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 July 12, 2010
021 * Author: Mark Chapman
022 */
023
024package org.biojava.nbio.alignment;
025
026import org.biojava.nbio.alignment.Alignments.PairInProfileScorerType;
027import org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType;
028import org.biojava.nbio.alignment.template.AbstractScorer;
029import org.biojava.nbio.core.alignment.template.Profile;
030import org.biojava.nbio.alignment.template.RescoreRefiner;
031import org.biojava.nbio.core.sequence.template.Compound;
032import org.biojava.nbio.core.sequence.template.Sequence;
033
034public class StandardRescoreRefiner<S extends Sequence<C>, C extends Compound> extends AbstractScorer
035                implements RescoreRefiner<S, C> {
036
037        private PairInProfileScorerType pips;
038        private ProfileProfileAlignerType ppa;
039
040        public StandardRescoreRefiner(PairInProfileScorerType pips, ProfileProfileAlignerType ppa) {
041                this.pips = pips;
042                this.ppa = ppa;
043        }
044
045        // methods for RescoreRefiner
046
047        @Override
048        public PairInProfileScorerType getPairInProfileScorer() {
049                return pips;
050        }
051
052        @Override
053        public ProfileProfileAlignerType getProfileProfileAligner() {
054                return ppa;
055        }
056
057        // methods for Aligner
058
059        @Override
060        public long getComputationTime() {
061                // TODO Auto-generated method stub
062                return 0;
063        }
064
065        @Override
066        public Profile<S, C> getProfile() {
067                // TODO Auto-generated method stub
068                return null;
069        }
070
071        // methods for Scorer
072
073        @Override
074        public double getMaxScore() {
075                // TODO Auto-generated method stub
076                return 0;
077        }
078
079        @Override
080        public double getMinScore() {
081                // TODO Auto-generated method stub
082                return 0;
083        }
084
085        @Override
086        public double getScore() {
087                // TODO Auto-generated method stub
088                return 0;
089        }
090
091}