Package fr.ens.biologie.genomique.eoulsan.data

Class MapperIndexDataFormat

java.lang.Object

fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat

All Implemented Interfaces:

DataFormat, Serializable

public class MapperIndexDataFormat
extends Object
implements Serializable

This class define a DataFormat from an XML file.

Since:

2.6

Author:

Laurent Jourdren

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
MapperIndexDataFormat(fr.ens.biologie.genomique.kenetre.bio.readmapper.Mapper mapper)	Public constructor.
MapperIndexDataFormat(String mapperName)	Public constructor.

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object o)
String	getAlias()	Get the alias of the name of the format.
Checker	getChecker()	Get the checker needed to check data of this type.
String	getContentType()	Get the content type.
String	getDefaultExtension()	Get the default extension of the DataType.
String	getDescription()	Get the description of the format.
String	getDesignMetadataKeyName()	Get the name of the design metadata key of the design file that can provide the DataFile.
List<String>	getExtensions()	Get the extensions for the DataType
List<String>	getGalaxyFormatNames()	Get the extension from Galaxy tool file of the DataType.
Module	getGenerator()	Get the step needed to generate the DataType from DataTypes provided by the Design file.
int	getMaxFilesCount()	Get the maximal number of files used to store data of this format.
Merger	getMerger()	Get the merger class related to this type.
String	getName()	Get the name of the format.
String	getPrefix()	Get DataFormat prefix.
String	getSampleMetadataKeyName()	Get the name of the sample metadata key of the design file that can provide the DataFile.
Splitter	getSplitter()	Get the splitter class related to this type.
int	hashCode()
boolean	isChecker()	Test if a checker is available for this DataFormat.
boolean	isDataFormatFromDesignFile()	Test if the DataFormat is provided by the design file.
boolean	isGenerator()	Test if a generator is available for this DataFormat.
boolean	isMerger()	Test if a merger class is available for this DataFormat.
boolean	isOneFilePerAnalysis()	Test if there is only one file for this DataType per analysis.
boolean	isSplitter()	Test if a splitter class is available for this DataFormat.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

MapperIndexDataFormat

public MapperIndexDataFormat(fr.ens.biologie.genomique.kenetre.bio.readmapper.Mapper mapper)

Public constructor.

Parameters:

mapper - the mapper

MapperIndexDataFormat

public MapperIndexDataFormat(String mapperName)

Public constructor.

Parameters:

mapperName - name of the mapper

Method Detail

getName

public String getName()

Description copied from interface: DataFormat

Get the name of the format.

Specified by:

getName in interface DataFormat

Returns:

the name of the format

getAlias

public String getAlias()

Description copied from interface: DataFormat

Get the alias of the name of the format. The alias is optional.

Specified by:

getAlias in interface DataFormat

Returns:

the alias of the format if exist

getPrefix

public String getPrefix()

Description copied from interface: DataFormat

Get DataFormat prefix.

Specified by:

getPrefix in interface DataFormat

Returns:

the DataFormat prefix

isOneFilePerAnalysis

public boolean isOneFilePerAnalysis()

Description copied from interface: DataFormat

Test if there is only one file for this DataType per analysis.

Specified by:

isOneFilePerAnalysis in interface DataFormat

Returns:

true if there is only one file for this DataType per analysis

isDataFormatFromDesignFile

public boolean isDataFormatFromDesignFile()

Description copied from interface: DataFormat

Test if the DataFormat is provided by the design file.

Specified by:

isDataFormatFromDesignFile in interface DataFormat

Returns:

true if the DataType is provided by the design file

getDesignMetadataKeyName

public String getDesignMetadataKeyName()

Description copied from interface: DataFormat

Get the name of the design metadata key of the design file that can provide the DataFile.

Specified by:

getDesignMetadataKeyName in interface DataFormat

Returns:

the sample metadata key name

getSampleMetadataKeyName

public String getSampleMetadataKeyName()

Description copied from interface: DataFormat

Get the name of the sample metadata key of the design file that can provide the DataFile.

Specified by:

getSampleMetadataKeyName in interface DataFormat

Returns:

the sample metadata key name

getDefaultExtension

public String getDefaultExtension()

Description copied from interface: DataFormat

Get the default extension of the DataType.

Specified by:

getDefaultExtension in interface DataFormat

Returns:

the default extension

getExtensions

public List<String> getExtensions()

Description copied from interface: DataFormat

Get the extensions for the DataType

Specified by:

getExtensions in interface DataFormat

Returns:

an list of strings with the extension of the DataType

getGalaxyFormatNames

public List<String> getGalaxyFormatNames()

Description copied from interface: DataFormat

Get the extension from Galaxy tool file of the DataType.

Specified by:

getGalaxyFormatNames in interface DataFormat

Returns:

extension from Galaxy tool

isGenerator

public boolean isGenerator()

Description copied from interface: DataFormat

Test if a generator is available for this DataFormat.

Specified by:

isGenerator in interface DataFormat

Returns:

true if a generator is available for this DataFormat

isChecker

public boolean isChecker()

Description copied from interface: DataFormat

Test if a checker is available for this DataFormat.

Specified by:

isChecker in interface DataFormat

Returns:

true if a checker is available for this DataFormat

isSplitter

public boolean isSplitter()

Description copied from interface: DataFormat

Test if a splitter class is available for this DataFormat.

Specified by:

isSplitter in interface DataFormat

Returns:

true if a splitter class is available for this DataFormat

isMerger

public boolean isMerger()

Description copied from interface: DataFormat

Test if a merger class is available for this DataFormat.

Specified by:

isMerger in interface DataFormat

Returns:

true if a merger class is available for this DataFormat

getGenerator

public Module getGenerator()

Description copied from interface: DataFormat

Get the step needed to generate the DataType from DataTypes provided by the Design file.

Specified by:

getGenerator in interface DataFormat

Returns:

the Step needed to generated the DataType or null if no Step is available for this task

getChecker

public Checker getChecker()

Description copied from interface: DataFormat

Get the checker needed to check data of this type.

Specified by:

getChecker in interface DataFormat

Returns:

the Checker or null if no Checker is available for this task

getSplitter

public Splitter getSplitter()

Description copied from interface: DataFormat

Get the splitter class related to this type.

Specified by:

getSplitter in interface DataFormat

Returns:

The Splitter instanced class of null if no Splitter is available for this task

getMerger

public Merger getMerger()

Description copied from interface: DataFormat

Get the merger class related to this type.

Specified by:

getMerger in interface DataFormat

Returns:

The Merger instanced class of null if no Merger is available for this task

getContentType

public String getContentType()

Description copied from interface: DataFormat

Get the content type.

Specified by:

getContentType in interface DataFormat

Returns:

the content type of this format

getMaxFilesCount

public int getMaxFilesCount()

Description copied from interface: DataFormat

Get the maximal number of files used to store data of this format. This value cannot be lower than 1. Common values are 1 or 2.

Specified by:

getMaxFilesCount in interface DataFormat

Returns:

the number of maximal of files used to store data.

equals

public boolean equals(Object o)

hashCode

public int hashCode()

toString

public String toString()

getDescription

public String getDescription()

Description copied from interface: DataFormat

Get the description of the format.

Specified by:

getDescription in interface DataFormat

Returns:

the name of the format