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

Class WorkflowFileNaming

java.lang.Object

fr.ens.biologie.genomique.eoulsan.core.FileNaming

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

public class WorkflowFileNaming
extends FileNaming

This class contains methods to create workflow data file names.

Since:

2.0

Author:

Laurent Jourdren

Method Summary

Modifier and Type	Method	Description
static DataFile	file(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort port, fr.ens.biologie.genomique.eoulsan.core.workflow.DataElement data, int fileIndex)	Create a DataFile object for a file of the workflow.
static String	fileMiddle(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort port, fr.ens.biologie.genomique.eoulsan.core.workflow.DataElement data, int fileIndex)	Create the middle of a filename.
static String	fileMiddle(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort port, String dataName, int fileIndex, int part)	Create the middle of a filename.
static String	filename(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort port, fr.ens.biologie.genomique.eoulsan.core.workflow.DataElement data, int fileIndex)	Create the name of a data file of the workflow.
static String	filePrefix(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort port)	Create the prefix of a filename.
static String	fileSuffix(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort port)	Create the suffix of a filename.
static String	glob(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort port)	Create the glob for the port.

Methods inherited from class fr.ens.biologie.genomique.eoulsan.core.FileNaming

compatibilityFilename, dataEquals, dataEquals, dataEquals, fileMiddle, fileMiddle, filename, filename, filePrefix, filePrefix, filePrefix, fileSuffix, fileSuffix, fileSuffix, getCompression, getDataName, getFileIndex, getFormat, getPart, getPortName, getSampleNumber, getStepId, glob, isDataNameValid, isFilenameValid, isFilenameValid, isFilenameValid, isFormatPrefixValid, isPortNameValid, isStepIdValid, parse, parse, parse, set, setCompression, setDataName, setFileIndex, setFormat, setPart, setPortName, setSampleNumber, setStepId

Methods inherited from class java.lang.Object

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

Method Detail

filePrefix

public static String filePrefix(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort port)

Create the prefix of a filename.

Parameters:

port - output port that generate the file

Returns:

a String with the prefix of the file

glob

public static String glob(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort port)

Create the glob for the port.

Returns:

a glob in a string

fileMiddle

public static String fileMiddle(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort port,
                                fr.ens.biologie.genomique.eoulsan.core.workflow.DataElement data,
                                int fileIndex)

Create the middle of a filename.

Parameters:

port - output port that generate the file

data - the data

fileIndex - file index

Returns:

a String with the suffix of a file

fileMiddle

public static String fileMiddle(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort port,
                                String dataName,
                                int fileIndex,
                                int part)

Create the middle of a filename.

Parameters:

port - output port that generate the file

fileIndex - file index

part - file part

Returns:

a String with the suffix of a file

fileSuffix

public static String fileSuffix(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort port)

Create the suffix of a filename.

Parameters:

port - a workflow port

Returns:

a string with the suffix that correspond to the filename

filename

public static String filename(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort port,
                              fr.ens.biologie.genomique.eoulsan.core.workflow.DataElement data,
                              int fileIndex)

Create the name of a data file of the workflow.

Parameters:

port - port that generate the data

data - data

fileIndex - file index

Returns:

a String with the name of the file

file

public static DataFile file(fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputPort port,
                            fr.ens.biologie.genomique.eoulsan.core.workflow.DataElement data,
                            int fileIndex)

Create a DataFile object for a file of the workflow.

Parameters:

port - port that generate the data

data - data

fileIndex - file index

Returns:

a DataFile object