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

Packages that use PegasusFile
edu.isi.pegasus.planner.classes
edu.isi.pegasus.planner.parser.dax
edu.isi.pegasus.planner.refiner
edu.isi.pegasus.planner.refiner.cleanup

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

Subclasses of PegasusFile in edu.isi.pegasus.planner.classes
`class` `FileTransfer` This is a container for the storing the transfers that are required in between sites.

Fields in edu.isi.pegasus.planner.classes with type parameters of type PegasusFile
`protected java.util.List<PegasusFile>` CompoundTransformation.`mUses` The list of dependant executables

Methods in edu.isi.pegasus.planner.classes that return types with arguments of type PegasusFile
`java.util.List<PegasusFile>` CompoundTransformation.`getDependantFiles()` Returns the List of dependant files
`java.util.Set<PegasusFile>` Job.`getInputFiles()` Returns the set of input files associated with the job.
`java.util.Set<PegasusFile>` Job.`getOutputFiles()` Returns the set of output files associated with the job.

Methods in edu.isi.pegasus.planner.classes with parameters of type PegasusFile
`void` CompoundTransformation.`addDependantFile(PegasusFile pf)` Adds a dependant file.
`void` Job.`addInputFile(PegasusFile file)` Adds an input file to the underlying collection of input files associated with the job.
`void` Job.`addOutputFile(PegasusFile file)` Adds an output file to the underlying collection of output files associated with the job.

Method parameters in edu.isi.pegasus.planner.classes with type arguments of type PegasusFile
`void` Job.`setInputFiles(java.util.Set<PegasusFile> ipFiles)` Sets the input files associated with the job.
`void` Job.`setOutputFiles(java.util.Set<PegasusFile> opFiles)` Sets the output files associated with the job.

Constructors in edu.isi.pegasus.planner.classes with parameters of type PegasusFile
Constructor and Description
`FileTransfer(PegasusFile pf)` The overloaded constructor.

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

Fields in edu.isi.pegasus.planner.parser.dax declared as PegasusFile
`private PegasusFile` DAXParser2.`mUsesPegasusFile` The PegasusFile object that a uses tag corresponds to.

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

Methods in edu.isi.pegasus.planner.refiner that return types with arguments of type PegasusFile
`private java.util.Set<PegasusFile>` TransferEngine.`getOutputFiles(java.util.Collection<GraphNode> nodes)` It gets the output files for all the nodes which are specified in the nodes passed.

Methods in edu.isi.pegasus.planner.refiner with parameters of type PegasusFile
`private boolean` TransferEngine.`bypassStagingForInputFile(ReplicaCatalogEntry entry, PegasusFile file, java.lang.String computeSite)` Returns a boolean indicating whether to bypass first level staging for a file or not
`private FileTransfer` TransferEngine.`constructFileTX(PegasusFile pf, Job job, java.lang.String destSiteHandle, java.lang.String path, boolean localTransfer)` Constructs the FileTransfer object on the basis of the transiency information.
`private void` TransferEngine.`logRemoval(Job job, PegasusFile file, java.lang.String prefix, boolean removed)` Helped method for logging removal message.

### Uses of PegasusFile in edu.isi.pegasus.planner.refiner.cleanup

Fields in edu.isi.pegasus.planner.refiner.cleanup with type parameters of type PegasusFile
`private java.util.List<PegasusFile>` CleanupJobContent.`mToBeDeletedFiles` The list of files that need to be deleted and are associated with this job.

Methods in edu.isi.pegasus.planner.refiner.cleanup that return types with arguments of type PegasusFile
`java.util.List<PegasusFile>` CleanupJobContent.`getListOfFilesToDelete()` Returns the list of files to be deleted for a cleanupNode

Constructor parameters in edu.isi.pegasus.planner.refiner.cleanup with type arguments of type PegasusFile
Constructor and Description
`CleanupJobContent(GraphNode node, java.util.List<PegasusFile> files)`