Class StepOutputDataFile

    • Constructor Detail

      • 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 Detail

      • 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
      • 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