiteSelectorTimeout() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  It returns the timeout value in seconds after which to timeout in case of no activity from the external site selector.
getSitesSet(String) - Method in class edu.isi.pegasus.planner.selector.replica.Restricted
  Returns a set of third party sites.
getSitesTCEntries(String, List) - Method in class edu.isi.pegasus.planner.classes.TCMap
  Retrieves all the entries matching a particular lfn for the sites passed.
getSiteStore() - Method in interface edu.isi.pegasus.planner.parser.SiteCatalogXMLParser
  Returns the constructed site store object
getSiteStore() - Method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser3
  Returns the constructed site store object
getSiteStore() - Method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser4
  Returns the constructed site store object
getSiteTCEntries(String, String) - Method in class edu.isi.pegasus.planner.classes.TCMap
  This method returns a list of TransformationCatalogEntry objects for a given transformation and siteid
getSize() - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Returns the size for the file.
getSize() - Method in class edu.isi.pegasus.planner.dax.File
  Return the size of the file
getSize() - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor
getSLSInputLFN(Job) - Method in class edu.isi.pegasus.planner.transfer.sls.Condor
  Returns the LFN of sls input file.
getSLSInputLFN(Job) - Method in interface edu.isi.pegasus.planner.transfer.SLS
  Returns the LFN of sls input file.
getSLSInputLFN(Job) - Method in class edu.isi.pegasus.planner.transfer.sls.Transfer
  Returns the LFN of sls input file.
getSLSOutputLFN(Job) - Method in class edu.isi.pegasus.planner.transfer.sls.Condor
  Returns the LFN of sls output file.
getSLSOutputLFN(Job) - Method in interface edu.isi.pegasus.planner.transfer.SLS
  Returns the LFN of sls output file.
getSLSOutputLFN(Job) - Method in class edu.isi.pegasus.planner.transfer.sls.Transfer
  Returns the LFN of sls output file.
getSLSTransferArguments() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the extra arguments with which the transfer executable used in PegasusLite needs to be invoked.
getSLSTransferImplementation() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the sls transfer implementation that is to be used for constructing the transfer jobs.
getSourceURL() - Method in class edu.isi.pegasus.planner.classes.FileTransfer
  Returns a single source url associated with the transfer.
getSourceURL(boolean) - Method in class edu.isi.pegasus.planner.classes.FileTransfer
  Returns a single source url associated with the transfer.
getSpace(int, int) - Static method in class edu.isi.pegasus.planner.catalog.transformation.client.TCQuery
  Gets the required space for pretty printing.
getStackRSS() - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor.
getStagedExecutableBaseName() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the basename for the staged executable corresponding to the job.
getStagedExecutableBaseName(String, String, String) - Static method in class edu.isi.pegasus.planner.classes.Job
  Returns the basename for the staged executable corresponding to the job.
getStageInPoolTransfer(Map<String, Bundle.PoolTransfer>, String, int, boolean) - Method in class edu.isi.pegasus.planner.transfer.refiner.Cluster
  Returns the appropriate stagein pool transfer for a particular site.
getStageOutPoolTransfer(String, boolean, int) - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  Returns the appropriate pool transfer for a particular site.
getStageOutPoolTransfer(String, boolean, int) - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  Returns the appropriate pool transfer for a particular site.
getStagingDelimiter() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the delimiter to be used for constructing the staged executable name, during transfer of executables to remote sites.
getStagingSite(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the staging site for an execution site.
getStagingSite(String) - Method in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Returns the staging site for a particular execution site.
getStagingSite(Job) - Method in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  Returns the staging site to be used for a job.
getStagingSite(Job) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  Returns the staging site to be used for a job.
getStagingSiteHandle() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the staging site.
getStamp() - Method in class edu.isi.pegasus.planner.invocation.Machine
  Obtains the time stamp information when the remote machine element was recorded.
getStart() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor
getStart() - Method in class edu.isi.pegasus.planner.invocation.Job
  Accessor
getStartEventMessage() - Method in interface edu.isi.pegasus.common.logging.Event
  Creates the start message for the event.
getStartEventMessage() - Method in class edu.isi.pegasus.common.logging.format.AbstractLogFormatter
  Creates the start message for the event on top of the internal stack
getStartEventMessage() - Method in class edu.isi.pegasus.common.logging.format.NetloggerEvent
  Creates the start message for the event.
getStartEventMessage() - Method in class edu.isi.pegasus.common.logging.format.SimpleEvent
  Creates the start message for the event.
getStartEventMessage() - Method in interface edu.isi.pegasus.common.logging.LogFormatter
  Creates the start message for the event on top of the internal stack
getStartTime() - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Returns the start time for the planning operation as epoch with millisecond precision
getStatCall(int) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor: Obtains a stat at a certain position in the stat list.
getStatCount() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor: Obtains the size of the stat list.
getState() - Method in class edu.isi.pegasus.planner.transfer.RemoteTransfer.TransferState
  Returns the state.
getState() - Method in class edu.isi.pegasus.planner.transfer.TPT.TPTState
  Returns the state.
getStatement(int) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Singleton manager for prepared statements.
getStatement(int) - Method in class edu.isi.pegasus.planner.catalog.work.Database
  Singleton manager for prepared statements.
getStatement(int) - Method in class edu.isi.pegasus.planner.ranking.GetDAX
  Singleton manager for prepared statements.
getStatInfo() - Method in class edu.isi.pegasus.planner.invocation.StatCall
  Accessor
getStatList() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor: Gets an array of all values that constitute the current content.
getStatus() - Method in class edu.isi.pegasus.planner.invocation.Job
  Accessor
getStatus() - Method in class edu.isi.pegasus.planner.invocation.Status
  Accessor
getStdErr() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the file to which the stderr of the job is written to.
getStderr() - Method in class edu.isi.pegasus.planner.dax.AbstractJob
getStdIn() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the file from which the stdin is picked up.
getStdin() - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Get the STDIN file object
getStdOut() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the file to which the stdout of the job is written to.
getStdout() - Method in class edu.isi.pegasus.planner.dax.AbstractJob
getStorage() - Method in class edu.isi.pegasus.planner.catalog.site.classes.HeadNodeFS
  Returns the storage area on the head node.
getStorage() - Method in class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeFS
  Returns the storage area on the head node.
getStorageDirectory() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the storage directory suffix or absolute specified that is appended/replaced to the storage-mount-point specified in the pool catalog for the various pools.
getStringValue(Object) - Method in class edu.isi.pegasus.planner.namespace.Pegasus
  Returns a String value, that a particular key is mapped to in this namespace.
getSubmissionCredential() - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the credential to use for job submission.
getSubmitDirectory() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the path to the directory where the submit files are to be generated.
getSubmitFileDir() - Method in class edu.isi.pegasus.planner.common.UserOptions
  Returns the directory where the user wants the submit files to be generated.
getSubmitHostname() - Method in class edu.isi.pegasus.planner.code.generator.Braindump
  Returns the submit hostname
getSubmitHostPathToPegasusLiteCommon() - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Determines the path to common shell functions file that Pegasus Lite wrapped jobs use.
getSubmitHostPathToPegasusLiteLocal() - Method in class edu.isi.pegasus.planner.code.generator.condor.style.Condor
  Determines the path to PegasusLite local job
getSubmitHostPathToShellRunnerFunctions() - Method in class edu.isi.pegasus.planner.code.generator.Shell
  Determines the path to common shell functions file that the generated shell script will use.
getSubmitLogsDirectory() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the the path to the logs directory on the submit host.
getSubmitMode() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns which submit mode to be used to submit the jobs on to the grid.
getSupportedOperation() - Method in class edu.isi.pegasus.planner.catalog.site.classes.FileServerType
  Returns the operation supported by the file server
getSwaps() - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor: Obtains number of swap operations.
getSyncJob(String) - Method in class edu.isi.pegasus.planner.transfer.refiner.Cluster
  Returns the current synch job for a site.
getSyncJobBetweenLevelsName(String, int) - Method in class edu.isi.pegasus.planner.transfer.refiner.Cluster
  Returns the name of the job that acts as a synchronization node in between stage in jobs of different levels.
getSysConfDir() - Method in class edu.isi.pegasus.common.util.CommonProperties
  Accessor to $PEGASUS_HOME/etc.
getSysConfDir() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Accessor to $PEGASUS_HOME/etc.
getSysInfo() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Returns the System Information associated with the Site.
getSysInfo() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Returns the System Information associated with the Site.
getSysInfo(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  Returns the `SysInfo` for the site
getSysinfo(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.Abstract
  Returns the System information for a single site.
getSysinfo(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  Returns the System information for a single site.
getSysInfo() - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Returns the System Information associated with the transformation.
getSysInfoId(VDSSysInfo) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Gets the id for the system information entry.
getSysInfos(List<String>) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
getSysinfos(List) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.Abstract
  Returns the System information for a bunch of sites.
getSysinfos(List) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  Returns the System information for a bunch of sites.
getSystemName() - Method in class edu.isi.pegasus.planner.invocation.Architecture
  Accessor
getSystemTime() - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor: Obtains the system time from the object.
getTag() - Method in class edu.isi.pegasus.planner.invocation.Job
  Accessor
getTag() - Method in class edu.isi.pegasus.planner.invocation.MachineSpecific
  Accessor
getTaskCount(Job) - Method in class edu.isi.pegasus.planner.code.generator.NetloggerJobMapper
  Returns the task count for a job.
getTaskCount(Job) - Method in class edu.isi.pegasus.planner.code.generator.Stampede
  Returns the task count for a job.
getTC() - Method in class edu.isi.pegasus.planner.catalog.transformation.client.TCQuery
  Print all the contents of the TC in pretty print
getTCEntry(Job) - Method in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  Helper method to get an entry from the transformation catalog for an installed executable.
getTCEntry(String) - Method in class edu.isi.pegasus.planner.refiner.cleanup.Cleanup
  Returns the TCEntry object for the rm executable on a grid stagingSite.
getTCEntry(String) - Method in class edu.isi.pegasus.planner.refiner.cleanup.RM
  Returns the TCEntry object for the rm executable on a grid site.
getTCEntry(List) - Method in class edu.isi.pegasus.planner.selector.transformation.Installed
  Returns a list of TransformationCatalogEntry objects of type installed from a List of valid TCEntries
getTCEntry(List) - Method in class edu.isi.pegasus.planner.selector.transformation.Random
  This method randomly selects one of the records from numerous valid Transformation Catalog Entries returned by the TCMapper.
getTCEntry(List) - Method in class edu.isi.pegasus.planner.selector.transformation.RoundRobin
getTCEntry(List) - Method in class edu.isi.pegasus.planner.selector.transformation.Staged
  Takes a list of TransformationCatalogEntry objects and returns 1 or many TransformationCatalogEntry objects as a list by selecting only Static stageable binary's
getTCEntry(List) - Method in class edu.isi.pegasus.planner.selector.transformation.Submit
  This method returns a list of TransformationCatalogEntry objects of type STATIC_BINARY and only available on the Submit machine( "local" site).
getTCEntry(List) - Method in class edu.isi.pegasus.planner.selector.TransformationSelector
  Takes a list of TransformationCatalogEntry objects and returns 1 or many TransformationCatalogEntry objects as a list depending on the type of selection algorithm.
getTCList(String, String, String, String) - Method in class edu.isi.pegasus.planner.catalog.transformation.Mapper
  This method returns a List of TransformationCatalog Objects valid for a particular transformation and for a particular compute site
getTCLogicalNames(String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Get the list of LogicalNames available on a particular resource.
getTCLogicalNames(String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Get the list of LogicalNames available on a particular resource.
getTCLogicalNames(String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Get the list of LogicalNames available on a particular resource.
getTCLogicalNames(String, TCType) - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Get the list of LogicalNames available on a particular resource.
getTCMapperMode() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the mode for loading the transformation mapper that sits in front of the transformation catalog.
getTCMode() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the mode to be used for accessing the Transformation Catalog.
getTCPath() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the location of the transformation catalog.
getTCXML() - Method in class edu.isi.pegasus.planner.catalog.transformation.client.TCQuery
getTempFilename() - Method in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  Creates a temporary file and obtains its name.
getTerminate() - Static method in class edu.isi.pegasus.planner.invocation.SimpleServer
getTextToPoolConfig(String) - Method in class edu.isi.pegasus.planner.client.SCClient
  Generates the old site catalog object reading in from text file.
getThirdPartySites(String) - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the comma separated list of third party sites, specified in the properties.
getThirdPartySites(String) - Method in class edu.isi.pegasus.planner.transfer.RemoteTransfer
  Returns a set of third party sites.
getThirdPartySites(String) - Method in class edu.isi.pegasus.planner.transfer.TPT
  Returns a set of third party sites.
getThirdPartySitesRemote(String) - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the comma separated list of third party sites for which the third party transfers are executed on the remote sites.
getTimeStamp() - Method in class edu.isi.pegasus.common.logging.logger.Default
  Gets the timestamp nicely formatted.
getTimestamp() - Method in class edu.isi.pegasus.common.util.Version
getTo() - Method in class edu.isi.pegasus.planner.provisioner.Edge
  return the 'to' task
getTotalNodes() - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Returns the total number of nodes that this grid gateway talks to.
getTotalSize() - Method in class edu.isi.pegasus.planner.catalog.site.classes.FileSystemType
  Returns the total directory size.
getTransfer() - Method in class edu.isi.pegasus.planner.dax.File
  Get the transfer type of the file
getTransferArguments() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the arguments with which the transfer executable needs to be invoked.
getTransferContainerIterator() - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.PoolTransfer
  Returns the iterator to the list of transfer containers.
getTransferContainerIterator() - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle.PoolTransfer
  Returns the iterator to the list of transfer containers.
getTransferFlag() - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Returns the tristate transfer mode that is associated with the file.
getTransferImplementation() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the transfer implementation that is to be used for constructing the transfer jobs.
getTransferImplementation(String) - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the transfer implementation.
getTransferInterPriority() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the priority to be set for the interpool transfer job.
getTransferPriority(String) - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the transfer priority.
getTransferRefiner() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the transfer refiner that is to be used for adding in the transfer jobs in the workflow Referred to by the "pegasus.transfer.refiner" property.
getTransferStageInPriority() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the priority to be set for the stage in transfer job.
getTransferStageOutPriority() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the priority to be set for the stage out transfer job.
getTransformation() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor
getTransformation() - Method in class edu.isi.pegasus.planner.parser.TransformationCatalogTextParser
  Returns the transformation name, and moves the scanner to hold the next `TransformationCatalogReservedWord`.
getTransformationCatalogEntry(String) - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Returns the transformation catalog entry for kickstart on a site
getTransformationCatalogEntry(String, Profiles, boolean) - Method in class edu.isi.pegasus.planner.parser.TransformationCatalogTextParser
  Constructs a single transformation catalog entry and returns it.
getTransformationCatalogEntry(String, int) - Method in interface edu.isi.pegasus.planner.transfer.Implementation
  Retrieves the transformation catalog entry for the executable that is being used to transfer the files in the implementation.
getTransformationCatalogEntry(String, int) - Method in class edu.isi.pegasus.planner.transfer.implementation.GUC
  Retrieves the transformation catalog entry for the executable that is being used to transfer the files in the implementation.
getTransformationCatalogEntry(String, int) - Method in class edu.isi.pegasus.planner.transfer.implementation.Stork
  Retrieves the transformation catalog entry for the executable that is being used to transfer the files in the implementation.
getTransformationCatalogEntry(String, int) - Method in class edu.isi.pegasus.planner.transfer.implementation.T2
  Retrieves the transformation catalog entry for the executable that is being used to transfer the files in the implementation.
getTransformationCatalogEntry(String, int) - Method in class edu.isi.pegasus.planner.transfer.implementation.Transfer
  Retrieves the transformation catalog entry for the executable that is being used to transfer the files in the implementation.
getTransformationCatalogEntry(String) - Method in class edu.isi.pegasus.planner.transfer.sls.Transfer
  Retrieves the transformation catalog entry for the executable that is being used to transfer the files in the implementation.
getTransformations(String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.TransformationStore
  Returns a list of transformation names matching on a site and transformation type.
getTransformations() - Method in class edu.isi.pegasus.planner.dax.ADAG
  Returns a set of Transformation Objects (complex executables) stored in the DAX based Transformation Catalog
getTransformationStore() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the Transformation Store
getTransientRegFlag() - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Returns the transient registration flag (the value of dontRegister).
getTransientTransferFlag() - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Returns whether the transfer is transient or not.
getTruncated() - Method in class edu.isi.pegasus.planner.invocation.Data
  Accessor
getTXJobName(int, int, int) - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.PoolTransfer
  Generates the name of the transfer job, that is unique for the given workflow.
getTXJobName(int, int, int) - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle.PoolTransfer
  Generates the name of the transfer job, that is unique for the given workflow.
getTXJobName(int, int) - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle.PoolTransfer
  Generates the name of the transfer job, that is unique for the given workflow.
getTXName() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the name of the underlying transformation.
getTXName() - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.TransferContainer
  Returns the name of the transfer job.
getTXName() - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle.TransferContainer
  Returns the name of the transfer job.
getTXNamespace() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the namespace of the underlying transformation.
getTXPoolEntry(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  Gets the pool object to be used for the transfer universe.
getTXSelectorMode() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the mode for loading the transformation selector that selects amongst the various candidate transformation catalog entry objects.
getTXVersion() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the version of the underlying transformation.
getType() - Method in class edu.isi.pegasus.planner.catalog.site.classes.Directory
  Set the type of directory
getType() - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Returns the type of this grid gateway.
getType() - Method in class edu.isi.pegasus.planner.catalog.site.classes.ReplicaCatalog
  Returns the type of replica catalog.
getType() - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Returns the type of the transformation.
getType() - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Returns the tristate transfer mode that is associated with the file.
getType() - Method in class edu.isi.pegasus.planner.dax.MetaData
  Get the type of the metdata object
getUID() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor
getUID() - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor
getUMask() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor
getUname() - Method in class edu.isi.pegasus.planner.invocation.Machine
  Obtains the utsname generic system information record.
getUniverse() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the universe associated with the job.
getUnsharedRSS() - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor.
getUntarJobName(ADag, String) - Method in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  It returns the name of the untar job, that is to be assigned.
getUpLen() - Method in class edu.isi.pegasus.planner.provisioner.Node
  return the UpLength of this task.
getURL() - Method in class edu.isi.pegasus.planner.catalog.site.classes.FileServer
  Returns the externally accessible URL composed of url prefix and the mount point
getURL() - Method in class edu.isi.pegasus.planner.catalog.site.classes.ReplicaCatalog
  Returns the url for the replica catalog.
getURL() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.LRC
  Returns the LRC url associated with a pool.
getURL(Map, boolean) - Method in class edu.isi.pegasus.planner.classes.FileTransfer
  Returns a single url from the map passed.
getURL() - Method in class edu.isi.pegasus.planner.dax.PFN
getURLFor(String) - Method in class edu.isi.pegasus.gridftp.GridFTPConnection
  Return a gsiftp:// URL for path
getURLForRegistrationOnDestination() - Method in class edu.isi.pegasus.planner.classes.FileTransfer
  Sets the registration url for the destination.
getURLOnSharedScratch(SiteCatalogEntry, Job, FileServerType.OPERATION, String) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  Returns a URL on the shared scratch of the staging site
getURLPrefix() - Method in class edu.isi.pegasus.common.util.PegasusURL
  Returns the url prefix associated with the PegasusURL.
getURLPrefix() - Method in class edu.isi.pegasus.planner.catalog.site.classes.FileServerType
  Returns the url prefix .
getURLPrefix(boolean) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  A helper method that returns the url prefix for one of the gridftp server associated with the pool.
getURLPrefix(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  Returns the url prefix of a gridftp server on the pool.
getUsage() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor
getUsage() - Method in class edu.isi.pegasus.planner.invocation.Job
  Accessor
getUseOfSymbolicLinks() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  It returns whether the use of symbolic links in case where the source and destination files happen to be on the same file system.
getUser() - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Returns the username.
getUser() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor
getUser() - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor
getUserTime() - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor: Obtains the user time from the object.
getUses() - Method in class edu.isi.pegasus.planner.dax.AbstractJob
getUses() - Method in class edu.isi.pegasus.planner.dax.Transformation
  Get the List of files and/or executables being used by the transformation
getValue() - Method in class edu.isi.pegasus.planner.catalog.site.classes.Connection
  Returns the key value.
getValue() - Method in enum edu.isi.pegasus.planner.catalog.site.classes.Directory.TYPE
  The value associated with the enum
getValue(String) - Static method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolMode
  Deprecated.
getValue() - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.Arch
  Returns the value of the architecture as string.
getValue() - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.Os
  Returns the value of the operating system as string.
getValue() - Method in class edu.isi.pegasus.planner.classes.NameValue
  Returns the value associated with this tuple.
getValue() - Method in class edu.isi.pegasus.planner.dax.MetaData
  Get the value of the metdata object
getValue() - Method in class edu.isi.pegasus.planner.dax.Profile
  Get the value of this profile
getValue() - Method in class edu.isi.pegasus.planner.invocation.Architecture
  Accessor
getValue() - Method in class edu.isi.pegasus.planner.invocation.ArgEntry
  Accessor
getValue() - Method in class edu.isi.pegasus.planner.invocation.ArgString
  Accessor
getValue() - Method in class edu.isi.pegasus.planner.invocation.Arguments
  This abstract method is called by higher-level functions to obtain a single string representation of the arguments.
getValue() - Method in class edu.isi.pegasus.planner.invocation.ArgVector
  Returns the full argument vector as one single string.
getValue() - Method in class edu.isi.pegasus.planner.invocation.Boot
  Accessor
getValue() - Method in class edu.isi.pegasus.planner.invocation.CommandLine
  Accessor
getValue() - Method in class edu.isi.pegasus.planner.invocation.CPU
  Accessor
getValue() - Method in class edu.isi.pegasus.planner.invocation.Data
  Accessor
getValue() - Method in class edu.isi.pegasus.planner.invocation.EnvEntry
  Accessor
getValue() - Method in class edu.isi.pegasus.planner.invocation.File
  Accessor
getValue() - Method in interface edu.isi.pegasus.planner.invocation.HasText
  Accessor
getValue() - Method in class edu.isi.pegasus.planner.invocation.Ignore
  Accessor
getValue() - Method in class edu.isi.pegasus.planner.invocation.JobStatusFailure
  Accessor
getValue() - Method in class edu.isi.pegasus.planner.invocation.JobStatusSignal
  Accessor
getValue() - Method in class edu.isi.pegasus.planner.invocation.JobStatusSuspend
  Accessor
getValue() - Method in class edu.isi.pegasus.planner.invocation.Stamp
  Accessor
getValue() - Method in class edu.isi.pegasus.planner.invocation.Uname
  Accessor
getValue() - Method in class edu.isi.pegasus.planner.invocation.WorkingDir
  Accessor
getValue() - Method in class edu.isi.pegasus.planner.parser.tokens.Identifier
  Obtains the token value of a given reserved word token.
getValue() - Method in class edu.isi.pegasus.planner.parser.tokens.QuotedString
  Obtains the token value of a given string token.
getValue() - Method in class edu.isi.pegasus.planner.parser.tokens.SiteCatalogReservedWord
  Obtains the token value of a given reserved word token.
getValue() - Method in class edu.isi.pegasus.planner.parser.tokens.TransformationCatalogReservedWord
  Obtains the token value of a given reserved word token.
getValue() - Method in class edu.isi.pegasus.planner.refiner.ThreadPool.ConditionVariable
  Returns the value.
getValue() - Method in class edu.isi.pegasus.planner.selector.site.RoundRobin.NameValue
  Returns the value associated with this pair.
getVDS_HOME(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  Returns the value of VDS_HOME for a site.
getVDSHome() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Deprecated.
getVDSHome() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Deprecated.
getVDSHome(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  Deprecated.
getVDSKeyValue() - Method in interface edu.isi.pegasus.planner.code.GridStart
  Returns the value of the vds profile with key as VDS.GRIDSTART_KEY, that would result in the loading of this particular implementation.
getVDSKeyValue() - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Returns the value of the vds profile with key as Pegasus.GRIDSTART_KEY, that would result in the loading of this particular implementation.
getVDSKeyValue() - Method in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  Returns the value of the vds profile with key as Pegasus.GRIDSTART_KEY, that would result in the loading of this particular implementation.
getVDSKeyValue() - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Returns the value of the vds profile with key as Pegasus.GRIDSTART_KEY, that would result in the loading of this particular implementation.
getVDSProperties() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the VDS properties that were set by the user.
getVDSProperties() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the CommonProperties that this object encapsulates.
getVDSSuperNode() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the name of the compute job of Pegasus supernode containing this job.
getVDSSysInfo() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Returns the sysinfo for the site.
getVDSSysInfo() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Returns the sysinfo for the site.
getVDSSysInfo(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  Returns the `VDSSysInfo` for the site
getVDSSysInfo() - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Returns the System Information in the old VDS format associated with the transformation.
getVersion() - Method in class edu.isi.pegasus.common.util.CondorVersion.CondorVersionCallback
  Returns the condor version detected.
getVersion() - Method in class edu.isi.pegasus.common.util.Version
getVersion() - Method in class edu.isi.pegasus.planner.classes.CompoundTransformation
  Returns the version
getVersion() - Method in class edu.isi.pegasus.planner.dax.Executable
  Get the version of the executable
getVersion() - Method in class edu.isi.pegasus.planner.dax.File
  Get the version of the file
getVersion() - Method in class edu.isi.pegasus.planner.dax.Job
getVersion() - Method in class edu.isi.pegasus.planner.dax.Transformation
  Get the version of the transformation
getVersion() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor
getVersionOfDAX(String) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  A convenience method that tries to determine the version of the dax schema by reading ahead in the DAX file, and searching for the version attribue in the file.
getVOGroup() - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Returns the VO Group.
getVOGroup() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the VO Group to which the user belongs
getVoluntarySwitches() - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor: Obtains the voluntary context switches.
getWhat() - Method in class edu.isi.pegasus.planner.dax.Invoke
  Get what to invoke
getWhen() - Method in class edu.isi.pegasus.planner.dax.Invoke
  Get when to Invoke
getWingsPropertiesFile() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the path to the wings properties file.
getWingsRequestID() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns the request id.
getWorkerNodeDirectory(Job) - Method in interface edu.isi.pegasus.planner.code.GridStart
  Returns the directory in which the job executes on the worker node.
getWorkerNodeDirectory(Job) - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Returns the exectionSiteDirectory in which the constituentJob executes on the worker node.
getWorkerNodeDirectory(Job) - Method in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  Returns the directory in which the job executes on the worker node.
getWorkerNodeDirectory(Job) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Returns the directory in which the job executes on the worker node.
getWorkerNodeFS() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Returns the worker node filesystem.
getWorkerPackageMap() - Method in class edu.isi.pegasus.planner.classes.PegasusBag
  A convenice method to get the worker package
getWorkerSharedDirectory() - Method in class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeScratch
  Returns the directory shared amongst the worker nodes only.
getWorkerSharedDirectory() - Method in class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeStorage
  Returns the directory shared amongst the worker nodes only.
getWorkflow() - Method in class edu.isi.pegasus.planner.cluster.Horizontal
  Returns a reference to the workflow that is being refined by the refiner.
getWorkflow() - Method in class edu.isi.pegasus.planner.refiner.DataReuseEngine
  Returns a reference to the workflow that is being refined by the refiner.
getWorkflow() - Method in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  Returns a reference to the workflow that is being refined by the refiner.
getWorkflow() - Method in interface edu.isi.pegasus.planner.refiner.Refiner
  Returns a reference to the workflow that is being refined by the refiner.
getWorkflow() - Method in class edu.isi.pegasus.planner.transfer.AbstractRefiner
  Returns a reference to the workflow that is being refined by the refiner.
getWorkflowFileBasenamePrefix(PlannerOptions, String, String) - Method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
getWorkflowFileName(PlannerOptions, String, String, String) - Method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Constructs the basename to a workflow file that.
getWorkflowLabel() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor
getWorkflowMetrics() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the metrics about the workflow.
getWorkflowMetrics() - Method in class edu.isi.pegasus.planner.classes.DagInfo
  Returns the workflow metrics so far.
getWorkflowMetrics() - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Returns the workflow metrics.
getWorkflowTimestamp() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor
getWorkflowUUID() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the UUID for the workflow
getWorkflowUUID() - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Returns the UUID for the workflow
getWorkingDirectory() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor
getWriter(Job) - Method in class edu.isi.pegasus.planner.code.generator.Abstract
  Returns an open stream to the file that is used for writing out the job information for the job.
getWriter(Job) - Method in class edu.isi.pegasus.planner.code.generator.HashedFile
  Returns an open stream to the file that is used for writing out the job information for the job.
getXMLProducer() - Method in class edu.isi.pegasus.planner.cluster.Horizontal
  Returns a reference to the XMLProducer, that generates the XML fragment capturing the actions of the refiner.
getXMLProducer() - Method in class edu.isi.pegasus.planner.refiner.DataReuseEngine
  Returns a reference to the XMLProducer, that generates the XML fragment capturing the actions of the refiner.
getXMLProducer() - Method in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  Returns a reference to the XMLProducer, that generates the XML fragment capturing the actions of the refiner.
getXMLProducer() - Method in interface edu.isi.pegasus.planner.refiner.Refiner
  Returns a reference to the XMLProducer, that generates the XML fragment capturing the actions of the refiner.
getXMLProducer() - Method in class edu.isi.pegasus.planner.transfer.AbstractRefiner
  Returns a reference to the XMLProducer, that generates the XML fragment capturing the actions of the refiner.
gftp - Variable in class edu.isi.pegasus.planner.catalog.site.impl.XML2
gftp - Variable in class edu.isi.pegasus.planner.parser.ConfigXmlParser
glibc - Variable in class edu.isi.pegasus.planner.catalog.transformation.classes.VDSSysInfo
  Glibc version of the system
GLIDEIN_STYLE - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The style indicating that the submit files are to be generated for a glidein execution.
GLIDEIN_STYLE_IMPLEMENTING_CLASS - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactory
  The name of the class implementing the Condor GlideIN Style.
GLIDEINWMS_STYLE - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The style indicating that the submit files are to be generated for a glideinwms execution.
GLIDEINWMS_STYLE_IMPLEMENTING_CLASS - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactory
  The name of the class implementing the Condor GlideinWMS Style.
GLite - Class in edu.isi.pegasus.planner.code.generator.condor.style
  This implementation enables a job to be submitted via gLite to a grid sites.
GLite() - Constructor for class edu.isi.pegasus.planner.code.generator.condor.style.GLite
  The default Constructor.
GLITE_STYLE - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The style indicating that the submit files are to be generated for a glite execution.
GLITE_STYLE_IMPLEMENTING_CLASS - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactory
  The name of the class implementing the CondorG Style.
globallyIgnored(String) - Method in class edu.isi.pegasus.planner.selector.replica.Restricted
  Returns a boolean indicating whether a site is to be ignored as a replica source for all compute sites.
globallyPreferred(String) - Method in class edu.isi.pegasus.planner.selector.replica.Restricted
  Returns a boolean indicating whether a site is a preferred replica source for all compute sites.
GLOBUS - Static variable in class edu.isi.pegasus.planner.classes.Profile
Globus - Class in edu.isi.pegasus.planner.namespace
  This helper class helps in handling the globus rsl key value pairs that come through profile information for namespace Globus.
Globus() - Constructor for class edu.isi.pegasus.planner.namespace.Globus
  The default constructor.
Globus(Map) - Constructor for class edu.isi.pegasus.planner.namespace.Globus
  The overloaded constructor
GLOBUS_SCHEDULER_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Hints
  The globus scheduler hints key
GLOBUS_STYLE - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The style indicating that the submit files are to be generated for a CondorG execution.
GLOBUS_STYLE_IMPLEMENTING_CLASS - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactory
  The name of the class implementing the CondorG Style.
GLOBUS_UNIVERSE - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The condor universe key value for vanilla universe.
GLOBUS_VERSION - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPServer
  The constant to be passed to the accessor functions to get or set the globus version of the grid ftp server.
GLOBUS_VERSION - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The constant to be passed to the accessor functions to get or set the globus version.
globusRSL - Variable in class edu.isi.pegasus.planner.classes.Job
  The namespace object containing the globus rsl attributes which the user specifies in the dax, or the pool file or the properties file.
globusScheduler - Variable in class edu.isi.pegasus.planner.classes.Job
  The globus Scheduler for the job.
GlobusVersion - Class in edu.isi.pegasus.planner.catalog.site.impl.old.classes
  This is a data class that stores the globus version installed and to be used on a particular pool for the gridftp server or the jobmanagers.
GlobusVersion() - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GlobusVersion
  The default constructor.
GlobusVersion(String) - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GlobusVersion
  Overloaded constructor for the class;
GlobusVersion(int, int, int) - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GlobusVersion
  Constructor to set the version information
Graph - Interface in edu.isi.pegasus.planner.partitioner.graph
  The interface for the Graph Class.
GraphNode - Class in edu.isi.pegasus.planner.partitioner.graph
  Data class that allows us to construct information about the nodes in the abstract graph.
GraphNode() - Constructor for class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  The default constructor.
GraphNode(String) - Constructor for class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  The overloaded constructor.
GraphNode(String, GraphNodeContent) - Constructor for class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  The overloaded constructor.
GraphNode(String, String) - Constructor for class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  The overloaded constructor.
GraphNodeComparator() - Constructor for class edu.isi.pegasus.planner.partitioner.Horizontal.GraphNodeComparator
GraphNodeContent - Interface in edu.isi.pegasus.planner.partitioner.graph
  This inteface defines a common base for all the classes that can reside in a `GraphNode` object.
GRAY_COLOR - Static variable in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
GrepCallback(String) - Constructor for class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG.GrepCallback
  Overloaded Constructor.
GRID_DN_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The Grid DN of the user.
GRID_FTP_STANDARD_PORT - Static variable in class edu.isi.pegasus.planner.refiner.Authenticate
  The standard port at which Grid FTP runs.
GRID_JOB_TYPE_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The name of the key that specifies the grid job type.
GRID_JOB_TYPE_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Hints
  The jobmanager universe key.
GRID_RESOURCE_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.CondorC
  The key that designates the collector associated with the job
GRID_RESOURCE_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.CreamCE
  The key that designates the collector associated with the job
GRID_RESOURCE_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.SSH
  The key that designates the collector associated with the job
GRID_RESOURCE_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The condor key for designation the grid_resource.
GRID_UNIVERSE - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The condor universe key value for grid universe.
GRIDFTP - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  The constant to be passed to the accessor functions to get or set the list of `GridFTP` objects for the remote site.
GRIDFTP - Static variable in class edu.isi.pegasus.planner.parser.tokens.SiteCatalogReservedWord
  token value for the reserved word "gridftp".
GRIDFTP_RESOURCE - Static variable in class edu.isi.pegasus.planner.classes.AuthenticateRequest
  The type identifying that the resource to authenticate against is a grid ftp server.
GRIDFTP_URL - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPServer
  The constant to be passed to the accessor functions to get or set the url.
gridFTPAlive(String, int) - Method in class edu.isi.pegasus.planner.refiner.Authenticate
  It checks with a grid ftp server running at a particular host and port, to see if it is up or not.
GridFTPBandwidth - Class in edu.isi.pegasus.planner.catalog.site.impl.old.classes
  This is a data class to store information about gridftp bandwidths between various sites.
GridFTPBandwidth() - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPBandwidth
GRIDFTPBANDWIDTHINFO - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPBandwidth
GridFTPConnection - Class in edu.isi.pegasus.gridftp
  A connection to a GridFTP server
GridFTPConnection(String, int, GSSCredential) - Constructor for class edu.isi.pegasus.gridftp.GridFTPConnection
GridFTPConnection.StringBuilderDataSink - Class in edu.isi.pegasus.gridftp
  This class is used to collect data returned by the list command into a StringBuilder.
GridFTPException - Exception in edu.isi.pegasus.gridftp
GridFTPException(String) - Constructor for exception edu.isi.pegasus.gridftp.GridFTPException
GridFTPException(String, Throwable) - Constructor for exception edu.isi.pegasus.gridftp.GridFTPException
GRIDFTPINFO - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPServer
  Array storing the names of the attributes that are stored with the grid ftp server.
GridFTPServer - Class in edu.isi.pegasus.planner.catalog.site.impl.old.classes
  This is a data class that is used to store information about a grid ftp server.
GridFTPServer() - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPServer
  The default constructor.
GridFTPURL - Class in edu.isi.pegasus.gridftp
GridFTPURL(String) - Constructor for class edu.isi.pegasus.gridftp.GridFTPURL
GridGateway - Class in edu.isi.pegasus.planner.catalog.site.classes
  This class describes the Grid Gateway into a site.
GridGateway() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  The default constructor.
GridGateway(GridGateway.TYPE, String, GridGateway.SCHEDULER_TYPE) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  The overloaded constructor.
GridGateway.JOB_TYPE - Enum in edu.isi.pegasus.planner.catalog.site.classes
  An enumeration of types of jobs handled by an instance of a grid gateway.
GridGateway.SCHEDULER_TYPE - Enum in edu.isi.pegasus.planner.catalog.site.classes
  An enumeration of valid schedulers on the grid gateway.
GridGateway.TYPE - Enum in edu.isi.pegasus.planner.catalog.site.classes
  An enumeration of valid types of grid gateway.
GRIDLAUNCH - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  The constant to be passed to the accessor functions to get or set the path to kickstart.
GRIDLAUNCH - Static variable in class edu.isi.pegasus.planner.parser.tokens.SiteCatalogReservedWord
  token value for the reserved word "gridlaunch".
gridstart(PrintWriter, Job, boolean) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  This function creates the stdio handling with and without gridstart.
GridStart - Interface in edu.isi.pegasus.planner.code
  The interface that defines how a job specified in the abstract workflow is launched on the grid.
gridStart(String) - Method in class edu.isi.pegasus.planner.code.GridStartFactory
  Returns the cached implementation of GridStart from the implementing class table.
GRIDSTART_ARGUMENTS_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the profile key, that determines the arguments with which the GridStart that is used to launch a job on the remote site is invoked with.
GRIDSTART_IMPLEMENTING_CLASSES - Static variable in class edu.isi.pegasus.planner.code.GridStartFactory
  The known gridstart implementations.
GRIDSTART_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the profile key that determines the launching executable to be used to launch a job on the grid.
GRIDSTART_PATH_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the profile key that designates the path to a gridstart.
GRIDSTART_PREJOB - Static variable in class edu.isi.pegasus.planner.namespace.ENV
  The name of the environment variable that specifies the Gridstart PREJOB.
GRIDSTART_SHORT_NAMES - Static variable in class edu.isi.pegasus.planner.code.GridStartFactory
  The corresponding short names for the implementations.
GridStartFactory - Class in edu.isi.pegasus.planner.code
  An abstract factory class to load the appropriate type of GridStart implementations, and their corresponding POSTScript classes.
GridStartFactory() - Constructor for class edu.isi.pegasus.planner.code.GridStartFactory
  The default constructor.
GridStartFactoryException - Exception in edu.isi.pegasus.planner.code
  Class to notify of failures while instantiating GridStart implementations.
GridStartFactoryException(String) - Constructor for exception edu.isi.pegasus.planner.code.GridStartFactoryException
  Constructs a `GridStartFactoryException` with no detail message.
GridStartFactoryException(String, String) - Constructor for exception edu.isi.pegasus.planner.code.GridStartFactoryException
  Constructs a `GridStartFactoryException` with the specified detailed message.
GridStartFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.code.GridStartFactoryException
  Constructs a `GridStartFactoryException` with the specified detailed message and a cause.
GridStartFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.planner.code.GridStartFactoryException
  Constructs a `GridStartFactoryException` with the specified detailed message and a cause.
Group - Class in edu.isi.pegasus.planner.selector.site
  A site selector than ends up doing grouping jobs together on the basis of an identifier specifed in the dax for the jobs, and schedules them on to the same site.
Group() - Constructor for class edu.isi.pegasus.planner.selector.site.Group
  The default constructor.
GROUP_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the profile key in vds namespace that does the grouping.
GUC - Class in edu.isi.pegasus.planner.transfer.implementation
  The implementation that is used to create transfer jobs that callout to the new globus-url-copy client, that support multiple file transfers
GUC(PegasusBag) - Constructor for class edu.isi.pegasus.planner.transfer.implementation.GUC
  The overloaded constructor, that is called by the Factory to load the class.
Gvds_Pool_Gridlaunch - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
Gvds_Pool_Id - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
Gvds_Pool_Lrc - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
Gvds_Pool_Profile - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
Gvds_Pool_Storage - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
Gvds_Pool_Universe - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
Gvds_Pool_WorkDir - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery

## H

HANDLE - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  The name of the remote site.
handleAdagTagStart(String, Attributes) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Invoked when the starting of the adag element is got.
handleArgumentTagEnd() - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Invoked when the end of the Argument Tag is reached.
handleArgumentTagStart(String, Attributes) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Invoked when the starting of the Argument Tag is reached.
handleChildTagEnd() - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  This passes the child and it's parents list to the callback object.
handleChildTagStart(String, Attributes) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Invoked when the starting of the child element is got.
handleCondorVarForJob(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  It updates/adds the condor variables that are got through the Dax with the values specified in the properties file, pool config file or adds some variables internally.
handleConfigTagEnd() - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  Handles the end of the Xml files.
handleConfigTagEnd() - Static method in class edu.isi.pegasus.planner.parser.ConfigXmlParser
  Handles the end of the Xml files.
handleConfigTagStart() - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
handleConfigTagStart() - Method in class edu.isi.pegasus.planner.parser.ConfigXmlParser
handleDAGTagEnd() - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Invoked when the end of the dag tag is reached.
handleDAGTagStart(String, Attributes) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Invoked when the starting of the dax element is retrieved.
handleDAXTagEnd() - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Invoked when the end of the job tag is reached.
handleDAXTagStart(String, Attributes) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Invoked when the starting of the dax element is retrieved.
handleDependantExecutables(Job) - Method in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  Handles the dependant executables that need to be staged.
handleEnvVarForJob(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  It updates/adds the environment variables that are got through the Dax with the values specified in the properties file, pool config file or adds some variables internally.
handleExecutionTagEnd() - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Invoked when the end of the execution element is reached.
handleExecutionTagStart(String, Attributes) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Replaces the keys associated with the execution tag, with the corresponding keys in the hints profile namespace
handleFilenameTagStart(String, Attributes) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Invoked when the starting of the filename element is got.
handleGlobusRSLForJob(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  It updates/adds the the Globus RSL parameters got through the dax that are in Job object.
handleGridFtpBandwidthTagEnd() - Static method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
handleGridFtpBandwidthTagEnd() - Static method in class edu.isi.pegasus.planner.parser.ConfigXmlParser
handleGridFtpBandwidthTagStart(SiteInfo, Attributes) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  sk added function to handle gridftpbandwidth tag
handleGridFtpBandwidthTagStart(SiteInfo, Attributes) - Method in class edu.isi.pegasus.planner.parser.ConfigXmlParser
  sk added function to handle gridftpbandwidth tag
handleGridFtpTagEnd() - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  sk made changes to the following function to set GRIDFTPServer instead of setting it in fn handleGridFtpTagStart()
handleGridFtpTagEnd() - Method in class edu.isi.pegasus.planner.parser.ConfigXmlParser
  sk made changes to the following function to set GRIDFTPServer instead of setting it in fn handleGridFtpTagStart()
handleGridFtpTagStart(SiteInfo, Attributes) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
handleGridFtpTagStart(SiteInfo, Attributes) - Method in class edu.isi.pegasus.planner.parser.ConfigXmlParser
handleJobManagerTagEnd() - Static method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  Handles the end of the JobManager Tag
handleJobManagerTagEnd() - Static method in class edu.isi.pegasus.planner.parser.ConfigXmlParser
  Handles the end of the JobManager Tag
handleJobManagerTagStart(SiteInfo, Attributes) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  This method handles the start of a jobmanager tag.
handleJobManagerTagStart(SiteInfo, Attributes) - Static method in class edu.isi.pegasus.planner.parser.ConfigXmlParser
  This method handles the start of a jobmanager tag.
handleJobTagEnd() - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Invoked when the end of the job tag is reached.
handleJobTagStart(String, Attributes) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Invoked when the starting of the job element is got.
handleJobTagStart(Job) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Invoked when the starting of the job element is got.
handleLRCTagEnd() - Static method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  Handles the end of the LRC Tag
handleLRCTagEnd() - Static method in class edu.isi.pegasus.planner.parser.ConfigXmlParser
  Handles the end of the LRC Tag
handleLRCTagStart(SiteInfo, Attributes) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
handleLRCTagStart(SiteInfo, Attributes) - Static method in class edu.isi.pegasus.planner.parser.ConfigXmlParser
handleMetadataTagEnd() - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Resets the text content buffer
handleMetadataTagStart(String, Attributes) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Metadata parsing is ignored for time being.
handleParentTagStart(String, Attributes) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Invoked when the starting of the parent element is got.
handlePoolTagEnd() - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  Handles the end of the pool tag.
handlePoolTagEnd() - Static method in class edu.isi.pegasus.planner.parser.ConfigXmlParser
  Handles the end of the pool tag.
handlePoolTagStart(PoolConfig, Attributes) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
handlePoolTagStart(PoolConfig, Attributes) - Method in class edu.isi.pegasus.planner.parser.ConfigXmlParser
handleProfileTagEnd(SiteInfo) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  Handles the end of the Profile tag.
handleProfileTagEnd(SiteInfo) - Method in class edu.isi.pegasus.planner.parser.ConfigXmlParser
  Handles the end of the Profile tag.
handleProfileTagEnd() - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Invoked when the end of the profile element is got.
handleProfileTagStart(SiteInfo, Attributes) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
handleProfileTagStart(SiteInfo, Attributes) - Method in class edu.isi.pegasus.planner.parser.ConfigXmlParser
handleProfileTagStart(String, Attributes) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Invoked when the starting of the profile element is got.
handleRescueDAG(ADag, PlannerOptions) - Method in class edu.isi.pegasus.planner.client.CPlanner
  Checks for rescue dags, and determines whether to plan or not.
handleRescueDAG(String, String, int) - Method in class edu.isi.pegasus.planner.client.CPlanner
  Checks for rescue dags, and determines whether to submit a rescue dag or not.
handleStderrTagStart(String, Attributes) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Invoked when the starting of the stdout tag is reached.
handleStdinTagStart(String, Attributes) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Invoked when the starting of the stdin tag is reached.
handleStdoutTagStart(String, Attributes) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Invoked when the starting of the stdout tag is reached.
handleTransferOfExecutable(Job, String) - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  It changes the paths to the executable depending on whether we want to transfer the executable or not.
handleTransferOfExecutable(Job) - Method in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  It changes the paths to the executable depending on whether we want to transfer the executable or not.
handleUsesPFNTagStart(String, Attributes) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Invoked when start of the pfn element nested in uses element is encountered
handleUsesTagEnd() - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Handles the end of a uses tag.
handleUsesTagStart(String, Attributes) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Invoked when the starting of the uses element is got.
handleWorkDirectoryTagEnd(SiteInfo) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  This method handles the Workdirectory tg end.
handleWorkDirectoryTagEnd(SiteInfo) - Method in class edu.isi.pegasus.planner.parser.ConfigXmlParser
  This method handles the Workdirectory tg end.
handleWorkDirectoryTagStart(SiteInfo, Attributes) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  Handles the WorkDirectory Tag Start.
handleWorkDirectoryTagStart(SiteInfo, Attributes) - Static method in class edu.isi.pegasus.planner.parser.ConfigXmlParser
  Handles the WorkDirectory Tag Start.
hasAttribute(String) - Method in class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  Checks for the existence of an attribute key.
HasDescriptor - Interface in edu.isi.pegasus.planner.invocation
  This interface defines a common base for all File elements in an invocation record that carry a descriptor in their values.
HasFilename - Interface in edu.isi.pegasus.planner.invocation
  This interface defines a common base for all File elements in an invocation record that carry a filename in their values.
hasFileServerForGETOperations() - Method in class edu.isi.pegasus.planner.catalog.site.classes.DirectoryLayout
  A convenience method that retrieves whether the directory has a file server for get operations ( file server with type get and all )
hasFileServerForOperations(FileServerType.OPERATION) - Method in class edu.isi.pegasus.planner.catalog.site.classes.DirectoryLayout
  A convenience method that retrieves whether the directory has a file server for a particular operation.
hasFileServerForPUTOperations() - Method in class edu.isi.pegasus.planner.catalog.site.classes.DirectoryLayout
  A convenience method that retrieves whether the directory has a file server for put operations ( file server with type put and all )
hashCode() - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.Arch
hashCode() - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.Os
hashCode() - Method in class edu.isi.pegasus.planner.classes.CompoundTransformation
  Calculate a hash code value for the object to support hash tables.
hashCode() - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Calculate a hash code value for the object to support hash tables.
hashCode() - Method in class edu.isi.pegasus.planner.dax.AbstractJob
hashCode() - Method in class edu.isi.pegasus.planner.dax.Edge
hashCode() - Method in class edu.isi.pegasus.planner.dax.Executable
hashCode() - Method in class edu.isi.pegasus.planner.dax.File
  HashCode of this File
hashCode() - Method in class edu.isi.pegasus.planner.dax.Transformation
hashCode() - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  Calculate a hash code value for the object to support hash based Collections.
Hashed - Class in edu.isi.pegasus.planner.transfer.mapper.impl
  Maps the output files in a Hashed Directory structure on the output site.
Hashed() - Constructor for class edu.isi.pegasus.planner.transfer.mapper.impl.Hashed
HASHED_OUTPUT_MAPPER_IMPLEMENTATION - Static variable in class edu.isi.pegasus.planner.transfer.mapper.OutputMapperFactory
  The Hashed mapper implementation to be used.
HashedFile - Class in edu.isi.pegasus.planner.code.generator
  A Condor Submit Writer, that understands the notion of hashed file directories.
HashedFile() - Constructor for class edu.isi.pegasus.planner.code.generator.HashedFile
  The default constructor.
hashedOutputMapperUsed(PegasusProperties) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  Returns a boolean indicating whether the Hashed Output Mapper was used or not
hasMatchingAttr(ReplicaCatalogEntry, String, Object) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Looks for a match of an attribute value in a replica catalog entry.
hasMatchingAttr(ReplicaCatalogEntry, String, Object) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Looks for a match of an attribute value in a replica catalog entry.
hasMoreTokens() - Method in class edu.isi.pegasus.planner.parser.SiteCatalogTextScanner
  Checks for the availability of more input.
hasMoreTokens() - Method in class edu.isi.pegasus.planner.parser.TransformationCatalogTextScanner
  Checks for the availability of more input.
hasNext() - Method in class edu.isi.pegasus.planner.namespace.Namespace.EmptyIterator
  Always returns false, as an empty iterator.
hasNext() - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph.BottomUpIterator
  Always returns false, as an empty iterator.
hasNext() - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph.MapGraphIterator
  Always returns false, as an empty iterator.
hasNext() - Method in class edu.isi.pegasus.planner.partitioner.graph.TopologicalSortIterator
  Returns whether there are more nodes to be traversed in the graph or not.
HasText - Interface in edu.isi.pegasus.planner.invocation
  This interface defines a common base for all elements in an invocation record that can carry text in their values.
hasWorkflowRefinementStarted() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns a boolean indicating whether the workflow refinement has started or not
HEAD_INDEX - Static variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The index of the head job.
HeadNodeFS - Class in edu.isi.pegasus.planner.catalog.site.classes
  This data class describes the HeadNode Filesystem layout.
HeadNodeFS() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.HeadNodeFS
  The default constructor.
HeadNodeFS(HeadNodeScratch, HeadNodeStorage) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.HeadNodeFS
  The overloaded constructor.
HeadNodeScratch - Class in edu.isi.pegasus.planner.catalog.site.classes
  This data class describes the scratch area on a head node.
HeadNodeScratch() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.HeadNodeScratch
  The default constructor
HeadNodeScratch(StorageType) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.HeadNodeScratch
  The overloaded constructor
HeadNodeScratch(LocalDirectory, SharedDirectory) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.HeadNodeScratch
  The overloaded constructor.
HeadNodeStorage - Class in edu.isi.pegasus.planner.catalog.site.classes
  This data class describes the storage area on a node.
HeadNodeStorage() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.HeadNodeStorage
  The default constructor
HeadNodeStorage(StorageType) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.HeadNodeStorage
  The overloaded constructor
HeadNodeStorage(LocalDirectory, SharedDirectory) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.HeadNodeStorage
  The overloaded constructor.
HEFT(int) - Method in class edu.isi.pegasus.planner.provisioner.Estimator
Heft - Class in edu.isi.pegasus.planner.selector.site
  The HEFT based site selector.
Heft() - Constructor for class edu.isi.pegasus.planner.selector.site.Heft
  The default constructor.
HeftBag - Class in edu.isi.pegasus.planner.selector.site.heft
  A data class that implements the Bag interface and stores the extra information that is required by the HEFT algorithm for each node.
HeftBag() - Constructor for class edu.isi.pegasus.planner.selector.site.heft.HeftBag
  The default constructor.
HeftGraphNodeComparator - Class in edu.isi.pegasus.planner.selector.site.heft
  Comparator for GraphNode objects that allow us to sort on basis of the downward rank computed.
HeftGraphNodeComparator() - Constructor for class edu.isi.pegasus.planner.selector.site.heft.HeftGraphNodeComparator
HEFTINFO - Static variable in class edu.isi.pegasus.planner.selector.site.heft.HeftBag
  Array storing the names of the attributes that are stored with the site.
HIGHEST_RANK_VALUE - Static variable in class edu.isi.pegasus.planner.selector.replica.Regex
  The highest value of rank.
hints - Variable in class edu.isi.pegasus.planner.classes.Job
  To accomodate all the hints that maybe passed through the DAX.
HINTS - Static variable in class edu.isi.pegasus.planner.classes.Profile
Hints - Class in edu.isi.pegasus.planner.namespace
  An empty mechanical implementation for the namespace.
Hints() - Constructor for class edu.isi.pegasus.planner.namespace.Hints
  The default constructor.
Hints(Map) - Constructor for class edu.isi.pegasus.planner.namespace.Hints
  The overloaded constructor.
Horizontal - Class in edu.isi.pegasus.planner.cluster
  The horizontal clusterer, that clusters jobs on the same level.
Horizontal() - Constructor for class edu.isi.pegasus.planner.cluster.Horizontal
  The default constructor.
Horizontal - Class in edu.isi.pegasus.planner.partitioner
  Horizontal based partitioning scheme, that allows the user to configure the number of partitions per transformation name per level.
Horizontal(GraphNode, Map, PegasusProperties) - Constructor for class edu.isi.pegasus.planner.partitioner.Horizontal
  The overloaded constructor.
Horizontal.GraphNodeComparator - Class in edu.isi.pegasus.planner.partitioner
  A GraphNode comparator, that allows us to compare nodes according to the transformation logical names.
Horizontal.JobComparator - Class in edu.isi.pegasus.planner.cluster
  A job comparator, that allows me to compare jobs according to the transformation names.
HORIZONTAL_CLUSTERING_CLASS - Static variable in class edu.isi.pegasus.planner.cluster.ClustererFactory
  The name of the class implementing horizontal clustering.
HORIZONTAL_PARTITIONING_CLASS - Static variable in class edu.isi.pegasus.planner.partitioner.PartitionerFactory
  The name of the class that does horizontal based partitioning.
host - Variable in class edu.isi.pegasus.gridftp.GridFTPConnection
Host_Subnet_Id - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
HostPort(String, int) - Constructor for class edu.isi.pegasus.planner.refiner.Authenticate.HostPort
  The overloaded constructor
HourGlass - Class in edu.isi.pegasus.planner.refiner.createdir
  This class inserts the nodes for creating the random directories on the remote execution pools.
HourGlass() - Constructor for class edu.isi.pegasus.planner.refiner.createdir.HourGlass

## I

id - Variable in class edu.isi.pegasus.planner.provisioner.Node
idCounter() - Method in class edu.isi.pegasus.planner.partitioner.Horizontal
  Returns the current value of the ID counter.
Identifier - Class in edu.isi.pegasus.planner.parser.tokens
  Class to capture reserved words.
Identifier(String) - Constructor for class edu.isi.pegasus.planner.parser.tokens.Identifier
  Initializes an instance of an identifier.
IDLE_NODES - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The constant to be passed to the accessor functions to get or set the idle nodes.
ignorableWhitespace(char[], int, int) - Method in class edu.isi.pegasus.planner.client.DAXValidator
ignorableWhitespace(char[], int, int) - Method in class edu.isi.pegasus.planner.parser.InvocationParser
  Currently, ignorable whitespace will be ignored.
Ignore - Class in edu.isi.pegasus.planner.invocation
  This class is transient for XML parsing.
Ignore() - Constructor for class edu.isi.pegasus.planner.invocation.Ignore
  Default c'tor.
Ignore(String) - Constructor for class edu.isi.pegasus.planner.invocation.Ignore
  Constructs a piece of data.
ignore(String) - Method in class edu.isi.pegasus.planner.namespace.Dagman
  Helper method to decide whether a key has to be ignored or not.
ignore(String, String) - Method in class edu.isi.pegasus.planner.selector.replica.Restricted
  Returns a boolean indicating whether a source site is to be ignored for staging to a destination site
ignoreWhitespace(String) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Our own implementation for ignorable whitespace.
ignoreWhitespace(String) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser3.Arguments
  Our own implementation for ignorable whitespace.
ignoreWhitespace(String, boolean) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser3.Arguments
  Our own implementation for ignorable whitespace.
ignoreWhitespace(String) - Method in class edu.isi.pegasus.planner.parser.Parser
  Our own implementation for ignorable whitespace.
ignoreWhitespace(String, boolean) - Method in class edu.isi.pegasus.planner.parser.Parser
  Our own implementation for ignorable whitespace.
Implementation - Interface in edu.isi.pegasus.planner.refiner.createdir
  The interface that defines how the create dir job is created.
Implementation - Interface in edu.isi.pegasus.planner.transfer
  The interface defines the functions that a particular Transfer Implementation should implement.
ImplementationFactory - Class in edu.isi.pegasus.planner.transfer.implementation
  The factory class that loads an appropriate Transfer Immplementation class, as specified by the properties.
ImplementationFactory() - Constructor for class edu.isi.pegasus.planner.transfer.implementation.ImplementationFactory
implementingClassNameTable() - Static method in class edu.isi.pegasus.common.credential.CredentialHandlerFactory
  Returns a table that maps, the credential types to the implementing classes.
implementingClassNameTable() - Static method in class edu.isi.pegasus.planner.cluster.aggregator.JobAggregatorInstanceFactory
  Returns a table that maps, the Pegasus style keys to the names of implementing classes.
implementingClassNameTable() - Static method in class edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactory
  Returns a table that maps, the Pegasus style keys to the names of implementing classes.
implementingPOSTScriptClass(String) - Static method in class edu.isi.pegasus.planner.code.GridStartFactory
  Returns the name of the implementing POSTSCript class.
incorporateHint(Job, String) - Method in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  It incorporates a hint in the namespace to the job.
incorporateProfiles(Job) - Method in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  Incorporates the profiles from the various sources into the job.
increment(Job) - Method in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  Increment the metrics when on the basis of type of job.
increment() - Method in class edu.isi.pegasus.planner.refiner.ThreadPool.ConditionVariable
  It increments the value by 1.
increment() - Method in class edu.isi.pegasus.planner.selector.site.RoundRobin.NameValue
  Increments the int value by one.
incrementIDCounter() - Method in class edu.isi.pegasus.planner.partitioner.Horizontal
  Increments the ID counter by 1.
incrementIndentIndex() - Method in class edu.isi.pegasus.planner.catalog.site.classes.AbstractXMLPrintVisitor
  Increments the indent index
incrementJobMetrics(Job) - Method in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  Increment the metrics when on the basis of type of job.
incrementLogging() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Increments the logging level by 1.
incrementLogging() - Method in class edu.isi.pegasus.planner.client.SCClient
  Increments the logging level by 1.
incrementLogging() - Method in class edu.isi.pegasus.planner.client.TCConverter
  Increments the logging level by 1.
incrementTaskMetrics(Job) - Method in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  Increment the metrics when on the basis of type of job.
INDENT - Static variable in class edu.isi.pegasus.common.util.XMLWriter
indent(int) - Method in class edu.isi.pegasus.common.util.XMLWriter
index(String) - Method in class edu.isi.pegasus.planner.partitioner.graph.TopologicalSortIterator
  Returns the index of a particular node.
index(String) - Method in class edu.isi.pegasus.planner.partitioner.Topological
  Returns the index of a particular node.
inEdges - Variable in class edu.isi.pegasus.planner.provisioner.Node
INFO_MESSAGE_LEVEL - Static variable in class edu.isi.pegasus.common.logging.LogManager
  The level value, to indicate a INFO message.
INFO_MESSAGE_TYPE - Static variable in class edu.isi.pegasus.common.logging.logger.Default
  The type value to indicate an INFORMATIVE message.
infoAboutAllFilesRecv - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  A boolean variable set to true when we have got all the logical filenames.
init() - Static method in class edu.isi.ikcap.workflows.util.logging.EventLogMessage.Log4jFilter
init() - Method in class edu.isi.pegasus.planner.provisioner.Edge
  initiate bit and completion time variable used bt HEFT algorithm
init() - Method in class edu.isi.pegasus.planner.provisioner.Node
initalize(String[]) - Method in class edu.isi.pegasus.planner.client.PartitionDAX
  Initialize the PartitionDax object
initialiseList(List) - Method in class edu.isi.pegasus.planner.selector.site.RoundRobin
  It initialises the internal list.
initialize(PegasusBag) - Method in interface edu.isi.pegasus.common.credential.CredentialHandler
  Initializes the credential implementation.
initialize(PegasusBag) - Method in class edu.isi.pegasus.common.credential.CredentialHandlerFactory
  Initializes the Factory.
initialize(PegasusBag) - Method in class edu.isi.pegasus.common.credential.impl.Abstract
  Initializes the credential implementation.
initialize(PegasusBag) - Method in class edu.isi.pegasus.common.credential.impl.Irods
  Initializes the credential implementation.
initialize(PegasusBag) - Method in class edu.isi.pegasus.common.credential.impl.Proxy
  Initializes the credential implementation.
initialize(PegasusBag) - Method in class edu.isi.pegasus.common.credential.impl.S3CFG
  Initializes the credential implementation.
initialize(PegasusBag) - Method in class edu.isi.pegasus.common.credential.impl.Ssh
  Initializes the credential implementation.
initialize(LogFormatter, Properties) - Method in class edu.isi.pegasus.common.logging.logger.Default
  Sets the log formatter to use for formatting the messages.
initialize(LogFormatter, Properties) - Method in class edu.isi.pegasus.common.logging.logger.Log4j
  Sets the log formatter to use for formatting the messages.
initialize(LogFormatter, Properties) - Method in class edu.isi.pegasus.common.logging.LogManager
  Sets the log formatter to use for formatting the messages.
initialize(Writer) - Method in class edu.isi.pegasus.planner.catalog.site.classes.AbstractXMLPrintVisitor
  Initialize the visitor implementation
initialize(String, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.Connection
  Initializes the object.
initialize() - Method in class edu.isi.pegasus.planner.catalog.site.classes.DirectoryLayout
  Initializes the object
initialize(Map<FileServerType.OPERATION, List<FileServer>>, InternalMountPoint) - Method in class edu.isi.pegasus.planner.catalog.site.classes.DirectoryLayout
  Initializes the object
initialize(String, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.ReplicaCatalog
  Initialize the class.
initialize(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Initializes the object.
initialize(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Initializes the object.
initialize(Writer) - Method in interface edu.isi.pegasus.planner.catalog.site.classes.SiteDataVisitor
  Initialize the visitor implementation
initialize() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  The intialize method.
initialize() - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.TransformationStore
  Intializes the store.
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Initialize the implementation, and return an instance of the implementation.
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Initialize the implementation, and return an instance of the implementation.
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Initialize the implementation, and return an instance of the implementation.
initialize(PegasusBag) - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Initialize the implementation, and return an instance of the implementation.
initialize(PegasusBag, ADag) - Method in class edu.isi.pegasus.planner.classes.PlannerCache
  Initialize the replica catalog instances that make up the cache.
initialize(String[], char) - Method in class edu.isi.pegasus.planner.client.CPlanner
initialize(String[], char) - Method in class edu.isi.pegasus.planner.client.Executable
  Initialize the executable object
initialize(String[]) - Method in class edu.isi.pegasus.planner.client.Executable
  Initialize the executable object
initialize(String[]) - Method in class edu.isi.pegasus.planner.client.RankDAX
initialize(String[], char) - Method in class edu.isi.pegasus.planner.client.RCClient
  Initialize the RCClient object
initialize(String[]) - Method in class edu.isi.pegasus.planner.client.SCClient
initialize(String[]) - Method in class edu.isi.pegasus.planner.client.TCClient
initialize(String[]) - Method in class edu.isi.pegasus.planner.client.TCConverter
initialize(String[]) - Method in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
initialize(ADag, PegasusBag) - Method in class edu.isi.pegasus.planner.cluster.Abstract
  Initializes the Clusterer impelementation
initialize(ADag, PegasusBag) - Method in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  Initializes the JobAggregator impelementation
initialize(ADag, PegasusBag) - Method in class edu.isi.pegasus.planner.cluster.aggregator.JobAggregatorInstanceFactory
  Initializes the Factory.
initialize(ADag, PegasusBag) - Method in class edu.isi.pegasus.planner.cluster.aggregator.MPIExec
  Initializes the JobAggregator impelementation
initialize(ADag, PegasusBag) - Method in class edu.isi.pegasus.planner.cluster.aggregator.SeqExec
  Initializes the JobAggregator impelementation
initialize(ADag, PegasusBag) - Method in interface edu.isi.pegasus.planner.cluster.Clusterer
  Initializes the Clusterer impelementation
initialize(ADag, PegasusBag) - Method in class edu.isi.pegasus.planner.cluster.Horizontal
  Initializes the Clusterer impelementation
initialize(ADag, PegasusBag) - Method in interface edu.isi.pegasus.planner.cluster.JobAggregator
  Initializes the JobAggregator impelementation
initialize(PegasusBag) - Method in interface edu.isi.pegasus.planner.code.CodeGenerator
  Initializes the Code Generator implementation.
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.code.generator.Abstract
  Initializes the Code Generator implementation.
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.code.generator.Braindump
  Initializes the Code Generator implementation.
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Initializes the Code Generator implementation.
initialize(PegasusBag, CredentialHandlerFactory) - Method in interface edu.isi.pegasus.planner.code.generator.condor.CondorStyle
  Initializes the Code Style implementation.
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactory
  Initializes the Factory.
initialize(PegasusBag, CredentialHandlerFactory) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.Abstract
  Initializes the Code Style implementation.
initialize(PegasusBag, CredentialHandlerFactory) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.Condor
  Initializes the Code Style implementation.
initialize(PegasusBag, ADag, PrintWriter) - Method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Initializes the class.
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.code.generator.DAXReplicaStore
  Initializes the Code Generator implementation.
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.code.generator.Metrics
  Initializes the object
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.code.generator.MonitordNotify
  Initializes the Code Generator implementation.
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.code.generator.PBS
  Initializes the Code Generator implementation.
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.code.generator.PMC
  Initializes the Code Generator implementation.
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.code.generator.Shell
  Initializes the Code Generator implementation.
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.code.generator.Stampede
  Initializes the Code Generator implementation.
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.code.generator.Stork
  Initializes the Code Generator implementation.
initialize(PegasusBag, ADag) - Method in interface edu.isi.pegasus.planner.code.GridStart
  Initializes the GridStart implementation.
initialize(PegasusBag, ADag) - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Initializes the GridStart implementation.
initialize(PegasusProperties, String, String) - Method in class edu.isi.pegasus.planner.code.gridstart.NetloggerPostScript
  Initialize the POSTScript implementation.
initialize(PegasusBag, ADag) - Method in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  Initializes the GridStart implementation.
initialize(PegasusProperties, String, String) - Method in class edu.isi.pegasus.planner.code.gridstart.NoPOSTScript
  Initialize the POSTScript implementation.
initialize(PegasusProperties, String, String) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusExitCode
  Initialize the POSTScript implementation.
initialize(PegasusBag, ADag) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Initializes the GridStart implementation.
initialize(PegasusProperties, String, String) - Method in class edu.isi.pegasus.planner.code.gridstart.UserPOSTScript
  Initialize the POSTScript implementation.
initialize(PegasusBag, ADag) - Method in class edu.isi.pegasus.planner.code.GridStartFactory
  Initializes the factory with known GridStart implementations.
initialize(PegasusProperties, String, String) - Method in interface edu.isi.pegasus.planner.code.POSTScript
  Initialize the POSTScript implementation.
initialize(PegasusBag, String) - Method in interface edu.isi.pegasus.planner.parser.dax.Callback
  The overloaded constructor.
initialize(PegasusBag, String) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2CDAG
  The overloaded constructor.
initialize(PegasusBag, String) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2Graph
  The overloaded constructor.
initialize(PegasusBag, String) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2LabelGraph
  The overloaded constructor.
initialize(PegasusBag, String) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2Metadata
  The overloaded constructor.
initialize(PegasusBag, String) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2NewGraph
  The overloaded constructor.
initialize(PegasusBag, String) - Method in class edu.isi.pegasus.planner.parser.dax.ExampleDAXCallback
  The overloaded constructor.
initialize(PegasusProperties, Clusterer) - Method in class edu.isi.pegasus.planner.partitioner.ClustererCallback
  Initializes the callback.
initialize() - Method in class edu.isi.pegasus.planner.partitioner.graph.TopologicalSortIterator
  Initializes the inDegree for each node of the partition.
initialize() - Method in class edu.isi.pegasus.planner.partitioner.Topological
  Initializes the inDegree for each node of the partition.
initialize(PegasusProperties, String, String, String) - Method in class edu.isi.pegasus.planner.partitioner.WriterCallback
  Initializes the Writer Callback.
initialize(PegasusBag, List, String) - Method in class edu.isi.pegasus.planner.ranking.Rank
  Initializes the rank client.
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.refiner.cleanup.Cleanup
  Creates a new instance of InPlace
initialize(PegasusBag) - Method in interface edu.isi.pegasus.planner.refiner.cleanup.CleanupImplementation
  Intializes the class.
initialize(PegasusBag, CleanupImplementation) - Method in interface edu.isi.pegasus.planner.refiner.cleanup.CleanupStrategy
  Intializes the class.
initialize(PegasusBag, CleanupImplementation) - Method in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  Intializes the class.
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.refiner.cleanup.RM
  Intializes the class.
initialize(PegasusBag, Implementation) - Method in class edu.isi.pegasus.planner.refiner.createdir.AbstractStrategy
  Intializes the class.
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.refiner.createdir.DefaultImplementation
  Intializes the class.
initialize(PegasusBag, Implementation) - Method in class edu.isi.pegasus.planner.refiner.createdir.HourGlass
  Intializes the class.
initialize(PegasusBag) - Method in interface edu.isi.pegasus.planner.refiner.createdir.Implementation
  Intializes the class.
initialize(PegasusBag, Implementation) - Method in class edu.isi.pegasus.planner.refiner.createdir.Minimal
  Intializes the class.
initialize(PegasusBag, Implementation) - Method in interface edu.isi.pegasus.planner.refiner.createdir.Strategy
  Intializes the class.
initialize(PegasusBag, Implementation) - Method in class edu.isi.pegasus.planner.refiner.createdir.Tentacles
  Intializes the class.
initialize(ADag) - Method in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Initialize with the scheduled graph.
initialize(ADag, PegasusBag) - Method in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  Intialises the refiner.
initialize(ADag, PegasusProperties, PlannerOptions) - Method in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  Intialises the refiner.
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.selector.site.Abstract
  Initializes the site selector.
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.selector.site.Group
  Initializes the site selector.
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.selector.site.Heft
  Initializes the site selector.
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  Initializes the site selector.
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.selector.site.Random
  Initializes the site selector.
initialize(PegasusBag) - Method in interface edu.isi.pegasus.planner.selector.SiteSelector
  Initializes the site selector.
initialize(PegasusBag, ADag) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.AbstractFileFactoryBasedMapper
  Initializes the mappers.
initialize(PegasusBag, ADag) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Fixed
  Initializes the mappers.
initialize(PegasusBag, ADag) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Flat
  Initializes the mappers.
initialize(PegasusBag, ADag) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Hashed
  Initializes the mappers.
initialize(PegasusBag, ADag) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Replica
  Initializes the mappers.
initialize(PegasusBag, ADag) - Method in interface edu.isi.pegasus.planner.transfer.mapper.OutputMapper
  Initializes the mappers.
initialize(String, String, String) - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.BundleValue
  Initializes the implementation
initialize(String, String, String) - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle.BundleValue
  Initializes the implementation
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.transfer.sls.Condor
  Initializes the SLS implementation.
initialize(PegasusBag) - Method in interface edu.isi.pegasus.planner.transfer.SLS
  Initializes the SLS implementation.
initialize(PegasusBag) - Method in class edu.isi.pegasus.planner.transfer.sls.Transfer
  Initializes the SLS implementation.
initializeBundleValues() - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  Initializes the bundle value variables, that are responsible determining the bundle values.
initializeBundleValues() - Method in class edu.isi.pegasus.planner.transfer.refiner.Cluster
  Initializes the bundle value variables, that are responsible determining the bundle values.
initializeClusterValues() - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  Initializes the bundle value variables, that are responsible determining the bundle values.
initializeDagFileWriter(String, ADag) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Initializes the file handler to the dag file and writes the header to it.
initializeDatabase(String, String) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.CreateTCDatabase
  Initialize the database with given .sql file
initializePropertyFile(String) - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Gets the handle to the properties file.
initializeWorkflowCacheFile(ADag) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  Initializes a Replica Catalog Instance that is used to store the GET URL's for all files on the staging site ( inputs staged and outputs created ).
initializeWriteHandle(String) - Method in class edu.isi.pegasus.planner.code.generator.Shell
  It initializes the write handle to the output file.
initializeWriteHandle(int) - Method in class edu.isi.pegasus.planner.partitioner.DAXWriter
  This initializes the write handle a file in directory specified when creating the instance of this class.
initializeWriteHandle(String) - Method in class edu.isi.pegasus.planner.partitioner.DAXWriter
  This initializes the write handle to the file in directory specified when creating the instance of this class.
initOut(boolean, long) - Method in class edu.isi.pegasus.planner.provisioner.Node
  notify child nodes that this task will finish at time et
InMemory - Class in edu.isi.pegasus.planner.provenance.pasoa.producer
  An implementation of the XMLProducer interface backed by a StringBuffer.
InMemory() - Constructor for class edu.isi.pegasus.planner.provenance.pasoa.producer.InMemory
  The default constructor.
InMemory(int) - Constructor for class edu.isi.pegasus.planner.provenance.pasoa.producer.InMemory
  The overloaded constructor.
InPlace - Class in edu.isi.pegasus.planner.refiner.cleanup
  This generates cleanup jobs in the workflow itself.
InPlace() - Constructor for class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  The default constructor.
inputFiles - Variable in class edu.isi.pegasus.planner.classes.Job
  Contains the input files for the submit file.
insert(String, ReplicaCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Inserts a new mapping into the replica catalog.
insert(String, String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Inserts a new mapping into the replica catalog.
insert(Map) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Inserts multiple mappings into the replica catalog.
insert(String, ReplicaCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
  Inserts a new mapping into the replica catalog.
insert(String, String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
  Inserts a new mapping into the replica catalog.
insert(Map) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
  Inserts multiple mappings into the replica catalog.
insert(String, ReplicaCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Inserts a new mapping into the replica catalog.
insert(String, String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Inserts a new mapping into the replica catalog.
insert(Map) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Inserts multiple mappings into the replica catalog.
insert(String, String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Inserts a new mapping into the replica catalog.
insert(String, ReplicaCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Inserts a new mapping into the replica catalog.
insert(Map) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Inserts multiple mappings into the replica catalog.
insert(String, ReplicaCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Inserts a new mapping into the replica catalog.
insert(String, String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Inserts a new mapping into the replica catalog.
insert(Map) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Inserts multiple mappings into the replica catalog.
insert(String, ReplicaCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Inserts a new mapping into the replica catalog.
insert(String, String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Inserts a new mapping into the replica catalog.
insert(Map) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Inserts multiple mappings into the replica catalog.
insert(String, ReplicaCatalogEntry) - Method in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Inserts a new mapping into the replica catalog.
insert(String, String, String) - Method in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Inserts a new mapping into the replica catalog.
insert(Map) - Method in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Inserts multiple mappings into the replica catalog.
insert(SiteCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
insert(SiteCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML
  Not implemented as yet.
insert(SiteCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  Not implemented as yet.
insert(SiteCatalogEntry) - Method in interface edu.isi.pegasus.planner.catalog.SiteCatalog
  Inserts a new mapping into the Site catalog.
insert(List<TransformationCatalogEntry>) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Add multiple TCEntries to the Catalog.
insert(TransformationCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Add single TCEntry to the Catalog.
insert(TransformationCatalogEntry, boolean) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Add single TCEntry object temporarily to the in memory Catalog.
insert(String, String, String, String, TCType, String, List, List, SysInfo) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Add an single entry into the transformation catalog.
insert(List<TransformationCatalogEntry>) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Add multiple TCEntries to the Catalog.
insert(TransformationCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Add single TCEntry to the Catalog.
insert(TransformationCatalogEntry, boolean) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Add single TCEntry object temporarily to the in memory Catalog.
insert(String, String, String, String, TCType, String, List, List, SysInfo) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Add an single entry into the transformation catalog.
insert(List<TransformationCatalogEntry>) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Add multiple TCEntries to the Catalog.
insert(TransformationCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Add single TCEntry to the Catalog.
insert(TransformationCatalogEntry, boolean) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Add single TCEntry object temporarily to the in memory Catalog.
insert(String, String, String, String, TCType, String, List, List, SysInfo) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Add an single entry into the transformation catalog.
insert(List<TransformationCatalogEntry>) - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Add multiple TCEntries to the Catalog.
insert(TransformationCatalogEntry) - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Add single TCEntry to the Catalog.
insert(TransformationCatalogEntry, boolean) - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Add single TCEntry object temporarily to the in memory Catalog.
insert(String, String, String, String, TCType, String, List, List, SysInfo) - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Add an single entry into the transformation catalog.
insert(String, String, String, String, String, Date, Date, int) - Method in class edu.isi.pegasus.planner.catalog.work.Database
  Inserts a new mapping into the work catalog.
insert(String, String, String, String, String, Date, Date, int) - Method in interface edu.isi.pegasus.planner.catalog.WorkCatalog
  Inserts a new mapping into the work catalog.
insert(String, String, String, FileServerType.OPERATION) - Method in class edu.isi.pegasus.planner.classes.PlannerCache
  Inserts a new entry into the cache.
insert(Job) - Method in class edu.isi.pegasus.planner.selector.site.Group
  Inserts the job into the group map.
Installed - Class in edu.isi.pegasus.planner.catalog.transformation.mapper
  This class only generates maps for sites with installed transformations.
Installed(PegasusBag) - Constructor for class edu.isi.pegasus.planner.catalog.transformation.mapper.Installed
  The protected constructor.
Installed - Class in edu.isi.pegasus.planner.selector.transformation
  This implementation of the Selector returns a list of TransformationCatalogEntry objects of type INSTALLED y on the submit site.
Installed() - Constructor for class edu.isi.pegasus.planner.selector.transformation.Installed
instance() - Static method in class edu.isi.pegasus.common.util.CommonProperties
  Singleton threading: Creates the one and only instance of the properties in the current application.
instance() - Static method in class edu.isi.pegasus.common.util.Version
  Deprecated.
  Just create a new instance
instantiate(Object[]) - Method in class edu.isi.pegasus.common.util.DynamicLoader
  Dynamically instantiates a class from a contructor.
instantiate(Class[], Object[]) - Method in class edu.isi.pegasus.common.util.DynamicLoader
  Dynamically instantiates a class from a contructor.
instantiateFileFactory(PegasusBag, ADag) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.AbstractFileFactoryBasedMapper
  Method that instantiates the FileFactory
instantiateFileFactory(PegasusBag, ADag) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Flat
  Instantiates a Flat File Factory and returns it.
instantiateFileFactory(PegasusBag, ADag) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Hashed
  Method that instantiates the FileFactory
INTEL32 - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Arch
INTEL64 - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Arch
INTER_POOL_JOB - Static variable in class edu.isi.pegasus.planner.classes.Job
  Denotes a job that transfers the output of a compute node to the site where the child compute node is to be generated.
INTER_POOL_PREFIX - Static variable in interface edu.isi.pegasus.planner.transfer.Refiner
  The prefix for the jobs which are added to transfer the files generated by the parents of a job to the jobs execution pool.
INTER_REMOTE_TYPE - Static variable in class edu.isi.pegasus.planner.transfer.RemoteTransfer.TransferState
  The constant to denote that an inter site transfer is to be exectuted remotely
INTER_TPT_PROPERTY - Static variable in class edu.isi.pegasus.planner.transfer.TPT
  The property name to get the sites for which inter site transfers need to be TPT.
INTER_TPT_REMOTE - Static variable in class edu.isi.pegasus.planner.transfer.TPT.TPTState
  The constant to denote that an inter site transfer is to be executed on the remote site.
INTER_TPT_REMOTE_PROPERTY - Static variable in class edu.isi.pegasus.planner.transfer.TPT
  The property name to get the sites for which inter site TPT transfers need to be executed on the remote site.
INTER_TPT_TYPE - Static variable in class edu.isi.pegasus.planner.transfer.TPT.TPTState
  The constant to denote that an inter site transfer is to be third party.
INTER_TRANSFERS_REMOTE_PROPERTY - Static variable in class edu.isi.pegasus.planner.transfer.RemoteTransfer
  The property name to get the sites for which inter site transfers need to be executed remotely.
InternalMountPoint - Class in edu.isi.pegasus.planner.catalog.site.classes
  A data class to signify the Internal Mount Point for a filesystem.
InternalMountPoint() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.InternalMountPoint
  The default constructor.
InternalMountPoint(String) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.InternalMountPoint
  The overloaded constructor.
InternalMountPoint(String, String, String) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.InternalMountPoint
  The overloaded constructor.
interOnRemoteSite(String) - Method in class edu.isi.pegasus.planner.transfer.RemoteTransfer
  Returns a boolean indicating whether to execute inter site transfers on remote site or not.
InterPoolEngine - Class in edu.isi.pegasus.planner.refiner
  This engine calls out to the Site Selector selected by the user and maps the jobs in the workflow to the execution pools.
InterPoolEngine(PegasusBag) - Constructor for class edu.isi.pegasus.planner.refiner.InterPoolEngine
  Default constructor.
InterPoolEngine(ADag, PegasusBag) - Constructor for class edu.isi.pegasus.planner.refiner.InterPoolEngine
  Overloaded constructor.
interThirdParty(String) - Method in class edu.isi.pegasus.planner.transfer.TPT
  Returns a boolean indicating whether to use third party transfers for inter site transfers or not.
interThirdPartyRemote(String) - Method in class edu.isi.pegasus.planner.transfer.TPT
  Returns a boolean indicating whether to execute third party transfers for inter site on remote site or not.
intialize(String[]) - Method in class edu.isi.pegasus.planner.client.PegasusGetSites
  Initialize the PegasusGetSites object
intializeRCAsCache(ADag, FileServerType.OPERATION) - Method in class edu.isi.pegasus.planner.classes.PlannerCache
  Initializes the transient replica catalog and returns a handle to it.
introduceRootDependencies(ADag, Job) - Method in class edu.isi.pegasus.planner.refiner.createdir.HourGlass
  It traverses through the root jobs of the dag and introduces a new super root node to it.
intValue(String) - Static method in class edu.isi.pegasus.common.util.CondorVersion
  Deprecated.
invalidAttribute(String, String, String) - Method in class edu.isi.pegasus.planner.parser.PDAXParser
  Logs a message if an unknown key is come across, while parsing the xml document.
invalidValue(String, String, String) - Method in class edu.isi.pegasus.planner.parser.PDAXParser
  Logs a message if an unknown value is come across, while parsing the xml document.
INVOCATION - Static variable in class edu.isi.pegasus.planner.code.generator.MonitordNotify
  The constant string to write for invocation notifications.
Invocation - Class in edu.isi.pegasus.planner.invocation
  This abstract class defines a common base for all invocation record related Java objects.
Invocation() - Constructor for class edu.isi.pegasus.planner.invocation.Invocation
InvocationParser - Class in edu.isi.pegasus.planner.parser
  This class uses the Xerces SAX2 parser to validate and parse an XML document which contains information from kickstart generated invocation record.
InvocationParser(String) - Constructor for class edu.isi.pegasus.planner.parser.InvocationParser
  The class constructor.
InvocationRecord - Class in edu.isi.pegasus.planner.invocation
  This class is the container for an invocation record.
InvocationRecord() - Constructor for class edu.isi.pegasus.planner.invocation.InvocationRecord
  Default c'tor: Construct a hollow shell and allow further information to be added later.
invocationString(Job, File) - Method in class edu.isi.pegasus.planner.transfer.sls.Condor
  Constructs a command line invocation for a job, with a given sls file.
invocationString(Job, File) - Method in interface edu.isi.pegasus.planner.transfer.SLS
  Constructs a command line invocation for a job, with a given sls file.
invocationString(Job, File) - Method in class edu.isi.pegasus.planner.transfer.sls.Transfer
  Constructs a command line invocation for a job, with a given sls file.
Invoke - Class in edu.isi.pegasus.planner.dax
  The Notification invoke object for the Dax API
Invoke(Invoke) - Constructor for class edu.isi.pegasus.planner.dax.Invoke
  Copy Constructor
Invoke(Invoke.WHEN) - Constructor for class edu.isi.pegasus.planner.dax.Invoke
  Crete a new Invoke object
Invoke(Invoke.WHEN, String) - Constructor for class edu.isi.pegasus.planner.dax.Invoke
  Create a new Invoke object
Invoke.WHEN - Enum in edu.isi.pegasus.planner.dax
  WHEN To INVOKE
Irods - Class in edu.isi.pegasus.common.credential.impl
  A convenience class that allows us to determine the path to the user irodsEnvFile file.
Irods() - Constructor for class edu.isi.pegasus.common.credential.impl.Irods
  The default constructor.
IRODS_IMPLEMENTING_CLASS - Static variable in class edu.isi.pegasus.common.credential.CredentialHandlerFactory
IRODSENVFILE - Static variable in class edu.isi.pegasus.common.credential.impl.Irods
  The name of the environment variable that specifies the path to the irods configuration file.
IRODSENVFILE - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
IRODSENVFILE_PEGASUS_PROFILE_KEY - Static variable in class edu.isi.pegasus.common.credential.impl.Irods
isAnc(Node) - Method in class edu.isi.pegasus.planner.provisioner.Node
isAsciiPrintable(char) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusExitCodeEncode
  Checks whether the character is ASCII 7 bit printable.
isAvailable() - Method in class edu.isi.pegasus.planner.refiner.ThreadPool.AuthenticateThread
  Returns whether a thread is available to do some work or not.
isBottom() - Method in class edu.isi.pegasus.planner.provisioner.Node
  Check whether this task is the exit task or not.
isClosed() - Method in interface edu.isi.pegasus.planner.catalog.Catalog
  Predicate to check, if the connection with the catalog's implementation is still active.
isClosed() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Predicate to check, if the connection with the catalog's implementation is still active.
isClosed() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
  Predicate to check, if the connection with the catalog's implementation is still active.
isClosed() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Predicate to check, if the connection with the catalog's implementation is still active.
isClosed() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Predicate to check, if the connection with the catalog's implementation is still active.
isClosed() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Predicate to check, if the connection with the catalog's implementation is still active.
isClosed() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Predicate to check, if the connection with the catalog's implementation is still active.
isClosed() - Method in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  Returns if the connection is closed or not.
isClosed() - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML
  Returns if the connection is closed or not.
isClosed() - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  Returns if the connection is closed or not.
isClosed() - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
isClosed() - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
isClosed() - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Returns whether the connection is closed or not.
isClosed() - Method in class edu.isi.pegasus.planner.catalog.work.Database
  Predicate to check, if the connection with the catalog's implementation is still active.
isClosed() - Method in class edu.isi.pegasus.planner.ranking.GetDAX
  Predicate to check, if the connection with the catalog's implementation is still active.
isColor(int) - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  Returns if the color of the node is as specified.
isDAG() - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Is this Object a DAG
isDAG() - Method in class edu.isi.pegasus.planner.dax.DAG
  Is this Object a DAG
isDAX() - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Is this Object a DAX
isDAX() - Method in class edu.isi.pegasus.planner.dax.DAX
  Is this Object a DAX
isDeleted - Variable in class edu.isi.pegasus.planner.classes.PCRelation
  this is used for collapsing the dag during the reduction algorithm on the basis of the results returned from the Replica Catalog.
isDes(Node) - Method in class edu.isi.pegasus.planner.provisioner.Node
isDirectory() - Method in class edu.isi.pegasus.gridftp.FileInfo
isEmpty() - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Returns a boolean indicating if the object is empty.
isEmpty() - Method in class edu.isi.pegasus.planner.catalog.site.classes.DirectoryLayout
  A convenience method that returns true if all the attributes values are uninitialized or empty strings.
isEmpty() - Method in class edu.isi.pegasus.planner.catalog.site.classes.InternalMountPoint
  A convenience method that returns true if all the attributes values are uninitialized or empty strings.
isEmpty() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns a boolean if there are no nodes in the graph.
isEmpty() - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Returns a boolean if there are no nodes in the graph.
isEmpty() - Method in class edu.isi.pegasus.planner.classes.Notifications
  Returns a boolean indicating whether the notifications object is empty or not.
isEmpty() - Method in class edu.isi.pegasus.planner.classes.ReplicaStore
  Returns a boolean indicating whether a store is empty or not.
isEmpty() - Method in class edu.isi.pegasus.planner.namespace.Namespace
  Returns a boolean indicating if the object is empty.
isEmpty() - Method in interface edu.isi.pegasus.planner.partitioner.graph.Graph
  Returns a boolean if there are no nodes in the graph.
isEmpty() - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph
  Returns a boolean if there are no nodes in the graph.
isExecutable() - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Returns a boolean indicating if a file that is being staged is an executable or not (i.e is a data file).
isExecutable() - Method in class edu.isi.pegasus.planner.dax.CatalogType
isExecutable() - Method in class edu.isi.pegasus.planner.dax.Executable
isFile() - Method in class edu.isi.pegasus.planner.dax.CatalogType
isFile() - Method in class edu.isi.pegasus.planner.dax.File
isFree() - Method in class edu.isi.pegasus.planner.provisioner.Node
  used for DSC algorithm
isFSWritten - Variable in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
  Ensure that Directory information is written only once.
isIdenticalTo(String, String) - Method in class edu.isi.pegasus.planner.provenance.pasoa.pps.Empty
  isIdenticalTo
isIdenticalTo(String, String) - Method in interface edu.isi.pegasus.planner.provenance.pasoa.PPS
isInteger(String) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Returns a boolean indicating whether the value represented is an integer or not.
isInteger(String) - Method in class edu.isi.pegasus.planner.namespace.Condor
  Returns a boolean value indicating if the string passed is an integer or not
isJob() - Method in class edu.isi.pegasus.planner.dax.AbstractJob
  Is this Object a Job
isJob() - Method in class edu.isi.pegasus.planner.dax.Job
  Is this Object a Job
islfn - Variable in class edu.isi.pegasus.planner.client.TCClient
isMPIJob() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns a boolean value denoting whether the job is MPI or not.
isNamespaceValid(String) - Static method in class edu.isi.pegasus.planner.namespace.Namespace
  Checks if the namespace specified is valid or not.
isNodeIdValid(String) - Static method in class edu.isi.pegasus.planner.dax.Patterns
iso8601(boolean) - Static method in class edu.isi.pegasus.common.util.Currently
  Ignores any internal date format, and tries to show a complete date/timp stamp of the current time in extended ISO 8601 format.
iso8601(boolean, boolean, boolean, Date) - Static method in class edu.isi.pegasus.common.util.Currently
  Ignores any internal date format, and tries to show a complete date/timp stamp in extended ISO 8601 format.
isoldformat - Variable in class edu.isi.pegasus.planner.catalog.transformation.client.Client
isoldformat - Variable in class edu.isi.pegasus.planner.client.TCClient
isPartitionOf(String, List) - Method in class edu.isi.pegasus.planner.provenance.pasoa.pps.Empty
  isPartitionOf
isPartitionOf(String, List) - Method in interface edu.isi.pegasus.planner.provenance.pasoa.PPS
ispfn - Variable in class edu.isi.pegasus.planner.client.TCClient
isprofile - Variable in class edu.isi.pegasus.planner.client.TCClient
isRegex(ReplicaCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Checks if the 'regex' attribute is set to true for the given tuple
isresource - Variable in class edu.isi.pegasus.planner.client.TCClient
isSiteThirdParty(String, int) - Method in class edu.isi.pegasus.planner.transfer.AbstractRefiner
  Returns whether a Site is third party enabled or not.
isSiteThirdParty(String, int) - Method in interface edu.isi.pegasus.planner.transfer.Refiner
  Returns whether a Site is third party enabled or not.
isSiteValid(String, String, String, String) - Method in class edu.isi.pegasus.planner.catalog.transformation.Mapper
  Checks if a give site is valid for a given transformation.
isStageableMapper() - Method in class edu.isi.pegasus.planner.catalog.transformation.Mapper
  Returns whether this instance of mapper is an instance of a Stageable mapper or not.
isSupportedFormat(String) - Method in class edu.isi.pegasus.planner.client.TCConverter
  Checks if it is a supported transformation catalog format
issysinfo - Variable in class edu.isi.pegasus.planner.client.TCClient
isTop() - Method in class edu.isi.pegasus.planner.provisioner.Node
  Check whether this task is the entry task or not.
isTransferringExecutableFile() - Method in class edu.isi.pegasus.planner.classes.FileTransfer
  Returns a boolean indicating if a file that is being staged is an executable or not (i.e is a data file).
istype - Variable in class edu.isi.pegasus.planner.client.TCClient
isValid() - Method in class edu.isi.pegasus.planner.classes.FileTransfer
  Determines whether the transfer contained in this container is valid or not.
isValid(Pattern, String) - Static method in class edu.isi.pegasus.planner.dax.Patterns
isValidArchitecture(String) - Static method in class edu.isi.pegasus.planner.catalog.classes.SysInfo
  Checks if the architecture is a valid supported architecture
isValidOS(String) - Static method in class edu.isi.pegasus.planner.catalog.classes.SysInfo
  Checks if the operating system is a valid supported operating system
isVersionValid(String) - Static method in class edu.isi.pegasus.planner.dax.Patterns
isxml - Variable in class edu.isi.pegasus.planner.catalog.transformation.client.Client
isxml - Variable in class edu.isi.pegasus.planner.client.TCClient
iterateJob() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor: Enumerates the internal values that constitute the content of the job list.
iterateStatCall() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor: Enumerates the internal values that constitute the content of the stat list.
iterator() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns an iterator that traverses through the graph using a graph traversal algorithm.
iterator() - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Returns an iterator that traverses through the graph using a graph traversal algorithm.
iterator() - Method in class edu.isi.pegasus.planner.invocation.Environment
  Creates a sorted iterator
iterator() - Method in interface edu.isi.pegasus.planner.partitioner.graph.Graph
  Returns an iterator that traverses through the graph using a graph traversal algorithm.
iterator() - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph
  Returns an iterator that traverses through the graph using a graph traversal algorithm.
IterHEFT() - Method in class edu.isi.pegasus.planner.provisioner.Estimator
IVPTest - Class in edu.isi.pegasus.planner.parser
  This class is used to test the `InvocationParser` class.
IVPTest() - Constructor for class edu.isi.pegasus.planner.parser.IVPTest
IVSElement - Class in edu.isi.pegasus.planner.parser
  This class keeps the name of an element and its corresponding java object reference.
IVSElement(String, Invocation) - Constructor for class edu.isi.pegasus.planner.parser.IVSElement

