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 */ 021 022/* 023 * Created on 2005-08-03 024 */ 025package org.biojava.bio.alignment; 026 027import java.util.LinkedList; 028import java.util.List; 029import java.util.NoSuchElementException; 030 031import org.biojava.bio.seq.Sequence; 032import org.biojava.bio.seq.SequenceIterator; 033import org.biojava.bio.seq.db.SequenceDB; 034import org.biojava.bio.symbol.SymbolList; 035 036/** 037 * This Interface provides methods for the alignment of bio-sequences. 038 * 039 * @author Andreas Dräger <andreas.draeger@uni-tuebingen.de> 040 * @author Mark Schreiber 041 */ 042public abstract class AlignmentAlgorithm { 043 044 /** 045 * @param source 046 * a SequenceIterator containing a set of sequences to be aligned 047 * with 048 * @param subjectDB 049 * the SequenceDB containing another set of sequences. 050 * @return a list containing the results of all single alignments performed 051 * by this method. 052 * @throws NoSuchElementException 053 * @throws Exception 054 */ 055 public List<AlignmentPair> alignAll(SequenceIterator source, 056 SequenceDB subjectDB) throws Exception { 057 List<AlignmentPair> l = new LinkedList<AlignmentPair>(); 058 while (source.hasNext()) { 059 Sequence query = source.nextSequence(); 060 // compare all the sequences of both sets. 061 SequenceIterator target = subjectDB.sequenceIterator(); 062 while (target.hasNext()) 063 try { 064 l.add(pairwiseAlignment(query, target.nextSequence())); 065 // pairwiseAlignment(query, target.nextSequence()); 066 } catch (Exception exc) { 067 exc.printStackTrace(); 068 } 069 } 070 return l; 071 } 072 073 /** 074 * Performs a pairwise sequence alignment of the two given sequences. 075 * 076 * @param query 077 * @param subject 078 * @return score of the alignment or the distance. 079 * @throws Exception 080 */ 081 public abstract AlignmentPair pairwiseAlignment(SymbolList query, SymbolList subject) 082 throws Exception; 083}