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

Class FileNaming

java.lang.Object

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

Direct Known Subclasses:

WorkflowFileNaming

public class FileNaming
extends Object

This class contains methods to create workflow data file names.

Since:

2.0

Author:

Laurent Jourdren

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	FileNaming()	Private constructor.

Method Summary

Modifier and Type	Method	Description
String	compatibilityFilename()	Return the filename using Eoulsan 1.x naming.
static boolean	dataEquals(DataFile file1, DataFile file2)	Test if two files are related to the same data.
static boolean	dataEquals(File file1, File file2)	Test if two files are related to the same data.
static boolean	dataEquals(String filename1, String filename2)	Test if two filenames are related to the same data.
String	fileMiddle()	Return the middle string of the filename.
static String	fileMiddle(String dataName, int fileIndex, int part)	Create the middle of a filename.
String	filename()	Return the filename.
static String	filename(String stepId, String portName, DataFormat format, String dataName, int fileIndex, int part, fr.ens.biologie.genomique.kenetre.io.CompressionType compression)	Create the filename from several parameters.
String	filePrefix()	Return the file prefix.
static String	filePrefix(String stepId, String portName, DataFormat format)	Create the prefix of a filename.
static String	filePrefix(String stepId, String portName, String formatPrefix)	Create the prefix of a filename.
String	fileSuffix()	Return the file suffix.
static String	fileSuffix(DataFormat format, fr.ens.biologie.genomique.kenetre.io.CompressionType compression)	Create the suffix of a file.
static String	fileSuffix(String extension, String compression)	Create the suffix of a file.
fr.ens.biologie.genomique.kenetre.io.CompressionType	getCompression()	Get the compression.
String	getDataName()	Get the data name.
int	getFileIndex()	Get the file index.
DataFormat	getFormat()	Get the format.
int	getPart()	Get the file part.
String	getPortName()	Get the port name.
int	getSampleNumber()	Get the sample number related to the data.
String	getStepId()	Get Step Id.
String	glob()	Get a glob for the filename.
static boolean	isDataNameValid(String dataName)	Test if a data name is valid.
static boolean	isFilenameValid(DataFile file)	Test if a filename is valid.
static boolean	isFilenameValid(File file)	Test if a filename is valid.
static boolean	isFilenameValid(String filename)	Test if a filename is valid.
static boolean	isFormatPrefixValid(String formatPrefix)	Test if a format prefix id is valid.
static boolean	isPortNameValid(String portName)	Test if a port name is valid.
static boolean	isStepIdValid(String stepId)	Test if a step id is valid.
static FileNaming	parse(DataFile file)	Create a FileNaming object from a DataFile object.
static FileNaming	parse(File file)	Create a FileNaming object from a File object.
static FileNaming	parse(String filename)	Create a FileNaming object from a filename.
protected void	set(Data data)	Set several field of the object from a Data object.
void	setCompression(fr.ens.biologie.genomique.kenetre.io.CompressionType compression)	Set the compression
void	setDataName(String dataName)	Set the data name.
void	setFileIndex(int fileIndex)	Set the file index.
void	setFormat(DataFormat format)	Set the format.
void	setPart(int part)	Set the part number.
void	setPortName(String portName)	Set the port name.
void	setSampleNumber(int sampleNumber)	Set the sample number related to the data.
void	setStepId(String stepId)	Set the step id.

Methods inherited from class java.lang.Object

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

Constructor Detail

FileNaming

protected FileNaming()

Private constructor.

Method Detail

getStepId

public String getStepId()

Get Step Id.

Returns:

the step Id

getPortName

public String getPortName()

Get the port name.

Returns:

the port name

getDataName

public String getDataName()

Get the data name.

Returns:

the data name

getSampleNumber

public int getSampleNumber()

Get the sample number related to the data. This value is only use when generate compatible filenames.

Returns:

the number of the sample related to the file or -1 if not known

getFormat

public DataFormat getFormat()

Get the format.

Returns:

the format

getFileIndex

public int getFileIndex()

Get the file index.

Returns:

the file index

getPart

public int getPart()

Get the file part.

Returns:

the file part

getCompression

public fr.ens.biologie.genomique.kenetre.io.CompressionType getCompression()

Get the compression.

Returns:

the compression

setStepId

public void setStepId(String stepId)

Set the step id.

Parameters:

stepId - the step id

setPortName

public void setPortName(String portName)

Set the port name.

Parameters:

portName - the port name

setDataName

public void setDataName(String dataName)

Set the data name.

Parameters:

dataName - the data name

setSampleNumber

public void setSampleNumber(int sampleNumber)

Set the sample number related to the data. This value is only use when generate compatible filenames.

Parameters:

sampleNumber - the number of the sample related to the file or -1 if not known

setFormat

public void setFormat(DataFormat format)

Set the format.

Parameters:

format - the format

setFileIndex

public void setFileIndex(int fileIndex)

Set the file index.

