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.sequence.template.Compound; 027import org.biojava.nbio.core.sequence.template.Sequence; 028 029/** 030 * Defines a data structure for the results of pairwise sequence alignment. 031 * 032 * @author Mark Chapman 033 * @author Paolo Pavan 034 * @param <S> each element of the alignment {@link Profile} is of type S 035 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C 036 */ 037public interface SequencePair<S extends Sequence<C>, C extends Compound> extends Profile<S, C> { 038 039 /** 040 * Returns the {@link Compound} in query sequence at given column index in alignment. 041 * 042 * @param alignmentIndex column index in alignment 043 * @return the query sequence element 044 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} 045 */ 046 C getCompoundInQueryAt(int alignmentIndex); 047 048 /** 049 * Returns the {@link Compound} in target sequence at given column index in alignment. 050 * 051 * @param alignmentIndex column index in alignment 052 * @return the target sequence element 053 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} 054 */ 055 C getCompoundInTargetAt(int alignmentIndex); 056 057 /** 058 * Returns the query index corresponding to a given alignment column. 059 * 060 * @param alignmentIndex column index in alignment 061 * @return index in query {@link Sequence} 062 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} 063 */ 064 int getIndexInQueryAt(int alignmentIndex); 065 066 /** 067 * Returns the query index corresponding to a given target index. 068 * 069 * @param targetIndex index in target {@link Sequence} 070 * @return index in query {@link Sequence} 071 * @throws IndexOutOfBoundsException if targetIndex < 1 or targetIndex > {@link #getTarget()}.getLength() 072 */ 073 int getIndexInQueryForTargetAt(int targetIndex); 074 075 /** 076 * Returns the target index corresponding to a given alignment column. 077 * 078 * @param alignmentIndex column index in alignment 079 * @return index in target {@link Sequence} 080 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()} 081 */ 082 int getIndexInTargetAt(int alignmentIndex); 083 084 /** 085 * Returns the target index corresponding to a given query index. 086 * 087 * @param queryIndex index in query {@link Sequence} 088 * @return index in target {@link Sequence} 089 * @throws IndexOutOfBoundsException if queryIndex < 1 or queryIndex > {@link #getQuery()}.getLength() 090 */ 091 int getIndexInTargetForQueryAt(int queryIndex); 092 093 /** 094 * Returns the number of indices for which both the query and target sequences have an identical {@link Compound}. 095 * 096 * @return the number of identical indices 097 */ 098 int getNumIdenticals(); 099 100 /** 101 * Returns the number of indices for which both the query and target sequences have a similar {@link Compound}. 102 * 103 * @return the number of similar indices 104 */ 105 int getNumSimilars(); 106 107 /** 108 * Returns the first {@link AlignedSequence} of the pair. 109 * 110 * @return the first {@link AlignedSequence} of the pair 111 */ 112 AlignedSequence<S, C> getQuery(); 113 114 /** 115 * Returns the second {@link AlignedSequence} of the pair. 116 * 117 * @return the second {@link AlignedSequence} of the pair 118 */ 119 AlignedSequence<S, C> getTarget(); 120 121}