Package fr.ens.biologie.genomique.eoulsan.core.workflow

Class StepOutputDataFile

java.lang.Object
fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile
All Implemented Interfaces:
Comparable<StepOutputDataFile>
public final class StepOutputDataFile extends Object implements Comparable<StepOutputDataFile>
This class define an output file of workflow set.
Since:
2.0
Author:
Laurent Jourdren

  • Constructor Details

    • StepOutputDataFile

      public StepOutputDataFile(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort outputPort, Sample sample)
      Constructor.
      Parameters:
      outputPort - output port that create the file
      sample - sample of the file

    • StepOutputDataFile

      public StepOutputDataFile(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort outputPort, Sample sample, int fileIndex)
      Constructor.
      Parameters:
      outputPort - output port that create the file
      sample - sample of the file
      fileIndex - file index of the file for multi-file data

  • Method Details

    • getStep

      public AbstractStep getStep()
      Get the workflow step that produced the file.
      Returns:
      the workflow step

    • getPortName

      public String getPortName()
      Get the port name that produced the file.
      Returns:
      the port name

    • getFormat

      public DataFormat getFormat()
      Get the format of the output
      Returns:
      the DataFormat of the output

    • getSample

      public Sample getSample()
      Get the sample that produced the file.
      Returns:
      the Sample

    • getFileIndex

      public int getFileIndex()
      Get file index.
      Returns:
      the file index

    • isMayNotExist

      public boolean isMayNotExist()

    • getDataFile

      public DataFile getDataFile()
      Get the file as a DataFile.
      Returns:
      a DataFile

    • compareTo

      public int compareTo(StepOutputDataFile o)
      Specified by:
      compareTo in interface Comparable<StepOutputDataFile>

    • equals

      public boolean equals(Object o)
      Overrides:
      equals in class Object

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • newStandardFilename

      public static String newStandardFilename(Step step, String portName, DataFormat format, Sample sample, int fileIndex, fr.ens.biologie.genomique.kenetre.io.CompressionType compression)
      Create a standard filename.
      Parameters:
      step - the step that generated the file
      portName - the port name that generated the file
      format - the format of the file
      sample - the sample of the file
      fileIndex - file index of the file for multi-file data
      compression - the compression of the file
      Returns:
      a file name as a String

    • dataFileCount

      public static int dataFileCount(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort outputPort, Sample sample, boolean existingFiles)
      Get the count of files that exists for a step, a format and sample (case of multi-files data).
      Parameters:
      outputPort - output port that create the file
      sample - sample of the file
      existingFiles - true if existence of file must be tested. If false the return value will be the maximum number files
      Returns:
      the number of files