## Uses of Class
edu.isi.pegasus.planner.classes.ADag

Packages that use ADag
edu.isi.pegasus.planner.classes
edu.isi.pegasus.planner.client
edu.isi.pegasus.planner.cluster
edu.isi.pegasus.planner.cluster.aggregator
edu.isi.pegasus.planner.code
edu.isi.pegasus.planner.code.generator
edu.isi.pegasus.planner.code.generator.condor
edu.isi.pegasus.planner.code.gridstart
edu.isi.pegasus.planner.parser.dax
edu.isi.pegasus.planner.parser.pdax
edu.isi.pegasus.planner.refiner
edu.isi.pegasus.planner.refiner.createdir
edu.isi.pegasus.planner.selector: Provides the interface and call-out to the site selector mechanism.
edu.isi.pegasus.planner.selector.site
edu.isi.pegasus.planner.selector.site.heft
edu.isi.pegasus.planner.transfer
edu.isi.pegasus.planner.transfer.mapper
edu.isi.pegasus.planner.transfer.mapper.impl
edu.isi.pegasus.planner.transfer.refiner

### Uses of ADag in edu.isi.pegasus.planner.classes

Methods in edu.isi.pegasus.planner.classes with parameters of type ADag
`private java.lang.String` PlannerCache.`getCacheFileName(ADag adag, FileServerType.OPERATION operation)` Constructs the basename to the cache file that is to be used to log the transient files.
`void` PlannerCache.`initialize(PegasusBag bag, ADag dag)` Initialize the replica catalog instances that make up the cache.
`private ReplicaCatalog` PlannerCache.`intializeRCAsCache(ADag dag, FileServerType.OPERATION type)` Initializes the transient replica catalog and returns a handle to it.

### Uses of ADag in edu.isi.pegasus.planner.client

Methods in edu.isi.pegasus.planner.client that return ADag
`private ADag` CPlanner.`parseDAX(java.lang.String dax)` Parses the DAX and returns the associated ADag object

Methods in edu.isi.pegasus.planner.client with parameters of type ADag
`protected java.lang.String` CPlanner.`determineRelativeSubmitDirectory(ADag dag, java.lang.String dir, java.lang.String user, java.lang.String vogroup, boolean timestampBased)` Creates the submit directory for the workflow.
`private java.lang.String` CPlanner.`determineRootWorkflowUUID(ADag dag, PlannerOptions options, PegasusProperties properties)` Determines the workflow uuid for a workflow
`private void` CPlanner.`generateStampedeEventsForAbstractWorkflow(ADag workflow, PegasusBag bag)` Generates events for the abstract workflow.
`protected java.lang.String` CPlanner.`getDAGFilename(ADag dag, PlannerOptions options)` Returns the basename of the dag file
`java.lang.String` CPlanner.`getNOOPJobName(ADag dag)` Returns the name of the noop job.
`protected java.lang.String` CPlanner.`getRandomDirectory(ADag dag)` Sets the basename of the random directory that is created on the remote sites per workflow.
`protected boolean` CPlanner.`handleRescueDAG(ADag dag, PlannerOptions options)` Checks for rescue dags, and determines whether to plan or not.

### Uses of ADag in edu.isi.pegasus.planner.cluster

Fields in edu.isi.pegasus.planner.cluster declared as ADag
`protected ADag` Abstract.`mScheduledDAG` ADag object containing the jobs that have been scheduled by the site selector.
`private ADag` Horizontal.`mScheduledDAG` ADag object containing the jobs that have been scheduled by the site selector.

Methods in edu.isi.pegasus.planner.cluster that return ADag
`ADag` Abstract.`getClusteredDAG()` Returns the clustered workflow.
`ADag` Clusterer.`getClusteredDAG()` Returns the clustered workflow.
`ADag` Horizontal.`getClusteredDAG()` Returns the clustered workflow.
`ADag` Horizontal.`getWorkflow()` Returns a reference to the workflow that is being refined by the refiner.

