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91 lines (75 loc) · 2.17 KB
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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
* Created on July 12, 2010
* Author: Mark Chapman
*/
package org.biojava.nbio.alignment;
import org.biojava.nbio.alignment.Alignments.PairInProfileScorerType;
import org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType;
import org.biojava.nbio.alignment.template.AbstractScorer;
import org.biojava.nbio.core.alignment.template.Profile;
import org.biojava.nbio.alignment.template.RescoreRefiner;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;
public class StandardRescoreRefiner<S extends Sequence<C>, C extends Compound> extends AbstractScorer
implements RescoreRefiner<S, C> {
private PairInProfileScorerType pips;
private ProfileProfileAlignerType ppa;
public StandardRescoreRefiner(PairInProfileScorerType pips, ProfileProfileAlignerType ppa) {
this.pips = pips;
this.ppa = ppa;
}
// methods for RescoreRefiner
@Override
public PairInProfileScorerType getPairInProfileScorer() {
return pips;
}
@Override
public ProfileProfileAlignerType getProfileProfileAligner() {
return ppa;
}
// methods for Aligner
@Override
public long getComputationTime() {
// TODO Auto-generated method stub
return 0;
}
@Override
public Profile<S, C> getProfile() {
// TODO Auto-generated method stub
return null;
}
// methods for Scorer
@Override
public double getMaxScore() {
// TODO Auto-generated method stub
return 0;
}
@Override
public double getMinScore() {
// TODO Auto-generated method stub
return 0;
}
@Override
public double getScore() {
// TODO Auto-generated method stub
return 0;
}
}