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 Summary

Constructors

Constructor	Description
StepOutputDataFile(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort outputPort, Sample sample)	Constructor.
StepOutputDataFile(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort outputPort, Sample sample, int fileIndex)	Constructor.

Method Summary

Modifier and Type	Method	Description
int	compareTo(StepOutputDataFile o)
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).
boolean	equals(Object o)
DataFile	getDataFile()	Get the file as a DataFile.
int	getFileIndex()	Get file index.
DataFormat	getFormat()	Get the format of the output
String	getPortName()	Get the port name that produced the file.
Sample	getSample()	Get the sample that produced the file.
AbstractStep	getStep()	Get the workflow step that produced the file.
int	hashCode()
boolean	isMayNotExist()
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.

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

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

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