Methods in edu.isi.pegasus.planner.cluster with parameters of type ADag
`void` Abstract.`initialize(ADag dag, PegasusBag bag)` Initializes the Clusterer impelementation
`void` JobAggregator.`initialize(ADag dag, PegasusBag bag)` Initializes the JobAggregator impelementation
`void` Clusterer.`initialize(ADag dag, PegasusBag bag)` Initializes the Clusterer impelementation
`void` Horizontal.`initialize(ADag dag, PegasusBag bag)` Initializes the Clusterer impelementation
`static Clusterer` ClustererFactory.`loadClusterer(ADag dag, PegasusBag bag, java.lang.String type)` Loads the appropriate clusterer on the basis of the clustering type specified in the options passed to the planner.

### Uses of ADag in edu.isi.pegasus.planner.cluster.aggregator

Fields in edu.isi.pegasus.planner.cluster.aggregator declared as ADag
`protected ADag` Abstract.`mClusteredADag` The handle to the ADag object that contains the workflow being clustered.
`private ADag` JobAggregatorInstanceFactory.`mDAG` ADag object containing the jobs that have been scheduled by the site selector.

Methods in edu.isi.pegasus.planner.cluster.aggregator with parameters of type ADag
`void` SeqExec.`initialize(ADag dag, PegasusBag bag)` Initializes the JobAggregator impelementation
`void` Abstract.`initialize(ADag dag, PegasusBag bag)` Initializes the JobAggregator impelementation
`void` JobAggregatorInstanceFactory.`initialize(ADag dag, PegasusBag bag)` Initializes the Factory.
`void` MPIExec.`initialize(ADag dag, PegasusBag bag)` Initializes the JobAggregator impelementation
`static JobAggregator` JobAggregatorFactory.`loadInstance(ADag dag, PegasusBag bag)` Loads the implementing class corresponding to the mode specified by the user at runtime in the properties file.
`static JobAggregator` JobAggregatorFactory.`loadInstance(java.lang.String className, ADag dag, PegasusBag bag)` Loads the implementing class corresponding to the class passed.

### Uses of ADag in edu.isi.pegasus.planner.code

Fields in edu.isi.pegasus.planner.code declared as ADag
`private ADag` GridStartFactory.`mDAG` The workflow object.

Methods in edu.isi.pegasus.planner.code with parameters of type ADag
`java.util.Collection<java.io.File>` CodeGenerator.`generateCode(ADag dag)` Generates the code for the concrete workflow in the input format of the workflow executor being used.
`void` CodeGenerator.`generateCode(ADag dag, Job job)` Generates the code for a single job in the input format of the workflow executor being used.
`void` GridStartFactory.`initialize(PegasusBag bag, ADag dag)` Initializes the factory with known GridStart implementations.
`void` GridStart.`initialize(PegasusBag bag, ADag dag)` Initializes the GridStart implementation.
`private GridStart` GridStartFactory.`loadGridStart(PegasusBag bag, ADag dag, java.lang.String className)` Loads the implementing class corresponding to the class.