## J

JAVA_COMMAND_LINE_PROPERTY_REGEX - Static variable in class edu.isi.pegasus.planner.client.CPlanner
  The regex used to match against a java property that is set using -Dpropertyname=value in the argument string
JDBCRC - Class in edu.isi.pegasus.planner.catalog.replica.impl
  This class implements a replica catalog on top of a simple table in a JDBC database.
JDBCRC(String, String, String, String) - Constructor for class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Convenience c'tor: Establishes the connection to the replica catalog database.
JDBCRC() - Constructor for class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Default empty constructor creates an object that is not yet connected to any database.
Job - Class in edu.isi.pegasus.planner.classes
  The object of this class holds the information to generate a submit file about one particular job making the Dag.
Job() - Constructor for class edu.isi.pegasus.planner.classes.Job
  Intialises the member variables.
Job(Job) - Constructor for class edu.isi.pegasus.planner.classes.Job
  Overloaded constructor.
JOB - Static variable in class edu.isi.pegasus.planner.code.generator.MonitordNotify
  The constant string to write for job notifications.
Job - Class in edu.isi.pegasus.planner.dax
Job(String, String) - Constructor for class edu.isi.pegasus.planner.dax.Job
Job(String, String, String) - Constructor for class edu.isi.pegasus.planner.dax.Job
Job(String, String, String, String) - Constructor for class edu.isi.pegasus.planner.dax.Job
Job(Job) - Constructor for class edu.isi.pegasus.planner.dax.Job
Job(String, String, String, String, String) - Constructor for class edu.isi.pegasus.planner.dax.Job
Job - Class in edu.isi.pegasus.planner.invocation
  This class is contains the record from each jobs that ran in every invocation.
Job(String) - Constructor for class edu.isi.pegasus.planner.invocation.Job
JOB_AGGREGATOR_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the key that determines the clusterig executable to be used to run the merged/collapsed job.
JOB_ARGUMENTS - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
JOB_ARGUMENTS - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
JOB_CLASS_AD_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.ClassADSGenerator
  The class ad for job Class.
JOB_CLUSTER_SIZE_AD_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.ClassADSGenerator
  The class ad to designate the size of the clustered jobs.
JOB_CLUSTERED_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The attribute key for whether a job is clustered or not
JOB_EDGE_EVENT_NAME - Static variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The event name for job edge
JOB_ENVIRONMENTVARIABLE - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
JOB_ENVIRONMENTVARIABLE - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
JOB_EVENT_NAME - Static variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The event name for a job
JOB_EXECUTABLE_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The attribute key for the executable
JOB_EXITCODE - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
JOB_EXITTCODE - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
JOB_ID - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
JOB_ID - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
JOB_ID_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The attribute key for job id
JOB_INPUTS - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
JOB_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The name of the key that indicates the path to the corresponding submit file for the job.
JOB_MAX_RETRIES_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The attribute key for how many times a job is retried
JOB_NUMBER - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
JOB_NUMBER - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
JOB_OUTPUTS - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
JOB_PREFIX - Static variable in class edu.isi.pegasus.planner.classes.DAGJob
  The prefix to be attached for the DAX jobs
JOB_PREFIX - Static variable in class edu.isi.pegasus.planner.classes.DAXJob
  The prefix to be attached for the DAX jobs
JOB_RESOURCE_INFORMATION - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
JOB_RESOURCE_INFORMATION - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
JOB_RUN_TIME - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the key that if set in the Pegasus namespace specifies the approximate runtime of the job.
JOB_RUNTIME_AD_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.ClassADSGenerator
  The class ad for the expected job value
JOB_SUBMIT_FILE_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Stampede
  Teh attribute key for the submit file
JOB_TASK_COUNT_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The attribute key for the number of tasks in the job
JOB_TYPE() - Constructor for enum edu.isi.pegasus.planner.catalog.site.classes.GridGateway.JOB_TYPE
JobAggregator - Interface in edu.isi.pegasus.planner.cluster
  The interface that dictates how the jobs are clumped together into one single larger job.
JobAggregatorFactory - Class in edu.isi.pegasus.planner.cluster.aggregator
  A factory class to load the appropriate JobAggregator implementations while clustering jobs.
JobAggregatorFactory() - Constructor for class edu.isi.pegasus.planner.cluster.aggregator.JobAggregatorFactory
JobAggregatorFactoryException - Exception in edu.isi.pegasus.planner.cluster.aggregator
  Class to notify of failures while instantiating JobAggregator implementations.
JobAggregatorFactoryException(String) - Constructor for exception edu.isi.pegasus.planner.cluster.aggregator.JobAggregatorFactoryException
  Constructs a `JobAggregatorFactoryException` with no detail message.
JobAggregatorFactoryException(String, String) - Constructor for exception edu.isi.pegasus.planner.cluster.aggregator.JobAggregatorFactoryException
  Constructs a `JobAggregatorFactoryException` with the specified detailed message.
JobAggregatorFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.cluster.aggregator.JobAggregatorFactoryException
  Constructs a `JobAggregatorFactoryException` with the specified detailed message and a cause.
JobAggregatorFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.planner.cluster.aggregator.JobAggregatorFactoryException
  Constructs a `JobAggregatorFactoryException` with the specified detailed message and a cause.
JobAggregatorInstanceFactory - Class in edu.isi.pegasus.planner.cluster.aggregator
  A JobAggergator factory that caches up the loaded implementations.
JobAggregatorInstanceFactory() - Constructor for class edu.isi.pegasus.planner.cluster.aggregator.JobAggregatorInstanceFactory
  The default constructor.
jobClass - Variable in class edu.isi.pegasus.planner.classes.Job
  The type of the job.
jobComparator() - Method in class edu.isi.pegasus.planner.cluster.Horizontal
  Singleton access to the job comparator.
JobComparator() - Constructor for class edu.isi.pegasus.planner.cluster.Horizontal.JobComparator
jobID - Variable in class edu.isi.pegasus.planner.classes.Job
  Identifies of which Pegasus Super Node is a job associated with.
jobIterator() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns an iterator for traversing through the jobs in the workflow.
JobManager - Class in edu.isi.pegasus.planner.catalog.site.impl.old.classes
  This is a data class that is used to store information about a jobmanager and the information that it reports about a remote pool.
JobManager() - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  Default constructor for the class.
JOBMANAGER - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  The constant to be passed to the accessor functions to get or set the list of `JobManager` objects for the remote site.
JOBMANAGER_RESOURCE - Static variable in class edu.isi.pegasus.planner.classes.AuthenticateRequest
  The type identifying that the resource to authenticate against is a job manager.
JOBMANAGER_TYPE - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The constant to be passed to the accessor functions to get or set the jobmanager type.
JOBMANAGER_TYPE_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The name of the key that specifies the jobmanager type.
JOBMANAGERINFO - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  Array storing the names of the attributes that are stored with the jobmanager.
jobName - Variable in class edu.isi.pegasus.planner.classes.Job
  The name of the job.
JOBS_IN_QUEUE - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The constant to be passed to the accessor functions to get or set the number of the jobs in the queue attribute.
JOBSTATE_JOB_PREFIX - Static variable in class edu.isi.pegasus.planner.code.generator.Shell
  The prefix for events associated with job in jobstate.log file
JOBSTATE_POST_SCRIPT_PREFIX - Static variable in class edu.isi.pegasus.planner.code.generator.Shell
  The prefix for events associated with POST_SCRIPT in jobstate.log file
JOBSTATE_PRE_SCRIPT_PREFIX - Static variable in class edu.isi.pegasus.planner.code.generator.Shell
  The prefix for events associated with job in jobstate.log file
JobStatus - Class in edu.isi.pegasus.planner.invocation
  This abstract class is the interface for all classes that describe the job exit, which describes more clearly failure, regular execution, signal and suspension.
JobStatus() - Constructor for class edu.isi.pegasus.planner.invocation.JobStatus
JobStatusFailure - Class in edu.isi.pegasus.planner.invocation
  This class is transient for XML parsing.
JobStatusFailure() - Constructor for class edu.isi.pegasus.planner.invocation.JobStatusFailure
  Default c'tor: Construct a hollow shell and allow further information to be added later.
JobStatusFailure(int) - Constructor for class edu.isi.pegasus.planner.invocation.JobStatusFailure
  Constructs an error number without reason text.
JobStatusFailure(int, String) - Constructor for class edu.isi.pegasus.planner.invocation.JobStatusFailure
  Constructs a piece of data.
JobStatusRegular - Class in edu.isi.pegasus.planner.invocation
  This class is transient for XML parsing.
JobStatusRegular() - Constructor for class edu.isi.pegasus.planner.invocation.JobStatusRegular
  Default c'tor: Construct a hollow shell and allow further information to be added later.
JobStatusRegular(short) - Constructor for class edu.isi.pegasus.planner.invocation.JobStatusRegular
  Constructs an exit code.
JobStatusSignal - Class in edu.isi.pegasus.planner.invocation
  This class is transient for XML parsing.
JobStatusSignal() - Constructor for class edu.isi.pegasus.planner.invocation.JobStatusSignal
  Default c'tor: Construct a hollow shell and allow further information to be added later.
JobStatusSignal(short) - Constructor for class edu.isi.pegasus.planner.invocation.JobStatusSignal
  Constructs an error number without reason text.
JobStatusSignal(short, boolean) - Constructor for class edu.isi.pegasus.planner.invocation.JobStatusSignal
  Constructs a piece of data.
JobStatusSignal(short, boolean, String) - Constructor for class edu.isi.pegasus.planner.invocation.JobStatusSignal
  Constructs a piece of data.
JobStatusSuspend - Class in edu.isi.pegasus.planner.invocation
  This class is transient for XML parsing.
JobStatusSuspend() - Constructor for class edu.isi.pegasus.planner.invocation.JobStatusSuspend
  Default c'tor: Construct a hollow shell and allow further information to be added later.
JobStatusSuspend(short) - Constructor for class edu.isi.pegasus.planner.invocation.JobStatusSuspend
  Constructs an error number without reason text.
JobStatusSuspend(short, String) - Constructor for class edu.isi.pegasus.planner.invocation.JobStatusSuspend
  Constructs a piece of data.
JOBTYPE - Static variable in class edu.isi.pegasus.planner.dax.AbstractJob
jobType2GridGatewayJobType(int) - Static method in class edu.isi.pegasus.planner.classes.Job
  Returns an appropriate grid gateway job type corresponding to a job type
join(long) - Method in class edu.isi.pegasus.planner.refiner.ThreadPool.AuthenticateThread
  Calls the corresponding join method of the thread associated with this class.
joinLFN(String, String, String) - Static method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Joins the 3 components into a fully qualified logical mName of the format NS::NAME:VER

## K

KEEP_ALWAYS - Static variable in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  The state denoting always to keep the temporary files.
KEEP_NEVER - Static variable in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  The state denoting never to keep the temporary files.
KEEP_ONERROR - Static variable in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  The state denoting to keep the temporary files only in case of error.
keySet() - Method in class edu.isi.pegasus.planner.namespace.Namespace
  Returns the key set associated with the namespace.
Kickstart - Class in edu.isi.pegasus.planner.code.gridstart
  This enables a constituentJob to be run on the grid, by launching it through kickstart.
Kickstart() - Constructor for class edu.isi.pegasus.planner.code.gridstart.Kickstart
KICKSTART_CLEANUP - Static variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  The environment variable used to the set Kickstart CLEANUP JOB.
KICKSTART_INDEX - Static variable in class edu.isi.pegasus.planner.code.GridStartFactory
  The index in the constant arrays for NoGridStart.
KICKSTART_INPUT_SUFFIX - Static variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  The suffix for the kickstart input file, that is generated to use invoke at the remote end.
KICKSTART_POSTJOB - Static variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  The environment variable used to the set Kickstart POSTJOB.
KICKSTART_PREJOB - Static variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  The environment variable used to the set Kickstart PREJOB.
KICKSTART_SETUP - Static variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  The environment variable used to the set Kickstart SETUP JOB.

## L

Label - Class in edu.isi.pegasus.planner.partitioner
  This partitioner partitions the DAX into smaller partitions as specified by the labels associated with the jobs.
Label(GraphNode, Map, PegasusProperties) - Constructor for class edu.isi.pegasus.planner.partitioner.Label
  The overloaded constructor.
LABEL_BASED_PARTITIONING_CLASS - Static variable in class edu.isi.pegasus.planner.partitioner.PartitionerFactory
  The name of the class that does label based partitioning.
LABEL_CALLBACK_CLASS - Static variable in class edu.isi.pegasus.planner.parser.DAXParserFactory
  The default callback for label partitioning.
LABEL_CLUSTERING_TYPE - Static variable in class edu.isi.pegasus.planner.cluster.ClustererFactory
  The type corresponding to label based clustering.
LABEL_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the profile key in vds namespace that does the labelling by default.
LABEL_KEY - Static variable in class edu.isi.pegasus.planner.partitioner.graph.LabelBag
  The default key that is associated with label.
LabelBag - Class in edu.isi.pegasus.planner.partitioner.graph
  A bag implementation that just holds a particular value for the label key.
LabelBag() - Constructor for class edu.isi.pegasus.planner.partitioner.graph.LabelBag
  The default constructor.
labelBasedSubmitDirectoryForSubWorkflows() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a boolean indicating whether the submit directory for the sub workflows should include the label of the sub workflow or not.
lastAddedNode() - Method in class edu.isi.pegasus.planner.partitioner.Partition
  Returns the last added node to the partition.
lb - Variable in class edu.isi.pegasus.planner.provisioner.Node
level - Variable in class edu.isi.pegasus.planner.classes.Job
  Identifies the level of the job in the dax.
LEVEL_BASED_PARTITIONING_CLASS - Static variable in class edu.isi.pegasus.planner.partitioner.PartitionerFactory
  The name of the class that does level based partitioning.
LEVEL_KW - Static variable in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
lfn - Variable in class edu.isi.pegasus.planner.catalog.transformation.client.Client
lfn - Variable in class edu.isi.pegasus.planner.client.TCClient
LFN_DOES_NOT_EXIST_MSG - Static variable in class edu.isi.pegasus.planner.client.RCClient
  The message for LFN's not found.
LFNComparator() - Constructor for class edu.isi.pegasus.planner.catalog.transformation.client.TCQuery.LFNComparator
lfnDoesNotExist(String) - Method in class edu.isi.pegasus.planner.client.RCClient
  Writes out a message about LFN not existing.
lfnMap - Variable in class edu.isi.pegasus.planner.classes.DagInfo
  Contains a unique ordered listing of the logical names referred to by the dag.
LIGO_VO - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  The name of the LIGO VO
LINK() - Constructor for enum edu.isi.pegasus.planner.dax.File.LINK
LINKAGE() - Constructor for enum edu.isi.pegasus.planner.classes.PegasusFile.LINKAGE
LINUX - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Os
list(PrintStream) - Method in class edu.isi.pegasus.common.util.CommonProperties
  Print out the property list onto the specified stream.
list() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Lists all logical filenames in the catalog.
list(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Lists a subset of all logical filenames in the catalog.
list() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
list(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
list() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Lists all logical filenames in the catalog.
list(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Lists a subset of all logical filenames in the catalog.
list(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Lists a subset of all logical filenames in the catalog.
list() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Lists all logical filenames in the catalog.
list() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Lists all logical filenames in the catalog.
list(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Lists a subset of all logical filenames in the catalog.
list() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Lists all logical filenames in the catalog.
list(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Lists a subset of all logical filenames in the catalog.
list() - Method in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Lists all logical filenames in the catalog.
list(String) - Method in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Lists a subset of all logical filenames in the catalog.
list() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  Returns the list of sites, in the store.
list() - Method in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
list() - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML
  Lists the site handles for all the sites in the Site Catalog.
list() - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  Lists the site handles for all the sites in the Site Catalog.
list() - Method in interface edu.isi.pegasus.planner.catalog.SiteCatalog
  Lists the site handles for all the sites in the Site Catalog.
ListCallback() - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.OSGMM.ListCallback
  Default Constructor.
ListCommand - Class in edu.isi.pegasus.gridftp
  Implements the ls command for remote GridFTP servers
ListCommand(boolean, boolean) - Constructor for class edu.isi.pegasus.gridftp.ListCommand
listIterateJob() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor: Enumerates the internal values that constitute the content of the job list.
listIterateStatCall() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor: Enumerates the internal values that constitute the content of the stat list.
ll(String) - Method in class edu.isi.pegasus.gridftp.GridFTPConnection
  List contents of path in long format
load(List<String>) - Method in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  Loads up the Site Catalog implementation with the sites whose site handles are specified.
load(List<String>) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML
  Loads up the Site Catalog implementation with the sites whose site handles are specified.
load(List<String>) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  Loads up the Site Catalog implementation with the sites whose site handles are specified.
load(List<String>) - Method in interface edu.isi.pegasus.planner.catalog.SiteCatalog
  Loads up the Site Catalog implementation with the sites whose site handles are specified.
Load - Class in edu.isi.pegasus.planner.invocation
  The RAM element.
Load() - Constructor for class edu.isi.pegasus.planner.invocation.Load
  The default constructor
loadCacheFiles(Set) - Method in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  Ends up loading the cache files so as to enable the lookup for the transient files created by the parent jobs.
loadCleanupImplementationInstance(PegasusBag) - Static method in class edu.isi.pegasus.planner.refiner.cleanup.CleanupFactory
  Loads the implementing class corresponding to the mode specified by the user at runtime.
loadCleanupStraegyInstance(PegasusBag) - Static method in class edu.isi.pegasus.planner.refiner.cleanup.CleanupFactory
  Loads the implementing class corresponding to the mode specified by the user at runtime.
loadClusterer(ADag, PegasusBag, String) - Static method in class edu.isi.pegasus.planner.cluster.ClustererFactory
  Loads the appropriate clusterer on the basis of the clustering type specified in the options passed to the planner.
loadConfigurationProperties(PegasusProperties) - Method in class edu.isi.pegasus.planner.common.PegasusConfiguration
  Loads configuration specific properties into PegasusProperties
loadConfigurationPropertiesAndOptions(PegasusProperties, PlannerOptions) - Method in class edu.isi.pegasus.planner.common.PegasusConfiguration
  Loads configuration specific properties into PegasusProperties, and adjusts planner options accordingly.
loadCreateDirectoryImplementationInstance(PegasusBag) - Static method in class edu.isi.pegasus.planner.refiner.CreateDirectory
  Loads the implementing class corresponding to the mode specified by the user at runtime.
loadCreateDirectoryStraegyInstance(PegasusBag) - Static method in class edu.isi.pegasus.planner.refiner.CreateDirectory
  Loads the implementing class corresponding to the mode specified by the user at runtime.
loadDAXParser(PegasusBag, String, String) - Static method in class edu.isi.pegasus.planner.parser.DAXParserFactory
  Loads the appropriate DAXParser looking at the dax schema that is specified by the user.
loadDAXParser(PegasusBag, Callback, String) - Static method in class edu.isi.pegasus.planner.parser.DAXParserFactory
  Loads the appropriate DAXParser looking at the dax schema that is specified in the DAX file.
loadDAXParser(String, PegasusBag, Callback) - Static method in class edu.isi.pegasus.planner.parser.DAXParserFactory
  Loads the appropriate DAXParser looking at the dax schema that is specified by the user.
loadDAXParserCallback(String, PegasusBag, String) - Static method in class edu.isi.pegasus.planner.parser.DAXParserFactory
  Loads the implementing class corresponding to the type specified by the user.
loadDAXParserCallback(PegasusBag, String, String) - Static method in class edu.isi.pegasus.planner.parser.DAXParserFactory
  Loads the implementing class corresponding to the type specified by the user.
loadDeployWorkerPackage(PegasusBag) - Static method in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Loads the implementing class corresponding to the mode specified by the user at runtime.
loadEnvironmentVariables() - Method in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  Initializes the internal hash that collects environment variables.
loadGridStart(Job, String) - Method in class edu.isi.pegasus.planner.code.GridStartFactory
  Loads the appropriate gridstart implementation for a job on the basis of the value of the GRIDSTART_KEY in the Pegasus namepsace.
loadGridStart(PegasusBag, ADag, String) - Method in class edu.isi.pegasus.planner.code.GridStartFactory
  Loads the implementing class corresponding to the class.
loadImplementations(PegasusBag) - Method in class edu.isi.pegasus.planner.transfer.MultipleFTPerXFERJobRefiner
  Loads the appropriate implementations that is required by this refinement strategy for different types of transfer jobs.
loadImplementations(PegasusBag) - Method in interface edu.isi.pegasus.planner.transfer.Refiner
  Loads the appropriate implementations that is required by this refinement strategy for different types of transfer jobs.
loadImplementations(PegasusBag) - Method in class edu.isi.pegasus.planner.transfer.SingleFTPerXFERJobRefiner
  Loads the appropriate implementations that is required by this refinement strategy for different types of transfer jobs.
loadInheritedReplicaStore(Set) - Method in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  Ends up loading the inherited replica files.
loadInstance(CredentialHandler.TYPE) - Method in class edu.isi.pegasus.common.credential.CredentialHandlerFactory
  This method loads the appropriate implementing CondorStyle as specified by the user at runtime.
loadInstance(PegasusBag, String) - Method in class edu.isi.pegasus.common.credential.CredentialHandlerFactory
  This method loads the appropriate CredentialHandler using reflection.
loadInstance(PegasusProperties) - Static method in class edu.isi.pegasus.common.logging.LogFormatterFactory
  Loads the appropriate LogFormatter class as specified by properties.
loadInstance(String) - Static method in class edu.isi.pegasus.common.logging.LogFormatterFactory
  Loads the Log Formatter specified.
loadInstance(PegasusProperties) - Static method in class edu.isi.pegasus.common.logging.LogManagerFactory
  Loads the appropriate LogManager class as specified by properties.
loadInstance(String, String, Properties) - Static method in class edu.isi.pegasus.common.logging.LogManagerFactory
  Loads the Log Formatter specified.
loadInstance(PegasusProperties) - Static method in class edu.isi.pegasus.planner.catalog.replica.ReplicaFactory
  Connects the interface with the replica catalog implementation.
loadInstance(CommonProperties) - Static method in class edu.isi.pegasus.planner.catalog.replica.ReplicaFactory
  Connects the interface with the replica catalog implementation.
loadInstance(String, Properties) - Static method in class edu.isi.pegasus.planner.catalog.replica.ReplicaFactory
  Connects the interface with the replica catalog implementation.
loadInstance() - Static method in class edu.isi.pegasus.planner.catalog.replica.ReplicaFactory
  Connects the interface with the replica catalog implementation.
loadInstance(PegasusProperties, boolean) - Static method in class edu.isi.pegasus.planner.catalog.site.impl.old.SiteFactory
  Connects the interface with the site catalog implementation.
loadInstance() - Static method in class edu.isi.pegasus.planner.catalog.site.SiteFactory
  Connects the interface with the transformation catalog implementation.
loadInstance(PegasusProperties) - Static method in class edu.isi.pegasus.planner.catalog.site.SiteFactory
  Connects the interface with the site catalog implementation.
loadInstance(String, Properties) - Static method in class edu.isi.pegasus.planner.catalog.site.SiteFactory
  Connects the interface with the site catalog implementation.
loadInstance() - Static method in class edu.isi.pegasus.planner.catalog.transformation.TCMode
  The overloaded method which is to be used internally in Pegasus.
loadInstance(String, Object[]) - Static method in class edu.isi.pegasus.planner.catalog.transformation.TCMode
  Loads the appropriate TC implementing Class with the given arguments.
loadInstance() - Static method in class edu.isi.pegasus.planner.catalog.transformation.TransformationFactory
  Connects the interface with the transformation catalog implementation.
loadInstance(PegasusProperties) - Static method in class edu.isi.pegasus.planner.catalog.transformation.TransformationFactory
  Connects the interface with the transformation catalog implementation.
loadInstance(PegasusProperties, LogManager) - Static method in class edu.isi.pegasus.planner.catalog.transformation.TransformationFactory
  Connects the interface with the transformation catalog implementation.
loadInstance(PegasusBag) - Static method in class edu.isi.pegasus.planner.catalog.transformation.TransformationFactory
  Connects the interface with the transformation catalog implementation.
loadInstance(PegasusProperties) - Static method in class edu.isi.pegasus.planner.catalog.work.WorkFactory
  Connects the interface with the work catalog implementation.
loadInstance(CommonProperties) - Static method in class edu.isi.pegasus.planner.catalog.work.WorkFactory
  Connects the interface with the work catalog implementation.
loadInstance(String, Properties) - Static method in class edu.isi.pegasus.planner.catalog.work.WorkFactory
  Connects the interface with the work catalog implementation.
loadInstance(ADag, PegasusBag) - Static method in class edu.isi.pegasus.planner.cluster.aggregator.JobAggregatorFactory
  Loads the implementing class corresponding to the mode specified by the user at runtime in the properties file.
loadInstance(String, ADag, PegasusBag) - Static method in class edu.isi.pegasus.planner.cluster.aggregator.JobAggregatorFactory
  Loads the implementing class corresponding to the class passed.
loadInstance(Job) - Method in class edu.isi.pegasus.planner.cluster.aggregator.JobAggregatorInstanceFactory
  Returns the appropriate handle to the JobAggregator that is to be used for a particular type of job.
loadInstance(PegasusBag) - Static method in class edu.isi.pegasus.planner.code.CodeGeneratorFactory
  This method loads the appropriate implementing code generator as specified by the user at runtime.
loadInstance(PegasusBag, String) - Static method in class edu.isi.pegasus.planner.code.CodeGeneratorFactory
  This method loads the appropriate code generator as specified by the user at runtime.
loadInstance(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactory
  This method loads the appropriate implementing CondorStyle as specified by the user at runtime.
loadInstance(PegasusBag, String) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactory
  This method loads the appropriate Condor Style using reflection.
loadInstance(PegasusProperties, PlannerOptions, String) - Static method in class edu.isi.pegasus.planner.parser.pdax.PDAXCallbackFactory
  Loads the implementing class corresponding to the type specified by the user.
loadInstance(PegasusProperties, PlannerOptions, String, String) - Static method in class edu.isi.pegasus.planner.parser.pdax.PDAXCallbackFactory
  Loads the implementing class corresponding to the type specified by the user.
loadInstance(PegasusProperties, String, String) - Static method in class edu.isi.pegasus.planner.partitioner.DAXWriter
  The ends up loading the PDAXWriter.
loadInstance(String, PegasusProperties, String, String) - Static method in class edu.isi.pegasus.planner.partitioner.DAXWriter
  Loads the implementing PDAXWriter.
loadInstance(PegasusProperties, GraphNode, Map, String) - Static method in class edu.isi.pegasus.planner.partitioner.PartitionerFactory
  Loads the implementing class corresponding to the type specified by the user.
loadInstance() - Static method in class edu.isi.pegasus.planner.selector.replica.ReplicaSelectorFactory
  A no hassle factory method that loads the replica selector specified in the properties.
loadInstance(PegasusProperties) - Static method in class edu.isi.pegasus.planner.selector.replica.ReplicaSelectorFactory
  Loads the implementing class corresponding to the mode specified by the user at runtime in the properties file.
loadInstance(PegasusProperties, String) - Static method in class edu.isi.pegasus.planner.selector.replica.ReplicaSelectorFactory
  Loads the implementing class corresponding to the class.
loadInstance(PegasusBag) - Static method in class edu.isi.pegasus.planner.selector.site.SiteSelectorFactory
  Loads the implementing class corresponding to the mode specified by the user at runtime in the properties file.
loadInstance(PegasusBag, int) - Static method in class edu.isi.pegasus.planner.transfer.implementation.ImplementationFactory
  Loads the implementing class corresponding to the type specified by the user.
loadInstance(String, PegasusBag) - Static method in class edu.isi.pegasus.planner.transfer.implementation.ImplementationFactory
  Loads the implementing class corresponding to the class.
loadInstance(ADag, PegasusBag) - Static method in class edu.isi.pegasus.planner.transfer.mapper.OutputMapperFactory
  Loads the implementing class corresponding to the value specified in the properties.
loadInstance(String, PegasusBag, ADag) - Static method in class edu.isi.pegasus.planner.transfer.mapper.OutputMapperFactory
  Loads the implementing class corresponding to the class.
loadInstance(ADag, PegasusBag) - Static method in class edu.isi.pegasus.planner.transfer.refiner.RefinerFactory
  Loads the implementing class corresponding to the value specified in the properties.
loadInstance(String, PegasusBag, ADag) - Static method in class edu.isi.pegasus.planner.transfer.refiner.RefinerFactory
  Loads the implementing class corresponding to the class.
loadInstance(PegasusBag) - Static method in class edu.isi.pegasus.planner.transfer.sls.SLSFactory
  This method loads the appropriate implementing code generator as specified by the user at runtime.
loadInstance(PegasusBag, String) - Static method in class edu.isi.pegasus.planner.transfer.sls.SLSFactory
  This method loads the appropriate code generator as specified by the user at runtime.
loadLocalEnvVariables() - Method in class edu.isi.pegasus.planner.refiner.ThreadPool
  Reads in the environment variables into memory from the properties file and the pool catalog.
loadNonSingletonObjects(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  It loads the objects using their non singleton implementations.
loadPartitioner(PegasusProperties, String, GraphNode, Map) - Static method in class edu.isi.pegasus.planner.cluster.ClustererFactory
  Loads the appropriate partitioner on the basis of the clustering type specified in the options passed to the planner.
loadPoolInstance(String, String, int) - Static method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolMode
  Loads the pool info provider class using the reflection package in java at runtime.
loadPoolInstance(String, String, String, int) - Static method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolMode
  Loads the pool info provider class using the reflection package in java at runtime.
loadPoolInstance(String, int, Object[]) - Static method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolMode
  Loads the appropriate class that implements a particular pool mode using the reflection package in java at runtime.
loadPOSTScript(Job, GridStart) - Method in class edu.isi.pegasus.planner.code.GridStartFactory
  Loads the appropriate POST Script implementation for a job on the basis of the value of the Pegasus profile GRIDSTART_KEY, and the DAGMan profile POST_SCRIPT_KEY in the Pegasus namepsace.
loadPOSTScript(PegasusProperties, String, String, String) - Method in class edu.isi.pegasus.planner.code.GridStartFactory
  Loads the implementing class corresponding to the class.
loadPPS(PegasusProperties) - Static method in class edu.isi.pegasus.planner.provenance.pasoa.pps.PPSFactory
  Loads the appropriate PPS implementation on the basis of the property set in the properties.
loadProperties() - Method in class edu.isi.pegasus.planner.client.CPlanner
  Loads all the properties that are needed by this class.
loadProperties() - Method in class edu.isi.pegasus.planner.client.Executable
  Loads all the properties that would be needed by the Toolkit classes.
loadProperties() - Method in class edu.isi.pegasus.planner.client.PartitionDAX
  Loads all the properties that are needed by this class.
loadProperties() - Method in class edu.isi.pegasus.planner.client.PegasusGetSites
  An empty implementation.
loadProperties() - Method in class edu.isi.pegasus.planner.client.RankDAX
  Loads all the properties that would be needed by the Toolkit classes.
loadProperties() - Method in class edu.isi.pegasus.planner.client.SCClient
  Loads all the properties that would be needed by the Toolkit classes
loadProperties() - Method in class edu.isi.pegasus.planner.client.TCClient
loadProperties() - Method in class edu.isi.pegasus.planner.client.TCConverter
  Loads all the properties that would be needed by the Toolkit classes
loadProperties() - Method in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  Loads all the properties that would be needed by the Toolkit classes.
loadProperties() - Method in class edu.isi.pegasus.planner.refiner.Engine
  Loads all the properties that are needed by the Engine classes.
loadSingletonInstance(String) - Static method in class edu.isi.pegasus.common.logging.LogFormatterFactory
  Loads the appropriate LogFormatter class as specified by properties.
loadSingletonInstance() - Static method in class edu.isi.pegasus.common.logging.LogManagerFactory
  Loads the appropriate LogManager class as specified by properties.
loadSingletonInstance(PegasusProperties) - Static method in class edu.isi.pegasus.common.logging.LogManagerFactory
  Loads the appropriate LogManager class as specified by properties.
loadSingletonObjects() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  It loads the objects that the pool providers need in a singleton manner, wherever possible.
loadSite(SiteCatalogEntry3) - Method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser3
  Whether to laod a site or not in the `SiteStore`
loadSite(SiteCatalogEntry) - Method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser4
  Whether to laod a site or not in the `SiteStore`
loadSiteCatalogParser(String, PegasusBag, List<String>) - Static method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParserFactory
  Loads the appropriate Site Catalog Parser looking at the dax schema that is specified by the user.
loadSiteCatalogXMLParser(PegasusBag, String, List<String>) - Static method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParserFactory
  Loads the appropriate DAXParser looking at the dax schema that is specified by the user.
loadSiteStore(Collection<String>, PegasusBag) - Static method in class edu.isi.pegasus.planner.catalog.site.SiteFactory
loadSiteStore(Set<String>) - Method in class edu.isi.pegasus.planner.client.CPlanner
  Loads the sites from the site catalog into the site store
loadTCMapper(String, PegasusBag) - Static method in class edu.isi.pegasus.planner.catalog.transformation.Mapper
  Loads the implementing class corresponding to the mode specified by the user at runtime in the properties file.
loadTXSelector(String) - Static method in class edu.isi.pegasus.planner.selector.TransformationSelector
  Loads the implementing class corresponding to the mode specified by the user at runtime in the properties file.
loadXMLProducer(PegasusProperties) - Static method in class edu.isi.pegasus.planner.provenance.pasoa.producer.XMLProducerFactory
  Loads the appropriate XMLProducer on the basis of the property set in the properties.
Local - Class in edu.isi.pegasus.planner.selector.replica
  This replica selector only prefers replicas from the local host and that start with a file: URL scheme.
Local(PegasusProperties) - Constructor for class edu.isi.pegasus.planner.selector.replica.Local
  The overloaded constructor, that is called by load method.
LOCAL_PREFIX - Static variable in interface edu.isi.pegasus.planner.transfer.Refiner
  The prefix for all local transfer jobs.
LOCAL_SITE_HANDLE - Static variable in interface edu.isi.pegasus.planner.selector.ReplicaSelector
  The local site handle.
LOCAL_UNIVERSE - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.Condor
LOCAL_UNIVERSE - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The condor universe key value for local universe.
LocalDirectory - Class in edu.isi.pegasus.planner.catalog.site.classes
  This data class represents a local directory on a site.
LocalDirectory() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.LocalDirectory
  The default constructor.
LocalDirectory(Map<FileServerType.OPERATION, List<FileServer>>, InternalMountPoint) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.LocalDirectory
  The overloaded constructor
lockTaskMetrics(boolean) - Method in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  Sets the lock task metrics parameters.
log(String, Exception, int) - Method in class edu.isi.pegasus.common.logging.logger.Default
  Logs the exception on the appropriate queue if the level of the message is less than or equal to the level set for the Logger.
log(String, int, boolean) - Method in class edu.isi.pegasus.common.logging.logger.Default
  Logs the message on the appropriate queue if the level of the message is less than or equal to the level set for the Logger.
log(String, Exception, int) - Method in class edu.isi.pegasus.common.logging.logger.Log4j
  Logs the exception on the appropriate queue if the level of the message is less than or equal to the level set for the Logger.
log(int) - Method in class edu.isi.pegasus.common.logging.LogManager
  Log the message represented by the internal log buffer.
log(String, Exception, int) - Method in class edu.isi.pegasus.common.logging.LogManager
  Logs the exception on the appropriate queue if the level of the message is less than or equal to the level set for the Logger.
log(String, int) - Method in class edu.isi.pegasus.common.logging.LogManager
  Logs the message on the appropriate queue if the level of the message is less than or equal to the level set for the Logger.
log(String, int) - Method in class edu.isi.pegasus.planner.client.Executable
  Logs messages to the singleton logger.
log(Level, String) - Static method in class edu.isi.pegasus.planner.client.RCClient
  Logs messages from main() method.
log(Level, String) - Method in class edu.isi.pegasus.planner.invocation.SimpleServerThread
log(String, String, String) - Method in class edu.isi.pegasus.planner.parser.InvocationParser
  Small helper method to bundle repetitive parameters in a template for reporting progress.
log(String, String, String) - Method in class edu.isi.pegasus.planner.parser.StackBasedXMLParser
Log4j - Class in edu.isi.pegasus.common.logging.logger
  A Log4j implementation of the LogManager interface.
Log4j() - Constructor for class edu.isi.pegasus.common.logging.logger.Log4j
  The constructor.
LOG4J_CONF_PROPERTY - Static variable in class edu.isi.pegasus.common.logging.logger.Log4j
  The property that specifies the path to the log4j properties file.
LOG4J_CONF_PROPERTY - Static variable in class edu.isi.pegasus.planner.code.gridstart.NetloggerPostScript
  The LOG4j system configuration property.
LOG4J_LOGGER - Static variable in class edu.isi.pegasus.common.logging.LogManager
  The Log4j logger.
Log4jFilter() - Constructor for class edu.isi.ikcap.workflows.util.logging.EventLogMessage.Log4jFilter
logAlreadyFormattedMessage(String, int) - Method in class edu.isi.pegasus.common.logging.logger.Default
  Logs the message on the appropriate queue if the level of the message is less than or equal to the level set for the Logger.
logAlreadyFormattedMessage(String, int) - Method in class edu.isi.pegasus.common.logging.logger.Log4j
  Logs the message on the appropriate queue if the level of the message is less than or equal to the level set for the Logger.
logAlreadyFormattedMessage(String, int) - Method in class edu.isi.pegasus.common.logging.LogManager
  A stop gap function .
logAndReset(int) - Method in class edu.isi.pegasus.common.logging.LogManager
  Creates a log message with the contents of the internal log buffer.
logConfigMessages() - Method in class edu.isi.pegasus.planner.transfer.AbstractRefiner
  Logs configuration messages regarding the type of implementations loaded for various type of transfer node creations.
logDeprecatedWarning(String, String) - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Logs a warning about the deprecated property.
logEntityHierarchyMessage(String, String, String, Collection<String>) - Method in class edu.isi.pegasus.common.logging.logger.Log4j
  Log a message that connects the parent entities with the children.
logEntityHierarchyMessage(String, String, String, Collection<String>) - Method in class edu.isi.pegasus.common.logging.LogManager
  Log a message that connects the parent entities with the children.
logEntityHierarchyMessage(String, String, String, Collection<String>, int) - Method in class edu.isi.pegasus.common.logging.LogManager
  Log a message that connects the parent entities with the children.
LogEvent - Class in edu.isi.ikcap.workflows.util.logging
LogEvent(String, String, String, String) - Constructor for class edu.isi.ikcap.workflows.util.logging.LogEvent
LogEvent(String, String, Map<String, String>) - Constructor for class edu.isi.ikcap.workflows.util.logging.LogEvent
LogEvent(String, String) - Constructor for class edu.isi.ikcap.workflows.util.logging.LogEvent
logEventCompletion(int) - Method in class edu.isi.pegasus.common.logging.logger.Default
  Logs the completion message on the basis of the debug level.
logEventCompletion(int) - Method in class edu.isi.pegasus.common.logging.logger.Log4j
  Logs the completion message on the basis of the debug level.
logEventCompletion() - Method in class edu.isi.pegasus.common.logging.LogManager
  Logs the completion message on the basis of the debug level.
logEventCompletion(int) - Method in class edu.isi.pegasus.common.logging.LogManager
  Logs the completion message on the basis of the debug level.
logEventStart(String, String, String) - Method in class edu.isi.pegasus.common.logging.LogManager
  Log an event start message to INFO level
logEventStart(String, String, String, int) - Method in class edu.isi.pegasus.common.logging.LogManager
  Log an event start message.
logEventStart(String, Map<String, String>) - Method in class edu.isi.pegasus.common.logging.LogManager
  Log an event start message to the INFO Level
logEventStart(String, Map<String, String>, int) - Method in class edu.isi.pegasus.common.logging.LogManager
  Log an event start message.
logFile(AggregatedJob) - Method in class edu.isi.pegasus.planner.cluster.aggregator.SeqExec
  Returns the name of the log file to used on the remote site, for the seqexec job.
LogFormatter - Interface in edu.isi.pegasus.common.logging
  The interface that defines how the messages need to be formatted for logging
LogFormatterFactory - Class in edu.isi.pegasus.common.logging
  A factory class to load the appropriate implementation of LogFormatter as specified by properties.
LogFormatterFactory() - Constructor for class edu.isi.pegasus.common.logging.LogFormatterFactory
LogFormatterFactoryException - Exception in edu.isi.pegasus.common.logging
  Class to notify of failures while instantiating Log Formatter implementations.
LogFormatterFactoryException(String) - Constructor for exception edu.isi.pegasus.common.logging.LogFormatterFactoryException
  Constructs a `LogFormatterFactoryException` with no detail message.
LogFormatterFactoryException(String, String) - Constructor for exception edu.isi.pegasus.common.logging.LogFormatterFactoryException
  Constructs a `LogFormatterFactoryException` with the specified detailed message.
LogFormatterFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.common.logging.LogFormatterFactoryException
  Constructs a `LogFormatterFactoryException` with the specified detailed message and a cause.
LogFormatterFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.common.logging.LogFormatterFactoryException
  Constructs a `LogFormatterFactoryException` with the specified detailed message and a cause.
logger - Static variable in class edu.isi.pegasus.common.logging.logger.Default
  Ensures only one object is created always.
logger - Variable in class edu.isi.pegasus.gridftp.Command
logger - Variable in class edu.isi.pegasus.gridftp.GridFTPConnection
logger - Variable in class edu.isi.pegasus.gridftp.ListCommand
logger - Variable in class edu.isi.pegasus.gridftp.MakeDirectoryCommand
logger - Static variable in class edu.isi.pegasus.gridftp.PegasusGridFTP
logger - Variable in class edu.isi.pegasus.gridftp.RemoveCommand
LoggingKeys - Interface in edu.isi.ikcap.workflows.util.logging
  Defines keys for creating logs within the workflow system
LoggingKeys - Class in edu.isi.pegasus.common.logging
  Some predifined logging keys to be used for logging.
LoggingKeys() - Constructor for class edu.isi.pegasus.common.logging.LoggingKeys
logicalId - Variable in class edu.isi.pegasus.planner.classes.Job
  The logical id of the job as referred to in the dax.
logicalName - Variable in class edu.isi.pegasus.planner.classes.Job
  The logical name of the transformation which is executed as a part of this job.
logJobAggregatorProgress() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns whether the seqexec job aggregator should log progress to a log or not.
logJobAggregatorProgressToGlobal() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns whether the seqexec job aggregator should write to a global log or not.
LogManager - Class in edu.isi.pegasus.common.logging
  The logging class that to log messages at different levels.
LogManager() - Constructor for class edu.isi.pegasus.common.logging.LogManager
  The constructor.
LogManagerFactory - Class in edu.isi.pegasus.common.logging
  A factory class to load the appropriate implementation of Logger API as specified by properties.
LogManagerFactory() - Constructor for class edu.isi.pegasus.common.logging.LogManagerFactory
LogManagerFactoryException - Exception in edu.isi.pegasus.common.logging
  Class to notify of failures while instantiating Log Factory implementations.
LogManagerFactoryException(String) - Constructor for exception edu.isi.pegasus.common.logging.LogManagerFactoryException
  Constructs a `LogManagerFactoryException` with no detail message.
LogManagerFactoryException(String, String) - Constructor for exception edu.isi.pegasus.common.logging.LogManagerFactoryException
  Constructs a `LogManagerFactoryException` with the specified detailed message.
LogManagerFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.common.logging.LogManagerFactoryException
  Constructs a `LogManagerFactoryException` with the specified detailed message and a cause.
LogManagerFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.common.logging.LogManagerFactoryException
  Constructs a `LogManagerFactoryException` with the specified detailed message and a cause.
logMemoryUsage() - Method in class edu.isi.pegasus.planner.client.CPlanner
  Logs memory usage of the JVM
logMemoryUsage() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a boolean indicating whether to log JVM memory usage or not.
logMessage(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  Logs the message to a logging stream.
logMessage(String) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Logs the message to a logging stream.
logMessage(String) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Logs the message to a logging stream.
logMetrics(PlannerMetrics) - Method in class edu.isi.pegasus.planner.code.generator.Metrics
  Logs the metrics to the metrics server and to the submit directory
logRefinerAction(AggregatedJob, JobAggregator) - Method in class edu.isi.pegasus.planner.cluster.Horizontal
  Records the refiner action into the Provenace Store as a XML fragment.
logRefinerAction(Job) - Method in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  Logs the action taken by the refiner on a job as a XML fragment in the XML Producer.
logRefinerAction(Job, Job, Collection, String) - Method in class edu.isi.pegasus.planner.transfer.refiner.Basic
  Records the refiner action into the Provenace Store as a XML fragment.
logRemoval(Job, PegasusFile, String, boolean) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  Helped method for logging removal message.
logSuccessfulCompletion(boolean) - Method in class edu.isi.pegasus.planner.client.CPlanner
  Logs the successful completion message.
longFormat - Variable in class edu.isi.pegasus.gridftp.FileInfo
longFormat - Variable in class edu.isi.pegasus.gridftp.ListCommand
lookup(String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Retrieves the entry for a given directory and site handle from the replica catalog.
lookup(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Retrieves all entries for a given LFN from the replica catalog.
lookup(Set) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Retrieves multiple entries for a given logical directory, up to the complete catalog.
lookup(Set, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Retrieves multiple entries for a given logical directory, up to the complete catalog.
lookup(Map) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Retrieves multiple entries for a given logical directory, up to the complete catalog.
lookup(String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
lookup(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
lookup(Set) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
lookup(Set, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
lookup(Map) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
lookup(String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Retrieves the entry for a given filename and site handle from the replica catalog.
lookup(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Retrieves all entries for a given LFN from the replica catalog.
lookup(Set) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookup(Set, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookup(Map) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookup(String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Retrieves the entry for a given filename and resource handle from the replica catalog.
lookup(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Retrieves all entries for a given LFN from the replica catalog.
lookup(Set, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookup(Map) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookup(Set) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookup(String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Retrieves the entry for a given filename and site handle from the replica catalog.
lookup(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Retrieves all entries for a given LFN from the replica catalog.
lookup(Set) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookup(Set, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookup(Map) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookup(String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Retrieves the entry for a given filename and site handle from the replica catalog.
lookup(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Retrieves all entries for a given LFN from the replica catalog.
lookup(Set) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookup(Set, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookup(Map) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookup(String, String) - Method in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Retrieves the entry for a given filename and resource handle from the replica catalog.
lookup(String) - Method in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Retrieves all entries for a given LFN from the replica catalog.
lookup(Set) - Method in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookup(Set, String) - Method in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookup(Map) - Method in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookup(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  Returns SiteCatalogEntry matching a site handle.
lookup(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
lookup(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML
  Retrieves the `SiteCatalogEntry` for a site.
lookup(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  Retrieves the `SiteCatalogEntry` for a site.
lookup(String) - Method in interface edu.isi.pegasus.planner.catalog.SiteCatalog
  Retrieves the `SiteCatalogEntry` for a site.
lookup(String, String, String, String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Returns TC entries for a particular logical transformation and/or on a particular resource and/or of a particular type.
lookup(String, String, String, List, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Returns TC entries for a particular logical transformation and/or on a number of resources and/or of a particular type.
lookup(String, String, String, List, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Returns TC entries for a particular logical transformation and/or on a number of resources and/or of a particular type.
lookup(String, String, String, String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Returns TC entries for a particular logical transformation and/or on a particular resource and/or of a particular type.
lookup(String, String, String, List, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Returns TC entries for a particular logical transformation and/or on a number of resources and/or of a particular type.
lookup(String, String, String, String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Returns TC entries for a particular logical transformation and/or on a particular resource and/or of a particular type.
lookup(String, String, String, String, TCType) - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Returns TC entries for a particular logical transformation and/or on a particular resource and/or of a particular type.
lookup(String, String, String, List, TCType) - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Returns TC entries for a particular logical transformation and/or on a number of resources and/or of a particular type.
lookup(String, FileServerType.OPERATION) - Method in class edu.isi.pegasus.planner.classes.PlannerCache
  Retrieves all entries for a given LFN from the replica catalog.
lookup(String, String, FileServerType.OPERATION) - Method in class edu.isi.pegasus.planner.classes.PlannerCache
  Retrieves the entry for a given filename and resource handle from the replica catalog.
lookupConfProperty(String[], char) - Method in class edu.isi.pegasus.planner.client.Executable
  Looks up for the conf property in the arguments passed to the executable
lookupConfProperty(String[], char) - Method in class edu.isi.pegasus.planner.client.RCClient
  Looks up for the conf property in the command line arguments passed to the RCClient
lookupLFNProfiles(String, String, String) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Get the list of Profiles associated with a particular logical transformation.
lookupLFNProfiles(String, String, String) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Get the list of Profiles associated with a particular logical transformation.
lookupLFNProfiles(String, String, String) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Get the list of Profiles associated with a particular logical transformation.
lookupLFNProfiles(String, String, String) - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Get the list of Profiles associated with a particular logical transformation.
lookupNoAttributes(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Retrieves all entries for a given LFN from the replica catalog.
lookupNoAttributes(Set) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Retrieves multiple entries for a given logical directory, up to the complete catalog.
lookupNoAttributes(Set, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Retrieves multiple entries for a given logical directory, up to the complete catalog.
lookupNoAttributes(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
lookupNoAttributes(Set) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
lookupNoAttributes(Set, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
lookupNoAttributes(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Retrieves all entries for a given LFN from the replica catalog.
lookupNoAttributes(Set) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookupNoAttributes(Set, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookupNoAttributes(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Retrieves all entries for a given LFN from the replica catalog.
lookupNoAttributes(Set) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookupNoAttributes(Set, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookupNoAttributes(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Retrieves all entries for a given LFN from the replica catalog.
lookupNoAttributes(Set) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookupNoAttributes(Set, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookupNoAttributes(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Retrieves all entries for a given LFN from the replica catalog.
lookupNoAttributes(Set) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookupNoAttributes(Set, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookupNoAttributes(String) - Method in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Retrieves all entries for a given LFN from the replica catalog.
lookupNoAttributes(Set) - Method in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookupNoAttributes(Set, String) - Method in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Retrieves multiple entries for a given logical filename, up to the complete catalog.
lookupNoProfiles(String, String, String, String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Get the list of PhysicalNames for a particular transformation on a site/sites for a particular type/types;
lookupNoProfiles(String, String, String, String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Get the list of PhysicalNames for a particular transformation on a site/sites for a particular type/types;
lookupNoProfiles(String, String, String, String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Get the list of PhysicalNames for a particular transformation on a site/sites for a particular type/types;
lookupNoProfiles(String, String, String, String, TCType) - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Get the list of PhysicalNames for a particular transformation on a site/sites for a particular type/types;
lookupPFNProfiles(String, String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Get the list of Profiles associated with a particular physical transformation.
lookupPFNProfiles(String, String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Get the list of Profiles associated with a particular physical transformation.
lookupPFNProfiles(String, String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Get the list of Profiles associated with a particular physical transformation.
lookupPFNProfiles(String, String, TCType) - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Get the list of Profiles associated with a particular physical transformation.
lookupSites(String, String, String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Get the list of Resource ID's where a particular transformation may reside.
lookupSites(String, String, String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Get the list of Resource ID's where a particular transformation may reside.
lookupSites(String, String, String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Get the list of Resource ID's where a particular transformation may reside.
lookupSites(String, String, String, TCType) - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Get the list of Resource ID's where a particular transformation may reside.
lookupStorageDirectory(String) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.AbstractFileFactoryBasedMapper
  Looks up the site catalog to return the storage directory for a site
lookupWithHandle(String, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
LOWEST_RANK_VALUE - Static variable in class edu.isi.pegasus.planner.selector.replica.Regex
  The lowest rank value
LRC - Class in edu.isi.pegasus.planner.catalog.site.impl.old.classes
  This is a data class that is used to store information about a local replica catalog, that is associated with a site in the pool configuration catalog.
LRC(String) - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.old.classes.LRC
  Constructor for the class.
LRC - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  The constant to be passed to the accessor functions to get or set the list of `LRC` objects for the remote site.
LRC - Static variable in class edu.isi.pegasus.planner.parser.tokens.SiteCatalogReservedWord
  token value for the reserved word "lrc".
ls(String) - Method in class edu.isi.pegasus.gridftp.GridFTPConnection
  List contents of path in short (filename only) format
ls(String, boolean) - Method in class edu.isi.pegasus.gridftp.GridFTPConnection
  List contents of path.

