Class IntervalListReferenceSequenceMask

    • Constructor Detail

      • IntervalListReferenceSequenceMask

        public IntervalListReferenceSequenceMask​(IntervalList intervalList)
    • Method Detail

      • get

        public boolean get​(int sequenceIndex,
                           int position)
        It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
        Specified by:
        get in interface ReferenceSequenceMask
        Returns:
        true if the mask is set for the given sequence and position
      • nextPosition

        public int nextPosition​(int sequenceIndex,
                                int position)
        It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
        Specified by:
        nextPosition in interface ReferenceSequenceMask
        Returns:
        the next pos on the given sequence >= position that is set, or -1 if there are no more set positions