### Uses of ADag in edu.isi.pegasus.planner.code.generator

Methods in edu.isi.pegasus.planner.code.generator with parameters of type ADag
`java.util.Map<java.lang.String,java.lang.String>` Braindump.`defaultBrainDumpEntries(ADag workflow)` Returns default braindump entries.
`java.util.Collection<java.io.File>` PMC.`generateCode(ADag dag)` Generates the code for the concrete workflow in the GRMS input format.
`java.util.Collection<java.io.File>` Stork.`generateCode(ADag dag)` Generates the code for the concrete workflow in the input format of the workflow executor being used.
`java.util.Collection<java.io.File>` Braindump.`generateCode(ADag dag)` Generates the code for the executable workflow in terms of a braindump file that contains workflow metadata useful for monitoring daemons etc.
`java.util.Collection<java.io.File>` MonitordNotify.`generateCode(ADag dag)` Generates the notifications input file.
`java.util.Collection<java.io.File>` DAXReplicaStore.`generateCode(ADag dag)` Generates the notifications input file.
`java.util.Collection<java.io.File>` PBS.`generateCode(ADag dag)` Generates the code for the concrete workflow in the GRMS input format.
`java.util.Collection<java.io.File>` Shell.`generateCode(ADag dag)` Generates the code for the concrete workflow in the GRMS input format.
`java.util.Collection<java.io.File>` Stampede.`generateCode(ADag dag)` Generates the code for the executable workflow in terms of a braindump file that contains workflow metadata useful for monitoring daemons etc.
`void` PMC.`generateCode(ADag dag, Job job)` Generates the code for a single job in the input format of the workflow executor being used.
`void` Stork.`generateCode(ADag dag, Job job)` Generates the code for a single job in the Stork format.
`void` Braindump.`generateCode(ADag dag, Job job)` Method not implemented.
`void` MonitordNotify.`generateCode(ADag dag, Job job)` Not implemented
`void` DAXReplicaStore.`generateCode(ADag dag, Job job)` Not implemented
`void` PBS.`generateCode(ADag dag, Job job)` Generates the code for a single job in the input format of the workflow executor being used.
`void` Shell.`generateCode(ADag dag, Job job)` Generates the code for a single job in the input format of the workflow executor being used.
`void` Stampede.`generateCode(ADag dag, Job job)` Method not implemented.
`java.util.Collection<java.io.File>` Braindump.`generateCode(ADag dag, java.util.Map<java.lang.String,java.lang.String> additionalEntries)` Generates the code for the executable workflow in terms of a braindump file that contains workflow metadata useful for monitoring daemons etc.
`protected void` Stampede.`generateEventsForDAXTask(java.io.PrintWriter writer, ADag workflow, Job job)` Generates stampede events corresponding to jobs/tasks in the DAX
`protected void` Stampede.`generateEventsForExecutableJob(java.io.PrintWriter writer, ADag dag, Job job)` Generates stampede events corresponding to an executable job
`protected void` Stampede.`generateTaskMapEvents(java.io.PrintWriter writer, ADag dag, Job job)` Generates the task.map events that link the jobs in the DAX with the jobs in the executable workflow
`abstract java.util.Map<java.lang.String,java.lang.String>` Abstract.`getAdditionalBraindumpEntries(ADag workflow)` Returns a Map containing additional metrics entries that are specific to a Code Generator
`java.util.Map<java.lang.String,java.lang.String>` PMC.`getAdditionalBraindumpEntries(ADag workflow)` Returns a Map containing additional braindump entries that are specific to a Code Generator.
`java.util.Map<java.lang.String,java.lang.String>` Stork.`getAdditionalBraindumpEntries(ADag workflow)` Returns an empty map
`java.util.Map<java.lang.String,java.lang.String>` PBS.`getAdditionalBraindumpEntries(ADag workflow)` Returns a Map containing additional braindump entries that are specific to a Code Generator
`java.util.Map<java.lang.String,java.lang.String>` Shell.`getAdditionalBraindumpEntries(ADag workflow)` Returns a Map containing additional braindump entries that are specific to a Code Generator
`protected java.lang.String` Abstract.`getDAGFilename(ADag dag, java.lang.String suffix)` Returns the name of the file on the basis of the metadata associated with the DAG.
`protected java.lang.String` PBS.`getPathtoPBSFile(ADag dag)` Returns the basename for the PBS script file for the dag
`protected java.lang.String` PMC.`getPathtoPMCFile(ADag dag)` Returns the basename for the pmc file for the dag
`protected java.lang.String` Shell.`getPathToShellScript(ADag dag)` Returns path to the shell script that is generated
`protected java.lang.String` PBS.`pbsBasename(ADag dag)` Returns the basename for the PBS file for the dag
`protected java.lang.String` PMC.`pmcBasename(ADag dag)` Returns the basename for the pmc file for the dag
`protected void` Abstract.`writeOutBraindump(ADag workflow)` Writes out the metrics file for the workflow
`protected void` Abstract.`writeOutDAXReplicaStore(ADag workflow)` Writes out the DAX replica store
`void` NetloggerJobMapper.`writeOutMappings(java.io.Writer writer, ADag dag)` Writes out the job mappings for a workflow.
`protected void` Abstract.`writeOutNotifications(ADag workflow)` Writes out the generator input file for the work-flow.
`protected void` Abstract.`writeOutStampedeEvents(ADag workflow)` Writes out the stampedeEventGenerator events for the workflow.

