Interface ReferenceSequenceMask

    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      boolean get​(int sequenceIndex, int position)
      It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
      int getMaxPosition()  
      int getMaxSequenceIndex()  
      int nextPosition​(int sequenceIndex, int position)
      It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
    • Method Detail

      • get

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

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

        int getMaxSequenceIndex()
        Returns:
        Largest sequence index for which there are set bits.
      • getMaxPosition

        int getMaxPosition()
        Returns:
        the largest position on the last sequence index