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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 17, 2010
* Author: Mark Chapman
*/
package org.biojava.nbio.alignment.template;
import org.biojava.nbio.core.alignment.template.SequencePair;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.CompoundSet;
import org.biojava.nbio.core.sequence.template.Sequence;
import java.util.ArrayList;
import java.util.List;
/**
* Implements common code for an {@link Aligner} for a pair of {@link Sequence}s.
*
* @author Mark Chapman
* @param each {@link Sequence} of the alignment pair is of type S
* @param each element of an {@link AlignedSequence} is a {@link Compound} of type C
*/
public abstract class AbstractPairwiseSequenceAligner, C extends Compound>
extends AbstractMatrixAligner implements PairwiseSequenceAligner {
// additional input fields
private S query, target;
// additional output field
protected SequencePair pair;
/**
* Before running a pairwise global sequence alignment, data must be sent in via calls to
* {@link #setQuery(Sequence)}, {@link #setTarget(Sequence)}, {@link #setGapPenalty(GapPenalty)}, and
* {@link #setSubstitutionMatrix(SubstitutionMatrix)}.
*/
protected AbstractPairwiseSequenceAligner() {
}
/**
* Prepares for a pairwise global sequence alignment.
*
* @param query the first {@link Sequence} of the pair to align
* @param target the second {@link Sequence} of the pair to align
* @param gapPenalty the gap penalties used during alignment
* @param subMatrix the set of substitution scores used during alignment
*/
protected AbstractPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty,
SubstitutionMatrix subMatrix) {
this(query, target, gapPenalty, subMatrix, false);
}
/**
* Prepares for a pairwise sequence alignment.
*
* @param query the first {@link Sequence} of the pair to align
* @param target the second {@link Sequence} of the pair to align
* @param gapPenalty the gap penalties used during alignment
* @param subMatrix the set of substitution scores used during alignment
* @param local if true, find a region of similarity rather than aligning every compound
*/
protected AbstractPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty,
SubstitutionMatrix subMatrix, boolean local) {
super(gapPenalty, subMatrix, local);
this.query = query;
this.target = target;
reset();
}
/**
* Sets the query {@link Sequence}.
*
* @param query the first {@link Sequence} of the pair to align
*/
public void setQuery(S query) {
this.query = query;
reset();
}
/**
* Sets the target {@link Sequence}.
*
* @param target the second {@link Sequence} of the pair to align
*/
public void setTarget(S target) {
this.target = target;
reset();
}
// method for PairwiseSequenceAligner
@Override
public SequencePair getPair() {
if (pair == null) {
align();
}
return pair;
}
// methods for PairwiseSequenceScorer
@Override
public S getQuery() {
return query;
}
@Override
public S getTarget() {
return target;
}
// methods for AbstractMatrixAligner
@Override
protected CompoundSet getCompoundSet() {
return (query == null) ? null : query.getCompoundSet();
}
@Override
protected List getCompoundsOfQuery() {
return (query == null) ? new ArrayList() : query.getAsList();
}
@Override
protected List getCompoundsOfTarget() {
return (target == null) ? new ArrayList() : target.getAsList();
}
@Override
protected int[] getScoreMatrixDimensions() {
return new int[] { (query == null) ? 1 : query.getLength() + 1, (target == null) ? 1 : target.getLength() + 1,
(getGapPenalty() == null || getGapPenalty().getType() == GapPenalty.Type.LINEAR) ? 1 : 3 };
}
@Override
protected int getSubstitutionScore(int queryColumn, int targetColumn) {
return getSubstitutionMatrix().getValue(query.getCompoundAt(queryColumn), target.getCompoundAt(targetColumn));
}
@Override
protected boolean isReady() {
return query != null && target != null && getGapPenalty() != null && getSubstitutionMatrix() != null &&
query.getCompoundSet().equals(target.getCompoundSet());
}
@Override
protected void reset() {
super.reset();
pair = null;
if (query != null && target != null && getGapPenalty() != null && getSubstitutionMatrix() != null &&
query.getCompoundSet().equals(target.getCompoundSet())) {
int maxq = 0, maxt = 0;
for (C c : query) {
maxq += getSubstitutionMatrix().getValue(c, c);
}
for (C c : target) {
maxt += getSubstitutionMatrix().getValue(c, c);
}
max = Math.max(maxq, maxt);
score = min = isLocal() ? 0 : (int) (2 * getGapPenalty().getOpenPenalty() + (query.getLength() +
target.getLength()) * getGapPenalty().getExtensionPenalty());
}
}
}