### Uses of ADag in edu.isi.pegasus.planner.code.generator.condor

Fields in edu.isi.pegasus.planner.code.generator.condor declared as ADag
`protected ADag` CondorGenerator.`mConcreteWorkflow` The workflow for which the code has to be generated.
`private ADag` SUBDAXGenerator.`mDAG`

Methods in edu.isi.pegasus.planner.code.generator.condor with parameters of type ADag
`protected void` CondorGenerator.`concreteDagEmpty(java.lang.String filename, ADag dag)` A callout method that dictates what needs to be done in case the concrete plan that is generated is empty.
`protected java.lang.String` SUBDAXGenerator.`createSubmitDirectory(ADag dag, java.lang.String dir, java.lang.String user, java.lang.String vogroup, boolean timestampBased)` Creates the submit directory for the workflow.
`static void` ClassADSGenerator.`generate(java.io.PrintWriter writer, ADag dag)` Writes out the classads for a workflow to corresponding writer stream.
`static void` ClassADSGenerator.`generate(java.io.PrintWriter writer, ADag dag, Job job)` Writes out the classads for a job to corresponding writer stream.
`java.util.Collection<java.io.File>` CondorGenerator.`generateCode(ADag dag)` Generates the code for the concrete workflow in Condor DAGMAN and CondorG input format.
`void` CondorGenerator.`generateCode(ADag dag, Job job)` Generates the code (condor submit file) for a single job.
`java.util.Map<java.lang.String,java.lang.String>` CondorGenerator.`getAdditionalBraindumpEntries(ADag workflow)` Returns a Map containing additional braindump entries that are specific to a Code Generator.
`protected java.lang.String` CondorGenerator.`getCondorLogInSubmitDirectory(ADag dag)` Returns the path to the condor log file in the submit directory.
`protected java.lang.String` CondorGenerator.`getDAGMANOutFilename(ADag dag)` Returns the basename of the file, that contains the output of the dagman while running the dag generated for the workflow.
`void` SUBDAXGenerator.`initialize(PegasusBag bag, ADag dag, java.io.PrintWriter dagWriter)` Initializes the class.
`protected java.io.File` CondorGenerator.`initializeDagFileWriter(java.lang.String filename, ADag workflow)` Initializes the file handler to the dag file and writes the header to it.
`protected void` CondorGenerator.`writeDagFileTail(ADag dag)` It writes the relations making up the DAG in the dag file and and closes the file handle to it.
`protected void` CondorGenerator.`writeDOTFile(java.lang.String filename, ADag dag)` Writes out the DOT file in the submit directory.
`protected void` CondorGenerator.`writeJobMapFile(java.lang.String filename, ADag dag)` Writes out the job map file in the submit directory.

### Uses of ADag in edu.isi.pegasus.planner.code.gridstart

Fields in edu.isi.pegasus.planner.code.gridstart declared as ADag
`private ADag` Kickstart.`mConcDAG` The handle to the workflow that is being enabled.
`private ADag` PegasusLite.`mDAG`
`private ADag` NoGridStart.`mDAG`

Methods in edu.isi.pegasus.planner.code.gridstart with parameters of type ADag
`void` PegasusLite.`initialize(PegasusBag bag, ADag dag)` Initializes the GridStart implementation.
`void` Kickstart.`initialize(PegasusBag bag, ADag dag)` Initializes the GridStart implementation.
`void` NoGridStart.`initialize(PegasusBag bag, ADag dag)` Initializes the GridStart implementation.

### Uses of ADag in edu.isi.pegasus.planner.parser.dax

Fields in edu.isi.pegasus.planner.parser.dax declared as ADag
`private ADag` DAX2CDAG.`mDag` The ADag object which contains information corresponding to the ADag in the XML file.

### Uses of ADag in edu.isi.pegasus.planner.parser.pdax

Fields in edu.isi.pegasus.planner.parser.pdax declared as ADag
`private ADag` PDAX2MDAG.`mMegaDAG` The abstract dag object that ends up holding the megadag.