## M

m_application - Variable in class edu.isi.pegasus.planner.client.VersionNumber
  application's own name.
m_archmode - Variable in class edu.isi.pegasus.planner.invocation.Architecture
  Describes the architecture runtime mode.
m_arguments - Variable in class edu.isi.pegasus.planner.invocation.Job
  Command-line arguments.
m_argv - Variable in class edu.isi.pegasus.planner.invocation.ArgVector
  This is the (new) alternative explicit argument vector.
m_atime - Variable in class edu.isi.pegasus.planner.invocation.StatInfo
  Contains the last access time timestamp.
m_attributeMap - Variable in class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  Any optional attributes associated with the PFN.
m_autoinc - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Remembers if obtaining generated keys will work or not.
m_autoinc - Variable in class edu.isi.pegasus.planner.catalog.work.Database
  Remembers if obtaining generated keys will work or not.
m_avg_line_size - Static variable in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
  No.
m_batch - Variable in class edu.isi.pegasus.planner.client.RCClient
  Indication of batch mode.
m_binDir - Variable in class edu.isi.pegasus.common.util.CommonProperties
  The bin dir of the Pegasus install
m_blksize - Variable in class edu.isi.pegasus.planner.invocation.StatInfo
  Stores the blocksize of the file.
m_blocks - Variable in class edu.isi.pegasus.planner.invocation.StatInfo
  Stores the number of blocks of the file.
m_buffer_size - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
  No.
m_chunk_factor - Variable in class edu.isi.pegasus.planner.client.RCClient
  The number of lines that are to be parsed for chunking up large input files.
m_classname - Variable in class edu.isi.pegasus.common.util.DynamicLoader
  Stores the fully qualified class name to dynamically instantiate.
m_coarse - Variable in class edu.isi.pegasus.planner.parser.InvocationParser
  Parsing for ISO dates without milliseconds
m_conf_property_file - Variable in class edu.isi.pegasus.planner.client.RCClient
  Reference to the property file passed using the --conf option
m_core - Variable in class edu.isi.pegasus.planner.invocation.JobStatusSignal
  This flag signals, if a core file was generated.
m_count - Variable in class edu.isi.pegasus.planner.invocation.Fifo
  optional message count for the FIFO.
m_ctime - Variable in class edu.isi.pegasus.planner.invocation.StatInfo
  Contains the creation time timestamp.
m_cwd - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Working directory at startup.
m_data - Variable in class edu.isi.pegasus.planner.invocation.StatCall
  Optional data gleaned from stdout or stderr.
m_dbschema - Variable in class edu.isi.pegasus.planner.invocation.SimpleServer
m_depth - Variable in class edu.isi.pegasus.planner.parser.InvocationParser
  Count the depths of elements in the document
m_derivation - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Name of the Derivation that produced this invocation.
m_descriptor - Variable in class edu.isi.pegasus.planner.invocation.Descriptor
  Descriptor of the file.
m_descriptor - Variable in class edu.isi.pegasus.planner.invocation.Temporary
  Descriptor of the file.
m_domainname - Variable in class edu.isi.pegasus.planner.invocation.Architecture
  Contains the optional domain name on the network.
m_duration - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  total duration of call.
m_duration - Variable in class edu.isi.pegasus.planner.invocation.Job
  Duration of the job.
m_emptyFail - Variable in class edu.isi.pegasus.planner.invocation.SimpleServer
m_environment - Variable in class edu.isi.pegasus.planner.invocation.Environment
  Mappings of keys to values
m_environment - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Environment settings.
m_errno - Variable in class edu.isi.pegasus.planner.invocation.JobStatusFailure
  This is the errno value with the reason that the invocation of the application failed.
m_errno - Variable in class edu.isi.pegasus.planner.invocation.StatCall
  value of errno after calling any stat function, or -1 for failure.
m_errors - Variable in class edu.isi.pegasus.planner.client.DAXValidator
  Counts the number of errors.
m_escapable - Variable in class edu.isi.ikcap.workflows.util.logging.Escape
  Defines the set of characters that require escaping.
m_escapable - Variable in class edu.isi.pegasus.common.util.Escape
  Defines the set of characters that require escaping.
m_escape - Variable in class edu.isi.ikcap.workflows.util.logging.Escape
  Defines the character used to escape characters.
m_escape - Variable in class edu.isi.pegasus.common.util.Escape
  Defines the character used to escape characters.
m_executable - Variable in class edu.isi.pegasus.planner.invocation.Arguments
  This is the executable that was run.
m_executable - Variable in class edu.isi.pegasus.planner.invocation.CommandLine
  This is the executable that was run.
m_executable - Variable in class edu.isi.pegasus.planner.invocation.Job
  Stat call of the executable.
m_exitcode - Variable in class edu.isi.pegasus.planner.invocation.JobStatusRegular
  This is exit code returned by the application.
m_fatals - Variable in class edu.isi.pegasus.planner.client.DAXValidator
  Counts the number of fatal errors.
m_file - Variable in class edu.isi.pegasus.planner.invocation.StatCall
  the object (fn,fd) that the stat call was taken on.
m_filename - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Records the name of the on-disk representation.
m_filename - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Records the name of the on-disk representation.
m_filename - Variable in class edu.isi.pegasus.planner.invocation.Regular
  Name of the file.
m_filename - Variable in class edu.isi.pegasus.planner.invocation.Temporary
  Name of the file.
m_fine - Variable in class edu.isi.pegasus.planner.parser.InvocationParser
  Parsing for ISO dates with millisecond extension.
m_formatter - Variable in class edu.isi.pegasus.common.util.Currently
  This is used to format the time stamp.
m_forward - Variable in class edu.isi.pegasus.planner.parser.InvocationParser
  A Hashmap to forward resolve namespaces that were encountered during parsing.
m_gid - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  numerical group id of the effective user.
m_gid - Variable in class edu.isi.pegasus.planner.invocation.StatInfo
  group id of the owner of the file.
m_group - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  symbolical group name of the effective user.
m_group - Variable in class edu.isi.pegasus.planner.invocation.StatInfo
  symbolical group name of the effective user.
m_handle - Variable in class edu.isi.pegasus.planner.invocation.StatCall
  optional handle for stat calls of the invocation record
m_hexbyte - Variable in class edu.isi.pegasus.planner.invocation.File
  optional first 16 byte of file, or less if shorter.
m_hostaddr - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  host address where gridlaunch ran (primary interface).
m_hostname - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Symbolic hostname where gridlaunch ran (primary interface).
m_identifiers - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
m_idrss - Variable in class edu.isi.pegasus.planner.invocation.Usage
  integral unshared data size, or private integral resident set size.
m_in - Variable in class edu.isi.pegasus.planner.parser.SiteCatalogTextScanner
  Stores the stream from which we are currently scanning.
m_inblock - Variable in class edu.isi.pegasus.planner.invocation.Usage
  block input operations.
m_info - Variable in class edu.isi.pegasus.planner.invocation.MachineSpecific
  The List of `MachineInfo` elements associated with the machine.
m_inode - Variable in class edu.isi.pegasus.planner.invocation.StatInfo
  We store the inode number, which let's us reference a file uniquely per filesystem.
m_instance - Static variable in class edu.isi.pegasus.common.util.CommonProperties
  implements the singleton access via class variable.
m_interface - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Symbolic name of primary interface we used to determine host-name and -address.
m_isrss - Variable in class edu.isi.pegasus.planner.invocation.Usage
  integral stoack size.
m_ixrss - Variable in class edu.isi.pegasus.planner.invocation.Usage
  integral shared memory size.
m_job - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Job records: prejob, main job, postjob
m_jobStatus - Variable in class edu.isi.pegasus.planner.invocation.Status
  This member variable contains the real status of the job.
m_key - Variable in class edu.isi.pegasus.planner.catalog.site.impl.XML2
m_key - Variable in class edu.isi.pegasus.planner.invocation.EnvEntry
  environment handle
m_key - Variable in class edu.isi.pegasus.planner.parser.ConfigXmlParser
m_lfn - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Maintains a memory slurp of the file representation.
m_lfn - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Maintains a memory slurp of the file representation.
m_lfn - Variable in class edu.isi.pegasus.planner.invocation.StatCall
  optional logical filename associated with this stat call
m_lfn_pattern - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
m_lfn_regex - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
m_line_count - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
  No.
m_lineno - Variable in exception edu.isi.pegasus.planner.parser.ScannerException
m_location - Variable in class edu.isi.pegasus.planner.client.DAXValidator
  Keep the location within the document.
m_location - Variable in class edu.isi.pegasus.planner.parser.InvocationParser
  Keep the location within the document
m_log - Variable in class edu.isi.pegasus.planner.client.RCClient
  Our own logger.
m_log - Variable in class edu.isi.pegasus.planner.parser.InvocationParser
  Obtain our logger once for multiple uses.
m_logger - Variable in class edu.isi.pegasus.planner.parser.SiteCatalogTextParser
  The handle to the logger used to log messages.
m_lookAhead - Variable in class edu.isi.pegasus.planner.parser.SiteCatalogTextParser
  Stores the look-ahead symbol.
m_lookAhead - Variable in class edu.isi.pegasus.planner.parser.SiteCatalogTextScanner
  Captures the look-ahead character.
m_machine - Variable in class edu.isi.pegasus.planner.invocation.Architecture
  Contains the machine's hardware description.
m_machine - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  The Machine object capturing machine information.
m_majflt - Variable in class edu.isi.pegasus.planner.invocation.Usage
  major page faults - incurred subsystem IO, sometimes includes swap.
m_maxrss - Variable in class edu.isi.pegasus.planner.invocation.Usage
  maximum resident set size.
m_minflt - Variable in class edu.isi.pegasus.planner.invocation.Usage
  minor page faults - sometimes also recovered pages.
m_mode - Variable in class edu.isi.pegasus.planner.invocation.StatInfo
  Is the number for the file mode.
m_msgrcv - Variable in class edu.isi.pegasus.planner.invocation.Usage
  messages received.
m_msgsnd - Variable in class edu.isi.pegasus.planner.invocation.Usage
  messages sent.
m_mtime - Variable in class edu.isi.pegasus.planner.invocation.StatInfo
  Contains the last modification time timestamp;
m_name - Variable in class edu.isi.pegasus.planner.parser.IVSElement
m_namespace - Variable in class edu.isi.pegasus.planner.catalog.site.impl.XML2
m_namespace - Variable in class edu.isi.pegasus.planner.parser.ConfigXmlParser
m_next_exception - Variable in exception edu.isi.pegasus.planner.catalog.CatalogException
  chains the next exception into line.
m_nivcsw - Variable in class edu.isi.pegasus.planner.invocation.Usage
  involuntary conext switches.
m_nlink - Variable in class edu.isi.pegasus.planner.invocation.StatInfo
  Stores the number of hard links to the file.
m_noDBase - Variable in class edu.isi.pegasus.planner.invocation.SimpleServer
m_nodename - Variable in class edu.isi.pegasus.planner.invocation.Architecture
  Describes the machine's network node hostname.
m_nsignals - Variable in class edu.isi.pegasus.planner.invocation.Usage
  number of signals sent to process.
m_nswap - Variable in class edu.isi.pegasus.planner.invocation.Usage
  number of swap operations - unused in Linux unless kernel patched.
m_nvcsw - Variable in class edu.isi.pegasus.planner.invocation.Usage
  voluntary context switches.
m_obj - Variable in class edu.isi.pegasus.planner.parser.IVSElement
m_out - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
  A buffered writer, to buffer all file writes being performed.
m_outblock - Variable in class edu.isi.pegasus.planner.invocation.Usage
  block output operations.
m_pagesize - Variable in class edu.isi.pegasus.planner.invocation.Machine
  The only attribute to the machine element is required.
m_parser - Variable in class edu.isi.pegasus.planner.invocation.SimpleServer
m_parser - Variable in class edu.isi.pegasus.planner.parser.InvocationParser
  Holds the instance of a `XMLReader` class.
m_pconfig - Variable in class edu.isi.pegasus.planner.catalog.site.impl.XML2
m_pconfig - Variable in class edu.isi.pegasus.planner.parser.ConfigXmlParser
m_pegasus_props - Variable in class edu.isi.pegasus.planner.client.RCClient
  The object holding all the properties pertaining to Pegasus.
m_pfn - Variable in class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  The physical filename.
m_pid - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  process id of gridlaunch itself.
m_pid - Variable in class edu.isi.pegasus.planner.invocation.Job
  Process id assigned to the job.
m_pmem - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Records the physical memory on the remote machine, if available.
m_pool_info - Variable in class edu.isi.pegasus.planner.catalog.site.impl.XML2
m_pool_info - Variable in class edu.isi.pegasus.planner.parser.ConfigXmlParser
m_position - Variable in exception edu.isi.pegasus.common.util.ProfileParserException
  Remembers the position that cause the exception to be thrown.
m_position - Variable in class edu.isi.pegasus.planner.invocation.ArgEntry
  argument vector position
m_prefs - Variable in class edu.isi.pegasus.planner.client.RCClient
  Maintains instance-local settings on user preferences.
m_props - Variable in class edu.isi.pegasus.common.util.CommonProperties
  internal set of properties.
m_quote - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Records the quoting mode for LFNs and PFNs.
m_quote - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Records the quoting mode for LFNs and PFNs.
m_rc - Variable in class edu.isi.pegasus.planner.client.RCClient
  Maintains the interface to the replica catalog implementation.
m_reader - Variable in class edu.isi.pegasus.planner.client.DAXValidator
  Holds the instance of a `XMLReader` class.
m_readonly - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  A boolean indicating whether the catalog is read only or not.
m_readonly - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  A boolean indicating whether the catalog is read only or not.
m_release - Variable in class edu.isi.pegasus.planner.invocation.Architecture
  Contains the operating system's version string.
m_remote - Variable in class edu.isi.pegasus.planner.invocation.SimpleServerThread
m_resource - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Resource, site or pool at which the jobs was run.
m_result - Variable in class edu.isi.pegasus.planner.parser.InvocationParser
  Holds the result, will be overwritten by each invocation of parse().
m_reverse - Variable in class edu.isi.pegasus.planner.parser.InvocationParser
  A Hashmap to reverse resolve namespaces that were encountered during parsing.
m_rls_logger - Variable in class edu.isi.pegasus.planner.client.RCClient
  Logger for RLS implementation for the time being.
m_root - Static variable in class edu.isi.pegasus.planner.client.RCClient
  Keeps track of log4j's root logger as singleton.
m_rsize - Variable in class edu.isi.pegasus.planner.invocation.Fifo
  optional number of bytes read from FIFO.
m_scanner - Variable in class edu.isi.pegasus.planner.parser.SiteCatalogTextParser
  The access to the lexical scanner is stored here.
m_schemaDir - Variable in class edu.isi.pegasus.common.util.CommonProperties
  Location of our schemas
m_schemafile - Variable in class edu.isi.pegasus.planner.client.DAXValidator
  what is the name of the schema file in the filename hint?
m_server - Variable in class edu.isi.pegasus.planner.invocation.SimpleServer
m_server - Variable in class edu.isi.pegasus.planner.invocation.SimpleServerThread
m_sharedStateDir - Variable in class edu.isi.pegasus.common.util.CommonProperties
  GNU: modifiable architecture-independent data in DIR [PREFIX/share/pegasus].
m_signo - Variable in class edu.isi.pegasus.planner.invocation.JobStatusSignal
  This is the signal number that led to the process termination.
m_signo - Variable in class edu.isi.pegasus.planner.invocation.JobStatusSuspend
  This is the signal number that led to the suspension.
m_size - Variable in class edu.isi.pegasus.planner.invocation.StatInfo
  Denotes the size of the file.
m_socket - Variable in class edu.isi.pegasus.planner.invocation.SimpleServerThread
m_specific - Variable in class edu.isi.pegasus.planner.invocation.Machine
  This is a grouping element for the remaining machine-specific items.
m_stack - Variable in class edu.isi.pegasus.planner.parser.InvocationParser
  A stack of namespaces?
m_stamp - Variable in class edu.isi.pegasus.planner.invocation.Machine
  The time when the snapshot was taken.
m_start - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  start of gridlaunch timestamp.
m_start - Variable in class edu.isi.pegasus.planner.invocation.Job
  Start time of this job.
m_stat - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Array with stat() and fstat() information about various files.
m_statinfo - Variable in class edu.isi.pegasus.planner.invocation.StatCall
  the stat information itself, only present for unfailed calls.
m_status - Variable in class edu.isi.pegasus.planner.invocation.Job
  Exit condition of the job.
m_status - Variable in class edu.isi.pegasus.planner.invocation.Status
  The raw exit code, unparsed and unprepared.
m_stime - Variable in class edu.isi.pegasus.planner.invocation.Usage
  system time - time spent in system mode, seconds with fraction.
m_symbolTable - Static variable in class edu.isi.pegasus.planner.parser.tokens.SiteCatalogReservedWord
  Singleton implementation of a symbol table for reserved words.
m_sysConfDir - Variable in class edu.isi.pegasus.common.util.CommonProperties
  GNU: read-only single-machine data in DIR [PREFIX/etc].
m_sysname - Variable in class edu.isi.pegasus.planner.invocation.Architecture
  Describes the operating system name.
m_tag - Variable in class edu.isi.pegasus.planner.invocation.Job
  This is the tag to produce the job for.
m_tag - Variable in class edu.isi.pegasus.planner.invocation.MachineSpecific
  This is the tag to group the machine-specific information.
m_total_lines_succ_worked - Variable in class edu.isi.pegasus.planner.client.RCClient
  The total number of lines on which the client has successfully worked on till yet.
m_total_lines_worked - Variable in class edu.isi.pegasus.planner.client.RCClient
  The total number of lines on which the client has worked on till yet.
m_transformation - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Name of the: Transformation that produced this invocation.
m_truncated - Variable in class edu.isi.pegasus.planner.invocation.Data
  Indicates, if the data is only partial.
m_uid - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  numerical user id of the effective user.
m_uid - Variable in class edu.isi.pegasus.planner.invocation.StatInfo
  user id of the owner of the file.
m_umask - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Currently active umask while kickstart was executing.
m_uname - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Architectural information.
m_uname - Variable in class edu.isi.pegasus.planner.invocation.Machine
  The uname child element is mandatory.
m_usage - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Total resource consumption by gridlaunch and all siblings.
m_usage - Variable in class edu.isi.pegasus.planner.invocation.Job
  Resource usage of this job.
m_usage1 - Static variable in class edu.isi.pegasus.planner.client.ExitCode
  Just a string to denote the short usage.
m_user - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  symbolical user name of the effective user.
m_user - Variable in class edu.isi.pegasus.planner.invocation.StatInfo
  symbolical user name of the effective user.
m_utime - Variable in class edu.isi.pegasus.planner.invocation.Usage
  user time - time spent in user mode, seconds with fraction.
m_value - Variable in class edu.isi.pegasus.planner.invocation.Architecture
  This is the data contained between the tags.
m_value - Variable in class edu.isi.pegasus.planner.invocation.ArgEntry
  argument vector value
m_value - Variable in class edu.isi.pegasus.planner.invocation.ArgString
  This is the data contained between the tags.
m_value - Variable in class edu.isi.pegasus.planner.invocation.CommandLine
  This is the data contained between the tags.
m_value - Variable in class edu.isi.pegasus.planner.invocation.Data
  This is the data contained between the tags.
m_value - Variable in class edu.isi.pegasus.planner.invocation.EnvEntry
  environment value
m_value - Variable in class edu.isi.pegasus.planner.invocation.JobStatusFailure
  This is the data contained between the tags.
m_value - Variable in class edu.isi.pegasus.planner.invocation.JobStatusSignal
  This is the signal name or message contained between the tags.
m_value - Variable in class edu.isi.pegasus.planner.invocation.JobStatusSuspend
  This is the data contained between the tags.
m_value - Variable in class edu.isi.pegasus.planner.invocation.WorkingDir
  This is the data contained between the tags.
m_value - Variable in class edu.isi.pegasus.planner.parser.tokens.Identifier
  This instance variable captures the token value for the reserved word.
m_value - Variable in class edu.isi.pegasus.planner.parser.tokens.QuotedString
  This instance variable captures the token value for the quoted string.
m_value - Variable in class edu.isi.pegasus.planner.parser.tokens.SiteCatalogReservedWord
  This instance variable captures the token value for the reserved word.
m_verbose - Variable in class edu.isi.pegasus.planner.client.DAXValidator
  How verbose should we be?
m_version - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  protocol version information.
m_warnings - Variable in class edu.isi.pegasus.planner.client.DAXValidator
  Counts the number of warnings.
m_wf_label - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Workflow label, currently optional?
m_wf_stamp - Variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Workflow timestamp to make the label more unique.
m_wsize - Variable in class edu.isi.pegasus.planner.invocation.Fifo
  optional number of bytes written - but not to the FIFO.
mAbstractChildID - Variable in class edu.isi.pegasus.planner.classes.PCRelation
  The abstract id for the child node.
mAbstractDag - Variable in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  The abstract DAG.
mAbstractGraph - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2Graph
  The map containing the a graph node for each of the jobs referred to in the dax.
mAbstractParentID - Variable in class edu.isi.pegasus.planner.classes.PCRelation
  The abstract id for the parent node.
Machine - Class in edu.isi.pegasus.planner.invocation
  The Machine element groups a time stamp, the page size, the generic utsname information, and a machine-specific content collecting element.
Machine() - Constructor for class edu.isi.pegasus.planner.invocation.Machine
  Default constructor.
MACHINE_ATTRIBUTE_KEY - Static variable in class edu.isi.pegasus.planner.invocation.Uname
  The release attribute for the uname
MachineInfo - Class in edu.isi.pegasus.planner.invocation
  An abstract class that is used for all the child elements that appear in the machine element.
MachineInfo() - Constructor for class edu.isi.pegasus.planner.invocation.MachineInfo
  Default constructor.
MachineSpecific - Class in edu.isi.pegasus.planner.invocation
  This class collects the various OS-specific elements that we are capturing machine information for.
MachineSpecific(String) - Constructor for class edu.isi.pegasus.planner.invocation.MachineSpecific
  Default constructor.
mAddDataDependencies - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2CDAG
  To track whether we auto detect data dependancies or not.
mAddNodesForSettingXBit - Variable in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  A boolean indicating whether chmod jobs should be created that set the xbit in case of executable staging.
mAddNodesForSettingXBit - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  A boolean indicating whether chmod jobs should be created that set the xbit in case of executable staging.
mAddNodesForSettingXBit - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  A boolean indicating whether chmod jobs should be created that set the xbit in case of executable staging.
mAdjFName - Variable in class edu.isi.pegasus.planner.parser.Parser
  Boolean flag to ensure that two adjacent filenames are separated by a whitespace.
mAggregatorTable - Static variable in class edu.isi.pegasus.planner.namespace.Globus
  The table that maps the various globus profile keys to their aggregator functions.
main(String[]) - Static method in class edu.isi.ikcap.workflows.util.logging.Escape
  Test program.
main(String[]) - Static method in class edu.isi.pegasus.common.logging.TestLogFormatter
main(String[]) - Static method in class edu.isi.pegasus.common.util.CommonProperties
main(String[]) - Static method in class edu.isi.pegasus.common.util.CondorVersion
  The main program to test.
main(String[]) - Static method in class edu.isi.pegasus.common.util.Escape
  Test program.
main(String[]) - Static method in class edu.isi.pegasus.common.util.FindExecutable
  Test function for the class
main(String[]) - Static method in class edu.isi.pegasus.common.util.PegasusURL
  Test program
main(String[]) - Static method in class edu.isi.pegasus.common.util.ProfileParser
  Test program.
main(String[]) - Static method in class edu.isi.pegasus.common.util.Separator2Test
main(String[]) - Static method in class edu.isi.pegasus.common.util.SeparatorTest
main(String[]) - Static method in class edu.isi.pegasus.gridftp.PegasusGridFTP
main(String[]) - Static method in class edu.isi.pegasus.planner.catalog.classes.Profiles
main(String[]) - Static method in class edu.isi.pegasus.planner.catalog.classes.VDSSysInfo2NMI
main(String[]) - Static method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  The main program
main(String[]) - Static method in class edu.isi.pegasus.planner.catalog.replica.TestReplicaCatalog
  The main program.
main(String[]) - Static method in class edu.isi.pegasus.planner.catalog.site.classes.CreateSampleSiteCatalog
  The main program
main(String[]) - Static method in class edu.isi.pegasus.planner.catalog.site.impl.old.TestSiteCatalog
  The main program.
main(String[]) - Static method in class edu.isi.pegasus.planner.catalog.site.TestSiteCatalog
  The main program.
main(String[]) - Static method in class edu.isi.pegasus.planner.catalog.site.TestVORSSiteCatalog
  The main program.
main(String[]) - Static method in class edu.isi.pegasus.planner.catalog.transformation.TestTransformationCatalog
  The main program.
main(String[]) - Static method in class edu.isi.pegasus.planner.client.CPlanner
  The main program for the CPlanner.
main(String[]) - Static method in class edu.isi.pegasus.planner.client.DAXValidator
main(String[]) - Static method in class edu.isi.pegasus.planner.client.ExitCode
main(String[]) - Static method in class edu.isi.pegasus.planner.client.PartitionDAX
  The main function of the class, that is invoked by the jvm.
main(String[]) - Static method in class edu.isi.pegasus.planner.client.PegasusGetSites
  The main program
main(String[]) - Static method in class edu.isi.pegasus.planner.client.RankDAX
  The main program for the CPlanner.
main(String[]) - Static method in class edu.isi.pegasus.planner.client.RCClient
  Manipulate entries in a given replica catalog implementation.
main(String[]) - Static method in class edu.isi.pegasus.planner.client.SCClient
main(String[]) - Static method in class edu.isi.pegasus.planner.client.TCClient
main(String[]) - Static method in class edu.isi.pegasus.planner.client.TCConverter
  The main function
main(String[]) - Static method in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  The main test program.
main(String[]) - Static method in class edu.isi.pegasus.planner.client.VersionNumber
main(String[]) - Static method in class edu.isi.pegasus.planner.code.generator.condor.CondorQuoteParser
  A Test program.
main(String[]) - Static method in class edu.isi.pegasus.planner.code.gridstart.PegasusExitCodeEncode
  Test program.
main(String[]) - Static method in class edu.isi.pegasus.planner.dax.ADAG
  Create an example DIAMOND DAX
main(String[]) - Static method in class edu.isi.pegasus.planner.dax.examples.Diamond
  Create an example DIAMOND DAX
main(String[]) - Static method in class edu.isi.pegasus.planner.dax.examples.Pipeline
main(String[]) - Static method in class edu.isi.pegasus.planner.invocation.SimpleServer
main(String[]) - Static method in class edu.isi.pegasus.planner.namespace.TestNamespace
main(String[]) - Static method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  The main program.
main(String[]) - Static method in class edu.isi.pegasus.planner.parser.dax.DAXParser3
main(String[]) - Static method in class edu.isi.pegasus.planner.parser.IVPTest
main(String[]) - Static method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser3
main(String[]) - Static method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser4
main(String[]) - Static method in class edu.isi.pegasus.planner.parser.TestDAXParser
  The main program to TestDAXParser.
main(String[]) - Static method in class edu.isi.pegasus.planner.parser.TransformationCatalogTextParser
  Test function.
main(String[]) - Static method in class edu.isi.pegasus.planner.provisioner.Estimator
main(String[]) - Static method in class edu.isi.pegasus.planner.ranking.GetDAX
  For Testing purposes only.
main(String[]) - Static method in class edu.isi.pegasus.planner.refiner.Authenticate
main(String[]) - Static method in class edu.isi.pegasus.planner.refiner.AuthenticateEngine
  The main testing method.
main(String[]) - Static method in class edu.isi.pegasus.planner.refiner.TestReduceEdges
main(String[]) - Static method in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  The main program that allows you to test.
main(String[]) - Static method in class edu.isi.pegasus.planner.transfer.TestTPT
main(String[]) - Static method in class ShowProperties
  Runs the main program.
MainEngine - Class in edu.isi.pegasus.planner.refiner
  The central class that calls out to the various other components of Pegasus.
MainEngine(ADag, PegasusBag) - Constructor for class edu.isi.pegasus.planner.refiner.MainEngine
  This constructor initialises the class variables to the variables passed.
MAJOR - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GlobusVersion
  The constant for the major version type.
makeAbstractAggregatedJobConcrete(AggregatedJob) - Method in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  Enables the abstract clustered job for execution and converts it to it's executable form
makeAbstractAggregatedJobConcrete(AggregatedJob) - Method in class edu.isi.pegasus.planner.cluster.aggregator.MPIExec
  Enables the abstract clustered job for execution and converts it to it's executable form.
makeAbstractAggregatedJobConcrete(AggregatedJob) - Method in class edu.isi.pegasus.planner.cluster.aggregator.SeqExec
  Enables the abstract clustered job for execution and converts it to it's executable form.
makeAbstractAggregatedJobConcrete(AggregatedJob) - Method in interface edu.isi.pegasus.planner.cluster.JobAggregator
  Enables the abstract clustered job for execution and converts it to it's executable form
makeCreateDirJob(String, String, String) - Method in class edu.isi.pegasus.planner.refiner.createdir.DefaultImplementation
  It creates a make directoryURL job that creates a directoryURL on the remote pool using the perl executable that Gaurang wrote.
makeCreateDirJob(String, String, String) - Method in interface edu.isi.pegasus.planner.refiner.createdir.Implementation
  It creates a make directory job that creates a directory on the remote pool using the perl executable that Gaurang wrote.
MakeDirectoryCommand - Class in edu.isi.pegasus.gridftp
  Implements the mkdir command for remote GridFTP servers
MakeDirectoryCommand(boolean, boolean) - Constructor for class edu.isi.pegasus.gridftp.MakeDirectoryCommand
makeDummyConcatJob(ADag) - Method in class edu.isi.pegasus.planner.refiner.createdir.HourGlass
  It creates a dummy concat job that is run at the local submit host.
makeIntermediate - Variable in class edu.isi.pegasus.gridftp.MakeDirectoryCommand
makeRCRegNode(String, Job, Collection) - Method in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  It constructs the Job object for the registration node, which registers the materialized files on the output pool in the RLS.
makeRemoveDirJob(String, String) - Method in class edu.isi.pegasus.planner.refiner.RemoveDirectory
  It creates a remove directory job that creates a directory on the remote pool using the perl executable that Gaurang wrote.
makeRemoveDirJob(String, String, List<String>) - Method in class edu.isi.pegasus.planner.refiner.RemoveDirectory
  It creates a remove directory job that creates a directory on the remote pool using the perl executable that Gaurang wrote.
makeUntarJob(String, String, String) - Method in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  It creates a untar job , that untars the worker package that is staged by the setup transfer job.
MALFORMED_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Namespace
  Either the key or the value specified is null or malformed.
malformedKey(String, String) - Method in class edu.isi.pegasus.planner.namespace.Namespace
  Warns about a namespace profile key-value pair that is malformed.
mAliases - Variable in class edu.isi.pegasus.planner.catalog.site.classes.ReplicaCatalog
  Set of alias names to be used for lookup.
mAllDeletedJobs - Variable in class edu.isi.pegasus.planner.refiner.DataReuseEngine
  List of all deleted jobs during workflow reduction.
mAllDeletedNodes - Variable in class edu.isi.pegasus.planner.refiner.DataReuseEngine
  List of all deleted jobs during workflow reduction.
map(String) - Method in class edu.isi.pegasus.planner.parser.InvocationParser
  Helper function to map prefixes correctly onto the elements.
map(String, String, FileServerType.OPERATION) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.AbstractFileFactoryBasedMapper
  Maps a LFN to a location on the filsystem of a site and returns a single externally accessible URL corresponding to that location.
map(String, String, FileServerType.OPERATION, boolean) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.AbstractFileFactoryBasedMapper
  Maps a LFN to a location on the filsystem of a site and returns a single externally accessible URL corresponding to that location.
map(String, String, FileServerType.OPERATION) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Fixed
  Maps a LFN to a location on the filsystem of a site and returns a single externally accessible URL corresponding to that location.
map(String, String, FileServerType.OPERATION, boolean) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Fixed
  Maps a LFN to a location on the filsystem of a site and returns a single externally accessible URL corresponding to that location.
map(String, String, FileServerType.OPERATION) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Replica
  Maps a LFN to a location on the filsystem of a site and returns a single externally accessible URL corresponding to that location.
map(String, String, FileServerType.OPERATION, boolean) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Replica
  Maps a LFN to a location on the filsystem of a site and returns a single externally accessible URL corresponding to that location.
map(String, String, FileServerType.OPERATION) - Method in interface edu.isi.pegasus.planner.transfer.mapper.OutputMapper
  Maps a LFN to a location on the filsystem of a site and returns a single externally accessible URL corresponding to that location.
map(String, String, FileServerType.OPERATION, boolean) - Method in interface edu.isi.pegasus.planner.transfer.mapper.OutputMapper
  Maps a LFN to a location on the filsystem of a site and returns a single externally accessible URL corresponding to that location.
mapAll(String, String, FileServerType.OPERATION) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.AbstractFileFactoryBasedMapper
  Maps a LFN to a location on the filsystem of a site and returns all the possible equivalent externally accessible URL corresponding to that location.
mapAll(String, String, FileServerType.OPERATION) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Fixed
  Maps a LFN to a location on the filesystem of a site and returns all the possible equivalent externally accessible URL corresponding to that location.
mapAll(String, String, FileServerType.OPERATION) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Replica
  Maps a LFN to a location on the filsystem of a site and returns all the possible equivalent externally accessible URL corresponding to that location.
mapAll(String, String, FileServerType.OPERATION) - Method in interface edu.isi.pegasus.planner.transfer.mapper.OutputMapper
  Maps a LFN to a location on the filsystem of a site and returns all the possible equivalent externally accessible URL corresponding to that location.
MapGraph - Class in edu.isi.pegasus.planner.partitioner.graph
  An implementation of the Graph that is backed by a Map.
MapGraph() - Constructor for class edu.isi.pegasus.planner.partitioner.graph.MapGraph
  The default constructor.
MapGraph(boolean) - Constructor for class edu.isi.pegasus.planner.partitioner.graph.MapGraph
  The overloaded constructor
MapGraph.BottomUpIterator - Class in edu.isi.pegasus.planner.partitioner.graph
  An inner iterator class that traverses through the Graph bottom up.
MapGraph.MapGraphIterator - Class in edu.isi.pegasus.planner.partitioner.graph
  An inner iterator class that traverses through the Graph.
MapGraphIterator() - Constructor for class edu.isi.pegasus.planner.partitioner.graph.MapGraph.MapGraphIterator
  The default constructor.
mapJob(Job, List) - Method in class edu.isi.pegasus.planner.selector.site.AbstractPerJob
  Maps a job in the workflow to the various grid sites.
mapJob(Job, List) - Method in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  Calls out to the external site selector.
mapJob(Job, List) - Method in class edu.isi.pegasus.planner.selector.site.Random
  Maps a job in the workflow to an execution site.
mapJob(Job, List) - Method in class edu.isi.pegasus.planner.selector.site.RoundRobin
  Maps a job in the workflow to an execution site.
mapJob2ExecPool(Job, List) - Method in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  The call out to the site selector to determine on what pool the job should be scheduled.
Mapper - Class in edu.isi.pegasus.planner.catalog.transformation
  This is an interface for generating valid TC maps which will be used for executable staging.
Mapper(PegasusBag) - Constructor for class edu.isi.pegasus.planner.catalog.transformation.Mapper
  The private constructor.
Mapper - Interface in edu.isi.pegasus.planner.transfer.mapper
  An empty interface for all transfer Mappers that determine where a File should be on a particular site.
MapperException - Exception in edu.isi.pegasus.planner.transfer.mapper
  The baseclass of the exception that is thrown by all Mappers.
MapperException() - Constructor for exception edu.isi.pegasus.planner.transfer.mapper.MapperException
  Constructs a `MapperException` with no detail message.
MapperException(String) - Constructor for exception edu.isi.pegasus.planner.transfer.mapper.MapperException
  Constructs a `MapperException` with the specified detailed message.
MapperException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.transfer.mapper.MapperException
  Constructs a `MapperException` with the specified detailed message and a cause.
MapperException(Throwable) - Constructor for exception edu.isi.pegasus.planner.transfer.mapper.MapperException
  Constructs a `MapperException` with the specified just a cause.
mApplicationMetrics - Variable in class edu.isi.pegasus.planner.classes.PlannerMetrics
  The application metrics that need to be forwarded
mapWorkflow(ADag, List) - Method in class edu.isi.pegasus.planner.selector.site.AbstractPerJob
  Maps the jobs in the workflow to the various grid sites.
mapWorkflow(ADag, List) - Method in class edu.isi.pegasus.planner.selector.site.Group
  The call out to map a list of jobs on to the execution pools.
mapWorkflow(ADag, List) - Method in class edu.isi.pegasus.planner.selector.site.Heft
  Maps the jobs in the workflow to the various grid sites.
mapWorkflow(ADag, List, String) - Method in class edu.isi.pegasus.planner.selector.site.Heft
  Maps the jobs in the workflow to the various grid sites.
mapWorkflow(ADag, List) - Method in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  Maps the jobs in the workflow to the various grid sites.
mapWorkflow(ADag, List) - Method in interface edu.isi.pegasus.planner.selector.SiteSelector
  Maps the jobs in the workflow to the various grid sites.
mArch - Variable in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  An optional architecture type for the grid gateway.
mArch - Variable in class edu.isi.pegasus.planner.dax.Executable
  Architecture the executable is compiled for
mArchitecture - Variable in class edu.isi.pegasus.planner.catalog.classes.SysInfo
  The architecture.
mArchType - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The architecture type of the remote machines to which the jobmanager talks to.
mArguments - Variable in class edu.isi.pegasus.planner.dax.AbstractJob
mArgumentTag - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser2
mAssignDefaultJobPriorities - Variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Boolean indicating whether to assign job priorities or not.
matches() - Method in class edu.isi.pegasus.common.util.Version
  Determines, if the compiled version and the installed version match.
matches(String) - Method in class edu.isi.pegasus.planner.selector.replica.Regex.Rank
  Matches a string against the compiled regex expression
matchForStarProperties(String) - Method in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  Returns a matching pegasus property for a VDS star property.
matchingSubset(String, boolean) - Method in class edu.isi.pegasus.common.util.CommonProperties
  Extracts a specific property key subset from the known properties.
matchingSubset(Properties, String, boolean) - Static method in class edu.isi.pegasus.common.util.CommonProperties
  Extracts a specific property key subset from the properties passed.
matchingSubset(Properties, String, boolean) - Method in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  Extracts a specific property key subset from the known properties.
matchingSubset(String, boolean) - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Extracts a specific property key subset from the known properties.
matchMe(ReplicaCatalogEntry, ReplicaCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Attempts to see, if all keys in the partial replica catalog entry are contained in the full replica catalog entry.
matchMe(ReplicaCatalogEntry, ReplicaCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Attempts to see, if all keys in the partial replica catalog entry are contained in the full replica catalog entry.
matchMe(ReplicaCatalogEntry, ReplicaCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Attempts to see, if all keys in the partial replica catalog entry are contained in the full replica catalog entry.
mAttributeMap - Variable in class edu.isi.pegasus.planner.invocation.MachineInfo
  An internal maps that is indexed by attribute keys.
mAttributes - Variable in class edu.isi.pegasus.common.util.XMLWriter
mAuthEng - Variable in class edu.isi.pegasus.planner.refiner.MainEngine
  The handle to the Authentication Engine that performs the authentication with the various sites.
mAuthenticate - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  Whether to attempt authentication against the jobmanagers for the pools specified at runtime.
mAuthRequest - Variable in class edu.isi.pegasus.planner.refiner.Authenticate
  The object containing the authenticate request.
mAvailable - Variable in class edu.isi.pegasus.planner.refiner.ThreadPool.AuthenticateThread
  Whether the thread is available to do some work or not.
mAverageCommunicationCost - Variable in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  The average communication cost between nodes.
mAvgComputeTime - Variable in class edu.isi.pegasus.planner.selector.site.heft.HeftBag
  The average compute time for a node.
MAX - Class in edu.isi.pegasus.planner.namespace.aggregator
  An implementation of the Aggregator interface that takes the maximum of the profile values.
MAX() - Constructor for class edu.isi.pegasus.planner.namespace.aggregator.MAX
max - Variable in class edu.isi.pegasus.planner.provisioner.OccupationDiagram
max_bandwidth - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPBandwidth
Max_Bandwidth - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
MAX_BW - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPBandwidth
MAX_CACHE_ENTRIES - Static variable in class edu.isi.pegasus.planner.transfer.mapper.impl.Hashed
  The maximum number of entries in the map, before the output site map is cleared.
MAX_COUNT - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The constant to be passed to the accessor functions to get or set the maximum number of jobs that can be in the queue.
MAX_CPU_TIME - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The constant to be passed to the accessor functions to get or set the maxwalltime for the jobs.
MAX_KEYS_PREFIX - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The prefix for the max keys
MAX_NUMBER_OF_VERSION_COMPONENTS - Static variable in class edu.isi.pegasus.common.util.CondorVersion
  The maximum number of components version can have.
MAX_RUN_TIME - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the key that if set in the Pegasus namespace specifies the maximum amount of time for which a cluster should run.
MAX_VERSION_PRECISION - Static variable in class edu.isi.pegasus.common.util.CondorVersion
  The maximum number of digits each component of version can have.
MAXIDLE_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The key name for max idle setting for dagman
MAXIMUM_FINISH_TIME - Static variable in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  The maximum finish time possible for a job.
maxIndex - Variable in class edu.isi.pegasus.planner.provisioner.OccupationDiagram
MAXJOBS_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The key name for max jobs setting for dagman
MAXPOST_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The key name for max post setting for dagman
MAXPRE_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The key name for max pre setting for dagman
mBag - Variable in class edu.isi.pegasus.common.credential.CredentialHandlerFactory
  Handle to the PegasusBag
mBag - Variable in class edu.isi.pegasus.planner.catalog.site.impl.XML
  The bag of Pegasus Initialization objects
mBag - Variable in class edu.isi.pegasus.planner.client.CPlanner
  The object containing the bag of pegasus objects
mBag - Variable in class edu.isi.pegasus.planner.client.RankDAX
  The bag of objects that Pegasus requires.
mBag - Variable in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  Bag of initialization objects.
mBag - Variable in class edu.isi.pegasus.planner.cluster.aggregator.JobAggregatorInstanceFactory
  The bag of initialization objects
mBag - Variable in class edu.isi.pegasus.planner.code.generator.Abstract
  The bag of initialization objects.
mBag - Variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The bag of initialization objects.
mBag - Variable in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Bag of Pegasus objects
mBag - Variable in class edu.isi.pegasus.planner.code.generator.DAXReplicaStore
  The bag of initialization objects.
mBag - Variable in class edu.isi.pegasus.planner.code.generator.MonitordNotify
  The bag of initialization objects.
mBag - Variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The bag of initialization objects.
mBag - Variable in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
mBag - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
mBag - Variable in class edu.isi.pegasus.planner.code.GridStartFactory
  The bag of objects used for initialization.
mBag - Variable in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  A Bag of objects that maybe associated with the node.
mBag - Variable in class edu.isi.pegasus.planner.ranking.Rank
  The pegasus bag.
mBag - Variable in class edu.isi.pegasus.planner.refiner.Engine
  The bag of initialization objects
mBag - Variable in class edu.isi.pegasus.planner.refiner.NodeCollapser
  The bag of initialization objects.
mBag - Variable in class edu.isi.pegasus.planner.selector.site.Abstract
  The bag of Pegasus objects.
mBandWidths - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPServer
mBaseDir - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  The base submit directory.
mBaseDir - Variable in class edu.isi.pegasus.planner.client.RankDAX
  The base directory where the ranked daxes are kept.
mBasenamePrefix - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  The basename prefix that is to be given to the per workflow file, like the log file, the .dag file, the .cache files etc.
mBaseSubmitDirectory - Variable in class edu.isi.pegasus.planner.classes.PlannerMetrics
  The base submit directory where the files are being created.
mBoolean - Variable in class edu.isi.pegasus.planner.refiner.DataReuseEngine.BooleanBag
  The boolean value
mBuffer - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser3.Arguments
  Handle to a job arguments to handle mixed content.
mBundles - Variable in class edu.isi.pegasus.planner.transfer.refiner.Chain.SiteTransfer
  The list of `Chain` object.
mBypassStagingForInputs - Variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  A boolean indicating whether to bypass first level staging for inputs
mBypassStagingForInputs - Variable in class edu.isi.pegasus.planner.transfer.sls.Condor
  A boolean indicating whether to bypass first level staging for inputs
mBypassStagingForInputs - Variable in class edu.isi.pegasus.planner.transfer.sls.Transfer
  A boolean indicating whether to bypass first level staging for inputs
mCacheFiles - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  Set of cache files that need to be used, to determine the location of the transiency files.
mCacheStore - Variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  The replica store in which we store all the results that are queried from the cache replica catalogs.
mCallback - Variable in class edu.isi.pegasus.common.util.StreamGobbler
  The callback to be used.
mCallback - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  The handle to the class implementing the callback interface.
mCallback - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser3
  Handle to the callback
mCallback - Variable in class edu.isi.pegasus.planner.parser.PDAXParser
  The callback handler to which the callbacks are sent during designated points of parsing the pdax.
mCapacity - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.PoolTransfer
  The maximum number of transfer jobs that are allowed for this particular pool.
mCapacity - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle.PoolTransfer
  The maximum number of transfer jobs that are allowed for this particular pool.
mCapacity - Variable in class edu.isi.pegasus.planner.transfer.refiner.Chain.SiteTransfer
  The maximum number of transfer jobs that are allowed for this particular site.
mCatalog - Variable in class edu.isi.pegasus.planner.client.PegasusGetSites
mChain - Variable in class edu.isi.pegasus.planner.transfer.refiner.Chain.TransferChain
  The linked list that maintians the chain of names of the transfer jobs.
mChild - Variable in class edu.isi.pegasus.planner.dax.Edge
  The parent of the child
mChild - Variable in class edu.isi.pegasus.planner.parser.PDAXParser
  The current child.
mChildren - Variable in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  The list of children of the job/node in the abstract graph.
mChmodDisabledForAllSites - Variable in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  A boolean indicating whether chmod is disabled for all sites.
mChmodOnExecutionSiteMap - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  A map indexed by the execution site and value is the path to chmod on that site.
mClassname - Variable in exception edu.isi.pegasus.common.util.FactoryException
  The name of the class that was trying to be instantiated when this error occured, or some other signifier like module name.
mCleanup - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  An enum tracking what type of cleanup needs to be done.
mCleanupDag - Variable in class edu.isi.pegasus.planner.refiner.MainEngine
  The cleanup dag for the final concrete dag.
mCleanupJobsPerLevel - Variable in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  The number of cleanup jobs per level to be created
mCleanupJobsSize - Variable in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  the number of cleanup jobs clustered into a clustered cleanup job
mCleanupScope - Variable in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  The cleanup scope for the workflows.
mCleanupScope - Variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The cleanup scope for the workflows.
mClient - Variable in class edu.isi.pegasus.planner.classes.PlannerMetrics
  The name of the client
mClosedElement - Variable in class edu.isi.pegasus.common.util.XMLWriter
mClusteredADag - Variable in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  The handle to the ADag object that contains the workflow being clustered.
mClusteredRelations - Variable in class edu.isi.pegasus.planner.cluster.Abstract
  The collection of relations, that is constructed for the clustered workflow.
mClusterer - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  Denotes what type of clustering needs to be done
mClusterer - Variable in class edu.isi.pegasus.planner.partitioner.ClustererCallback
  The handle to the clusterer that does the clustering.
mClustererTable - Static variable in class edu.isi.pegasus.planner.cluster.ClustererFactory
  The table that maps a clustering technique to a clustering impelemntation.
mCollapseMap - Variable in class edu.isi.pegasus.planner.cluster.Horizontal
  Map to hold the collapse values for the various execution pools.
mCollectorHost - Variable in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  The collector host to query to.
mColor - Variable in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  The color the node is colored.
mCompiledPatterns - Static variable in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  Stores compiled patterns at first use, quasi-Singleton.
mCompoundTransformations - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2CDAG
  Map of Compound Transformations indexed by complete name of the compound transformation.
mConcDAG - Variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  The handle to the workflow that is being enabled.
mConcDag - Variable in class edu.isi.pegasus.planner.refiner.RemoveDirectory
  The concrete dag so far, for which the clean up dag needs to be generated.
mConcreteWorkflow - Variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  The workflow for which the code has to be generated.
mCondorStatusError - Variable in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  The List storing the stderr of condor-status.
mCondorStatusOutput - Variable in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  The List storing the output of condor-status.
mCondorVersion - Variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  The long value of condor version.
mCondorVersion - Variable in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  The long value of condor version.
mCondorVersion - Variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The long value of condor version.
mConfFile - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  The conf option passed to the planner pointing to the properties file.
mConnection - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Maintains the connection to the database over the lifetime of this instance.
mConnection - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.CreateTCDatabase
  Maintains the connection to the database over the lifetime of this instance.
mConnection - Variable in class edu.isi.pegasus.planner.catalog.work.Database
  Maintains the connection to the database over the lifetime of this instance.
mConnection - Variable in class edu.isi.pegasus.planner.ranking.GetDAX
  Maintains the connection to the database over the lifetime of this instance.
mConnectionError - Static variable in class edu.isi.pegasus.planner.catalog.work.Database
  This message is sent whenever one of the member function is executed which relies on an established database context.
mConnectionParams - Variable in class edu.isi.pegasus.planner.catalog.site.classes.ReplicaCatalog
  Collection of connection parameters to use for connecting to that replica catalog.
mConstructFlatLFN - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  A boolean indicating whether the catalog is to construct flat lfns or not
mContact - Variable in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  The contact string for the grid gateway.
mContent - Variable in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  The content associated with this node.
mCount - Variable in class edu.isi.pegasus.planner.classes.DagInfo
  Refers to the number of the Abstract Dags which are being sent to the Concrete Planner in response to the user's request.
mCount - Variable in class edu.isi.pegasus.planner.dax.ADAG
  The Count of the number of dax objects : N
mCount - Variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG.GrepCallback
  The number of times the word appears.
mCreateEng - Variable in class edu.isi.pegasus.planner.refiner.MainEngine
  The engine that ends up creating random directories in the remote execution pools.
mCreateRegistrationJobs - Variable in class edu.isi.pegasus.planner.transfer.refiner.Basic
  Boolean indicating whether to create registration jobs or not.
mCreateRegistrationJobs - Variable in class edu.isi.pegasus.planner.transfer.refiner.Empty
  Boolean indicating whether to create registration jobs or not.
mCredential - Variable in class edu.isi.pegasus.planner.refiner.Authenticate
  The credential to be used while authentication to jobmanager.
mCredential - Variable in class edu.isi.pegasus.planner.refiner.ThreadPool
  The credential loaded from the non default location if specified.
mCredentialFactory - Variable in class edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactory
  Handler to the Credential Handler factory.
mCredentialFactory - Variable in class edu.isi.pegasus.planner.code.generator.condor.style.Abstract
  Handle to the Credential Handler Factory
mCredentialsType - Variable in class edu.isi.pegasus.planner.classes.Job
  Set of credential types required by a job to execute remotely.
mCStatements - Static variable in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  The statement to prepare to slurp attributes.
mCStatements - Static variable in class edu.isi.pegasus.planner.catalog.work.Database
  The statement to prepare to slurp attributes.
mCStatements - Static variable in class edu.isi.pegasus.planner.ranking.GetDAX
  The statement to prepare to slurp attributes.
mCurrentChildId - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  These store the current child element for the child parent relationship.
mCurrentDag - Variable in class edu.isi.pegasus.planner.refiner.CreateDirectory
  It is a reference to the Concrete Dag so far.
mCurrentDag - Variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  It is a reference to the Concrete Dag so far.
mCurrentDAGCacheFile - Variable in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Cache file for the current DAG
mCurrentDepth - Variable in class edu.isi.pegasus.planner.parser.PDAXParser
  The current depth of parsing through the xml structure.
mCurrentDepth - Variable in class edu.isi.pegasus.planner.partitioner.BFS
  The current depth of the nodes that are being traversed in the BFS.
mCurrentDepth - Variable in class edu.isi.pegasus.planner.partitioner.graph.MapGraph.BottomUpIterator
  The current height of the nodes that are being traversed in the BFS starting from the leaf.
mCurrentDepth - Variable in class edu.isi.pegasus.planner.partitioner.graph.MapGraph.MapGraphIterator
  The current depth of the nodes that are being traversed in the BFS.
mCurrentIndentIndex - Variable in class edu.isi.pegasus.planner.catalog.site.classes.AbstractXMLPrintVisitor
  The number of tabs to use for current indent
mCurrentJobSubInfo - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Holds information regarding the current job being parsed.
mCurrentLevel - Variable in class edu.isi.pegasus.planner.selector.site.RoundRobin
  The current level in the abstract workflow.
mCurrentNum - Variable in class edu.isi.pegasus.planner.partitioner.MultipleLook
  The number of jobs about which the callback interface has knowledge.
mCurrentNum - Variable in class edu.isi.pegasus.planner.partitioner.SingleLook
  The number of jobs about which the callback interface has knowledge.
mCurrentNum - Variable in class edu.isi.pegasus.planner.refiner.ThreadPool
  The condition variable that is used to synchronize the shutdown.
mCurrentProcessorIndex - Variable in class edu.isi.pegasus.planner.selector.site.heft.Site
  The index to the processor that is to be used for scheduling a job.
mCurrentSILevel - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  The current level of the jobs being traversed.
mCurrentSILevel - Variable in class edu.isi.pegasus.planner.transfer.refiner.Cluster
  The current level of the jobs being traversed.
mCurrentSOLevel - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  The current level of the jobs being traversed.
mCurrentSOLevel - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  The current level of the jobs being traversed.
mDAG - Variable in class edu.isi.pegasus.planner.cluster.aggregator.JobAggregatorInstanceFactory
  ADag object containing the jobs that have been scheduled by the site selector.
mDAG - Variable in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
mDAG - Variable in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
mDAG - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
mDAG - Variable in class edu.isi.pegasus.planner.code.GridStartFactory
  The workflow object.
mDag - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2CDAG
  The ADag object which contains information corresponding to the ADag in the XML file.
mDag - Variable in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  ADag object corresponding to the Dag whose jobs we want to schedule.
mDag - Variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  The DAG being worked upon.
mDag - Variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  The DAG object to which the transfer nodes are to be added.
mDAG - Variable in class edu.isi.pegasus.planner.transfer.AbstractRefiner
  The ADag object associated with the Dag.
mDAGFile - Variable in class edu.isi.pegasus.planner.classes.DAGJob
  The DAG File that the job refers to.
mDAGInfo - Variable in class edu.isi.pegasus.planner.classes.ADag
  The DagInfo object which contains the information got from parsing the dax file.
mDAGLFN - Variable in class edu.isi.pegasus.planner.classes.DAGJob
  The DAG LFN.
mDAGLFN - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  The file attribute encountered in the dag element.
mDAGManKnobs - Variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Any extra arguments that need to be passed to dagman, as determined from the properties file.
mDagWriter - Variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  The file handle to the .dag file.
mDAGWriter - Variable in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  The print writer handle to DAG file being written out.
mDatabase - Variable in class edu.isi.pegasus.planner.client.TCConverter
  The database type.
mDatabaseAbsolutePath - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.CreateTCDatabase
  Stores the absolute path to the mysql home directory
mDatabaseHost - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.CreateTCDatabase
  Stores the database host name
mDatabaseHost - Variable in class edu.isi.pegasus.planner.client.TCConverter
  The database host .
mDatabaseName - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.CreateTCDatabase
  Stores the database name
mDatabaseName - Variable in class edu.isi.pegasus.planner.client.TCConverter
  The database name.
mDatabasePassword - Variable in class edu.isi.pegasus.planner.client.TCConverter
  The database user password.
mDatabaseTC - Static variable in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
mDatabaseURL - Variable in class edu.isi.pegasus.planner.client.TCConverter
  The database type.
mDatabaseUserName - Variable in class edu.isi.pegasus.planner.client.TCConverter
  The database user name.
mDataConfiguration - Variable in class edu.isi.pegasus.planner.classes.PlannerMetrics
  The UUID associated with the workflow.
mDate - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  Stores the time at which the planning process started.
mDAXFile - Variable in class edu.isi.pegasus.planner.classes.DAXJob
  The DAX File that the job refers to.
mDAXFile - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  The dax file which contains the abstract dag.
mDAXFile - Variable in class edu.isi.pegasus.planner.client.PartitionDAX
  The path to the dax file that is to be partitioned.
mDaxFile - Variable in class edu.isi.pegasus.planner.partitioner.DAXWriter
  The dax file that is being partitioned.
mDAXInMemory - Variable in class edu.isi.pegasus.planner.partitioner.SingleLook
  The flag to identify that dax is in memory.
mDAXJobIDToSubmitDirectoryCacheFile - Variable in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Maps a sub dax job id to it's submit directory.
mDAXLabel - Variable in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  The label of the dax.
mDAXLFN - Variable in class edu.isi.pegasus.planner.classes.DAXJob
  The DAX LFN.
mDAXLFN - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  The file attribute encountered in the dax element.
mDAXMTime - Variable in class edu.isi.pegasus.planner.classes.DagInfo
  Keeps the last modified time of the DAX.
mDAXPath - Variable in class edu.isi.pegasus.planner.classes.PlannerMetrics
  The path to the DAX that was planned by the workflow.
mDAXReplicaStore - Variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  The DAX Replica Store.
mDaxSchemaVersion - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser2
mDAXTransformationStore - Variable in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  Handle to the transformation store that stores the transformation catalog user specifies in the DAX
mDAXVersion - Variable in class edu.isi.pegasus.planner.classes.DagInfo
  The DAX Version
mDAXWriter - Variable in class edu.isi.pegasus.planner.partitioner.WriterCallback
  The handle to the dax writer that writes out the dax corresponding to the partition identified.
mDebugLevel - Variable in class edu.isi.pegasus.common.logging.LogManager
  The debug level.
mDeepStorageStructure - Variable in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  A boolean indicating whether to have a deep directory structure for the storage directory or not.
mDeepStorageStructure - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  A boolean indicating whether to have a deep directory structure for the storage directory or not.
mDefaultAggregator - Static variable in class edu.isi.pegasus.planner.namespace.Globus
  The default aggregator to be used for profile aggregation, if none specified in the aggregator table;
mDefaultBundleValue - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.BundleValue
  The default bundle value to use.
mDefaultBundleValue - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle.BundleValue
  The default bundle value to use.
mDefaultCallback - Variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  An instance of the default stream gobbler callback implementation that is used for creating symbolic links.
mDefaultGroup - Static variable in class edu.isi.pegasus.planner.selector.site.Group
  The name of the group into which jobs are grouped if no group is specified in the dax.
mDefaultPoolFile - Variable in class edu.isi.pegasus.planner.common.PegasusProperties
  The default path to the pool file.
mDefaultProfileKey - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.BundleValue
  The Default Pegasus profile key to use for lookup
mDefaultProfileKey - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle.BundleValue
  The Default Pegasus profile key to use for lookup
mDefaultTC - Variable in class edu.isi.pegasus.planner.common.PegasusProperties
  The default path to the transformation catalog.
mDefaultTCRCCreated - Variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  A boolean indicating whether the attempt to create a default tc entry has happened or not.
mDefaultTCRCEntry - Variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  The default tc entry.
mDefaultTransferPriority - Variable in class edu.isi.pegasus.planner.common.PegasusProperties
  The default transfer priority that needs to be applied to the transfer jobs.
mDeferredRun - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  A boolean indicating whether the planner invocation is part of a larger deferred planning run.
mDeletedJobs - Variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  Holds all the jobs deleted by the reduction algorithm.
mDependencies - Variable in class edu.isi.pegasus.planner.dax.ADAG
  Map of Dependencies between Job,DAX,DAG objects.
mDeprecatedProperties - Variable in class edu.isi.pegasus.planner.common.PegasusProperties
  The set containing the deprecated properties specified by the user.
mDeprecatedTable - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The table containing the mapping of the deprecated keys to the newer keys.
mDepth - Variable in class edu.isi.pegasus.planner.parser.StackBasedXMLParser
  Count the depths of elements in the document
mDepth - Variable in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  The depth of the node from the root or any arbitary node.
mDescription - Static variable in class edu.isi.pegasus.planner.selector.replica.Default
  A short description of the replica selector.
mDescription - Static variable in class edu.isi.pegasus.planner.selector.replica.Local
  A short description of the replica selector.
mDescription - Static variable in class edu.isi.pegasus.planner.selector.replica.Regex
  A short description of the replica selector.
mDescription - Static variable in class edu.isi.pegasus.planner.selector.replica.Restricted
  A short description of the replica selector.
mDescription - Static variable in class edu.isi.pegasus.planner.selector.site.Group
  The description of the site selector.
mDescription - Static variable in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  The description of the site selector.
mDestMap - Variable in class edu.isi.pegasus.planner.classes.FileTransfer
  The map containing all the destination urls keyed by the pool id/name.
mDirectories - Variable in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  A Map of different directories indexed by Directory.TYPE associated with the site catalog entry
mDirectory - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Records the name of the on-disk representation.
mDirectory - Variable in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
  Keep track of which directories are found in the site.
mDirectory - Variable in class edu.isi.pegasus.planner.classes.DAGJob
  The directory in which the DAG needs to execute.
mDirectory - Variable in class edu.isi.pegasus.planner.classes.DAXJob
  The directory in which the DAX needs to execute.
mDirectory - Variable in class edu.isi.pegasus.planner.classes.Job
  The directory in which the job should run.
mDirectory - Variable in class edu.isi.pegasus.planner.client.PartitionDAX
  The directory in which the partition daxes are generated.
mDirectory - Variable in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  The directory, where the stdin file of the fat jobs are created.
mDirectory - Variable in class edu.isi.pegasus.planner.refiner.NodeCollapser
  The directory, where the stdin file of the fat jobs are created.
mDirectoryReplicaStore - Variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  The replica store where we store all the results that are queried from the input directory specified at the command line.
mDirectoryURL - Variable in class edu.isi.pegasus.planner.transfer.mapper.impl.Fixed
  Externally accessible URL
mDisabledChmodSites - Variable in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  The set of sites for which chmod job creation has to be disabled while doing executable staging.
mDisableInvokeFunctionality - Variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Boolean indicating whether to disable invoke functionality.
mDisplayHelp - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  To Display help or not.
mDone - Variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  A boolean indicating whether the files have been generated or not.
mDone - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2CDAG
  A flag to specify whether the graph has been generated for the partition or not.
mDone - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2Graph
  A flag to specify whether the graph has been generated for the partition or not.
mDone - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2Metadata
  A flag to specify whether the graph has been generated for the partition or not.
mDone - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2NewGraph
  A flag to specify whether the graph has been generated for the partition or not.
mDone - Variable in class edu.isi.pegasus.planner.parser.dax.ExampleDAXCallback
mDone - Variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  A flag to store whether the parsing is complete or not.
mDoNotClean - Variable in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  HashSet of Files that should not be cleaned up
mDoStat - Variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  A boolean indicating whether to stat files or not.
mDownwardRank - Variable in class edu.isi.pegasus.planner.selector.site.heft.HeftBag
  The downward rank for a node.
mDriver - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.CreateTCDatabase
  Stores the driver string
Mds_Computer_Isa - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
Mds_Computer_Total_Free_NodeCount - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
Mds_Computer_Total_NodeCount - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
Mds_Gram_Job_Queue_MaxCount - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
Mds_Gram_Job_Queue_MaxCpuTime - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
Mds_Gram_Job_Queue_MaxJobsInQueue - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
Mds_Gram_Job_Queue_MaxRunningJobs - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
Mds_Memory_Ram_FreeSizeMB - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
Mds_Memory_Ram_Total_SizeMB - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
Mds_Os_Name - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
Mds_Service_Gram_SchedulerType - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
Mds_Subnetid - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
mdsbaseDN - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
mdshost - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
mdsport - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
MdsQuery - Class in edu.isi.pegasus.planner.catalog.site.impl.old
  This Class queries the GT2 based Monitoring and Discovery Service (MDS) and stores the remote sites information into a single data class.
MdsQuery() - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
  C'tor for the class.
MdsQuery(String, int) - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
  Valid C'tor for the class to create a MdsQuery object.
mDuration - Variable in class edu.isi.pegasus.planner.classes.PlannerMetrics
  The planning duration
mDynamicDeployment - Variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  A boolean indicating whether kickstart is deployed dynamically or not.
mElement - Variable in class edu.isi.pegasus.planner.parser.ParserStackElement
mElement - Variable in class edu.isi.pegasus.planner.parser.SiteCatalogXMLMetadataParser
  The root element name to look for.
mEmptyElement - Variable in class edu.isi.pegasus.common.util.XMLWriter
mEnablingPartOfAggregatedJob - Variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  An instance variable to track if enabling is happening as part of a clustered constituentJob.
mEnablingPartOfAggregatedJob - Variable in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  An instance variable to track if enabling is happening as part of a clustered job.
mEnablingPartOfAggregatedJob - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  An instance variable to track if enabling is happening as part of a clustered job.
mEncode - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusExitCodeEncode
  The value to encode to
mEncodeable - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusExitCodeEncode
  Defines the character that requires encoding
mEnd - Variable in class edu.isi.pegasus.common.logging.format.SimpleEvent
  The time when end message for the event was generated
mEndSeparator - Static variable in class edu.isi.pegasus.planner.code.generator.Stork
  The nice end separator, define once, use often.
mEndTime - Variable in class edu.isi.pegasus.planner.classes.PlannerMetrics
  The end time for the planning.
mEndTime - Variable in class edu.isi.pegasus.planner.selector.site.heft.HeftBag
  The estimated end time for a job.
mEndTime - Variable in class edu.isi.pegasus.planner.selector.site.heft.Processor
  The end time of the current scheduled job.
mEnvVar - Variable in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  The map that contains the environment variables including the default ones that are set while calling out to the site selector unless they are overridden by the values set in the properties file.
merge(ReplicaCatalogEntry, ReplicaCatalogEntry, boolean) - Static method in class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  Merges the attribute maps of two entries in a controlled fashion.
merge(ReplicaCatalogEntry, boolean) - Method in class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  Merges the attribute maps in a controlled fashion.
merge(ReplicaLocation) - Method in class edu.isi.pegasus.planner.classes.ReplicaLocation
  Merges the `ReplicaLocation` object to the existing one, only if the logical filenames match.
merge(Namespace) - Method in class edu.isi.pegasus.planner.namespace.Condor
  Merge the profiles in the namespace in a controlled manner.
merge(Namespace) - Method in class edu.isi.pegasus.planner.namespace.Dagman
  Merge the profiles in the namespace in a controlled manner.
merge(Namespace) - Method in class edu.isi.pegasus.planner.namespace.ENV
  Merge the profiles in the namespace in a controlled manner.
merge(Namespace) - Method in class edu.isi.pegasus.planner.namespace.Globus
  Merge the profiles in the namespace in a controlled manner.
merge(Namespace) - Method in class edu.isi.pegasus.planner.namespace.Hints
  Merge the profiles in the namespace in a controlled manner.
merge(Namespace) - Method in class edu.isi.pegasus.planner.namespace.Namespace
  Merge the profiles in the namespace in a controlled manner.
merge(Namespace) - Method in class edu.isi.pegasus.planner.namespace.Pegasus
  UniqueMerge the profiles in the namespace in a controlled manner.
merge(Namespace) - Method in class edu.isi.pegasus.planner.namespace.Selector
  Merge the profiles in the namespace in a controlled manner.
merge(Namespace) - Method in class edu.isi.pegasus.planner.namespace.Stat
  Merge the profiles in the namespace in a controlled manner.
mergeProfiles(Job) - Method in class edu.isi.pegasus.planner.classes.Job
  Merges profiles from another job to this job in a controlled fashion.
mErrorMessage - Variable in class edu.isi.pegasus.planner.classes.PlannerMetrics
  The error message to be logged
mErrStream - Variable in class edu.isi.pegasus.common.logging.logger.Default
  The stream to which all the error messages are logged.By default it is System.err
mEscapable - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusExitCodeEncode
  Defines the set of characters that require escaping.
mEscape - Static variable in class edu.isi.pegasus.planner.classes.Profile
  A private static handle to the escape class.
mEscape - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusExitCodeEncode
  Defines the character used to escape characters.
MESSAGE_DONE_PREFIX - Static variable in class edu.isi.pegasus.common.logging.LogManager
  Suffx for an event completion message.
MetaData - Class in edu.isi.pegasus.planner.dax
  Metadata object for the DAX API
MetaData(MetaData) - Constructor for class edu.isi.pegasus.planner.dax.MetaData
  Copy constructor
MetaData(String, String) - Constructor for class edu.isi.pegasus.planner.dax.MetaData
  Create a new Metadata object
MetaData(String, String, String) - Constructor for class edu.isi.pegasus.planner.dax.MetaData
  Create a new Metadata object
method - Variable in class edu.isi.pegasus.planner.provisioner.Estimator
Metrics - Class in edu.isi.pegasus.planner.code.generator
  Logs workflow metrics to a file in the submit directory and also sends them over a HTTP connection to a Metrics Server.
Metrics() - Constructor for class edu.isi.pegasus.planner.code.generator.Metrics
METRICS_FILE_SUFFIX - Static variable in class edu.isi.pegasus.planner.code.generator.Metrics
  The suffix to use while constructing the name of the metrics file
METRICS_SEND_TIMEOUT - Static variable in class edu.isi.pegasus.planner.code.generator.Metrics
  The timeout in seconds for sending the metrics to the server
METRICS_SERVER_DEFAULT_URL - Static variable in class edu.isi.pegasus.planner.code.generator.Metrics
  The default URL for the metrics server to use
mEventBuffer - Variable in class edu.isi.pegasus.common.logging.format.SimpleEvent
  The buffer that stores information about the event
mExecPools - Variable in class edu.isi.pegasus.planner.refiner.AuthenticateEngine
  The Set of pools that need to be authenticated against.
mExecPools - Variable in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  Set of the execution pools which the user has specified.
mExecPools - Variable in class edu.isi.pegasus.planner.refiner.MainEngine
  The pools on which the Dag should be executed as specified by the user.
mExecPools - Variable in class edu.isi.pegasus.planner.refiner.ThreadPool
  The Set of pools that need to be authenticated against.
mExecPools - Variable in class edu.isi.pegasus.planner.selector.site.RoundRobin
  The list of pools that have been given by the user at run time or has been authenticated against.
mExecutable - Variable in class edu.isi.pegasus.planner.dax.File
  Is the file an executable.
mExecutables - Variable in class edu.isi.pegasus.planner.dax.ADAG
  The list of Executable objects
mExecutionToHintsNamespace - Static variable in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  The map that maps keys in execution tag to hints namespace.
mExitcode - Variable in class edu.isi.pegasus.planner.classes.PlannerMetrics
  the exitcode of the planner
mExitParserArguments - Variable in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  The argument string containing the arguments with which the exitcode is invoked on kickstart output.
mExitParserPath - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusExitCode
  The path to the exitcode client that parses the exit status of the kickstart.
mExtraArguments - Variable in class edu.isi.pegasus.planner.transfer.sls.Transfer
  Any extra arguments that need to be passed ahead to the s3 client invocation.
mFactory - Variable in class edu.isi.pegasus.planner.code.generator.Shell
  Handle to the Credential Factory
mFactory - Variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The handle to the file factory, that is used to create the top level directories for each of the partitions.
mFactory - Variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  The handle to the file factory, that is used to create the top level directories for each of the partitions.
mFactory - Variable in class edu.isi.pegasus.planner.transfer.mapper.impl.AbstractFileFactoryBasedMapper
mFailOnFirstError - Variable in class edu.isi.pegasus.planner.cluster.aggregator.SeqExec
  Flag indicating whether to fail on first hard error or not.
mFileCreationMap - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2CDAG
  Map to track a LFN with the job that creates the file corresponding to the LFN.
mFilename - Variable in class edu.isi.pegasus.planner.catalog.site.impl.XML
  The Site Catalog file to be parser.
mFilename - Variable in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  The Site Catalog file to be parser.
mFileName - Variable in class edu.isi.pegasus.planner.partitioner.PDAXWriter
  The fully qaulified path to the file being written.
mFiles - Variable in class edu.isi.pegasus.planner.dax.ADAG
  The list of edu.isi.pegasus.planner.dax.File objects
mFileServer - Variable in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
  Keep track of which file servers are listed in the specified directories.
mFileServers - Variable in class edu.isi.pegasus.planner.catalog.site.classes.DirectoryLayout
  The list of file servers that can be used to write to access this directory indexed by operation type.
mFileTable - Variable in class edu.isi.pegasus.planner.transfer.refiner.Basic
  A Map containing information about which logical file has been transferred to which site and the name of the stagein transfer node that is transferring the file from the location returned from the replica catalog.
mFileTable - Variable in class edu.isi.pegasus.planner.transfer.refiner.Empty
  A Map containing information about which logical file has been transferred to which site and the name of the stagein transfer node that is transferring the file from the location returned from the replica catalog.
mFileTXList - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.TransferContainer
  The collection of `FileTransfer` objects containing the transfers the job is responsible for.
mFileTXList - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle.TransferContainer
  The collection of `FileTransfer` objects containing the transfers the job is responsible for.
mFlags - Variable in class edu.isi.pegasus.planner.classes.PegasusFile
  The transient flags field which is kept as a bit field.
mFlowID - Variable in class edu.isi.pegasus.planner.classes.DagInfo
  It is a unique identifier identifying the concrete DAG generated by Pegasus.
mFlowIDName - Variable in class edu.isi.pegasus.planner.classes.DagInfo
  It is the name of the dag as generated by Chimera in the dax.
mFlowTimestamp - Variable in class edu.isi.pegasus.planner.classes.DagInfo
  The ISO timestamp corresponding to the time when Pegasus is invoked for a dax.
mFlushOnClose - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Boolean indicating whether to flush the contents back to the file on close.
mFlushOnClose - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Boolean indicating whether to flush the contents back to the file on close.
mForce - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  The force option to make a build dag from scratch.
mForceReplan - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the force replan option
mFormatter - Static variable in class edu.isi.pegasus.common.logging.logger.Default
  This is used to format the time stamp.
mForwardOptions - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  The options that need to be passed forward to pegasus-run.
mFreeMem - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The free memory that the jobmanager reports.
mFreeSize - Variable in class edu.isi.pegasus.planner.catalog.site.classes.FileSystemType
  The free space on the file system.
mFreeSize - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPServer
  The free space at the grid ftp server.
mFreeSize - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.WorkDir
  The free space available at the file system under this directory.
mFTMap - Variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The FileTransfer map indexed by site id.
mGenerateLOF - Variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  A boolean indicating whether to generate lof files or not.
mGenerateLOF - Variable in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  A boolean indicating whether to generate lof files or not.
mGenerateLOF - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  A boolean indicating whether to generate lof files or not.
mGenRandomDir - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  Whether to create a random directory in the execution directory that is determined from the exec mount point in the pool configuration file.
mGetOperations - Static variable in enum edu.isi.pegasus.planner.catalog.site.classes.FileServerType.OPERATION
mGetRCCache - Variable in class edu.isi.pegasus.planner.classes.PlannerCache
  The cache storing the GET urls for the files in the workflow
mGlibc - Variable in class edu.isi.pegasus.planner.catalog.classes.SysInfo
  The Glibc version.
mGlibc - Variable in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Optional information about the glibc.
mGlibc - Variable in class edu.isi.pegasus.planner.dax.Executable
  Glibc the executable is compiled for
mGlobalIgnoredSites - Variable in class edu.isi.pegasus.planner.selector.replica.Restricted
  The Set of ignored sites, that are ignored for selecting replicas for all sites.
mGlobalLog - Variable in class edu.isi.pegasus.planner.cluster.aggregator.SeqExec
  Flag indicating whether a global log file or per job file.
mGlobalPreferredSites - Variable in class edu.isi.pegasus.planner.selector.replica.Restricted
  The set of preferred sites, that are preferred stagein sites for all sites.
mGlobusVersion - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPServer
  The version of Globus Toolkit that was used to install the grid ftp server.
mGlobusVersion - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The globus version that is installed on the remote site.
mGraph - Variable in class edu.isi.pegasus.planner.partitioner.graph.TopologicalSortIterator
  The partition that has to be sorted.
mGraph - Variable in class edu.isi.pegasus.planner.partitioner.Partitioner
  The map containing all the graph nodes.
mGraph - Variable in class edu.isi.pegasus.planner.refiner.NodeCollapser
  The internal map that contains the adjacency list representation of the Graph referred to by the workflow.
mGraphImplementor - Variable in class edu.isi.pegasus.planner.classes.ADag
  Handle to the Graph implementor.
mGraphImplementor - Variable in class edu.isi.pegasus.planner.classes.AggregatedJob
  Handle to the Graph implementor.
mGrid - Variable in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  The grid to which the user belongs to.
mGrid - Variable in class edu.isi.pegasus.planner.client.PegasusGetSites
mGridFTPList - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  The list of `GridFTPServer` objects that contain the information about the gridftp servers on the remote site.
mGridGateways - Variable in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Map of grid gateways at the site for submitting different job types.
mGridGateways - Variable in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Map of grid gateways at the site for submitting different job types.
mGridLaunch - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  The path to the kickstart on the remote site.
mGridStartFactory - Variable in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  The handle to the GridStart Factory.
mGridStartFactory - Variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  The handle to the GridStart Factory.
mGridStartFactory - Variable in class edu.isi.pegasus.planner.code.generator.PMC
  The handle to the GridStart Factory.
mGridStartFactory - Variable in class edu.isi.pegasus.planner.code.generator.Shell
  The handle to the GridStart Factory.
mGridStartImplementationTable - Variable in class edu.isi.pegasus.planner.code.GridStartFactory
  A table that maps short names of `GridStart` implementations with the implementations themselves.
mGroupMap - Variable in class edu.isi.pegasus.planner.selector.site.Group
  The map containing the the jobs grouped by the key group.
mHandle - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  The handle to the site, usually name of the site.
mHasBeenRenderedToExecutableForm - Variable in class edu.isi.pegasus.planner.classes.AggregatedJob
  Boolean indicating whether a job has been fully rendered to an executable job or not i.e the aggregated job has been mapped to the aggregator and the constituent jobs have been gridstarted or not.
mHeader - Variable in class edu.isi.pegasus.common.util.XMLWriter
mHeadFS - Variable in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  The handle to the head node filesystem.
mHeft - Variable in class edu.isi.pegasus.planner.ranking.Rank
  The handle to the ranking algorithm.
mHeftImpl - Variable in class edu.isi.pegasus.planner.selector.site.Heft
  An instance of the class that implements the HEFT algorithm.
mHost - Variable in class edu.isi.pegasus.common.util.PegasusURL
  The hostname referred to by the PegasusURL.
mHost - Variable in class edu.isi.pegasus.planner.refiner.Authenticate.HostPort
  The host at which the server is running.
micro0 - Static variable in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
micro1 - Static variable in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
micro2 - Variable in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
mID - Variable in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  The site identifier.
mID - Variable in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  The site identifier.
mId - Variable in class edu.isi.pegasus.planner.dax.AbstractJob
mID - Variable in class edu.isi.pegasus.planner.partitioner.Partition
  The partition id of the partition.
mIDCounter - Variable in class edu.isi.pegasus.planner.partitioner.Horizontal
  The global counter that is used to assign ID's to the partitions.
mIdleNodes - Variable in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  The number of idle nodes.
mIdleNodes - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The total number of idle nodes that the jobmanager reports are on the remote site.
mIgnoredSitesMap - Variable in class edu.isi.pegasus.planner.selector.replica.Restricted
  A Map indexed by site handles, that contains a set of site handles.
mImpl - Variable in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  The handle to the CleanupImplementation instance that creates the jobs for us.
mImpl - Variable in class edu.isi.pegasus.planner.refiner.createdir.AbstractStrategy
  The implementation instance that is used to create a create dir job.
mImplementingClassNameTable - Static variable in class edu.isi.pegasus.common.credential.CredentialHandlerFactory
  A table that maps, Pegasus style keys to the names of the corresponding classes implementing the CondorStyle interface.
mImplementingClassNameTable - Static variable in class edu.isi.pegasus.planner.cluster.aggregator.JobAggregatorInstanceFactory
  A table that maps, Pegasus style keys to the names of the corresponding classes implementing the CondorStyle interface.
mImplementingClassNameTable - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactory
  A table that maps, Pegasus style keys to the names of the corresponding classes implementing the CondorStyle interface.
mImplementingClassTable - Variable in class edu.isi.pegasus.common.credential.CredentialHandlerFactory
  A table that maps, Pegasus style keys to appropriate classes implementing the CredentialHandler interface
mImplementingClassTable - Variable in class edu.isi.pegasus.planner.cluster.aggregator.JobAggregatorInstanceFactory
  A table that maps, Pegasus style keys to appropriate classes implementing the JobAggregator interface
mImplementingClassTable - Variable in class edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactory
  A table that maps, Pegasus style keys to appropriate classes implementing the CondorStyle interface
MIN - Class in edu.isi.pegasus.planner.namespace.aggregator
  An implementation of the Aggregator interface that takes the minimum of the profile values.
MIN() - Constructor for class edu.isi.pegasus.planner.namespace.aggregator.MIN
min_bandwidth - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPBandwidth
Min_Bandwidth - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
MIN_BW - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPBandwidth
mInDegree - Variable in class edu.isi.pegasus.planner.partitioner.graph.TopologicalSortIterator
  An array that contains the number of incoming edges to a node.
mInDegree - Variable in class edu.isi.pegasus.planner.partitioner.Topological
  An array that contains the number of incoming edges to a node.
mIndex - Variable in class edu.isi.pegasus.planner.classes.DagInfo
  Refers to the number of the Dag.
mIndex - Variable in class edu.isi.pegasus.planner.dax.ADAG
  The Index of the dax object.
mIndex - Variable in class edu.isi.pegasus.planner.partitioner.MultipleLook
  The index of the partition that is being written out.
mIndex - Variable in class edu.isi.pegasus.planner.partitioner.Partition
  The index associated with the partition.
mIndex - Variable in class edu.isi.pegasus.planner.refiner.ThreadPool.AuthenticateThread
  The unique identifying id of the thread.
mIndexMap - Variable in class edu.isi.pegasus.planner.partitioner.graph.TopologicalSortIterator
  A Map that returns the index into mInDegree map for a particular node in graph.
mIndexMap - Variable in class edu.isi.pegasus.planner.partitioner.Topological
  A Map that returns the index into mInDegree map for a particular node in graph.
mInheritedRCFiles - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  Set of replica catalog files that are inherited by a planning instance.
mInheritedReplicaStore - Variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  The inherited Replica Store
Minimal - Class in edu.isi.pegasus.planner.refiner.createdir
  This strategy for adding create dir jobs to the workflow only adds the minimum number of edges from the create dir job to the compute jobs in the workflow.
Minimal() - Constructor for class edu.isi.pegasus.planner.refiner.createdir.Minimal
mInitialized - Variable in class edu.isi.pegasus.common.credential.CredentialHandlerFactory
  A boolean indicating that the factory has been initialized.
mInitialized - Variable in class edu.isi.pegasus.planner.cluster.aggregator.JobAggregatorInstanceFactory
  A boolean indicating that the factory has been initialized.
mInitialized - Variable in class edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactory
  A boolean indicating that the factory has been initialized.
mInitialized - Variable in class edu.isi.pegasus.planner.code.GridStartFactory
  A boolean indicating that the factory has been initialized.
mInitializeGridStart - Variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  A boolean indicating whether grid start has been initialized or not.
mInitializeGridStart - Variable in class edu.isi.pegasus.planner.code.generator.PBS
  A boolean indicating whether grid start has been initialized or not.
mInitializeGridStart - Variable in class edu.isi.pegasus.planner.code.generator.PMC
  A boolean indicating whether grid start has been initialized or not.
mInitializeGridStart - Variable in class edu.isi.pegasus.planner.code.generator.Shell
  A boolean indicating whether grid start has been initialized or not.
MINOR - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GlobusVersion
  The constant for the minor version type.
mInputDir - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  the input directory
mInputFile - Variable in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  The input directory containing the kickstart records.
mInputFiles - Variable in class edu.isi.pegasus.planner.client.SCClient
  The input files.
mInputFiles - Variable in class edu.isi.pegasus.planner.client.TCConverter
  The input files.
mInputFormat - Variable in class edu.isi.pegasus.planner.client.SCClient
  The input format for the site catalog.
mInputFormat - Variable in class edu.isi.pegasus.planner.client.TCConverter
  The input format for the transformation catalog.
mInputReader - Variable in class edu.isi.pegasus.planner.parser.TransformationCatalogTextScanner
  Stores the stream from which we are currently scanning.
mInstalled - Variable in class edu.isi.pegasus.planner.dax.Executable
  Flag to mark if the executable is installed or can be staged.
mInstance - Static variable in class edu.isi.pegasus.planner.provenance.pasoa.pps.PPSFactory
  The singleton instance of the PPS implementation that is returned.
mInternalMount - Variable in class edu.isi.pegasus.planner.catalog.site.classes.DirectoryLayout
  The internal mount point for the directory.
mInvokeAlways - Variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  A boolean indicating whether to use invoke always or not.
mInvokeLength - Variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  The invoke limit trigger.
mInvokeMap - Variable in class edu.isi.pegasus.planner.classes.Notifications
  An enum map that associates the various notification events with the list of actions that need to be taken.
mInvokes - Variable in class edu.isi.pegasus.planner.dax.AbstractJob
mInvokes - Variable in class edu.isi.pegasus.planner.dax.ADAG
  List of Notification objects
mInvokes - Variable in class edu.isi.pegasus.planner.dax.Executable
  List of Notification objects
mInvokes - Variable in class edu.isi.pegasus.planner.dax.Transformation
mIPEng - Variable in class edu.isi.pegasus.planner.refiner.MainEngine
  The handle to the InterPool Engine that calls out to the Site Selector and maps the jobs.
mIPStream - Variable in class edu.isi.pegasus.common.util.StreamGobbler
  The input stream that is to be read from.
missingKeyError(Job, String) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.GLite
  Constructs an error message in case of style mismatch.
mJob - Variable in class edu.isi.pegasus.planner.classes.FileTransfer
  The logical name of the asssociated VDS super node, with which the file is associated.
mJobAggregator - Variable in class edu.isi.pegasus.planner.classes.AggregatedJob
  Handle to the JobAggregator that created this job.
mJobAggregatorFactory - Variable in class edu.isi.pegasus.planner.cluster.Abstract
  The handle to the job aggregator factory.
mJobAggregatorFactory - Variable in class edu.isi.pegasus.planner.cluster.Horizontal
  The handle to the job aggregator factory.
mJobComparator - Static variable in class edu.isi.pegasus.planner.cluster.Horizontal
  A singleton access to the job comparator.
mJobExecutablesStaged - Variable in class edu.isi.pegasus.planner.classes.Job
  Boolean indicating whether the job executables were staged for it or not.
mJobManagerList - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  The list of `JobManager` objects that contain the information about the jobmanagers associated with the remote site.
mJobManagerType - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The type of remote scheduler to which the jobmanager talks to.
mJobMap - Variable in class edu.isi.pegasus.planner.cluster.Horizontal
  Map to hold the jobs sorted by the label of jobs in dax.
mJobMap - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2CDAG
  The mapping of the idrefs of a job to the job name.
mJobMap - Variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The internal map that maps the partition id to the job responsible for executing the partition..
mJobMap - Variable in class edu.isi.pegasus.planner.partitioner.SingleLook
  The map containing all the jobs in the dax indexed by the job id.
mJobName - Variable in class edu.isi.pegasus.planner.namespace.Dagman
  The name of the job (jobname) to which the profiles for this namespace belong.
mJobPrefix - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  The prefix that is to be applied while constructing job names.
mJobPrefix - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  The job prefix that needs to be applied to the job file basenames.
mJobPrefix - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser3
  A job prefix specifed at command line.
mJobPrefix - Variable in class edu.isi.pegasus.planner.refiner.createdir.AbstractStrategy
  The job prefix that needs to be applied to the job file basenames.
mJobPrefix - Variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The job prefix that needs to be applied to the job file basenames.
mJobPrefix - Variable in class edu.isi.pegasus.planner.refiner.RemoveDirectory
  The job prefix that needs to be applied to the job file basenames.
mJobPrefix - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  The job prefix that needs to be applied to the job file basenames.
mJobPrefix - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  The job prefix that needs to be applied to the job file basenames.
mJobs - Variable in class edu.isi.pegasus.planner.dax.ADAG
  The List of Job,DAX and DAG objects
mJobsInQueue - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The number of jobs in the remote queue at the remote site.
mJobType - Variable in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  The type of jobs that this grid gateway can accept.
mkdir(String) - Method in class edu.isi.pegasus.gridftp.GridFTPConnection
  Create directory path
mkdir(GridFTPConnection, String) - Method in class edu.isi.pegasus.gridftp.MakeDirectoryCommand
mKeepTMP - Variable in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  The tristate value for whether keeping the temporary files generated or not.
mKey - Variable in class edu.isi.pegasus.planner.catalog.site.classes.Connection
  The connection key.
mKey - Variable in class edu.isi.pegasus.planner.classes.Profile
mKey - Variable in class edu.isi.pegasus.planner.dax.MetaData
  Metadata Key
mKey - Variable in class edu.isi.pegasus.planner.dax.Profile
  Key of the profile
mKeys - Variable in class edu.isi.pegasus.planner.namespace.aggregator.UniqueMerge
mKickstartGridStartImpl - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Handle to kickstart GridStart implementation.
mKickstartLabel - Variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  The label that is passed to kickstart.
mLabel - Variable in class edu.isi.pegasus.planner.dax.Edge
  The edge label for the parent child relationship.
mLabel - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2Graph
  The label of the abstract dax as set by Chimera.
mLabel - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2NewGraph
  The label of the abstract dax.
mLabel - Variable in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  The label of the workflow.
mLabelKey - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2LabelGraph
  The profile key that is used for the labelling.
mLastAddedNode - Variable in class edu.isi.pegasus.planner.partitioner.Partition
  A pointer to the last added node to the partition.
mLastDirectoryTraversed - Variable in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
  Track which type of directory was traversed last.
mLDAGs - Variable in class edu.isi.pegasus.planner.dax.ADAG
mLDAXs - Variable in class edu.isi.pegasus.planner.dax.ADAG
mLevel - Variable in class edu.isi.pegasus.common.util.DefaultStreamGobblerCallback
  The level on which the messages are to be logged.
mLevelList - Variable in class edu.isi.pegasus.planner.partitioner.graph.MapGraph.BottomUpIterator
  A temporary list that stores all the nodes on a particular level.
mLevelList - Variable in class edu.isi.pegasus.planner.partitioner.graph.MapGraph.MapGraphIterator
  A temporary list that stores all the nodes on a particular level.
mLFN - Variable in class edu.isi.pegasus.planner.classes.ReplicaLocation
  The LFN associated with the entry.
mLFNMap - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Maintains a memory slurp of the file representation.
mLineSeparator - Variable in class edu.isi.pegasus.common.util.XMLWriter
mLink - Variable in class edu.isi.pegasus.planner.classes.PegasusFile
  Linkage of the file.
mLink - Variable in class edu.isi.pegasus.planner.dax.File
mList - Variable in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM.ListCallback
  The ArrayList where the lines are stored.
mLJobs - Variable in class edu.isi.pegasus.planner.dax.ADAG
mLoadAll - Variable in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser3
  A boolean indicating whether to load all sites.
mLoadAll - Variable in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser4
  A boolean indicating whether to load all sites.
mLocalCredentialPath - Variable in class edu.isi.pegasus.common.credential.impl.Irods
  The local path to the credential
mLocalCredentialPath - Variable in class edu.isi.pegasus.common.credential.impl.S3CFG
  The local path to the credential
mLocalCredentialPath - Variable in class edu.isi.pegasus.common.credential.impl.Ssh
  The local path to the credential
mLocalDirectory - Variable in class edu.isi.pegasus.planner.catalog.site.classes.StorageType
  The local directory on the node.
mLocalEnv - Variable in class edu.isi.pegasus.planner.refiner.ThreadPool
  The namespace object holding the environment variables for local pool.
mLocalIrodsEnv - Variable in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  The path to the irodsEnv file on the submit host (local pool).
mLocalIrodsEnvBasename - Variable in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  The basename of the user irodsEnv file
mLocalPathToPegasusLiteCommon - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  The local path on the submit host to pegasus-lite-common.sh
mLocalProxyPath - Variable in class edu.isi.pegasus.common.credential.impl.Proxy
  The local path to the user proxy
mLocalS3cfg - Variable in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  The path to the s3cfg file on the submit host (local pool).
mLocalS3cfgBasename - Variable in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  The basename of the user s3cfg file
mLocalTransfer - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.PoolTransfer
  boolean indicating whether the transfer job needs to run on local site
mLocalTransfer - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle.PoolTransfer
  boolean indicating whether the transfer job needs to run on local site
mLocalTransfers - Variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Map that indicates whether we need local setup transfer jobs for a site or not.
mLocalUserProxy - Variable in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  The path to the user proxy on the submit host (local pool), that is picked up for use in transfer of proxies.
mLocalUserProxyBasename - Variable in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  The basename of the user proxy , that is picked up for use in transfer of proxies.
mLocator - Variable in class edu.isi.pegasus.planner.parser.Parser
  Locator object to determine on which line in the xml has the error occured.
mLockTaskMetrics - Variable in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  A boolean indicating whether to update task metrics
mLog4jConf - Variable in class edu.isi.pegasus.planner.code.gridstart.NetloggerPostScript
  The log4j system property
mLogBuffer - Variable in class edu.isi.pegasus.common.logging.format.SimpleEvent
  The buffer that stores information about the log message
mLogEvent - Variable in class edu.isi.pegasus.common.logging.format.NetloggerEvent
  The current event object.
mLogFormatter - Variable in class edu.isi.pegasus.common.logging.LogManager
  The LogFormatter to use to format the message.
mLogFormatter - Variable in class edu.isi.pegasus.planner.code.generator.NetloggerJobMapper
  The handle to the netlogger log formatter.
mLogFormatter - Variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The handle to the netlogger log formatter.
mLogger - Variable in class edu.isi.pegasus.common.credential.impl.Abstract
  A handle to the logging object.
mLogger - Variable in class edu.isi.pegasus.common.logging.logger.Log4j
  The handle to a log4j logger object.
mLogger - Static variable in class edu.isi.pegasus.common.logging.LogManager
