Class ExternalCompressor

java.lang.Object
htsjdk.samtools.cram.compression.ExternalCompressor
Direct Known Subclasses:
BZIP2ExternalCompressor, FQZCompExternalCompressor, GZIPExternalCompressor, LZMAExternalCompressor, NameTokeniserExternalCompressor, RangeExternalCompressor, RANS4x8ExternalCompressor, RANSNx16ExternalCompressor, RAWExternalCompressor, TrialCompressor
public abstract class ExternalCompressor extends Object
Abstract base class for CRAM external block compressors. Each subclass wraps a specific compression algorithm (GZIP, rANS, BZIP2, etc.) and provides compress/uncompress operations on raw byte arrays. Instances are typically obtained via getCompressorForMethod(BlockCompressionMethod, int).

  • Field Details

  • Constructor Details

    • ExternalCompressor

      protected ExternalCompressor(BlockCompressionMethod method)
      Parameters:
      method - the compression method for this compressor, or null if the method will be determined later (e.g., by TrialCompressor after its first trial)

  • Method Details

    • setMethod

      protected void setMethod(BlockCompressionMethod method)
      Set the compression method. For use by subclasses like TrialCompressor that determine their method after construction.
      Parameters:
      method - the compression method to set

    • compress

      public abstract byte[] compress(byte[] data, CRAMCodecModelContext contextModel)
      Compress the data using the codec-specific context model.
      Parameters:
      data - the data to compress
      contextModel - the context model to use for compression; may be null
      Returns:
      the compressed data

    • uncompress

      public abstract byte[] uncompress(byte[] data)
      Decompress the data.
      Parameters:
      data - the compressed data
      Returns:
      the decompressed data

    • getMethod

      public BlockCompressionMethod getMethod()
      Returns:
      the compression method used by this compressor
      Throws:
      IllegalStateException - if the method has not been determined yet (compress() must be called first for compressors like TrialCompressor)

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • equals

      public boolean equals(Object o)
      Overrides:
      equals in class Object

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • getCompressorForMethod

      public static ExternalCompressor getCompressorForMethod(BlockCompressionMethod compressionMethod, int compressorSpecificArg)
      Return an ExternalCompressor subclass based on the BlockCompressionMethod. Compressor-specific arguments must be populated by the caller.
      Parameters:
      compressionMethod - the type of compressor required (BlockCompressionMethod)
      compressorSpecificArg - the required order for RANS compressors; or the desired write compression level for GZIP
      Returns:
      an ExternalCompressor of the requested type, populated with an compressor-specific args