### Uses of ADag in edu.isi.pegasus.planner.refiner

Fields in edu.isi.pegasus.planner.refiner declared as ADag
`private ADag` MainEngine.`mCleanupDag` The cleanup dag for the final concrete dag.
`private ADag` RemoveDirectory.`mConcDag` The concrete dag so far, for which the clean up dag needs to be generated.
`protected ADag` DeployWorkerPackage.`mCurrentDag` It is a reference to the Concrete Dag so far.
`protected ADag` CreateDirectory.`mCurrentDag` It is a reference to the Concrete Dag so far.
`private ADag` TransferEngine.`mDag` The DAG object to which the transfer nodes are to be added.
`private ADag` ReplicaCatalogBridge.`mDag` The DAG being worked upon.
`private ADag` InterPoolEngine.`mDag` ADag object corresponding to the Dag whose jobs we want to schedule.
`private ADag` MainEngine.`mOriginalDag` The Original Dag object which is constructed by parsing the dag file.
`private ADag` MainEngine.`mReducedDag` The reduced Dag object which is got from the Reduction Engine.
`private ADag` DataReuseEngine.`mWorkflow` The workflow object being worked upon.

Methods in edu.isi.pegasus.planner.refiner that return ADag
`ADag` CleanupEngine.`addCleanupJobs(ADag dag)` Adds the cleanup jobs in the workflow that removes the files staged to the remote site.
`ADag` DeployWorkerPackage.`addCleanupNodesForWorkerPackage(ADag dag)` Adds cleanup nodes in the workflow for sites specified.
`ADag` CreateDirectory.`addCreateDirectoryNodes(ADag dag)` It modifies the concrete dag passed in the constructor and adds the create random directory nodes to it at the root level.
`ADag` RemoveDirectory.`addRemoveDirectoryNodes(ADag dag)` Modifies the workflow to add remove directory nodes.
`ADag` RemoveDirectory.`addRemoveDirectoryNodes(ADag workflow, java.util.Set<java.lang.String> sites)` Adds create dir nodes to the workflow.
`ADag` DeployWorkerPackage.`addSetupNodes(ADag dag)` 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.
`private ADag` DeployWorkerPackage.`addSetupNodesWithoutUntarNodes(ADag dag, java.util.Set<java.lang.String> deploymentSites)` Adds only the stage worker nodes to the workflow.
`private ADag` DeployWorkerPackage.`addSetupNodesWithUntarNodes(ADag dag, java.util.Set<java.lang.String> deploymentSites)` Adds untar nodes to the workflow, in addition to the stage worker nodes
`ADag` NodeCollapser.`cluster(ADag dag)` Clusters the jobs in the workflow.
`ADag` NodeCollapser.`cluster(ADag dag, java.lang.String type)` Clusters the jobs in the workflow.
`ADag` TestReduceEdges.`createTest1()`
`ADag` TestReduceEdges.`createTest2()`
`ADag` MainEngine.`getCleanupDAG()` Returns the cleanup dag for the concrete dag.
`ADag` Refiner.`getWorkflow()` Returns a reference to the workflow that is being refined by the refiner.
`ADag` DataReuseEngine.`getWorkflow()` Returns a reference to the workflow that is being refined by the refiner.
`ADag` InterPoolEngine.`getWorkflow()` Returns a reference to the workflow that is being refined by the refiner.
`ADag` ReduceEdges.`reduce(ADag dag)` Prunes redundant edges from the workflow.
`ADag` DataReuseEngine.`reduceWorkflow(ADag workflow, ReplicaCatalogBridge rcb)` Reduces the workflow on the basis of the existence of lfn's in the replica catalog.
`ADag` MainEngine.`runPlanner()` The main function which calls the other engines and does the necessary work.

