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:

  • Constructor Details

    • 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 Details

    • 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