Class ReferenceSequence


  • public class ReferenceSequence
    extends Object
    Wrapper around a reference sequence that has been read from a reference file.
    • Constructor Detail

      • ReferenceSequence

        public ReferenceSequence​(String name,
                                 int index,
                                 byte[] bases)
        creates a fully formed ReferenceSequence
        Parameters:
        name - the name of the sequence from the source file
        index - the zero based index of this contig in the source file
        bases - the bases themselves stored as one-byte characters
    • Method Detail

      • getName

        public String getName()
        Gets the set of names given to this sequence in the source file.
      • getBases

        public byte[] getBases()
        Gets the array of bases that define this sequence. The bases can include any letter and possibly include masking information in the form of lower case letters. This array is mutable (obviously!) and it NOT a clone of the array held interally. Do not modify it!!!
      • getBaseString

        public String getBaseString()
        Returns the bases represented by this ReferenceSequence as a String. Since this will copy the bases and convert them to two-byte characters, this should not be used on very long reference sequences, but as a convenience when manipulating short sequences returned by ReferenceSequenceFile.getSubsequenceAt(String, long, long)
        Returns:
        The set of bases represented by this ReferenceSequence, as a String
      • getContigIndex

        public int getContigIndex()
        Gets the 0-based index of this contig in the source file from which it came.
      • length

        public int length()
        Gets the length of this reference sequence in bases.