Methods in edu.isi.pegasus.planner.refiner with parameters of type ADag
`ADag` CleanupEngine.`addCleanupJobs(ADag dag)` Adds the cleanup jobs in the workflow that removes the files staged to the remote site.
`ADag` DeployWorkerPackage.`addCleanupNodesForWorkerPackage(ADag dag)` Adds cleanup nodes in the workflow for sites specified.
`ADag` CreateDirectory.`addCreateDirectoryNodes(ADag dag)` It modifies the concrete dag passed in the constructor and adds the create random directory nodes to it at the root level.
`ADag` RemoveDirectory.`addRemoveDirectoryNodes(ADag dag)` Modifies the workflow to add remove directory nodes.
`ADag` RemoveDirectory.`addRemoveDirectoryNodes(ADag workflow, java.util.Set<java.lang.String> sites)` Adds create dir nodes to the workflow.
`ADag` DeployWorkerPackage.`addSetupNodes(ADag dag)` 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.
`private ADag` DeployWorkerPackage.`addSetupNodesWithoutUntarNodes(ADag dag, java.util.Set<java.lang.String> deploymentSites)` Adds only the stage worker nodes to the workflow.
`private ADag` DeployWorkerPackage.`addSetupNodesWithUntarNodes(ADag dag, java.util.Set<java.lang.String> deploymentSites)` Adds untar nodes to the workflow, in addition to the stage worker nodes
`ADag` NodeCollapser.`cluster(ADag dag)` Clusters the jobs in the workflow.
`ADag` NodeCollapser.`cluster(ADag dag, java.lang.String type)` Clusters the jobs in the workflow.
`protected java.util.Map` NodeCollapser.`edgeList2Graph(ADag dag, java.util.Map nameIDMap)` Returns an adjacency list representation of the graph referred to by the list of edges.
`private java.lang.String` TransferEngine.`getCacheFileName(ADag adag)` Constructs the basename to the cache file that is to be used to log the transient files.
`protected java.lang.String` DeployWorkerPackage.`getCleanupJobname(ADag dag, java.lang.String site)` It returns the name of the untar job, that is to be assigned.
`protected java.util.Set` RemoveDirectory.`getCreateDirSites(ADag dag)` Retrieves the sites for which the create dir jobs need to be created.
`protected java.lang.String` DeployWorkerPackage.`getDeployJobName(ADag dag, java.lang.String site, boolean localTransfer)` It returns the name of the deployment job, that is to be assigned.
`protected java.util.Set` DeployWorkerPackage.`getDeploymentSites(ADag dag)` Retrieves the sites for which the deployment jobs need to be created.
`private java.lang.String` RemoveDirectory.`getRemoveDirJobName(ADag dag, java.lang.String site)` It returns the name of the remove directory job, that is to be assigned.
`protected java.lang.String` DeployWorkerPackage.`getUntarJobName(ADag dag, java.lang.String site)` It returns the name of the untar job, that is to be assigned.
`void` DeployWorkerPackage.`initialize(ADag scheduledDAG)` Initialize with the scheduled graph.
`void` ReplicaCatalogBridge.`initialize(ADag dag, PegasusBag bag)` Intialises the refiner.
`void` ReplicaCatalogBridge.`initialize(ADag dag, PegasusProperties properties, PlannerOptions options)` Intialises the refiner.
`private ReplicaCatalog` TransferEngine.`initializeWorkflowCacheFile(ADag dag)` 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 ).
`ADag` ReduceEdges.`reduce(ADag dag)` Prunes redundant edges from the workflow.
`ADag` DataReuseEngine.`reduceWorkflow(ADag workflow, ReplicaCatalogBridge rcb)` Reduces the workflow on the basis of the existence of lfn's in the replica catalog.
`void` InterPoolEngine.`scheduleJobs(ADag dag, java.util.List sites)` It schedules a list of jobs on the execution pools by calling out to the site selector specified.

Constructors in edu.isi.pegasus.planner.refiner with parameters of type ADag
Constructor and Description
`DataReuseEngine(ADag orgDag, PegasusBag bag)` The constructor
`InterPoolEngine(ADag aDag, PegasusBag bag)` Overloaded constructor.
`MainEngine(ADag orgDag, PegasusBag bag)` This constructor initialises the class variables to the variables passed.
`RemoveDirectory(ADag concDag, PegasusBag bag, java.lang.String submitDirectory)` The overloaded constructor that sets the dag for which we have to generated the cleanup dag for.
`ReplicaCatalogBridge(ADag dag, PegasusBag bag)` The overloaded constructor.
`TransferEngine(ADag reducedDag, PegasusBag bag, java.util.List<Job> deletedJobs, java.util.List<Job> deletedLeafJobs)` Overloaded constructor.

