Class XMLDataFormat

    • Constructor Detail

      • XMLDataFormat

        public XMLDataFormat​(InputStream is,
                             String source)
                      throws EoulsanException
        Public constructor.
        Parameters:
        is - input stream that contains the value of the data format
        source - source of the format
        Throws:
        EoulsanException - if an error occurs while reading or parsing XML file
    • 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