  Ensures only one object is created always.
mLogger - Variable in class edu.isi.pegasus.common.util.CondorVersion
  The default logger.
mLogger - Variable in class edu.isi.pegasus.common.util.DefaultStreamGobblerCallback
  The instance to the logger to log messages.
mLogger - Variable in class edu.isi.pegasus.common.util.StreamGobbler
  The handle to the logging object.
mLogger - Variable in class edu.isi.pegasus.common.util.XMLWriter
mLogger - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  The handle to the logging object.
mLogger - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  The handle to the logging manager.
mLogger - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.PoolConfig
  The handle to the logging object.
mLogger - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  The LogManager object which is used to log all the messages.
mLogger - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolMode
mLogger - Variable in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  The handle to the log manager.
mLogger - Variable in class edu.isi.pegasus.planner.catalog.site.impl.XML
  The handle to the log manager.
mLogger - Variable in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  The Logging instance.
mLogger - Variable in class edu.isi.pegasus.planner.catalog.transformation.client.Client
mLogger - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.CreateTCDatabase
  The default logger.
mLogger - Static variable in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  The LogManager object which is used to log all the messages.
mLogger - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  The LogManager object which is used to log all the messages.
mLogger - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  The LogManager object which is used to log all the messages.
mLogger - Variable in class edu.isi.pegasus.planner.catalog.transformation.Mapper
  Handle to the logger.
mLogger - Static variable in class edu.isi.pegasus.planner.catalog.transformation.TCMode
mLogger - Variable in class edu.isi.pegasus.planner.catalog.work.Database
  The handle to the logging object.
mLogger - Variable in class edu.isi.pegasus.planner.classes.Data
  The LogManager object which is used to log all the messages.
mLogger - Variable in class edu.isi.pegasus.planner.classes.PegasusBag
  The handle to the LogManager.
mLogger - Variable in class edu.isi.pegasus.planner.classes.TCMap
mLogger - Variable in class edu.isi.pegasus.planner.client.Executable
  The LogManager object which is used to log all the messages.
mLogger - Variable in class edu.isi.pegasus.planner.cluster.Abstract
  The handle to the logger object.
mLogger - Variable in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  The handle to the LogManager that logs all the messages.
mLogger - Variable in class edu.isi.pegasus.planner.cluster.Horizontal
  The handle to the logger object.
mLogger - Variable in class edu.isi.pegasus.planner.code.generator.Abstract
  The LogManager object which is used to log all the messages.
mLogger - Variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The handle to the logging object.
mLogger - Variable in class edu.isi.pegasus.planner.code.generator.condor.style.Abstract
  A handle to the logging object.
mLogger - Variable in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Handle to the logging manager.
mLogger - Variable in class edu.isi.pegasus.planner.code.generator.DAXReplicaStore
  The handle to the logging object.
mLogger - Variable in class edu.isi.pegasus.planner.code.generator.Metrics
  The logger object
mLogger - Variable in class edu.isi.pegasus.planner.code.generator.MonitordNotify
  The handle to the logging object.
mLogger - Variable in class edu.isi.pegasus.planner.code.generator.NetloggerJobMapper
  The handle to pegasus logger used for run.
mLogger - Variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The handle to the logging object.
mLogger - Variable in class edu.isi.pegasus.planner.code.generator.Stork
  The LogManager object which is used to log all the messages.
mLogger - Variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  The LogManager object which is used to log all the messages.
mLogger - Variable in class edu.isi.pegasus.planner.code.gridstart.NetloggerPostScript
  The LogManager object which is used to log all the messages.
mLogger - Variable in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  The LogManager object which is used to log all the messages.
mLogger - Variable in class edu.isi.pegasus.planner.code.gridstart.NoPOSTScript
  The LogManager object which is used to log all the messages.
mLogger - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusExitCode
  The LogManager object which is used to log all the messages.
mLogger - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  The LogManager object which is used to log all the messages.
mLogger - Variable in class edu.isi.pegasus.planner.code.gridstart.UserPOSTScript
  The LogManager object which is used to log all the messages.
mLogger - Variable in class edu.isi.pegasus.planner.common.PegasusConfiguration
  The logger to use.
mLogger - Variable in class edu.isi.pegasus.planner.common.UserOptions
  The Logger object used to log the messages.
mLogger - Static variable in class edu.isi.pegasus.planner.dax.AbstractJob
mLogger - Variable in class edu.isi.pegasus.planner.dax.ADAG
mLogger - Variable in class edu.isi.pegasus.planner.dax.CatalogType
mLogger - Variable in class edu.isi.pegasus.planner.namespace.Namespace
  The LogManager object which is used to log all the messages.
mLogger - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2CDAG
  The handle to the logger
mLogger - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2Graph
  The logging object.
mLogger - Variable in class edu.isi.pegasus.planner.parser.Parser
  The LogManager object which logs the Pegasus messages.
mLogger - Variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The handle to the logging object.
mLogger - Variable in class edu.isi.pegasus.planner.parser.TransformationCatalogTextParser
  The transformation to the logger used to log messages.
mLogger - Variable in class edu.isi.pegasus.planner.parser.XMLErrorHandler
  The handle to the logging object that is used to log the messages.
mLogger - Variable in class edu.isi.pegasus.planner.partitioner.DAXWriter
  The handle to the logging object.
mLogger - Variable in class edu.isi.pegasus.planner.partitioner.graph.MapGraph
  The handle to the logging manager.
mLogger - Variable in class edu.isi.pegasus.planner.partitioner.Label
  The handle to the Logging object.
mLogger - Variable in class edu.isi.pegasus.planner.partitioner.Partitioner
  The handle to the internal logging object.
mLogger - Variable in class edu.isi.pegasus.planner.partitioner.PDAXWriter
  The handle to the logging object.
mLogger - Variable in class edu.isi.pegasus.planner.partitioner.WriterCallback
  The handle to the logger object.
mLogger - Variable in class edu.isi.pegasus.planner.ranking.GetDAX
  The instance to the Logging manager.
mLogger - Variable in class edu.isi.pegasus.planner.ranking.Rank
  The handle to the logging object.
mLogger - Variable in class edu.isi.pegasus.planner.refiner.Authenticate
  The handle to the LogManager object.
mLogger - Variable in class edu.isi.pegasus.planner.refiner.cleanup.Cleanup
  The handle to the logger.
mLogger - Variable in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  The handle to the logging object used for logging.
mLogger - Variable in class edu.isi.pegasus.planner.refiner.createdir.AbstractStrategy
  The handle to the logging object, that is used to log the messages.
mLogger - Variable in class edu.isi.pegasus.planner.refiner.createdir.DefaultImplementation
  The handle to the logging object.
mLogger - Variable in class edu.isi.pegasus.planner.refiner.Engine
  The logging object which is used to log all the messages.
mLogger - Variable in class edu.isi.pegasus.planner.refiner.NodeCollapser
  The handle to the logger object.
mLogger - Variable in class edu.isi.pegasus.planner.refiner.ThreadPool
  The handle to the LogManager object.
mLogger - Variable in class edu.isi.pegasus.planner.selector.replica.Default
  The handle to the logging object that is used to log the various debug messages.
mLogger - Variable in class edu.isi.pegasus.planner.selector.replica.Local
  The handle to the logging object that is used to log the various debug messages.
mLogger - Variable in class edu.isi.pegasus.planner.selector.site.Abstract
  The handle to the logger.
mLogger - Variable in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  The handle to the LogManager
mLogger - Variable in class edu.isi.pegasus.planner.selector.TransformationSelector
mLogger - Variable in class edu.isi.pegasus.planner.transfer.AbstractRefiner
  The logging object which is used to log all the messages.
mLogger - Variable in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  The logging object which is used to log all the messages.
mLogger - Variable in class edu.isi.pegasus.planner.transfer.mapper.impl.AbstractFileFactoryBasedMapper
  The handle to the logger.
mLogger - Variable in class edu.isi.pegasus.planner.transfer.mapper.impl.Fixed
  The handle to the logger.
mLogger - Variable in class edu.isi.pegasus.planner.transfer.mapper.impl.Replica
  The handle to the logger.
mLogger - Variable in class edu.isi.pegasus.planner.transfer.RemoteTransfer
  The handle to the logging object.
mLogger - Variable in class edu.isi.pegasus.planner.transfer.sls.Condor
  The handle to the logging manager.
mLogger - Variable in class edu.isi.pegasus.planner.transfer.sls.Transfer
  The handle to the logging manager.
mLogger - Variable in class edu.isi.pegasus.planner.transfer.TPT
  The handle to the logging object.
mLoggingLevel - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  Denotes the logging level that is to be used for logging the messages.
mLoggingLevel - Variable in class edu.isi.pegasus.planner.client.SCClient
  Denotes the logging level that is to be used for logging the messages.
mLoggingLevel - Variable in class edu.isi.pegasus.planner.client.TCConverter
  Denotes the logging level that is to be used for logging the messages.
mLogicalFile - Variable in class edu.isi.pegasus.planner.classes.PegasusFile
  The logical name of the file.
mLogicalID - Variable in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  The logical id of the job as identified in the dax.
mLogicalName - Variable in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  The logical name of the node as identified in the dax.
mLogMsg - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  The String holding the log message.
mLogMsg - Variable in class edu.isi.pegasus.planner.classes.Data
  The String which stores the message to be stored.
mLogMsg - Variable in class edu.isi.pegasus.planner.client.Executable
  The error message to be logged.
mLogMsg - Variable in class edu.isi.pegasus.planner.parser.Parser
  The String which contains the messages to be logged.
mLogMsg - Variable in class edu.isi.pegasus.planner.refiner.Engine
  Contains the message which is to be logged by Pegasus.
mLogMsg - Variable in class edu.isi.pegasus.planner.transfer.refiner.Basic
  The string holding the logging messages
mLogMsg - Variable in class edu.isi.pegasus.planner.transfer.refiner.Empty
  The string holding the logging messages
mLogProgress - Variable in class edu.isi.pegasus.planner.cluster.aggregator.SeqExec
  Flag to indicate whether to log progress or not.
mLookAhead - Variable in class edu.isi.pegasus.planner.parser.TransformationCatalogTextParser
  Stores the look-ahead symbol.
mLookAhead - Variable in class edu.isi.pegasus.planner.parser.TransformationCatalogTextScanner
  Captures the look-ahead character.
mLRCList - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  The list of `LRC` objects that contain the information about the various LRCs associated with the remote site.
mLRCURL - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.LRC
  The contact string to the lrc e.g rls://sukhna.isi.edu .
mMajorVersion - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GlobusVersion
  This variable defines the major version number.
mMajorVersionLevel - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Stores the major version of the planner.
mMask - Variable in class edu.isi.pegasus.common.logging.logger.Default
  The mask that needs to be deployed to determine what messages are to be logged.
mMaxCount - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The maximum number of jobs that can be running on the remote site.
mMaxCPUTime - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The max walltime of the jobs that are run on the remote site.
mMaxDepth - Variable in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  The max depth of any job in the workflow useful for a priorityQueue implementation in an array
mMDAGPropertiesFile - Variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The path to the properties file that is written out and shared by all partitions in the mega DAG.
mMegadag - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  The megadag generation mode.
mMegaDAG - Variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The abstract dag object that ends up holding the megadag.
mMessage - Variable in class edu.isi.pegasus.common.logging.format.NetloggerEvent
  The current log event message.
mMetadata - Variable in class edu.isi.pegasus.planner.dax.CatalogType
mMetadata - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2Metadata
  The metadata of the workflow.
mMetadata - Variable in class edu.isi.pegasus.planner.parser.SiteCatalogXMLMetadataParser
  The Metadata object that has to be returned.
mMetrics - Variable in class edu.isi.pegasus.planner.code.generator.SendMetrics
mMetricsFileInSubmitDirectory - Variable in class edu.isi.pegasus.planner.classes.PlannerMetrics
mMetricsServers - Variable in class edu.isi.pegasus.planner.code.generator.Metrics
  The List of URLS for the metrics servers to report to.
mMinorVersion - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GlobusVersion
  This variable defines the minor version number.
mMinorVersionLevel - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Stores the major version of the planner.
mMountPoint - Variable in class edu.isi.pegasus.planner.catalog.site.classes.FileServerType
  The mount point for the server.
mMountPoint - Variable in class edu.isi.pegasus.planner.catalog.site.classes.FileSystemType
  The mount point for the file system.
mName - Variable in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  The logical mName of the transformation.
mName - Variable in class edu.isi.pegasus.planner.classes.CompoundTransformation
  The name of the tranformation.
mName - Variable in class edu.isi.pegasus.planner.dax.AbstractJob
mName - Variable in class edu.isi.pegasus.planner.dax.ADAG
  The Name / Label of the DAX
mName - Variable in class edu.isi.pegasus.planner.dax.Executable
  Name of the executable
mName - Variable in class edu.isi.pegasus.planner.dax.File
  The logical name of the file.
mName - Variable in class edu.isi.pegasus.planner.dax.Transformation
  Name of the transformation
mName - Variable in class edu.isi.pegasus.planner.partitioner.Partition
  The name of the partition.
mName - Variable in class edu.isi.pegasus.planner.partitioner.PDAXWriter
  The name assigned to the pdax file being written.
mName - Variable in class edu.isi.pegasus.planner.ranking.Ranking
  The name of the DAX.
mName - Variable in class edu.isi.pegasus.planner.selector.site.heft.Site
  The logical name assigned to the site.
mNameOfADag - Variable in class edu.isi.pegasus.planner.classes.DagInfo
  The name of the Abstract Dag taken from the adag element of the DAX generated by the Abstract Planner.
mNamepsaceToPropertiesPrefix - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
mNamespace - Variable in class edu.isi.pegasus.common.util.XMLWriter
mNamespace - Variable in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  The logical mNamespace of the transformation
mNamespace - Variable in class edu.isi.pegasus.planner.classes.CompoundTransformation
  The namespace of the compound transformation.
mNamespace - Variable in class edu.isi.pegasus.planner.classes.Profile
mNamespace - Variable in class edu.isi.pegasus.planner.dax.AbstractJob
mNamespace - Variable in class edu.isi.pegasus.planner.dax.Executable
  Namespace of the executable
mNamespace - Variable in class edu.isi.pegasus.planner.dax.File
  The namespace on a file.
mNamespace - Variable in class edu.isi.pegasus.planner.dax.Profile
  Namespace of the profile
mNamespace - Variable in class edu.isi.pegasus.planner.dax.Transformation
  Namespace of the Transformation
mNamespace - Variable in class edu.isi.pegasus.planner.namespace.Condor
  The name of the implementing namespace.
mNamespace - Variable in class edu.isi.pegasus.planner.namespace.Dagman
  The name of the implementing namespace.
mNamespace - Variable in class edu.isi.pegasus.planner.namespace.ENV
  The name of the implementing namespace.
mNamespace - Variable in class edu.isi.pegasus.planner.namespace.Globus
  The name of the implementing namespace.
mNamespace - Variable in class edu.isi.pegasus.planner.namespace.Hints
  The name of the implementing namespace.
mNamespace - Variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the implementing namespace.
mNamespace - Variable in class edu.isi.pegasus.planner.namespace.Selector
  The name of the implementing namespace.
mNamespace - Variable in class edu.isi.pegasus.planner.namespace.Stat
  The name of the implementing namespace.
mNamespace - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  For holding the namespace if specified in the Profile Element.
mNewLine - Variable in class edu.isi.pegasus.planner.catalog.site.classes.AbstractXMLPrintVisitor
  The new line character to be used
mNext - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.PoolTransfer
  The index of the job to which the next transfer for the pool would be scheduled.
mNext - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle.PoolTransfer
  The index of the job to which the next transfer for the pool would be scheduled.
mNext - Variable in class edu.isi.pegasus.planner.transfer.refiner.Chain.SiteTransfer
  The index of the bundle to which the next transfer for the site would be added to.
mNMIArchToVDSArchMap - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.NMI2VDSSysInfo
  The map storing architecture to corresponding NMI architecture platforms.
mNMIOSToVDSOSMap - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.NMI2VDSSysInfo
  The map storing OS to corresponding NMI OS platforms.
mNode - Variable in class edu.isi.pegasus.planner.refiner.cleanup.CleanupJobContent
  The graph cleanupNode object for the associated job whose files are being deleted.
mNodeCollapser - Variable in class edu.isi.pegasus.planner.refiner.MainEngine
  The handle to the node collapser.
mNodeComparator - Variable in class edu.isi.pegasus.planner.partitioner.Horizontal
  A static instance of GraphNode comparator.
mNodeIdPattern - Static variable in class edu.isi.pegasus.planner.dax.Patterns
mNodeLabel - Variable in class edu.isi.pegasus.planner.dax.AbstractJob
mNodeList - Variable in class edu.isi.pegasus.planner.partitioner.Partition
  The list of `GraphNode`objects corresponding to the nodes making the partiition.``
mNodeSet - Variable in class edu.isi.pegasus.planner.partitioner.MultipleLook
  The set of job id's in the partition.
mNodeSet - Variable in class edu.isi.pegasus.planner.partitioner.Partition
  The set of node id's in the partition.
mNodeSet - Variable in class edu.isi.pegasus.planner.partitioner.SingleLook
  The set of job id's in the partition.
mNoGridStartImpl - Variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Handle to NoGridStart implementation.
mNonStandardJavaOptions - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  The set of non standard java options that need to be passed to the JVM
mNonTPTSite - Variable in class edu.isi.pegasus.planner.classes.TransferJob
  The site at which the transfer jobs would have run, had it been running in a peer 2 peer transfer mode (non third party mode).
mNotifications - Variable in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  All the notifications associated with the job
mNotifications - Variable in class edu.isi.pegasus.planner.classes.ADag
  All the notifications associated with the job
mNotifications - Variable in class edu.isi.pegasus.planner.classes.CompoundTransformation
  All the notifications associated with the job
mNotifications - Variable in class edu.isi.pegasus.planner.classes.Job
  All the notifications associated with the job
mNotifications - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2CDAG
  All the notifications associated with the adag
mNotificationsWriter - Variable in class edu.isi.pegasus.planner.code.generator.MonitordNotify
  The handle to the PrintWriter that writes out the notifications file
mNumberOfExistingLFNS - Variable in class edu.isi.pegasus.planner.transfer.mapper.impl.Hashed
mNumChmodJobs - Variable in class edu.isi.pegasus.planner.classes.WorkflowMetrics
mNumCleanupJobs - Variable in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  The number of cleanup jobs.
mNumClusteredJobs - Variable in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  The number of clustered compute jobs.
mNumComputeJobs - Variable in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  The number of compute jobs.
mNumComputeTasks - Variable in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  The number of compute tasks in the DAX
mNumCreateDirJobs - Variable in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  The number of create dir jobs.
mNumDAGJobs - Variable in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  The number of DAG jobs in the workflow
mNumDAGTasks - Variable in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  The number of DAG tasks in the DAX.
mNumDAXJobs - Variable in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  The number of dax jobs in the workflow
mNumDAXTasks - Variable in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  The number of DAX tasks in the DAX
mNumFormatter - Variable in class edu.isi.pegasus.planner.classes.PlannerMetrics
  The number formatter to format the run submit dir entries.
mNumFormatter - Variable in class edu.isi.pegasus.planner.client.CPlanner
  The number formatter to format the run submit dir entries.
mNumFormatter - Variable in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  The number formatter to format the run submit dir entries.
mNumFormatter - Variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The number formatter to format the run submit dir entries.
mNumInterTxJobs - Variable in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  The number of inter-site transfer jobs.
mNumOfJobs - Variable in class edu.isi.pegasus.planner.partitioner.MultipleLook
  The number of jobs that are in the partition.
mNumOfJobs - Variable in class edu.isi.pegasus.planner.partitioner.SingleLook
  The number of jobs that are in the partition.
mNumOfPools - Variable in class edu.isi.pegasus.planner.refiner.ThreadPool
  The number of pools that one has to authenticate against.
mNumOfRescueTries - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  The numer of rescue's to try before replanning.
mNumOfTXProcesses - Variable in class edu.isi.pegasus.planner.transfer.implementation.T2
  The number of g-u-c processes that are spawned to transfer the files in one transfer job.
mNumOfTXStreams - Variable in class edu.isi.pegasus.planner.transfer.implementation.GUC
  The number of streams that each g-u-c process opens to do the ftp transfer.
mNumOfTXStreams - Variable in class edu.isi.pegasus.planner.transfer.implementation.T2
  The number of streams that each g-u-c process opens to do the ftp transfer.
mNumProcessors - Variable in class edu.isi.pegasus.planner.selector.site.heft.Site
  The number of processors making up a site.
mNumRegJobs - Variable in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  The number of registration jobs.
mNumSITxJobs - Variable in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  The number of stage in transfer jobs.
mNumSOTxJobs - Variable in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  The number of stage-out transfer jobs.
mNumTotalJobs - Variable in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  The total number of jobs in the executable workflow.
mNumTotalTasks - Variable in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  The total number of tasks in the executable workflow.
mObject - Variable in class edu.isi.pegasus.planner.parser.ParserStackElement
MODIFY_FOR_FILE_URLS_KEY - Static variable in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Property specify whether to modify file url or not.
modifyFileURL - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Boolean indicating whether to modify the file URL or not
modifyFileURL - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Boolean indicating whether to modify the file URL or not
modifyForFileURLS(TransformationCatalogEntry) - Static method in class edu.isi.pegasus.planner.catalog.transformation.impl.Abstract
  Modifies a Transformation Catalog Entry to handle file URL's.
modifyForFileURLS(String, String) - Static method in class edu.isi.pegasus.planner.catalog.transformation.impl.Abstract
  Modifies a Transformation Catalog Entry to handle file URL's.
modifyJobForFirstLevelStaging(Job, String, String, String) - Method in class edu.isi.pegasus.planner.transfer.sls.Condor
  Modifies a job for the first level staging to headnode.This is to add any files that needs to be staged to the head node for a job specific to the SLS implementation.
modifyJobForWorkerNodeExecution(Job, String, String, String) - Method in class edu.isi.pegasus.planner.transfer.sls.Condor
  Modifies a compute job for second level staging.
modifyJobForWorkerNodeExecution(Job, String, String, String) - Method in interface edu.isi.pegasus.planner.transfer.SLS
  Modifies a compute job for second level staging.
modifyJobForWorkerNodeExecution(Job, String, String, String) - Method in class edu.isi.pegasus.planner.transfer.sls.Transfer
  Modifies a compute job for second level staging.
modifyURL - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Boolean indicating whether to modify the file URL or not
MONITORD_COMMENT_MARKER - Static variable in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  The marker to designate a line in the input file reserved for monitord purposes.
MonitordNotify - Class in edu.isi.pegasus.planner.code.generator
  A MonitordNotify Input File Generator that generates the input file required for pegasus-monitord.
MonitordNotify() - Constructor for class edu.isi.pegasus.planner.code.generator.MonitordNotify
mOperation - Variable in class edu.isi.pegasus.planner.catalog.site.classes.FileServerType
  The operations supported by the file server
mOPStream - Variable in class edu.isi.pegasus.common.util.StreamGobbler
  The output stream to which the contents have to be redirected to.
mOptArg - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  Designates if the optional argument to the random directory was given.
mOptional - Variable in class edu.isi.pegasus.planner.dax.File
  Is the file optional
mOrder - Variable in class edu.isi.pegasus.planner.partitioner.graph.TopologicalSortIterator
  The number of nodes in the graph.
mOriginalArgumentString - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  The argument string with which the planner was invoked.
mOriginalDag - Variable in class edu.isi.pegasus.planner.refiner.MainEngine
  The Original Dag object which is constructed by parsing the dag file.
mOS - Variable in class edu.isi.pegasus.planner.catalog.classes.SysInfo
  The Operating System.
mOS - Variable in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  An optional os type for the grid gateway.
mOs - Variable in class edu.isi.pegasus.planner.dax.Executable
  Os the executable is compiled for
mOSRelease - Variable in class edu.isi.pegasus.planner.catalog.classes.SysInfo
  The Operating System Release.
mOSRelease - Variable in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Optional information about the os release.
mOsRelease - Variable in class edu.isi.pegasus.planner.dax.Executable
  Os release the executable is compiled for
mOSToNMIOSReleaseAndVersion - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The map storing OS to corresponding NMI OS platforms.
mOSType - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The operating system type type of the remote machines to which the jobmanager talks to.
mOSVersion - Variable in class edu.isi.pegasus.planner.catalog.classes.SysInfo
  The Operating System Version.
mOSVersion - Variable in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Optional information about the version.
mOsVersion - Variable in class edu.isi.pegasus.planner.dax.Executable
  OS version the executable is compiled for
mOutputDir - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  the output directory
mOutputDir - Variable in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  The output directory where to generate the ploticus output.
mOutputFile - Variable in class edu.isi.pegasus.planner.client.RankDAX
  The output file that lists the daxes in sorted order.
mOutputFile - Variable in class edu.isi.pegasus.planner.client.SCClient
  The output file that is written out.
mOutputFile - Variable in class edu.isi.pegasus.planner.client.TCConverter
  The output file that is written out.
mOutputFormat - Variable in class edu.isi.pegasus.planner.client.SCClient
  The output format for the site catalog.
mOutputFormat - Variable in class edu.isi.pegasus.planner.client.TCConverter
  The output format for the transformation catalog.
mOutputMapper - Variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  Handle to an OutputMapper that tells what
mOutputPool - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  The output pool on which the data products are needed to be transferred to.
mOutputPool - Static variable in class edu.isi.pegasus.planner.refiner.Engine
  The pool on which all the output data should be transferred.
mOutputSite - Variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  The output site where files need to be staged to.
mOutputSite - Variable in class edu.isi.pegasus.planner.transfer.mapper.impl.AbstractFileFactoryBasedMapper
  The output site where the data needs to be placed.
mOutputSite - Variable in class edu.isi.pegasus.planner.transfer.mapper.impl.Fixed
  The output site where the data needs to be placed.
mOutputSite - Variable in class edu.isi.pegasus.planner.transfer.mapper.impl.Replica
  The output site where the data needs to be placed.
mOutStream - Variable in class edu.isi.pegasus.common.logging.logger.Default
  The stream to which one writes.
moveLeft(LinkedList[], int, long) - Method in class edu.isi.pegasus.planner.provisioner.Node
  Redistribute this task to the earlier time.
moveRight(LinkedList[], int, long) - Method in class edu.isi.pegasus.planner.provisioner.Node
  Redistribute this task to the later time.
mParent - Variable in class edu.isi.pegasus.planner.dax.Edge
  The parent of the parent
mParents - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  The list of parents of a node referred to by mCurrentChildId.
mParents - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser3
  List of parents for a child node in the graph
mParents - Variable in class edu.isi.pegasus.planner.parser.PDAXParser
  List of parents for a particular child.
mParents - Variable in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  The list of parents of the job/node in the abstract graph.
mParentsMap - Variable in class edu.isi.pegasus.planner.partitioner.Partition
  A map containing a node and it's parents ids in the partition.
mParser - Variable in class edu.isi.pegasus.planner.catalog.site.impl.XML
  The handle to parser instance that will parse the site catalog.
mParser - Variable in class edu.isi.pegasus.planner.parser.Parser
  The object which is used to parse the dax.
mParsingDone - Variable in class edu.isi.pegasus.planner.parser.SiteCatalogXMLMetadataParser
  A boolean indicating that parsing is done.
mParsingDone - Variable in class edu.isi.pegasus.planner.parser.StackBasedXMLParser
  A boolean indicating that parsing is done.
mPartADAG - Variable in class edu.isi.pegasus.planner.partitioner.MultipleLook
  The ADAG object containing the partitioned dax.
mPartADAG - Variable in class edu.isi.pegasus.planner.partitioner.SingleLook
  The ADAG object containing the partitioned dax.
mPartition - Variable in class edu.isi.pegasus.planner.parser.PDAXParser
  The object holding the contents of one partition as indicated in the pdax.
mPartition - Variable in class edu.isi.pegasus.planner.partitioner.Topological
  The partition that has to be sorted.
mPartitionClusterMap - Variable in class edu.isi.pegasus.planner.cluster.Abstract
  A Map that indexes the partition ID to the clustered job.
mPartitionerTable - Static variable in class edu.isi.pegasus.planner.cluster.ClustererFactory
  The table that maps clustering technique to a partitioner.
mPartitionID - Variable in class edu.isi.pegasus.planner.partitioner.graph.LabelBag
  The value for the partition key.
mPartitioningStarted - Variable in class edu.isi.pegasus.planner.partitioner.WriterCallback
  A boolean indicating that the partitioning has started.
mPartitioningType - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  Stores the type of partitioning to be done.
mPartitionMap - Variable in class edu.isi.pegasus.planner.partitioner.Horizontal
  A map indexed by the partition ID.
mPartitionMap - Variable in class edu.isi.pegasus.planner.partitioner.Label
  A map indexed by the label.
mPartitionName - Variable in class edu.isi.pegasus.planner.partitioner.DAXWriter
  The name of the partition dax that are generated.
mPassword - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.CreateTCDatabase
  Stores the MySQL password
mPatchVersion - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GlobusVersion
  This variable defines the patch version number.
mPatchVersionLevel - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Stores the major version of the planner.
mPath - Variable in class edu.isi.pegasus.common.util.PegasusURL
  The path referred to by the PegasusURL
mPattern - Static variable in class edu.isi.pegasus.common.util.CondorVersion
  Stores compiled patterns at first use, quasi-Singleton.
mPattern - Static variable in class edu.isi.pegasus.common.util.PegasusURL
  Stores compiled patterns at first use, quasi-Singleton.
mPattern - Variable in class edu.isi.pegasus.planner.client.SubmitDirectoryFilenameFilter
  Stores compiled patterns at first use, quasi-Singleton.
mPattern - Static variable in class edu.isi.pegasus.planner.common.RunDirectoryFilenameFilter
  Stores compiled patterns at first use, quasi-Singleton.
mPattern - Static variable in class edu.isi.pegasus.planner.parser.pdax.RunDirectoryFilenameFilter
  Stores compiled patterns at first use, quasi-Singleton.
mPattern - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Stores compiled patterns at first use, quasi-Singleton.
mPattern - Variable in class edu.isi.pegasus.planner.selector.replica.Regex.Rank
  The compiled regex expression
mPBS - Variable in class edu.isi.pegasus.planner.code.generator.PMC
  Handle to the PBS Code generator.
mPDAX - Variable in class edu.isi.pegasus.planner.partitioner.WriterCallback
  The path to the PDAX file written out.
mPDAXDirectory - Variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The directory in which the daxes corresponding to the partitions are kept.
mPDAXDirectory - Variable in class edu.isi.pegasus.planner.partitioner.DAXWriter
  The directory in which the daxes corresponding to the partition are generated.
mPDAXFile - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  The path to the pdax file that contains the partition graph.
mPDAXWriter - Variable in class edu.isi.pegasus.planner.partitioner.WriterCallback
  The handle to the partition graph writer.
mPegasusHome - Variable in class edu.isi.pegasus.planner.common.PegasusProperties
  The value of the PEGASUS_HOME environment variable.
mPegasusLiteEnabled - Variable in class edu.isi.pegasus.planner.code.generator.condor.style.Condor
  A boolean indicating whether pegasus lite mode is picked up or not.
mPegasusLiteLocalWrapper - Variable in class edu.isi.pegasus.planner.code.generator.condor.style.Condor
  Path to Pegasus Lite local wrapper script.
mPegasusPlanOptions - Variable in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  The object containing all the options passed to the Concrete Planner.
mPegasusProfilesInProperties - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  Pegasus Profiles specified in the properties.
mPegasusProfilesInProperties - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  Pegasus Profiles specified in the properties.
mPFN - Variable in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  The physical path on the resource for a particular arch, os and type.
mPFNList - Variable in class edu.isi.pegasus.planner.classes.ReplicaLocation
  A list of `ReplicaCatalogEntry` objects containing the PFN's and associated attributes.
mPFNs - Variable in class edu.isi.pegasus.planner.dax.CatalogType
MPI_EXEC_CLASS - Static variable in class edu.isi.pegasus.planner.cluster.aggregator.JobAggregatorFactory
  The name of the class in this package, that corresponds to mpiexec.
MPIExec - Class in edu.isi.pegasus.planner.cluster.aggregator
  This class aggregates the smaller jobs in a manner such that they are launched at remote end, by mpiexec on n nodes where n is the nodecount associated with the aggregated job that is being lauched by mpiexec.
MPIExec() - Constructor for class edu.isi.pegasus.planner.cluster.aggregator.MPIExec
  The default constructor.
mPlannerCache - Variable in class edu.isi.pegasus.planner.classes.PegasusBag
  The transient replica catalog that tracks the files created or transferred during the workflow
mPlannerCache - Variable in class edu.isi.pegasus.planner.refiner.cleanup.Cleanup
  Handle to the transient replica catalog.
mPlannerCache - Variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  A SimpleFile Replica Catalog, that tracks all the files that are being materialized as part of workflow executaion.
mPlannerCache - Variable in class edu.isi.pegasus.planner.transfer.sls.Condor
  A SimpleFile Replica Catalog, that tracks all the files that are being materialized as part of workflow execution.
mPlannerCache - Variable in class edu.isi.pegasus.planner.transfer.sls.Transfer
  A SimpleFile Replica Catalog, that tracks all the files that are being materialized as part of workflow execution.
mPlannerOptions - Variable in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
mPlannerOptions - Variable in class edu.isi.pegasus.planner.client.RankDAX
  The options to be passed ahead to pegasus plan.
mPlannerOptions - Variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  The planner options passed to the planner
mPlannerOpts - Variable in class edu.isi.pegasus.planner.common.UserOptions
  The object containing all the user options.
mPMetrics - Variable in class edu.isi.pegasus.planner.classes.PegasusBag
  The planner metrics to use.
mPMetrics - Variable in class edu.isi.pegasus.planner.client.CPlanner
  The PlannerMetrics object storing the metrics about this planning instance.
mPool - Variable in class edu.isi.pegasus.planner.classes.AuthenticateRequest
  The pool id at of the pool which the resource is .
mPool - Variable in class edu.isi.pegasus.planner.refiner.ThreadPool.AuthenticateThread
  The pool against which to authenticate.
mPool - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.PoolTransfer
  The staging site for which these transfers are grouped.
mPool - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle.PoolTransfer
  The remote pool for which these transfers are grouped.
mPoolClass - Variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Specifies the implementing class for the pool interface.
mPoolConfig - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.Abstract
  Handle to the PoolConfig object
mPoolFile - Variable in class edu.isi.pegasus.planner.refiner.Engine
  The path to the file containing the pool information.
mPoolHandle - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.Text
  The internal singleton handle.
mPoolHandle - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.XML
mPoolHandle - Variable in class edu.isi.pegasus.planner.refiner.Authenticate
  The handle to the Pool Info Provider.
mPoolHandle - Variable in class edu.isi.pegasus.planner.refiner.ThreadPool
  The handle to the Pool Info Provider.
mPoolProvider - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  The path to the pool information provider.
mPOptions - Variable in class edu.isi.pegasus.planner.classes.PegasusBag
  The options passed to the planner.
mPOptions - Variable in class edu.isi.pegasus.planner.classes.PlannerCache
  The planner options
mPOptions - Variable in class edu.isi.pegasus.planner.client.CPlanner
  The object containing all the options passed to the Concrete Planner.
mPOptions - Variable in class edu.isi.pegasus.planner.code.generator.Abstract
  The object containing the command line options specified to the planner at runtime.
mPOptions - Variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The object containing the command line options specified to the planner at runtime.
mPOptions - Variable in class edu.isi.pegasus.planner.code.generator.DAXReplicaStore
  The object containing the command line options specified to the planner at runtime.
mPOptions - Variable in class edu.isi.pegasus.planner.code.generator.MonitordNotify
  The object containing the command line options specified to the planner at runtime.
mPOptions - Variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The object containing the command line options specified to the planner at runtime.
mPOptions - Variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  The options passed to the planner.
mPOptions - Variable in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  The options passed to the planner.
mPOptions - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  The options passed to the planner.
mPOptions - Static variable in class edu.isi.pegasus.planner.common.UserOptions
  The object holding the Singleton instance.
mPOptions - Variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The object containing the options that were given to the concrete planner at runtime.
mPOptions - Variable in class edu.isi.pegasus.planner.refiner.Engine
  Contains the various options to the Planner as passed by the user at runtime.
mPOptions - Variable in class edu.isi.pegasus.planner.transfer.AbstractRefiner
  The options passed to the planner at runtime.
mPOptions - Variable in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  Contains the various options to the Planner as passed by the user at runtime.
mPOptions - Variable in class edu.isi.pegasus.planner.transfer.sls.Condor
  The handle to the planner options.
mPort - Variable in class edu.isi.pegasus.planner.refiner.Authenticate.HostPort
  The port at which the server is running.
mPosition - Variable in exception edu.isi.pegasus.planner.code.generator.condor.CondorQuoteParserException
  Remembers the position that cause the exception to be thrown.
mPOSTScriptImplementationTable - Variable in class edu.isi.pegasus.planner.code.GridStartFactory
  A table that maps short names of `POSTScript` implementations with the implementations themselves.
mPOSTScriptPath - Variable in class edu.isi.pegasus.planner.code.gridstart.NetloggerPostScript
  The path to the user postscript on the submit host.
mPOSTScriptPath - Variable in class edu.isi.pegasus.planner.code.gridstart.UserPOSTScript
  The path to the user postscript on the submit host.
mPostScriptProperties - Variable in class edu.isi.pegasus.planner.code.gridstart.NetloggerPostScript
  The path to the properties file created in submit directory.
mPostScriptProperties - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusExitCode
  The properties that need to be passed to the postscript invocation on the command line in the java format.
mPPS - Variable in class edu.isi.pegasus.planner.cluster.Horizontal
  The handle to the provenance store implementation.
mPPS - Variable in class edu.isi.pegasus.planner.transfer.refiner.Basic
  The handle to the provenance store implementation.
mPPS - Variable in class edu.isi.pegasus.planner.transfer.refiner.Empty
  The handle to the provenance store implementation.
mPreferredSitesMap - Variable in class edu.isi.pegasus.planner.selector.replica.Restricted
  A Map indexed by site handles, that contains a set of site handles.
mPreviousToken - Variable in class edu.isi.pegasus.planner.parser.TransformationCatalogTextScanner
  Captures the previous token.
mPriority - Variable in class edu.isi.pegasus.planner.classes.FileTransfer
  A priority associated with the FileTransfer
mProcessors - Variable in class edu.isi.pegasus.planner.selector.site.heft.Site
  A list of processors making up the site.
mProfileKey - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  For holding the key attribute in profile tag.
mProfileKey - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.BundleValue
  The pegasus profile key to use for lookup
mProfileKey - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle.BundleValue
  The pegasus profile key to use for lookup
mProfileList - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  The list of `Profile` objects that contain the profile information associated with the remote site.
mProfileMap - Variable in class edu.isi.pegasus.planner.catalog.classes.Profiles
  An enum map that associates the enum keys with the corresponding namespace objects.
mProfileMap - Variable in class edu.isi.pegasus.planner.namespace.Namespace
  The Map object that contains the profiles for a particular namespace.
mProfiles - Variable in class edu.isi.pegasus.planner.catalog.site.classes.FileServerType
  The profiles associated with the FileSystem.
mProfiles - Variable in class edu.isi.pegasus.planner.catalog.site.classes.HeadNodeFS
  The profiles associated with the headnode filesystem.
mProfiles - Variable in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  The profiles asscociated with the site.
mProfiles - Variable in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  The profiles asscociated with the site.
mProfiles - Variable in class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeFS
  The profiles associated with the headnode filesystem.
mProfiles - Variable in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  The profiles associated with the site.
mProfiles - Variable in class edu.isi.pegasus.planner.common.PegasusProperties
  Profiles that are specified in the properties
mProfiles - Variable in class edu.isi.pegasus.planner.dax.AbstractJob
mProfiles - Variable in class edu.isi.pegasus.planner.dax.CatalogType
mProfiles - Variable in class edu.isi.pegasus.planner.dax.PFN
mProfileTag - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Set as and when Profile and Argument tags are started and ended.
mProgram - Variable in class edu.isi.pegasus.common.logging.format.AbstractLogFormatter
  The name of the program.
mProgram - Variable in class edu.isi.pegasus.common.logging.format.NetloggerEvent
  The name of the program.
mProgram - Variable in class edu.isi.pegasus.common.logging.format.SimpleEvent
  The name of the program.
mPrompt - Variable in class edu.isi.pegasus.common.util.StreamGobbler
  The prompt that is to be written to the output stream.
mProperties - Variable in class edu.isi.pegasus.common.logging.logger.Log4j
  The properties passed at runtime
mProperties - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  The properties container for properties specified on the commandline in the DAX dax elements.
mPropertiesFilename - Variable in class edu.isi.pegasus.planner.client.PegasusGetSites
mPropertiesPath - Variable in class edu.isi.pegasus.planner.classes.PlannerMetrics
  The pointer to the properties file that was used.
mPropertyTable - Static variable in class edu.isi.pegasus.planner.transfer.RemoteTransfer
  An internal table that maps remote transfer type to the corresponding property.
mPropertyTable - Static variable in class edu.isi.pegasus.planner.transfer.TPT
  An internal table that maps third party transfer type to the corresponding property.
mProps - Variable in class edu.isi.pegasus.common.credential.impl.Abstract
  The object holding all the properties pertaining to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  The object holding all the properties pertaining to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  The handle to the properties object.
mProps - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  The handle to the properties object.
mProps - Variable in class edu.isi.pegasus.planner.catalog.transformation.Mapper
  Handle to Pegasus Properties
mProps - Variable in class edu.isi.pegasus.planner.classes.PegasusBag
  The handle to the `PegasusProperties`.
mProps - Variable in class edu.isi.pegasus.planner.classes.PlannerCache
  The PegasusProperties
mProps - Variable in class edu.isi.pegasus.planner.client.Executable
  The object holding all the properties pertaining to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.cluster.Abstract
  The handle to the properties object holding all the properties.
mProps - Variable in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  The object holding all the properties pertaining to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.cluster.aggregator.JobAggregatorInstanceFactory
  The handle to the properties object holding all the properties.
mProps - Variable in class edu.isi.pegasus.planner.cluster.Horizontal
  The handle to the properties object holding all the properties.
mProps - Variable in class edu.isi.pegasus.planner.code.generator.Abstract
  The object holding all the properties pertaining to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The object holding all the properties pertaining to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.code.generator.condor.style.Abstract
  The object holding all the properties pertaining to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  The handle to Pegasus Properties.
mProps - Variable in class edu.isi.pegasus.planner.code.generator.DAXReplicaStore
  The object holding all the properties pertaining to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.code.generator.MonitordNotify
  The object holding all the properties pertaining to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The object holding all the properties pertaining to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  The object holding all the properties pertaining to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.code.gridstart.NetloggerPostScript
  The object holding all the properties pertaining to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  The object holding all the properties pertaining to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.code.gridstart.NoPOSTScript
  The object holding all the properties pertaining to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusExitCode
  The object holding all the properties pertaining to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  The object holding all the properties pertaining to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.code.gridstart.UserPOSTScript
  The object holding all the properties pertaining to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.code.GridStartFactory
  The properties object holding all the properties.
mProps - Variable in class edu.isi.pegasus.planner.common.PegasusProperties
  The object holding all the properties pertaining to the VDS system.
mProps - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2CDAG
  The handle to the properties object.
mProps - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2Graph
  The handle to the properties object.
mProps - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2Metadata
  The handle to the properties object.
mProps - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2NewGraph
  The handle to the properties object.
mProps - Variable in class edu.isi.pegasus.planner.parser.Parser
  The object holding all the properties pertaining to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The handle to the properties file.
mProps - Variable in class edu.isi.pegasus.planner.partitioner.ClustererCallback
  The handle to the properties object.
mProps - Variable in class edu.isi.pegasus.planner.partitioner.Partitioner
  The object holding all the properties pertaining to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.partitioner.WriterCallback
  Handle to the properties available.
mProps - Variable in class edu.isi.pegasus.planner.ranking.GetDAX
  The properties passed to the client.
mProps - Variable in class edu.isi.pegasus.planner.refiner.Authenticate
  The handle to the PegasusProperties object.
mProps - Variable in class edu.isi.pegasus.planner.refiner.cleanup.Cleanup
  The handle to the properties passed to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  The handle to the properties passed to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.refiner.cleanup.RM
  The handle to the properties passed to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.refiner.createdir.DefaultImplementation
  The handle to the pegasus properties.
mProps - Variable in class edu.isi.pegasus.planner.refiner.Engine
  The object holding all the properties pertaining to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.refiner.ThreadPool
  The handle to the properties object.
mProps - Variable in class edu.isi.pegasus.planner.selector.replica.Default
  The properties object containing the properties passed to the planner.
mProps - Variable in class edu.isi.pegasus.planner.selector.replica.Local
  The properties object containing the properties passed to the planner.
mProps - Variable in class edu.isi.pegasus.planner.selector.site.Abstract
  The properties passed to Pegasus at runtime.
mProps - Variable in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  The handle to the properties.
mProps - Variable in class edu.isi.pegasus.planner.transfer.AbstractRefiner
  The handle to the properties object holding the properties relevant to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  The handle to the properties object holding the properties relevant to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.transfer.RemoteTransfer
  The handle to the properties object holding the properties relevant to Pegasus.
mProps - Variable in class edu.isi.pegasus.planner.transfer.sls.Condor
  The handle to the properties.
mProps - Variable in class edu.isi.pegasus.planner.transfer.sls.Transfer
  The handle to the properties.
mProps - Variable in class edu.isi.pegasus.planner.transfer.TPT
  The handle to the properties object holding the properties relevant to Pegasus.
mPropsInSubmitDir - Variable in class edu.isi.pegasus.planner.common.PegasusProperties
  The pointer to the properties file that is written out in the submit directory.
mProtocol - Variable in class edu.isi.pegasus.common.util.PegasusURL
  The protocol referred to by the PegasusURL
mProtocol - Variable in class edu.isi.pegasus.planner.catalog.site.classes.FileServerType
  The protocol used by the file server.
mPutOperations - Static variable in enum edu.isi.pegasus.planner.catalog.site.classes.FileServerType.OPERATION
mPutRCCache - Variable in class edu.isi.pegasus.planner.classes.PlannerCache
  The cache storing the PUT urls for the files in the workflow
mQueue - Variable in class edu.isi.pegasus.planner.partitioner.BFS
  The first in first out queue, that manages the set of gray vertices in a breadth first search.
mQueue - Variable in class edu.isi.pegasus.planner.partitioner.graph.MapGraph.BottomUpIterator
  The first in first out queue, that manages the set of gray vertices in a breadth first search.
mQueue - Variable in class edu.isi.pegasus.planner.partitioner.graph.MapGraph.MapGraphIterator
  The first in first out queue, that manages the set of gray vertices in a breadth first search.
mQueue - Variable in class edu.isi.pegasus.planner.partitioner.graph.TopologicalSortIterator
  The internal list of nodes that contains the nodes to be traversed.
mQueue - Variable in class edu.isi.pegasus.planner.partitioner.Label
  The first in first out queue, that manages the set of gray vertices in a breadth first search.
mQueue - Variable in class edu.isi.pegasus.planner.refiner.ThreadPool
  The request queue that holds the authenticate requests.
mRandom - Static variable in class edu.isi.pegasus.planner.common.PegRandom
  The object containing the instance of the java.util.Random class.
mRandomDirName - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  If the genRandomDir flag is set, then this contains the name of the random directory.
mRank - Variable in class edu.isi.pegasus.planner.ranking.Ranking
  Rank of the dax.
mRank - Variable in class edu.isi.pegasus.planner.selector.replica.Regex.Rank
  The rank value.
MRC - Class in edu.isi.pegasus.planner.catalog.replica.impl
  A multiple replica catalog implementation that allows users to query different multiple catalogs at the same time.
MRC() - Constructor for class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  The default constructor.
mRCB - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  The handle to the replica catalog bridge.
mRCB - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  The handle to the replica catalog bridge.
mRCBridge - Variable in class edu.isi.pegasus.planner.refiner.MainEngine
  The bridge to the Replica Catalog.
mRCBridge - Variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  The bridge to the Replica Catalog.
mRCCatalog - Variable in class edu.isi.pegasus.planner.transfer.mapper.impl.Replica
mRCDown - Variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  A boolean variable to desingnate whether the RLI queried was down or not.
mRCHandle - Variable in class edu.isi.pegasus.planner.classes.PegasusBag
  The handle to the replica catalog.
mRCList - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  The list of replica catalogs that need to be queried for.
mReadOnly - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  A boolean indicating whether the catalog is read only or not.
mRedEng - Variable in class edu.isi.pegasus.planner.refiner.MainEngine
  The handle to the Reduction Engine that performs reduction on the graph.
mReducedDag - Variable in class edu.isi.pegasus.planner.refiner.MainEngine
  The reduced Dag object which is got from the Reduction Engine.
mRefiner - Variable in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  The handle to the refiner that loaded this implementation.
mRegexExpression - Static variable in class edu.isi.pegasus.common.util.CondorVersion
  Store the regular expressions necessary to parse the output of condor_version.
mRegexExpression - Static variable in class edu.isi.pegasus.common.util.PegasusURL
  Stores the regular expressions necessary to parse a PegasusURL into 3 components protocol, host and path
mRegexExpression - Variable in class edu.isi.pegasus.planner.client.SubmitDirectoryFilenameFilter
  Store the regular expressions necessary to parse kickstart output files
mRegexExpression - Static variable in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  Store the regular expressions necessary to match the * properties.
mRegexExpression - Static variable in class edu.isi.pegasus.planner.common.RunDirectoryFilenameFilter
  Store the regular expressions necessary to parse kickstart output files
mRegexExpression - Static variable in class edu.isi.pegasus.planner.parser.pdax.RunDirectoryFilenameFilter
  Store the regular expressions necessary to parse kickstart output files
mRegexExpression - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Store the regular expressions necessary to parse the basename from the worker package url to retrieve the version of pegasus.
mRegFiles - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.TransferContainer
  The collection of `FileTransfer` objects containing the files that need to be registered.
mRegFiles - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle.TransferContainer
  The collection of `FileTransfer` objects containing the files that need to be registered.
mRegister - Variable in class edu.isi.pegasus.planner.dax.File
  Should the file be registered in the replica catalog
mRegName - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.TransferContainer
  The name of the registration job.
mRegName - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle.TransferContainer
  The name of the registration job.
mRelationsMap - Variable in class edu.isi.pegasus.planner.partitioner.MultipleLook
  A map containing the relations between the jobs making up the partition.
mRelationsMap - Variable in class edu.isi.pegasus.planner.partitioner.SingleLook
  A map containing the relations between the jobs making up the partition.
mRelationsMap - Variable in class edu.isi.pegasus.planner.transfer.refiner.Basic
  The map indexed by a node name, where the associated value is the set of child nodes.
mRelationsParentMap - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  The map indexed by compute jobnames that contains the list of stagin job names that are being added during the traversal of the workflow.
mRelationsParentMap - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  The map indexed by compute jobnames that contains the list of stagin job names that are being added during the traversal of the workflow.
mRelativeDir - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  The relative directory for the submit directory and remote execution directory
mRelativeSubmitDir - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  The relative directory for the submit directory.
mRelativeSubmitDirectory - Variable in class edu.isi.pegasus.planner.classes.PlannerMetrics
  The relative submit directory for this run.
mReleaseVersion - Variable in class edu.isi.pegasus.planner.classes.DagInfo
  Identifies the release version of the VDS software that was used to generate the workflow.
mRemoteTransfers - Variable in class edu.isi.pegasus.planner.transfer.AbstractRefiner
  The handle to the Remote Transfers State machinery.
mRemoveEng - Variable in class edu.isi.pegasus.planner.refiner.MainEngine
  The engine that ends up creating the cleanup dag for the dag.
mReplacementTable - Variable in class edu.isi.pegasus.planner.cluster.Horizontal
  Replacement table, that identifies the corresponding fat job for a job.
mReplicaCatalog - Variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  The handle to the main Replica Catalog.
mReplicaCatalogs - Variable in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  The list of replica catalog associated with the site.
mReplicaCatalogs - Variable in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  The list of replica catalog associated with the site.
mReplicaSelector - Variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  The handle to the replica selector that is to used to select the various replicas.
mReplicaStore - Variable in class edu.isi.pegasus.planner.classes.ADag
  Handle to the replica store that stores the replica catalog user specifies in the DAX
mReplicaStore - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2CDAG
  Handle to the replica store that stores the replica catalog user specifies in the DAX
mReplicaStore - Variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  The replica store in which we store all the results that are queried from the main replica catalog.
mRequestID - Variable in class edu.isi.pegasus.planner.classes.ADag
  The optional request ID associated with the DAX.
mRequestID - Variable in class edu.isi.pegasus.planner.client.RankDAX
  The request id to get the daxes.
mRequestID - Variable in class edu.isi.pegasus.planner.ranking.Rank
  The optional request id.
mRequestID - Variable in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  The request id associated with the DAX.
mResMap - Variable in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  The mapping to siteHandle to all the jobs that are mapped to it mapping to siteHandle(String) to Set<GraphNodes>
mResMapLeaves - Variable in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  The mapping of siteHandle to all subset of the jobs mapped to it that are leaves in the workflow mapping to siteHandle(String) to Set<GraphNodes>.
mResMapRoots - Variable in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  The mapping of siteHandle to all subset of the jobs mapped to it that are roots in the workflow mapping to siteHandle(String) to Set<GraphNodes>.
mResourceContact - Variable in class edu.isi.pegasus.planner.classes.AuthenticateRequest
  The contact string to the resource.
mResourceID - Variable in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  The Id of the resource on which the transformation is installed.
mResponseCode - Variable in class edu.isi.pegasus.planner.code.generator.SendMetricsResult
mResponseMessage - Variable in class edu.isi.pegasus.planner.code.generator.SendMetricsResult
mResult - Variable in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser3
  The final result constructed.
mResult - Variable in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser4
  The final result constructed.
mRLIUrl - Variable in class edu.isi.pegasus.planner.refiner.Engine
  The Replica Location Index URL got from vds.rls.url property
mRoot - Static variable in class edu.isi.pegasus.common.logging.logger.Log4j
  Keeps track of log4j's root logger as singleton.
mRoot - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2Graph
  The root node for the graph that is constructed.
mRoot - Variable in class edu.isi.pegasus.planner.partitioner.Partitioner
  The root node of the graph from where to start the BFS.
mRootWorkflowUUID - Variable in class edu.isi.pegasus.planner.classes.ADag
  The Root Workflow UUID.
mRootWorkflowUUID - Variable in class edu.isi.pegasus.planner.classes.PlannerMetrics
  The Root Workflow UUID.
mRunningJobs - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The number of jobs in the remote queue that are running at the remote site.
mRuntime - Variable in class edu.isi.pegasus.planner.classes.Job
  The expected runtime for a job.
mRuntime - Variable in class edu.isi.pegasus.planner.ranking.Ranking
  The runtime of the dax in seconds.
mSanitizePath - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  A boolean storing whether to sanitize paths or not
mScanner - Variable in class edu.isi.pegasus.planner.parser.TransformationCatalogTextParser
  The access to the lexical scanner is stored here.
mSCFile - Variable in class edu.isi.pegasus.planner.client.PegasusGetSites
mScheduledDAG - Variable in class edu.isi.pegasus.planner.cluster.Abstract
  ADag object containing the jobs that have been scheduled by the site selector.
mScheduledDAG - Variable in class edu.isi.pegasus.planner.cluster.Horizontal
  ADag object containing the jobs that have been scheduled by the site selector.
mScheduledSite - Variable in class edu.isi.pegasus.planner.selector.site.heft.HeftBag
  The site where a job is scheduled to run.
mScheduler - Variable in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  The scheduler type with which it interfaces.
mScratch - Variable in class edu.isi.pegasus.planner.catalog.site.classes.HeadNodeFS
  The scratch area on the head node.
mScratch - Variable in class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeFS
  The scratch area on the head node.
mSearchFiles - Variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  The Vector of `String` objects containing the logical filenames of the files whose locations are to be searched in the Replica Catalog.
mSelector - Variable in class edu.isi.pegasus.planner.selector.site.Group
  The handle to the internal site selector that is used to schedule jobs amongst the groups.
mSendMetrics - Variable in class edu.isi.pegasus.planner.client.CPlanner
  A boolean indicating whether metrics should be sent to metrics server or not
mSendMetricsToServer - Variable in class edu.isi.pegasus.planner.code.generator.Metrics
  boolean indicating whether to log metrics or not
mSeparator - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  The nice separator, define once, use often.
mSeparator - Static variable in interface edu.isi.pegasus.planner.code.GridStart
  The File separator to be used on the submit host.
mSeparator - Static variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The file Separator to be used on the submit host.
mSeqExecGridStartUsed - Variable in class edu.isi.pegasus.planner.transfer.sls.Transfer
  Boolean to track whether the gridstart used in PegasusLite or not
mSetupForCondorIO - Variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  A boolean to track whether condor file io is used for the workflow or not.
mSetupMap - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  The map indexed by staged executable logical name.
mSetupMap - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  The map indexed by staged executable logical name.
mSetupTransferImplementation - Variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The transfer implementation to be used for staging in the data as part of setup job.
mSetXBit - Variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Whether kickstart should set the X Bit on the staged executables.
MSG - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
MSG_ID - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
mSharedDirectory - Variable in class edu.isi.pegasus.planner.catalog.site.classes.StorageType
  The shared directory on the node.
mShiwaBundle - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  the path to the shiwa bundle
mShutdown - Variable in class edu.isi.pegasus.planner.refiner.ThreadPool.AuthenticateThread
  Whether to shutdown or not.
mSIBundleMap - Variable in class edu.isi.pegasus.planner.transfer.refiner.Chain
  The map containing the stage in bundle values indexed by the name of the site.
mSingletonInstance - Static variable in class edu.isi.pegasus.common.logging.LogFormatterFactory
  Holds a singleton instance that is populated via the loadSingletonInstance() method.
mSingletonInstance - Static variable in class edu.isi.pegasus.common.logging.LogManagerFactory
  Holds a singleton instance that is populated via the loadSingletonInstance() method.
mSite - Variable in class edu.isi.pegasus.planner.dax.PFN
mSite - Variable in class edu.isi.pegasus.planner.transfer.refiner.Chain.SiteTransfer
  The site for which these transfers are grouped.
mSiteCatalog - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.PoolConfig
  The map indexed by the site handle.
mSiteHandle - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  The site handle to use.
mSiteLFNAddOnMap - Variable in class edu.isi.pegasus.planner.transfer.mapper.impl.Hashed
  A Map that tracks for each output site, the LFN to the Add on's
mSiteMap - Variable in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  Map containing the number of free nodes for each site.
mSites - Variable in class edu.isi.pegasus.planner.client.RankDAX
  The list of grid sites where the daxes can run.
mSites - Variable in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser3
  The set of sites that need to be parsed.
mSites - Variable in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser4
  The set of sites that need to be parsed.
mSites - Variable in class edu.isi.pegasus.planner.ranking.Rank
  The list of candidate grid sites.
mSites - Variable in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  The list of sites where the workflow can run.
mSiteSelector - Variable in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  Handle to the site selector.
mSiteSelectorPath - Variable in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  The path to the site selector.
mSiteStore - Variable in class edu.isi.pegasus.common.credential.impl.Abstract
  The handle to the Site Catalog Store.
mSiteStore - Variable in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  The SiteStore object where information about the sites is stored.
mSiteStore - Variable in class edu.isi.pegasus.planner.catalog.site.impl.XML
  Stores sites in memory
mSiteStore - Variable in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  Stores sites in memory
mSiteStore - Variable in class edu.isi.pegasus.planner.catalog.transformation.Mapper
  The handle to the RIC.
mSiteStore - Variable in class edu.isi.pegasus.planner.classes.PegasusBag
  The site store containing the sites that need to be used.
mSiteStore - Variable in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  Handle to the site catalog store
mSiteStore - Variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  The handle to the site catalog store.
mSiteStore - Variable in class edu.isi.pegasus.planner.code.generator.condor.style.Abstract
  The handle to the Site Catalog Store.
mSiteStore - Variable in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
mSiteStore - Variable in class edu.isi.pegasus.planner.code.generator.Shell
  Handle to the Site Store.
mSiteStore - Variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Handle to the site catalog store.
mSiteStore - Variable in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  Handle to the site catalog store.
mSiteStore - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Handle to the site catalog store.
mSiteStore - Variable in class edu.isi.pegasus.planner.refiner.cleanup.Cleanup
  Handle to the stagingSite catalog.
mSiteStore - Variable in class edu.isi.pegasus.planner.refiner.cleanup.RM
  Handle to the site catalog.
mSiteStore - Variable in class edu.isi.pegasus.planner.refiner.createdir.AbstractStrategy
  The Site Store handle.
mSiteStore - Variable in class edu.isi.pegasus.planner.refiner.createdir.DefaultImplementation
  The handle to the SiteStore.
mSiteStore - Variable in class edu.isi.pegasus.planner.refiner.Engine
  The handle to the Pool Info Provider.
mSiteStore - Variable in class edu.isi.pegasus.planner.selector.site.Abstract
  The handle to the site catalog.
mSiteStore - Variable in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  Handle to the site catalog.
mSiteStore - Variable in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  The handle to the Pool Info Provider.
mSiteStore - Variable in class edu.isi.pegasus.planner.transfer.mapper.impl.AbstractFileFactoryBasedMapper
  Handle to the Site Catalog contents.
mSiteStore - Variable in class edu.isi.pegasus.planner.transfer.mapper.impl.Fixed
  Handle to the Site Catalog contents.
mSiteStore - Variable in class edu.isi.pegasus.planner.transfer.mapper.impl.Replica
  Handle to the Site Catalog contents.
mSiteStore - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  Handle to the SiteStore
mSiteStore - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  Handle to the SiteStore
mSiteStore - Variable in class edu.isi.pegasus.planner.transfer.refiner.Chain
  The handle to the Site Catalog.
mSiteStore - Variable in class edu.isi.pegasus.planner.transfer.sls.Condor
  The handle to the site catalog.
mSiteStore - Variable in class edu.isi.pegasus.planner.transfer.sls.Transfer
  The handle to the site catalog.
mSiteToPegasusHomeMap - Variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Maps a site to the the directory where the pegasus worker package has been untarred during workflow execution.
mSize - Variable in class edu.isi.pegasus.planner.classes.PegasusFile
  The size of the file.
mSize - Variable in class edu.isi.pegasus.planner.dax.File
  File size of the file no units required
mSize - Variable in class edu.isi.pegasus.planner.provenance.pasoa.producer.InMemory
  The initial size of the buffer.
mSLS - Variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  The handle to the SLS implementor
mSLS - Variable in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  The handle to the SLS implementor
mSLS - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  The handle to the SLS implementor
mSLS - Variable in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  The handle to the SLS implementor
mSortedRegexSet - Variable in class edu.isi.pegasus.planner.selector.replica.Regex
  The Set of regular expressions that orders the regex expressions to use in ascending order.
mSource - Variable in class edu.isi.pegasus.planner.client.PegasusGetSites
  The default source to query for generating a site catalog.
mSourceMap - Variable in class edu.isi.pegasus.planner.classes.FileTransfer
  The map containing all the source urls keyed by the pool id/name.
mSRMServiceURLToMountPointMap - Variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  A map that associates the site name with the SRM server url and mount point.
mStack - Variable in class edu.isi.pegasus.common.logging.format.AbstractLogFormatter
  The Stack of event objects maintained internally
mStack - Variable in class edu.isi.pegasus.common.util.XMLWriter
mStack - Variable in class edu.isi.pegasus.planner.parser.StackBasedXMLParser
  The stack of objects kept around.
mStageinLocalBundleValue - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  The BundleValue that evaluates for local stage in jobs.
mStageinLocalBundleValue - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  The BundleValue that evaluates for local stage in jobs.
mStageInLocalMap - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  The map containing the list of stage in transfer jobs that are being created for the workflow indexed by the execution poolname.
mStageInLocalMapPerLevel - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  The map containing the list of stage in transfer jobs that are being created for the workflow indexed by the execution poolname.
mStageInLocalMapPerLevel - Variable in class edu.isi.pegasus.planner.transfer.refiner.Cluster
  A map indexed by site name, that contains the pointer to the stage in PoolTransfer objects for that site.
mStageInMap - Variable in class edu.isi.pegasus.planner.transfer.refiner.Chain
  A map indexed by execution sites.
mStageInRemoteBundleValue - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  The BundleValue that evaluates for remote stage-in jobs.
mStageInRemoteBundleValue - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  The BundleValue that evaluates for remote stage-in jobs.
mStageInRemoteMap - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  The map containing the list of stage in transfer jobs that are being created for the workflow indexed by the execution poolname.
mStageInRemoteMapPerLevel - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  The map containing the list of stage in transfer jobs that are being created for the workflow indexed by the execution poolname.
mStageInRemoteMapPerLevel - Variable in class edu.isi.pegasus.planner.transfer.refiner.Cluster
  A map indexed by site name, that contains the pointer to the symlink stage in PoolTransfer objects for that site.
mStageoutDirectory - Variable in class edu.isi.pegasus.planner.transfer.mapper.impl.AbstractFileFactoryBasedMapper
  The stage out directory where the outputs are staged to.
mStageOutLocalBundleValue - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  The BundleValue that evaluates for local stage out jobs.
mStageOutLocalBundleValue - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  The BundleValue that evaluates for local stage out jobs.
mStageOutLocalMapPerLevel - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  A map indexed by site name, that contains the pointer to the local stage out PoolTransfer objects for that site.
mStageOutLocalMapPerLevel - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  A map indexed by site name, that contains the pointer to the local stage out PoolTransfer objects for that site.
mStageOutRemoteBundleValue - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  The BundleValue that evaluates for remote stage out jobs.
mStageOutRemoteBundleValue - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  The BundleValue that evaluates for remote stage out jobs.
mStageOutRemoteMapPerLevel - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  A map indexed by site name, that contains the pointer to the remote stage out PoolTransfer objects for that site.
mStageOutRemoteMapPerLevel - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  A map indexed by site name, that contains the pointer to the remote stage out PoolTransfer objects for that site.
mStageSLSFile - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Boolean to track whether to stage sls file or not
mStageSLSFile - Variable in class edu.isi.pegasus.planner.transfer.sls.Transfer
  Boolean to track whether to stage sls file or not
mStagingSite - Variable in class edu.isi.pegasus.planner.classes.Job
  The staging site associated with the job
mStagingSitesMap - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  A map that maps an execution site to a staging site.
mStarReplacements - Static variable in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  Replacement 2 D Array for the above properties.
mStart - Variable in class edu.isi.pegasus.common.logging.format.SimpleEvent
  The start time when start message for the event was generated
mStarted - Variable in class edu.isi.pegasus.common.util.StreamGobbler
  A boolean indicating whether the thread has started or not.
mStartSeparator - Static variable in class edu.isi.pegasus.planner.code.generator.Stork
  The nice start separator, define once, use often.
mStartTime - Variable in class edu.isi.pegasus.planner.classes.PlannerMetrics
  The start time for the planning.
mStartTime - Variable in class edu.isi.pegasus.planner.selector.site.heft.HeftBag
  The estimated start time for a job.
mStartTime - Variable in class edu.isi.pegasus.planner.selector.site.heft.Processor
  The start time of the current scheduled job.
mState - Variable in class edu.isi.pegasus.planner.transfer.RemoteTransfer.TransferState
  Stores the state as an integer.
mState - Variable in class edu.isi.pegasus.planner.transfer.TPT.TPTState
  Stores the state as an integer.
mStateMap - Variable in class edu.isi.pegasus.planner.transfer.RemoteTransfer
  The map indexed by site name, that contains the state for all the sites.
mStateMap - Variable in class edu.isi.pegasus.planner.transfer.TPT
  The map indexed by site name, that contains the state for all the sites.
mStatements - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Maintains an essential set of prepared statement, ready to use.
mStatements - Variable in class edu.isi.pegasus.planner.catalog.work.Database
  Maintains an essential set of prepared statement, ready to use.
mStatements - Variable in class edu.isi.pegasus.planner.ranking.GetDAX
  Maintains an essential set of prepared statement, ready to use.
mStderr - Variable in class edu.isi.pegasus.planner.dax.AbstractJob
mStdin - Variable in class edu.isi.pegasus.planner.dax.AbstractJob
mStdout - Variable in class edu.isi.pegasus.planner.dax.AbstractJob
mStorage - Variable in class edu.isi.pegasus.planner.catalog.site.classes.HeadNodeFS
  The storage area on the head node.
mStorage - Variable in class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeFS
  The storage area on the head node.
mStorageDir - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPServer
  The storage mount point for the grid ftp server.
mStorageDir - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  This contains the storage directory relative to the se mount point of the pool.
mStore - Variable in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  The internal map that maps a site catalog entry to the site handle.
mStore - Variable in class edu.isi.pegasus.planner.classes.ReplicaStore
  The replica store.
mStore - Variable in class edu.isi.pegasus.planner.partitioner.graph.MapGraph
  The map indexed by the id of the `GraphNode`, used for storing the nodes of the Graph.
mStore - Variable in class edu.isi.pegasus.planner.provenance.pasoa.producer.InMemory
  The StringBuffer store.
mStyleFactory - Variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Handle to the Style factory, that is used for this workflow.
mSubInfoMap - Variable in class edu.isi.pegasus.planner.cluster.Abstract
  A Map to store all the job(Job) objects indexed by their logical ID found in the dax.
mSubInfoMap - Variable in class edu.isi.pegasus.planner.cluster.Horizontal
  A Map to store all the job(Job) objects indexed by their logical ID found in the dax.
mSubmissionCredential - Variable in class edu.isi.pegasus.planner.classes.Job
  The credential to use for job submission if required.
mSubmit - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  If specified, then it submits to the underlying CondorG using the kickstart-Condorscript provided.
mSubmitDir - Variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  The submit exectionSiteDirectory where the submit files are being generated for the workflow.
mSubmitDir - Variable in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  The submit directory where the submit files are being generated for the workflow.
mSubmitDir - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusExitCode
  The submit directory where the submit files are being generated for the workflow.
mSubmitDir - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  The submit directory where the submit files are being generated for the workflow.
mSubmitDir - Variable in class edu.isi.pegasus.planner.code.GridStartFactory
  The submit directory where the submit files are being generated for the workflow.
mSubmitDirectory - Variable in class edu.isi.pegasus.planner.classes.ADag
  The root of the submit directory hierarchy for the DAG.
mSubmitDirectory - Variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The root of the submit directory where all the submit directories for the various partitions reside.
mSubmitDirectory - Variable in class edu.isi.pegasus.planner.refiner.cleanup.Cleanup
  The submit directory where the output files have to be written.
mSubmitDirectory - Variable in class edu.isi.pegasus.planner.refiner.RemoveDirectory
  The submit directory for the workflow.
mSubmitFileDir - Variable in class edu.isi.pegasus.planner.code.generator.Abstract
  The directory where all the submit files are to be generated.
mSubmitFileDir - Variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The directory where all the submit files are to be generated.
mSubmitFileDir - Variable in class edu.isi.pegasus.planner.code.generator.DAXReplicaStore
  The directory where all the submit files are to be generated.
mSubmitFileDir - Variable in class edu.isi.pegasus.planner.code.generator.MonitordNotify
  The directory where all the submit files are to be generated.
mSubmitFileDir - Variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The directory where all the submit files are to be generated.
mSupportedOSReleaseVersions - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  A set of supported OS release and versions that our build process builds for.
mSymbolTable - Static variable in class edu.isi.pegasus.planner.parser.tokens.TransformationCatalogReservedWord
  Singleton implementation of a symbol table for reserved words.
mSyncJobMap - Variable in class edu.isi.pegasus.planner.transfer.refiner.Cluster
  Maps the site name to the current synch job
mSysInfo - Variable in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  The System Information for the Site.
mSysInfo - Variable in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  The System Information for the Site.
mSysInfo - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  The system information of the remote site.
mSysInfo - Variable in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  The System Info for the transformation.
mTCFile - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  The path to the file based TC.
mTCFile - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  The path to the file based TC.
mTCFile - Variable in class edu.isi.pegasus.planner.refiner.Engine
  The path to the file containing the pool information.
mTCFileHandle - Static variable in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  The singleton handler to the contents of the transformation catalog.
mTCHandle - Variable in class edu.isi.pegasus.planner.catalog.transformation.Mapper
  The handle to the tranformation catalog.
mTCHandle - Variable in class edu.isi.pegasus.planner.classes.PegasusBag
  The handle to the transformation catalog.
mTCHandle - Variable in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  The handle to the transformation catalog.
mTCHandle - Variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Handle to the Transformation Catalog.
mTCHandle - Variable in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  The handle to the transformation catalog
mTCHandle - Variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Handle to Transformation Catalog.
mTCHandle - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Handle to Transformation Catalog.
mTCHandle - Variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The handle to the transformation catalog.
mTCHandle - Variable in class edu.isi.pegasus.planner.refiner.cleanup.Cleanup
  The handle to the transformation catalog.
mTCHandle - Variable in class edu.isi.pegasus.planner.refiner.cleanup.RM
  The handle to the transformation catalog.
mTCHandle - Variable in class edu.isi.pegasus.planner.refiner.createdir.DefaultImplementation
  The handle to the transformation catalog.
mTCHandle - Variable in class edu.isi.pegasus.planner.refiner.Engine
  The handle to the Transformation Catalog.
mTCHandle - Variable in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  The handle to the transformation catalog.
mTCHandle - Variable in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  The handle to the Transformation Catalog.
mTCHandle - Variable in class edu.isi.pegasus.planner.transfer.sls.Transfer
  The handle to the transformation catalog.
mTCMap - Variable in class edu.isi.pegasus.planner.catalog.transformation.Mapper
  Handle to the TCMap
mTCMap - Variable in class edu.isi.pegasus.planner.classes.TCMap
  The TCMap for a dag is stored in this HashMap.
mTCMapper - Variable in class edu.isi.pegasus.planner.classes.PegasusBag
  The handle to the Transformation Mapper.
mTCMapper - Variable in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  The handle to the transformation catalog mapper object that caches the queries to the transformation catalog, and indexes them according to lfn's.
mTCMapper - Variable in class edu.isi.pegasus.planner.selector.site.Abstract
  The handle to the TCMapper object.
mTCMapper - Variable in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  Handle to the TCMapper.
mTCMode - Variable in class edu.isi.pegasus.planner.refiner.Engine
  Defines the read mode for transformation catalog.
mTCStore - Variable in class edu.isi.pegasus.planner.catalog.transformation.classes.TransformationStore
  The internal store map.
mTCStore - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  The transformation store containing the transformations after parsing the file.
mTempLogFile - Variable in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  The name of the log file in the /tmp directory
mTextContent - Variable in class edu.isi.pegasus.planner.parser.Parser
  Holds the text in an element (text between start and final tags if any).
mTextParser - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Instance to the TextParser.
mTextString - Variable in class edu.isi.pegasus.planner.parser.Parser
  A String that holds the contents of data passed as text.
mThread - Variable in class edu.isi.pegasus.planner.refiner.ThreadPool.AuthenticateThread
  The thread object that is used to launch the thread.
mTimeout - Variable in class edu.isi.pegasus.planner.refiner.Authenticate
  The timeout value that is to be used in milliseconds
mTimeout - Variable in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  The timeout value in seconds after which to timeout, in the case where the external site selector does nothing (nothing on stdout nor stderr).
mToBeDeletedFiles - Variable in class edu.isi.pegasus.planner.refiner.cleanup.CleanupJobContent
  The list of files that need to be deleted and are associated with this job.
mTopNum - Variable in class edu.isi.pegasus.planner.client.RankDAX
  The top n workflows to execute and put in the rankings file
mTotalMem - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The total memory that the jobmanager reports.
mTotalNodes - Variable in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  The number of total nodes
mTotalNodes - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The total number of nodes that the jobmanager reports are on the remote site.
mTotalSize - Variable in class edu.isi.pegasus.planner.catalog.site.classes.FileSystemType
  The total size of file system.
mTotalSize - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPServer
  The total storage space at the grid ftp server.
mTotalSize - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.WorkDir
  The total space available at the file system under this directory.
mTPT - Variable in class edu.isi.pegasus.planner.transfer.AbstractRefiner
  The handle to the Third Party State machinery.
mTransEng - Variable in class edu.isi.pegasus.planner.refiner.MainEngine
  The handle to the Transfer Engine that adds the transfer nodes in the graph to transfer the files from one site to another.
mTransfer - Variable in class edu.isi.pegasus.planner.dax.File
  Should the file be transferred on generation.
mTransferFlag - Variable in class edu.isi.pegasus.planner.classes.PegasusFile
  The transfer flag associated with the file containing tristate of transfer,dontTransfer and optional.
mTransferFromSubmitHost - Variable in class edu.isi.pegasus.planner.refiner.RemoveDirectory
  Boolean indicating whether we need to transfer dirmanager from the submit host.
mTransferType - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.TransferContainer
  The type of the transfers the job is responsible for.
mTransferType - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle.TransferContainer
  The type of the transfers the job is responsible for.
mTransferWorkerPackage - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Boolean indicating whether worker package transfer is enabled or not
mTransferWorkerPackage - Variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Boolean indicating whether user wants the worker package to be transferred or not.
mTransformations - Variable in class edu.isi.pegasus.planner.dax.ADAG
  The List of Transformation objects
mTransformationStore - Variable in class edu.isi.pegasus.planner.classes.ADag
  Handle to the transformation store that stores the transformation catalog user specifies in the DAX
mTransformationStore - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2CDAG
  Handle to the transformation store that stores the transformation catalog user specifies in the DAX
mTreatCacheAsRC - Variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  A boolean indicating whether the cache file needs to be treated as a replica catalog or not.
mTreeMap - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  The Tree Map which stores the contents of the file.
mTXContainers - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.PoolTransfer
  The list of `TransferContainer` that correspond to each transfer job.
mTXContainers - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle.PoolTransfer
  The list of `TransferContainer` that correspond to each transfer job.
mTXFERImplTable - Static variable in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  An internal table that resolves the old transfer mode property, to the corresponding transfer implementation.
mTXFERRefinerTable - Static variable in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  An internal table that resolves the old transfer mode property, to the corresponding transfer refiner.
mTXInterImplementation - Variable in class edu.isi.pegasus.planner.transfer.AbstractRefiner
  The inter transfer implementation that the refiner requires.
mTXName - Variable in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.TransferContainer
  The name of the transfer job.
mTXName - Variable in class edu.isi.pegasus.planner.transfer.refiner.Bundle.TransferContainer
  The name of the transfer job.
mTXRefiner - Variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  The handle to the transfer refiner that adds the transfer nodes into the workflow.
mTXSelector - Variable in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  The handle to the transformation selector, that ends up selecting what transformations to pick up.
mTXStageInImplementation - Variable in class edu.isi.pegasus.planner.transfer.AbstractRefiner
  The stage-in transfer implementation that the refiner requires.
mTXStageOutImplementation - Variable in class edu.isi.pegasus.planner.transfer.AbstractRefiner
  The stage-out transfer implementation that the refiner requires.
mTXSymbolicLinkImplementation - Variable in class edu.isi.pegasus.planner.transfer.AbstractRefiner
  The stage-in symbolic link transfer implementation that refiner requires.
mType - Variable in class edu.isi.pegasus.planner.catalog.site.classes.Directory
  The type of directory
mType - Variable in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  The grid type associated with this instance.
mType - Variable in class edu.isi.pegasus.planner.catalog.site.classes.ReplicaCatalog
  The type of the replica catalog implementation to use.
mType - Variable in class edu.isi.pegasus.planner.classes.AuthenticateRequest
  Specifies what type of resource you are authenticating to.
mType - Variable in class edu.isi.pegasus.planner.classes.PegasusFile
  The type associated with the file.
mType - Variable in class edu.isi.pegasus.planner.classes.PlannerMetrics
  The name of the client
mType - Variable in class edu.isi.pegasus.planner.client.PartitionDAX
  The type of the partitioner to be used.
mType - Variable in class edu.isi.pegasus.planner.dax.MetaData
  Metadata type
MULTIPLE_READ - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolMode
  Constants for multiple read.
MULTIPLE_READ - Static variable in class edu.isi.pegasus.planner.catalog.transformation.TCMode
MultipleFTPerXFERJob - Interface in edu.isi.pegasus.planner.transfer
  An empty interface, that allows for grouping of implementations that can handle multiple file transfers per transfer job like old guc and Stork.
MultipleFTPerXFERJobRefiner - Class in edu.isi.pegasus.planner.transfer
  The refiner interface, that determines the functions that need to be implemented to add various types of transfer nodes to the workflow.
MultipleFTPerXFERJobRefiner(ADag, PegasusBag) - Constructor for class edu.isi.pegasus.planner.transfer.MultipleFTPerXFERJobRefiner
  The overloaded constructor.
MultipleLook - Class in edu.isi.pegasus.planner.partitioner
  This class ends up writing a partitioned dax, that corresponds to one partition as defined by the Partitioner.
MultipleLook(String, String) - Constructor for class edu.isi.pegasus.planner.partitioner.MultipleLook
  The overloaded constructor.
MultipleLook.MyCallBackHandler - Class in edu.isi.pegasus.planner.partitioner
  The internal callback handler for the DAXParser in Euryale.
mUniverse - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The VDS universe with which the jobmanager is associated with.
mUpwardRank - Variable in class edu.isi.pegasus.planner.selector.site.heft.HeftBag
  The upward rank for a node.
mURL - Variable in class edu.isi.pegasus.planner.catalog.site.classes.ReplicaCatalog
  The url for the catalog.
mURL - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPServer
  The url string of the gridftp that contains the host and the port.
mURL - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The url to the jobmanager on the remote site.
mUrl - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.CreateTCDatabase
  Stores the database url
mURL - Variable in class edu.isi.pegasus.planner.code.generator.SendMetrics
mURL - Variable in class edu.isi.pegasus.planner.dax.PFN
mURLForRegistrationOnDestination - Variable in class edu.isi.pegasus.planner.classes.FileTransfer
  The registration URL for the file
mURLPrefix - Variable in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  The URL prefix to use
mURLPrefix - Variable in class edu.isi.pegasus.planner.catalog.site.classes.FileServerType
  The URL prefix for the server.
mUseDoubleNegative - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  A boolean indicating whether to use the double negative flags for transfer and register or not.
mUseForce - Variable in class edu.isi.pegasus.planner.transfer.implementation.GUC
  Whether to use force option for the transfer executable or not.
mUseForce - Variable in class edu.isi.pegasus.planner.transfer.implementation.T2
  Whether to use force option for the transfer executable or not.
mUseFullPathToGridStart - Variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Boolean indicating whether to use full path or not
mUseMkdir - Variable in class edu.isi.pegasus.planner.refiner.createdir.AbstractStrategy
  Whether we want to use dirmanager or mkdir directly.
mUseMkdir - Variable in class edu.isi.pegasus.planner.refiner.createdir.DefaultImplementation
  Whether we want to use dirmanager or mkdir directly.
mUser - Variable in class edu.isi.pegasus.planner.classes.PlannerMetrics
  The user who planned the workflow.
mUser - Variable in class edu.isi.pegasus.planner.client.CPlanner
  The user name of the user running Pegasus.
mUser - Variable in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  The username of the user running the program.
mUser - Variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The user name of the user running Pegasus.
mUsername - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.CreateTCDatabase
  Stores the user name
mUserOpts - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  Handle to the Singleton instance containing the options passed to the planner at run time.
mUserSpecifiedSourceLocation - Variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The user specified location from where to stage the worker packages.
mUses - Variable in class edu.isi.pegasus.planner.classes.CompoundTransformation
  The list of dependant executables
mUses - Variable in class edu.isi.pegasus.planner.dax.AbstractJob
mUses - Variable in class edu.isi.pegasus.planner.dax.Transformation
  List of executable of files used by the transformation
mUseSizeFactor - Variable in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  A boolean indicating whether we prefer use the size factor or the num factor
mUsesLinkType - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  The uses link type for a file when uses tag is parsed.
mUsesPegasusFile - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  The PegasusFile object that a uses tag corresponds to.
mUsesPMC - Variable in class edu.isi.pegasus.planner.classes.PegasusBag
  A boolean indicating whether we use PMC or not
mUseSymLinks - Variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  This member variable if set causes the destination URL for the symlink jobs to have symlink:// url if the pool attributed associated with the pfn is same as a particular jobs execution pool.
mUseSymLinks - Variable in class edu.isi.pegasus.planner.transfer.sls.Transfer
  This member variable if set causes the destination URL for the symlink jobs to have symlink:// url if the pool attributed associated with the pfn is same as a particular jobs execution pool.
mUseUserSpecifiedSourceLocation - Variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Boolean indicating whether to use the user specified location or not
mValue - Variable in class edu.isi.pegasus.planner.catalog.site.classes.Connection
  The value of the connection key.
mValue - Variable in enum edu.isi.pegasus.planner.catalog.site.classes.Directory.TYPE
mValue - Variable in class edu.isi.pegasus.planner.classes.Profile
mValue - Variable in class edu.isi.pegasus.planner.dax.MetaData
  Metadata value
mValue - Variable in class edu.isi.pegasus.planner.dax.Profile
  Value of the profile
mValue - Variable in class edu.isi.pegasus.planner.invocation.Boot
  The text value
mValue - Variable in class edu.isi.pegasus.planner.invocation.CPU
  The text value
mValue - Variable in class edu.isi.pegasus.planner.invocation.Stamp
  The text value
mValue - Variable in class edu.isi.pegasus.planner.invocation.Uname
  The text value
mValue - Variable in class edu.isi.pegasus.planner.parser.tokens.TransformationCatalogReservedWord
  This instance variable captures the token value for the reserved word.
mValue - Variable in class edu.isi.pegasus.planner.partitioner.graph.LabelBag
  The value for the Label.
mVDSArchToNMIArch - Static variable in class edu.isi.pegasus.planner.catalog.classes.VDSSysInfo2NMI
  The map storing architecture to corresponding NMI architecture platforms.
mVDSOSToNMIOS - Static variable in class edu.isi.pegasus.planner.catalog.classes.VDSSysInfo2NMI
  The map storing OS to corresponding NMI OS platforms.
mVDSProps - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  The list of VDS properties set at runtime by the user on commandline.
mVDSToPegasusPropertiesTable - Static variable in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  The handle to the internal map, that maps vds properties to pegasus properties.
mVersion - Variable in class edu.isi.pegasus.common.util.CondorVersion.CondorVersionCallback
  The version detected.
mVersion - Variable in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  The mVersion of the transformation.
mVersion - Variable in class edu.isi.pegasus.planner.classes.CompoundTransformation
  The version
mVersion - Variable in class edu.isi.pegasus.planner.classes.PlannerMetrics
  The planner version
mVersion - Variable in class edu.isi.pegasus.planner.client.Executable
  It stores the verison of the Griphyn Virtual Data System software.
mVersion - Variable in class edu.isi.pegasus.planner.dax.AbstractJob
mVersion - Variable in class edu.isi.pegasus.planner.dax.Executable
  Version of the executable
mVersion - Variable in class edu.isi.pegasus.planner.dax.File
  The logical version of the file.
mVersion - Variable in class edu.isi.pegasus.planner.dax.Transformation
  Version of the transformation
mVersionPattern - Static variable in class edu.isi.pegasus.planner.dax.Patterns
mvExecPools - Variable in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  The List containing the user specified list of pools on which he wants the dag to run.
mvExecPools - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  List of execution pools on which the user wants the Dag to be executed.
mVJobInpFiles - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Holds the input files for a particular job making the aDag.
mVJobOutFiles - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Holds the output files for a particular job making the aDag.
mVO - Variable in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  The VO to which the user belongs to.
mVO - Variable in class edu.isi.pegasus.planner.client.PegasusGetSites
mVOGroup - Variable in class edu.isi.pegasus.planner.classes.PlannerMetrics
  The VOGroup to which the user belonged to.
mVOGroup - Variable in class edu.isi.pegasus.planner.classes.PlannerOptions
  The VOGroup to which the user belongs to.
mWFMetrics - Variable in class edu.isi.pegasus.planner.classes.DagInfo
  The workflow metric objects that contains metrics about the workflow being planned.
mWFMetrics - Variable in class edu.isi.pegasus.planner.classes.PlannerMetrics
  The metrics about the workflow.
mWhat - Variable in class edu.isi.pegasus.planner.dax.Invoke
  What to invoke
mWhen - Variable in class edu.isi.pegasus.planner.dax.Invoke
  WHen to Invoke
mWholeCommandString - Variable in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  All the arguments to a particular job.
mWord - Variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG.GrepCallback
  The word that is to be searched for.
mWordLength - Variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG.GrepCallback
  The length of the word to be searched for.
mWorkDir - Variable in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  The work dir path from the properties.
mWorkDir - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  Contains the information about the work directory on the remote site.
mWorkDir - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.WorkDir
  The path to the work directory.
mWorkDir - Variable in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  The working directory relative to the mount point of the execution pool.
mWorkDir - Variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  The working directory relative to the mount point of the execution pool.
mWorkerFS - Variable in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  The handle to the worker node filesystem.
mWorkerNodeExecution - Variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  A boolean indicating whether to have worker node execution or not.
mWorkerNodeExecution - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  A boolean indicating whether to have worker node execution or not.
mWorkerNodeExecution - Variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Boolean indicating worker node execution.
mWorkerNodeExecution - Variable in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  A boolean indicating whether to have worker node execution or not.
mWorkerNodeExecution - Variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  A boolean indicating whether we are doing worker node execution or not.
mWorkerPackageMap - Variable in class edu.isi.pegasus.planner.classes.PegasusBag
  Worker Package Map, that indexes execution site with the location of the corresponding worker package in the submit directory
mWorkerPackageMap - Variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  A map indexed by execution site and the corresponding worker package location in the submit directory
mWorkerPackageStagingEnabled - Variable in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  Boolean indicating whether worker package staging is enabled or not.
mWorkers - Variable in class edu.isi.pegasus.planner.refiner.ThreadPool
  The handle to the pool of threads that this thread pool is reponsible for.
mWorkerShared - Variable in class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeScratch
  The directory shared only amongst the worker nodes.
mWorkerShared - Variable in class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeStorage
  The directory shared only amongst the worker nodes.
mWorkflow - Variable in class edu.isi.pegasus.planner.parser.dax.DAX2NewGraph
  The Graph instance that stores the abstract workflow as a Graph.
mWorkflow - Variable in class edu.isi.pegasus.planner.refiner.DataReuseEngine
  The workflow object being worked upon.
mWorkflow - Variable in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  The workflow in the graph format, that needs to be scheduled.
mWorkflowCache - Variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  A Replica Catalog, that tracks all the GET URL's for the files on the staging sites.
mWorkflowID - Variable in class edu.isi.pegasus.planner.code.gridstart.NetloggerPostScript
  the workflow id used.
mWorkflowRefinementStarted - Variable in class edu.isi.pegasus.planner.classes.ADag
  Boolean indicating whether the refinement process on the workflow has started or not.
mWorkflowUUID - Variable in class edu.isi.pegasus.planner.classes.ADag
  The UUID associated with the workflow.
mWorkflowUUID - Variable in class edu.isi.pegasus.planner.classes.PlannerMetrics
  The UUID associated with the workflow.
mWriteHandle - Variable in class edu.isi.pegasus.planner.code.generator.Shell
  The handle to the output file that is being written to.
mWriteHandle - Variable in class edu.isi.pegasus.planner.partitioner.DAXWriter
  The write handle to the xml file being written.
mWriteHandle - Variable in class edu.isi.pegasus.planner.partitioner.PDAXWriter
  The write handle to the xml file being written.
mWriteLine - Variable in class edu.isi.pegasus.common.util.XMLWriter
mWriter - Variable in class edu.isi.pegasus.common.util.XMLWriter
mWriter - Variable in class edu.isi.pegasus.planner.catalog.site.classes.AbstractXMLPrintVisitor
  The internal writer
mWriter - Variable in class edu.isi.pegasus.planner.dax.ADAG
  Handle the XML writer
mXMLStore - Variable in class edu.isi.pegasus.planner.cluster.Horizontal
  The XML Producer object that records the actions.
mXMLStore - Variable in class edu.isi.pegasus.planner.refiner.DataReuseEngine
  The XML Producer object that records the actions.
mXMLStore - Variable in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  The XML Producer object that records the actions.
mXMLStore - Variable in class edu.isi.pegasus.planner.transfer.AbstractRefiner
  The XML Producer object that records the actions.
MyCallBackHandler() - Constructor for class edu.isi.pegasus.planner.partitioner.MultipleLook.MyCallBackHandler
  The empty constructor.
MyCallBackHandler() - Constructor for class edu.isi.pegasus.planner.partitioner.SingleLook.MyCallBackHandler
  The empty constructor.
myquote(String) - Method in class edu.isi.pegasus.planner.invocation.Architecture
  Quotes an input string for XML attributes while converting nulls.

