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

Class DataFormatRegistry

java.lang.Object
fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry
public class DataFormatRegistry extends Object
this class register DataFormat to allow get the DataFormat of a file from its filename.
Since:
1.0
Author:
Laurent Jourdren

  • Method Details

    • register

      public void register(DataFormat df) throws EoulsanException
      Register a DataFormat.
      Parameters:
      df - the DataFormat to register
      Throws:
      EoulsanException - if the DataFormat is not valid

    • register

      public void register(DataFormat[] array) throws EoulsanException
      Register DataFormats.
      Parameters:
      array - Array with DataFormats to register
      Throws:
      EoulsanException - if the DataFormat is not valid

    • getDataFormatFromFilename

      public DataFormat getDataFormatFromFilename(String prefix, String extension)
      Get a DataFormat From a file prefix and extension
      Parameters:
      prefix - the prefix of the file
      extension - the extension of the file without compression extension
      Returns:
      a DataFormat or null if the DataFormat was not found

    • getDataFormatFromFilename

      public DataFormat getDataFormatFromFilename(String filename)
      Get the DataFormat of a file from its filename
      Parameters:
      filename - the filename of the file
      Returns:
      a DataFormat or null if the DataFormat was not found

    • getDataFormatFromName

      public DataFormat getDataFormatFromName(String dataFormatName)
      Get a DataFormat from its name.
      Parameters:
      dataFormatName - the name of the DataFormat to get
      Returns:
      a DataFormat if found or null

    • getDataFormatFromAlias

      public DataFormat getDataFormatFromAlias(String dataFormatAlias)
      Get a DataFormat from its alias.
      Parameters:
      dataFormatAlias - the name of the DataFormat to get
      Returns:
      a DataFormat if found or null

    • getDataFormatFromGalaxyFormatName

      public DataFormat getDataFormatFromGalaxyFormatName(String formatName)
      Get DataFormat from an Galaxy format name.
      Parameters:
      formatName - Galaxy name extension.
      Returns:
      DataFormat

    • getDataFormatFromNameOrAlias

      public DataFormat getDataFormatFromNameOrAlias(String name)
      Get a DataFormat from its alias.
      Parameters:
      name - the name of the DataFormat to get
      Returns:
      a DataFormat if found or null

    • getDataFormatFromGalaxyFormatNameOrNameOrAlias

      public DataFormat getDataFormatFromGalaxyFormatNameOrNameOrAlias(String name)
      Get a DataFormat from its Galaxy format name or its name or alias.
      Parameters:
      name - the name of the DataFormat to get
      Returns:
      a DataFormat if found or null

    • getDataFormatsFromExtension

      public Set<DataFormat> getDataFormatsFromExtension(String extension)
      Get DataFormats from an extension.
      Parameters:
      extension - the extension of the file without compression extension
      Returns:
      a set of DataFormat

    • getAllFormats

      public Set<DataFormat> getAllFormats()
      Get all the registered formats.
      Returns:
      a set with all the registered formats

    • getDataFormatForDesignMetadata

      public DataFormat getDataFormatForDesignMetadata(String key)
      Get the DataFormat that define a metadata entry in the design file.
      Parameters:
      key - the name of the metadata key
      Returns:
      a DataFormat

    • getDataFormatForSampleMetadata

      public DataFormat getDataFormatForSampleMetadata(String key)
      Get the DataFormat that define a metadata entry of a sample in the design file.
      Parameters:
      key - the name of the metadata key
      Returns:
      a DataFormat

    • getDesignMetadataKeyForDataFormat

      public String getDesignMetadataKeyForDataFormat(Design design, DataFormat dataformat)
      Get the field name in a Design object that correspond to a dataformat.
      Parameters:
      design - design object
      dataformat - dataformat to search
      Returns:
      the field name if found or null

    • getSampleMetadataKeyForDataFormat

      public String getSampleMetadataKeyForDataFormat(Sample sample, DataFormat dataformat)
      Get the field name in a Sample object that correspond to a dataformat.
      Parameters:
      sample - sample object
      dataformat - dataformat to search
      Returns:
      the field name if found or null

    • reload

      public void reload()
      Reload the list of the available data types.

    • getInstance

      public static DataFormatRegistry getInstance()
      Get the singleton instance of DataFormatRegistry
      Returns:
      the DataFormatRegistry singleton