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 17, 2010
021 * Author: Mark Chapman
022 */
023
024package org.biojava.nbio.alignment.template;
025
026import org.biojava.nbio.core.alignment.template.SequencePair;
027import org.biojava.nbio.core.sequence.template.Compound;
028import org.biojava.nbio.core.sequence.template.Sequence;
029
030import java.util.concurrent.Callable;
031
032/**
033 * Implements a concurrency wrapper for a {@link PairwiseSequenceAligner}.
034 *
035 * @author Mark Chapman
036 * @param <S> each {@link Sequence} of the alignment pair is of type S
037 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
038 */
039public class CallablePairwiseSequenceAligner<S extends Sequence<C>, C extends Compound>
040                implements Callable<SequencePair<S, C>> {
041
042        private PairwiseSequenceAligner<S, C> psa;
043
044        /**
045         * Creates a pairwise sequence alignment task for simplified parallel execution.
046         *
047         * @param psa already initialized pairwise sequence aligner
048         */
049        public CallablePairwiseSequenceAligner(PairwiseSequenceAligner<S, C> psa) {
050                this.psa = psa;
051        }
052
053        @Override
054        public SequencePair<S, C> call() {
055                return psa.getPair();
056        }
057
058}