## N

NAME - Static variable in class edu.isi.pegasus.common.util.Separator
  This constant defines the separator between an identifier and its version.
name - Variable in class edu.isi.pegasus.gridftp.FileInfo
NAME - Static variable in class edu.isi.pegasus.gridftp.PegasusGridFTP
name - Variable in class edu.isi.pegasus.planner.catalog.transformation.client.Client
name - Variable in class edu.isi.pegasus.planner.classes.NameValue
  stores the name of the pair.
name - Variable in class edu.isi.pegasus.planner.selector.site.RoundRobin.NameValue
  Stores the name of the pair (the left handside of the mapping).
NAMESPACE - Static variable in class edu.isi.pegasus.common.util.Separator
  This constant defines the separator between a namespace and the identifier.
namespace - Variable in class edu.isi.pegasus.planner.catalog.transformation.client.Client
namespace - Variable in class edu.isi.pegasus.planner.classes.Job
  The namespace to which the transformation is bound.
NAMESPACE - Static variable in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  The namespace to which the job in the MEGA DAG being created refer to.
NAMESPACE() - Constructor for enum edu.isi.pegasus.planner.dax.Profile.NAMESPACE
Namespace - Class in edu.isi.pegasus.planner.namespace
  The base namespace class that all the othernamepsace handling classes extend.
Namespace() - Constructor for class edu.isi.pegasus.planner.namespace.Namespace
NAMESPACE - Static variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The namespace to which the job in the MEGA DAG being created refer to.
NAMESPACE - Static variable in interface edu.isi.pegasus.planner.provenance.pasoa.PPS
  A namespace we can use to identify relationships and concepts defined for Pegasus' provenance data
Namespace.EmptyIterator - Class in edu.isi.pegasus.planner.namespace
  An empty iterator that allows me to traverse in case of null objects.
NAMESPACE_NAME - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The name of the namespace that this class implements.
NAMESPACE_NAME - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The name of the namespace that this class implements.
NAMESPACE_NAME - Static variable in class edu.isi.pegasus.planner.namespace.ENV
  The name of the namespace that this class implements.
NAMESPACE_NAME - Static variable in class edu.isi.pegasus.planner.namespace.Globus
  The name of the namespace that this class implements.
NAMESPACE_NAME - Static variable in class edu.isi.pegasus.planner.namespace.Hints
  The name of the namespace that this class implements.
NAMESPACE_NAME - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the namespace that this class implements.
NAMESPACE_NAME - Static variable in class edu.isi.pegasus.planner.namespace.Selector
  The name of the namespace that this class implements.
NAMESPACE_NAME - Static variable in class edu.isi.pegasus.planner.namespace.Stat
  The name of the namespace that this class implements.
namespaceName() - Method in class edu.isi.pegasus.planner.namespace.Condor
  Returns the name of the namespace associated with the profile implementations.
namespaceName() - Method in class edu.isi.pegasus.planner.namespace.Dagman
  Returns the name of the namespace associated with the profile implementations.
namespaceName() - Method in class edu.isi.pegasus.planner.namespace.ENV
  Returns the name of the namespace associated with the profile implementations.
namespaceName() - Method in class edu.isi.pegasus.planner.namespace.Globus
  Returns the name of the namespace associated with the profile implementations.
namespaceName() - Method in class edu.isi.pegasus.planner.namespace.Hints
  Returns the name of the namespace associated with the profile implementations.
namespaceName() - Method in class edu.isi.pegasus.planner.namespace.Namespace
  Returns the name of the namespace associated with the profile implementations.
namespaceName() - Method in class edu.isi.pegasus.planner.namespace.Pegasus
  Returns the name of the namespace associated with the profile implementations.
namespaceName() - Method in class edu.isi.pegasus.planner.namespace.Selector
  Returns the name of the namespace associated with the profile implementations.
namespaceName() - Method in class edu.isi.pegasus.planner.namespace.Stat
  Returns the name of the namespace associated with the profile implementations.
NAMESPACES() - Constructor for enum edu.isi.pegasus.planner.catalog.classes.Profiles.NAMESPACES
namespaceToPropertiesPrefix() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
namespaceValid(String) - Static method in class edu.isi.pegasus.planner.classes.Profile
  Returns a boolean indicating whether the namespace is valid or not.
NameValue - Class in edu.isi.pegasus.planner.classes
  The object of this class holds the name value pair.
NameValue() - Constructor for class edu.isi.pegasus.planner.classes.NameValue
  the default constructor which initialises the class member variables.
NameValue(String, String) - Constructor for class edu.isi.pegasus.planner.classes.NameValue
  Initialises the class member variables to the values passed in the arguments.
NameValue() - Constructor for class edu.isi.pegasus.planner.selector.site.RoundRobin.NameValue
  The default constructor which initialises the class member variables.
NameValue(String, int) - Constructor for class edu.isi.pegasus.planner.selector.site.RoundRobin.NameValue
  Initialises the class member variables to the values passed in the arguments.
nano0 - Static variable in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
needsSLSInputTransfers(Job) - Method in class edu.isi.pegasus.planner.transfer.sls.Condor
  Returns a boolean indicating whether it will an input file for a job to do the transfers.
needsSLSInputTransfers(Job) - Method in interface edu.isi.pegasus.planner.transfer.SLS
  Returns a boolean indicating whether it will an input file for a job to do the transfers.
needsSLSInputTransfers(Job) - Method in class edu.isi.pegasus.planner.transfer.sls.Transfer
  Returns a boolean indicating whether it will an input file for a job to do the transfers.
needsSLSOutputTransfers(Job) - Method in class edu.isi.pegasus.planner.transfer.sls.Condor
  Returns a boolean indicating whether it will an output file for a job to do the transfers.
needsSLSOutputTransfers(Job) - Method in interface edu.isi.pegasus.planner.transfer.SLS
  Returns a boolean indicating whether it will an output file for a job to do the transfers.
needsSLSOutputTransfers(Job) - Method in class edu.isi.pegasus.planner.transfer.sls.Transfer
  Returns a boolean indicating whether it will an output file for a job to do the transfers.
Netlogger - Class in edu.isi.pegasus.common.logging.format
  This formatter formats the messages in the netlogger format.
Netlogger() - Constructor for class edu.isi.pegasus.common.logging.format.Netlogger
  The default constructor.
NETLOGGER_BP_FILE_SUFFIX - Static variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The suffix to use while constructing the name of the metrics file
NETLOGGER_LOG_FORMATTER_IMPLEMENTOR - Static variable in class edu.isi.pegasus.planner.code.generator.NetloggerJobMapper
NETLOGGER_LOG_FORMATTER_IMPLEMENTOR - Static variable in class edu.isi.pegasus.planner.code.generator.Stampede
NetloggerEvent - Class in edu.isi.pegasus.common.logging.format
  The netlogger event.
NetloggerEvent() - Constructor for class edu.isi.pegasus.common.logging.format.NetloggerEvent
  The default constructor.
NetloggerJobMapper - Class in edu.isi.pegasus.planner.code.generator
  This class can write out the job mappings that link jobs with jobs in the DAX to a Writer stream in the netlogger format.
NetloggerJobMapper(LogManager) - Constructor for class edu.isi.pegasus.planner.code.generator.NetloggerJobMapper
  The default constructor.
NetloggerPostScript - Class in edu.isi.pegasus.planner.code.gridstart
  This postscript invokes the netlogger-exitcode to parse the kickstart output and write out in netlogger format.
NetloggerPostScript() - Constructor for class edu.isi.pegasus.planner.code.gridstart.NetloggerPostScript
  The default constructor.
next() - Method in class edu.isi.pegasus.planner.namespace.Namespace.EmptyIterator
  Returns a null as we are iterating over nothing.
next() - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph.BottomUpIterator
  Returns the next object in the traversal order.
next() - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph.MapGraphIterator
  Returns the next object in the traversal order.
next() - Method in class edu.isi.pegasus.planner.partitioner.graph.TopologicalSortIterator
  Returns the next node to be traversed
nextDouble() - Static method in class edu.isi.pegasus.planner.common.PegRandom
  Returns a double value between 0.0 and 1.0.
nextGaussian() - Static method in class edu.isi.pegasus.planner.common.PegRandom
  Returns a normally distributed (gaussian) random variable between 0.0 and 1.0.
nextToken() - Method in class edu.isi.pegasus.planner.parser.SiteCatalogTextScanner
  Obtains the next token from the input stream.
nextToken() - Method in class edu.isi.pegasus.planner.parser.TransformationCatalogTextScanner
  Obtains the next token from the input stream.
niceString(String) - Method in class edu.isi.pegasus.planner.parser.SiteCatalogTextParser
  Remove potential leading and trainling quotes from a string.
niceString(String) - Method in class edu.isi.pegasus.planner.parser.TransformationCatalogTextParser
  Remove potential leading and trainling quotes from a string.
NMI2VDSSysInfo - Class in edu.isi.pegasus.planner.catalog.transformation.classes
  An Adapter class that translates the new NMI based Architecture and OS specifications to VDS ( VDS era ) Arch and Os objects
NMI2VDSSysInfo() - Constructor for class edu.isi.pegasus.planner.catalog.transformation.classes.NMI2VDSSysInfo
nmiArchToVDSArch(SysInfo.Architecture) - Static method in class edu.isi.pegasus.planner.catalog.transformation.classes.NMI2VDSSysInfo
  Returns the the VDS Arch object corresponding to the new NMI Architecture object .
nmiArchToVDSArch(String) - Static method in class edu.isi.pegasus.planner.catalog.transformation.classes.NMI2VDSSysInfo
  Returns the VDS Arch object corresponding to the new NMI Architecture object .
NMIArchToVDSArchMap() - Static method in class edu.isi.pegasus.planner.catalog.transformation.classes.NMI2VDSSysInfo
  Singleton access to the NMI arch to VDS arch map.
nmiOSToVDSOS(SysInfo.OS) - Static method in class edu.isi.pegasus.planner.catalog.transformation.classes.NMI2VDSSysInfo
  Returns the VDS Os object corresponding to the new NMI OS object .
nmiOSToVDSOS(String) - Static method in class edu.isi.pegasus.planner.catalog.transformation.classes.NMI2VDSSysInfo
  Returns the VDS Os object corresponding to the new NMI OS object .
NMIOSToVDSOSMap() - Static method in class edu.isi.pegasus.planner.catalog.transformation.classes.NMI2VDSSysInfo
  Singleton access to the os to NMI os map.
nmiToVDSSysInfo(SysInfo) - Static method in class edu.isi.pegasus.planner.catalog.transformation.classes.NMI2VDSSysInfo
  Returns the VDSSysInfo object.
nmiToVDSSysInfo(SysInfo.Architecture, SysInfo.OS, String) - Static method in class edu.isi.pegasus.planner.catalog.transformation.classes.NMI2VDSSysInfo
  Returns the VDS VDSSysInfo object corresponding to the NMI arch and OS
NO_GRIDSTART_INDEX - Static variable in class edu.isi.pegasus.planner.code.GridStartFactory
  The index in the constant arrays for NoGridStart.
NO_MATCH - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
NO_OF_TRANSIENT_FLAGS - Static variable in class edu.isi.pegasus.planner.classes.PegasusFile
  The number of transient flags.
Node - Class in edu.isi.pegasus.planner.provisioner
  An instance of this class represents an independent task of a workflow.
Node(String, String, long) - Constructor for class edu.isi.pegasus.planner.provisioner.Node
  constructor
Node(String, String, int, long) - Constructor for class edu.isi.pegasus.planner.provisioner.Node
Node(String) - Constructor for class edu.isi.pegasus.planner.provisioner.Node
NodeCollapser - Class in edu.isi.pegasus.planner.refiner
  This collapses the nodes of the same logical name scheduled on the same pool into fewer fat nodes.
NodeCollapser(PegasusBag) - Constructor for class edu.isi.pegasus.planner.refiner.NodeCollapser
  The overloaded constructor.
NodeComp() - Constructor for class edu.isi.pegasus.planner.provisioner.OccupationDiagram.NodeComp
nodeComparator() - Method in class edu.isi.pegasus.planner.partitioner.Horizontal
  Singleton access to the job comparator.
nodeIterator() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns an iterator for the nodes in the Graph.
nodeIterator() - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Returns an iterator for the nodes in the Graph.
nodeIterator() - Method in interface edu.isi.pegasus.planner.partitioner.graph.Graph
  Returns an iterator for the nodes in the Graph.
nodeIterator() - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph
  Returns an iterator for the nodes in the Graph.
NODENAME_ATTRIBUTE_KEY - Static variable in class edu.isi.pegasus.planner.invocation.Uname
  The nodename attribute for the uname
nodes - Variable in class edu.isi.pegasus.planner.provisioner.Estimator
nodes - Variable in class edu.isi.pegasus.planner.provisioner.OccupationDiagram
NoGridStart - Class in edu.isi.pegasus.planner.code.gridstart
  This class ends up running the job directly on the grid, without wrapping it in any other launcher executable.
NoGridStart() - Constructor for class edu.isi.pegasus.planner.code.gridstart.NoGridStart
noHassleInstance() - Static method in class edu.isi.pegasus.common.util.CommonProperties
  Singleton interface: Creates the one and only instance of the properties in the current application, and does not bother the programmer with exceptions.
noLine() - Method in class edu.isi.pegasus.common.util.XMLWriter
NON_SHARED_FS_CONFIGURATION_VALUE - Static variable in class edu.isi.pegasus.planner.common.PegasusConfiguration
  The value for the non shared filesystem configuration.
NON_SINGLETON_LOAD - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolMode
NON_SINGLETON_LOAD - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.SiteFactory
NonJavaCallout - Class in edu.isi.pegasus.planner.selector.site
  This is the class that implements a call-out to a site selector which is an application or executable script.
NonJavaCallout() - Constructor for class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  The default constructor.
nonSingletonInstance(String) - Static method in class edu.isi.pegasus.common.util.CommonProperties
  Create a temporary property that is not attached to the Singleton.
nonSingletonInstance(String, String) - Static method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  The method that returns a Non Singleton instance of the dervived InfoProvider class.
nonSingletonInstance(String, String) - Static method in class edu.isi.pegasus.planner.catalog.site.impl.old.Text
  The method that returns a Non Singleton instance of the dervived InfoProvider class.
nonSingletonInstance(String, String) - Static method in class edu.isi.pegasus.planner.catalog.site.impl.old.XML
  The method that returns a Non Singleton instance of the dervived InfoProvider class.
nonSingletonInstance(String) - Static method in class edu.isi.pegasus.planner.common.PegasusProperties
  To get a reference to the the object.
nonSingletonInstance() - Static method in class edu.isi.pegasus.planner.common.PegasusProperties
  To get a reference to the the object.
NOOP_PREFIX - Static variable in class edu.isi.pegasus.planner.client.CPlanner
  The prefix for the NoOP jobs that are created.
NOOP_PREFIX - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  The prefix for the NoOP jobs that are created.
NoPOSTScript - Class in edu.isi.pegasus.planner.code.gridstart
  This class refers to having no postscript associated with the job.
NoPOSTScript() - Constructor for class edu.isi.pegasus.planner.code.gridstart.NoPOSTScript
  The default constructor.
noquote(String) - Method in class edu.isi.pegasus.planner.client.RCClient
  Removes a pair of outer quotes, which are optional.
normalize() - Method in class edu.isi.pegasus.planner.invocation.Architecture
  Normalizes a misconfigured nodename that contains a domainname.
NoSuchFileException - Exception in edu.isi.pegasus.gridftp
NoSuchFileException(String) - Constructor for exception edu.isi.pegasus.gridftp.NoSuchFileException
NoSuchFileException(String, Throwable) - Constructor for exception edu.isi.pegasus.gridftp.NoSuchFileException
NOT_PERMITTED_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Namespace
  The key is not permitted in as it clashes with default Pegasus constructs.
Notifications - Class in edu.isi.pegasus.planner.classes
  A container class that stores all the notifications that need to be done indexed by the various conditions.
Notifications() - Constructor for class edu.isi.pegasus.planner.classes.Notifications
  The default constructor.
NOTIFICATIONS_FILE_SUFFIX - Static variable in class edu.isi.pegasus.planner.code.generator.MonitordNotify
  The suffix to use while constructing the name of the metrics file
notPermitted(String) - Method in class edu.isi.pegasus.planner.namespace.Namespace
  Warns about a namespace profile key that cannot be permitted.
now() - Method in class edu.isi.pegasus.common.util.Currently
  Obtains the current time as formatted string according to the format option.
now(Date) - Method in class edu.isi.pegasus.common.util.Currently
  Obtains the current time as formatted string according to the format option.
NPbalance(LinkedList[], int, boolean) - Method in class edu.isi.pegasus.planner.provisioner.Node
  Non-propagate redistribution of this task
NUM_OF_EXPANDED_JOBS - Static variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The number of jobs into which each job in the partition graph is expanded to.
NUMBER_OF_THREADS - Static variable in class edu.isi.pegasus.planner.refiner.ThreadPool
  The maximum number of authentication threads that are spawned.
numberOfConsitutentJobs() - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Returns the number of constituent jobs.
numericValue(String) - Static method in class edu.isi.pegasus.common.util.CondorVersion
  Converts a string into the corresponding numeric value.
numericValue() - Method in class edu.isi.pegasus.common.util.CondorVersion
  Returns the condor version parsed by executing the condor_version command.

## O

OccupationDiagram - Class in edu.isi.pegasus.planner.provisioner
  This class keeps structure of an Occupation Diagram and conduct BTS algorithm
OccupationDiagram(long) - Constructor for class edu.isi.pegasus.planner.provisioner.OccupationDiagram
  Constructor
OccupationDiagram.NodeComp - Class in edu.isi.pegasus.planner.provisioner
  Comparator which compare the schedulable duration of two nodes
olb - Variable in class edu.isi.pegasus.planner.provisioner.Node
OLD_XML3_IMPLEMENTING_CLASS_BASENAME - Static variable in class edu.isi.pegasus.planner.catalog.site.SiteFactory
  The name of old XML3 implementation class.
OLDFILE_TC_CLASS - Static variable in class edu.isi.pegasus.planner.catalog.transformation.TCMode
One2One - Class in edu.isi.pegasus.planner.partitioner
  This partitioning technique considers each of the job in the dax as a separate partition.
One2One(GraphNode, Map, PegasusProperties) - Constructor for class edu.isi.pegasus.planner.partitioner.One2One
  The overloaded constructor.
ONTOLOGY_LOCATION - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
OpenBrace - Class in edu.isi.pegasus.planner.parser.tokens
  Class to convey a opened brace, no token value necessary.
OpenBrace() - Constructor for class edu.isi.pegasus.planner.parser.tokens.OpenBrace
OpenParanthesis - Class in edu.isi.pegasus.planner.parser.tokens
  Class to convey a closed paranthesis, no token value necessary.
OpenParanthesis() - Constructor for class edu.isi.pegasus.planner.parser.tokens.OpenParanthesis
OPERATION() - Constructor for enum edu.isi.pegasus.planner.catalog.site.classes.FileServerType.OPERATION
operationsFor(FileServerType.OPERATION) - Static method in enum edu.isi.pegasus.planner.catalog.site.classes.FileServerType.OPERATION
  Returns a collection of operations corresponding to a get or put operation
operationsForGET() - Static method in enum edu.isi.pegasus.planner.catalog.site.classes.FileServerType.OPERATION
  Returns a collection of get operations.
operationsForPUT() - Static method in enum edu.isi.pegasus.planner.catalog.site.classes.FileServerType.OPERATION
  Returns a collection of get operations.
OPTIONAL_BIT_FLAG - Static variable in class edu.isi.pegasus.planner.classes.PegasusFile
  The index of the flags field which when set indicates that the file is to be considered optional.
optionalArgSet() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the flag to denote whether the optional argument for the random was specified or not.
options() - Static method in class edu.isi.pegasus.gridftp.PegasusGridFTP
orb - Variable in class edu.isi.pegasus.planner.provisioner.Node
order(Partition) - Method in class edu.isi.pegasus.planner.cluster.Abstract
  Returns the nodes in the partition as a List in a particular order.
order(Partition) - Method in class edu.isi.pegasus.planner.cluster.Vertical
  Returns the nodes in the partition as a List in the topologically sorted order.
OS() - Constructor for enum edu.isi.pegasus.planner.catalog.classes.SysInfo.OS
Os - Class in edu.isi.pegasus.planner.catalog.transformation.classes
Os(String) - Constructor for class edu.isi.pegasus.planner.catalog.transformation.classes.Os
os - Variable in class edu.isi.pegasus.planner.catalog.transformation.classes.VDSSysInfo
  Os of the system.
OS() - Constructor for enum edu.isi.pegasus.planner.dax.Executable.OS
OS - Static variable in class edu.isi.pegasus.planner.parser.tokens.TransformationCatalogReservedWord
  token value for the reserved word "os".
OS_COMBINE_SEPARATOR - Static variable in class edu.isi.pegasus.planner.catalog.classes.VDSSysInfo2NMI
  The separator used to combine OS version and release.
OS_COMBINE_SEPARATOR - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.NMI2VDSSysInfo
  The separator used to combine OS version and release.
OS_TYPE - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The constant to be passed to the accessor functions to get or set the operating system type of the remote machines to which the jobmanager talks to.
OSGMM - Class in edu.isi.pegasus.planner.catalog.site.impl
  The OSGMM implementation of the Site Catalog interface.
OSGMM() - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  The default constructor.
OSGMM.ListCallback - Class in edu.isi.pegasus.planner.catalog.site.impl
  An inner class, that implements the StreamGobblerCallback to store all the lines in a List
OSRELEASE - Static variable in class edu.isi.pegasus.planner.parser.tokens.TransformationCatalogReservedWord
  token value for the reserved word "osrelease".
osToOSReleaseAndVersion() - Static method in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Maps each to OS to a specific OS release for purposes of picking up the correct worker package for a site.
osversion - Variable in class edu.isi.pegasus.planner.catalog.transformation.classes.VDSSysInfo
  Os version of the system.
OSVERSION - Static variable in class edu.isi.pegasus.planner.parser.tokens.TransformationCatalogReservedWord
  token value for the reserver word "osversion".
OTHER_FILE - Static variable in class edu.isi.pegasus.planner.classes.PegasusFile
  The type denoting that a logical file is an other file.
OTHER_TYPE - Static variable in class edu.isi.pegasus.planner.classes.PegasusFile
  The string value of a file that is of type other.
outEdges - Variable in class edu.isi.pegasus.planner.provisioner.Node
OUTPUT_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The name of the key that determines the file on the submit host on which postscript is to be invoked.
outputFiles - Variable in class edu.isi.pegasus.planner.classes.Job
  Contains the output files for the submit file.
OutputMapper - Interface in edu.isi.pegasus.planner.transfer.mapper
  The interface that defines how to map the output files to a stage out site.
OutputMapperFactory - Class in edu.isi.pegasus.planner.transfer.mapper
  The factory class that loads an appropriate Transfer OutputMapper class, as specified by the properties.
OutputMapperFactory() - Constructor for class edu.isi.pegasus.planner.transfer.mapper.OutputMapperFactory
OutputMapperFactoryException - Exception in edu.isi.pegasus.planner.transfer.mapper
  Class to notify of failures while instantiating Output Mappers.
OutputMapperFactoryException(String) - Constructor for exception edu.isi.pegasus.planner.transfer.mapper.OutputMapperFactoryException
  Constructs a `OutputMapperFactoryException` with no detail message.
OutputMapperFactoryException(String, String) - Constructor for exception edu.isi.pegasus.planner.transfer.mapper.OutputMapperFactoryException
  Constructs a `OutputMapperFactoryException` with the specified detailed message.
OutputMapperFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.transfer.mapper.OutputMapperFactoryException
  Constructs a `OutputMapperFactoryException` with the specified detailed message and a cause.
OutputMapperFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.planner.transfer.mapper.OutputMapperFactoryException
  Constructs a `OutputMapperFactoryException` with the specified detailed message and a cause.

## P

PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolMode
PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.catalog.transformation.Mapper
  The name of the package where the implementing classes reside.
PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.catalog.transformation.TCMode
  Default PACKAGE PATH for the TC implementing classes
PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.partitioner.DAXWriter
  The name of the package in which the writers are implemented.
PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.partitioner.Partitioner
  The package name where the implementing classes of this interface reside.
PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.refiner.CreateDirectory
  The name of the package in which all the implementing classes are.
PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The name of the package in which all the implementing classes are.
PACKAGE_NAME - Static variable in class edu.isi.pegasus.planner.selector.TransformationSelector
PARALLEL_UNIVERSE - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.Condor
PARALLEL_UNIVERSE - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The condor universe key value for parallel universe.
parent - Variable in class edu.isi.pegasus.planner.classes.PCRelation
  the parent making up the parent child relationship pair in a dag
PARENT_JOB_ID_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The atrribute key for parent job id.
PARENT_TASK_ID_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The atrribute key for parent task id.
parents(String, List) - Method in class edu.isi.pegasus.planner.cluster.Abstract
  Associates the relations between the partitions with the corresponding relations between the clustered jobs that are created for each Partition.
parents(String, List) - Method in interface edu.isi.pegasus.planner.cluster.Clusterer
  Associates the relations between the partitions with the corresponding relations between the clustered jobs that are created for each Partition.
parents(String, List) - Method in class edu.isi.pegasus.planner.cluster.Horizontal
  Am empty implementation of the callout, as state is maintained internally to determine the relations between the jobs.
parentsColored(int) - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  Returns if all the parents of that node have the color that is specified.
parentsToString() - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  A convenience methods that generates a comma separated list of parents as String
parse(String) - Static method in class edu.isi.pegasus.common.util.Boolean
  Converts a boolean string representation into a boolean value.
parse(String, boolean) - Static method in class edu.isi.pegasus.common.util.Boolean
  Converts a boolean string representation into a boolean value.
parse(String) - Static method in class edu.isi.pegasus.common.util.Currently
  Parses one of the ISO 8601 that it produces.
parse(String) - Method in class edu.isi.pegasus.common.util.PegasusURL
  Parses the url and populates the internal member variables that can be accessed via the appropriate accessor methods
parse(String) - Static method in class edu.isi.pegasus.common.util.ProfileParser
  Parses a given user profile specification into a map of maps.
parse(String, int) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Parses a line from the file replica catalog
parse(String, int) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Parses a line from the file replica catalog
parse(String) - Method in class edu.isi.pegasus.planner.client.DAXValidator
parse(String) - Method in class edu.isi.pegasus.planner.client.RCClient
  Consumes commands that control the replica management.
parse(String, String) - Method in class edu.isi.pegasus.planner.client.RCClient
  Consumes commands that control the replica management.
parse(InputStream) - Method in class edu.isi.pegasus.planner.parser.InvocationParser
  This function parses a XML source from an InputStream source, and creates java class instances that correspond to different elements in the XML source.
parse(Reader) - Method in class edu.isi.pegasus.planner.parser.InvocationParser
  This function parses a XML source from the new Reader source, and creates java class instances that correspond to different elements in the XML source.
parse() - Method in class edu.isi.pegasus.planner.parser.SiteCatalogTextParser
  Parses the complete input stream, into the PoolConfig data object that holds the contents of all the sites referred to in the stream.
parse(boolean) - Method in class edu.isi.pegasus.planner.parser.TransformationCatalogTextParser
  Parses the complete input stream, into the PoolConfig data object that holds the contents of all the sites referred to in the stream.
parseCommandLineArguments(String[]) - Method in class edu.isi.pegasus.planner.client.CPlanner
  Parses the command line arguments using GetOpt and returns a `PlannerOptions` contains all the options passed by the user at the command line.
parseCommandLineArguments(String[], boolean) - Method in class edu.isi.pegasus.planner.client.CPlanner
  Parses the command line arguments using GetOpt and returns a `PlannerOptions` contains all the options passed by the user at the command line.
parseCommandLineArguments(String[]) - Method in class edu.isi.pegasus.planner.client.PegasusGetSites
  Parses the command line arguments using GetOpt and sets the class member variables.
parseCommandLineArguments(String[]) - Method in class edu.isi.pegasus.planner.client.RankDAX
  Parses the command line arguments using GetOpt and sets the class member variables.
parseCommandLineArguments(String[]) - Method in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  Parses the command line arguments using GetOpt and returns a `PlannerOptions` contains all the options passed by the user at the command line.
parseDate(String) - Method in class edu.isi.pegasus.planner.parser.InvocationParser
  Small helper to parse the different date varieties and deal with Java obnoxeity.
parseDAX(String) - Method in class edu.isi.pegasus.planner.client.CPlanner
  Parses the DAX and returns the associated ADag object
parseGridFTPResponse(String, char) - Method in class edu.isi.pegasus.planner.refiner.Authenticate
  The parses the grid ftp server response and returns if the response was valid or not.
parseInputFiles(List<String>, String, String) - Method in class edu.isi.pegasus.planner.client.SCClient
  Parses the input files in the input format and returns a String in the output format.
parseInt(String) - Static method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Parses a string into an integer.
parseInt(String, String) - Method in class edu.isi.pegasus.planner.namespace.aggregator.Abstract
  Formats the String value as an integer.
parseInt(String) - Static method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Parses a string into an integer.
Parser - Class in edu.isi.pegasus.planner.parser
  This is the base class which all the xml parsing classes extend.
Parser(PegasusBag) - Constructor for class edu.isi.pegasus.planner.parser.Parser
  Intialises the parser.
Parser(PegasusProperties) - Constructor for class edu.isi.pegasus.planner.parser.Parser
  Intialises the parser.
ParserStackElement - Class in edu.isi.pegasus.planner.parser
  This class keeps the name of an element and its corresponding java object reference.
ParserStackElement(String, Object) - Constructor for class edu.isi.pegasus.planner.parser.ParserStackElement
  The overloaded constructor
parseStdOut(Job, String) - Method in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  Extracts the chosen site from the site selector's answer.
parseTC(PegasusProperties) - Method in class edu.isi.pegasus.planner.client.TCConverter
  Parses the input format specified in the properties file and returns list of TransfromationCatalogEntry
PARSING_DONE_ERROR_MESSAGE - Static variable in class edu.isi.pegasus.planner.parser.dax.DAX2Metadata
  The parsing completed message.
Partition - Class in edu.isi.pegasus.planner.partitioner
  This is an abstract container for a partition in the graph.
Partition() - Constructor for class edu.isi.pegasus.planner.partitioner.Partition
  The default constructor.
Partition(List, String) - Constructor for class edu.isi.pegasus.planner.partitioner.Partition
  The overloaded constructor.
PARTITION_KEY - Static variable in class edu.isi.pegasus.planner.partitioner.graph.LabelBag
  The key that designates the partition to which a node belongs to.
PARTITION_PREFIX - Static variable in class edu.isi.pegasus.planner.partitioner.DAXWriter
  The prefix added to the name of the dax to identify it is a partitioned dax.
PartitionDAX - Class in edu.isi.pegasus.planner.client
  The class ends up partitioning the dax into smaller daxes according to the various algorithms/criteria, to be used for deferred planning.
PartitionDAX() - Constructor for class edu.isi.pegasus.planner.client.PartitionDAX
  The default constructor.
partitionDAX(PegasusProperties, String, String, String) - Method in class edu.isi.pegasus.planner.client.PartitionDAX
Partitioner - Class in edu.isi.pegasus.planner.partitioner
  The abstract class that lays out the api to do the partitioning of the dax into smaller daxes.
Partitioner(GraphNode, Map, PegasusProperties) - Constructor for class edu.isi.pegasus.planner.partitioner.Partitioner
  The overloaded constructor.
PartitionerFactory - Class in edu.isi.pegasus.planner.partitioner
  A Factory class to load the right type of partitioner at runtime, as specified by the Properties.
PartitionerFactory() - Constructor for class edu.isi.pegasus.planner.partitioner.PartitionerFactory
PartitionerFactoryException - Exception in edu.isi.pegasus.planner.partitioner
  Class to notify of failures while instantiating Partitioner implementations.
PartitionerFactoryException(String) - Constructor for exception edu.isi.pegasus.planner.partitioner.PartitionerFactoryException
  Constructs a `PartitionerFactoryException` with no detail message.
PartitionerFactoryException(String, String) - Constructor for exception edu.isi.pegasus.planner.partitioner.PartitionerFactoryException
  Constructs a `PartitionerFactoryException` with the specified detailed message.
PartitionerFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.partitioner.PartitionerFactoryException
  Constructs a `PartitionerFactoryException` with the specified detailed message and a cause.
PartitionerFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.planner.partitioner.PartitionerFactoryException
  Constructs a `PartitionerFactoryException` with the specified detailed message and a cause.
partitionerTable() - Static method in class edu.isi.pegasus.planner.cluster.ClustererFactory
  Returns a table that maps, the clustering technique to an appropriate partitioning technique.
PARTITIONING_CLASSES - Static variable in class edu.isi.pegasus.planner.partitioner.PartitionerFactory
  An array of known partitioning classes.
partitionRelation2XML(String, String) - Method in class edu.isi.pegasus.planner.partitioner.WriterCallback
  Returns the xml description of a relation between 2 partitions.
partitionRelation2XML(String, List) - Method in class edu.isi.pegasus.planner.partitioner.WriterCallback
  Returns the xml description of a relation between 2 partitions.
partitionRelation2XML(String, Set) - Method in class edu.isi.pegasus.planner.partitioner.WriterCallback
  Returns the xml description of a relation between 2 partitions.
partOfDeferredRun() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns a boolean indicating whether this invocation is part of a deferred execution or not.
PASOA_PPS_PROVIDER - Static variable in class edu.isi.pegasus.planner.provenance.pasoa.pps.PPSFactory
  The default Pasoa PPS implementation to be used.
PATCH - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GlobusVersion
  The constant for patche version type.
PATH_VALUE - Static variable in class edu.isi.pegasus.planner.refiner.createdir.DefaultImplementation
  The path to be set for create dir jobs.
PATH_VALUE - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The path to be set for create dir jobs.
Patterns - Class in edu.isi.pegasus.planner.dax
Patterns() - Constructor for class edu.isi.pegasus.planner.dax.Patterns
PBS - Class in edu.isi.pegasus.planner.code.generator
  This code generator generates a PBS submit script for the workflow, that can be submitted directly using qsub.
PBS() - Constructor for class edu.isi.pegasus.planner.code.generator.PBS
  The default constructor.
pbsBasename(ADag) - Method in class edu.isi.pegasus.planner.code.generator.PBS
  Returns the basename for the PBS file for the dag
PCRelation - Class in edu.isi.pegasus.planner.classes
  Captures the parent child relationship between the jobs in the ADAG.
PCRelation() - Constructor for class edu.isi.pegasus.planner.classes.PCRelation
  the default constructor
PCRelation(String, String, boolean) - Constructor for class edu.isi.pegasus.planner.classes.PCRelation
  the overloaded constructor
PCRelation(String, String) - Constructor for class edu.isi.pegasus.planner.classes.PCRelation
  the overloaded constructor
PDAX2MDAG - Class in edu.isi.pegasus.planner.parser.pdax
  This callback ends up creating the megadag that contains the smaller dags each corresponding to the one level as identified in the pdax file generated by the partitioner.
PDAX2MDAG(String, PegasusProperties, PlannerOptions) - Constructor for class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The overloaded constructor.
PDAX2MDAG.GrepCallback - Class in edu.isi.pegasus.planner.parser.pdax
  An inner class, that implements the StreamGobblerCallback to count the occurences of a word in a document.
PDAXCallbackFactory - Class in edu.isi.pegasus.planner.parser.pdax
  A factory class to load the appropriate DAX callback implementations that need to be passed to the DAX Parser.
PDAXCallbackFactory() - Constructor for class edu.isi.pegasus.planner.parser.pdax.PDAXCallbackFactory
PDAXCallbackFactoryException - Exception in edu.isi.pegasus.planner.parser.pdax
  Class to notify of failures while instantiating PDAXCallback implementations.
PDAXCallbackFactoryException(String) - Constructor for exception edu.isi.pegasus.planner.parser.pdax.PDAXCallbackFactoryException
  Constructs a `PDAXCallbackFactoryException` with no detail message.
PDAXCallbackFactoryException(String, String) - Constructor for exception edu.isi.pegasus.planner.parser.pdax.PDAXCallbackFactoryException
  Constructs a `PDAXCallbackFactoryException` with the specified detailed message.
PDAXCallbackFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.parser.pdax.PDAXCallbackFactoryException
  Constructs a `PDAXCallbackFactoryException` with the specified detailed message and a cause.
PDAXCallbackFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.planner.parser.pdax.PDAXCallbackFactoryException
  Constructs a `PDAXCallbackFactoryException` with the specified detailed message and a cause.
PDAXParser - Class in edu.isi.pegasus.planner.parser
  This is a parser class for the parsing the pdax that contain the jobs in the various partitions and the relations between the partitions.
PDAXParser(PegasusProperties) - Constructor for class edu.isi.pegasus.planner.parser.PDAXParser
  The default constructor.
PDAXParser(String, PegasusProperties) - Constructor for class edu.isi.pegasus.planner.parser.PDAXParser
  The constructor initialises the parser, and turns on the validation feature in Xerces.
PDAXWriter - Class in edu.isi.pegasus.planner.partitioner
  It writes out the partition graph in xml form.
PDAXWriter(String, String) - Constructor for class edu.isi.pegasus.planner.partitioner.PDAXWriter
  The overloaded constructor.
Pegasus - Class in edu.isi.pegasus.planner.namespace
  A Planner specific namespace.
Pegasus() - Constructor for class edu.isi.pegasus.planner.namespace.Pegasus
  The default constructor.
Pegasus(Map) - Constructor for class edu.isi.pegasus.planner.namespace.Pegasus
  The overloaded constructor.
PEGASUS - Static variable in interface edu.isi.pegasus.planner.provenance.pasoa.PPS
PEGASUS_APP_METRICS_PREFIX - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
PEGASUS_BIN_DIR - Static variable in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  The name of the environment variable PEGASUS_BIN_DIR.
PEGASUS_BIN_DIR - Static variable in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  The name of the environment variable PEGASUS_BIN_DIR.
PEGASUS_CONFIGURATION_PROPERTY_KEY - Static variable in class edu.isi.pegasus.planner.common.PegasusConfiguration
  The property key for pegasus configuration.
PEGASUS_CONNECT_STDIN_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.Condor
  Whether to connect stdin or not
PEGASUS_EXECUTE_IN_INITIAL_DIR - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.Condor
  The name of the environment variable that determines if job should be executed in initial dir or not
PEGASUS_HOME - Static variable in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  The name of the environment variable PEGASUS_HOME.
PEGASUS_HOME - Static variable in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  The name of the environment variable PEGASUS_HOME.
PEGASUS_HOME - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  The name of the environment variable PEGASUS_HOME.
PEGASUS_INFO - Static variable in class edu.isi.pegasus.planner.classes.PegasusBag
  Array storing the names of the attributes that are stored with the site.
PEGASUS_INITIAL_DIR_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.Condor
  The name of the environment variable for the initial dir for pegasus lite local
PEGASUS_LITE_COMMON_FILE_BASENAME - Static variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  The basename of the pegasus lite common shell functions file.
PEGASUS_LITE_EXITCODE_SUCCESS_MESSAGE - Static variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  The pegasus lite exitcode success message.
PEGASUS_LITE_LOCAL_FILE_BASENAME - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.Condor
  The Pegasus Lite local wrapper basename.
PEGASUS_LOGMANAGER - Static variable in class edu.isi.pegasus.planner.classes.PegasusBag
  The constant to be passed to the accessor functions to get or set the handle to the Logging manager
PEGASUS_MONITORD_LAUNCH_PROPERTY_KEY - Static variable in class edu.isi.pegasus.planner.client.CPlanner
  The name of the property key that determines whether pegasus-run should monitord or not.
PEGASUS_PROPERTIES - Static variable in class edu.isi.pegasus.planner.classes.PegasusBag
  The constant to be passed to the accessor functions to get or set the PegasusProperties.
PEGASUS_PROPERTY_PREFIX - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
  The pegasus property prefix.
PEGASUS_REPLICA_CATALOG_FILE_PROPERTY - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
PEGASUS_REPLICA_CATALOG_PROPERTY - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
PEGASUS_SHELL_RUNNER_FUNCTIONS_BASENAME - Static variable in class edu.isi.pegasus.planner.code.generator.Shell
PEGASUS_SITE_CATALOG_FILE_PROPERTY - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
PEGASUS_SITE_CATALOG_PROPERTY - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
PEGASUS_TRANSFER_INPUT_FILES_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.Condor
  The name of the environment variable for transferring input files
PEGASUS_TRANSFER_OUTPUT_FILES_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.Condor
  The name of the environment variable for transferring output files
PEGASUS_TRANSFER_WORKER_PACKAGE_PROPERTY - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
PEGASUS_TRANSFORMATION_CATALOG_FILE_PROPERTY - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
PEGASUS_TRANSFORMATION_CATALOG_PROPERTY - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
PEGASUS_VERSION - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The version of pegasus matching the planner.
PEGASUS_WORKER_EXECUTABLES - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Array storing the names of the executables in the $PEGASUS_HOME/bin directory Associates the transformation name with the executable basenames
PEGASUS_WORKER_NODE_EXECUTION_PROPERTY - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
PegasusBag - Class in edu.isi.pegasus.planner.classes
  A bag of objects that needs to be passed to various refiners.
PegasusBag() - Constructor for class edu.isi.pegasus.planner.classes.PegasusBag
  The default constructor.
PegasusConfiguration - Class in edu.isi.pegasus.planner.common
  A utility class that returns JAVA Properties that need to be set based on a configuration value
PegasusConfiguration(LogManager) - Constructor for class edu.isi.pegasus.planner.common.PegasusConfiguration
  Overloaded Constructor
PegasusExitCode - Class in edu.isi.pegasus.planner.code.gridstart
  The exitcode wrapper, that can parse kickstart output's and put them in the database also.
PegasusExitCode() - Constructor for class edu.isi.pegasus.planner.code.gridstart.PegasusExitCode
  The default constructor.
PegasusExitCodeEncode - Class in edu.isi.pegasus.planner.code.gridstart
  This class tries to define a mechanism to encode arguments for pegasus-exitcode, as DAGMan does not handle whitespaces correctly for postscript arguments.
PegasusExitCodeEncode() - Constructor for class edu.isi.pegasus.planner.code.gridstart.PegasusExitCodeEncode
  Defines the default encoding rules escape + with \+ encode single whitespace with +
PegasusExitCodeEncode(String, char) - Constructor for class edu.isi.pegasus.planner.code.gridstart.PegasusExitCodeEncode
  Constructs arbitrary escaping rules.
PegasusFile - Class in edu.isi.pegasus.planner.classes
  The logical file object that contains the logical filename which is got from the DAX, and the associated set of flags specifying the transient characteristics.
PegasusFile() - Constructor for class edu.isi.pegasus.planner.classes.PegasusFile
  The default constructor.
PegasusFile(String) - Constructor for class edu.isi.pegasus.planner.classes.PegasusFile
  The overloaded constructor.
PegasusFile.LINKAGE - Enum in edu.isi.pegasus.planner.classes
  Enumeration for denoting type of linkage
PegasusGetSites - Class in edu.isi.pegasus.planner.client
  The client that replaces the perl based pegasus-get-sites.
PegasusGetSites() - Constructor for class edu.isi.pegasus.planner.client.PegasusGetSites
  The default constructor.
PegasusGridFTP - Class in edu.isi.pegasus.gridftp
  Implements a command-line utility for performing file and directory operations on remote GridFTP servers.
PegasusGridFTP() - Constructor for class edu.isi.pegasus.gridftp.PegasusGridFTP
PegasusLite - Class in edu.isi.pegasus.planner.code.gridstart
  This class launches all the jobs using Pegasus Lite a shell script based wrapper.
PegasusLite() - Constructor for class edu.isi.pegasus.planner.code.gridstart.PegasusLite
PegasusProperties - Class in edu.isi.pegasus.planner.common
  A Central Properties class that keeps track of all the properties used by Pegasus.
PegasusProperties(String) - Constructor for class edu.isi.pegasus.planner.common.PegasusProperties
  The constructor that constructs the default paths to the various configuration files, and populates the singleton instance as required.
PegasusProperties.CLEANUP_SCOPE - Enum in edu.isi.pegasus.planner.common
  An enum defining The scope for cleanup algorithm
PegasusURL - Class in edu.isi.pegasus.common.util
  A common PegasusURL class to use by the planner and other components.
PegasusURL() - Constructor for class edu.isi.pegasus.common.util.PegasusURL
  The default constructor.
PegasusURL(String) - Constructor for class edu.isi.pegasus.common.util.PegasusURL
  The overloaded constructor.
PegRandom - Class in edu.isi.pegasus.planner.common
  A Helper class that returns the Random values using java.util.Random class.
PegRandom() - Constructor for class edu.isi.pegasus.planner.common.PegRandom
PERFMETRIC_CPU_UTILIZATION - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
PERFMETRIC_CPU_UTILIZATION - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
PERFMETRIC_MEMORY_UTILIZATION - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
PERFMETRIC_MEMORY_UTILIZATION - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
PERFMETRIC_NETWORK_BANDWIDTH - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
PERFMETRIC_NETWORK_BANDWIDTH - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
PERFMETRIC_TIME_DURATION - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
PERFMETRIC_TIME_DURATION - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
PERIODIC_RELEASE_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The name of the key that specifies the peridic release
PERIODIC_REMOVE_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The name of the key that specifies the peridic remove
PermissionDeniedException - Exception in edu.isi.pegasus.gridftp
PermissionDeniedException(String) - Constructor for exception edu.isi.pegasus.gridftp.PermissionDeniedException
PermissionDeniedException(String, Throwable) - Constructor for exception edu.isi.pegasus.gridftp.PermissionDeniedException
pfn - Variable in class edu.isi.pegasus.planner.catalog.transformation.client.Client
pfn - Variable in class edu.isi.pegasus.planner.client.TCClient
PFN - Class in edu.isi.pegasus.planner.dax
PFN(String) - Constructor for class edu.isi.pegasus.planner.dax.PFN
PFN(String, String) - Constructor for class edu.isi.pegasus.planner.dax.PFN
PFN - Static variable in class edu.isi.pegasus.planner.parser.tokens.TransformationCatalogReservedWord
  token value for the reserved word "pfn".
PFN_HINT_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Hints
  The pfnHint key
pfnIterator() - Method in class edu.isi.pegasus.planner.classes.ReplicaLocation
  Returns an iterator to the list of `ReplicaCatalogEntry` objects.
pickPath(String, String) - Method in class edu.isi.pegasus.common.util.CommonProperties
Pipeline - Class in edu.isi.pegasus.planner.dax.examples
Pipeline() - Constructor for class edu.isi.pegasus.planner.dax.examples.Pipeline
PLANNER_ARGUMENTS_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The arguments passed to the planner.
PLANNER_CACHE - Static variable in class edu.isi.pegasus.planner.classes.PegasusBag
  The constant to be passed to the accessor functions to get or set the handle to the planner cache for planning purposes.
PLANNER_CACHE_REPLICA_CATALOG_IMPLEMENTER - Static variable in class edu.isi.pegasus.planner.classes.PlannerCache
  The name of the Replica Catalog Implementer that serves as the source for cache files.
PLANNER_CACHE_REPLICA_CATALOG_KEY - Static variable in class edu.isi.pegasus.planner.classes.PlannerCache
  The name of the source key for Replica Catalog Implementer that serves as cache
PLANNER_METRICS - Static variable in class edu.isi.pegasus.planner.classes.PegasusBag
  The constant to be passed to the accessor functions to get or set the the planner metrics that are logged during the planning purpose
PLANNER_OPTIONS - Static variable in class edu.isi.pegasus.planner.classes.PegasusBag
  The constant to be passed to the accessor functions to get or set the options passed to the planner.
PLANNER_VERSION_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The Key for the planner version
PlannerCache - Class in edu.isi.pegasus.planner.classes
  A data class that is used to track the various files placed by the mapper on the staging sites for the workflow.
PlannerCache() - Constructor for class edu.isi.pegasus.planner.classes.PlannerCache
  The default constructor.
PlannerMetrics - Class in edu.isi.pegasus.planner.classes
  A Data class containing the metrics about the planning instance.
PlannerMetrics() - Constructor for class edu.isi.pegasus.planner.classes.PlannerMetrics
  The default metrics.
PlannerOptions - Class in edu.isi.pegasus.planner.classes
  Holds the information about thevarious options which user specifies to the Concrete Planner at runtime.
PlannerOptions() - Constructor for class edu.isi.pegasus.planner.classes.PlannerOptions
  Default Constructor.
PlannerOptions.CLEANUP_OPTIONS - Enum in edu.isi.pegasus.planner.classes
  The various cleanup options supported by the planner
plannerUsesPMC() - Method in class edu.isi.pegasus.planner.classes.PegasusBag
  A convenice method to return whether the planner used PMC or not
PMC - Class in edu.isi.pegasus.planner.code.generator
  This code generator generates a shell script in the submit directory.
PMC() - Constructor for class edu.isi.pegasus.planner.code.generator.PMC
  The default constructor.
PMC_PRIORITY_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  A key to designate a priority to the jobs run by pegasus-mpi-cluster.
PMC_REQUEST_CPUS_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  A key to designate the number of CPU's requested by pegasus-mpi-cluster.
PMC_REQUEST_MEMORY_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  A key to designate the memory required by a job in MB by pegasus-mpi-cluster.
PMC_TASK_ARGUMENTS - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  Arguments that need to be passed to the PMC clustering executable.
pmcBasename(ADag) - Method in class edu.isi.pegasus.planner.code.generator.PMC
  Returns the basename for the pmc file for the dag
PoolConfig - Class in edu.isi.pegasus.planner.catalog.site.impl.old.classes
  A data class to store information about the various remote sites.
PoolConfig() - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.old.classes.PoolConfig
  The default constructor.
PoolInfoProvider - Class in edu.isi.pegasus.planner.catalog.site.impl.old
  This is an abstract class which defines the interface for the information providers like sites.xml, sites.catalog.
PoolInfoProvider() - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
PoolMode - Class in edu.isi.pegasus.planner.catalog.site.impl.old
  This class determines at runtime which implementing class to use as a Pool Handle.
PoolMode() - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.old.PoolMode
poolNotFoundMsg(String, String) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  This generates a error message for pool not found in the pool config file.
PoolTransfer() - Constructor for class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.PoolTransfer
  The default constructor.
PoolTransfer(String, boolean, int) - Constructor for class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.PoolTransfer
  Convenience constructor.
PoolTransfer() - Constructor for class edu.isi.pegasus.planner.transfer.refiner.Bundle.PoolTransfer
  The default constructor.
PoolTransfer(String, boolean, int) - Constructor for class edu.isi.pegasus.planner.transfer.refiner.Bundle.PoolTransfer
  Convenience constructor.
popEvent() - Method in class edu.isi.pegasus.common.logging.format.AbstractLogFormatter
  Pop the event on top of the internal stack.
popEvent() - Method in interface edu.isi.pegasus.common.logging.LogFormatter
  Pop the event on top of the internal stack.
populate(SiteInfo) - Method in class edu.isi.pegasus.planner.parser.SiteCatalogTextParser
  Populates all the attributes except the handle, associated with the site in the `SiteInfo` object.
populatePeriodicReleaseAndRemoveInJob(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Populates the periodic release and remove values in the job.
populateSiteMap(List) - Method in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  Populates the number of free nodes for each site, by querying the Site Catalog.
populateSiteMaps(String) - Method in class edu.isi.pegasus.planner.selector.replica.Restricted
  Builds up the set of preferred and ignored sites for a site.
populateTC(InputStream) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Populates the internal copy of the transformation catalog from a byte stream (input stream).
populateTC() - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Populates the internal copy of the transformation catalog from the file containing the transformation catalog in the 6 column format.
populateTC(Reader) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Adds multiple entries into the TC.
port - Variable in class edu.isi.pegasus.gridftp.GridFTPConnection
port - Static variable in class edu.isi.pegasus.planner.invocation.SimpleServer
PORTFOLIO_ID - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
PORTFOLIO_ID - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
POST_SCRIPT_ARGUMENTS_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The name of the key that determines the arguments that need to be passed to the postscript.
POST_SCRIPT_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The name of the key that determines what post script is to be invoked when the job completes.
POST_SCRIPT_PATH_PREFIX - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The key prefix that determines the path to a postscript
POST_SCRIPT_REPLACEMENT_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The key name for the post script that is put in the .dag file.
POST_SCRIPT_SCOPE_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The key prefix that determines the path to a postscript
postProcess(TransferJob) - Method in class edu.isi.pegasus.planner.transfer.implementation.AbstractMultipleFTPerXFERJob
  An optional method that allows the derived classes to do their own post processing on the the transfer job before it is returned to the calling module.
postProcess(TransferJob) - Method in class edu.isi.pegasus.planner.transfer.implementation.GUC
  Makes sure the stdin is transferred by the Condor File Transfer Mechanism.
postProcess(TransferJob) - Method in class edu.isi.pegasus.planner.transfer.implementation.TPTGUC
  Makes sure the stdin is transferred by the Condor File Transfer Mechanism.
postProcess(TransferJob) - Method in class edu.isi.pegasus.planner.transfer.implementation.Transfer
  An optional method that allows the derived classes to do their own post processing on the the transfer job before it is returned to the calling module.
postScript(String) - Method in class edu.isi.pegasus.planner.code.GridStartFactory
  Returns the cached implementation of `POSTScript` from the implementing class table.
POSTScript - Interface in edu.isi.pegasus.planner.code
  The interface that defines the creation of a POSTSCRIPT for a job.
POSTSCRIPT_ARGUMENTS_FOR_ONLY_ROTATING_LOG_FILE - Static variable in class edu.isi.pegasus.planner.code.gridstart.PegasusExitCode
  The arguments for pegasus-exitcode when you only want the log files to be rotated.
POSTSCRIPT_ARGUMENTS_FOR_ONLY_ROTATING_LOG_FILE - Static variable in class edu.isi.pegasus.planner.refiner.createdir.DefaultImplementation
  The arguments for pegasus-exitcode when you only want the log files to be rotated.
POSTSCRIPT_ARGUMENTS_FOR_ONLY_ROTATING_LOG_FILE - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The arguments for pegasus-exitcode when you only want the log files to be rotated.
POSTSCRIPT_IMPLEMENTING_CLASS_TABLE - Static variable in class edu.isi.pegasus.planner.code.GridStartFactory
  A table that associates POSTScript implementing classes with their SHORT_NAMES.
PPS - Interface in edu.isi.pegasus.planner.provenance.pasoa
  Pegasus P-assertion Support interface Classes that implement this interface assist in the creation of p-assertions for the Pegasus workflow refinement system.
PPSFactory - Class in edu.isi.pegasus.planner.provenance.pasoa.pps
  The factory for instantiating an XMLProducer.
PPSFactory() - Constructor for class edu.isi.pegasus.planner.provenance.pasoa.pps.PPSFactory
PPSFactoryException - Exception in edu.isi.pegasus.planner.provenance.pasoa.pps
  Class to notify of failures while instantiating PPS implementations.
PPSFactoryException(String) - Constructor for exception edu.isi.pegasus.planner.provenance.pasoa.pps.PPSFactoryException
  Constructs a `PPSFactoryException` with no detail message.
PPSFactoryException(String, String) - Constructor for exception edu.isi.pegasus.planner.provenance.pasoa.pps.PPSFactoryException
  Constructs a `PPSFactoryException` with the specified detailed message.
PPSFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.provenance.pasoa.pps.PPSFactoryException
  Constructs a `PPSFactoryException` with the specified detailed message and a cause.
PPSFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.planner.provenance.pasoa.pps.PPSFactoryException
  Constructs a `PPSFactoryException` with the specified detailed message and a cause.
PRE_SCRIPT_ARGUMENTS_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The name of the key that determines the arguments that need to be passed to the postscript.
PRE_SCRIPT_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The name of the key that determines what pre script is to be invoked when the job is run.
PRE_SCRIPT_REPLACEMENT_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The key name for the pre script that is put in the .dag file.
prec - Variable in class edu.isi.pegasus.planner.provisioner.Estimator
prefer(String, String) - Method in class edu.isi.pegasus.planner.selector.replica.Restricted
  Returns a boolean indicating whether a source site is to be preffered for staging to a destination site
PREFIX_PROPERTIES - Static variable in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  The prefix of the property names that specify the environment variables that need to be set before calling out to the site selector.
PREFIX_TEMPORARY_FILE - Static variable in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  The prefix to be used while creating a temporary file to pass to the external siteselector.
prepareInputFile(Job, List) - Method in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  Writes job knowledge into the temporary file passed to the external site selector.
prepareSTDINAndAssociateCredentials(TransferJob, Collection, String, int) - Method in class edu.isi.pegasus.planner.transfer.implementation.AbstractMultipleFTPerXFERJob
  Prepares the stdin for the transfer job.
preserveParserLineBreaks() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a boolean indicating whether to preserver line breaks.
PRIMARY_METRICS_SERVER_URL_ENV_VARIABLE - Static variable in class edu.isi.pegasus.planner.code.generator.Metrics
  The name of the environment variable that overrides the default server url
print(boolean) - Static method in class edu.isi.pegasus.common.util.Boolean
  Converts a boolean value into a strict representation of it.
print() - Method in class edu.isi.pegasus.planner.provisioner.Edge
print() - Method in class edu.isi.pegasus.planner.provisioner.Node
print() - Method in class edu.isi.pegasus.planner.transfer.RemoteTransfer
  Prints out the third party state for the various sites.
print() - Method in class edu.isi.pegasus.planner.transfer.TPT
  Prints out the third party state for the various sites.
printDagString(String) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Writes a string to the dag file.
printList(List) - Method in class edu.isi.pegasus.planner.cluster.Horizontal
  A utility method to print short description of jobs in a list.
printLongVersion() - Method in class edu.isi.pegasus.planner.client.CPlanner
  Prints the long description, displaying in detail what the various options to the command stand for.
printLongVersion() - Method in class edu.isi.pegasus.planner.client.Executable
  This method is used to print the long version of the command.
printLongVersion() - Method in class edu.isi.pegasus.planner.client.PartitionDAX
  Generated the long version of the help on the stdout.
printLongVersion() - Method in class edu.isi.pegasus.planner.client.PegasusGetSites
  Prints out the long help.
printLongVersion() - Method in class edu.isi.pegasus.planner.client.RankDAX
  This method is used to print the long version of the command.
printLongVersion() - Method in class edu.isi.pegasus.planner.client.SCClient
printLongVersion() - Method in class edu.isi.pegasus.planner.client.TCClient
printLongVersion() - Method in class edu.isi.pegasus.planner.client.TCConverter
printLongVersion() - Method in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  Prints the long description, displaying in detail what the various options to the command stand for.
printNodes() - Method in class edu.isi.pegasus.planner.provisioner.OccupationDiagram
printShortHelp() - Method in class edu.isi.pegasus.planner.client.RankDAX
  This is used to print the short version of the command.
printShortVersion() - Method in class edu.isi.pegasus.planner.client.CPlanner
  Prints out a short description of what the command does.
printShortVersion() - Method in class edu.isi.pegasus.planner.client.Executable
  This is used to print the short version of the command.
printShortVersion() - Method in class edu.isi.pegasus.planner.client.PartitionDAX
  Generates the short version of the help on the stdout.
printShortVersion() - Method in class edu.isi.pegasus.planner.client.PegasusGetSites
  The short help version.
printShortVersion() - Method in class edu.isi.pegasus.planner.client.RankDAX
  This is used to print the short version of the command.
printShortVersion() - Method in class edu.isi.pegasus.planner.client.SCClient
  Returns the short help.
printShortVersion() - Method in class edu.isi.pegasus.planner.client.TCClient
printShortVersion() - Method in class edu.isi.pegasus.planner.client.TCConverter
  Prints the short help.
printShortVersion() - Method in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  Prints out a short description of what the command does.
printVector(String, Vector) - Method in class edu.isi.pegasus.planner.refiner.Engine
  It prints the contents of the Vector, with the first line being the heading.
printXMLFormat(TransformationStore) - Static method in class edu.isi.pegasus.planner.catalog.transformation.client.TCFormatUtility
  Prints the transformations in XML format
PRIORITY_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The name of the key that specifies the priority for the job.
PRIORITY_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The name of the key that determines the priority a job is assigned.
Proc - Class in edu.isi.pegasus.planner.invocation
  The proc element.
Proc() - Constructor for class edu.isi.pegasus.planner.invocation.Proc
  The default constructor
PROCESS_CATALOG_IMPL_PROPERTY - Static variable in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  The property that designates which Process catalog impl to pick up.
processingInstruction(String, String) - Method in class edu.isi.pegasus.planner.parser.InvocationParser
  Receive a processing instruction.
Processor - Class in edu.isi.pegasus.planner.selector.site.heft
  A data class that is used to simulate a processor on a site.
Processor() - Constructor for class edu.isi.pegasus.planner.selector.site.heft.Processor
  The default constructor.
processParents(Job, Collection<GraphNode>) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  It processes a nodes parents and determines if nodes are to be added or not.
PROFILE - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  The constant to be passed to the accessor functions to get or set the list of `Profile` objects for the remote site.
profile - Variable in class edu.isi.pegasus.planner.catalog.transformation.client.Client
Profile - Class in edu.isi.pegasus.planner.classes
  This Class hold informations about profiles associated with a tc.
Profile() - Constructor for class edu.isi.pegasus.planner.classes.Profile
  C'tpr for the class;
Profile(String, String, String) - Constructor for class edu.isi.pegasus.planner.classes.Profile
  This constructor allows to set the namespace , key and value of the PoolProfile.
profile - Variable in class edu.isi.pegasus.planner.client.TCClient
Profile - Class in edu.isi.pegasus.planner.dax
  Profile Object for the DAX API
Profile(String, String) - Constructor for class edu.isi.pegasus.planner.dax.Profile
  Create a new Profile object
Profile(String, String, String) - Constructor for class edu.isi.pegasus.planner.dax.Profile
  Create a new Profile object
Profile(Profile.NAMESPACE, String, String) - Constructor for class edu.isi.pegasus.planner.dax.Profile
Profile(Profile) - Constructor for class edu.isi.pegasus.planner.dax.Profile
  Copy constructor
PROFILE - Static variable in class edu.isi.pegasus.planner.parser.tokens.SiteCatalogReservedWord
  token value for the reserver word "profile".
PROFILE - Static variable in class edu.isi.pegasus.planner.parser.tokens.TransformationCatalogReservedWord
  token value for the reserved word "profile".
Profile.NAMESPACE - Enum in edu.isi.pegasus.planner.dax
  Supported NAMESPACES.
ProfileParser - Class in edu.isi.pegasus.common.util
  Converts between the string version of a profile specification and the parsed triples and back again.
ProfileParser() - Constructor for class edu.isi.pegasus.common.util.ProfileParser
ProfileParserException - Exception in edu.isi.pegasus.common.util
  This class is used to signal errors while parsing profile strings
ProfileParserException(String, int) - Constructor for exception edu.isi.pegasus.common.util.ProfileParserException
ProfileParserException(String, int, Throwable) - Constructor for exception edu.isi.pegasus.common.util.ProfileParserException
Profiles - Class in edu.isi.pegasus.planner.catalog.classes
  Maintains profiles for different namespaces.
Profiles() - Constructor for class edu.isi.pegasus.planner.catalog.classes.Profiles
  The default constructor.
profiles - Variable in class edu.isi.pegasus.planner.catalog.transformation.client.Client
Profiles.NAMESPACES - Enum in edu.isi.pegasus.planner.catalog.classes
  The enumeration of valid namespaces.
PROG - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
PROG_SETUP - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
prop(String, Object) - Method in class edu.isi.pegasus.planner.client.DAXValidator
  Sets a SAX property while capturing failed features right here.
PROPERTIES_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The path to the pegasus properties file
PROPERTIES_PREFIX - Static variable in class edu.isi.pegasus.common.logging.LogManager
  Prefix for the property subset to use with the LogManager
PROPERTY_FILENAME - Static variable in class edu.isi.pegasus.common.util.CommonProperties
  Basename of the file to read to obtain system properties
PROPERTY_IGNORE_SUFFIX - Static variable in class edu.isi.pegasus.planner.selector.replica.Restricted
  The property suffix for determining the ignored sites for a site x.
PROPERTY_KEY - Static variable in class edu.isi.pegasus.planner.transfer.mapper.OutputMapperFactory
  The prefix for the property subset for connecting to the individual catalogs.
PROPERTY_PREFER_SUFFIX - Static variable in class edu.isi.pegasus.planner.selector.replica.Restricted
  The property suffix for determining the preferred sites for a site x.
PROPERTY_PREFIX - Static variable in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  The prefix for the property subset for connecting to the individual catalogs.
PROPERTY_PREFIX - Static variable in class edu.isi.pegasus.planner.selector.replica.Regex
  The property prefix for all Regex rank property.
PROPERTY_PREFIX - Static variable in class edu.isi.pegasus.planner.selector.replica.Restricted
  The property prefix for all properties used by this selector.
PROPERTY_PREFIX - Static variable in class edu.isi.pegasus.planner.transfer.mapper.impl.Fixed
  The prefix for the property subset for this mapper implementation
PROPERTY_PREFIX - Static variable in class edu.isi.pegasus.planner.transfer.mapper.impl.Replica
  The prefix for the property subset for connecting to the individual catalogs.
propertyNames() - Method in class edu.isi.pegasus.common.util.CommonProperties
  Accessor: enumerate all keys known to this property collection
propertyTable() - Static method in class edu.isi.pegasus.planner.transfer.RemoteTransfer
  Singleton access to the type table Contains the mapping of a property to the third party transfer type
propertyTable() - Static method in class edu.isi.pegasus.planner.transfer.TPT
  Singleton access to the type table Contains the mapping of a property to the third party transfer type
props - Variable in class edu.isi.pegasus.common.util.Version
Proxy - Class in edu.isi.pegasus.common.credential.impl
  A convenice class that allows us to determine the path to the user proxy.
Proxy() - Constructor for class edu.isi.pegasus.common.credential.impl.Proxy
  The default constructor.
PROXY_KEY - Static variable in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  The key that if set, specifies the proxy to be picked up while connecting to the RLS.
purgePools() - Method in class edu.isi.pegasus.planner.refiner.AuthenticateEngine
  It removies from the list of pools the pool that was not authenticated against.
pushedChildren(long) - Method in class edu.isi.pegasus.planner.provisioner.Node
pushedParents(long) - Method in class edu.isi.pegasus.planner.provisioner.Node
put(CredentialHandler.TYPE, CredentialHandler) - Method in class edu.isi.pegasus.common.credential.CredentialHandlerFactory
  Inserts an entry into the implementing class table.
put(String, ReplicaLocation) - Method in class edu.isi.pegasus.planner.classes.ReplicaStore
  Inserts entry in the store overwriting any existing entry.
put(String, Object) - Method in class edu.isi.pegasus.planner.cluster.aggregator.JobAggregatorInstanceFactory
  Inserts an entry into the implementing class table.
put(String, Object) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactory
  Inserts an entry into the implementing class table.
put(Object, Object) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2Graph
  It puts the key and the value in the internal map.
put(String, RemoteTransfer.TransferState) - Method in class edu.isi.pegasus.planner.transfer.RemoteTransfer
  Inserts an entry in to the State Map, that maintains state of various sites.
put(String, TPT.TPTState) - Method in class edu.isi.pegasus.planner.transfer.TPT
  Inserts an entry in to the State Map, that maintains state of various sites.

## Q

query - Variable in class edu.isi.pegasus.planner.client.TCClient
QUERY_ARGUMENTS - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
QUERY_ARGUMENTS - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
QUERY_ID - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
QUERY_ID - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
QUERY_INPUT - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
QUERY_INPUT - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
QUERY_NAME - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
QUERY_NAME - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
QUERY_NUMBER - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
QUERY_NUMBER - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
QUERY_OUTPUT - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
QUERY_OUTPUT - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
QUERY_RESPONSE - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
QUERY_RESPONSE - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
QUEUED_TEMPLATES - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
quote(String, boolean) - Static method in class edu.isi.pegasus.common.util.XMLOutput
  Escapes certain characters inappropriate for XML content output.
quote(Escape, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
  Quotes a string only if necessary.
quote(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Quotes a string that may contain special SQL characters.
quote(Escape, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Quotes a string only if necessary.
quote(Escape, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Quotes a string only if necessary.
quote(String) - Static method in class edu.isi.pegasus.planner.catalog.transformation.client.TCFormatUtility
  Quotes a String.
quote(String) - Static method in class edu.isi.pegasus.planner.code.generator.condor.CondorQuoteParser
  Parses a string and condor quotes it.
quote(String, boolean) - Static method in class edu.isi.pegasus.planner.code.generator.condor.CondorQuoteParser
  Parses a string and condor quotes it.
quote(String) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.GLite
  Condor Quotes a string
quote(String) - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Condor Quotes a string
QuotedString - Class in edu.isi.pegasus.planner.parser.tokens
  Class to capture the content within a quoted string.
QuotedString(String) - Constructor for class edu.isi.pegasus.planner.parser.tokens.QuotedString
  Initializes an instance of a quoted string.
quoteTransferURL() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns whether to introduce quotes around url's before handing to g-u-c and condor.

