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 Detail

      • 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.