001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 * Created on June 7, 2010
021 * Author: Mark Chapman
022 */
023
024package org.biojava.nbio.core.alignment.template;
025
026import org.biojava.nbio.core.alignment.template.AlignedSequence;
027import org.biojava.nbio.core.sequence.location.template.Location;
028import org.biojava.nbio.core.sequence.template.Compound;
029import org.biojava.nbio.core.sequence.template.Sequence;
030
031/**
032 * Defines a mutable (editable) data structure for an {@link AlignedSequence}.
033 *
034 * @author Mark Chapman
035 * @author Paolo Pavan
036 * @param <C> each element of the {@link AlignedSequence} is a {@link Compound} of type C
037 * @param <S> the sequence type
038 */
039public interface MutableAlignedSequence<S extends Sequence<C>, C extends Compound> extends AlignedSequence<S, C> {
040
041        /**
042         * Sets the position of the {@link AlignedSequence} to the given {@link Location} (start, gaps, end).
043         *
044         * @param location new location for this sequence
045         * @throws IllegalArgumentException if location is invalid
046         */
047        void setLocationInAlignment(Location location);
048
049        /**
050         * Slides a part of the {@link AlignedSequence}.
051         *
052         * @param location portion of sequence moved in alignment coordinates
053         * @param shift amount the alignment index changes for each contained element
054         * @throws IllegalArgumentException if location is invalid or the shift causes a collision with stationary elements
055         */
056        void shiftAtAlignmentLocation(Location location, int shift);
057
058        /**
059         * Slides a part of the {@link AlignedSequence}.
060         *
061         * @param location portion of sequence moved in sequence coordinates
062         * @param shift amount the alignment index changes for each contained element
063         * @throws IllegalArgumentException if location is invalid or the shift causes a collision with stationary elements
064         */
065        void shiftAtSequenceLocation(Location location, int shift);
066
067}