## R

RAM - Class in edu.isi.pegasus.planner.invocation
  The RAM element.
RAM() - Constructor for class edu.isi.pegasus.planner.invocation.RAM
  The default constructor
Random - Class in edu.isi.pegasus.planner.selector.site
  A random site selector that maps to a job to a random pool, amongst the subset of pools where that particular job can be executed.
Random() - Constructor for class edu.isi.pegasus.planner.selector.site.Random
  The default constructor.
Random - Class in edu.isi.pegasus.planner.selector.transformation
  This implemenation of the TCSelector selects a random TransformationCatalogEntry from a List of entries.
Random() - Constructor for class edu.isi.pegasus.planner.selector.transformation.Random
Rank - Class in edu.isi.pegasus.planner.ranking
  The Rank class that ranks the DAX'es
Rank() - Constructor for class edu.isi.pegasus.planner.ranking.Rank
  The default constructor.
rank(Collection<String>) - Method in class edu.isi.pegasus.planner.ranking.Rank
  Ranks the daxes, and returns a sort collection of Ranking objects.
Rank(int, String) - Constructor for class edu.isi.pegasus.planner.selector.replica.Regex.Rank
  The default constructor.
RankDAX - Class in edu.isi.pegasus.planner.client
  A client that ranks the DAX'es corresponding to the request id.
RankDAX() - Constructor for class edu.isi.pegasus.planner.client.RankDAX
  The default constructor.
Ranking - Class in edu.isi.pegasus.planner.ranking
  A Data class that associates a DAX with the rank.
Ranking(String, long) - Constructor for class edu.isi.pegasus.planner.ranking.Ranking
  The overloaded constructor.
rb - Variable in class edu.isi.pegasus.planner.provisioner.Node
RC_DERIVATION_NAME - Static variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  The derivation name for the transfer jobs.
RC_DERIVATION_NS - Static variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  The derivation namespace for the transfer jobs.
RC_DERIVATION_VERSION - Static variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  The version number for the derivations for registration jobs.
RC_TRANSFORMATION_NAME - Static variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  The logical name of the transformation used.
RC_TRANSFORMATION_NS - Static variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  The transformation namespace for the regostration jobs.
RC_TRANSFORMATION_VERSION - Static variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  The logical name of the transformation used.
RCClient - Class in edu.isi.pegasus.planner.client
  This class interfaces the with the replica catalog API to delve into the underlying true catalog without knowing (once instantiated) which one it is.
RCClient(String) - Constructor for class edu.isi.pegasus.planner.client.RCClient
  ctor: Constructs a new instance of the commandline interface to replica catalogs.
rcIterator() - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Returns an iterator to iterate through the list of ReplicaCatalogs that MRC is associated with.
READ_ONLY_KEY - Static variable in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  The name of the key that disables writing back to the cache file.
READ_ONLY_KEY - Static variable in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  The name of the key that disables writing back to the cache file.
READ_ONLY_KEY - Static variable in class edu.isi.pegasus.planner.transfer.mapper.impl.Replica
  The name of the key that disables writing back to the cache file.
readDAX() - Method in class edu.isi.pegasus.planner.provisioner.Estimator
readURLs(File) - Static method in class edu.isi.pegasus.gridftp.PegasusGridFTP
recursive - Variable in class edu.isi.pegasus.gridftp.RemoveCommand
redirect(OutputStream, String) - Method in class edu.isi.pegasus.common.util.StreamGobbler
  Sets the output stream to which to redirect the contents of the input stream.
reduce(ADag) - Method in class edu.isi.pegasus.planner.refiner.ReduceEdges
  Prunes redundant edges from the workflow.
reduce(Graph) - Method in class edu.isi.pegasus.planner.refiner.ReduceEdges
  Prunes redundant edges from the workflow.
reduceDependency(GraphNode) - Method in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  Reduces the number of edges between the nodes and it's parents.
ReduceEdges - Class in edu.isi.pegasus.planner.refiner
  An algorithm to reduce remove edges in the workflow, based on a DFS of a graph and doing least common ancestor tranversals to detect duplicate edges.
ReduceEdges() - Constructor for class edu.isi.pegasus.planner.refiner.ReduceEdges
reduceWorkflow(ADag, ReplicaCatalogBridge) - Method in class edu.isi.pegasus.planner.refiner.DataReuseEngine
  Reduces the workflow on the basis of the existence of lfn's in the replica catalog.
reduceWorkflow(Graph, ReplicaCatalogBridge) - Method in class edu.isi.pegasus.planner.refiner.DataReuseEngine
  Reduces the workflow on the basis of the existence of lfn's in the replica catalog.
REFINEMENT_CLUSTER - Static variable in interface edu.isi.pegasus.planner.provenance.pasoa.PPS
REFINEMENT_REDUCE - Static variable in interface edu.isi.pegasus.planner.provenance.pasoa.PPS
REFINEMENT_REGISTER - Static variable in interface edu.isi.pegasus.planner.provenance.pasoa.PPS
REFINEMENT_SITE_SELECT - Static variable in interface edu.isi.pegasus.planner.provenance.pasoa.PPS
REFINEMENT_STAGE - Static variable in interface edu.isi.pegasus.planner.provenance.pasoa.PPS
Refiner - Interface in edu.isi.pegasus.planner.refiner
  A first cut at a separate refiner interface.
Refiner - Interface in edu.isi.pegasus.planner.transfer
  The refiner interface, that determines the functions that need to be implemented to add various types of transfer nodes to the workflow.
REFINER_NAME - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The name of the refiner for purposes of error logging
REFINER_NAME - Static variable in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  The name of the refiner for purposes of error logging
REFINER_NAME - Static variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  The name of the refiner for purposes of error logging
RefinerFactory - Class in edu.isi.pegasus.planner.transfer.refiner
  The factory class that loads an appropriate Transfer Refiner class, as specified by the properties.
RefinerFactory() - Constructor for class edu.isi.pegasus.planner.transfer.refiner.RefinerFactory
refinerPreferenceForLocalTransferJobs(int) - Method in class edu.isi.pegasus.planner.transfer.AbstractRefiner
  Boolean indicating Refiner preference for transfer jobs to run locally.
refinerPreferenceForLocalTransferJobs(int) - Method in interface edu.isi.pegasus.planner.transfer.Refiner
  Boolean indicating Refiner preference for transfer jobs to run locally.
refinerPreferenceForTransferJobLocation() - Method in class edu.isi.pegasus.planner.transfer.AbstractRefiner
  Boolean indicating whether the Transfer Refiner has a preference for where a transfer job is run.
refinerPreferenceForTransferJobLocation() - Method in interface edu.isi.pegasus.planner.transfer.Refiner
  Boolean indicating whether the Transfer Refiner has a preference for where a transfer job is run.
Regex - Class in edu.isi.pegasus.planner.catalog.replica.impl
  This class implements a replica catalog on top of a simple file with regular expression based entries, which contains two or more columns.
Regex() - Constructor for class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Default empty constructor creates an object that is not yet connected to any database.
Regex - Class in edu.isi.pegasus.planner.selector.replica
  A replica selector that allows the user to specific regex expressions that can be used to rank various PFN's returned from the Replica Catalog for a particular LFN.
Regex(PegasusProperties) - Constructor for class edu.isi.pegasus.planner.selector.replica.Regex
  The overloaded constructor, that is called by load method.
Regex.Rank - Class in edu.isi.pegasus.planner.selector.replica
  A Data class that allows us to compile a regex expression and associate a rank value with it.
REGEX_KEY - Static variable in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
REGISTER_PREFIX - Static variable in interface edu.isi.pegasus.planner.transfer.Refiner
  The prefix for the jobs which register the newly materialized files in the Replica Catalog.
registerGridStart(String, GridStart) - Method in class edu.isi.pegasus.planner.code.GridStartFactory
  Inserts an entry into the implementing class table.
registerPOSTScript(String, POSTScript) - Method in class edu.isi.pegasus.planner.code.GridStartFactory
  Inserts an entry into the implementing class table.
REGISTRATION_UNIVERSE - Static variable in class edu.isi.pegasus.planner.refiner.Engine
registrationIntroducedFor(String, String) - Method in class edu.isi.pegasus.planner.provenance.pasoa.pps.Empty
  registrationIntroducedFor
registrationIntroducedFor(String, String) - Method in interface edu.isi.pegasus.planner.provenance.pasoa.PPS
Regular - Class in edu.isi.pegasus.planner.invocation
  This class is the container for a regular file object.
Regular() - Constructor for class edu.isi.pegasus.planner.invocation.Regular
  Default c'tor: Construct a hollow shell and allow further information to be added later.
Regular(String) - Constructor for class edu.isi.pegasus.planner.invocation.Regular
  Constructs a regular file.
RELEASE_ATTRIBUTE_KEY - Static variable in class edu.isi.pegasus.planner.invocation.Uname
  The release attribute for the uname
REMOTE_INITIALDIR_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the key that sets a remote initial dir for a condor globus job.
REMOTE_PREFIX - Static variable in interface edu.isi.pegasus.planner.transfer.Refiner
  The prefix for all remote transfer jobs
REMOTE_SHOULD_TRANSFER_FILES_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.CondorC
  The corresponding remote kye name that designates that files should be transferred via Condor File Transfer mechanism.
REMOTE_SHOULD_TRANSFER_FILES_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The corresponding remote kye name that designates that files should be transferred via Condor File Transfer mechanism.
REMOTE_UNIVERSE_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.CondorC
  The constant for the remote universe key.
REMOTE_UNIVERSE_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The name of the key that denotes the remote condor universe key.
REMOTE_WHEN_TO_TRANSFER_OUTPUT_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.CondorC
  The corresponding name of the remote key that designated when to transfer output.
REMOTE_WHEN_TO_TRANSFER_OUTPUT_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The corresponding name of the remote key that designated when to transfer output.
RemoteTransfer - Class in edu.isi.pegasus.planner.transfer
  A common class, that builds up the state from the properties to determine whether a user wants certain type of transfer jobs for particular site to run remotely.
RemoteTransfer() - Constructor for class edu.isi.pegasus.planner.transfer.RemoteTransfer
  The default constructor.
RemoteTransfer(PegasusProperties) - Constructor for class edu.isi.pegasus.planner.transfer.RemoteTransfer
  The overloaded constructor.
RemoteTransfer.TransferState - Class in edu.isi.pegasus.planner.transfer
  An inner class that holds the state for a particular site,as to whether to execute transfers remotely or not.
remove(GridFTPConnection, File) - Method in class edu.isi.pegasus.gridftp.RemoveCommand
remove(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Removes all mappings for an LFN from the replica catalog.
remove(Set) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Removes all mappings for a set of LFNs.
remove(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
remove(Set) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
remove(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Removes all mappings for an LFN from the replica catalog.
remove(Set) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Removes all mappings for a set of LFNs.
remove(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Removes all mappings for an LFN from the replica catalog.
remove(Set) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Removes all mappings for a set of LFNs.
remove(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Removes all mappings for an LFN from the replica catalog.
remove(Set) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Removes all mappings for a set of LFNs.
remove(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Removes all mappings for an LFN from the replica catalog.
remove(Set) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Removes all mappings for a set of LFNs.
remove(String) - Method in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Removes all mappings for an LFN from the replica catalog.
remove(Set) - Method in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Removes all mappings for a set of LFNs.
remove(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM
remove(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML
  Not yet implemented as yet.
remove(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  Not yet implemented as yet.
remove(String) - Method in interface edu.isi.pegasus.planner.catalog.SiteCatalog
  Removes a site catalog entry matching the the handle.
remove(Job) - Method in class edu.isi.pegasus.planner.classes.ADag
  Removes a particular job from the workflow.
remove(String) - Method in class edu.isi.pegasus.planner.classes.ADag
  Removes a node from the Graph.
remove(String) - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Removes a node from the Graph.
remove() - Method in class edu.isi.pegasus.planner.namespace.Namespace.EmptyIterator
  Returns a false, as no removal
remove(String) - Method in interface edu.isi.pegasus.planner.partitioner.graph.Graph
  Removes a node from the Graph.
remove() - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph.BottomUpIterator
  Method is not supported.
remove() - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph.MapGraphIterator
  Method is not supported.
remove(String) - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph
  Removes a node from the Graph.
remove() - Method in class edu.isi.pegasus.planner.partitioner.graph.TopologicalSortIterator
  Removes a node from the graph.
REMOVE_DIR_EXECUTABLE_BASENAME - Static variable in class edu.isi.pegasus.planner.refiner.RemoveDirectory
  The basename of the pegasus dirmanager executable.
REMOVE_DIR_SUFFIX - Static variable in class edu.isi.pegasus.planner.refiner.RemoveDirectory
  Constant suffix for the names of the remote directory nodes.
removeAllAttribute() - Method in class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  Removes all attributes associated with a PFN.
removeAllJob() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor: Removes all values from the job list.
removeAllStatCall() - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor: Removes all values from the stat list.
removeAttribute(String) - Method in class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  Removes a specific attribute.
removeByAttribute(String, Object) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Removes all entries from the replica catalog where the PFN attribute is found, and matches exactly the object value.
removeByAttribute(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Removes all entries associated with a particular resource handle.
removeByAttribute(String, Object) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
removeByAttribute(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
removeByAttribute(String, Object) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Removes all entries from the replica catalog where the PFN attribute is found, and matches exactly the object value.
removeByAttribute(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.JDBCRC
  Removes all entries associated with a particular resource handle.
removeByAttribute(String, Object) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Removes all entries from the replica catalog where the PFN attribute is found, and matches exactly the object value.
removeByAttribute(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  Removes all entries associated with a particular resource handle.
removeByAttribute(String, Object) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Removes all entries from the replica catalog where the PFN attribute is found, and matches exactly the object value.
removeByAttribute(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
  Removes all entries associated with a particular resource handle.
removeByAttribute(String, Object) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Removes all entries from the replica catalog where the PFN attribute is found, and matches exactly the object value.
removeByAttribute(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Removes all entries associated with a particular resource handle.
removeByAttribute(String, Object) - Method in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Removes all entries from the replica catalog where the PFN attribute is found, and matches exactly the object value.
removeByAttribute(String) - Method in interface edu.isi.pegasus.planner.catalog.ReplicaCatalog
  Removes all entries associated with a particular resource handle.
removeByLFN(String, String, String, String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Delete all entries in the transformation catalog for a give logical transformation and/or on a resource and/or of a particular type
removeByLFN(String, String, String, String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Delete all entries in the transformation catalog for a give logical tranformation and/or on a resource and/or of a particular type
removeByLFN(String, String, String, String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Delete all entries in the transformation catalog for a give logical transformation and/or on a resource and/or of a particular type
removeByLFN(String, String, String, String, TCType) - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Delete all entries in the transformation catalog for a give logical transformation and/or on a resource and/or of a particular type
removeByPFN(String, String, String, String, String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Delete all entries in the transformation catalog for pair of logical and physical transformation.
removeByPFN(String, String, String, String, String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Delete all entries in the transformation catalog for pair of logical and physical transformation.
removeByPFN(String, String, String, String, String, TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Delete all entries in the transformation catalog for pair of logical and physical transformation.
removeByPFN(String, String, String, String, String, TCType) - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Delete all entries in the transformation catalog for pair of logical and physical transformation.
removeBySiteID(String) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Delete all entries on a particular resource from the transformation catalog.
removeBySiteID(String) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Delete all entries on a particular resource from the transformation catalog.
removeBySiteID(String) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Delete all entries on a particular resource from the transformation catalog.
removeBySiteID(String) - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Delete all entries on a particular resource from the transformation catalog.
removeBySysInfo(SysInfo) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Deletes entries from the catalog which have a particular system information.
removeBySysInfo(SysInfo) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Deletes entries from the catalog which have a particular system information.
removeBySysInfo(SysInfo) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Deletes entries from the catalog which have a particular system information.
removeBySysInfo(SysInfo) - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Deletes entries from the catalog which have a particular system information.
removeByType(TCType, String) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Database
  Delete a particular type of transformation, and/or on a particular resource
removeByType(TCType, String) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
  Delete a particular type of transformation, and/or on a particular resource
removeByType(TCType, String) - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Delete a particular type of transformation, and/or on a particular resource
removeByType(TCType, String) - Method in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  Delete a particular type of transformation, and/or on a particular resource
removeChild(GraphNode) - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  Removes a child linkage to the node.
RemoveCommand - Class in edu.isi.pegasus.gridftp
  Implements the rm command for remote GridFTP servers
RemoveCommand(boolean, boolean) - Constructor for class edu.isi.pegasus.gridftp.RemoveCommand
removeDestURL() - Method in class edu.isi.pegasus.planner.classes.FileTransfer
  Removes a single destination url associated with the transfer.
removeDir(GridFTPConnection, File) - Method in class edu.isi.pegasus.gridftp.RemoveCommand
RemoveDirectory - Class in edu.isi.pegasus.planner.refiner
  Ends up creating a cleanup dag that deletes the remote directories that were created by the create dir jobs.
RemoveDirectory(ADag, PegasusBag, String) - Constructor for class edu.isi.pegasus.planner.refiner.RemoveDirectory
  The overloaded constructor that sets the dag for which we have to generated the cleanup dag for.
removeDirectoryKey(Job) - Method in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  Returns a boolean indicating whether to remove remote directory information or not from the job.
removeDirectoryKey(Job) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Returns a boolean indicating whether to remove remote directory information or not from the job.
removeFileServer(String, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  This is a soft state remove, that removes a file server from a particular pool entry.
removeFileURL(ReplicaCatalogEntry, String, boolean) - Method in class edu.isi.pegasus.planner.selector.replica.Default
  A convenience function that determines whether we should be removing a file URL from replica selection or not.
removeFileURL(String, String, String, boolean) - Method in class edu.isi.pegasus.planner.selector.replica.Default
  A convenience function that determines whether we should be removing a file URL from replica selection or not.
removeGridFtp(String, String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.Abstract
  This is a soft state remove, that removes a gridftp server from a particular pool entry.
removeGridFtp(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  Removes a grid ftp server from the soft state associated with the pool.
removeGridFtp(String, String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  This is a soft state remove, that removes a gridftp server from a particular pool entry.
removeGridGateway(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  This is a soft state remove, that removes a GridGateway from a particular site.
removeGridGateway(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  This is a soft state remove, that removes a GridGateway from a particular site.
removeGridGateway(String, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  This is a soft state remove, that removes a GridGateway from a particular site.
removeIn(Edge) - Method in class edu.isi.pegasus.planner.provisioner.Node
  remove a specified data dependency edge from this task
removeIPFilesForTransfer() - Method in class edu.isi.pegasus.planner.namespace.Condor
  Remove the input files that were designated for transfer using Condor File Transfer Mechanism.
removeJob(int) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor: Removes a specific job from the job list.
removeJobManager(String, String, String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.Abstract
  This is a soft state remove, that removes a jobmanager from a particular pool entry.
removeJobmanager(String, String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  It removes a jobmanager from the pool.
removeJobManager(String, String, String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  This is a soft state remove, that removes a jobmanager from a particular pool entry.
removeKey(Object) - Method in class edu.isi.pegasus.planner.namespace.Namespace
  Removes the key from the namespace.
removeOut(Edge) - Method in class edu.isi.pegasus.planner.provisioner.Node
  remove a specified data dependency edge from this task
removeOutputFilesForTransfer() - Method in class edu.isi.pegasus.planner.namespace.Condor
  Remove the output files that were designated for transfer using Condor File Transfer Mechanism.
removeParent(GraphNode) - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  Removes a parent linkage to the node.
removeResource(AuthenticateRequest) - Method in class edu.isi.pegasus.planner.refiner.Authenticate
  It tries to remove a resource from the soft state of the pool.
removeSourceURL() - Method in class edu.isi.pegasus.planner.classes.FileTransfer
  Removes a single source url associated with the transfer.
removeStatCall(int) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor: Removes a specific stat from the stat list.
removeURL(Map) - Method in class edu.isi.pegasus.planner.classes.FileTransfer
  Removes a single url from the map passed.
renderedToExecutableForm() - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Returns a boolean indicating whether a job has been rendered to an executable form or not
replaceJobs() - Method in class edu.isi.pegasus.planner.cluster.Horizontal
  The relations/edges are changed in local graph structure.
replacementKey(String) - Method in class edu.isi.pegasus.planner.namespace.Dagman
  Returns the replacement key that needs to be printed in .dag file in lieu of the key.
replacementValue(String) - Method in class edu.isi.pegasus.planner.namespace.Dagman
  Returns the replacement value that needs to be printed in .dag file for a key.
replaceProtocolFromURL(String) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  Replaces the gsiftp URL scheme from the url, and replaces it with the symlink url scheme and returns in a new object.
replaceSourceProtocolFromURL(ReplicaCatalogEntry) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  Replaces the SRM URL scheme from the url, and replaces it with the file url scheme and returns in a new object if replacement happens.
Replica - Class in edu.isi.pegasus.planner.transfer.mapper.impl
  This class connects to a Replica Catalog backend to determine where an output file should be placed on the output site.
Replica() - Constructor for class edu.isi.pegasus.planner.transfer.mapper.impl.Replica
  The default constructor.
REPLICA_CATALOG - Static variable in class edu.isi.pegasus.planner.classes.PegasusBag
  The constant to be passed to the accessor functions to get or set the handle to the replica catalog
REPLICA_CATALOG_URL_KEY - Static variable in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  The name of the URL key for the replica catalog impelementer to be picked up.
REPLICA_REG_JOB - Static variable in class edu.isi.pegasus.planner.classes.Job
  Denotes a job that registers in the replica mechanism the materialized files.
ReplicaCatalog - Interface in edu.isi.pegasus.planner.catalog
  This interface describes a minimum set of essential tasks required from a replica catalog.
ReplicaCatalog - Class in edu.isi.pegasus.planner.catalog.site.classes
  This data class describes the Replica Catalog associated with the site.
ReplicaCatalog() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.ReplicaCatalog
  The default constrcutor.
ReplicaCatalog(String, String) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.ReplicaCatalog
  The overloaded constructor.
ReplicaCatalogBridge - Class in edu.isi.pegasus.planner.refiner
  This coordinates the look up to the Replica Location Service, to determine the logical to physical mappings.
ReplicaCatalogBridge(ADag, PegasusBag) - Constructor for class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  The overloaded constructor.
ReplicaCatalogEntry - Class in edu.isi.pegasus.planner.catalog.replica
  The entry is a high-level logical structure representing the physical filename, the site handle, and optional attributes related to the PFN as one entity.
ReplicaCatalogEntry() - Constructor for class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  Default constructor for arrays.
ReplicaCatalogEntry(String) - Constructor for class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  Convenience constructor initializes the PFN.
ReplicaCatalogEntry(String, String) - Constructor for class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  Convenience constructor initializes the PFN and the resource handle.
ReplicaCatalogEntry(String, Map) - Constructor for class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  Standard constructor initializes the PFN and arbitrary attributes.
ReplicaCatalogException - Exception in edu.isi.pegasus.planner.catalog.replica
  Class to notify of failures.
ReplicaCatalogException() - Constructor for exception edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogException
ReplicaCatalogException(String) - Constructor for exception edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogException
  Constructs a `ReplicaCatalogException` with the specified detailed message.
ReplicaCatalogException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogException
  Constructs a `ReplicaCatalogException` with the specified detailed message and a cause.
ReplicaCatalogException(Throwable) - Constructor for exception edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogException
  Constructs a `ReplicaCatalogException` with the specified just a cause.
ReplicaFactory - Class in edu.isi.pegasus.planner.catalog.replica
  This factory loads a replica catalog, as specified by the properties.
ReplicaFactory() - Constructor for class edu.isi.pegasus.planner.catalog.replica.ReplicaFactory
ReplicaLocation - Class in edu.isi.pegasus.planner.classes
  A Data Class that associates a LFN with the PFN's.
ReplicaLocation() - Constructor for class edu.isi.pegasus.planner.classes.ReplicaLocation
  Default constructor.
ReplicaLocation(String, List) - Constructor for class edu.isi.pegasus.planner.classes.ReplicaLocation
  Overloaded constructor.
ReplicaLocation(String, Collection) - Constructor for class edu.isi.pegasus.planner.classes.ReplicaLocation
  Overloaded constructor.
replicaLocationIterator() - Method in class edu.isi.pegasus.planner.classes.ReplicaStore
  Returns an iterator to the list of `ReplicaLocation` objects stored in the store.
ReplicaSelector - Interface in edu.isi.pegasus.planner.selector
  A prototypical interface for a replica selector.
ReplicaSelectorFactory - Class in edu.isi.pegasus.planner.selector.replica
  A factory class to load the appropriate type of Replica Selector, as specified by the user at runtime in properties.
ReplicaSelectorFactory() - Constructor for class edu.isi.pegasus.planner.selector.replica.ReplicaSelectorFactory
ReplicaSelectorFactoryException - Exception in edu.isi.pegasus.planner.selector.replica
  Class to notify of failures while instantiating ReplicaSelector implementations.
ReplicaSelectorFactoryException(String) - Constructor for exception edu.isi.pegasus.planner.selector.replica.ReplicaSelectorFactoryException
  Constructs a `ReplicaSelectorFactoryException` with no detail message.
ReplicaSelectorFactoryException(String, String) - Constructor for exception edu.isi.pegasus.planner.selector.replica.ReplicaSelectorFactoryException
  Constructs a `ReplicaSelectorFactoryException` with the specified detailed message.
ReplicaSelectorFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.selector.replica.ReplicaSelectorFactoryException
  Constructs a `ReplicaSelectorFactoryException` with the specified detailed message and a cause.
ReplicaSelectorFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.planner.selector.replica.ReplicaSelectorFactoryException
  Constructs a `ReplicaSelectorFactoryException` with the specified detailed message and a cause.
ReplicaStore - Class in edu.isi.pegasus.planner.classes
  A Replica Store that allows us to store the entries from a replica catalog.
ReplicaStore() - Constructor for class edu.isi.pegasus.planner.classes.ReplicaStore
  Default constructor.
ReplicaStore(Map) - Constructor for class edu.isi.pegasus.planner.classes.ReplicaStore
  Overloaded constructor.
REQUEST_CPUS_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The Condor Key designating the numnber of cpu's to request.
REQUEST_DISK_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The Condor Key designating the amount of disk to request.
REQUEST_ID - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
REQUEST_ID - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
REQUEST_MEMORY_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The Condor Key designating the amount of memory to request.
requestInvalid() - Method in class edu.isi.pegasus.planner.classes.AuthenticateRequest
  Checks if the request is invalid or not.
REQUIREMENTS_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The name of the key that denotes the requirements of the job.
requiresCredentials() - Method in class edu.isi.pegasus.planner.classes.Job
  A boolean method indicating whether credentials are associated with the job
requiresToSetDirectory(Job) - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Returns a boolean indicating whether we need to set the directory for the job or not.
requiresToSetDirectory(Job) - Method in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  Returns a boolean indicating whether we need to set the directory for the job or not.
reset() - Method in interface edu.isi.pegasus.common.logging.Event
  Reset the internal log message buffer associated with the event
reset() - Method in class edu.isi.pegasus.common.logging.format.NetloggerEvent
  Reset the internal log message buffer associated with the event
reset() - Method in class edu.isi.pegasus.common.logging.format.SimpleEvent
  Reset the internal log message buffer associated with the event
reset() - Method in class edu.isi.pegasus.common.util.PegasusURL
  Resets the internal member variables
reset() - Method in class edu.isi.pegasus.planner.classes.Notifications
  Resets the internal invoke map.
reset(boolean) - Method in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  Resets the internal counters to zero.
reset() - Method in interface edu.isi.pegasus.planner.code.CodeGenerator
  Resets the Code Generator implementation.
reset() - Method in class edu.isi.pegasus.planner.code.generator.Abstract
  Resets the Code Generator implementation.
reset() - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Resets the Code Generator implementation.
reset() - Method in class edu.isi.pegasus.planner.code.generator.DAXReplicaStore
  Not implemented
reset() - Method in class edu.isi.pegasus.planner.code.generator.MonitordNotify
  Not implemented
reset() - Method in class edu.isi.pegasus.planner.code.generator.Stampede
reset() - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser3.Arguments
  Resets the internal buffer
reset() - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG.GrepCallback
  Resets the internal counters.
reset() - Method in class edu.isi.pegasus.planner.provenance.pasoa.producer.InMemory
  Resets the internal store.
reset() - Method in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  Resets the internal data structures.
reset(Graph) - Method in class edu.isi.pegasus.planner.refiner.ReduceEdges
  Resets internal depth and color counters associated with the nodes in the workflow, before doing any graph traversals.
resetCredentialTypes() - Method in class edu.isi.pegasus.planner.classes.Job
  Resets the credential types required by a job.
resetEdges() - Method in class edu.isi.pegasus.planner.classes.ADag
  Resets all the dependencies in the Graph, while preserving the nodes.
resetEdges() - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Resets all the dependencies in the Graph, while preserving the nodes.
resetEdges() - Method in interface edu.isi.pegasus.planner.partitioner.graph.Graph
  Resets all the dependencies in the Graph, while preserving the nodes.
resetEdges() - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  Reset all the edges associated with this node.
resetEdges() - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph
  Resets all the dependencies in the Graph, while preserving the nodes.
resetFileServers() - Method in class edu.isi.pegasus.planner.catalog.site.classes.DirectoryLayout
  Resets the internal collection of file servers
resetLFNAddOnCache() - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Hashed
  Resets the internal cache.
resetNotifications() - Method in class edu.isi.pegasus.planner.classes.Job
  Resets the notifications associated with the job
resetProfiles() - Method in class edu.isi.pegasus.planner.classes.Job
  Resets all the profiles associated with the job.
resetStageInMap(Map<String, BalancedCluster.PoolTransfer>, Implementation, int, boolean) - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  Signals that the traversal of the workflow is done.
resetStageInMap(Map<String, Bundle.PoolTransfer>, Implementation, Map<String, Job>, int, boolean, boolean) - Method in class edu.isi.pegasus.planner.transfer.refiner.Cluster
  Resets the stage in map and adds the stage in jobs for each site per level.
resetStageInMaps() - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  Resets the local and remote stage out maps.
resetStageInMaps() - Method in class edu.isi.pegasus.planner.transfer.refiner.Cluster
  Resets the stage in map and adds the stage in jobs for each site per level.
resetStageOutMap(Map<String, BalancedCluster.PoolTransfer>, boolean) - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  Resets a single map
resetStageOutMap(Map<String, Bundle.PoolTransfer>, boolean) - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  Resets a single map
resetStageOutMaps() - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster
  Resets the local and remote stage out maps.
resetStageOutMaps() - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle
  Resets the local and remote stage out maps.
resetStores() - Method in class edu.isi.pegasus.planner.classes.ADag
  Resets the replica and transformation stores;
resource - Variable in class edu.isi.pegasus.planner.catalog.transformation.client.Client
resource - Variable in class edu.isi.pegasus.planner.client.TCClient
RESOURCE_AD_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.ClassADSGenerator
  The class ad to store the execution pool at which the job is run.
RESOURCE_HANDLE - Static variable in class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  The (reserved) attribute name used for the resource handle.
Restricted - Class in edu.isi.pegasus.planner.selector.replica
  A replica selector, that allows the user to specify good sites and bad sites for staging in data to a compute site.
Restricted(PegasusProperties) - Constructor for class edu.isi.pegasus.planner.selector.replica.Restricted
  The overloaded constructor, that is called by load method.
retrieveFromCache(String) - Method in class edu.isi.pegasus.planner.refiner.ReplicaCatalogBridge
  Retrieves a location from the cache table, that contains the contents of the cache files specified at runtime.
retrieveLocationForWorkerPackageFromTC(String) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Retrieves the location for the pegasus worker package from the TC for a site
retrieveProfilesFromProperties() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Retrieves profiles from the properties
retrieveProfilesFromProperties(CommonProperties) - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Retrieves profiles from the properties
RETRY_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The name of the key that determines how many times DAGMAN should be retrying the job.
RETRY_LOGICAL_NAME - Static variable in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  The planner utility that needs to be called as a prescript.
RETRY_LOGICAL_NAME - Static variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The planner utility that needs to be called as a prescript.
RFT - Variable in class edu.isi.pegasus.planner.provisioner.Estimator
RFT - Variable in class edu.isi.pegasus.planner.provisioner.OccupationDiagram
rm(String) - Method in class edu.isi.pegasus.gridftp.GridFTPConnection
  Remove path
RM - Class in edu.isi.pegasus.planner.refiner.cleanup
  Use's RM to do removal of the files on the remote sites.
RM() - Constructor for class edu.isi.pegasus.planner.refiner.cleanup.RM
  The default constructor.
rmdir(String) - Method in class edu.isi.pegasus.gridftp.GridFTPConnection
  Remove directory path
ROOT_UUID_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The key for UUID of the workflow.
ROOT_WF_UUID_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.ClassADSGenerator
  The classad for the root workflow uuid
ROOT_WORKFLOW_UUID_PROPERTY_KEY - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
  The property key designated the root workflow uuid.
RoundRobin - Class in edu.isi.pegasus.planner.selector.site
  This ends up scheduling the jobs in a round robin manner.
RoundRobin() - Constructor for class edu.isi.pegasus.planner.selector.site.RoundRobin
  The default constructor.
RoundRobin - Class in edu.isi.pegasus.planner.selector.transformation
  This implementation of the Selector select a transformation from a list in a round robin fashion.
RoundRobin() - Constructor for class edu.isi.pegasus.planner.selector.transformation.RoundRobin
RoundRobin.NameValue - Class in edu.isi.pegasus.planner.selector.site
  A inner name value class that associates a string with an int value.
run() - Method in class edu.isi.pegasus.common.util.StreamGobbler
  The main method of the gobbler, that does all the work.
run(GridFTPURL) - Method in class edu.isi.pegasus.gridftp.Command
run(GridFTPURL) - Method in class edu.isi.pegasus.gridftp.ListCommand
run(GridFTPURL) - Method in class edu.isi.pegasus.gridftp.MakeDirectoryCommand
run(GridFTPURL) - Method in class edu.isi.pegasus.gridftp.RemoveCommand
run() - Method in class edu.isi.pegasus.planner.invocation.SimpleServerThread
run() - Method in class edu.isi.pegasus.planner.refiner.ThreadPool.AuthenticateThread
  The runnable method of the thread, that is called when the thread is started.
RunDirectoryFilenameFilter - Class in edu.isi.pegasus.planner.common
  A filename filter for identifying the run directory
RunDirectoryFilenameFilter() - Constructor for class edu.isi.pegasus.planner.common.RunDirectoryFilenameFilter
RunDirectoryFilenameFilter - Class in edu.isi.pegasus.planner.parser.pdax
  A filename filter for identifying the run directory
RunDirectoryFilenameFilter() - Constructor for class edu.isi.pegasus.planner.parser.pdax.RunDirectoryFilenameFilter
runInWorkDirectory() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns whether a job should be run in the work directory or not.
RUNNING_JOBS - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The constant to be passed to the accessor functions to get or set the number of running jobs attribute.
runPlanner() - Method in class edu.isi.pegasus.planner.refiner.MainEngine
  The main function which calls the other engines and does the necessary work.
RUNTIME_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the profile key when associated with a transformation in the transformation catalog gives expected runtime in seconds.
RUNTIME_PROFILE_KEY - Static variable in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  The pegasus profile key that gives us the expected runtime.
runTPTOnRemoteSite(String, int) - Method in class edu.isi.pegasus.planner.transfer.AbstractRefiner
  Returns whether the third party transfers for a particular site are to be run on the remote site or the submit host.
runTPTOnRemoteSite(String, int) - Method in interface edu.isi.pegasus.planner.transfer.Refiner
  Returns whether the third party transfers for a particular site are to be run on the remote site or the submit host.
runTransferOnLocalSite(Refiner, String, String, int) - Method in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Returns whether to run a transfer job on local site or not.
runTransferOnLocalSite(String, String, int) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  Returns whether to run a transfer job on local site or not.
runTransferRemotely(String, int) - Method in class edu.isi.pegasus.planner.transfer.AbstractRefiner
  Returns whether a Site prefers transfers to be run on it i.e remote transfers enabled.
runTransferRemotely(String, int) - Method in interface edu.isi.pegasus.planner.transfer.Refiner
  Returns whether a Site prefers transfers to be run on it i.e remote transfers enabled.

