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}