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114 lines (98 loc) · 2.83 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 June 21, 2010
* Author: Mark Chapman
*/
package org.biojava.nbio.alignment;
import org.biojava.nbio.core.alignment.template.SequencePair;
import org.biojava.nbio.alignment.template.*;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;
/**
* Implements an algorithm which computes a score for a sequence alignment pair. The reported score is the number of
* alignment columns which have similar {@link Compound}s.
*
* @author Mark Chapman
* @param <S> each {@link Sequence} of the alignment pair is of type S
* @param <C> each element of a sequence is a {@link Compound} of type C
*/
public class FractionalSimilarityScorer<S extends Sequence<C>, C extends Compound> extends AbstractScorer
implements PairwiseSequenceScorer<S, C> {
// always stored
private S query, target;
private int max, score;
// optional cached input field
private PairwiseSequenceAligner<S, C> aligner;
/**
* Creates a fractional similarity scorer for a pair of sequences aligned by the given pairwise sequence aligner.
*
* @param aligner a pairwise sequence aligner
*/
public FractionalSimilarityScorer(PairwiseSequenceAligner<S, C> aligner) {
query = aligner.getQuery();
target = aligner.getTarget();
this.aligner = aligner;
}
/**
* Creates a fractional similarity scorer for an aligned pair of sequences.
*
* @param pair an aligned pair of sequences
*/
public FractionalSimilarityScorer(SequencePair<S, C> pair) {
query = pair.getQuery().getOriginalSequence();
target = pair.getTarget().getOriginalSequence();
max = pair.getLength();
score = pair.getNumSimilars();
}
// methods for PairwiseSequenceScorer
@Override
public S getQuery() {
return query;
}
@Override
public S getTarget() {
return target;
}
// methods for Scorer
@Override
public double getMaxScore() {
if (aligner != null) {
align();
}
return max;
}
@Override
public double getMinScore() {
return 0;
}
@Override
public double getScore() {
if (aligner != null) {
align();
}
return score;
}
// helper method for initialization from an aligner
private void align() {
max = aligner.getPair().getLength();
score = aligner.getPair().getNumSimilars();
aligner = null;
}
}