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.SequencePair;
027import org.biojava.nbio.core.alignment.template.AlignedSequence;
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 the results of pairwise sequence alignment.
033 *
034 * @author Mark Chapman
035 * @author Paolo Pavan
036 * @param <S> each element of the alignment {@link Profile} is of type S
037 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
038 */
039public interface MutableSequencePair<S extends Sequence<C>, C extends Compound> extends MutableProfile<S, C>,
040                SequencePair<S, C> {
041
042        /**
043         * Sets both {@link AlignedSequence}s of the pair.
044         *
045         * @param query becomes the first {@link AlignedSequence} of the pair
046         * @param target becomes the second {@link AlignedSequence} of the pair
047         * @throws IllegalArgumentException if query and target are different lengths
048         */
049        void setPair(AlignedSequence<S, C> query, AlignedSequence<S, C> target);
050
051        /**
052         * Sets the first {@link AlignedSequence} of the pair.
053         *
054         * @param query becomes the first {@link AlignedSequence} of the pair
055         * @throws IllegalArgumentException if (new) query and (old) target are different lengths
056         */
057        void setQuery(AlignedSequence<S, C> query);
058
059        /**
060         * Sets the second {@link AlignedSequence} of the pair.
061         *
062         * @param target becomes the second {@link AlignedSequence} of the pair
063         * @throws IllegalArgumentException if (old) query and (new) target are different lengths
064         */
065        void setTarget(AlignedSequence<S, C> target);
066
067}