Parameters:

fileIndex - the file index

setPart

public void setPart(int part)

Set the part number.

Parameters:

part - the part number

setCompression

public void setCompression(fr.ens.biologie.genomique.kenetre.io.CompressionType compression)

Set the compression

Parameters:

compression - the compression type

set

protected void set(Data data)

Set several field of the object from a Data object.

Parameters:

data - the data object

filePrefix

public String filePrefix()

Return the file prefix.

Returns:

a string with the file prefix

fileSuffix

public String fileSuffix()

Return the file suffix.

Returns:

q string with the file suffix

fileMiddle

public String fileMiddle()

Return the middle string of the filename.

Returns:

a string with the middle string of the filename

filename

public String filename()

Return the filename.

Returns:

a string with the filename

glob

public String glob()

Get a glob for the filename.

Returns:

a glob in a string

compatibilityFilename

public String compatibilityFilename()

Return the filename using Eoulsan 1.x naming.

Returns:

a string with the filename using Eoulsan 1.x naming

filePrefix

public static String filePrefix(String stepId,
                                String portName,
                                DataFormat format)

Create the prefix of a filename.

Parameters:

stepId - step id

portName - port name

format - format of the file

Returns:

a String with the prefix of the file

filePrefix

public static String filePrefix(String stepId,
                                String portName,
                                String formatPrefix)

Create the prefix of a filename.

Parameters:

stepId - step id

portName - port name

formatPrefix - format prefix of the file

Returns:

a String with the prefix of the file

fileMiddle

public static String fileMiddle(String dataName,
                                int fileIndex,
                                int part)

Create the middle of a filename.

Parameters:

dataName - data name

fileIndex - file index

part - file part

Returns:

a String with the suffix of a file

fileSuffix

public static String fileSuffix(DataFormat format,
                                fr.ens.biologie.genomique.kenetre.io.CompressionType compression)

Create the suffix of a file.

Parameters:

format - format of the file

compression - file compression

Returns:

a String with the suffix of a file

fileSuffix

public static String fileSuffix(String extension,
                                String compression)

Create the suffix of a file.

Parameters:

extension - file extension

compression - file compression

Returns:

a String with the suffix of a file

filename

public static String filename(String stepId,
                              String portName,
                              DataFormat format,
                              String dataName,
                              int fileIndex,
                              int part,
                              fr.ens.biologie.genomique.kenetre.io.CompressionType compression)

Create the filename from several parameters.

Parameters:

stepId - the step id

portName - the port name

format - the format

dataName - the data name

fileIndex - the file index

part - the part

compression - the compression type

Returns:

a string with the filename

parse

public static FileNaming parse(File file)

Create a FileNaming object from a File object.

Parameters:

file - the file

Returns:

a new FileNaming object

parse

public static FileNaming parse(DataFile file)

Create a FileNaming object from a DataFile object.

Parameters:

file - the file

Returns:

a new FileNaming object

parse

public static FileNaming parse(String filename)

Create a FileNaming object from a filename.

Parameters:

filename - the filename

Returns:

a new FileNaming object

isStepIdValid

public static boolean isStepIdValid(String stepId)

Test if a step id is valid.

Parameters:

stepId - the step id to check

Returns:

true if the step id is valid

isFormatPrefixValid

public static boolean isFormatPrefixValid(String formatPrefix)

Test if a format prefix id is valid.

Parameters:

formatPrefix - the format prefix to check

Returns:

true if the format prefix is valid

isPortNameValid

public static boolean isPortNameValid(String portName)

Test if a port name is valid.

Parameters:

portName - port name to check

Returns:

true if the port name is valid

isDataNameValid

public static boolean isDataNameValid(String dataName)

Test if a data name is valid.

Parameters:

dataName - data name to check

Returns:

true if the data name is valid

isFilenameValid

public static boolean isFilenameValid(DataFile file)

Test if a filename is valid.

Parameters:

file - the file to test.

Returns:

true if the filename is valid

isFilenameValid

public static boolean isFilenameValid(File file)

Test if a filename is valid.

Parameters:

file - the file to test.

Returns:

true if the filename is valid

isFilenameValid

public static boolean isFilenameValid(String filename)

Test if a filename is valid.

Parameters:

filename - the file to test.

Returns:

true if the filename is valid

dataEquals

public static boolean dataEquals(File file1,
                                 File file2)

Test if two files are related to the same data.

Parameters:

file1 - the first file

file2 - the second file

Returns:

true if the two files are related to the same data

dataEquals

public static boolean dataEquals(DataFile file1,
                                 DataFile file2)

Test if two files are related to the same data.

Parameters:

file1 - the first file

file2 - the second file

Returns:

true if the two files are related to the same data

dataEquals

public static boolean dataEquals(String filename1,
                                 String filename2)

Test if two filenames are related to the same data.

Parameters:

filename1 - the first filename

filename2 - the second filename

Returns:

true if the two files are related to the same data