### Uses of ADag in edu.isi.pegasus.planner.refiner.createdir

Methods in edu.isi.pegasus.planner.refiner.createdir that return ADag
`ADag` Tentacles.`addCreateDirectoryNodes(ADag dag)` Modifies the workflow to add create directory nodes.
`ADag` HourGlass.`addCreateDirectoryNodes(ADag dag)` It modifies the concrete dag passed in the constructor and adds the create random directory nodes to it at the root level.
`ADag` Strategy.`addCreateDirectoryNodes(ADag dag)` Modifies the workflow to add create directory nodes.
`ADag` Minimal.`addCreateDirectoryNodes(ADag dag)` Modifies the workflow to add create directory nodes.
`ADag` Minimal.`addCreateDirectoryNodes(ADag workflow, java.util.Set<java.lang.String> sites)` Adds create dir nodes to the workflow.

Methods in edu.isi.pegasus.planner.refiner.createdir with parameters of type ADag
`ADag` Tentacles.`addCreateDirectoryNodes(ADag dag)` Modifies the workflow to add create directory nodes.
`ADag` HourGlass.`addCreateDirectoryNodes(ADag dag)` It modifies the concrete dag passed in the constructor and adds the create random directory nodes to it at the root level.
`ADag` Strategy.`addCreateDirectoryNodes(ADag dag)` Modifies the workflow to add create directory nodes.
`ADag` Minimal.`addCreateDirectoryNodes(ADag dag)` Modifies the workflow to add create directory nodes.
`ADag` Minimal.`addCreateDirectoryNodes(ADag workflow, java.util.Set<java.lang.String> sites)` Adds create dir nodes to the workflow.
`protected java.lang.String` HourGlass.`getConcatJobname(ADag dag)` Returns the name of the concat job
`java.lang.String` AbstractStrategy.`getCreateDirJobName(ADag dag, java.lang.String pool)` It returns the name of the create directory job, that is to be assigned.
`static java.util.Set` AbstractStrategy.`getCreateDirSites(ADag dag)` Retrieves the sites for which the create dir jobs need to be created.
`private void` HourGlass.`introduceRootDependencies(ADag dag, Job newRoot)` It traverses through the root jobs of the dag and introduces a new super root node to it.
`Job` HourGlass.`makeDummyConcatJob(ADag dag)` It creates a dummy concat job that is run at the local submit host.

### Uses of ADag in edu.isi.pegasus.planner.selector

Methods in edu.isi.pegasus.planner.selector with parameters of type ADag
`void` SiteSelector.`mapWorkflow(ADag workflow, java.util.List sites)` Maps the jobs in the workflow to the various grid sites.

### Uses of ADag in edu.isi.pegasus.planner.selector.site

Fields in edu.isi.pegasus.planner.selector.site declared as ADag
`private ADag` NonJavaCallout.`mAbstractDag` The abstract DAG.

Methods in edu.isi.pegasus.planner.selector.site with parameters of type ADag
`void` Group.`mapWorkflow(ADag workflow, java.util.List sites)` The call out to map a list of jobs on to the execution pools.
`void` Heft.`mapWorkflow(ADag workflow, java.util.List sites)` Maps the jobs in the workflow to the various grid sites.
`void` AbstractPerJob.`mapWorkflow(ADag workflow, java.util.List sites)` Maps the jobs in the workflow to the various grid sites.
`void` NonJavaCallout.`mapWorkflow(ADag workflow, java.util.List sites)` Maps the jobs in the workflow to the various grid sites.
`void` Heft.`mapWorkflow(ADag workflow, java.util.List sites, java.lang.String label)` Maps the jobs in the workflow to the various grid sites.

