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 22, 2010 021 * Author: Mark Chapman 022 */ 023 024package org.biojava.nbio.core.alignment; 025 026import org.biojava.nbio.core.alignment.template.AlignedSequence; 027import org.biojava.nbio.core.alignment.template.AlignedSequence.Step; 028import org.biojava.nbio.core.alignment.template.Profile; 029import org.biojava.nbio.core.alignment.template.ProfilePair; 030import org.biojava.nbio.core.sequence.template.Compound; 031import org.biojava.nbio.core.sequence.template.Sequence; 032 033import java.util.List; 034 035/** 036 * Implements a data structure for the results of the alignment of a pair of {@link Profile}s. 037 * 038 * @author Mark Chapman 039 * @author Paolo Pavan 040 * @param <S> each element of an alignment {@link Profile} is of type S 041 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C 042 */ 043public class SimpleProfilePair<S extends Sequence<C>, C extends Compound> extends SimpleProfile<S, C> 044 implements ProfilePair<S, C> { 045 046 047 private static final long serialVersionUID = 1L; 048 049 private Profile<S, C> query, target; 050 051 /** 052 * Creates a pair profile for the given profiles. 053 * 054 * @param query the first profile of the pair 055 * @param target the second profile of the pair 056 * @param sx lists whether the query profile aligns a {@link Compound} or gap at each index of the alignment 057 * @param sy lists whether the target profile aligns a {@link Compound} or gap at each index of the alignment 058 * @throws IllegalArgumentException if alignments differ in size or given profiles do not fit in alignments 059 */ 060 public SimpleProfilePair(Profile<S, C> query, Profile<S, C> target, List<Step> sx, List<Step> sy) { 061 super(query, target, sx, sy); 062 this.query = query; 063 this.target = target; 064 } 065 066 @Override 067 public Profile<S, C> getQuery() { 068 return query; 069 } 070 071 @Override 072 public Profile<S, C> getTarget() { 073 return target; 074 } 075 076}