Package org.biojava.nbio.core.alignment.template

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

Type Parameters:
C - each element of the AlignedSequence is a Compound of type C
All Superinterfaces:
Accessioned, AlignedSequence<S,C>, Iterable<C>, Sequence<C>
public interface MutableAlignedSequence<S extends Sequence<C>,C extends Compound> extends AlignedSequence<S,C>
Defines a mutable (editable) data structure for an AlignedSequence.
Author:
Mark Chapman, Paolo Pavan

  • Method Details

    • 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:
      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:
      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:
      IllegalArgumentException - if location is invalid or the shift causes a collision with stationary elements