Class XMLDataFormat
- java.lang.Object
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- fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
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- All Implemented Interfaces:
DataFormat
,Serializable
public final class XMLDataFormat extends Object implements Serializable
This class define a DataFormat from an XML file.- Since:
- 1.2
- Author:
- Laurent Jourdren
- See Also:
- Serialized Form
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Constructor Summary
Constructors Constructor Description XMLDataFormat(InputStream is, String source)
Public constructor.
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Method Summary
All Methods Instance Methods Concrete Methods 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 DataTypeList<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()
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Constructor Detail
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XMLDataFormat
public XMLDataFormat(InputStream is, String source) throws EoulsanException
Public constructor.- Parameters:
is
- input stream that contains the value of the data formatsource
- source of the format- Throws:
EoulsanException
- if an error occurs while reading or parsing XML file
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Method Detail
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getName
public String getName()
Description copied from interface:DataFormat
Get the name of the format.- Specified by:
getName
in interfaceDataFormat
- Returns:
- the name of the format
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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 interfaceDataFormat
- Returns:
- the alias of the format if exist
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getPrefix
public String getPrefix()
Description copied from interface:DataFormat
Get DataFormat prefix.- Specified by:
getPrefix
in interfaceDataFormat
- Returns:
- the DataFormat prefix
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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 interfaceDataFormat
- Returns:
- true if there is only one file for this DataType per analysis
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isDataFormatFromDesignFile
public boolean isDataFormatFromDesignFile()
Description copied from interface:DataFormat
Test if the DataFormat is provided by the design file.- Specified by:
isDataFormatFromDesignFile
in interfaceDataFormat
- Returns:
- true if the DataType is provided by the design file
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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 interfaceDataFormat
- Returns:
- the sample metadata key name
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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 interfaceDataFormat
- Returns:
- the sample metadata key name
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getDefaultExtension
public String getDefaultExtension()
Description copied from interface:DataFormat
Get the default extension of the DataType.- Specified by:
getDefaultExtension
in interfaceDataFormat
- Returns:
- the default extension
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getExtensions
public List<String> getExtensions()
Description copied from interface:DataFormat
Get the extensions for the DataType- Specified by:
getExtensions
in interfaceDataFormat
- Returns:
- an list of strings with the extension of the DataType
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getGalaxyFormatNames
public List<String> getGalaxyFormatNames()
Description copied from interface:DataFormat
Get the extension from Galaxy tool file of the DataType.- Specified by:
getGalaxyFormatNames
in interfaceDataFormat
- Returns:
- extension from Galaxy tool
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isGenerator
public boolean isGenerator()
Description copied from interface:DataFormat
Test if a generator is available for this DataFormat.- Specified by:
isGenerator
in interfaceDataFormat
- Returns:
- true if a generator is available for this DataFormat
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isChecker
public boolean isChecker()
Description copied from interface:DataFormat
Test if a checker is available for this DataFormat.- Specified by:
isChecker
in interfaceDataFormat
- Returns:
- true if a checker is available for this DataFormat
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isSplitter
public boolean isSplitter()
Description copied from interface:DataFormat
Test if a splitter class is available for this DataFormat.- Specified by:
isSplitter
in interfaceDataFormat
- Returns:
- true if a splitter class is available for this DataFormat
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isMerger
public boolean isMerger()
Description copied from interface:DataFormat
Test if a merger class is available for this DataFormat.- Specified by:
isMerger
in interfaceDataFormat
- Returns:
- true if a merger class is available for this DataFormat
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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 interfaceDataFormat
- Returns:
- the Step needed to generated the DataType or null if no Step is available for this task
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getChecker
public Checker getChecker()
Description copied from interface:DataFormat
Get the checker needed to check data of this type.- Specified by:
getChecker
in interfaceDataFormat
- Returns:
- the Checker or null if no Checker is available for this task
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getSplitter
public Splitter getSplitter()
Description copied from interface:DataFormat
Get the splitter class related to this type.- Specified by:
getSplitter
in interfaceDataFormat
- Returns:
- The Splitter instanced class of null if no Splitter is available for this task
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getMerger
public Merger getMerger()
Description copied from interface:DataFormat
Get the merger class related to this type.- Specified by:
getMerger
in interfaceDataFormat
- Returns:
- The Merger instanced class of null if no Merger is available for this task
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getContentType
public String getContentType()
Description copied from interface:DataFormat
Get the content type.- Specified by:
getContentType
in interfaceDataFormat
- Returns:
- the content type of this format
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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 interfaceDataFormat
- Returns:
- the number of maximal of files used to store data.
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equals
public boolean equals(Object o)
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hashCode
public int hashCode()
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toString
public String toString()
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getDescription
public String getDescription()
Description copied from interface:DataFormat
Get the description of the format.- Specified by:
getDescription
in interfaceDataFormat
- Returns:
- the name of the format
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