Interface MutableAlignedSequence<S extends Sequence<C>,​C extends Compound>

    • Method Detail

      • setLocationInAlignment

        void setLocationInAlignment​(Location location)
        Sets the position of the AlignedSequence to the given Location (start, gaps, end).
        Parameters:
        location - new location for this sequence
        Throws:
        java.lang.IllegalArgumentException - if location is invalid
      • shiftAtAlignmentLocation

        void shiftAtAlignmentLocation​(Location location,
                                      int shift)
        Slides a part of the AlignedSequence.
        Parameters:
        location - portion of sequence moved in alignment coordinates
        shift - amount the alignment index changes for each contained element
        Throws:
        java.lang.IllegalArgumentException - if location is invalid or the shift causes a collision with stationary elements
      • shiftAtSequenceLocation

        void shiftAtSequenceLocation​(Location location,
                                     int shift)
        Slides a part of the AlignedSequence.
        Parameters:
        location - portion of sequence moved in sequence coordinates
        shift - amount the alignment index changes for each contained element
        Throws:
        java.lang.IllegalArgumentException - if location is invalid or the shift causes a collision with stationary elements