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

Interface DataFormat

All Known Implementing Classes:
MapperIndexDataFormat, XMLDataFormat
public interface DataFormat
This interface define a DataFormat.
Since:
1.0
Author:
Laurent Jourdren

  • Method Details

    • getName

      String getName()
      Get the name of the format.
      Returns:
      the name of the format

    • getDescription

      String getDescription()
      Get the description of the format.
      Returns:
      the name of the format

    • getAlias

      String getAlias()
      Get the alias of the name of the format. The alias is optional.
      Returns:
      the alias of the format if exist

    • getPrefix

      String getPrefix()
      Get DataFormat prefix.
      Returns:
      the DataFormat prefix

    • isOneFilePerAnalysis

      boolean isOneFilePerAnalysis()
      Test if there is only one file for this DataType per analysis.
      Returns:
      true if there is only one file for this DataType per analysis

    • isDataFormatFromDesignFile

      boolean isDataFormatFromDesignFile()
      Test if the DataFormat is provided by the design file.
      Returns:
      true if the DataType is provided by the design file

    • getDesignMetadataKeyName

      String getDesignMetadataKeyName()
      Get the name of the design metadata key of the design file that can provide the DataFile.
      Returns:
      the sample metadata key name

    • getSampleMetadataKeyName

      String getSampleMetadataKeyName()
      Get the name of the sample metadata key of the design file that can provide the DataFile.
      Returns:
      the sample metadata key name

    • getContentType

      String getContentType()
      Get the content type.
      Returns:
      the content type of this format

    • getDefaultExtension

      String getDefaultExtension()
      Get the default extension of the DataType.
      Returns:
      the default extension

    • getExtensions

      List<String> getExtensions()
      Get the extensions for the DataType
      Returns:
      an list of strings with the extension of the DataType

    • getGalaxyFormatNames

      List<String> getGalaxyFormatNames()
      Get the extension from Galaxy tool file of the DataType.
      Returns:
      extension from Galaxy tool

    • isGenerator

      boolean isGenerator()
      Test if a generator is available for this DataFormat.
      Returns:
      true if a generator is available for this DataFormat

    • isChecker

      boolean isChecker()
      Test if a checker is available for this DataFormat.
      Returns:
      true if a checker is available for this DataFormat

    • isSplitter

      boolean isSplitter()
      Test if a splitter class is available for this DataFormat.
      Returns:
      true if a splitter class is available for this DataFormat

    • isMerger

      boolean isMerger()
      Test if a merger class is available for this DataFormat.
      Returns:
      true if a merger class is available for this DataFormat

    • getGenerator

      Module getGenerator()
      Get the step needed to generate the DataType from DataTypes provided by the Design file.
      Returns:
      the Step needed to generated the DataType or null if no Step is available for this task

    • getChecker

      Checker getChecker()
      Get the checker needed to check data of this type.
      Returns:
      the Checker or null if no Checker is available for this task

    • getSplitter

      Splitter getSplitter()
      Get the splitter class related to this type.
      Returns:
      The Splitter instanced class of null if no Splitter is available for this task

    • getMerger

      Merger getMerger()
      Get the merger class related to this type.
      Returns:
      The Merger instanced class of null if no Merger is available for this task

    • getMaxFilesCount

      int getMaxFilesCount()
      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.
      Returns:
      the number of maximal of files used to store data.