## S

S3_IMPLEMENTING_CLASS - Static variable in class edu.isi.pegasus.common.credential.CredentialHandlerFactory
S3CFG - Class in edu.isi.pegasus.common.credential.impl
  A convenience class that allows us to determine the path to the user s3cfg file.
S3CFG() - Constructor for class edu.isi.pegasus.common.credential.impl.S3CFG
  The default constructor.
S3CFG - Static variable in class edu.isi.pegasus.planner.namespace.ENV
  The name of the environment variable that specifies the s3cfg path
S3CFG_FILE_VARIABLE - Static variable in class edu.isi.pegasus.common.credential.impl.S3CFG
  The name of the environment variable that specifies the path to the s3cfg file.
S3CFG_FILE_VARIABLE - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
S3CFG_PEGASUS_PROFILE_KEY - Static variable in class edu.isi.pegasus.common.credential.impl.S3CFG
sanitize(List) - Method in class edu.isi.pegasus.planner.classes.ReplicaLocation
  Sanitizes a tuple list .
sanitize(ReplicaCatalogEntry) - Method in class edu.isi.pegasus.planner.classes.ReplicaLocation
  Sanitizes a tuple .
sanitizePath(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  A small utility method that santizes the url, converting it from relative to absolute.
sanitizePathForProperty(Properties, String) - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Santizes the value in the properties .
SANITY_CHECK_ERROR_MESSAGE_PREFIX - Static variable in class edu.isi.pegasus.planner.selector.replica.Local
  Sanity Check Error Message.
sanityCheck(File) - Static method in class edu.isi.pegasus.planner.client.CPlanner
  Checks the destination location for existence, if it can be created, if it is writable etc.
sanityCheck(File) - Static method in class edu.isi.pegasus.planner.client.RankDAX
  Checks the destination location for existence, if it can be created, if it is writable etc.
sanityCheck(File) - Static method in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  Checks the destination location for existence, if it can be created, if it is writable etc.
sanityCheck(File) - Static method in class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  Checks the destination location for existence, if it can be created, if it is writable etc.
sanityCheck(File) - Static method in class edu.isi.pegasus.planner.common.PegasusProperties
  Checks the destination location for existence, if it can be created, if it is writable etc.
sanityCheck(File) - Static method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Checks the destination location for existence, if it can be created, if it is writable etc.
sanityCheck(File) - Static method in class edu.isi.pegasus.planner.ranking.GetDAX
  Checks the destination location for existence, if it can be created, if it is writable etc.
sanityCheckOnDirectory(File) - Static method in class edu.isi.pegasus.common.logging.LogManager
  Checks the destination location for existence, if it can be created, if it is writable etc.
sanityCheckOnFile(File) - Static method in class edu.isi.pegasus.common.logging.LogManager
  Checks the destination location for existence, if it can be created, if it is writable etc.
sanityCheckOnProperties() - Method in class edu.isi.pegasus.planner.client.Executable
  Does a sanity check on the properties to make sure that all the required properties are loaded.
sanityCheckOnVersion(String) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser3
  Sanity check on the version that this parser works on.
SC_PARSER3_CLASS - Static variable in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParserFactory
  The SC Parser classname
SC_VERSION_2_0_0 - Static variable in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParserFactory
SC_VERSION_3_0_0 - Static variable in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParserFactory
SC_VERSION_4_0_0 - Static variable in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParserFactory
SC_XML3_FILE - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
SC_XML_FILE - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
ScannerException - Exception in edu.isi.pegasus.planner.parser
  This class is used to signal errors while scanning or parsing.
ScannerException(LineNumberReader, String) - Constructor for exception edu.isi.pegasus.planner.parser.ScannerException
ScannerException(int, String) - Constructor for exception edu.isi.pegasus.planner.parser.ScannerException
SCClient - Class in edu.isi.pegasus.planner.client
  A client to convert site catalog between different formats.
SCClient() - Constructor for class edu.isi.pegasus.planner.client.SCClient
  The default constructor.
schedule(ADag, List) - Method in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  Schedules the workflow using the heft.
schedule(ADag, List, String) - Method in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  Schedules the workflow according to the HEFT algorithm.
SCHEDULED_SITE - Static variable in class edu.isi.pegasus.planner.selector.site.heft.HeftBag
  The site where the job is scheduled.
scheduleJob(String, long, long) - Method in class edu.isi.pegasus.planner.selector.site.heft.Algorithm
  Schedules a job to a site.
scheduleJob(long, long) - Method in class edu.isi.pegasus.planner.selector.site.heft.Processor
  Schedules a job on to a processor.
scheduleJob(long, long) - Method in class edu.isi.pegasus.planner.selector.site.heft.Site
  Schedules a job to the site.
scheduleJobs(ADag, List) - Method in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  It schedules a list of jobs on the execution pools by calling out to the site selector specified.
SCHEDULER_TYPE() - Constructor for enum edu.isi.pegasus.planner.catalog.site.classes.GridGateway.SCHEDULER_TYPE
SCHEDULER_UNIVERSE - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.Condor
SCHEDULER_UNIVERSE - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The condor universe key value for scheduler universe.
SCHEMA_LOCATION - Static variable in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
  The "not-so-official" location URL of the DAX schema definition.
SCHEMA_LOCATION - Static variable in class edu.isi.pegasus.planner.catalog.site.classes.XML4PrintVisitor
  The "not-so-official" location URL of the DAX schema definition.
SCHEMA_LOCATION - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  The "not-so-official" location URL of the VDLx schema definition.
SCHEMA_LOCATION - Static variable in class edu.isi.pegasus.planner.dax.ADAG
  The "not-so-official" location URL of the DAX schema definition.
SCHEMA_LOCATION - Static variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  The "not-so-official" location URL of the invocation record definition.
SCHEMA_LOCATION - Static variable in class edu.isi.pegasus.planner.parser.ConfigXmlParser
  The "not-so-official" location URL of the VDLx schema definition.
SCHEMA_LOCATION - Static variable in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  The "not-so-official" location URL of the DAX schema definition.
SCHEMA_LOCATION - Static variable in class edu.isi.pegasus.planner.parser.dax.DAXParser3
  The "not-so-official" location URL of the Site Catalog Schema.
SCHEMA_LOCATION - Static variable in class edu.isi.pegasus.planner.parser.PDAXParser
  The "not-so-official" location URL of the DAX schema definition.
SCHEMA_LOCATION - Static variable in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser3
  The "not-so-official" location URL of the Site Catalog Schema.
SCHEMA_LOCATION - Static variable in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser4
  The "not-so-official" location URL of the Site Catalog Schema.
SCHEMA_NAMESPACE - Static variable in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
  The "official" namespace URI of the site catalog schema.
SCHEMA_NAMESPACE - Static variable in class edu.isi.pegasus.planner.catalog.site.classes.XML4PrintVisitor
  The "official" namespace URI of the site catalog schema.
SCHEMA_NAMESPACE - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.XML2
  uri namespace
SCHEMA_NAMESPACE - Static variable in class edu.isi.pegasus.planner.client.DAXValidator
  URI namespace for DAX schema.
SCHEMA_NAMESPACE - Static variable in class edu.isi.pegasus.planner.dax.ADAG
  The "official" namespace URI of the site catalog schema.
SCHEMA_NAMESPACE - Static variable in class edu.isi.pegasus.planner.invocation.InvocationRecord
  The "official" namespace URI of the invocation record schema.
SCHEMA_NAMESPACE - Static variable in class edu.isi.pegasus.planner.parser.ConfigXmlParser
  uri namespace
SCHEMA_NAMESPACE - Static variable in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  URI namespace
SCHEMA_NAMESPACE - Static variable in class edu.isi.pegasus.planner.parser.dax.DAXParser3
  uri namespace
SCHEMA_NAMESPACE - Static variable in class edu.isi.pegasus.planner.parser.PDAXParser
  URI namespace
SCHEMA_NAMESPACE - Static variable in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser3
  uri namespace
SCHEMA_NAMESPACE - Static variable in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser4
  uri namespace
SCHEMA_NAMESPACE_XSI - Static variable in class edu.isi.pegasus.planner.dax.ADAG
  XSI SCHEMA NAMESPACE
SCHEMA_VERSION - Static variable in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
  The version to report.
SCHEMA_VERSION - Static variable in class edu.isi.pegasus.planner.catalog.site.classes.XML4PrintVisitor
  The version to report.
SCHEMA_VERSION - Static variable in class edu.isi.pegasus.planner.dax.ADAG
  The version to report.
searchMDS(LdapContext, String, String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
  Still Thinking how to eable this option.
SECONDARY_METRICS_SERVER_URL_ENV_VARIABLE - Static variable in class edu.isi.pegasus.planner.code.generator.Metrics
  The name of the environment variable that overrides the default server url
SEED - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
SEED_ID - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
SEED_ID - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
SEED_NAME - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
SEED_NAME - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
selectFileServer(FileServerType.OPERATION) - Method in class edu.isi.pegasus.planner.catalog.site.classes.DirectoryLayout
  Selects a random file server and returns it matching an operation type.
selectGridFTP(boolean) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  Returns a gridftp server from the list of gridftp servers associated with the site.
selectGridFtp(ArrayList) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  Return a random gridftp url from the list of gridftp url's.
selectGridGateway(GridGateway.JOB_TYPE) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Selects a grid gateway object corresponding to a job type.
selectGridGateway(GridGateway.JOB_TYPE) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Selects a grid gateway object corresponding to a job type.
selectHeadNodeScratchSharedFileServer(FileServerType.OPERATION) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  A convenience method to select the FileServer for the shared scratch space on the HeadNode.
selectHeadNodeScratchSharedFileServerURLPrefix(FileServerType.OPERATION) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Deprecated.
  should be removed
selectJobManager(String, boolean) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  Returns a selected jobmanager corresponding to a particular VDS universe.
selectLRC(boolean) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  Returns an LRC from the list of LRCs associated with the site.
selectLRC(ArrayList) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  Return a random lrc url from the list of lrc url's.
SELECTOR - Static variable in class edu.isi.pegasus.planner.classes.Profile
Selector - Class in edu.isi.pegasus.planner.namespace
  The selector namespace object.
Selector() - Constructor for class edu.isi.pegasus.planner.namespace.Selector
  The default constructor.
Selector(Map) - Constructor for class edu.isi.pegasus.planner.namespace.Selector
  The overloaded constructor.
selectRandomSite(List) - Method in class edu.isi.pegasus.planner.selector.site.Random
  The random selection that selects randomly one of the records returned by the transformation catalog.
selectReplica(ReplicaLocation, String, boolean) - Method in class edu.isi.pegasus.planner.selector.replica.Default
  This chooses a location amongst all the locations returned by the replica location service.
selectReplica(ReplicaLocation, String, boolean) - Method in class edu.isi.pegasus.planner.selector.replica.Local
  Selects a random replica from all the replica's that have their site handle set to local and the pfn's start with a file url scheme.
selectReplica(ReplicaLocation, String, boolean) - Method in class edu.isi.pegasus.planner.selector.replica.Regex
  This chooses a location amongst all the locations returned by the replica location service.
selectReplica(ReplicaLocation, String, boolean) - Method in class edu.isi.pegasus.planner.selector.replica.Restricted
  This chooses a location amongst all the locations returned by the replica location service.
selectReplica(ReplicaLocation, String, boolean) - Method in interface edu.isi.pegasus.planner.selector.ReplicaSelector
  Selects a single replica amongst all the replicas returned by the implementing Replica Mechanism.
selectReplicaCatalog() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Selects a Random ReplicaCatalog.
selectReplicaCatalog() - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Selects a Random ReplicaCatalog.
selectReplicas(ReplicaLocation, String, boolean) - Method in class edu.isi.pegasus.planner.selector.replica.Default
  This chooses a location amongst all the locations returned by the Replica Mechanism.
selectReplicas(ReplicaLocation, String, boolean) - Method in class edu.isi.pegasus.planner.selector.replica.Local
  This chooses a location amongst all the locations returned by the Replica Mechanism.
selectReplicas(ReplicaLocation, String, boolean) - Method in interface edu.isi.pegasus.planner.selector.ReplicaSelector
  Selects a replica amongst all the replicas returned by the implementing Replica Mechanism.
selectStorageFileServerForStageout(FileServerType.OPERATION) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  A convenience method that selects a file server for staging the data out to a site.
selectTCEntry(List, Job, String) - Method in class edu.isi.pegasus.planner.refiner.InterPoolEngine
  Calls out to the transformation selector to select an entry from a list of valid transformation catalog entries.
selectWorkdir(WorkDir) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  Returns the path to the execution mount point (The Workdir).
send(PlannerMetrics, String) - Method in class edu.isi.pegasus.planner.code.generator.SendMetrics
  Sends the planner metrics to the metrics server
SendMetrics - Class in edu.isi.pegasus.planner.code.generator
  A Send metrics class that is used to send metrics to the metrics server using HTTP POST methods
SendMetrics(PlannerMetrics, String) - Constructor for class edu.isi.pegasus.planner.code.generator.SendMetrics
sendMetricsAsynchronously(PlannerMetrics, String) - Method in class edu.isi.pegasus.planner.code.generator.Metrics
  Sends the planner metrics to the metrics server asynchrnously with a timeout of 5 seconds
SendMetricsResult - Class in edu.isi.pegasus.planner.code.generator
SendMetricsResult() - Constructor for class edu.isi.pegasus.planner.code.generator.SendMetricsResult
SendMetricsResult(int, String) - Constructor for class edu.isi.pegasus.planner.code.generator.SendMetricsResult
sendMetricsSynchronously(PlannerMetrics, String) - Method in class edu.isi.pegasus.planner.code.generator.Metrics
  Sends the planner metrics to the metrics server
Separator - Class in edu.isi.pegasus.common.util
  This class solely defines the separators used in the textual in- and output between namespace, name and version(s).
Separator() - Constructor for class edu.isi.pegasus.common.util.Separator
Separator2Test - Class in edu.isi.pegasus.common.util
  This is the test program for the Separator class.
Separator2Test() - Constructor for class edu.isi.pegasus.common.util.Separator2Test
SeparatorTest - Class in edu.isi.pegasus.common.util
  This is the test program for the Separator class.
SeparatorTest() - Constructor for class edu.isi.pegasus.common.util.SeparatorTest
SEQ_EXEC_CLASS - Static variable in class edu.isi.pegasus.planner.cluster.aggregator.JobAggregatorFactory
  The name of the class in this package, that corresponds to seqexec.
SeqExec - Class in edu.isi.pegasus.planner.cluster.aggregator
  This class aggregates the smaller jobs in a manner such that they are launched at remote end, sequentially on a single node using seqexec.
SeqExec() - Constructor for class edu.isi.pegasus.planner.cluster.aggregator.SeqExec
  The default constructor.
SEQEXEC_INDEX - Static variable in class edu.isi.pegasus.planner.code.GridStartFactory
  The index in constant arrays for SeqExec
SEQEXEC_PROGRESS_REPORT_SUFFIX - Static variable in class edu.isi.pegasus.planner.cluster.aggregator.SeqExec
  The suffix to be applied to seqexec progress report file.
serialVersionUID - Static variable in exception edu.isi.pegasus.gridftp.DirectoryNotEmptyException
serialVersionUID - Static variable in exception edu.isi.pegasus.gridftp.DirectoryRemovalException
serialVersionUID - Static variable in exception edu.isi.pegasus.gridftp.FileExistsException
serialVersionUID - Static variable in exception edu.isi.pegasus.gridftp.GridFTPException
serialVersionUID - Static variable in exception edu.isi.pegasus.gridftp.NoSuchFileException
serialVersionUID - Static variable in exception edu.isi.pegasus.gridftp.PermissionDeniedException
set(String, boolean) - Method in class edu.isi.pegasus.planner.client.DAXValidator
  Sets a feature while capturing failed features right here.
set(String, boolean) - Method in class edu.isi.pegasus.planner.parser.InvocationParser
  Sets a feature while capturing failed features right here.
set(int) - Method in class edu.isi.pegasus.planner.transfer.RemoteTransfer.TransferState
  Sets a type of transfer to be third party.
set(int) - Method in class edu.isi.pegasus.planner.transfer.TPT.TPTState
  Sets a type of transfer to be third party.
SET_XBIT_PREFIX - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  The prefix for the jobs which are added to set X bit for the staged executables.
setAbortOnFirstJobFailure(boolean) - Method in class edu.isi.pegasus.planner.cluster.aggregator.MPIExec
  Setter method to indicate , failure on first consitutent job should result in the abort of the whole aggregated job.
setAbortOnFirstJobFailure(boolean) - Method in class edu.isi.pegasus.planner.cluster.aggregator.SeqExec
  Setter method to indicate , failure on first consitutent job should result in the abort of the whole aggregated job.
setAbortOnFirstJobFailure(boolean) - Method in interface edu.isi.pegasus.planner.cluster.JobAggregator
  Setter method to indicate , failure on first consitutent job should result in the abort of the whole aggregated job.
setAbstractChildID(String) - Method in class edu.isi.pegasus.planner.classes.PCRelation
  Sets the abstract child id associated with the edge.
setAbstractParentID(String) - Method in class edu.isi.pegasus.planner.classes.PCRelation
  Sets the abstract parent id associated with the edge.
setAccessTime(Date) - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor.
setApplicationMetrics(Properties) - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Sets the app metrics that need to be forwarded.
setApplicationMetrics(PegasusProperties) - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Sets the app metrics that need to be forwarded.
setArch(Arch) - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.VDSSysInfo
  Sets the architecture of the system.
setArchitecture(SysInfo.Architecture) - Method in class edu.isi.pegasus.planner.catalog.classes.SysInfo
  Sets the architecture of the site.
setArchitecture(SysInfo.Architecture) - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Sets the architecture of the nodes that this grid gateway talks to.
setArchitecture(SysInfo.Architecture) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Sets the architecture of the site.
setArchitecture(SysInfo.Architecture) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Sets the architecture of the site.
setArchitecture(Executable.ARCH) - Method in class edu.isi.pegasus.planner.dax.Executable
  Set the architecture the executable is compiled for
setArchitecture(Architecture) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setArchMode(String) - Method in class edu.isi.pegasus.planner.invocation.Architecture
  Accessor.
setArguments(String) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the argument string with which the job has to be invoked.
setArguments(Arguments) - Method in class edu.isi.pegasus.planner.invocation.Job
  Accessor.
setAttribute(String, Object) - Method in class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  Adds a new or overwrites an existing attribute.
setAttribute(Map) - Method in class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  Replaces all existing attributes with new attributes.
setAuthentication(boolean) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the authenticate flag to the value passed.
setBag(Bag) - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  Sets the bag of objects associated with the node.
setBasenamePrefix(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the basename prefix for the per workflow files.
setBaseSubmitDirectory(String) - Method in class edu.isi.pegasus.planner.classes.ADag
  Sets the submit directory for the workflow.
setBaseSubmitDirectory(String) - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Sets the path to the base submit directory.
setBaseSubmitDirectory(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the path to the base submitdirectory where the submit files are to be generated.
setBlocks(long) - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor.
setBlockSize(long) - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor.
setBufferSize(int) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
  Set buffer size i.e.
setCacheFiles(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the caches files.
setCacheFiles(Set) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the caches files.
setCallback(Callback) - Method in class edu.isi.pegasus.planner.parser.PDAXParser
  Sets the callback handler for this parsing instance.
setChild(String) - Method in class edu.isi.pegasus.planner.classes.PCRelation
  Sets the child of the edge.
setChild(String) - Method in class edu.isi.pegasus.planner.dax.Edge
setChildren(Collection<GraphNode>) - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  It sets the children to the node.
setClassName(String) - Method in class edu.isi.pegasus.common.util.DynamicLoader
  Sets the fully-qualified class name to load.
setCleanup(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the cleanup option for the planner.
setCleanup(PlannerOptions.CLEANUP_OPTIONS) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the cleanup option for the planner.
setClusteringTechnique(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the clustering option.
setCode(int) - Method in class edu.isi.pegasus.planner.code.generator.SendMetricsResult
setColor(int) - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  Sets the color of the node to the color specified
setConfFile(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the property file pointed to by the --conf option passed to the planner
setContact(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Sets the contact string for the Grid gateway
setContent(GraphNodeContent) - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  Sets the content associated with the node.
setCoreFlag(boolean) - Method in class edu.isi.pegasus.planner.invocation.JobStatusSignal
  Accessor.
setCost(long) - Method in class edu.isi.pegasus.planner.provisioner.Edge
setCount(String) - Method in class edu.isi.pegasus.planner.classes.ADag
  Set the count of the workflow, that was specified in the DAX.
setCount(String) - Method in class edu.isi.pegasus.planner.classes.DagInfo
  Set the count of the workflow, that was specified in the DAX.
setCount(int) - Method in class edu.isi.pegasus.planner.invocation.Fifo
  Accessor.
setCreationTime(Date) - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor.
setCredential(GSSCredential) - Method in class edu.isi.pegasus.planner.refiner.Authenticate
  Sets the credential that has to be used for authentication.
setDAGFile(String) - Method in class edu.isi.pegasus.planner.classes.DAGJob
  Sets the DAG file
setDAGLFN(String) - Method in class edu.isi.pegasus.planner.classes.DAGJob
  Sets the DAG file LFN
setData(String) - Method in class edu.isi.pegasus.planner.invocation.StatCall
  Accessor.
setData(Data) - Method in class edu.isi.pegasus.planner.invocation.StatCall
  Conversion accessor.
setDataConfiguration(String) - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  The data configuration
setDateFormat(SimpleDateFormat) - Method in class edu.isi.pegasus.common.util.Currently
  Accessor: Sets the default timestamp format for all queues.
setDateFormat(String) - Method in class edu.isi.pegasus.common.util.Currently
  Accessor: Sets the default timestamp format for all queues.
setDAX(String) - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Sets the path to the DAX.
setDAX(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the DAX that has to be worked on by the planner.
setDAXCallback(Callback) - Method in interface edu.isi.pegasus.planner.parser.dax.DAXParser
  Set the DAXCallback for the parser to call out to.
setDAXCallback(Callback) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Set the DAXCallback for the parser to call out to.
setDAXCallback(Callback) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser3
  Set the DAXCallback for the parser to call out to.
setDAXFile(String) - Method in class edu.isi.pegasus.planner.classes.DAXJob
  Sets the DAX file
setDAXLFN(String) - Method in class edu.isi.pegasus.planner.classes.DAXJob
  Sets the DAX file LFN
setDAXMTime(File) - Method in class edu.isi.pegasus.planner.classes.ADag
  Sets the mtime (last modified time) for the DAX.
setDAXMTime(File) - Method in class edu.isi.pegasus.planner.classes.DagInfo
  Sets the mtime (last modified time) for the DAX.
setDAXMTime(String) - Method in class edu.isi.pegasus.planner.classes.DagInfo
  Sets the mtime (last modified time) for the DAX.
setDAXVersion(String) - Method in class edu.isi.pegasus.planner.classes.ADag
  Sets the dax version
setDAXVersion(String) - Method in class edu.isi.pegasus.planner.classes.DagInfo
  Sets the dax version
setDepth(int) - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  Sets the depth associated with the node.
setDepth_ResMap(List) - Method in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  A BFS implementation to set depth value (roots have depth 1) and also to populate mResMap ,mResMapLeaves,mResMapRoots which contains all the jobs that are assigned to a particular resource
setDerivation(String, String, String) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the various attributes of underlying derivation.
setDerivation(String) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setDescriptor(int) - Method in class edu.isi.pegasus.planner.invocation.Descriptor
  Accessor.
setDescriptor(int) - Method in interface edu.isi.pegasus.planner.invocation.HasDescriptor
  Accessor: Sets the descriptor number of a file object.
setDescriptor(int) - Method in class edu.isi.pegasus.planner.invocation.Temporary
  Accessor.
setDirectory(Directory) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Sets a directory corresponding to a particular type
setDirectory(String) - Method in class edu.isi.pegasus.planner.classes.DAGJob
  Sets the directory in which the dag needs to execute.
setDirectory(String) - Method in class edu.isi.pegasus.planner.classes.DAXJob
  Sets the directory in which the dag needs to execute.
setDirectory(String) - Method in class edu.isi.pegasus.planner.classes.Job
  Setter method to set the name of the job.
setDirectory(String) - Method in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  Sets the directory where the stdin files are to be generated.
setDirectory(String) - Method in class edu.isi.pegasus.planner.refiner.NodeCollapser
  Sets the directory where the stdin files are to be generated.
setDocumentLocator(Locator) - Method in class edu.isi.pegasus.planner.client.DAXValidator
setDocumentLocator(Locator) - Method in class edu.isi.pegasus.planner.parser.InvocationParser
  Obtains the document locator from the parser.
setDocumentLocator(Locator) - Method in class edu.isi.pegasus.planner.parser.Parser
  Overrides the empty implementation provided by Default Handler and sets the locator variable for the locator.
setDomainName(String) - Method in class edu.isi.pegasus.planner.invocation.Architecture
  Accessor.
setDuration(double) - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Sets the user.
setDuration(double) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setDuration(double) - Method in class edu.isi.pegasus.planner.invocation.Job
  Accessor.
setDVName(String) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the derivation name of the underlying derivation.
setDVNamespace(String) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the derivation namespace to be associated with the job.
setDVVersion(String) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the version of the underlying derivation.
setElementRelation(String, Object, Object) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser3
  This method sets the relations between the currently finished XML element(child) and its containing element in terms of Java objects.
setElementRelation(char, Invocation, Invocation) - Method in class edu.isi.pegasus.planner.parser.InvocationParser
  This method sets the relations between the currently finished XML element and its containing element in terms of Java objects.
setElementRelation(String, Object, Object) - Method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser3
  This method sets the relations between the currently finished XML element and its containing element in terms of Java objects.
setElementRelation(String, Object, Object) - Method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser4
  This method sets the relations between the currently finished XML element and its containing element in terms of Java objects.
setElementRelation(String, Object, Object) - Method in class edu.isi.pegasus.planner.parser.StackBasedXMLParser
  This method sets the relations between the currently finished XML element(child) and its containing element in terms of Java objects.
setEndTime(Date) - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Set the end time for the planning operation.
setEndTime(double) - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Set the end time for the planning operation.
setEnvironment(Environment) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setError(int) - Method in class edu.isi.pegasus.planner.invocation.JobStatusFailure
  Accessor.
setError(int) - Method in class edu.isi.pegasus.planner.invocation.StatCall
  Accessor.
setErrorMessage(String) - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Set the error message that we want to log
setErrorWriter(String) - Method in class edu.isi.pegasus.common.logging.logger.Default
  Certains levels like FATAL, ERROR and WARN can be set to log to a different stream, than the default stream used for writing other messages.
setErrorWriter(OutputStream) - Method in class edu.isi.pegasus.common.logging.logger.Default
  Certains levels like FATAL, ERROR and WARN can be set to log to a different stream, than the default stream used for writing other messages.
setEvent(String, String, String) - Method in interface edu.isi.pegasus.common.logging.Event
  Set the event that is to be associated with the log messages.
setEvent(String, Map<String, String>) - Method in interface edu.isi.pegasus.common.logging.Event
  Adds the event that is to be associated with the log messages onto an internal stack
setEvent(String, String, String) - Method in class edu.isi.pegasus.common.logging.format.NetloggerEvent
  Set the event that is to be associated with the log messages.
setEvent(String, Map<String, String>) - Method in class edu.isi.pegasus.common.logging.format.NetloggerEvent
  Adds the event that is to be associated with the log messages onto an internal stack
setEvent(String, String, String) - Method in class edu.isi.pegasus.common.logging.format.SimpleEvent
  Set the event that is to be associated with the log messages.
setEvent(String, Map<String, String>) - Method in class edu.isi.pegasus.common.logging.format.SimpleEvent
  Adds the event that is to be associated with the log messages onto an internal stack
setExecutable(boolean) - Method in class edu.isi.pegasus.planner.dax.File
  Mark the file as executable.
setExecutable() - Method in class edu.isi.pegasus.planner.dax.File
  Mark the file as executable.
setExecutable(String) - Method in class edu.isi.pegasus.planner.invocation.Arguments
  Accessor.
setExecutable(String) - Method in class edu.isi.pegasus.planner.invocation.CommandLine
  Accessor.
setExecutable(StatCall) - Method in class edu.isi.pegasus.planner.invocation.Job
  Accessor.
setExecutableForTransfer() - Method in class edu.isi.pegasus.planner.namespace.Condor
  Adds the executable for transfer via the condor file transfer mechanism.
setExecutableStagingForJob(boolean) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the executable staging flag in the job to the value passed.
setExecutionSites(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the names of the execution sites where the concrete workflow can be run.
setExecutionSites(Collection) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the names of the execution sites where the concrete workflow can be run.
setExecutionSites(Collection) - Method in class edu.isi.pegasus.planner.common.UserOptions
  Sets the execution sites.
setExitcode(int) - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Sets the exitcode for the planner.
setExitCode(short) - Method in class edu.isi.pegasus.planner.invocation.JobStatusRegular
  Accessor.
setFile(File) - Method in class edu.isi.pegasus.planner.invocation.StatCall
  Accessor.
setFilename(String) - Method in interface edu.isi.pegasus.planner.invocation.HasFilename
  Accessor: Sets the name of an file object.
setFilename(String) - Method in class edu.isi.pegasus.planner.invocation.Regular
  Accessor.
setFilename(String) - Method in class edu.isi.pegasus.planner.invocation.Temporary
  Accessor.
setFileOptional() - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Sets the optional flag denoting the file to be optional to true.
setFileServers(List<FileServer>) - Method in class edu.isi.pegasus.planner.catalog.site.classes.DirectoryLayout
  Sets the list of FileServers that can access this directory.
setFlowTimestamp(String) - Method in class edu.isi.pegasus.planner.classes.ADag
  Sets the flow timestamp for the workflow.
setFlowTimestamp(String) - Method in class edu.isi.pegasus.planner.classes.DagInfo
  Sets the flow timestamp for the workflow.
setForce(boolean) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the force option for the planner.
setForceReplan(boolean) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the force replan option
setForCleanup() - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Sets the cleanup flag denoting the file can be cleaned up to true.
setForCleanup(boolean) - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Sets the cleanup flag to the value passed
setForPlannerUse(PegasusProperties, PlannerOptions) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  A setter method that is to be set to use getWorkDirectory functions, correctly.
setFreeSize(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.FileSystemType
  Sets the free directory size
setFrom(Node) - Method in class edu.isi.pegasus.planner.provisioner.Edge
  set the 'from' task
setGID(int) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setGID(int) - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor.
setGlibc(String) - Method in class edu.isi.pegasus.planner.catalog.classes.SysInfo
  Sets the glibc version on the site.
setGlibc(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Sets the glibc version on the site.
setGlibc(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Sets the glibc version on the site.
setGlibc(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Sets the glibc version on the site.
setGlibc(String) - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.VDSSysInfo
  Sets the glibc version of the system
setGlibc(String) - Method in class edu.isi.pegasus.planner.dax.Executable
  Set the glibc this executable is compiled for
setGridFTPBandwidthInfo(GridFTPBandwidth) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPServer
  It fills information in the mBandWidths ArrayList.
setGroup(String) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setGroup(String) - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor.
setHandle(String) - Method in class edu.isi.pegasus.planner.invocation.StatCall
  Accessor.
setHeadNodeFS(HeadNodeFS) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Sets the headnode filesystem.
setHelp(boolean) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the help option for the planner.
setHostAddress(InetAddress) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setHostname(String) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setID(String) - Method in class edu.isi.pegasus.planner.partitioner.Partition
  It sets the id of the partition.
setIdleNodes(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Sets the number of idle nodes that this grid gateway talks to.
setIdleNodes(int) - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Sets the number of idle nodes that this grid gateway talks to.
setIndex(String) - Method in class edu.isi.pegasus.planner.classes.ADag
  Set the index of the workflow, that was specified in the DAX.
setIndex(String) - Method in class edu.isi.pegasus.planner.classes.DagInfo
  Set the index of the workflow, that was specified in the DAX.
setIndex(int) - Method in class edu.isi.pegasus.planner.partitioner.Partition
  It sets the index associated with this partition to the value passed.
setInfo(int, String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPBandwidth
  This method sets the info about gridftpbw based on the gridftpbwkey
setInfo(int, String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPServer
  Sets an attribute associated with the grid ftp server.
setInfo(int, String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  Sets an attribute associated with the jobmanager.
setInfo(int, Object) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  Sets an attribute associated with the remote site.
setInfo(int, String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.WorkDir
  Sets an attribute associated with the work directory.
setInheritedRCFiles(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the inherited RC Files.
setInheritedRCFiles(Set) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the inherited RC Files.
setINode(long) - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor.
setInputBlocks(int) - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor.
setInputDirectory(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Set the input directory.
setInputFiles(Set<PegasusFile>) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the input files associated with the job.
setInputSize(long) - Method in class edu.isi.pegasus.planner.invocation.Fifo
  Accessor.
setInstalled() - Method in class edu.isi.pegasus.planner.dax.Executable
  set the installed flag on the executable.
setInstalled(boolean) - Method in class edu.isi.pegasus.planner.dax.Executable
  Set the installed flag on the executable.
setInterface(String) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setInternalMountPoint(InternalMountPoint) - Method in class edu.isi.pegasus.planner.catalog.site.classes.DirectoryLayout
  Sets the internal mount point for the directory.
setInvoluntarySwitches(int) - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor: Sets the number of involuntary context switches.
setJob(int, Job) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor: Overwrites a job at a certain position.
setJob(Collection) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor: Overwrites internal list with an external list representing jobs.
setJobAggregator(JobAggregator) - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Sets the JobAggregator that created this aggregated job.
setJobManager(String) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the remote jobmanager on which the job has to run.
setJobName(String) - Method in class edu.isi.pegasus.planner.namespace.Dagman
  It sets the name of the job that is associated with the profiles contained in this placeholder.
setJobnamePrefix(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the job prefix to be used while constructing the job names.
setJobStatus(JobStatus) - Method in class edu.isi.pegasus.planner.invocation.Status
  Accessor.
setJobType(GridGateway.JOB_TYPE) - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Sets the type of jobs that run via this grid gateway.
setJobType(int) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the type of the job.
setKey(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.Connection
  Returns the connection key.
setKey(String) - Method in class edu.isi.pegasus.planner.classes.NameValue
  Sets the key associated with this tuple.
setKey(String) - Method in class edu.isi.pegasus.planner.invocation.EnvEntry
  Accessor.
setLabel(String) - Method in class edu.isi.pegasus.planner.classes.ADag
  Sets the label for the workflow.
setLabel(String) - Method in class edu.isi.pegasus.planner.classes.DagInfo
  Sets the label for the workflow.
setLabel(String) - Method in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  Sets the DAXlabel.
setLabel(String) - Method in class edu.isi.pegasus.planner.dax.Edge
setLabelKey(String) - Method in class edu.isi.pegasus.planner.parser.dax.DAX2LabelGraph
  Set the profile key that is to be used to pick up the labels.
setLabelKey(String) - Static method in class edu.isi.pegasus.planner.partitioner.graph.LabelBag
  Sets the label key that is to be associated with the bag.
setLdapConnectionEnv(String, String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
  Enables a user to set new or overide existing connection settings to the MDS.
setLdapSearchConstraints() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
setLevel(Level) - Method in class edu.isi.pegasus.common.logging.logger.Default
  Sets the debug level.
setLevel(int) - Method in class edu.isi.pegasus.common.logging.logger.Default
  Sets the debug level.
setLevel(int, boolean) - Method in class edu.isi.pegasus.common.logging.logger.Default
  Sets the debug level.
setLevel(Level) - Method in class edu.isi.pegasus.common.logging.logger.Log4j
  Sets the debug level.
setLevel(int) - Method in class edu.isi.pegasus.common.logging.logger.Log4j
  Sets the debug level.
setLevel(int, boolean) - Method in class edu.isi.pegasus.common.logging.logger.Log4j
  Sets the debug level.
setLevel(Level, boolean) - Method in class edu.isi.pegasus.common.logging.logger.Log4j
  Sets the debug level.
setLevel(Level) - Method in class edu.isi.pegasus.common.logging.LogManager
  Sets the debug level.
setLevel(int) - Method in class edu.isi.pegasus.common.logging.LogManager
  Sets the debug level.
setLevel(int, boolean) - Method in class edu.isi.pegasus.common.logging.LogManager
  Sets the debug level.
setLevel(int) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the level for the job.
setLevel(int) - Method in class edu.isi.pegasus.planner.client.RCClient
  Sets a logging level.
setLFN(String) - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  It sets the logical filename of the file that is being transferred.
setLFN(String) - Method in class edu.isi.pegasus.planner.classes.ReplicaLocation
  Sets the LFN.
setLFN(String) - Method in class edu.isi.pegasus.planner.invocation.StatCall
  Accessor.
setLink(File.LINK) - Method in class edu.isi.pegasus.planner.dax.File
  Set the file linkage
setLinkage(PegasusFile.LINKAGE) - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Sets the linkage for the file during parsing.
setLinkCount(long) - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor.
setLocalDirectory(LocalDirectory) - Method in class edu.isi.pegasus.planner.catalog.site.classes.StorageType
  Sets the local directory.
setLocalDirectory(Directory) - Method in class edu.isi.pegasus.planner.catalog.site.classes.StorageType
  Sets the local directory.
setLoggingLevel(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the logging level for logging of messages.
setLogicalID(String) - Method in class edu.isi.pegasus.planner.classes.Job
  Setter method to set the logical id of the job.
setLogicalName(String) - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Set the logical mName of the transformation.
setLogicalNamespace(String) - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Set the logical mNamespace of the transformation.
setLogicalTransformation(String) - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Set the logical transformation with a fully qualified tranformation String of the format NS::NAME:Ver
setLogicalTransformation(String, String, String) - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Set the logical transformation by providing the mNamespace, mName and mVersion as seperate strings.
setLogicalVersion(String) - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Set the logical mVersion of the transformation.
setMachine(String) - Method in class edu.isi.pegasus.planner.invocation.Architecture
  Accessor.
setMachine(Machine) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setMachineSpecific(MachineSpecific) - Method in class edu.isi.pegasus.planner.invocation.Machine
  Sets the machine-specific grouping element.
setMajorFaults(int) - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor: Sets the number of major page faults.
setMaximumRSS(int) - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor.
setMegaDAGMode(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the megadag generation option
setMetricsFileLocationInSubmitDirectory(File) - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Sets the metrics file location in the submit directory
setMetricsType(String) - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Sets the metrics
setMetricsTypeToError() - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Convenience setter method
setMinorFaults(int) - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor: Sets the number of minor faults.
setMode(int) - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor.
setModificationTime(Date) - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor.
setMountPoint(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.FileServerType
  Returns the mount point.
setMountPoint(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.FileSystemType
  Sets the mount point for the file system type.
setName(String) - Method in class edu.isi.pegasus.planner.classes.Job
  Setter method to set the name of the job.
setName(String) - Method in class edu.isi.pegasus.planner.partitioner.Partition
  It sets the partition name to the value passed.
setName(String) - Method in class edu.isi.pegasus.planner.ranking.Ranking
  Sets the name.
setNextException(CatalogException) - Method in exception edu.isi.pegasus.planner.catalog.CatalogException
  Adds an `CatalogException`object to the end of the chain.``
setNodeLabel(String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setNodeName(String) - Method in class edu.isi.pegasus.planner.invocation.Architecture
  Accessor.
setNonThirdPartySite(String) - Method in class edu.isi.pegasus.planner.classes.TransferJob
  Sets the non third party site for the transfer job.
setNumberOfRescueTries(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the number of times to try for rescue dag submission.
setNumberOfRescueTries(int) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the number of times to try for rescue dag submission.
setOptional(boolean) - Method in class edu.isi.pegasus.planner.dax.File
  Set the optional flag on the file.
setOptionalArg(boolean) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the flag to denote that the optional argument for the random was specified.
setOriginalArgString(String[]) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the argument string of how planner was invoked.
setOS(SysInfo.OS) - Method in class edu.isi.pegasus.planner.catalog.classes.SysInfo
  Sets the OS of the site.
setOS(SysInfo.OS) - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Sets the OS of the nodes that this grid gateway talks to.
setOS(SysInfo.OS) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Sets the OS of the site.
setOS(SysInfo.OS) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Sets the OS of the site.
setOs(Os) - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.VDSSysInfo
  Sets the Os of the sytem.
setOS(Executable.OS) - Method in class edu.isi.pegasus.planner.dax.Executable
  Set the OS the executable is compiled for
setOSRelease(String) - Method in class edu.isi.pegasus.planner.catalog.classes.SysInfo
  Sets the OS release of the site.
setOSRelease(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Sets the OS release of the site.
setOSRelease(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Sets the OS release of the site.
setOSRelease(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Sets the OS release of the site.
setOSRelease(String) - Method in class edu.isi.pegasus.planner.dax.Executable
  Set the osrelease the executable is compiled for
setOSVersion(String) - Method in class edu.isi.pegasus.planner.catalog.classes.SysInfo
  Sets the OS version of the site.
setOSVersion(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Sets the OS version of the site.
setOSVersion(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Sets the OS version of the site.
setOSVersion(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Sets the OS version of the site.
setOsversion(String) - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.VDSSysInfo
  Sets the Os version of the system.
setOSVersion(String) - Method in class edu.isi.pegasus.planner.dax.Executable
  Set the osversion the executable is compiled for
setOutputBlocks(int) - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor.
setOutputDirectory(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Set the output directory.
setOutputFiles(Set<PegasusFile>) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the output files associated with the job.
setOutputSite(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the output site specified by the user.
setOutputSize(long) - Method in class edu.isi.pegasus.planner.invocation.Fifo
  Accessor.
setOutputWriter(String) - Method in class edu.isi.pegasus.common.logging.logger.Default
  Sets the writer associated with the class to the one specified for all type of messages other than error messages.
setOutputWriter(OutputStream) - Method in class edu.isi.pegasus.common.logging.logger.Default
  Sets the writer associated with the class to the one specified for all type of messages other than error messages.
setPageSize(long) - Method in class edu.isi.pegasus.planner.invocation.Machine
  Sets the page size.
setParent(String) - Method in class edu.isi.pegasus.planner.classes.PCRelation
  Sets the parent of the edge.
setParent(String) - Method in class edu.isi.pegasus.planner.dax.Edge
setParents(Collection<GraphNode>) - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  It adds the parents to the node.
setParserFeature(String, boolean) - Method in class edu.isi.pegasus.planner.parser.Parser
  Sets a parser feature, and fails here enabling us to set all the following features.
setPartitioningType(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the partitioning type in case of partition and plan.
setPartitionName(String) - Method in class edu.isi.pegasus.planner.partitioner.DAXWriter
  It sets the name of the partition in the dax that is generated.
setPartOfDeferredRun(boolean) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the flag to denote that the run is part of a larger deferred run.
setPDAX(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the PDAX that has to be worked on by the planner.
setPFN(String) - Method in class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  Accessor: Sets a new PFN to remember.
setPhysicalMemory(long) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setPhysicalTransformation(String) - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Set the physical location of the transformation.
setPID(int) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setPID(int) - Method in class edu.isi.pegasus.planner.invocation.Job
  Accessor.
setPosition(int) - Method in class edu.isi.pegasus.planner.invocation.ArgEntry
  Accessor.
setPostSCRIPTDebugON() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a boolean indicating whether to turn debug on or not for exitcode.
setPreScript(String) - Method in class edu.isi.pegasus.planner.classes.Job
  It sets the prescript for the job.
setPreScript(String, String) - Method in class edu.isi.pegasus.planner.classes.Job
  It sets the prescript for the job.
setPrescript(Job, String, String) - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Sets the prescript that ends up calling to the default wrapper that introduces retry into Pegasus for a particular job.
setPrescript(Job, String, String, String, String, String) - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Sets the prescript that ends up calling to the default wrapper that introduces retry into Pegasus for a particular job.
setPriority(int) - Method in class edu.isi.pegasus.planner.classes.FileTransfer
  Sets the priority for the File Transfer
setProfile(String, String, String) - Method in class edu.isi.pegasus.planner.classes.Profile
  This method allows to set the namespace , key and value of the Profile.
setProfileKey(String) - Method in class edu.isi.pegasus.planner.classes.Profile
  Sets the profile key
setProfileNamespace(String) - Method in class edu.isi.pegasus.planner.classes.Profile
  Sets the NameSpace of the Profile
setProfiles(Profiles) - Method in class edu.isi.pegasus.planner.catalog.site.classes.FileServerType
  Sets the profiles associated with the file server.
setProfiles(Profiles) - Method in class edu.isi.pegasus.planner.catalog.site.classes.HeadNodeFS
  Sets the profiles associated with the file server.
setProfiles(Profiles) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Sets the profiles associated with the file server.
setProfiles(Profiles) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Sets the profiles associated with the file server.
setProfiles(Profiles) - Method in class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeFS
  Sets the profiles associated with the file server.
setProfileValue(String) - Method in class edu.isi.pegasus.planner.classes.Profile
  Sets the profile value
setProgramName(String) - Method in interface edu.isi.pegasus.common.logging.Event
  Sets the program name for the software whose log statement are logged.
setProgramName(String) - Method in class edu.isi.pegasus.common.logging.format.AbstractLogFormatter
  Sets the program name for the software whose log statement are logged.
setProgramName(String) - Method in class edu.isi.pegasus.common.logging.format.NetloggerEvent
  Sets the program name for the software whose log statement are logged.
setProgramName(String) - Method in class edu.isi.pegasus.common.logging.format.SimpleEvent
  Sets the program name for the software whose log statement are logged.
setProgramName(String) - Method in interface edu.isi.pegasus.common.logging.LogFormatter
  Sets the program name for the software whose log statement are logged.
setProperties(String) - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Sets the path to the properties file for the run.
setProperty(String, String) - Method in class edu.isi.pegasus.common.util.CommonProperties
  Accessor: Overwrite any properties from within the program.
setProperty(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets a property passed on the command line.
setProperty(String, String) - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Accessor: Overwrite any properties from within the program.
setProtocol(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.FileServerType
  Set the protocol implemented by the file server.
setRandomDir(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the random directory in which the jobs are run.
setRank(long) - Method in class edu.isi.pegasus.planner.ranking.Ranking
  Sets the rank.
setReceived(int) - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor.
setRefiner(Refiner) - Method in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  Sets the callback to the refiner, that has loaded this implementation.
setRefiner(Refiner) - Method in interface edu.isi.pegasus.planner.transfer.Implementation
  Sets the callback to the refiner, that has loaded this implementation.
setRegister(boolean) - Method in class edu.isi.pegasus.planner.dax.File
  Set the register flag of the file.
setRegisterFlag(boolean) - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Sets the transient registration flag to value specified.
setRegName(String) - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.TransferContainer
  Sets the name of the registration job.
setRegName(String) - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle.TransferContainer
  Sets the name of the registration job.
setRelativeDirectory(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the path to the relative directory where the submit files are to be generated.
setRelativeSubmitDirectory(String) - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Sets the path to the submit directory relative to the base.
setRelativeSubmitDirectory(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the path to the directory where the submit files are to be generated.
setRelease(String) - Method in class edu.isi.pegasus.planner.invocation.Architecture
  Accessor.
setReleaseVersion() - Method in class edu.isi.pegasus.planner.classes.ADag
  Grabs the release version from VDS.Properties file.
setReleaseVersion() - Method in class edu.isi.pegasus.planner.classes.DagInfo
  Grabs the release version from VDS.Properties file.
setRemoteExecutable(String) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the path to the executable on the remote grid site.
setRenderedToExecutableForm(boolean) - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Returns a boolean indicating whether a job has been rendered to an executable form or not
setReplicaStore(ReplicaStore) - Method in class edu.isi.pegasus.planner.classes.ADag
  Sets the Replica Store
setRequestID(String) - Method in class edu.isi.pegasus.planner.classes.ADag
  Sets the request id.
setResource(String) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setResourceHandle(String) - Method in class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  Sets a new resource handle to remember as PFN attribute.
setResourceId(String) - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Set the mResourceID where the transformation is available.
setResponseMessage(String) - Method in class edu.isi.pegasus.planner.code.generator.SendMetricsResult
setRootWorkflowUUID(String) - Method in class edu.isi.pegasus.planner.classes.ADag
  Sets the root UUID for the workflow
setRootWorkflowUUID(String) - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Sets the root UUID for the workflow
setRuntime(String) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the expected runtime for the job.
setRuntime(double) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the expected runtime for the job.
setRuntime(long) - Method in class edu.isi.pegasus.planner.ranking.Ranking
  Sets the runtime.
setSanitizePath(boolean) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the flag denoting whether to sanitize path or not.
setScheduler(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Sets the the underlying scheduler that gateway talks to.
setScheduler(GridGateway.SCHEDULER_TYPE) - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Sets the the underlying scheduler that gateway talks to.
setSchemaLocations(String) - Method in class edu.isi.pegasus.planner.parser.InvocationParser
  Sets the list of external real locations where the XML schema may be found.
setSchemaLocations(String) - Method in class edu.isi.pegasus.planner.parser.Parser
  Sets the list of external real locations where the XML schema may be found.
setScratch(HeadNodeScratch) - Method in class edu.isi.pegasus.planner.catalog.site.classes.HeadNodeFS
  Sets the scratch area on the head node.
setScratch(WorkerNodeScratch) - Method in class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeFS
  Sets the scratch area on the head node.
setSent(int) - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor.
setSharedDirectory(SharedDirectory) - Method in class edu.isi.pegasus.planner.catalog.site.classes.StorageType
  Sets the shared directory.
setSharedDirectory(Directory) - Method in class edu.isi.pegasus.planner.catalog.site.classes.StorageType
  Sets the shared directory.
setSharedRSS(int) - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor.
setShiwaBundle(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the path to the Shiwa Bundle to be used.
setSignalNumber(short) - Method in class edu.isi.pegasus.planner.invocation.JobStatusSignal
  Accessor.
setSignalNumber(short) - Method in class edu.isi.pegasus.planner.invocation.JobStatusSuspend
  Accessor.
setSignals(int) - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor: Sets the number of signalss sent.
setSite(String) - Method in class edu.isi.pegasus.planner.dax.PFN
setSiteHandle(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Sets the site handle for the site
setSiteHandle(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Sets the site handle for the site
setSiteHandle(String) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the site handle of the site, where teh job is to be executed
setSiteMap(String, Map) - Method in class edu.isi.pegasus.planner.classes.TCMap
  This method allows to associate a site map with a particular logical transformation
setSiteTCEntries(String, String, TransformationCatalogEntry) - Method in class edu.isi.pegasus.planner.classes.TCMap
  This method allows to add a TransformationCatalogEntry object in the map to a particular transformation for a particular site
setSize(double) - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Sets the size for the file.
setSize(String) - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Sets the size for the file.
setSize(String) - Method in class edu.isi.pegasus.planner.dax.File
  Set the size of the file.
setSize(long) - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor.
setStackRSS(int) - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor.
setStagingSiteHandle(String) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the staging site.
setStamp(Stamp) - Method in class edu.isi.pegasus.planner.invocation.Machine
  Sets the time stamp when the machine info was obtained.
setStart(Date) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setStart(Date) - Method in class edu.isi.pegasus.planner.invocation.Job
  Accessor.
setStartTime(Date) - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Set the start time for the planning operation.
setStartTime(double) - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Set the start time for the planning operation.
setStatCall(int, StatCall) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor: Overwrites a stat at a certain position.
setStatCall(Collection) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor: Overwrites internal list with an external list representing stats.
setStatInfo(StatInfo) - Method in class edu.isi.pegasus.planner.invocation.StatCall
  Accessor.
setStatus(Status) - Method in class edu.isi.pegasus.planner.invocation.Job
  Accessor.
setStatus(int) - Method in class edu.isi.pegasus.planner.invocation.Status
  Accessor.
setStdErr(String) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the file to which the stderr of the job needs to be written to at the remote grid site.
setStderr(File) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStderr(File, File.TRANSFER) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStderr(File, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStderr(File, File.TRANSFER, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStderr(File, File.TRANSFER, boolean, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStderr(String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStderr(String, File.TRANSFER) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStderr(String, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStderr(String, File.TRANSFER, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStderr(String, File.TRANSFER, boolean, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStdIn(String) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the file to from which to pick up the stdin for the job.
setStdin(File) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStdin(File, File.TRANSFER) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStdin(File, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStdin(File, File.TRANSFER, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStdin(File, File.TRANSFER, boolean, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStdin(String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStdin(String, File.TRANSFER) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStdin(String, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStdin(String, File.TRANSFER, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStdin(String, File.TRANSFER, boolean, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStdOut(String) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the file to which the stdout of the job needs to be written to at the remote grid site.
setStdout(File) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStdout(File, File.TRANSFER) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStdout(File, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStdout(File, File.TRANSFER, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStdout(File, File.TRANSFER, boolean, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStdout(String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStdout(String, File.TRANSFER) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStdout(String, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStdout(String, File.TRANSFER, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStdout(String, File.TRANSFER, boolean, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
setStorage(HeadNodeStorage) - Method in class edu.isi.pegasus.planner.catalog.site.classes.HeadNodeFS
  Sets the storage area on the head node.
setStorage(WorkerNodeStorage) - Method in class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeFS
  Sets the storage area on the head node.
setSubmissionCredential(CredentialHandler.TYPE) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the credential to use for job submission.
setSubmitDirectory(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the path to the directory where the submit files are to be generated.
setSubmitDirectory(File) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the path to the directory where the submit files are to be generated.
setSubmitDirectory(String, String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the path to the directory where the submit files are to be generated.
setSubmitToScheduler(boolean) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns whether to submit the workflow or not.
setSupportedOperation(FileServerType.OPERATION) - Method in class edu.isi.pegasus.planner.catalog.site.classes.FileServerType
  The operation supported by the file server
setSwaps(int) - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor: Sets the number of swap ops.
setSysInfo(SysInfo) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Sets the System Information associated with the Site.
setSysInfo(SysInfo) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Sets the System Information associated with the Site.
setSysInfo(SysInfo) - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Sets the system information for the entry.
setSystemName(String) - Method in class edu.isi.pegasus.planner.invocation.Architecture
  Accessor.
setSystemTime(double) - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor: Sets the system time.
setTag(String) - Method in class edu.isi.pegasus.planner.invocation.Job
  Accessor.
setTag(String) - Method in class edu.isi.pegasus.planner.invocation.MachineSpecific
  Accessor.
setTerminate(boolean) - Static method in class edu.isi.pegasus.planner.invocation.SimpleServer
setTimeStampMillis(long) - Method in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
  Set the timestamp from milliseconds returned by System.currentTimeMillis().
setTimeStampNanos(long) - Method in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
  Set the timestamp from nanoseconds returned by System.nanoTime().
setTo(Node) - Method in class edu.isi.pegasus.planner.provisioner.Edge
  set the 'to' task
setToString(Set, String) - Method in class edu.isi.pegasus.planner.classes.Data
  A small helper method that displays the contents of a Set in a String.
setToString(Set, String) - Method in class edu.isi.pegasus.planner.refiner.MainEngine
  A small helper method that displays the contents of a Set in a String.
setTotalNodes(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Sets the number of total nodes that this grid gateway talks to.
setTotalNodes(int) - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Sets the total number of nodes that this grid gateway talks to.
setTotalSize(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.FileSystemType
  Sets the directory size
setTransfer(File.TRANSFER) - Method in class edu.isi.pegasus.planner.dax.File
  Set the transfer type of the file
setTransferFlag(int) - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Sets the transient transfer flag to value passed.
setTransferFlag(String) - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Sets the transient transfer flag corresponding to the string value of transfer mode passed.
setTransferFlag(String, boolean) - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Sets the transient transfer flag corresponding to the string value of transfer mode passed.
setTransferType(int) - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.TransferContainer
  Sets the transfer type for the transfers associated.
setTransferType(int) - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle.TransferContainer
  Sets the transfer type for the transfers associated.
setTransformation(String, String, String) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the various attributes of underlying transformation.
setTransformation(String) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setTransformationStore(TransformationStore) - Method in class edu.isi.pegasus.planner.classes.ADag
  Sets the Transformation Store
setTransientRegFlag() - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Deprecated.
setTruncated(boolean) - Method in class edu.isi.pegasus.planner.invocation.Data
  Accessor.
setTXName(String) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the transformation name of the underlying transformation.
setTXName(String) - Method in class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.TransferContainer
  Sets the name of the transfer job.
setTXName(String) - Method in class edu.isi.pegasus.planner.transfer.refiner.Bundle.TransferContainer
  Sets the name of the transfer job.
setTXNamespace(String) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the transformation namespace to be associated with the job.
setTXVersion(String) - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the version of the underlying transformation.
setType(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.Directory
  Set the type of directory
setType(Directory.TYPE) - Method in class edu.isi.pegasus.planner.catalog.site.classes.Directory
  Set the type of directory
setType(GridGateway.TYPE) - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Sets the type of grid gateway.
setType(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.ReplicaCatalog
  Sets the type of replica catalog.
setType(TCType) - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Set the type of the transformation.
setType(int) - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Sets the type flag to value passed.
setType(String) - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Sets the transient transfer flag to value passed.
setTypeRecursive() - Method in class edu.isi.pegasus.planner.classes.Job
  Sets the job to be recursive.
setUID(int) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setUID(int) - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor.
setUMask(int) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setUname(Uname) - Method in class edu.isi.pegasus.planner.invocation.Machine
  Sets the utsname generic system information record.
setUniverse(String) - Method in class edu.isi.pegasus.planner.classes.Job
  Set the universe associated with the job.
setUnsharedRSS(int) - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor.
setupForCondorIO(PegasusProperties) - Method in class edu.isi.pegasus.planner.common.PegasusConfiguration
  Returns a boolean indicating if properties are setup for condor io
setupJob(Job, List, List) - Method in class edu.isi.pegasus.planner.parser.InvocationParser
  Small helper method to set up the attributes for the job elements.
setupLogging(LogManager, PegasusProperties) - Method in class edu.isi.pegasus.planner.client.Executable
  Sets up the logging options for this class.
setupLogging() - Method in class edu.isi.pegasus.planner.client.PegasusGetSites
  Sets up the logging options for this class.
setupLogging() - Method in class edu.isi.pegasus.planner.client.SCClient
  Sets up the logging options for this class.
setupLogging() - Method in class edu.isi.pegasus.planner.client.TCClient
  Sets up the logging options for this class.
setupLogging() - Method in class edu.isi.pegasus.planner.client.TCConverter
  Sets up the logging options for this class.
setURL(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.ReplicaCatalog
  Sets the url for the replica catalog.
setURL(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.LRC
  Sets the url of the LRC associated with the object.
setURLForRegistrationOnDestination(String) - Method in class edu.isi.pegasus.planner.classes.FileTransfer
  Sets the registration url for the destination.
setURLPrefix(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.FileServerType
  Sets the url prefix .
setUsage(Usage) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setUsage(Usage) - Method in class edu.isi.pegasus.planner.invocation.Job
  Accessor.
setUser(String) - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Sets the user.
setUser(String) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setUser(String) - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Accessor.
setUserTime(double) - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor: Sets the user time.
setValue(String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.Connection
  Returns the key value.
setValue(String) - Method in class edu.isi.pegasus.planner.classes.NameValue
  Sets the value associated with this tuple.
setValue(String) - Method in class edu.isi.pegasus.planner.dax.MetaData
  Set the value of the metadata
setValue(String) - Method in class edu.isi.pegasus.planner.dax.Profile
  Set the value of this Profile
setValue(String) - Method in class edu.isi.pegasus.planner.invocation.Architecture
  Accessor.
setValue(String) - Method in class edu.isi.pegasus.planner.invocation.ArgEntry
  Accessor.
setValue(String) - Method in class edu.isi.pegasus.planner.invocation.ArgString
  Accessor.
setValue(int, String) - Method in class edu.isi.pegasus.planner.invocation.ArgVector
  Sets the argument vector at the specified location.
setValue(String) - Method in class edu.isi.pegasus.planner.invocation.Boot
  Accessor.
setValue(String) - Method in class edu.isi.pegasus.planner.invocation.CommandLine
  Accessor.
setValue(String) - Method in class edu.isi.pegasus.planner.invocation.CPU
  Accessor.
setValue(String) - Method in class edu.isi.pegasus.planner.invocation.Data
  Accessor.
setValue(String) - Method in class edu.isi.pegasus.planner.invocation.EnvEntry
  Accessor.
setValue(String) - Method in class edu.isi.pegasus.planner.invocation.File
  Accessor.
setValue(String) - Method in interface edu.isi.pegasus.planner.invocation.HasText
  Accessor.
setValue(String) - Method in class edu.isi.pegasus.planner.invocation.Ignore
  Accessor.
setValue(String) - Method in class edu.isi.pegasus.planner.invocation.JobStatusFailure
  Accessor.
setValue(String) - Method in class edu.isi.pegasus.planner.invocation.JobStatusSignal
  Accessor.
setValue(String) - Method in class edu.isi.pegasus.planner.invocation.JobStatusSuspend
  Accessor.
setValue(String) - Method in class edu.isi.pegasus.planner.invocation.Stamp
  Accessor.
setValue(String) - Method in class edu.isi.pegasus.planner.invocation.Uname
  Accessor.
setValue(String) - Method in class edu.isi.pegasus.planner.invocation.WorkingDir
  Accessor.
setValue(int) - Method in class edu.isi.pegasus.planner.selector.site.RoundRobin.NameValue
  The set method to set the value.
setVDSProperties(List) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Sets the VDS properties specifed by the user at the command line.
setVDSSuperNode(String) - Method in class edu.isi.pegasus.planner.classes.Job
  Setter method to the name of the compute job of Pegasus supernode containing this job.
setVDSSysInfo(VDSSysInfo) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Sets the sysinfo for the site.
setVDSSysInfo(VDSSysInfo) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Sets the sysinfo for the site.
setVDSSysInfo(VDSSysInfo) - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Set the System Information associated with the transformation.
setVersion(String) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setVOGroup(String) - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Sets the vo group
setVOGroup(String) - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Set the VO Group to which the user belongs
setVoluntarySwitches(int) - Method in class edu.isi.pegasus.planner.invocation.Usage
  Accessor: Sets the number of voluntary context switches.
setWeight(long) - Method in class edu.isi.pegasus.planner.provisioner.Node
  set execution time of this task
setWhat(String) - Method in class edu.isi.pegasus.planner.dax.Invoke
  Set what executable to invoke and how
setWhen(Invoke.WHEN) - Method in class edu.isi.pegasus.planner.dax.Invoke
  Set when to invoke
setWorkerNodeFS(WorkerNodeFS) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Sets the worker node filesystem.
setWorkerSharedDirectory(WorkerSharedDirectory) - Method in class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeScratch
  Sets the directory shared amongst the worker nodes only.
setWorkerSharedDirectory(WorkerSharedDirectory) - Method in class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeStorage
  Sets the directory shared amongst the worker nodes only.
setWorkflowLabel(String) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setWorkflowMetrics(WorkflowMetrics) - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Sets the workflow metrics.
setWorkflowRefinementStarted(boolean) - Method in class edu.isi.pegasus.planner.classes.ADag
  Sets whether the workflow refinement has started or not
setWorkflowTimestamp(Date) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setWorkflowUUID(String) - Method in class edu.isi.pegasus.planner.classes.ADag
  Sets the UUID for the workflow
setWorkflowUUID(String) - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Sets the UUID for the workflow
setWorkingDirectory(String) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setWorkingDirectory(WorkingDir) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Accessor.
setWriters(String) - Method in class edu.isi.pegasus.common.logging.logger.Default
  Sets both the output writer and the error writer to the same underlying writer.
setWriters(String) - Method in class edu.isi.pegasus.common.logging.logger.Log4j
  Sets both the output writer and the error writer to the same underlying writer.
setWriters(String) - Method in class edu.isi.pegasus.common.logging.LogManager
  Sets both the output writer and the error writer to the same underlying writer.
setXBitOnFile(String) - Method in class edu.isi.pegasus.planner.code.generator.Shell
  Sets the xbit on the file.
setXBitOnFile(String) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Sets the xbit on the file.
setXBitWithKickstart() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a boolean indicating whether kickstart should set x bit on staged executables before launching them.
SHARED_FS_CONFIGURATION_VALUE - Static variable in class edu.isi.pegasus.planner.common.PegasusConfiguration
  The value for the non shared filesystem configuration.
SharedDirectory - Class in edu.isi.pegasus.planner.catalog.site.classes
  This data class represents a shared directory on a site.
SharedDirectory() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.SharedDirectory
  The default constructor.
SharedDirectory(Map<FileServerType.OPERATION, List<FileServer>>, InternalMountPoint) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.SharedDirectory
  The overloaded constructor
Shell - Class in edu.isi.pegasus.planner.code.generator
  This code generator generates a shell script in the submit directory.
Shell() - Constructor for class edu.isi.pegasus.planner.code.generator.Shell
  The default constructor.
shiftRight(String) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Returns a float with the decimal point shifted right till the end.
SHORT_NAME - Static variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  The SHORTNAME for this implementation.
SHORT_NAME - Static variable in class edu.isi.pegasus.planner.code.gridstart.NetloggerPostScript
  The SHORTNAME for this implementation.
SHORT_NAME - Static variable in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  The SHORTNAME for this implementation.
SHORT_NAME - Static variable in class edu.isi.pegasus.planner.code.gridstart.NoPOSTScript
  The SHORTNAME for this implementation.
SHORT_NAME - Static variable in class edu.isi.pegasus.planner.code.gridstart.PegasusExitCode
  The SHORTNAME for this implementation.
SHORT_NAME - Static variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  The SHORTNAME for this implementation.
SHORT_NAME - Static variable in class edu.isi.pegasus.planner.code.gridstart.UserPOSTScript
  The SHORTNAME for this implementation.
SHORT_NAME - Static variable in class edu.isi.pegasus.planner.transfer.mapper.impl.Fixed
SHORT_NAME - Static variable in class edu.isi.pegasus.planner.transfer.mapper.impl.Flat
  The short name for the mapper
SHORT_NAME - Static variable in class edu.isi.pegasus.planner.transfer.mapper.impl.Hashed
  The short name for the mapper
SHORT_NAME - Static variable in class edu.isi.pegasus.planner.transfer.mapper.impl.Replica
  The short name for this backend.
shortDescribe() - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Returns a short textual description in the form of the name of the class.
shortDescribe() - Method in class edu.isi.pegasus.planner.code.gridstart.NetloggerPostScript
  Returns a short textual description of the implementing class.
shortDescribe() - Method in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
  Returns a short textual description in the form of the name of the class.
shortDescribe() - Method in class edu.isi.pegasus.planner.code.gridstart.NoPOSTScript
  Returns a short textual description of the implementing class.
shortDescribe() - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusExitCode
  Returns a short textual description of the implementing class.
shortDescribe() - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Returns a short textual description in the form of the name of the class.
shortDescribe() - Method in interface edu.isi.pegasus.planner.code.GridStart
  Returns a short textual description of the implementing class.
shortDescribe() - Method in class edu.isi.pegasus.planner.code.gridstart.UserPOSTScript
  Returns a short textual description of the implementing class.
shortDescribe() - Method in interface edu.isi.pegasus.planner.code.POSTScript
  Returns a short textual description of the implementing class.
SHOULD_TRANSFER_FILES_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.CondorC
  The name of the key that designates that files should be transferred via Condor File Transfer mechanism.
SHOULD_TRANSFER_FILES_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The name of the key that designates that files should be transferred via Condor File Transfer mechanism.
show(String) - Static method in class edu.isi.pegasus.common.util.Separator2Test
show(String) - Static method in class edu.isi.pegasus.common.util.SeparatorTest
show(String, ReplicaCatalogEntry) - Method in class edu.isi.pegasus.planner.client.RCClient
  Preliminary implementation of output method.
showHelp() - Method in class edu.isi.pegasus.planner.client.RCClient
  Prints internal command help.
ShowProperties - Class in <Unnamed>
  Displays single specific values or all values from the current system properties.
ShowProperties() - Constructor for class ShowProperties
showThreads() - Method in class edu.isi.pegasus.planner.client.ExitCode
showUsage() - Method in class edu.isi.pegasus.planner.client.ExitCode
  Implements printing the usage string onto stdout.
showUsage() - Method in class edu.isi.pegasus.planner.client.RCClient
  Prints the usage string on stdout.
showUsage() - Method in class edu.isi.pegasus.planner.client.VersionNumber
  Prints the usage string.
showUsage() - Method in class edu.isi.pegasus.planner.invocation.SimpleServer
showVersion(Version, boolean) - Static method in class edu.isi.pegasus.planner.client.VersionNumber
  Print the version information onto stdout.
shutdown() - Method in class edu.isi.pegasus.planner.refiner.ThreadPool.AuthenticateThread
  Sets the shutdown flag to true.
shutdown() - Method in class edu.isi.pegasus.planner.refiner.ThreadPool
  This method is called to ensure the clean shutdown of threads, and waits till all the requests have been serviced.
Simple - Class in edu.isi.pegasus.common.logging.format
  This formatter formats the messages in the simple format.
Simple() - Constructor for class edu.isi.pegasus.common.logging.format.Simple
  The default constructor.
SimpleEvent - Class in edu.isi.pegasus.common.logging.format
  A Simple LogEvent implementation that is back by a StringBuffer.
SimpleEvent() - Constructor for class edu.isi.pegasus.common.logging.format.SimpleEvent
  The default constructor.
SimpleFile - Class in edu.isi.pegasus.planner.catalog.replica.impl
  This class implements a replica catalog on top of a simple file which contains two or more columns.
SimpleFile() - Constructor for class edu.isi.pegasus.planner.catalog.replica.impl.SimpleFile
  Default empty constructor creates an object that is not yet connected to any database.
SimpleServer - Class in edu.isi.pegasus.planner.invocation
SimpleServer(int) - Constructor for class edu.isi.pegasus.planner.invocation.SimpleServer
SimpleServerThread - Class in edu.isi.pegasus.planner.invocation
SimpleServerThread(SimpleServer, Socket) - Constructor for class edu.isi.pegasus.planner.invocation.SimpleServerThread
SINGLE_READ - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolMode
  Constants for single read.
SINGLE_READ - Static variable in class edu.isi.pegasus.planner.catalog.transformation.TCMode
  Constants for backward compatibility.
SingleFTPerXFERJob - Interface in edu.isi.pegasus.planner.transfer
  An empty interface, that allows for grouping of implementations that can handle only one file transfer per transfer job like old guc and Stork.
SingleFTPerXFERJobRefiner - Class in edu.isi.pegasus.planner.transfer
  The refiner interface, that determines the functions that need to be implemented to add various types of transfer nodes to the workflow.
SingleFTPerXFERJobRefiner(ADag, PegasusBag) - Constructor for class edu.isi.pegasus.planner.transfer.SingleFTPerXFERJobRefiner
  The overloaded constructor.
SingleLook - Class in edu.isi.pegasus.planner.partitioner
  This class ends up writing a partitioned dax, that corresponds to one partition as defined by the Partitioner.
SingleLook(String, String) - Constructor for class edu.isi.pegasus.planner.partitioner.SingleLook
  The overloaded constructor.
SingleLook.MyCallBackHandler - Class in edu.isi.pegasus.planner.partitioner
  The internal callback handler for the DAXParser in Euryale.
SINGLETON_LOAD - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolMode
  Constants to specify how to load the class, as singleton or non singleton.
SINGLETON_LOAD - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.SiteFactory
  Constants to specify how to load the class, as singleton or non singleton.
singletonInstance(String) - Static method in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  The method which returns a Singleton instance of the derived InfoProvider class.
singletonInstance(String, String) - Static method in class edu.isi.pegasus.planner.catalog.site.impl.old.Text
  The method returns a singleton instance of the derived InfoProvider class.
singletonInstance(String, String) - Static method in class edu.isi.pegasus.planner.catalog.site.impl.old.XML
  The method returns a singleton instance of the derived InfoProvider class.
SITE - Static variable in class edu.isi.pegasus.planner.parser.tokens.SiteCatalogReservedWord
  token value for the reserved word "site".
SITE - Static variable in class edu.isi.pegasus.planner.parser.tokens.TransformationCatalogReservedWord
  token value for the reserved word "site".
Site - Class in edu.isi.pegasus.planner.selector.site.heft
  A data class that models a site as a collection of processors.
Site(String) - Constructor for class edu.isi.pegasus.planner.selector.site.heft.Site
  The default constructor.
Site(String, int) - Constructor for class edu.isi.pegasus.planner.selector.site.heft.Site
  The overloaded constructor.
SITE_CATALOG - Static variable in class edu.isi.pegasus.planner.classes.PegasusBag
  The constant to be passed to the accessor functions to get or set the handle to the site catalog.
SITE_NOT_FOUND - Static variable in interface edu.isi.pegasus.planner.selector.SiteSelector
  The value for the pool handle, when the pool is not found.
SITE_PROPERTY_KEY - Static variable in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  The name of the key that specifies the site attribute to be associated
SITE_STORE - Static variable in class edu.isi.pegasus.planner.classes.PegasusBag
  The constant to be passed to the accessor functions to get or set the handle to the Site Store
SiteCatalog - Interface in edu.isi.pegasus.planner.catalog
SiteCatalogEntry - Class in edu.isi.pegasus.planner.catalog.site.classes
  This data class describes a site in the site catalog.
SiteCatalogEntry() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  The default constructor.
SiteCatalogEntry(String) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  The overloaded constructor.
SiteCatalogEntry3 - Class in edu.isi.pegasus.planner.catalog.site.classes
  This data class describes a site in the site catalog.
SiteCatalogEntry3() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  The default constructor.
SiteCatalogEntry3(String) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  The overloaded constructor.
SiteCatalogException - Exception in edu.isi.pegasus.planner.catalog.site
  Class to notify of failures.
SiteCatalogException() - Constructor for exception edu.isi.pegasus.planner.catalog.site.SiteCatalogException
  Constructs a `SiteCatalogException` with no detail message.
SiteCatalogException(String) - Constructor for exception edu.isi.pegasus.planner.catalog.site.SiteCatalogException
  Constructs a `SiteCatalogException` with the specified detailed message.
SiteCatalogException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.catalog.site.SiteCatalogException
  Constructs a `SiteCatalogException` with the specified detailed message and a cause.
SiteCatalogException(Throwable) - Constructor for exception edu.isi.pegasus.planner.catalog.site.SiteCatalogException
  Constructs a `SiteCatalogException` with the specified just a cause.
SiteCatalogReservedWord - Class in edu.isi.pegasus.planner.parser.tokens
  Class to capture reserved words.
SiteCatalogReservedWord(int) - Constructor for class edu.isi.pegasus.planner.parser.tokens.SiteCatalogReservedWord
  Initializes an instance of a reserved word token.
SiteCatalogTextParser - Class in edu.isi.pegasus.planner.parser
  Parses the input stream and generates site configuration map as output.
SiteCatalogTextParser(Reader) - Constructor for class edu.isi.pegasus.planner.parser.SiteCatalogTextParser
  Initializes the parser with an input stream to read from.
SiteCatalogTextScanner - Class in edu.isi.pegasus.planner.parser
  Implements the scanner for reserved words and other tokens that are generated from the input stream.
SiteCatalogTextScanner(Reader) - Constructor for class edu.isi.pegasus.planner.parser.SiteCatalogTextScanner
  Starts to scan the given stream.
SiteCatalogXMLMetadataParser - Class in edu.isi.pegasus.planner.parser
  A lightweight XML Parser class to just retrieve the meta data in first instance of an element in a XML Document.
SiteCatalogXMLMetadataParser(PegasusBag, String) - Constructor for class edu.isi.pegasus.planner.parser.SiteCatalogXMLMetadataParser
  The overloaded constructor
SiteCatalogXMLMetadataParser.StopParserException - Exception in edu.isi.pegasus.planner.parser
  Private RuntimeException to stop the SAX Parser
SiteCatalogXMLParser - Interface in edu.isi.pegasus.planner.parser
  An empty interface for Site Catalog XML parsers
SiteCatalogXMLParser3 - Class in edu.isi.pegasus.planner.parser
  This class uses the Xerces SAX2 parser to validate and parse an XML document conforming to the Site Catalog schema v3.0
SiteCatalogXMLParser3(PegasusBag, List<String>) - Constructor for class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser3
  The overloaded constructor.
SiteCatalogXMLParser4 - Class in edu.isi.pegasus.planner.parser
  This class uses the Xerces SAX2 parser to validate and parse an XML document conforming to the Site Catalog schema v4.0
SiteCatalogXMLParser4(PegasusBag, List<String>) - Constructor for class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser4
  The overloaded constructor.
SiteCatalogXMLParserFactory - Class in edu.isi.pegasus.planner.parser
  A factory class to load the appropriate Site Catalog Parser implementations based on version in the site catalog element of the XML document
SiteCatalogXMLParserFactory() - Constructor for class edu.isi.pegasus.planner.parser.SiteCatalogXMLParserFactory
SiteCatalogXMLParserFactoryException - Exception in edu.isi.pegasus.planner.parser
  Class to notify of failures while instantiating DAXCallback implementations.
SiteCatalogXMLParserFactoryException(String) - Constructor for exception edu.isi.pegasus.planner.parser.SiteCatalogXMLParserFactoryException
  Constructs a `DAXParserFactoryException` with no detail message.
SiteCatalogXMLParserFactoryException(String, String) - Constructor for exception edu.isi.pegasus.planner.parser.SiteCatalogXMLParserFactoryException
  Constructs a `DAXParserFactoryException` with the specified detailed message.
SiteCatalogXMLParserFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.parser.SiteCatalogXMLParserFactoryException
  Constructs a `DAXParserFactoryException` with the specified detailed message and a cause.
SiteCatalogXMLParserFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.planner.parser.SiteCatalogXMLParserFactoryException
  Constructs a `DAXParserFactoryException` with the specified detailed message and a cause.
SiteData - Class in edu.isi.pegasus.planner.catalog.site.classes
  The abstract base class for all site catalog classes.
SiteData() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.SiteData
SiteDataVisitor - Interface in edu.isi.pegasus.planner.catalog.site.classes
  The Visitor interface for the Site Catalog Data Classes.
SiteFactory - Class in edu.isi.pegasus.planner.catalog.site.impl.old
  A factory class to load the appropriate implementation of Transformation Catalog as specified by properties.
SiteFactory() - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.old.SiteFactory
SiteFactory - Class in edu.isi.pegasus.planner.catalog.site
  A factory class to load the appropriate implementation of Site Catalog as specified by properties.
SiteFactory() - Constructor for class edu.isi.pegasus.planner.catalog.site.SiteFactory
SiteFactoryException - Exception in edu.isi.pegasus.planner.catalog.site.impl.old
  Class to notify of failures while instantiating Site Catalog implementations.
SiteFactoryException(String) - Constructor for exception edu.isi.pegasus.planner.catalog.site.impl.old.SiteFactoryException
  Constructs a `SiteFactoryException` with no detail message.
SiteFactoryException(String, String) - Constructor for exception edu.isi.pegasus.planner.catalog.site.impl.old.SiteFactoryException
  Constructs a `SiteFactoryException` with the specified detailed message.
SiteFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.catalog.site.impl.old.SiteFactoryException
  Constructs a `SiteFactoryException` with the specified detailed message and a cause.
SiteFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.planner.catalog.site.impl.old.SiteFactoryException
  Constructs a `SiteFactoryException` with the specified detailed message and a cause.
SiteFactoryException - Exception in edu.isi.pegasus.planner.catalog.site
  Class to notify of failures while instantiating Site Catalog implementations.
SiteFactoryException(String) - Constructor for exception edu.isi.pegasus.planner.catalog.site.SiteFactoryException
  Constructs a `SiteFactoryException` with no detail message.
SiteFactoryException(String, String) - Constructor for exception edu.isi.pegasus.planner.catalog.site.SiteFactoryException
  Constructs a `SiteFactoryException` with the specified detailed message.
SiteFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.catalog.site.SiteFactoryException
  Constructs a `SiteFactoryException` with the specified detailed message and a cause.
SiteFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.planner.catalog.site.SiteFactoryException
  Constructs a `SiteFactoryException` with the specified detailed message and a cause.
SiteInfo - Class in edu.isi.pegasus.planner.catalog.site.impl.old.classes
  This is a data class that is used to store information about a single remote site (pool).
SiteInfo() - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  Default Constructor.
SITEINFO - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  Array storing the names of the attributes that are stored with the site.
SiteInfo2SiteCatalogEntry - Class in edu.isi.pegasus.planner.catalog.site.classes
  An adapter class that converts SiteInfo object to SiteCatalogEntry object.
SiteInfo2SiteCatalogEntry() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.SiteInfo2SiteCatalogEntry
siteSelectionFor(String, String) - Method in class edu.isi.pegasus.planner.provenance.pasoa.pps.Empty
  siteSelectionFor
siteSelectionFor(String, String) - Method in interface edu.isi.pegasus.planner.provenance.pasoa.PPS
SiteSelector - Interface in edu.isi.pegasus.planner.selector
  The interface for the Site Selector.
SiteSelectorFactory - Class in edu.isi.pegasus.planner.selector.site
  A factory class to load the appropriate type of Site Selector, as specified by the user at runtime in properties.
SiteSelectorFactory() - Constructor for class edu.isi.pegasus.planner.selector.site.SiteSelectorFactory
SiteSelectorFactoryException - Exception in edu.isi.pegasus.planner.selector.site
  Class to notify of failures while instantiating SiteSelector implementations.
SiteSelectorFactoryException(String) - Constructor for exception edu.isi.pegasus.planner.selector.site.SiteSelectorFactoryException
  Constructs a `SiteSelectorFactoryException` with no detail message.
SiteSelectorFactoryException(String, String) - Constructor for exception edu.isi.pegasus.planner.selector.site.SiteSelectorFactoryException
  Constructs a `SiteSelectorFactoryException` with the specified detailed message.
SiteSelectorFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.selector.site.SiteSelectorFactoryException
  Constructs a `SiteSelectorFactoryException` with the specified detailed message and a cause.
SiteSelectorFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.planner.selector.site.SiteSelectorFactoryException
  Constructs a `SiteSelectorFactoryException` with the specified detailed message and a cause.
SiteStore - Class in edu.isi.pegasus.planner.catalog.site.classes
  The site store contains the collection of sites backed by a HashMap.
SiteStore() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  The default constructor.
SiteTransfer() - Constructor for class edu.isi.pegasus.planner.transfer.refiner.Chain.SiteTransfer
  The default constructor.
SiteTransfer(String, int) - Constructor for class edu.isi.pegasus.planner.transfer.refiner.Chain.SiteTransfer
  Convenience constructor.
size() - Method in class edu.isi.pegasus.common.util.CommonProperties
  Accessor: Obtains the number of properties known to the project.
size() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the number of nodes in the graph.
size() - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Returns the number of nodes in the graph.
size() - Method in interface edu.isi.pegasus.planner.partitioner.graph.Graph
  Returns the number of nodes in the graph.
size() - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph
  Returns the number of nodes in the graph.
size() - Method in class edu.isi.pegasus.planner.partitioner.Partition
  Returns the number of nodes in the partition.
skippedEntity(String) - Method in class edu.isi.pegasus.planner.parser.InvocationParser
  Receive a notification that an entity was skipped.
skipWhitespace() - Method in class edu.isi.pegasus.planner.parser.SiteCatalogTextScanner
  Skips any white space and comments in the input.
skipWhitespace() - Method in class edu.isi.pegasus.planner.parser.TransformationCatalogTextScanner
  Skips any white space and comments in the input.
SLS - Interface in edu.isi.pegasus.planner.transfer
  This interface defines the second level staging process, that manages the transfer of files from the headnode to the worker node temp and back.
SLSFactory - Class in edu.isi.pegasus.planner.transfer.sls
  A factory class to load the appropriate type of SLS Implementation to do the Second Level Staging.
SLSFactory() - Constructor for class edu.isi.pegasus.planner.transfer.sls.SLSFactory
SLSFactoryException - Exception in edu.isi.pegasus.planner.transfer.sls
  Class to notify of failures while instantiating SLS implementations.
SLSFactoryException(String) - Constructor for exception edu.isi.pegasus.planner.transfer.sls.SLSFactoryException
  Constructs a `SLSFactoryException` with no detail message.
SLSFactoryException(String, String) - Constructor for exception edu.isi.pegasus.planner.transfer.sls.SLSFactoryException
  Constructs a `SLSFactoryException` with the specified detailed message.
SLSFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.transfer.sls.SLSFactoryException
  Constructs a `SLSFactoryException` with the specified detailed message and a cause.
SLSFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.planner.transfer.sls.SLSFactoryException
  Constructs a `SLSFactoryException` with the specified detailed message and a cause.
slurpInFile(String, String) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Convenience method to slurp in contents of a file into memory.
SOLUTION_PREFIX - Static variable in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  The prefix that the site selector writes out on its stdout to designate that it is sending a solution.
sort() - Method in class edu.isi.pegasus.planner.partitioner.Topological
  Topologically sorts the partition and returns a List of `GraphNode` elements.
SPARCV7 - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Arch
SPARCV9 - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Arch
SPECIALIZED_TEMPLATES_Q - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
split(String) - Static method in class edu.isi.pegasus.common.util.Separator
  Splits a fully-qualified identifier into its components.
splitFQDI(String) - Static method in class edu.isi.pegasus.common.util.Separator
  Splits a fully-qualified definition identifier into separate namespace, name and version.
splitLFN(String) - Static method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Splits the full qualified logical transformation into its components.
splitVersion() - Method in class edu.isi.pegasus.common.util.Version
SRM_MOUNT_POINT_PROPERTIES_SUFFIX - Static variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  The suffix to retrive the mount point for SRM server.
SRM_PROPERTIES_PREFIX - Static variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  The property prefix for retrieving SRM properties.
SRM_SERVICE_URL_PROPERTIES_SUFFIX - Static variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  The suffix to retrive the service url for SRM server.
Ssh - Class in edu.isi.pegasus.common.credential.impl
  A convenience class that allows us to determine the path to the user ssh private key file.
Ssh() - Constructor for class edu.isi.pegasus.common.credential.impl.Ssh
  The default constructor.
SSH - Class in edu.isi.pegasus.planner.code.generator.condor.style
  Enables a job to be directly submitted to a remote PBS cluster using direct ssh submission available as part of BOSCO The CREAM CE support in Condor is documented at the following link
SSH() - Constructor for class edu.isi.pegasus.planner.code.generator.condor.style.SSH
  The default constructor.
SSH_IMPLEMENTING_CLASS - Static variable in class edu.isi.pegasus.common.credential.CredentialHandlerFactory
SSH_PRIVATE_KEY_PEGASUS_PROFILE_KEY - Static variable in class edu.isi.pegasus.common.credential.impl.Ssh
SSH_PRIVATE_KEY_VARIABLE - Static variable in class edu.isi.pegasus.common.credential.impl.Ssh
  The name of the environment variable that specifies the path to the SSH key.
SSH_PRIVATE_KEY_VARIABLE - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
SSH_STYLE - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The style indicating that the submit files are to be generated for a direct ssh submission
SSH_STYLE_IMPLEMENTING_CLASS - Static variable in class edu.isi.pegasus.planner.code.generator.condor.CondorStyleFactory
  The name of the class implementing the CondorG Style.
st - Variable in class edu.isi.pegasus.planner.provisioner.Node
stack(boolean) - Method in class edu.isi.pegasus.planner.provisioner.OccupationDiagram
  Run Task placement phase of BTS algorithm
StackBasedXMLParser - Class in edu.isi.pegasus.planner.parser
  An abstract base class that XML Parsers can use if they use stack internally to store the elements encountered while parsing XML documents using SAX
StackBasedXMLParser(PegasusBag) - Constructor for class edu.isi.pegasus.planner.parser.StackBasedXMLParser
  The overloaded constructor.
stacked - Variable in class edu.isi.pegasus.planner.provisioner.Node
STAGE_IN_JOB - Static variable in class edu.isi.pegasus.planner.classes.Job
  Denotea a job that is used to stage in the input files for a compute job.
STAGE_IN_PREFIX - Static variable in interface edu.isi.pegasus.planner.transfer.Refiner
  The prefix for the jobs which are added to transfer the files to a job's execution pool from the location returned from the replica mechanism.
STAGE_IN_REMOTE_TYPE - Static variable in class edu.isi.pegasus.planner.transfer.RemoteTransfer.TransferState
  The constant to denote that a stage-in transfer is to be exectuted remotely
STAGE_IN_TPT_PROPERTY - Static variable in class edu.isi.pegasus.planner.transfer.TPT
  The property name to get the sites for which stage-in transfers need to be TPT.
STAGE_IN_TPT_REMOTE - Static variable in class edu.isi.pegasus.planner.transfer.TPT.TPTState
  The constant to denote that a stage-in transfer is to be executed on the remote site.
STAGE_IN_TPT_REMOTE_PROPERTY - Static variable in class edu.isi.pegasus.planner.transfer.TPT
  The property name to get the sites for which stage-in TPT transfers need to be executed on the remote site.
STAGE_IN_TPT_TYPE - Static variable in class edu.isi.pegasus.planner.transfer.TPT.TPTState
  The constant to denote that a stage-in transfer is to be third party.
STAGE_IN_TRANSFERS_REMOTE_PROPERTY - Static variable in class edu.isi.pegasus.planner.transfer.RemoteTransfer
  The property name to get the sites for which stage-in transfers need to be executed remotely.
STAGE_IN_WORKER_PACKAGE_JOB - Static variable in class edu.isi.pegasus.planner.classes.Job
  Denotes a job that stages the worker package.
STAGE_OUT_JOB - Static variable in class edu.isi.pegasus.planner.classes.Job
  Denotes a job that transfers the date generated by a compute job to the output pool specified by the user.
STAGE_OUT_PREFIX - Static variable in interface edu.isi.pegasus.planner.transfer.Refiner
  The prefix for the jobs which are added to transfer the files generated by a job on an execution pool to the output pool.
STAGE_OUT_REMOTE_TYPE - Static variable in class edu.isi.pegasus.planner.transfer.RemoteTransfer.TransferState
  The constant to denote that a stage-out transfer is to be exectuted remotely
STAGE_OUT_TPT_PROPERTY - Static variable in class edu.isi.pegasus.planner.transfer.TPT
  The property name to get the sites for which stage-out transfers need to be TPT.
STAGE_OUT_TPT_REMOTE - Static variable in class edu.isi.pegasus.planner.transfer.TPT.TPTState
  The constant to denote that a stage-out transfer is to be executed on the remote site.
STAGE_OUT_TPT_REMOTE_PROPERTY - Static variable in class edu.isi.pegasus.planner.transfer.TPT
  The property name to get the sites for which stage-out TPT transfers need to be executed on the remote site.
STAGE_OUT_TPT_TYPE - Static variable in class edu.isi.pegasus.planner.transfer.TPT.TPTState
  The constant to denote that a stage-out transfer is to be third party.
STAGE_OUT_TRANSFERS_REMOTE_PROPERTY - Static variable in class edu.isi.pegasus.planner.transfer.RemoteTransfer
  The property name to get the sites for which stage-out transfers need to be executed remotely.
Staged - Class in edu.isi.pegasus.planner.catalog.transformation.mapper
  This implementation only generates maps for sites where transformation can be staged
Staged(PegasusBag) - Constructor for class edu.isi.pegasus.planner.catalog.transformation.mapper.Staged
  The protected constructor.
Staged - Class in edu.isi.pegasus.planner.selector.transformation
  This implementation of the Selector select a transformation of type STAGEABLE on all sites.
Staged() - Constructor for class edu.isi.pegasus.planner.selector.transformation.Staged
stageInOnRemoteSite(String) - Method in class edu.isi.pegasus.planner.transfer.RemoteTransfer
  Returns a boolean indicating whether to execute stage-in transfers on remote site or not.
stageInThirdParty(String) - Method in class edu.isi.pegasus.planner.transfer.TPT
  Returns a boolean indicating whether to use third party transfers for stage-in transfers or not.
stageInThirdPartyRemote(String) - Method in class edu.isi.pegasus.planner.transfer.TPT
  Returns a boolean indicating whether to execute third party transfers for stage-in on remote site or not.
stageOutOnRemoteSite(String) - Method in class edu.isi.pegasus.planner.transfer.RemoteTransfer
  Returns a boolean indicating whether to execute stage-out transfers on remote site or not.
stageOutThirdParty(String) - Method in class edu.isi.pegasus.planner.transfer.TPT
  Returns a boolean indicating whether to use third party transfers for stage-out transfers or not.
stageOutThirdPartyRemote(String) - Method in class edu.isi.pegasus.planner.transfer.TPT
  Returns a boolean indicating whether to execute third party transfers for stage-out on remote site or not.
stageSLSFilesViaFirstLevelStaging() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a boolean indicating whether to stage sls files via Pegasus First Level Staging or let Condor do it.
stagingIntroducedFor(List, String) - Method in class edu.isi.pegasus.planner.provenance.pasoa.pps.Empty
  stagingIntroducedFor
stagingIntroducedFor(List, String) - Method in interface edu.isi.pegasus.planner.provenance.pasoa.PPS
stagingSiteMappingToString() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Convers the staging site mappings to comma separated list of executionsite=stagingsite mappings
Stamp - Class in edu.isi.pegasus.planner.invocation
  The Stamp element.
Stamp() - Constructor for class edu.isi.pegasus.planner.invocation.Stamp
  The default constructor
Stamp(String) - Constructor for class edu.isi.pegasus.planner.invocation.Stamp
  Constructs a piece of data.
STAMP_FILENAME - Static variable in class edu.isi.pegasus.common.util.Version
  Basename of the build stamp file.
Stampede - Class in edu.isi.pegasus.planner.code.generator
  A Stampede Events Code Generator that generates events in netlogger format for the exectuable workflow.
Stampede() - Constructor for class edu.isi.pegasus.planner.code.generator.Stampede
STAMPEDE_EVENT_GENERATOR_CLASS - Static variable in class edu.isi.pegasus.planner.code.CodeGeneratorFactory
  The name of the class implementing the Stampede Event Generator
STANDARD_UNIVERSE - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.Condor
STANDARD_UNIVERSE - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The condor universe key value for standard universe.
start() - Method in class edu.isi.pegasus.planner.refiner.ThreadPool.AuthenticateThread
  The start method for the thread.
START_COMMENT_TAG - Static variable in class edu.isi.pegasus.common.util.XMLWriter
START_ELEMENT_TAG - Static variable in class edu.isi.pegasus.common.util.XMLWriter
START_END_ELEMENT_TAG - Static variable in class edu.isi.pegasus.common.util.XMLWriter
START_POSTFIX - Static variable in class edu.isi.ikcap.workflows.util.logging.LogEvent
startDocument() - Method in class edu.isi.pegasus.planner.client.DAXValidator
startDocument() - Method in class edu.isi.pegasus.planner.parser.InvocationParser
  This method specifies what to do when the parser is at the beginning of the document.
startElement(String) - Method in class edu.isi.pegasus.common.util.XMLWriter
startElement(String, int) - Method in class edu.isi.pegasus.common.util.XMLWriter
startElement(String, String, String, Attributes) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
startElement(String, String, String, Attributes) - Method in class edu.isi.pegasus.planner.client.DAXValidator
startElement(String, String, String, Attributes) - Method in class edu.isi.pegasus.planner.parser.ConfigXmlParser
startElement(String, String, String, Attributes) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Overriding the empty implementation provided by DefaultHandler of ContentHandler.
startElement(String, String, String, Attributes) - Method in class edu.isi.pegasus.planner.parser.InvocationParser
  This method defines the action to take when the parser begins to parse an element.
startElement(String, String, String, Attributes) - Method in class edu.isi.pegasus.planner.parser.Parser
  An empty implementation is provided by DefaultHandler of ContentHandler.
startElement(String, String, String, Attributes) - Method in class edu.isi.pegasus.planner.parser.PDAXParser
  An empty implementation is provided by DefaultHandler of ContentHandler.
startElement(String, String, String, Attributes) - Method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLMetadataParser
  Start Element.
startElement(String, String, String, Attributes) - Method in class edu.isi.pegasus.planner.parser.StackBasedXMLParser
  This method defines the action to take when the parser begins to parse an element.
startMonitoring() - Method in interface edu.isi.pegasus.planner.code.CodeGenerator
  Starts monitoring of the workflow by invoking a workflow monitor daemon.
startMonitoring() - Method in class edu.isi.pegasus.planner.code.generator.Abstract
  Starts monitoring of the workflow by invoking a workflow monitor daemon.
startMonitoring() - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Starts monitoring of the workflow by invoking a workflow monitor daemon tailstatd.
startMonitoring() - Method in class edu.isi.pegasus.planner.code.generator.DAXReplicaStore
  Not implemented
startMonitoring() - Method in class edu.isi.pegasus.planner.code.generator.MonitordNotify
  Not implemented
startMonitoring() - Method in class edu.isi.pegasus.planner.code.generator.Stampede
startParser(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.XML2
startParser(String) - Method in class edu.isi.pegasus.planner.parser.ConfigXmlParser
startParser(String) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  This starts the parsing of the file by the parser.
startParser(String) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser3
  The main method that starts the parsing.
startParser(String) - Method in class edu.isi.pegasus.planner.parser.Parser
  Start the parser.
startParser(String) - Method in class edu.isi.pegasus.planner.parser.PDAXParser
  Ends up starting the parsing of the file , by the underlying parser.
startParser(String) - Method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLMetadataParser
  The function that starts the parser
startParser(String) - Method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser3
  The main method that starts the parsing.
startParser(String) - Method in class edu.isi.pegasus.planner.parser.SiteCatalogXMLParser4
  The main method that starts the parsing.
startPrefixMapping(String, String) - Method in class edu.isi.pegasus.planner.parser.InvocationParser
  There is a prefix or namespace defined, put the prefix and its URI in the HashMap.
stat(String) - Method in class edu.isi.pegasus.gridftp.GridFTPConnection
  Return information about path
STAT - Static variable in class edu.isi.pegasus.planner.classes.Profile
Stat - Class in edu.isi.pegasus.planner.namespace
  The stat namespace object.
Stat() - Constructor for class edu.isi.pegasus.planner.namespace.Stat
  The default constructor.
Stat(Map) - Constructor for class edu.isi.pegasus.planner.namespace.Stat
  The overloaded constructor.
StatCall - Class in edu.isi.pegasus.planner.invocation
  This class is the container for a complete call to stat() or fstat().
StatCall() - Constructor for class edu.isi.pegasus.planner.invocation.StatCall
  Default c'tor: Construct a hollow shell and allow further information to be added later.
StatCall(String) - Constructor for class edu.isi.pegasus.planner.invocation.StatCall
  Construct a specific but empty stat call object.
statemap - Static variable in class edu.isi.pegasus.common.util.Separator
  Maps the state and character class to the follow-up state.
statemap2 - Static variable in class edu.isi.pegasus.common.util.Separator
  Maps the new state from current state and character class.
static_method(String, Object[]) - Method in class edu.isi.pegasus.common.util.DynamicLoader
  Dynamically instantiates a class from a static method which constructs the resulting object.
StatInfo - Class in edu.isi.pegasus.planner.invocation
  This class is the container for the results of a call to either stat() or fstat().
StatInfo() - Constructor for class edu.isi.pegasus.planner.invocation.StatInfo
  Default c'tor: Construct a hollow shell and allow further information to be added later.
statistics() - Method in class edu.isi.pegasus.planner.client.DAXValidator
  Show how many warnings, errors and fatals were shown.
Status - Class in edu.isi.pegasus.planner.invocation
  This class encapsulates the exit code or reason of termination for a given job.
Status() - Constructor for class edu.isi.pegasus.planner.invocation.Status
  Default c'tor: Construct a hollow shell and allow further information to be added later.
Status(int) - Constructor for class edu.isi.pegasus.planner.invocation.Status
  Constructs a layer with the raw exit code.
Status(int, JobStatus) - Constructor for class edu.isi.pegasus.planner.invocation.Status
  Constructs the complete class with raw exit code and a status child describing the exit code.
stdErr - Variable in class edu.isi.pegasus.planner.classes.Job
  File which contains standard error.
stdIn - Variable in class edu.isi.pegasus.planner.classes.Job
  File which contains stdin (keyboard input).
stdOut - Variable in class edu.isi.pegasus.planner.classes.Job
  File which contains stdout.
StopParserException() - Constructor for exception edu.isi.pegasus.planner.parser.SiteCatalogXMLMetadataParser.StopParserException
STORAGE_DIR - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPServer
  The constant to be passed to the accessor functions to get or set the storage directory of the grid ftp server.
StorageType - Class in edu.isi.pegasus.planner.catalog.site.classes
  An Abstract Data class to describe the filesystem layout on a site, both shared and local on a site/node
StorageType() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.StorageType
  The default constructor
StorageType(LocalDirectory, SharedDirectory) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.StorageType
  The overloaded constructor.
store(Map) - Method in class edu.isi.pegasus.planner.classes.ReplicaStore
  Stores replica catalog entries into the store.
StoreGvdsMdsInfo(NamingEnumeration, String, PoolConfig) - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.MdsQuery
Stork - Class in edu.isi.pegasus.planner.code.generator
  This implementation generates files that can be understood by Stork.
Stork() - Constructor for class edu.isi.pegasus.planner.code.generator.Stork
  The default constructor.
Stork - Class in edu.isi.pegasus.planner.transfer.implementation
  The implementation that creates transfer jobs referring to the stork data placement scheduler that can handle only one transfer per job.
Stork(PegasusBag) - Constructor for class edu.isi.pegasus.planner.transfer.implementation.Stork
  The overloaded constructor, that is called by the Factory to load the class.
strargs - Variable in class edu.isi.pegasus.planner.classes.Job
  The arguements for the job.
Strategy - Interface in edu.isi.pegasus.planner.refiner.createdir
  The interface that defines how the cleanup job is invoked and created.
STREAM_STDERR_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The name of the key that specifies whether to stream stderr or not
STREAM_STDOUT_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The name of the key that specifies whether to stream stderr or not
StreamGobbler - Class in edu.isi.pegasus.common.util
  A Stream gobbler class to take care of reading from a stream and optionally write out to another stream.
StreamGobbler(InputStream, StreamGobblerCallback) - Constructor for class edu.isi.pegasus.common.util.StreamGobbler
  The overloaded constructor.
StreamGobblerCallback - Interface in edu.isi.pegasus.common.util
  This interface defines the callback calls that are called from within the StreamGobbler while working on a stream.
StringBuilderDataSink() - Constructor for class edu.isi.pegasus.gridftp.GridFTPConnection.StringBuilderDataSink
stringInList(String, List) - Method in class edu.isi.pegasus.planner.refiner.Engine
stringInPegVector(String, Vector) - Method in class edu.isi.pegasus.planner.refiner.Engine
  Returns true if a particular String is in the Vector of PegasusFile objects.
stringInVector(String, Vector) - Method in class edu.isi.pegasus.planner.refiner.Engine
  Returns true if a particular String is in the Vector of strings.
STYLE_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the key, that denotes the style of the dag that is constructed.
STYLE_NAME - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.Condor
  The name of the style being implemented.
STYLE_NAME - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.CondorC
  The name of the style being implemented.
STYLE_NAME - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.CondorG
  The name of the style being implemented.
STYLE_NAME - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.CondorGlideIN
  The name of the style being implemented.
STYLE_NAME - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.CondorGlideinWMS
  The name of the style being implemented.
STYLE_NAME - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.CreamCE
  The name of the style being implemented.
STYLE_NAME - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.GLite
  The name of the style being implemented.
STYLE_NAME - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.SSH
  The name of the style being implemented.
SUBDAG_EXTERNAL_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Dagman
  The name of the key that indicates the path to the external subdag
SUBDAXGenerator - Class in edu.isi.pegasus.planner.code.generator.condor
  The class that takes in a dax job specified in the DAX and renders it into a SUBDAG with pegasus-plan as the appropriate prescript.
SUBDAXGenerator() - Constructor for class edu.isi.pegasus.planner.code.generator.condor.SUBDAXGenerator
  The default constructor.
Submit - Class in edu.isi.pegasus.planner.catalog.transformation.mapper
  This implementation of the TCMapper returns a TCMap which only contains Stageable executables from the Local site.
Submit(PegasusBag) - Constructor for class edu.isi.pegasus.planner.catalog.transformation.mapper.Submit
  The protected constructor.
Submit - Class in edu.isi.pegasus.planner.selector.transformation
  This implementation of the Selector select a transformation of type STAGEABLE and only on the submit site.
Submit() - Constructor for class edu.isi.pegasus.planner.selector.transformation.Submit
SUBMIT_DIR_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The submit directory for the workflow.
SUBMIT_DIRECTORY_PREFIX - Static variable in class edu.isi.pegasus.planner.common.RunDirectoryFilenameFilter
  The prefix for the submit directory.
SUBMIT_DIRECTORY_PREFIX - Static variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The prefix for the submit directory.
SUBMIT_HOSTNAME_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The key for the submit hostname.
SubmitDirectoryFilenameFilter - Class in edu.isi.pegasus.planner.client
  A filename filter for identifying the submit directory
SubmitDirectoryFilenameFilter(String) - Constructor for class edu.isi.pegasus.planner.client.SubmitDirectoryFilenameFilter
  Overloaded constructor.
submitToScheduler() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns whether to submit the workflow or not.
submitWorkflow(String) - Method in class edu.isi.pegasus.planner.client.CPlanner
  Submits the workflow for execution using pegasus-run, a wrapper around pegasus-submit-dag.
SUCCESS_MESSAGE - Static variable in class edu.isi.pegasus.planner.client.CPlanner
  The message to be logged in case of empty executable workflow.
SUCCESS_MESSAGE_AGGREGATOR - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  Static Handle to the delimiter aggregator.
SUFFIX_TEMPORARY_FILE - Static variable in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  The suffix to be used while creating a temporary file to pass to the external siteselector.
Sum - Class in edu.isi.pegasus.planner.namespace.aggregator
  An implementation of the Aggregator interface that sums the profile values.
Sum() - Constructor for class edu.isi.pegasus.planner.namespace.aggregator.Sum
SUM_AGGREGATOR - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  Static Handle to the sum aggregator.
SUNOS - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Os
SUPPORTED_TRANSFORMATION_FORMAT - Static variable in class edu.isi.pegasus.planner.client.TCConverter
  The supported transformation formats.
supportedOSReleaseAndVersions() - Static method in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  A set of OS release and version combinations for which our build processes build Pegasus binaries.
Swap - Class in edu.isi.pegasus.planner.invocation
  The swap element.
Swap() - Constructor for class edu.isi.pegasus.planner.invocation.Swap
  The default constructor
symbolTable() - Static method in class edu.isi.pegasus.planner.parser.tokens.SiteCatalogReservedWord
  Singleton access to the symbol table as a whole.
symbolTable() - Static method in class edu.isi.pegasus.planner.parser.tokens.TransformationCatalogReservedWord
  Singleton access to the symbol table as a whole.
SYMLINK_URL_SCHEME - Static variable in class edu.isi.pegasus.common.util.PegasusURL
  The scheme name for file url.
symlinkCommonLog() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Completely disable placing a symlink for Condor common log (indiscriminately).
SysInfo - Class in edu.isi.pegasus.planner.catalog.classes
  A container class to keep system information associated with a Site entry in the Site Catalog or a Transformation in the Transformation Catalog.
SysInfo() - Constructor for class edu.isi.pegasus.planner.catalog.classes.SysInfo
  The default constructor.
SysInfo(String) - Constructor for class edu.isi.pegasus.planner.catalog.classes.SysInfo
  This constructor takes the system information in the format arch::os:osversion:glibc
SYSINFO - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  The constant to be passed to the accessor functions to get or set the `VDSSysInfo` site.
SYSINFO - Static variable in class edu.isi.pegasus.planner.parser.tokens.SiteCatalogReservedWord
  token value for the reserved work sysinfo.
SysInfo.Architecture - Enum in edu.isi.pegasus.planner.catalog.classes
  Enumerates the new architecture types supported in Pegasus.
SysInfo.OS - Enum in edu.isi.pegasus.planner.catalog.classes
  Enumerates the new OS types supported in Pegasus.
system - Variable in class edu.isi.pegasus.planner.catalog.transformation.client.Client
system - Variable in class edu.isi.pegasus.planner.client.TCClient
SYSTEM_ARCHITECTURE - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
SYSTEM_ARCHITECTURE - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
SYSTEM_ATTRIBUTE_KEY - Static variable in class edu.isi.pegasus.planner.invocation.Uname
  The system attribute for the uname
SYSTEM_HOSTADDR - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
SYSTEM_HOSTADDR - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
SYSTEM_HOSTNAME - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
SYSTEM_HOSTNAME - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
SYSTEM_NODENAME - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
SYSTEM_NODENAME - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
SYSTEM_NUMBEROFPROCESSORS - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
SYSTEM_NUMBEROFPROCESSORS - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
SYSTEM_OS - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
SYSTEM_OS - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
systemstring - Variable in class edu.isi.pegasus.planner.catalog.transformation.client.Client

