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}