### Uses of ADag in edu.isi.pegasus.planner.selector.site.heft

Methods in edu.isi.pegasus.planner.selector.site.heft with parameters of type ADag
`void` Algorithm.`schedule(ADag dag, java.util.List sites)` Schedules the workflow using the heft.
`void` Algorithm.`schedule(ADag workflow, java.util.List sites, java.lang.String label)` Schedules the workflow according to the HEFT algorithm.

### Uses of ADag in edu.isi.pegasus.planner.transfer

Fields in edu.isi.pegasus.planner.transfer declared as ADag
`protected ADag` AbstractRefiner.`mDAG` The ADag object associated with the Dag.

Methods in edu.isi.pegasus.planner.transfer that return ADag
`ADag` AbstractRefiner.`getWorkflow()` Returns a reference to the workflow that is being refined by the refiner.

Constructors in edu.isi.pegasus.planner.transfer with parameters of type ADag
Constructor and Description
`AbstractRefiner(ADag dag, PegasusBag bag)` The overloaded constructor.
`MultipleFTPerXFERJobRefiner(ADag dag, PegasusBag bag)` The overloaded constructor.
`SingleFTPerXFERJobRefiner(ADag dag, PegasusBag bag)` The overloaded constructor.

### Uses of ADag in edu.isi.pegasus.planner.transfer.mapper

Methods in edu.isi.pegasus.planner.transfer.mapper with parameters of type ADag
`void` OutputMapper.`initialize(PegasusBag bag, ADag workflow)` Initializes the mappers.
`static OutputMapper` OutputMapperFactory.`loadInstance(ADag dag, PegasusBag bag)` Loads the implementing class corresponding to the value specified in the properties.
`static OutputMapper` OutputMapperFactory.`loadInstance(java.lang.String className, PegasusBag bag, ADag dag)` Loads the implementing class corresponding to the class.

### Uses of ADag in edu.isi.pegasus.planner.transfer.mapper.impl

Methods in edu.isi.pegasus.planner.transfer.mapper.impl with parameters of type ADag
`void` AbstractFileFactoryBasedMapper.`initialize(PegasusBag bag, ADag workflow)` Initializes the mappers.
`void` Replica.`initialize(PegasusBag bag, ADag workflow)` Initializes the mappers.
`void` Hashed.`initialize(PegasusBag bag, ADag workflow)` Initializes the mappers.
`void` Fixed.`initialize(PegasusBag bag, ADag workflow)` Initializes the mappers.
`void` Flat.`initialize(PegasusBag bag, ADag workflow)` Initializes the mappers.
`abstract org.griphyn.vdl.euryale.FileFactory` AbstractFileFactoryBasedMapper.`instantiateFileFactory(PegasusBag bag, ADag workflow)` Method that instantiates the FileFactory
`org.griphyn.vdl.euryale.FileFactory` Hashed.`instantiateFileFactory(PegasusBag bag, ADag workflow)` Method that instantiates the FileFactory
`org.griphyn.vdl.euryale.FileFactory` Flat.`instantiateFileFactory(PegasusBag bag, ADag workflow)` Instantiates a Flat File Factory and returns it.

### Uses of ADag in edu.isi.pegasus.planner.transfer.refiner

Methods in edu.isi.pegasus.planner.transfer.refiner with parameters of type ADag
`static Refiner` RefinerFactory.`loadInstance(ADag dag, PegasusBag bag)` Loads the implementing class corresponding to the value specified in the properties.
`static Refiner` RefinerFactory.`loadInstance(java.lang.String className, PegasusBag bag, ADag dag)` Loads the implementing class corresponding to the class.

Constructors in edu.isi.pegasus.planner.transfer.refiner with parameters of type ADag
Constructor and Description
`BalancedCluster(ADag dag, PegasusBag bag)` The overloaded constructor.
`Basic(ADag dag, PegasusBag bag)` The overloaded constructor.
`Bundle(ADag dag, PegasusBag bag)` The overloaded constructor.
`Chain(ADag dag, PegasusBag bag)` The overloaded constructor.
`Cluster(ADag dag, PegasusBag bag)` The overloaded constructor.
`Empty(ADag dag, PegasusBag bag)` The overloaded constructor.