## T

T2 - Class in edu.isi.pegasus.planner.transfer.implementation
  The implementation that creates transfer jobs referring to the T2 executable distributed with the Pegasus.
T2(PegasusBag) - Constructor for class edu.isi.pegasus.planner.transfer.implementation.T2
  The overloaded constructor, that is called by the Factory to load the class.
TABSPACE - Static variable in class edu.isi.pegasus.planner.catalog.transformation.client.TCQuery
TAIL_INDEX - Static variable in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  The index of the tail job.
Task - Class in edu.isi.pegasus.planner.invocation
  The proc element.
Task() - Constructor for class edu.isi.pegasus.planner.invocation.Task
  The default constructor
TASK_EDGE_EVENT_NAME - Static variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The event name for task edge
TASK_EVENT_NAME - Static variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The event name for task info
TASK_ID_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The attribute key for task id
TASK_MAP_EVENT_NAME - Static variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The event name for task map event
TASK_TRANSFORMATION_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The attribute key for transformation
taskName - Variable in class edu.isi.pegasus.planner.provisioner.Node
tc - Variable in class edu.isi.pegasus.planner.catalog.transformation.client.Client
tc - Variable in class edu.isi.pegasus.planner.client.TCClient
TC_DATA_FILE - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
TC_INITIALIZATION_FILES - Static variable in class edu.isi.pegasus.planner.client.TCConverter
  List of sql initialization files
TC_TEXT_FILE - Static variable in class edu.isi.pegasus.planner.common.PegasusProperties
TCAdd - Class in edu.isi.pegasus.planner.catalog.transformation.client
TCAdd(TransformationCatalog, LogManager, Map) - Constructor for class edu.isi.pegasus.planner.catalog.transformation.client.TCAdd
TCClient - Class in edu.isi.pegasus.planner.client
  A common client to add, modify, delete, query any Transformation Catalog implementation.
TCClient() - Constructor for class edu.isi.pegasus.planner.client.TCClient
TCConverter - Class in edu.isi.pegasus.planner.client
  A client to convert transformation catalog between different formats.
TCConverter() - Constructor for class edu.isi.pegasus.planner.client.TCConverter
  The default constructor.
TCDelete - Class in edu.isi.pegasus.planner.catalog.transformation.client
  This is a TCClient class which handles the Delete Operations.
TCDelete(TransformationCatalog, LogManager, Map) - Constructor for class edu.isi.pegasus.planner.catalog.transformation.client.TCDelete
TCFormatUtility - Class in edu.isi.pegasus.planner.catalog.transformation.client
  This is a utility class for converting transformation catalog into different formats.
TCFormatUtility() - Constructor for class edu.isi.pegasus.planner.catalog.transformation.client.TCFormatUtility
tclist - Variable in class edu.isi.pegasus.planner.selector.transformation.RoundRobin
TCMap - Class in edu.isi.pegasus.planner.classes
  This is a data class to store the TCMAP for a particular dag.
TCMap() - Constructor for class edu.isi.pegasus.planner.classes.TCMap
  Default constructor.
TCMode - Class in edu.isi.pegasus.planner.catalog.transformation
  This class defines all the constants referring to the various interfaces to the transformation catalog, and used by the Concrete Planner.
TCMode() - Constructor for class edu.isi.pegasus.planner.catalog.transformation.TCMode
TCQuery - Class in edu.isi.pegasus.planner.catalog.transformation.client
TCQuery(TransformationCatalog, LogManager, Map) - Constructor for class edu.isi.pegasus.planner.catalog.transformation.client.TCQuery
TCQuery.LFNComparator - Class in edu.isi.pegasus.planner.catalog.transformation.client
  The comparator that is used to group the RLSAttributeObject objects by the value in the key field.
TCType - Enum in edu.isi.pegasus.planner.catalog.transformation.classes
  This is an enumerated data class for the different types of transformation.
TCType() - Constructor for enum edu.isi.pegasus.planner.catalog.transformation.classes.TCType
tempFT - Variable in class edu.isi.pegasus.planner.provisioner.Node
TEMPLATE - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
TEMPLATE_ID - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
TEMPLATE_ID - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
Temporary - Class in edu.isi.pegasus.planner.invocation
  This class is the container for a temporary file object.
Temporary() - Constructor for class edu.isi.pegasus.planner.invocation.Temporary
  Default c'tor: Construct a hollow shell and allow further information to be added later.
Temporary(String, int) - Constructor for class edu.isi.pegasus.planner.invocation.Temporary
  Constructs a temporary file object.
tempST - Variable in class edu.isi.pegasus.planner.provisioner.Node
Tentacles - Class in edu.isi.pegasus.planner.refiner.createdir
  This Strategy instance places the create directory jobs at the top of the graph.
Tentacles() - Constructor for class edu.isi.pegasus.planner.refiner.createdir.Tentacles
test(String) - Static method in class edu.isi.pegasus.planner.code.generator.condor.CondorQuoteParser
  Helper test method that tries and catches exception
test(String) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusExitCodeEncode
TestDAXParser - Class in edu.isi.pegasus.planner.parser
  A Test Class to demonstrate use of DAXParser and illustrates how to use the Callbacks for the parser.
TestDAXParser() - Constructor for class edu.isi.pegasus.planner.parser.TestDAXParser
testForFile(String) - Method in class edu.isi.pegasus.planner.parser.Parser
  Tests whether the file exists or not.
TestLogFormatter - Class in edu.isi.pegasus.common.logging
  Test program to test out LogFormatter API
TestLogFormatter() - Constructor for class edu.isi.pegasus.common.logging.TestLogFormatter
TestNamespace - Class in edu.isi.pegasus.planner.namespace
  Test Class for namespaces.
TestNamespace() - Constructor for class edu.isi.pegasus.planner.namespace.TestNamespace
TestReduceEdges - Class in edu.isi.pegasus.planner.refiner
TestReduceEdges() - Constructor for class edu.isi.pegasus.planner.refiner.TestReduceEdges
TestReplicaCatalog - Class in edu.isi.pegasus.planner.catalog.replica
  A Test program that shows how to load a Replica Catalog, and query for entries sites.
TestReplicaCatalog() - Constructor for class edu.isi.pegasus.planner.catalog.replica.TestReplicaCatalog
TestSiteCatalog - Class in edu.isi.pegasus.planner.catalog.site.impl.old
  A Test program that shows how to load a Site Catalog, and query for all sites.
TestSiteCatalog() - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.old.TestSiteCatalog
TestSiteCatalog - Class in edu.isi.pegasus.planner.catalog.site
  A Test program that shows how to load a Site Catalog, and query for all sites.
TestSiteCatalog() - Constructor for class edu.isi.pegasus.planner.catalog.site.TestSiteCatalog
TestTPT - Class in edu.isi.pegasus.planner.transfer
  Client for testing the TPT class.
TestTPT() - Constructor for class edu.isi.pegasus.planner.transfer.TestTPT
TestTransformationCatalog - Class in edu.isi.pegasus.planner.catalog.transformation
  A Test program that shows how to load a Replica Catalog, and query for entries sites.
TestTransformationCatalog() - Constructor for class edu.isi.pegasus.planner.catalog.transformation.TestTransformationCatalog
TestVORSSiteCatalog - Class in edu.isi.pegasus.planner.catalog.site
  A Test program that shows how to load a Site Catalog, and query for all sites.
TestVORSSiteCatalog() - Constructor for class edu.isi.pegasus.planner.catalog.site.TestVORSSiteCatalog
Text - Class in edu.isi.pegasus.planner.catalog.site.impl.old
  It gets the information about a pool by reading the multiline site catalog that is in a multiline format.
Text(String) - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.old.Text
  The private constructor that is called only once, when the Singleton is invoked for the first time.
Text(String, String) - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.old.Text
  The private constructor that is called to return a non singleton instance of the class.
Text - Class in edu.isi.pegasus.planner.catalog.transformation.impl
  A File based Transformation Catalog where each entry spans multiple lines.
Text() - Constructor for class edu.isi.pegasus.planner.catalog.transformation.impl.Text
  Default constructor.
TEXT_FORMAT - Static variable in class edu.isi.pegasus.planner.client.TCConverter
  The textual format.
TEXT_IMPLEMENTING_CLASS - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.SiteFactory
  The name of the class that connects to an multi line Text based Site Catalog.
TEXT_READ_CLASS - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolMode
TEXT_READ_VALUE - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolMode
  Constants for multiline text pool read.
ThreadPool - Class in edu.isi.pegasus.planner.refiner
  This maintains a pool of authenticate threads that authenticate against a particular resource.
ThreadPool(PegasusProperties, Set) - Constructor for class edu.isi.pegasus.planner.refiner.ThreadPool
  The overloaded constructor.
ThreadPool.AuthenticateThread - Class in edu.isi.pegasus.planner.refiner
  A thread as an inner class, that authenticates against one particular pool.
ThreadPool.ConditionVariable - Class in edu.isi.pegasus.planner.refiner
  A wrapper around an int that acts as a Condition Variable, and is used as such.
TIME_END - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
TIME_END - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
TIME_START - Static variable in interface edu.isi.ikcap.workflows.util.logging.LoggingKeys
TIME_START - Static variable in class edu.isi.pegasus.common.logging.LoggingKeys
timeMap - Variable in class edu.isi.pegasus.planner.provisioner.OccupationDiagram
TIMEOUT_VALUE - Static variable in class edu.isi.pegasus.planner.refiner.Authenticate
  The timeout in seconds.
TIMESTAMP_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The workflow timestamp.
timeString - Static variable in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
timeStringLock - Static variable in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
tlevel - Variable in class edu.isi.pegasus.planner.provisioner.Node
toArchitecture() - Method in class edu.isi.pegasus.planner.invocation.Uname
  An adapter method to convert the uname object to the architecture object.
toCondor() - Method in class edu.isi.pegasus.planner.namespace.Condor
  Converts the contents of the map into the string that can be put in the Condor file for printing.
toCondor() - Method in class edu.isi.pegasus.planner.namespace.Dagman
  Converts the contents of the map into the string that can be put in the Condor file for printing.
toCondor() - Method in class edu.isi.pegasus.planner.namespace.ENV
  Converts the contents of the map into the string that can be put in the Condor file for printing.
toCondor() - Method in class edu.isi.pegasus.planner.namespace.Globus
  Converts the contents of the map into the string that can be put in the Condor file for printing.
toCondor() - Method in class edu.isi.pegasus.planner.namespace.Hints
  Converts the contents of the map into the string that can be put in the Condor file for printing.
toCondor() - Method in class edu.isi.pegasus.planner.namespace.Namespace
  Returns a condor description that can be used to put the contents of the namespace into the condor submit file during code generation.
toCondor() - Method in class edu.isi.pegasus.planner.namespace.Pegasus
  Converts the contents of the map into the string that can be put in the Condor file for printing.
toCondor() - Method in class edu.isi.pegasus.planner.namespace.Selector
  Converts the contents of the map into the string that can be put in the Condor file for printing.
toCondor() - Method in class edu.isi.pegasus.planner.namespace.Stat
  Converts the contents of the map into the string that can be put in the Condor file for printing.
toDOT() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the DOT description of the object.
toDOT(Writer, String) - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the DOT description of the object.
toDOT() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the DOT description of the object.
toDOT(Writer, String) - Method in class edu.isi.pegasus.planner.classes.Job
  Returns the DOT description of the object.
toDOT() - Method in class edu.isi.pegasus.planner.classes.PCRelation
  Returns the DOT description of the object.
toDOT(Writer, String) - Method in class edu.isi.pegasus.planner.classes.PCRelation
  Returns the DOT description of the object.
toFile(String, String) - Method in class edu.isi.pegasus.planner.client.SCClient
  Writes out to a file, a string.
toJson() - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Converts the planner metrics to JSON
toJson() - Method in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  Converts the planner metrics to JSON
toJVMOptions() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Converts the vds properties that need to be passed to the jvm as an option.
Token - Interface in edu.isi.pegasus.planner.parser.tokens
  Base class for the tokens passed from the Text Scanner to the parser.
toMultiLine() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GlobusVersion
  Returns the textual description of the contents of `GlobusVersion` object in the multiline format.
toMultiLine() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPServer
  Returns the textual description of the contents of `GridFTPServer` object in the multiline format.
toMultiLine() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  Returns the textual description of the contents of `JobManager` object in the multiline format.
toMultiLine() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.LRC
  Returns the textual description of the contents of `LRC` object in the multiline format.
toMultiLine() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.PoolConfig
  Returns the textual description of the contents of `PoolConfig` object in the multiline format.
toMultiLine() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  Returns the textual description of the contents of `SiteInfo` object in the multiline format.
toMultiLine() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.WorkDir
  Returns the textual description of the contents of `WorkDir` object in the multiline format.
toMultiLine() - Method in class edu.isi.pegasus.planner.classes.Profile
  Returns the textual description of the contents of `Profile` object in the multiline format.
toMultiLine(PoolConfig) - Method in class edu.isi.pegasus.planner.client.SCClient
  Returns the String description of the contents of `PoolConfig` object passed.
toNode - Variable in class edu.isi.pegasus.planner.provisioner.Edge
toOptions() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Generates the argument string corresponding to these options that can be used to invoke Pegasus.
topNode - Variable in class edu.isi.pegasus.planner.provisioner.Estimator
Topological - Class in edu.isi.pegasus.planner.partitioner
  Does a topological sort on the Partition.
Topological(Partition) - Constructor for class edu.isi.pegasus.planner.partitioner.Topological
  The overloaded constructor.
topologicalOrderingRequired() - Method in class edu.isi.pegasus.planner.cluster.aggregator.MPIExec
  A boolean indicating whether ordering is important while traversing through the aggregated job.
topologicalOrderingRequired() - Method in class edu.isi.pegasus.planner.cluster.aggregator.SeqExec
  A boolean indicating whether ordering is important while traversing through the aggregated job.
topologicalOrderingRequired() - Method in interface edu.isi.pegasus.planner.cluster.JobAggregator
  A boolean indicating whether ordering is important while traversing through the aggregated job.
topologicalSortIterator() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns an iterator for the graph that traverses in topological sort order.
topologicalSortIterator() - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Returns an iterator for the graph that traverses in topological sort order.
topologicalSortIterator() - Method in interface edu.isi.pegasus.planner.partitioner.graph.Graph
  Returns an iterator for the graph that traverses in topological sort order.
topologicalSortIterator() - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph
  Returns an iterator for the graph that traverses in topological sort order.
TopologicalSortIterator - Class in edu.isi.pegasus.planner.partitioner.graph
  Does a topological sort on the Partition.
TopologicalSortIterator(Graph) - Constructor for class edu.isi.pegasus.planner.partitioner.graph.TopologicalSortIterator
  The overloaded constructor.
toPrettyJson() - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Converts the planner metrics to JSON
toPrettyJson() - Method in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  Converts the planner metrics to JSON
toString() - Method in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
  Format a message in CEDPS Best Practices format.
toString() - Method in class edu.isi.pegasus.common.util.PegasusURL
  The contents represented as a string
toString() - Method in class edu.isi.pegasus.common.util.Version
toString() - Method in class edu.isi.pegasus.gridftp.FileInfo
toString() - Method in class edu.isi.pegasus.gridftp.GridFTPConnection.StringBuilderDataSink
toString() - Method in class edu.isi.pegasus.gridftp.GridFTPURL
toString() - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Returns the string description of the object.
toString(Writer, String) - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Writes out the contents of the object as a String
toString() - Method in class edu.isi.pegasus.planner.catalog.classes.SysInfo
  Returns the output of the data class as string.
toString() - Method in class edu.isi.pegasus.planner.catalog.replica.ReplicaCatalogEntry
  Converts the contents into a string.
toString() - Method in class edu.isi.pegasus.planner.catalog.site.classes.AbstractSiteData
  Writes out the object as a string.
toString() - Method in enum edu.isi.pegasus.planner.catalog.site.classes.Directory.TYPE
  Override of the toString method to return
toString() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GlobusVersion
  Returns the textual description of the contents of `GlobusVersion` object.
toString() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPBandwidth
toString() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPServer
  Returns the textual description of the contents of `LRC` object.
toString() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  Returns the textual description of the contents of `JobManager` object.
toString() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.LRC
  Returns the textual description of the contents of `LRC` object.
toString() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  Returns the textual description of the contents of `SiteInfo` object.
toString() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.WorkDir
  Returns the textual description of the contents of `WorkDir` object.
toString() - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.Arch
  Returns the string value of the architecture.
toString() - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.Os
  Returns the string value of the operating system.
toString() - Method in class edu.isi.pegasus.planner.catalog.transformation.classes.VDSSysInfo
  Returns the output of the data class as string.
toString() - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  gets the String mVersion of the data class
toString() - Method in class edu.isi.pegasus.planner.classes.ADag
  Returns the String description of the dag associated with this object.
toString() - Method in class edu.isi.pegasus.planner.classes.AggregatedJob
  Returns a textual description of the object.
toString() - Method in class edu.isi.pegasus.planner.classes.AuthenticateRequest
  Returns a string version of this.
toString() - Method in class edu.isi.pegasus.planner.classes.CompoundTransformation
  Converts object to String
toString() - Method in class edu.isi.pegasus.planner.classes.DagInfo
  Returns the a textual description of the object.
toString() - Method in class edu.isi.pegasus.planner.classes.DAGJob
  Returns a textual description of the DAG Job.
toString() - Method in class edu.isi.pegasus.planner.classes.Data
  Returns the String version of the data object, which is in human readable form.
toString() - Method in class edu.isi.pegasus.planner.classes.DAXJob
  Returns a textual description of the DAX Job.
toString() - Method in class edu.isi.pegasus.planner.classes.FileTransfer
  Returns a textual interpretation of the object.
toString() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns a textual description of the object.
toString() - Method in class edu.isi.pegasus.planner.classes.NameValue
  Writes out the contents of the class to a String in form suitable for displaying.
toString() - Method in class edu.isi.pegasus.planner.classes.Notifications
  Returns a String description of the object
toString() - Method in class edu.isi.pegasus.planner.classes.PCRelation
  Returns the textual description.
toString() - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Returns the String version of the data object, which is in human readable form.
toString() - Method in class edu.isi.pegasus.planner.classes.PlannerCache
toString() - Method in class edu.isi.pegasus.planner.classes.PlannerMetrics
  Returns a textual description of the object.
toString() - Method in class edu.isi.pegasus.planner.classes.PlannerOptions
  Returns the textual description of all the options that were set for the planner.
toString() - Method in class edu.isi.pegasus.planner.classes.Profile
  This method returns a string of the contents of this object.
toString() - Method in class edu.isi.pegasus.planner.classes.ReplicaLocation
  Returns the textual description of the data class.
toString() - Method in class edu.isi.pegasus.planner.classes.ReplicaStore
  Returns the textual description of the data class.
toString() - Method in class edu.isi.pegasus.planner.classes.TCMap
  Returns the textual description of the contents of the object
toString(String) - Method in class edu.isi.pegasus.planner.classes.TCMap
  Returns a textual description of the object.
toString() - Method in class edu.isi.pegasus.planner.classes.TransferJob
  Returns a textual description of the Transfer Job.
toString() - Method in class edu.isi.pegasus.planner.classes.WorkflowMetrics
  Returns a textual description of the object.
toString() - Method in class edu.isi.pegasus.planner.code.generator.SendMetricsResult
toString() - Method in class edu.isi.pegasus.planner.dax.Edge
toString() - Method in class edu.isi.pegasus.planner.dax.Executable
toString() - Method in class edu.isi.pegasus.planner.dax.Invoke
  Returns the object as String
toString() - Method in class edu.isi.pegasus.planner.dax.Transformation
toString(Writer) - Method in class edu.isi.pegasus.planner.invocation.Architecture
  Converts the active state into something meant for human consumption.
toString(Writer) - Method in class edu.isi.pegasus.planner.invocation.ArgEntry
  Converts the active state into something meant for human consumption.
toString(Writer) - Method in class edu.isi.pegasus.planner.invocation.Arguments
  Converts the active state into something meant for human consumption.
toString(Writer) - Method in class edu.isi.pegasus.planner.invocation.CommandLine
  Converts the active state into something meant for human consumption.
toString(Writer) - Method in class edu.isi.pegasus.planner.invocation.Data
  Converts the active state into something meant for human consumption.
toString(Writer) - Method in class edu.isi.pegasus.planner.invocation.EnvEntry
  Converts the active state into something meant for human consumption.
toString(Writer) - Method in class edu.isi.pegasus.planner.invocation.Environment
  Converts the active state into something meant for human consumption.
toString(Writer) - Method in class edu.isi.pegasus.planner.invocation.File
  Converts the active state into something meant for human consumption.
toString(Writer) - Method in class edu.isi.pegasus.planner.invocation.Ignore
  Converts the active state into something meant for human consumption.
toString(Writer) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Converts the active state into something meant for human consumption.
toString(Writer) - Method in class edu.isi.pegasus.planner.invocation.Job
  Converts the active state into something meant for human consumption.
toString(Writer) - Method in class edu.isi.pegasus.planner.invocation.JobStatusFailure
  Converts the active state into something meant for human consumption.
toString(Writer) - Method in class edu.isi.pegasus.planner.invocation.JobStatusRegular
  Converts the active state into something meant for human consumption.
toString(Writer) - Method in class edu.isi.pegasus.planner.invocation.JobStatusSignal
  Converts the active state into something meant for human consumption.
toString(Writer) - Method in class edu.isi.pegasus.planner.invocation.JobStatusSuspend
  Converts the active state into something meant for human consumption.
toString(Writer) - Method in class edu.isi.pegasus.planner.invocation.Machine
  Converts the active state into something meant for human consumption.
toString(Writer) - Method in class edu.isi.pegasus.planner.invocation.MachineInfo
  Converts the active state into something meant for human consumption.
toString(Writer) - Method in class edu.isi.pegasus.planner.invocation.MachineSpecific
  Converts the active state into something meant for human consumption.
toString(Writer) - Method in class edu.isi.pegasus.planner.invocation.StatCall
  Converts the active state into something meant for human consumption.
toString(Writer) - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Converts the active state into something meant for human consumption.
toString(Writer) - Method in class edu.isi.pegasus.planner.invocation.Status
  Converts the active state into something meant for human consumption.
toString(Writer) - Method in class edu.isi.pegasus.planner.invocation.Usage
  Converts the active state into something meant for human consumption.
toString(Writer) - Method in class edu.isi.pegasus.planner.invocation.WorkingDir
  Converts the active state into something meant for human consumption.
toString(String) - Method in class edu.isi.pegasus.planner.namespace.Dagman
  Converts the contents of the map into the string that can be put in the Condor file for printing.
toString() - Method in class edu.isi.pegasus.planner.namespace.Namespace
  Returns the contents as String.
toString() - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser3.Arguments
  Returns the arguments as string
toString() - Method in class edu.isi.pegasus.planner.parser.tokens.Identifier
  Returns the textual description of the object.
toString() - Method in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
  The textual representation of the graph node.
toString() - Method in class edu.isi.pegasus.planner.partitioner.graph.LabelBag
  Returns a textual description of the Bag.
toString() - Method in class edu.isi.pegasus.planner.partitioner.graph.MapGraph
  The textual representation of the graph node.
toString() - Method in class edu.isi.pegasus.planner.partitioner.Partition
  Returns a String version of the object.
toString() - Method in class edu.isi.pegasus.planner.ranking.Ranking
  Returns a textual description.
toString() - Method in class edu.isi.pegasus.planner.refiner.Authenticate.HostPort
  Returns the string version of this object.
toString() - Method in class edu.isi.pegasus.planner.selector.replica.Regex.Rank
  Returns the textual representation of this
toString() - Method in class edu.isi.pegasus.planner.selector.site.RoundRobin.NameValue
  Writes out the contents of the class to a String in form suitable for displaying.
toString() - Method in class edu.isi.pegasus.planner.transfer.refiner.Chain.SiteTransfer
  Returns the textual description of the object.
toString() - Method in class edu.isi.pegasus.planner.transfer.refiner.Chain.TransferChain
  Returns the textual description of the object.
toString() - Method in class edu.isi.pegasus.planner.transfer.RemoteTransfer.TransferState
  Returns a textual description of the state as (stageinRemote,interRemote,stageoutRemote).
toString() - Method in class edu.isi.pegasus.planner.transfer.TPT.TPTState
  Returns a textual description of the state as (stageinRemote,interRemote,stageoutRemote,stageinTPT,interTPT,stageOutTPT).
TOTAL_MEM - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The constant to be passed to the accessor functions to get or set the total memory.
TOTAL_NODES - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The constant to be passed to the accessor functions to get or set the total number of nodes.
TOTAL_SIZE - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPServer
  The constant to be passed to the accessor functions to get or set the total size.
TOTAL_SIZE - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.WorkDir
  The constant to be passed to the accessor functions to get or set the total space available.
totalET - Variable in class edu.isi.pegasus.planner.provisioner.Estimator
toTCString() - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Prints out a TC file format String.
toText(TransformationCatalogEntry, String, String) - Static method in class edu.isi.pegasus.planner.catalog.transformation.client.TCFormatUtility
  Converts the transformation catalog entry object to the multi line textual representation.
toTextFormat(TransformationStore) - Static method in class edu.isi.pegasus.planner.catalog.transformation.client.TCFormatUtility
  Converts the transformations into multi line text format
toXML(String, String) - Method in class edu.isi.pegasus.common.util.XMLOutput
  Dumps the state of the current element as XML output.
toXML(Writer, String) - Method in class edu.isi.pegasus.common.util.XMLOutput
  Convenience adaptor method invoking the equivalent of:
toXML(Writer, String, String) - Method in class edu.isi.pegasus.common.util.XMLOutput
  Dump the state of the current element as XML output.
toXML(Writer, String) - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Writes out the xml description of the object.
toXML() - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Returns the xml description of the object.
toXML() - Method in class edu.isi.pegasus.planner.catalog.site.classes.AbstractSiteData
  Returns the xml description of the object.
toXML(Writer, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.AbstractSiteData
  Writes out the xml description of the object.
toXML(Writer, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.Connection
  Writes out the xml description of the object.
toXML(Writer, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.Directory
toXML(Writer, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.FileServer
  Writes out the xml description of the object.
toXML(Writer, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.GridGateway
  Writes out the xml description of the object.
toXML(Writer, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.HeadNodeFS
  Writes out the xml description of the object.
toXML(Writer, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.HeadNodeScratch
  Writes out the xml description of the object.
toXML(Writer, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.HeadNodeStorage
  Writes out the xml description of the object.
toXML(Writer, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.InternalMountPoint
  Writes out the xml description of the object.
toXML(Writer, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.LocalDirectory
  Writes out the xml description of the object.
toXML(Writer, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.ReplicaCatalog
  Writes out the xml description of the object.
toXML(Writer, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SharedDirectory
  Writes out the xml description of the object.
toXML(Writer, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  Writes out the xml description of the object.
toXML(Writer, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  Writes out the xml description of the object.
toXML(Writer, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.SiteStore
  Writes out the contents of the replica store as XML document
toXML(Writer, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.StorageType
toXML(Writer, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeFS
  Writes out the xml description of the object.
toXML(Writer, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeScratch
  Writes out the xml description of the object.
toXML(Writer, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeStorage
  Writes out the xml description of the object.
toXML(Writer, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.WorkerSharedDirectory
  Writes out the xml description of the object.
toXML() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPBandwidth
  Returns the XML description of the contents of Gridftp object.
toXML() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.GridFTPServer
  Returns the XML description of the contents of `LRC` object.
toXML() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  Returns the XML description of the contents of `JobManager` object.
toXML() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.LRC
  Returns the XML description of the contents of `LRC` object.
toXML() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.PoolConfig
  Returns the XML description of the contents of `PoolConfig` object.
toXML() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  Returns the XML description of the contents of `SiteInfo` object.
toXML() - Method in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.WorkDir
  Returns the XML description of the contents of `WorkDir` object.
toXML() - Method in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Returns an xml output of the contents of the data class.
toXML() - Method in class edu.isi.pegasus.planner.classes.Profile
  This method returns an xml of the contents of this object.
toXML(PoolConfig) - Method in class edu.isi.pegasus.planner.client.SCClient
  Returns the XML description of the contents of `PoolConfig` object passed, conforming to pool config schema found at http://pegasus.isi.edu/schema/sc-2.0.xsd.
toXML(XMLWriter) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
toXML(XMLWriter, int) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
toXML(XMLWriter) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Generates a DAX representation.
toXML(XMLWriter) - Method in class edu.isi.pegasus.planner.dax.CatalogType
  Write the XML representation of this object
toXML(XMLWriter, int) - Method in class edu.isi.pegasus.planner.dax.CatalogType
  Write the XML representation of this object
toXML(XMLWriter, int) - Method in class edu.isi.pegasus.planner.dax.DAG
toXML(XMLWriter, int) - Method in class edu.isi.pegasus.planner.dax.DAX
toXML(XMLWriter) - Method in class edu.isi.pegasus.planner.dax.Edge
toXML(XMLWriter, int) - Method in class edu.isi.pegasus.planner.dax.Edge
toXML(XMLWriter) - Method in class edu.isi.pegasus.planner.dax.Executable
toXML(XMLWriter, int) - Method in class edu.isi.pegasus.planner.dax.Executable
toXML(XMLWriter) - Method in class edu.isi.pegasus.planner.dax.File
  Write the file object
toXML(XMLWriter, int) - Method in class edu.isi.pegasus.planner.dax.File
  Write the file object, with indent level N
toXML(XMLWriter, int, String) - Method in class edu.isi.pegasus.planner.dax.File
  Write the file object as XML but render it as the elementname
toXML(XMLWriter) - Method in class edu.isi.pegasus.planner.dax.Invoke
toXML(XMLWriter, int) - Method in class edu.isi.pegasus.planner.dax.Invoke
toXML(XMLWriter, int) - Method in class edu.isi.pegasus.planner.dax.Job
  Overrides Base TOXML method.
toXML(XMLWriter) - Method in class edu.isi.pegasus.planner.dax.MetaData
toXML(XMLWriter, int) - Method in class edu.isi.pegasus.planner.dax.MetaData
toXML(XMLWriter) - Method in class edu.isi.pegasus.planner.dax.PFN
toXML(XMLWriter, int) - Method in class edu.isi.pegasus.planner.dax.PFN
toXML(XMLWriter) - Method in class edu.isi.pegasus.planner.dax.Profile
toXML(XMLWriter, int) - Method in class edu.isi.pegasus.planner.dax.Profile
toXML(XMLWriter) - Method in class edu.isi.pegasus.planner.dax.Transformation
toXML(XMLWriter, int) - Method in class edu.isi.pegasus.planner.dax.Transformation
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.Architecture
  Dump the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.ArgEntry
  Dumps the state of the current element as XML output.
toXML(String) - Method in class edu.isi.pegasus.planner.invocation.ArgString
  Dumps the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.ArgString
  Dump the state of the current element as XML output.
toXML(String) - Method in class edu.isi.pegasus.planner.invocation.ArgVector
  Dumps the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.ArgVector
  Dump the state of the current element as XML output.
toXML(String) - Method in class edu.isi.pegasus.planner.invocation.CommandLine
  Dumps the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.CommandLine
  Dump the state of the current element as XML output.
toXML(String) - Method in class edu.isi.pegasus.planner.invocation.Data
  Dumps the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.Data
  Dump the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.Descriptor
  Dump the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.EnvEntry
  Dumps the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.Environment
  Dump the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.Fifo
  Dump the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.Ignore
  Dump the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Dump the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.Job
  Dumps the state of the current element as XML output.
toXML(String) - Method in class edu.isi.pegasus.planner.invocation.JobStatusFailure
  Dumps the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.JobStatusFailure
  Dump the state of the current element as XML output.
toXML(String) - Method in class edu.isi.pegasus.planner.invocation.JobStatusRegular
  Dumps the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.JobStatusRegular
  Dump the state of the current element as XML output.
toXML(String) - Method in class edu.isi.pegasus.planner.invocation.JobStatusSignal
  Dumps the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.JobStatusSignal
  Dump the state of the current element as XML output.
toXML(String) - Method in class edu.isi.pegasus.planner.invocation.JobStatusSuspend
  Dumps the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.JobStatusSuspend
  Dump the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.Machine
  Dump the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.MachineInfo
  Dump the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.MachineSpecific
  Dump the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.Regular
  Dump the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.StatCall
  Dump the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.StatInfo
  Dump the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.Status
  Dump the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.Temporary
  Dump the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.Usage
  Dump the state of the current element as XML output.
toXML(String) - Method in class edu.isi.pegasus.planner.invocation.WorkingDir
  Dumps the state of the current element as XML output.
toXML(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.WorkingDir
  Dump the state of the current element as XML output.
toXML(Writer) - Method in class edu.isi.pegasus.planner.partitioner.Partition
  Returns the xml description of the object.
toXML() - Method in class edu.isi.pegasus.planner.partitioner.Partition
  Returns the xml description of the object.
toXML(Writer) - Method in class edu.isi.pegasus.planner.provenance.pasoa.producer.InMemory
  Returns the xml description of the object.
toXML() - Method in class edu.isi.pegasus.planner.provenance.pasoa.producer.InMemory
  Returns the interaction assertions as a XML blob.
toXML(Writer) - Method in interface edu.isi.pegasus.planner.provenance.pasoa.XMLProducer
  Returns the xml description of the object.
toXML() - Method in interface edu.isi.pegasus.planner.provenance.pasoa.XMLProducer
  Returns the interaction assertions as a XML blob.
toXMLParent(XMLWriter) - Method in class edu.isi.pegasus.planner.dax.Edge
toXMLParent(XMLWriter, int) - Method in class edu.isi.pegasus.planner.dax.Edge
TPT - Class in edu.isi.pegasus.planner.transfer
  A common class, that builds up the third party state for the sites from the properties file.
TPT() - Constructor for class edu.isi.pegasus.planner.transfer.TPT
  The default constructor.
TPT(PegasusProperties) - Constructor for class edu.isi.pegasus.planner.transfer.TPT
  The overloaded constructor.
TPT.TPTState - Class in edu.isi.pegasus.planner.transfer
  An inner class that holds the third party state for a particular site.
TPTGUC - Class in edu.isi.pegasus.planner.transfer.implementation
  The implementation that is used to create transfer jobs that callout to the new globus-url-copy client, that support multiple file transfers
TPTGUC(PegasusBag) - Constructor for class edu.isi.pegasus.planner.transfer.implementation.TPTGUC
  The overloaded constructor, that is called by the Factory to load the class.
TPTState() - Constructor for class edu.isi.pegasus.planner.transfer.TPT.TPTState
  The default constructor.
TRACE_MESSAGE_LEVEL - Static variable in class edu.isi.pegasus.common.logging.LogManager
  The level value, to indicate a DEBUG message.
TRACE_MESSAGE_TYPE - Static variable in class edu.isi.pegasus.common.logging.logger.Default
  The type value to indicate a DEBUG message.
trackInCaches(Job) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  Tracks the files created by a job in the both the planner and workflow cache The planner cache stores the put URL's and the GET URL is stored in the workflow cache.
trackInPlannerCache(String, String, String) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  Inserts an entry into the planner cache as a put URL.
trackInPlannerCache(String, String, String, FileServerType.OPERATION) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  Inserts an entry into the planner cache as a put URL.
trackInWorkflowCache(String, String, String) - Method in class edu.isi.pegasus.planner.refiner.TransferEngine
  Inserts an entry into the workflow cache that is to be written out to the submit directory.
trackLFNAddOn(String, String, String) - Method in class edu.isi.pegasus.planner.transfer.mapper.impl.Hashed
  Tracks the lfn with addOn's on the various sites.
TRANSFER() - Constructor for enum edu.isi.pegasus.planner.dax.File.TRANSFER
Transfer - Class in edu.isi.pegasus.planner.transfer.implementation
  The implementation that creates transfer jobs referring to the python based transfer script distributed with Pegasus since version 3.0
Transfer(PegasusBag) - Constructor for class edu.isi.pegasus.planner.transfer.implementation.Transfer
  The overloaded constructor, that is called by the Factory to load the class.
Transfer - Class in edu.isi.pegasus.planner.transfer.sls
  This uses the transfer executable distributed with Pegasus to do the second level staging.
Transfer() - Constructor for class edu.isi.pegasus.planner.transfer.sls.Transfer
  The default constructor.
TRANSFER_ARGUMENTS_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the profile key, that when associated with transfer jobs determines the arguments with which the transfer executable is invoked.
TRANSFER_EXECUTABLE_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.Condor
TRANSFER_EXECUTABLE_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The name of the key that specifies transfer of executable
TRANSFER_IP_FILES_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The name of the key that specifies transfer of input files.
TRANSFER_MANDATORY - Static variable in class edu.isi.pegasus.planner.classes.PegasusFile
  The mode where the transfer for this file to the pool is constructed and the transfer job fails if the transfer fails.
TRANSFER_NOT - Static variable in class edu.isi.pegasus.planner.classes.PegasusFile
  The mode where the transfer for this file is not constructed.
TRANSFER_OP_FILES_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The name of the key that specifies transfer of input files.
TRANSFER_OPTIONAL - Static variable in class edu.isi.pegasus.planner.classes.PegasusFile
  The mode where the transfer for this file to the pool is constructed, but the transfer job should not fail if the transfer fails.
TRANSFER_PROXY_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the profile key if associated with a job, results in an explicit transfer of the proxy from the submit host to the remote site, instead of banking upon CondorG to transfer the proxy.
TRANSFER_SLS_ARGUMENTS_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the profile key, that when associated with transfer jobs determines the arguments with which the transfer executable is invoked.
TRANSFER_SLS_THREADS_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the profile key, that when associated with transfer jobs determines the number of threads that pegasus-transfer uses to do the transfer
TRANSFER_THREADS_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the profile key, that when associated with transfer jobs determines the number of threads that pegasus-transfer uses to do the transfer
TRANSFER_UNIVERSE - Static variable in class edu.isi.pegasus.planner.refiner.Engine
TRANSFER_UNIVERSE - Static variable in interface edu.isi.pegasus.planner.transfer.Implementation
  The universe that applies for the transfer jobs.
TransferChain() - Constructor for class edu.isi.pegasus.planner.transfer.refiner.Chain.TransferChain
  The default constructor.
TransferContainer() - Constructor for class edu.isi.pegasus.planner.transfer.refiner.BalancedCluster.TransferContainer
  The default constructor.
TransferContainer() - Constructor for class edu.isi.pegasus.planner.transfer.refiner.Bundle.TransferContainer
  The default constructor.
TransferEngine - Class in edu.isi.pegasus.planner.refiner
  The transfer engine, which on the basis of the pools on which the jobs are to run, adds nodes to transfer the data products.
TransferEngine(ADag, PegasusBag, List<Job>, List<Job>) - Constructor for class edu.isi.pegasus.planner.refiner.TransferEngine
  Overloaded constructor.
TransferImplementationFactoryException - Exception in edu.isi.pegasus.planner.transfer.implementation
  Class to notify of failures while instantiating Transfer Implementations.
TransferImplementationFactoryException(String) - Constructor for exception edu.isi.pegasus.planner.transfer.implementation.TransferImplementationFactoryException
  Constructs a `TransferImplementationFactoryException` with no detail message.
TransferImplementationFactoryException(String, String) - Constructor for exception edu.isi.pegasus.planner.transfer.implementation.TransferImplementationFactoryException
  Constructs a `TransferImplementationFactoryException` with the specified detailed message.
TransferImplementationFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.transfer.implementation.TransferImplementationFactoryException
  Constructs a `TransferImplementationFactoryException` with the specified detailed message and a cause.
TransferImplementationFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.planner.transfer.implementation.TransferImplementationFactoryException
  Constructs a `TransferImplementationFactoryException` with the specified detailed message and a cause.
transferImplementationTable() - Static method in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  Singleton access to the transfer implementation table.
transferInRange(int) - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Returns whether the transfer value for the mode is in range or not.
TransferJob - Class in edu.isi.pegasus.planner.classes
  This is a data class that stores the contents of the transfer job that transfers the data.
TransferJob() - Constructor for class edu.isi.pegasus.planner.classes.TransferJob
  The default constructor.
TransferJob(Job) - Constructor for class edu.isi.pegasus.planner.classes.TransferJob
  The overloaded construct that constructs a GRMS job by wrapping around the `Job` job.
transferOutput(GraphNode) - Method in class edu.isi.pegasus.planner.refiner.DataReuseEngine
  Returns whether a user wants output transferred for a node or not.
TransferRefinerFactoryException - Exception in edu.isi.pegasus.planner.transfer.refiner
  Class to notify of failures while instantiating Transfer Refiners.
TransferRefinerFactoryException(String) - Constructor for exception edu.isi.pegasus.planner.transfer.refiner.TransferRefinerFactoryException
  Constructs a `TransferRefinerFactoryException` with no detail message.
TransferRefinerFactoryException(String, String) - Constructor for exception edu.isi.pegasus.planner.transfer.refiner.TransferRefinerFactoryException
  Constructs a `TransferRefinerFactoryException` with the specified detailed message.
TransferRefinerFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.transfer.refiner.TransferRefinerFactoryException
  Constructs a `TransferRefinerFactoryException` with the specified detailed message and a cause.
TransferRefinerFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.planner.transfer.refiner.TransferRefinerFactoryException
  Constructs a `TransferRefinerFactoryException` with the specified detailed message and a cause.
transferRefinerTable() - Static method in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  Singleton access to the transfer refiner table.
TransferState() - Constructor for class edu.isi.pegasus.planner.transfer.RemoteTransfer.TransferState
  The default constructor.
transferWorkerPackage() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  It specifies if the worker package needs to be staged to the remote site or not.
Transformation - Class in edu.isi.pegasus.planner.dax
  This Object is used to create a complex Transformation.
Transformation(String) - Constructor for class edu.isi.pegasus.planner.dax.Transformation
  Create a new Transformation object
Transformation(Transformation) - Constructor for class edu.isi.pegasus.planner.dax.Transformation
  Copy Constructor
Transformation(String, String, String) - Constructor for class edu.isi.pegasus.planner.dax.Transformation
  Create a new Transformation Object
TRANSFORMATION - Static variable in class edu.isi.pegasus.planner.parser.tokens.TransformationCatalogReservedWord
  token value for the reserved word "tr".
TRANSFORMATION_CATALOG - Static variable in class edu.isi.pegasus.planner.classes.PegasusBag
  The constant to be passed to the accessor functions to get or set the handle to the transformation catalog.
TRANSFORMATION_MAPPER - Static variable in class edu.isi.pegasus.planner.classes.PegasusBag
  The constant to be passed to the accessor functions to get or set the handle to the Transformation Mapper.
TRANSFORMATION_NAME - Static variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  The logical name of kickstart
TRANSFORMATION_NAME - Static variable in class edu.isi.pegasus.planner.refiner.cleanup.Cleanup
  The name of the underlying transformation that is queried for in the Transformation Catalog.
TRANSFORMATION_NAME - Static variable in class edu.isi.pegasus.planner.refiner.createdir.DefaultImplementation
  The logical name of the transformation that creates directories on the remote execution pools.
TRANSFORMATION_NAME - Static variable in class edu.isi.pegasus.planner.refiner.createdir.HourGlass
  The logical name of the transformation that creates directories on the remote execution pools.
TRANSFORMATION_NAME - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The logical name of the worker package
TRANSFORMATION_NAME - Static variable in class edu.isi.pegasus.planner.refiner.RemoveDirectory
  The logical name of the transformation that removes directories on the remote execution pools.
TRANSFORMATION_NAME - Static variable in class edu.isi.pegasus.planner.transfer.implementation.GUC
  The name of the underlying transformation that is queried for in the Transformation Catalog.
TRANSFORMATION_NAME - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Stork
  The name of the underlying transformation that is queried for in the Transformation Catalog.
TRANSFORMATION_NAME - Static variable in class edu.isi.pegasus.planner.transfer.implementation.T2
  The name of the underlying transformation that is queried for in the Transformation Catalog.
TRANSFORMATION_NAME - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Transfer
  The name of the underlying transformation that is queried for in the Transformation Catalog.
TRANSFORMATION_NAME - Static variable in class edu.isi.pegasus.planner.transfer.sls.Transfer
  The name of the underlying transformation that is queried for in the Transformation Catalog.
TRANSFORMATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  The transformation namespace for the cluster jobs.
TRANSFORMATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  The transformation namespace for the kickstart
TRANSFORMATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.refiner.cleanup.Cleanup
  The transformation namespace for the job.
TRANSFORMATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.refiner.createdir.DefaultImplementation
  The transformation namespace for the create dir jobs.
TRANSFORMATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.refiner.createdir.HourGlass
  The transformation namespace for the create dir jobs.
TRANSFORMATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The transformation namespace for the worker package
TRANSFORMATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.refiner.RemoveDirectory
  The transformation namespace for the create dir jobs.
TRANSFORMATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.transfer.implementation.GUC
  The transformation namespace for the transfer job.
TRANSFORMATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Stork
  The transformation namespace for the transfer job.
TRANSFORMATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.transfer.implementation.T2
  The transformation namespace for the transfer job.
TRANSFORMATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Transfer
  The transformation namespace for the transfer job.
TRANSFORMATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.transfer.sls.Transfer
  The transformation namespace for the transfer job.
TRANSFORMATION_VERSION - Static variable in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  The version number for the derivations for cluster jobs
TRANSFORMATION_VERSION - Static variable in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  The version number for kickstart.
TRANSFORMATION_VERSION - Static variable in class edu.isi.pegasus.planner.refiner.cleanup.Cleanup
  The version number for the job.
TRANSFORMATION_VERSION - Static variable in class edu.isi.pegasus.planner.refiner.createdir.DefaultImplementation
  The version number for the derivations for create dir jobs.
TRANSFORMATION_VERSION - Static variable in class edu.isi.pegasus.planner.refiner.createdir.HourGlass
  The version number for the derivations for create dir jobs.
TRANSFORMATION_VERSION - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The version number for the worker package.
TRANSFORMATION_VERSION - Static variable in class edu.isi.pegasus.planner.refiner.RemoveDirectory
  The version number for the derivations for create dir jobs.
TRANSFORMATION_VERSION - Static variable in class edu.isi.pegasus.planner.transfer.implementation.GUC
  The version number for the transfer job.
TRANSFORMATION_VERSION - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Stork
  The version number for the transfer job.
TRANSFORMATION_VERSION - Static variable in class edu.isi.pegasus.planner.transfer.implementation.T2
  The version number for the transfer job.
TRANSFORMATION_VERSION - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Transfer
  The version number for the transfer job.
TRANSFORMATION_VERSION - Static variable in class edu.isi.pegasus.planner.transfer.sls.Transfer
  The version number for the transfer job.
TransformationCatalog - Interface in edu.isi.pegasus.planner.catalog
  This class is an interface to the various TxCatalog implementations that Pegasus will use.
TransformationCatalogEntry - Class in edu.isi.pegasus.planner.catalog.transformation
  An object of this class corresponds to a tuple in the Transformation Catalog.
TransformationCatalogEntry() - Constructor for class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  The basic constructor
TransformationCatalogEntry(String, String, String) - Constructor for class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Optimized Constructor
TransformationCatalogEntry(String, String, String, String, String, TCType, List, VDSSysInfo) - Constructor for class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Optimized Constructor
TransformationCatalogEntry(String, String, String, String, String, TCType, Profiles, SysInfo) - Constructor for class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  Overloaded constructor.
TransformationCatalogReservedWord - Class in edu.isi.pegasus.planner.parser.tokens
  Class to capture reserved words for the textual format of Transformation Catalog
TransformationCatalogReservedWord(int) - Constructor for class edu.isi.pegasus.planner.parser.tokens.TransformationCatalogReservedWord
  Initializes an instance of a reserved word token.
TransformationCatalogTextParser - Class in edu.isi.pegasus.planner.parser
  Parses the input stream and generates the TransformationStore as output.
TransformationCatalogTextParser(Reader, LogManager) - Constructor for class edu.isi.pegasus.planner.parser.TransformationCatalogTextParser
  Initializes the parser with an input stream to read from.
TransformationCatalogTextScanner - Class in edu.isi.pegasus.planner.parser
  Implements the scanner for reserved words and other tokens that are generated from the input stream for the Transformation Catalog.
TransformationCatalogTextScanner(Reader) - Constructor for class edu.isi.pegasus.planner.parser.TransformationCatalogTextScanner
  Starts to scan the given stream.
TransformationFactory - Class in edu.isi.pegasus.planner.catalog.transformation
  A factory class to load the appropriate implementation of Transformation Catalog as specified by properties.
TransformationFactory() - Constructor for class edu.isi.pegasus.planner.catalog.transformation.TransformationFactory
TransformationFactoryException - Exception in edu.isi.pegasus.planner.catalog.transformation
  Class to notify of failures while instantiating Transformation Catalog implementations.
TransformationFactoryException(String) - Constructor for exception edu.isi.pegasus.planner.catalog.transformation.TransformationFactoryException
  Constructs a `TransformationFactoryException` with no detail message.
TransformationFactoryException(String, String) - Constructor for exception edu.isi.pegasus.planner.catalog.transformation.TransformationFactoryException
  Constructs a `TransformationFactoryException` with the specified detailed message.
TransformationFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.catalog.transformation.TransformationFactoryException
  Constructs a `TransformationFactoryException` with the specified detailed message and a cause.
TransformationFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.planner.catalog.transformation.TransformationFactoryException
  Constructs a `TransformationFactoryException` with the specified detailed message and a cause.
TransformationSelector - Class in edu.isi.pegasus.planner.selector
TransformationSelector() - Constructor for class edu.isi.pegasus.planner.selector.TransformationSelector
TransformationStore - Class in edu.isi.pegasus.planner.catalog.transformation.classes
  A container data class that is used to store transformations.
TransformationStore() - Constructor for class edu.isi.pegasus.planner.catalog.transformation.classes.TransformationStore
  The default constructor.
translateException(Exception, String) - Method in class edu.isi.pegasus.gridftp.GridFTPConnection
  Translate the exception e into one of the subclasses of GridFTPException
traverse(File, String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  Traverses a directory and populates the mappings in memory
treatCacheAsRC() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a boolean indicating whether to treat the entries in the cache files as a replica catalog or not.
trigger - Variable in class edu.isi.pegasus.planner.catalog.transformation.client.Client
TRUE - Static variable in class edu.isi.pegasus.common.util.Boolean
  The character representation of a `true` value.
TYPE() - Constructor for enum edu.isi.pegasus.common.credential.CredentialHandler.TYPE
TYPE(String) - Constructor for enum edu.isi.pegasus.planner.catalog.site.classes.Directory.TYPE
  The constructor
TYPE() - Constructor for enum edu.isi.pegasus.planner.catalog.site.classes.GridGateway.TYPE
type - Variable in class edu.isi.pegasus.planner.catalog.transformation.client.Client
type - Variable in class edu.isi.pegasus.planner.catalog.transformation.TransformationCatalogEntry
  The type of transformation.
type - Variable in class edu.isi.pegasus.planner.client.TCClient
TYPE - Static variable in class edu.isi.pegasus.planner.parser.tokens.TransformationCatalogReservedWord
  token value for the reserver word "osversion".
TYPE_DESCRIPTION_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The attribute key for type description
TYPE_KEY - Static variable in class edu.isi.pegasus.planner.catalog.replica.impl.MRC
  The property key that designates the type of replica catalog to connect to.
TYPE_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The attribute key for task type
TYPE_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The name of the key that denotes the type of the job.
TYPE_SETUP - Static variable in class edu.isi.pegasus.planner.transfer.implementation.ImplementationFactory
  The constant designating the implementation to be loaded for setup tx jobs.
TYPE_STAGE_IN - Static variable in class edu.isi.pegasus.planner.transfer.implementation.ImplementationFactory
  The constant designating the implementation be loaded for stage in jobs.
TYPE_STAGE_INTER - Static variable in class edu.isi.pegasus.planner.transfer.implementation.ImplementationFactory
  The constant designating the implementation be loaded for inter pool jobs.
TYPE_STAGE_OUT - Static variable in class edu.isi.pegasus.planner.transfer.implementation.ImplementationFactory
  The constant designating the implementation be loaded for stage out jobs.
TYPE_SYMLINK_STAGE_IN - Static variable in class edu.isi.pegasus.planner.transfer.implementation.ImplementationFactory
  The constant designating the implementation to be loaded for symbolic tx jobs.
typeInRange(int) - Static method in class edu.isi.pegasus.planner.classes.Job
  Returns whether the job type value for the job is in range or not.
typeNeedsCleanUp(GraphNode) - Method in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  Checks to see which job types are required to be looked at for cleanup.
typeNeedsCleanUp(int) - Method in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  Checks to see which job types are required to be looked at for cleanup.
typeRecursive() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns whether the job is recursive or not.
typeStageOut(int) - Method in class edu.isi.pegasus.planner.refiner.cleanup.InPlace
  Checks to see if job type is a stageout job type.
typeToString() - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Returns the type associated with the logical file.
typeValid(int) - Method in class edu.isi.pegasus.planner.classes.PegasusFile
  Returns whether the type of file value is valid or not.

## U

Uname - Class in edu.isi.pegasus.planner.invocation
  The uname element.
Uname() - Constructor for class edu.isi.pegasus.planner.invocation.Uname
  The default constructor
Uname(String) - Constructor for class edu.isi.pegasus.planner.invocation.Uname
  Constructs a piece of data.
unameToArchitecture(Uname) - Static method in class edu.isi.pegasus.planner.invocation.Uname
  An adapter method to convert the uname object to the architecture object.
UNASSIGNED_JOB - Static variable in class edu.isi.pegasus.planner.classes.Job
  Denotes a job that does not fall into the other categories.
UNDEFINED_ARCHMODE_VALUE - Static variable in class edu.isi.pegasus.planner.invocation.Uname
  The undefined value for archmode attribute.
UNDEFINED_READ_VALUE - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolMode
  Constants for mode not defined.
UNDEFINED_SITE - Static variable in class edu.isi.pegasus.planner.parser.dax.DAXParser3
  Constant denoting an undefined site
UNDEFINED_SITE_NAME - Static variable in class edu.isi.pegasus.planner.classes.ReplicaLocation
  The site name that is associated in the case the resource handle is not specified with the PFN.
unescape(String) - Method in class edu.isi.ikcap.workflows.util.logging.Escape
  Transforms a given string by unescaping all characters that are prefixed with the escape character.
unescape(String) - Method in class edu.isi.pegasus.common.util.Escape
  Transforms a given string by unescaping all characters that are prefixed with the escape character.
unescape(String) - Method in class edu.isi.pegasus.planner.client.RCClient
  Unescapes previously backslashed characters.
UniqueMerge - Class in edu.isi.pegasus.planner.namespace.aggregator
  Merges profile as a delimiter separated list.
UniqueMerge() - Constructor for class edu.isi.pegasus.planner.namespace.aggregator.UniqueMerge
UNIVERSE - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The constant to be passed to the accessor functions to get or set the universe.
UNIVERSE - Static variable in class edu.isi.pegasus.planner.parser.tokens.SiteCatalogReservedWord
  token value for the reserved word "universe".
UNIVERSE_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.Condor
UNIVERSE_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The name of the key that denotes the condor universe key.
UNKNOWN_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Namespace
  The key is unknown.
unknownKey(String, String) - Method in class edu.isi.pegasus.planner.namespace.Namespace
  Warns about an unknown profile key and constructs it anyway.
unknownKey(String, String) - Method in class edu.isi.pegasus.planner.namespace.Pegasus
  Warns about an unknown profile key and constructs it anyway.
unknownNamespaceMessage(String) - Static method in class edu.isi.pegasus.planner.classes.Profile
  Returns the unknown namespace message.
unmarkArgs() - Method in class edu.isi.pegasus.planner.refiner.MainEngine
  Deprecated.
unsetInstalled() - Method in class edu.isi.pegasus.planner.dax.Executable
  Unset the installed flag on the executable.
unSupportedNestingOfElements(String, String) - Method in class edu.isi.pegasus.planner.parser.StackBasedXMLParser
  Called when certain element nesting is allowed in the XML schema but is not supported in the code as yet.
UNTAR_DERIVATION_NAME - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The logical name of the transformation for the untar job.
UNTAR_DERIVATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The derivation namespace for the untar job.
UNTAR_DERIVATION_VERSION - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The version number for the derivations for untar job.
UNTAR_PREFIX - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  Constant suffix for the names of the deployment nodes.
UNTAR_TRANSFORMATION_NAME - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The logical name of the worker package
UNTAR_TRANSFORMATION_NAMESPACE - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The transformation namespace for the worker package
UNTAR_TRANSFORMATION_VERSION - Static variable in class edu.isi.pegasus.planner.refiner.DeployWorkerPackage
  The version number for the worker package.
Update - Class in edu.isi.pegasus.planner.namespace.aggregator
  An implementation of the Aggregator interface that always takes the new profile value.
Update() - Constructor for class edu.isi.pegasus.planner.namespace.aggregator.Update
updateDownLen() - Method in class edu.isi.pegasus.planner.provisioner.Node
updateETs() - Method in class edu.isi.pegasus.planner.provisioner.Estimator
updateLeftBound(long, TreeSet) - Method in class edu.isi.pegasus.planner.provisioner.Node
  update EST(earliest start time) of this task.
updateLFNMap(String, String) - Method in class edu.isi.pegasus.planner.classes.DagInfo
  Updates the lfn map, that contains the mapping of an lfn with the type.
updateProfiles(TransformationCatalogEntry) - Method in class edu.isi.pegasus.planner.classes.Job
  Updates all the profile namespaces with the information associated in the transformation catalog for this job.
updateProfiles(PegasusProperties) - Method in class edu.isi.pegasus.planner.classes.Job
  Updates all the profile namespaces with the information specified by the user in the properties file, that apply to this job.
updateProfiles(Profiles) - Method in class edu.isi.pegasus.planner.classes.Job
  Updates all the profile namespaces with the information specified in list of profile objects passed.
updateProfiles(List) - Method in class edu.isi.pegasus.planner.classes.Job
  Updates all the profile namespaces with the information specified in list of profile objects passed.
updateReplacementTable(List, Job) - Method in class edu.isi.pegasus.planner.cluster.Horizontal
  Updates the replacement table.
updateRightBound(long, TreeSet) - Method in class edu.isi.pegasus.planner.provisioner.Node
  update LFT(latest finish time) of this task.
updateSiteStoreAndOptions(SiteStore, PlannerOptions) - Method in class edu.isi.pegasus.planner.common.PegasusConfiguration
  Updates Site Store and options based on the planner options set by the user on the command line
updateUpLen() - Method in class edu.isi.pegasus.planner.provisioner.Node
upLen - Variable in class edu.isi.pegasus.planner.provisioner.Node
UPWARD_RANK - Static variable in class edu.isi.pegasus.planner.selector.site.heft.HeftBag
  The constant to be passed to the accessor functions to get or set the upward rank for a node.
url - Variable in class edu.isi.pegasus.gridftp.GridFTPURL
URL - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The constant to be passed to the accessor functions to get or set the url.
URL_PRFIX_PROPERTY_KEY - Static variable in class edu.isi.pegasus.planner.catalog.replica.impl.Directory
  The name of the key that specifies the url prefix to be associated with the PFN's
usage() - Static method in class edu.isi.pegasus.gridftp.PegasusGridFTP
usage(String) - Static method in class edu.isi.pegasus.gridftp.PegasusGridFTP
Usage - Class in edu.isi.pegasus.planner.invocation
  This class is contains some excerpt from the getrusage call.
Usage() - Constructor for class edu.isi.pegasus.planner.invocation.Usage
  Default c'tor: Construct a hollow shell and allow further information to be added later.
Usage(double, double, int, int, int, int, int, int, int, int, int, int, int, int, int, int) - Constructor for class edu.isi.pegasus.planner.invocation.Usage
  Full c'tor: All values are provided.
usecEnd - Variable in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
useCondorQuotingForArguments() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a boolean indicating whether we want to Condor Quote the arguments of the job or not.
usecStart - Variable in class edu.isi.ikcap.workflows.util.logging.EventLogMessage
useDeepStorageDirectoryStructure() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a boolean indicating whether to have a deep storage directory structure or not while staging out data to the output site.
useDoubleNegative(String) - Method in class edu.isi.pegasus.planner.parser.dax.DAXParser2
  Determines whether to use a doubleNegative or not.
useExtendedTimeStamp() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  It specifies whether to use the extended timestamp format for generation of timestamps that are used to create the random directory name, and for the classads generation.
useForceInTransfer() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  It specifies whether the underlying transfer mechanism being used should use the force option if available to transfer the files.
useFullPathToGridStarts(boolean) - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Setter method to control whether a full path to Gridstart should be returned while wrapping a job or not.
useFullPathToGridStarts(boolean) - Method in class edu.isi.pegasus.planner.code.gridstart.NoGridStart
useFullPathToGridStarts(boolean) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
useFullPathToGridStarts(boolean) - Method in interface edu.isi.pegasus.planner.code.GridStart
  Setter method to control whether a full path to Gridstart should be returned while wrapping a job or not.
useInvoke(Job, String, StringBuffer) - Method in class edu.isi.pegasus.planner.code.gridstart.Kickstart
  Triggers the creation of the kickstart input file, that contains the the remote executable and the arguments with which it has to be invoked.
useInvokeInGridStart() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a boolean indicating whether to use invoke in kickstart always or not.
USER_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The user who submitted the workflow.
USER_PROPERTY_FILENAME - Static variable in class edu.isi.pegasus.common.util.CommonProperties
  Basename of the (new) file to read for user properties.
userExecutablesStagedForJob() - Method in class edu.isi.pegasus.planner.classes.Job
  Returns whether user executables need to be staged for job or not.
UserOptions - Class in edu.isi.pegasus.planner.common
  A Singleton wrapper around the PlannerOptions class to get hold of the options specified by the user to run Pegasus.
UserOptions(PlannerOptions) - Constructor for class edu.isi.pegasus.planner.common.UserOptions
  The private constructor that initializes the user options.
UserPOSTScript - Class in edu.isi.pegasus.planner.code.gridstart
  A user defined post script.
UserPOSTScript() - Constructor for class edu.isi.pegasus.planner.code.gridstart.UserPOSTScript
  The default constructor.
uses(String, File.LINK) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
uses(String, File.LINK, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
uses(String, File.LINK, boolean, String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
uses(String, File.LINK, String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
uses(String, File.LINK, File.TRANSFER) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
uses(String, File.LINK, File.TRANSFER, String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
uses(String, File.LINK, File.TRANSFER, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
uses(String, File.LINK, File.TRANSFER, boolean, String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
uses(String, File.LINK, File.TRANSFER, boolean, boolean, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
uses(String, File.LINK, File.TRANSFER, boolean, boolean, boolean, String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
uses(File, File.LINK) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
uses(File, File.LINK, File.TRANSFER) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
uses(File, File.LINK, File.TRANSFER, String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
uses(File, File.LINK, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
uses(File, File.LINK, boolean, String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
uses(File, File.LINK, String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
uses(File, File.LINK, File.TRANSFER, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
uses(File, File.LINK, File.TRANSFER, boolean, String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
uses(File, File.LINK, File.TRANSFER, boolean, boolean, boolean) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
uses(File, File.LINK, File.TRANSFER, boolean, boolean, boolean, String) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
uses(List<File>, File.LINK) - Method in class edu.isi.pegasus.planner.dax.AbstractJob
uses(CatalogType) - Method in class edu.isi.pegasus.planner.dax.Transformation
  Set the file or executable being used by the transformation
uses(List<CatalogType>) - Method in class edu.isi.pegasus.planner.dax.Transformation
  Set the List of files and/or executables being used by the transformation
USES_PMC - Static variable in class edu.isi.pegasus.planner.classes.PegasusBag
  The constant to be passed to the accessor functions to get or set the whether the planner used PMC or not
useThirdPartyTransferAlways() - Method in class edu.isi.pegasus.planner.transfer.implementation.GUC
  Return a boolean indicating whether the transfers to be done always in a third party transfer mode.
useThirdPartyTransferAlways() - Method in class edu.isi.pegasus.planner.transfer.implementation.Stork
  Return a boolean indicating whether the transfers to be done always in a third party transfer mode.
useThirdPartyTransferAlways() - Method in class edu.isi.pegasus.planner.transfer.implementation.T2
  Return a boolean indicating whether the transfers to be done always in a third party transfer mode.
useThirdPartyTransferAlways() - Method in class edu.isi.pegasus.planner.transfer.implementation.TPTGUC
  Return a boolean indicating whether the transfers to be done always in a third party transfer mode.
useThirdPartyTransferAlways() - Method in class edu.isi.pegasus.planner.transfer.implementation.Transfer
  Return a boolean indicating whether the transfers to be done always in a third party transfer mode.
useThirdPartyTransferAlways() - Method in interface edu.isi.pegasus.planner.transfer.Implementation
  Return a boolean indicating whether the transfers to be done always in a third party transfer mode.
useTimestampForDirectoryStructure() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a boolean indicating whether to use timestamp for directory name creation or not.
UUID_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The key for UUID of the workflow.

## V

v_7_1_0 - Static variable in class edu.isi.pegasus.common.util.CondorVersion
  Predefined Constant for condor version 7.1.0
v_7_1_2 - Static variable in class edu.isi.pegasus.common.util.CondorVersion
  Predefined Constant for condor version 7.1.2
v_7_1_3 - Static variable in class edu.isi.pegasus.common.util.CondorVersion
  Predefined Constant for condor version 7.1.3
VALID_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Namespace
  The key is a valid key and can be put in the profiles.
validTypesToString() - Static method in class edu.isi.pegasus.planner.classes.Profile
  Returns a comma separated string containing the valid namespace types.
value(String) - Static method in enum edu.isi.pegasus.planner.catalog.site.classes.Directory.TYPE
value - Variable in class edu.isi.pegasus.planner.classes.NameValue
  stores the corresponding value to the name in the pair.
value - Variable in class edu.isi.pegasus.planner.refiner.ThreadPool.ConditionVariable
  The int that is associated with this object.
value - Variable in class edu.isi.pegasus.planner.selector.site.RoundRobin.NameValue
  Stores the corresponding value to the name in the pair.
valueOf(String) - Static method in enum edu.isi.pegasus.common.credential.CredentialHandler.TYPE
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.isi.pegasus.planner.catalog.classes.Profiles.NAMESPACES
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.isi.pegasus.planner.catalog.classes.SysInfo.Architecture
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.isi.pegasus.planner.catalog.classes.SysInfo.OS
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.isi.pegasus.planner.catalog.site.classes.Directory.TYPE
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.isi.pegasus.planner.catalog.site.classes.FileServerType.OPERATION
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.isi.pegasus.planner.catalog.site.classes.GridGateway.JOB_TYPE
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.isi.pegasus.planner.catalog.site.classes.GridGateway.SCHEDULER_TYPE
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.isi.pegasus.planner.catalog.site.classes.GridGateway.TYPE
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor.DirectoryTypes
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.isi.pegasus.planner.catalog.transformation.classes.TCType
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.isi.pegasus.planner.classes.PegasusFile.LINKAGE
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.isi.pegasus.planner.classes.PlannerOptions.CLEANUP_OPTIONS
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.isi.pegasus.planner.common.PegasusProperties.CLEANUP_SCOPE
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.isi.pegasus.planner.dax.Executable.ARCH
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.isi.pegasus.planner.dax.Executable.OS
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.isi.pegasus.planner.dax.File.LINK
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.isi.pegasus.planner.dax.File.TRANSFER
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.isi.pegasus.planner.dax.Invoke.WHEN
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.isi.pegasus.planner.dax.Profile.NAMESPACE
  Returns the enum constant of this type with the specified name.
values() - Static method in enum edu.isi.pegasus.common.credential.CredentialHandler.TYPE
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.isi.pegasus.planner.catalog.classes.Profiles.NAMESPACES
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.isi.pegasus.planner.catalog.classes.SysInfo.Architecture
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.isi.pegasus.planner.catalog.classes.SysInfo.OS
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.isi.pegasus.planner.catalog.site.classes.Directory.TYPE
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.isi.pegasus.planner.catalog.site.classes.FileServerType.OPERATION
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.isi.pegasus.planner.catalog.site.classes.GridGateway.JOB_TYPE
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.isi.pegasus.planner.catalog.site.classes.GridGateway.SCHEDULER_TYPE
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.isi.pegasus.planner.catalog.site.classes.GridGateway.TYPE
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor.DirectoryTypes
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.isi.pegasus.planner.catalog.transformation.classes.TCType
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.isi.pegasus.planner.classes.PegasusFile.LINKAGE
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.isi.pegasus.planner.classes.PlannerOptions.CLEANUP_OPTIONS
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.isi.pegasus.planner.common.PegasusProperties.CLEANUP_SCOPE
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.isi.pegasus.planner.dax.Executable.ARCH
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.isi.pegasus.planner.dax.Executable.OS
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.isi.pegasus.planner.dax.File.LINK
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.isi.pegasus.planner.dax.File.TRANSFER
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.isi.pegasus.planner.dax.Invoke.WHEN
  Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.isi.pegasus.planner.dax.Profile.NAMESPACE
  Returns an array containing the constants of this enum type, in the order they are declared.
VANILLA_JOBMANAGER_TYPE - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.JobManager
  The jobmanager type associated with the compute jobs.
VANILLA_UNIVERSE - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.Condor
VANILLA_UNIVERSE - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The condor universe key value for vanilla universe.
VDS - Static variable in class edu.isi.pegasus.planner.classes.Profile
VDS2PegasusProperties - Class in edu.isi.pegasus.planner.client
  A Central Properties class that keeps track of all the properties used by Pegasus.
VDS2PegasusProperties() - Constructor for class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  The default constructor.
VDS_HOME - Static variable in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry
  The name of the environment variable VDS_HOME.
VDS_HOME - Static variable in class edu.isi.pegasus.planner.catalog.site.classes.SiteCatalogEntry3
  The name of the environment variable VDS_HOME.
VDS_HOME - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolInfoProvider
  The name of the environment variable VDS_HOME.
vdsArchToNMIArch(Arch) - Static method in class edu.isi.pegasus.planner.catalog.classes.VDSSysInfo2NMI
  Returns the NMI Architecture object corresponding to the VDS Arch object
vdsArchToNMIArch(String) - Static method in class edu.isi.pegasus.planner.catalog.classes.VDSSysInfo2NMI
  Returns the NMI Architecture object corresponding to the VDS Arch object
vdsArchToNMIArchMap() - Static method in class edu.isi.pegasus.planner.catalog.classes.VDSSysInfo2NMI
  Singleton access to the architecture to NMI arch map.
vdsNS - Variable in class edu.isi.pegasus.planner.classes.Job
  The Pegasus namespace variable.
vdsOsToNMIOS(Os) - Static method in class edu.isi.pegasus.planner.catalog.classes.VDSSysInfo2NMI
  Returns the NMI OS object corresponding to the VDS Os object
vdsOsToNMIOS(String) - Static method in class edu.isi.pegasus.planner.catalog.classes.VDSSysInfo2NMI
  Returns the NMI OS object corresponding to the VDS Os object
vdsOsToNMIOSMap() - Static method in class edu.isi.pegasus.planner.catalog.classes.VDSSysInfo2NMI
  Singleton access to the os to NMI os map.
VDSSysInfo - Class in edu.isi.pegasus.planner.catalog.transformation.classes
  This class keeps the system information associated with a resource or transformation.
VDSSysInfo(Arch, Os, String, String) - Constructor for class edu.isi.pegasus.planner.catalog.transformation.classes.VDSSysInfo
  The secondary convenience constructor.
VDSSysInfo(String, String, String) - Constructor for class edu.isi.pegasus.planner.catalog.transformation.classes.VDSSysInfo
  Another convenience constructor that uses all entries as strings.
VDSSysInfo(String, String, String, String) - Constructor for class edu.isi.pegasus.planner.catalog.transformation.classes.VDSSysInfo
  Another convenience constructor that uses all entries as strings.
VDSSysInfo(String) - Constructor for class edu.isi.pegasus.planner.catalog.transformation.classes.VDSSysInfo
VDSSysInfo() - Constructor for class edu.isi.pegasus.planner.catalog.transformation.classes.VDSSysInfo
  The default constructor.
VDSSysInfo2NMI - Class in edu.isi.pegasus.planner.catalog.classes
  An Adapter class that translates the old ( VDS era ) Arch and Os objects to the new NMI based Architecture and OS objects.
VDSSysInfo2NMI() - Constructor for class edu.isi.pegasus.planner.catalog.classes.VDSSysInfo2NMI
vdsSysInfo2NMI(VDSSysInfo) - Static method in class edu.isi.pegasus.planner.catalog.classes.VDSSysInfo2NMI
  Converts VDS SysInfo to NMI based SysInfo object
vdsToPegasusPropertiesTable() - Static method in class edu.isi.pegasus.planner.client.VDS2PegasusProperties
  Singleton access to the transfer implementation table.
vectorToString(String, Vector) - Method in class edu.isi.pegasus.planner.classes.Data
  It converts the contents of the Vector to a String and returns it.
vectorToString(String, Vector) - Method in class edu.isi.pegasus.planner.refiner.Engine
  It prints the contents of the Vector, to a String with the first line being the heading.
vendorParserClass - Static variable in class edu.isi.pegasus.planner.client.DAXValidator
  Default parser is the Xerces parser.
vendorParserClass - Static variable in class edu.isi.pegasus.planner.parser.InvocationParser
  Default parser is the Xerces parser.
VERSION - Static variable in interface edu.isi.pegasus.common.credential.CredentialHandler
  The version of the API being used.
VERSION - Static variable in class edu.isi.pegasus.common.logging.LogManager
  The version of the Logging API
version() - Method in class edu.isi.pegasus.common.util.CondorVersion
  Returns the condor version parsed by executing the condor_version command.
VERSION - Static variable in class edu.isi.pegasus.common.util.Separator
  This constant defines the separator that denotes a version range.
Version - Class in edu.isi.pegasus.common.util
  This class solely defines the version numbers of PEGASUS.
Version() - Constructor for class edu.isi.pegasus.common.util.Version
VERSION - Static variable in interface edu.isi.pegasus.planner.catalog.SiteCatalog
  The version of the API
version - Variable in class edu.isi.pegasus.planner.catalog.transformation.client.Client
VERSION - Static variable in interface edu.isi.pegasus.planner.catalog.TransformationCatalog
  The version of the API
VERSION - Static variable in interface edu.isi.pegasus.planner.catalog.WorkCatalog
  The version of the API
version - Variable in class edu.isi.pegasus.planner.classes.Job
  The version of the transformation.
version - Variable in class edu.isi.pegasus.planner.client.TCClient
VERSION - Static variable in interface edu.isi.pegasus.planner.cluster.Clusterer
  The version number associated with this API of Code Generator.
VERSION - Static variable in interface edu.isi.pegasus.planner.cluster.JobAggregator
  The version number associated with this API of Job Aggregator.
VERSION - Static variable in interface edu.isi.pegasus.planner.code.CodeGenerator
  The version number associated with this API of Code Generator.
VERSION - Static variable in interface edu.isi.pegasus.planner.code.generator.condor.CondorStyle
  The version number associated with this API of Code Generator.
VERSION - Static variable in interface edu.isi.pegasus.planner.code.GridStart
  The version number associated with this API of GridStart.
VERSION - Static variable in interface edu.isi.pegasus.planner.code.POSTScript
  The version number associated with this API of GridStart.
VERSION - Static variable in interface edu.isi.pegasus.planner.namespace.aggregator.Aggregator
  The version number associated with this API of Profile Aggregators.
VERSION - Static variable in class edu.isi.pegasus.planner.namespace.Namespace
  The version number associated with this API of Profile Namespaces.
VERSION - Static variable in interface edu.isi.pegasus.planner.parser.dax.Callback
  The version of the Callback api
VERSION - Static variable in class edu.isi.pegasus.planner.parser.tokens.SiteCatalogReservedWord
  token value for the reserved word "version".
VERSION - Static variable in interface edu.isi.pegasus.planner.partitioner.graph.Graph
  The version number associated with this Graph API.
VERSION - Static variable in class edu.isi.pegasus.planner.partitioner.Partitioner
  The version number associated with this API of Code Generator.
VERSION - Static variable in interface edu.isi.pegasus.planner.refiner.cleanup.CleanupImplementation
  The version number associated with this API Cleanup CleanupImplementation.
VERSION - Static variable in interface edu.isi.pegasus.planner.refiner.cleanup.CleanupStrategy
  The version number associated with this API Cleanup CleanupStrategy.
VERSION - Static variable in interface edu.isi.pegasus.planner.refiner.createdir.Implementation
  The version number associated with this API.
VERSION - Static variable in interface edu.isi.pegasus.planner.refiner.createdir.Strategy
  The version number associated with this API Cleanup Strategy.
VERSION - Static variable in interface edu.isi.pegasus.planner.refiner.Refiner
  The version of the API.
VERSION - Static variable in interface edu.isi.pegasus.planner.selector.ReplicaSelector
  The version of this API.
VERSION - Static variable in class edu.isi.pegasus.planner.selector.site.NonJavaCallout
  The version number associated with this API of non java callout site selection.
VERSION - Static variable in interface edu.isi.pegasus.planner.selector.SiteSelector
  The version of the API of the Site Selector.
VERSION - Static variable in interface edu.isi.pegasus.planner.transfer.Implementation
  The version number associated with this API
VERSION - Static variable in interface edu.isi.pegasus.planner.transfer.mapper.OutputMapper
  The version of the API of the Output Mapper
VERSION - Static variable in interface edu.isi.pegasus.planner.transfer.SLS
  The version associated with the API.
VERSION_AD_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.ClassADSGenerator
  The class ad key for the version id.
VERSION_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The Key for the version id.
VersionNumber - Class in edu.isi.pegasus.planner.client
  This class just prints the current version number on stdout.
VersionNumber(String) - Constructor for class edu.isi.pegasus.planner.client.VersionNumber
  ctor: Constructs a new instance with the given application name.
Vertical - Class in edu.isi.pegasus.planner.cluster
  The vertical cluster, that extends the Default clusterer and topologically sorts the partition before clustering the jobs into aggregated jobs.
Vertical() - Constructor for class edu.isi.pegasus.planner.cluster.Vertical
  The default constructor.
VERTICAL_CLUSTERING_CLASS - Static variable in class edu.isi.pegasus.planner.cluster.ClustererFactory
  The name of the class implementing vertical clustering.
visit(SiteData) - Method in class edu.isi.pegasus.planner.catalog.site.classes.AbstractXMLPrintVisitor
visit(SiteStore) - Method in interface edu.isi.pegasus.planner.catalog.site.classes.SiteDataVisitor
  Visit the SiteStore object
visit(SiteCatalogEntry) - Method in interface edu.isi.pegasus.planner.catalog.site.classes.SiteDataVisitor
  Visit the Site CatalogEntry object
visit(GridGateway) - Method in interface edu.isi.pegasus.planner.catalog.site.classes.SiteDataVisitor
  Visit the GridGateway object
visit(Directory) - Method in interface edu.isi.pegasus.planner.catalog.site.classes.SiteDataVisitor
  Visit Directory site data object
visit(FileServer) - Method in interface edu.isi.pegasus.planner.catalog.site.classes.SiteDataVisitor
  Visit FileServer site data object
visit(ReplicaCatalog) - Method in interface edu.isi.pegasus.planner.catalog.site.classes.SiteDataVisitor
  Visit the ReplicaCatalog object
visit(Connection) - Method in interface edu.isi.pegasus.planner.catalog.site.classes.SiteDataVisitor
  Visit the connection object
visit(SiteData) - Method in interface edu.isi.pegasus.planner.catalog.site.classes.SiteDataVisitor
visit(SiteStore) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
  Visit the SiteStore object
visit(SiteCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
  Visit the Site CatalogEntry object
visit(GridGateway) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
  Visit the GridGateway object
visit(Directory) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
  Visit the directory object
visit(FileServer) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
  Visit FileServer site data object
visit(ReplicaCatalog) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
  Visit the ReplicaCatalog object
visit(Connection) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
  Visit the connection object
visit(SiteStore) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML4PrintVisitor
  Visit the SiteStore object
visit(SiteCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML4PrintVisitor
  Visit the Site CatalogEntry object
visit(GridGateway) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML4PrintVisitor
  Visit the GridGateway object
visit(Directory) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML4PrintVisitor
  Visit the directory object
visit(FileServer) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML4PrintVisitor
  Visit FileServer site data object
visit(ReplicaCatalog) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML4PrintVisitor
  Visit the ReplicaCatalog object
visit(Connection) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML4PrintVisitor
  Visit the connection object

## W

warning(SAXParseException) - Method in class edu.isi.pegasus.planner.client.DAXValidator
warning(SAXParseException) - Method in class edu.isi.pegasus.planner.parser.XMLErrorHandler
  Logs the warning messages in the SAX parser generates while validating the XML file against an XML Schema.
WARNING_MESSAGE_LEVEL - Static variable in class edu.isi.pegasus.common.logging.LogManager
  The level value, to indicate a WARNING error message.
WARNING_MESSAGE_TYPE - Static variable in class edu.isi.pegasus.common.logging.logger.Default
  The type value to indicate a WARNING message.
weight - Variable in class edu.isi.pegasus.planner.provisioner.Node
WF_NAME_AD_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.ClassADSGenerator
  The classad for the flow id.
WF_NAME_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The Key for the flow id.
WF_TIME_AD_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.ClassADSGenerator
  The classad for the timestamp.
WF_TIME_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The Key for the timestamp.
WF_TIMESTAMP_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Braindump
  The Key for the timestamp.
WF_UUID_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.ClassADSGenerator
  The classad for the workflow uuid
WHEN() - Constructor for enum edu.isi.pegasus.planner.dax.Invoke.WHEN
WHEN_TO_TRANSFER_OUTPUT_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.style.CondorC
  The name of key that designates when to transfer output.
WHEN_TO_TRANSFER_OUTPUT_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The name of key that designates when to transfer output.
where() - Method in class edu.isi.pegasus.planner.client.DAXValidator
where() - Method in class edu.isi.pegasus.planner.parser.InvocationParser
WHITE_COLOR - Static variable in class edu.isi.pegasus.planner.partitioner.graph.GraphNode
Whole - Class in edu.isi.pegasus.planner.partitioner
  This partitioning technique considers the whole DAX as a single partition.
Whole(GraphNode, Map, PegasusProperties) - Constructor for class edu.isi.pegasus.planner.partitioner.Whole
  The overloaded constructor.
WINDOWS - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Os
work(String) - Method in class edu.isi.pegasus.common.util.CondorVersion.CondorVersionCallback
  Callback whenever a line is read from the stream by the StreamGobbler.
work(String) - Method in class edu.isi.pegasus.common.util.DefaultStreamGobblerCallback
  Callback whenever a line is read from the stream by the StreamGobbler.
work(String) - Method in interface edu.isi.pegasus.common.util.StreamGobblerCallback
  Callback whenever a line is read from the stream by the StreamGobbler.
work(String) - Method in class edu.isi.pegasus.planner.catalog.site.impl.OSGMM.ListCallback
  Callback whenever a line is read from the stream by the StreamGobbler.
work(List, String) - Method in class edu.isi.pegasus.planner.client.RCClient
  Works on the command contained within chunk of lines.
work(List) - Method in class edu.isi.pegasus.planner.client.RCClient
  Works on the command contained within one line.
work(String) - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG.GrepCallback
  Callback whenever a line is read from the stream by the StreamGobbler.
WorkCatalog - Interface in edu.isi.pegasus.planner.catalog
  The catalog interface to the Work Catalog, the erstwhile Work DB, that is populated by tailstatd and associates.
WorkCatalogException - Exception in edu.isi.pegasus.planner.catalog.work
  Class to notify of failures.
WorkCatalogException() - Constructor for exception edu.isi.pegasus.planner.catalog.work.WorkCatalogException
WorkCatalogException(String) - Constructor for exception edu.isi.pegasus.planner.catalog.work.WorkCatalogException
  Constructs a `WorkCatalogException` with the specified detailed message.
WorkCatalogException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.catalog.work.WorkCatalogException
  Constructs a `WorkCatalogException` with the specified detailed message and a cause.
WorkCatalogException(Throwable) - Constructor for exception edu.isi.pegasus.planner.catalog.work.WorkCatalogException
  Constructs a `WorkCatalogException` with the specified just a cause.
WORKDIR - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.SiteInfo
  The constant to be passed to the accessor functions to get or set the List of `WorkDir` objects.
WorkDir - Class in edu.isi.pegasus.planner.catalog.site.impl.old.classes
  This is a data class that is used to store information about the scratch work directory or the execution mount point on the remote pool.
WorkDir() - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.old.classes.WorkDir
  The default constructor.
WORKDIR - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.WorkDir
  The constant to be passed to the accessor functions to get or set the path to the work directory.
WORKDIR - Static variable in class edu.isi.pegasus.planner.parser.tokens.SiteCatalogReservedWord
  token value for the reserved word "workdir".
WORKDIRINFO - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.classes.WorkDir
  Array storing the names of the attributes that are stored with the work directory.
WORKER_NODE_DIRECTORY_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
  The directory in which job needs to execute on worker node tmp.
WORKER_PACKAGE_MAP - Static variable in class edu.isi.pegasus.planner.classes.PegasusBag
  The constant to be passed to the accessor functions to get or set the handle to the worker package maps
WorkerNodeFS - Class in edu.isi.pegasus.planner.catalog.site.classes
  This data class describes the WorkerNode Filesystem layout.
WorkerNodeFS() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeFS
  The default constructor.
WorkerNodeFS(WorkerNodeScratch, WorkerNodeStorage) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeFS
  The overloaded constructor.
WorkerNodeScratch - Class in edu.isi.pegasus.planner.catalog.site.classes
  This data class describes the scratch area on a head node.
WorkerNodeScratch() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeScratch
  The default constructor
WorkerNodeScratch(StorageType) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeScratch
  The overloaded constructor
WorkerNodeScratch(LocalDirectory, SharedDirectory) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeScratch
  The overloaded constructor.
WorkerNodeStorage - Class in edu.isi.pegasus.planner.catalog.site.classes
  This data class describes the storage area on worker nodes.
WorkerNodeStorage() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeStorage
  The default constructor
WorkerNodeStorage(StorageType) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeStorage
  The overloaded constructor
WorkerNodeStorage(LocalDirectory, SharedDirectory) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.WorkerNodeStorage
  The overloaded constructor.
WorkerSharedDirectory - Class in edu.isi.pegasus.planner.catalog.site.classes
  This data class describes the directory shared only amongst worker nodes .
WorkerSharedDirectory() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.WorkerSharedDirectory
  The default constructor.
WorkerSharedDirectory(Map<FileServerType.OPERATION, List<FileServer>>, InternalMountPoint) - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.WorkerSharedDirectory
  The overloaded constructor
WorkFactory - Class in edu.isi.pegasus.planner.catalog.work
  This factory loads a work catalog, as specified by the properties.
WorkFactory() - Constructor for class edu.isi.pegasus.planner.catalog.work.WorkFactory
WorkFactoryException - Exception in edu.isi.pegasus.planner.catalog.work
  Class to notify of failures while instantiating Transformation Catalog implementations.
WorkFactoryException(String) - Constructor for exception edu.isi.pegasus.planner.catalog.work.WorkFactoryException
  Constructs a `WorkFactoryException` with no detail message.
WorkFactoryException(String, String) - Constructor for exception edu.isi.pegasus.planner.catalog.work.WorkFactoryException
  Constructs a `WorkFactoryException` with the specified detailed message.
WorkFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.catalog.work.WorkFactoryException
  Constructs a `WorkFactoryException` with the specified detailed message and a cause.
WorkFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.planner.catalog.work.WorkFactoryException
  Constructs a `WorkFactoryException` with the specified detailed message and a cause.
WORKFLOW - Static variable in class edu.isi.pegasus.planner.code.generator.MonitordNotify
  The constant string to write for work flow notifications.
WORKFLOW_CACHE_FILE_IMPLEMENTOR - Static variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  The name of the Replica Catalog Implementer that is used to write out the workflow cache file in the submit directory.
WORKFLOW_CACHE_REPLICA_CATALOG_KEY - Static variable in class edu.isi.pegasus.planner.refiner.TransferEngine
  The name of the source key for Replica Catalog Implementer that serves as cache
WORKFLOW_ID_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.Stampede
  The attribute key for workflow id.
WORKFLOW_ID_PROPERTY - Static variable in class edu.isi.pegasus.planner.code.gridstart.NetloggerPostScript
  The property to be set for postscript to pick up workflow id
WorkflowMetrics - Class in edu.isi.pegasus.planner.classes
  A Workflow metrics class that stores the metrics about the workflow.
WorkflowMetrics() - Constructor for class edu.isi.pegasus.planner.classes.WorkflowMetrics
  The default constructor.
WorkingDir - Class in edu.isi.pegasus.planner.invocation
  This class is transient for XML parsing.
WorkingDir() - Constructor for class edu.isi.pegasus.planner.invocation.WorkingDir
  Default c'tor: Construct a hollow shell and allow further information to be added later.
WorkingDir(String) - Constructor for class edu.isi.pegasus.planner.invocation.WorkingDir
  Constructs a piece of data.
wrapJobWithLocalPegasusLite(Job) - Method in class edu.isi.pegasus.planner.code.generator.condor.style.Condor
  Wraps the local universe jobs with a local Pegasus Lite wrapper to get around the Condor file IO bug for local universe job
wrapJobWithPegasusLite(Job, boolean) - Method in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  Generates a seqexec input file for the job.
write(Buffer) - Method in class edu.isi.pegasus.gridftp.GridFTPConnection.StringBuilderDataSink
write(String) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
write(Writer, Map<String, Collection<ReplicaCatalogEntry>>) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.Regex
write(Partition) - Method in class edu.isi.pegasus.planner.partitioner.PDAXWriter
  Writes out a partition to the associate XML stream.
write(String) - Method in class edu.isi.pegasus.planner.partitioner.PDAXWriter
  Writes out to the file.
writeAlias(Writer, String, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.ReplicaCatalog
  Renders alias as xml
writeAttribute(Writer, String, String) - Method in class edu.isi.pegasus.common.util.XMLOutput
  XML write helper method writes a quoted attribute onto a stream.
writeAttribute(String, String) - Method in class edu.isi.pegasus.common.util.XMLWriter
writeAttribute(Writer, String, String) - Method in class edu.isi.pegasus.planner.catalog.classes.Profiles
  Writes an attribute to the stream.
writeAttribute(Writer, String, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.AbstractSiteData
  Writes an attribute to the stream.
writeAttribute(String, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.AbstractXMLPrintVisitor
  Writes an attribute to the stream.
writeAttribute(Writer, String, String) - Method in class edu.isi.pegasus.planner.catalog.site.classes.AbstractXMLPrintVisitor
  Writes an attribute to the stream.
writeAttribute(Writer, String, String) - Method in class edu.isi.pegasus.planner.partitioner.Partition
  Writes an attribute to the stream.
writeAttribute2(Writer, String, String) - Method in class edu.isi.pegasus.common.util.XMLOutput
  Saner XML write helper method writes a quoted attribute onto a stream.
writeAttributes() - Method in class edu.isi.pegasus.common.util.XMLWriter
  Writes out the attributes of a given element to the writer
writeCData(String) - Method in class edu.isi.pegasus.common.util.XMLWriter
writeDagFileTail(ADag) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  It writes the relations making up the DAG in the dag file and and closes the file handle to it.
writeData(String) - Method in class edu.isi.pegasus.common.util.XMLWriter
writeDOTFile(String, ADag) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Writes out the DOT file in the submit directory.
writeDOTHeader(Writer, String) - Method in class edu.isi.pegasus.planner.classes.ADag
  Writes out the static DOT Header.
writeFileServer(Directory, XML3PrintVisitor.DirectoryTypes) - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
writeFS() - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
writeHeader() - Method in class edu.isi.pegasus.planner.partitioner.PDAXWriter
  Writes out the opening element of the xml document.
writeHeadFS() - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
writeHeadFSScratch() - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
writeHeadFSStorage() - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
writeJobMapFile(String, ADag) - Method in class edu.isi.pegasus.planner.code.generator.condor.CondorGenerator
  Writes out the job map file in the submit directory.
writeLine() - Method in class edu.isi.pegasus.common.util.XMLWriter
writeln(String) - Method in class edu.isi.pegasus.planner.partitioner.DAXWriter
  Writes out to the file.
writeln(String) - Method in class edu.isi.pegasus.planner.partitioner.PDAXWriter
  Writes out to the file.
writeOutBraindump(ADag) - Method in class edu.isi.pegasus.planner.code.generator.Abstract
  Writes out the metrics file for the workflow
writeOutBraindump(File, Partition, String, String) - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Writes out the braindump.txt file for a partition in the partition submit directory.
writeOutBraindumpFile(Map<String, String>) - Method in class edu.isi.pegasus.planner.code.generator.Braindump
  Writes out the braindump.txt file for a workflow in the submit directory.
writeOutDAXReplicaStore(ADag) - Method in class edu.isi.pegasus.planner.code.generator.Abstract
  Writes out the DAX replica store
writeOutInputFileForJobAggregator(AggregatedJob) - Method in class edu.isi.pegasus.planner.cluster.aggregator.Abstract
  Writes out the input file for the aggregated job
writeOutInputFileForJobAggregator(AggregatedJob) - Method in class edu.isi.pegasus.planner.cluster.aggregator.MPIExec
  Writes out the input file for the aggregated job
writeOutMappings(Writer, ADag) - Method in class edu.isi.pegasus.planner.code.generator.NetloggerJobMapper
  Writes out the job mappings for a workflow.
writeOutMetrics() - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Returns a boolean indicating whether to write out the planner metrics or not.
writeOutMetricsFile(PlannerMetrics) - Method in class edu.isi.pegasus.planner.code.generator.Metrics
  Writes out the workflow metrics file in the submit directory
writeOutNotifications(ADag) - Method in class edu.isi.pegasus.planner.code.generator.Abstract
  Writes out the generator input file for the work-flow.
writeOutProperties(String) - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Writes out the properties to a temporary file in the directory passed.
writeOutProperties(String, boolean) - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Writes out the properties to a temporary file in the directory passed.
writeOutProperties(String, boolean, boolean) - Method in class edu.isi.pegasus.planner.common.PegasusProperties
  Writes out the properties to a temporary file in the directory passed.
writeOutProperties(String) - Method in class edu.isi.pegasus.planner.parser.pdax.PDAX2MDAG
  Writes out the properties to a temporary file in the directory passed.
writeOutRankings(File, Collection<Ranking>) - Method in class edu.isi.pegasus.planner.client.RankDAX
  Writes out the ranking to the file.
writeOutStampedeEvents(ADag) - Method in class edu.isi.pegasus.planner.code.generator.Abstract
  Writes out the stampedeEventGenerator events for the workflow.
writePartitionDax(Partition) - Method in class edu.isi.pegasus.planner.partitioner.DAXWriter
  It writes out a dax consisting of the jobs as specified in the partition.
writePartitionDax(Partition, int) - Method in class edu.isi.pegasus.planner.partitioner.DAXWriter
  It writes out a dax consisting of the jobs as specified in the partition.
writePartitionDax(Partition, int) - Method in class edu.isi.pegasus.planner.partitioner.MultipleLook
  It writes out a dax consisting of the jobs as specified in the partition.
writePartitionDax(Partition, int) - Method in class edu.isi.pegasus.planner.partitioner.SingleLook
  It writes out a dax consisting of the jobs as specified in the partition.
WriterCallback - Class in edu.isi.pegasus.planner.partitioner
  This callback writes out a `DAX` file for each of the partitions, and also writes out a `PDAX` file that captures the relations between the partitions.
WriterCallback() - Constructor for class edu.isi.pegasus.planner.partitioner.WriterCallback
  The default constructor.
writeReplicaCatalogEntry(String, ReplicaCatalogEntry) - Method in class edu.isi.pegasus.planner.catalog.replica.impl.FlushedCache
  The method generate a String representation of the replica catalog entry.
writeStdInAndAssociateCredentials(TransferJob, FileWriter, Collection, String, int) - Method in class edu.isi.pegasus.planner.transfer.implementation.AbstractMultipleFTPerXFERJob
  Writes to a FileWriter stream the stdin which goes into the magic script via standard input
writeStdInAndAssociateCredentials(TransferJob, FileWriter, Collection, String, int) - Method in class edu.isi.pegasus.planner.transfer.implementation.GUC
  Writes to a FileWriter stream the stdin which goes into the magic script via standard input
writeStdInAndAssociateCredentials(TransferJob, FileWriter, Collection, String, int) - Method in class edu.isi.pegasus.planner.transfer.implementation.T2
  Writes to a FileWriter stream the stdin which T2 takes via standard input.
writeStdInAndAssociateCredentials(TransferJob, FileWriter, Collection, String, int) - Method in class edu.isi.pegasus.planner.transfer.implementation.Transfer
  Writes to a FileWriter stream the stdin which goes into the magic script via standard input
writeString(String) - Method in class edu.isi.pegasus.planner.code.generator.Shell
  Writes a string to the associated write handle with the class
writeTC() - Method in class edu.isi.pegasus.planner.catalog.transformation.impl.File
writeTestLog(LogFormatter) - Method in class edu.isi.pegasus.common.logging.TestLogFormatter
writeToFile(String) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Generate a DAX File out of this object;
writeToSTDOUT() - Method in class edu.isi.pegasus.planner.dax.ADAG
  Generate a DAX representation on STDOUT.
writeToWriter(Writer, boolean) - Method in class edu.isi.pegasus.planner.dax.ADAG
  Generate a DAX representation and pipe it into the Writer
writeUnEscapedData(String) - Method in class edu.isi.pegasus.common.util.XMLWriter
writeWorkerFS() - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
writeWorkerFSScratch() - Method in class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
writeXMLComment(String, boolean) - Method in class edu.isi.pegasus.common.util.XMLWriter
writeXMLComment(String) - Method in class edu.isi.pegasus.common.util.XMLWriter
writeXMLHeader() - Method in class edu.isi.pegasus.common.util.XMLWriter
writeXMLHeader(Writer, String, String) - Method in class edu.isi.pegasus.planner.invocation.InvocationRecord
  Writes the header of the XML output.

## X

x(String, int) - Static method in class edu.isi.pegasus.common.util.Separator2Test
X509_IMPLEMENTING_CLASS - Static variable in class edu.isi.pegasus.common.credential.CredentialHandlerFactory
  The name of the class implementing the x509 credentials
X509_USER_PROXY_KEY - Static variable in class edu.isi.pegasus.common.credential.impl.Proxy
  The name of the environment variable that specifies the path to the proxy.
X509_USER_PROXY_KEY - Static variable in class edu.isi.pegasus.planner.namespace.ENV
  The name of the environment variable that specifies the path to the proxy.
X509_USER_PROXY_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Pegasus
X509_USER_PROXY_PEGASUS_PROFILE_KEY - Static variable in class edu.isi.pegasus.common.credential.impl.Proxy
X509USERPROXY_KEY - Static variable in class edu.isi.pegasus.planner.namespace.Condor
  The key that overrides the default x509 proxy location.
XBIT_DERIVATION_NS - Static variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  The derivation namespace for the setXBit jobs.
XBIT_DERIVATION_NS - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  The derivation namespace for the setXBit jobs.
XBIT_DERIVATION_VERSION - Static variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  The version number for the derivations for setXBit jobs.
XBIT_DERIVATION_VERSION - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  The version number for the derivations for setXBit jobs.
XBIT_EXECUTABLE_BASENAME - Static variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  The basename of the pegasus dirmanager executable.
XBIT_EXECUTABLE_BASENAME - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  The basename of the pegasus dirmanager executable.
XBIT_TRANSFORMATION - Static variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  The logical name of the transformation that creates directories on the remote execution pools.
XBIT_TRANSFORMATION_NS - Static variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  The transformation namespace for the setXBit jobs.
XBIT_TRANSFORMATION_NS - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  The transformation namespace for the setXBit jobs.
XBIT_TRANSFORMATION_VERSION - Static variable in class edu.isi.pegasus.planner.code.gridstart.PegasusLite
  The version number for the derivations for setXBit jobs.
XBIT_TRANSFORMATION_VERSION - Static variable in class edu.isi.pegasus.planner.transfer.implementation.Abstract
  The version number for the derivations for setXBit jobs.
XFORMATION_AD_KEY - Static variable in class edu.isi.pegasus.planner.code.generator.condor.ClassADSGenerator
  The classad for the complete transformation name.
XML - Class in edu.isi.pegasus.planner.catalog.site.impl.old
  It gets the information about a pool by reading the pool config xml that is generated from querying mds or using the static information provided by the user at the submit host.
XML(String) - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.old.XML
  The private constructor that is called only once, when the Singleton is invoked for the first time.
XML(String, String) - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.old.XML
  The private constructor that is called to return a non singleton instance of the class.
XML - Class in edu.isi.pegasus.planner.catalog.site.impl
  An implementation of the Site Catalog interface that is backed up by an XML file conforming to site catalog xml schema version 3.
XML() - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.XML
  The default constructor.
XML2 - Class in edu.isi.pegasus.planner.catalog.site.impl
  A back port to old site catalog schema for the current Site Catalog API This class parses XML documents that conform to site catalog schema version 2.
XML2() - Constructor for class edu.isi.pegasus.planner.catalog.site.impl.XML2
  The default constructor.
XML3PrintVisitor - Class in edu.isi.pegasus.planner.catalog.site.classes
  Prints the Site Catalog compatible with Site Catalog schema version 3 https://pegasus.isi.edu/wms/docs/schemas/sc-4.0/sc-3.0.html
XML3PrintVisitor() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.XML3PrintVisitor
XML3PrintVisitor.DirectoryTypes - Enum in edu.isi.pegasus.planner.catalog.site.classes
XML4PrintVisitor - Class in edu.isi.pegasus.planner.catalog.site.classes
  Prints the Site Catalog compatible with Site Catalog schema version 4 https://pegasus.isi.edu/wms/docs/schemas/sc-4.0/sc-4.0.html
XML4PrintVisitor() - Constructor for class edu.isi.pegasus.planner.catalog.site.classes.XML4PrintVisitor
XML_HEADER - Static variable in class edu.isi.pegasus.common.util.XMLWriter
XML_IMPLEMENTING_CLASS - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.SiteFactory
  The name of the class that connects to an XML based Site Catalog.
XML_IMPLEMENTING_CLASS_BASENAME - Static variable in class edu.isi.pegasus.planner.catalog.site.SiteFactory
  For 4.2, the orginal XML3 class was renamed XML and it supports different schemas.
XML_NAMESPACE - Static variable in class edu.isi.pegasus.planner.catalog.transformation.client.TCQuery
XML_NAMESPACE - Static variable in class edu.isi.pegasus.planner.client.SCClient
XML_NAMESPACE - Static variable in class edu.isi.pegasus.planner.partitioner.PDAXWriter
XML_READ_CLASS - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolMode
XML_READ_VALUE - Static variable in class edu.isi.pegasus.planner.catalog.site.impl.old.PoolMode
  Constants for xml pool read.
XML_VERSION - Static variable in class edu.isi.pegasus.planner.catalog.transformation.client.TCQuery
XML_VERSION - Static variable in class edu.isi.pegasus.planner.client.SCClient
XML_VERSION - Static variable in class edu.isi.pegasus.planner.partitioner.PDAXWriter
  The version of the associated xml schema, to which the pdax files being written conform to.
XMLErrorHandler - Class in edu.isi.pegasus.planner.parser
  This class handles the errors which occur while enforcing validation against the XML Schema.
XMLErrorHandler() - Constructor for class edu.isi.pegasus.planner.parser.XMLErrorHandler
  The default constructor.
XMLOutput - Class in edu.isi.pegasus.common.util
  This abstract class defines a common base for certain classes that deal with the generation of XML files.
XMLOutput() - Constructor for class edu.isi.pegasus.common.util.XMLOutput
XMLProducer - Interface in edu.isi.pegasus.planner.provenance.pasoa
  A PASOA specific interface to generate various assertions as XML.
XMLProducerFactory - Class in edu.isi.pegasus.planner.provenance.pasoa.producer
  The factory for instantiating an XMLProducer.
XMLProducerFactory() - Constructor for class edu.isi.pegasus.planner.provenance.pasoa.producer.XMLProducerFactory
XMLProducerFactoryException - Exception in edu.isi.pegasus.planner.provenance.pasoa.producer
  Class to notify of failures while instantiating XMLProducer implementations.
XMLProducerFactoryException(String) - Constructor for exception edu.isi.pegasus.planner.provenance.pasoa.producer.XMLProducerFactoryException
  Constructs a `XMLProducerFactoryException` with no detail message.
XMLProducerFactoryException(String, String) - Constructor for exception edu.isi.pegasus.planner.provenance.pasoa.producer.XMLProducerFactoryException
  Constructs a `XMLProducerFactoryException` with the specified detailed message.
XMLProducerFactoryException(String, Throwable) - Constructor for exception edu.isi.pegasus.planner.provenance.pasoa.producer.XMLProducerFactoryException
  Constructs a `XMLProducerFactoryException` with the specified detailed message and a cause.
XMLProducerFactoryException(String, String, Throwable) - Constructor for exception edu.isi.pegasus.planner.provenance.pasoa.producer.XMLProducerFactoryException
  Constructs a `XMLProducerFactoryException` with the specified detailed message and a cause.
XMLWriter - Class in edu.isi.pegasus.common.util
XMLWriter(Writer) - Constructor for class edu.isi.pegasus.common.util.XMLWriter
XMLWriter(Writer, String) - Constructor for class edu.isi.pegasus.common.util.XMLWriter

## _

_ADD_BLOAT - Static variable in class edu.isi.ikcap.workflows.util.logging.LogEvent
  The variable that triggers generation of message id and the event id in the messages.
_AIX - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Os
_AMD64 - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Arch
_entityIdMap - Variable in class edu.isi.ikcap.workflows.util.logging.LogEvent
_eventId - Variable in class edu.isi.ikcap.workflows.util.logging.LogEvent
_eventName - Variable in class edu.isi.ikcap.workflows.util.logging.LogEvent
_INTEL32 - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Arch
_INTEL64 - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Arch
_LINUX - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Os
_progName - Variable in class edu.isi.ikcap.workflows.util.logging.LogEvent
_SPARCV7 - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Arch
_SPARCV9 - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Arch
_SUNOS - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Os
_table_ - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Arch
_table_ - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Os
_value_ - Variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Arch
_value_ - Variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Os
_WINDOWS - Static variable in class edu.isi.pegasus.planner.catalog.transformation.classes.Os

A B C D E F G H I J K L M N O P Q R S T U V W X _