org.biojava.nbio.alignment.SmithWaterman Maven / Gradle / Ivy
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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 24, 2010
* Author: Mark Chapman
*/
package org.biojava.nbio.alignment;
import org.biojava.nbio.core.alignment.SimpleSequencePair;
import org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner;
import org.biojava.nbio.core.alignment.template.AlignedSequence;
import org.biojava.nbio.core.alignment.template.AlignedSequence.Step;
import org.biojava.nbio.alignment.template.GapPenalty;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;
import java.util.List;
/**
* Smith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from each
* {@link Sequence}). This class performs such local sequence comparisons efficiently by dynamic programming.
*
* @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 class SmithWaterman, C extends Compound> extends AbstractPairwiseSequenceAligner {
/**
* Before running a pairwise local sequence alignment, data must be sent in via calls to
* {@link #setQuery(Sequence)}, {@link #setTarget(Sequence)}, {@link #setGapPenalty(GapPenalty)}, and
* {@link #setSubstitutionMatrix(SubstitutionMatrix)}.
*/
public SmithWaterman() {
super(null, null, null, null, true);
}
/**
* Prepares for a pairwise local 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
*/
public SmithWaterman(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix subMatrix) {
super(query, target, gapPenalty, subMatrix, true);
}
// method for AbstractMatrixAligner
@Override
protected void setProfile(List sx, List sy) {
profile = pair = new SimpleSequencePair<>(getQuery(), getTarget(), sx, xyStart[0],
getQuery().getLength() - xyMax[0], sy, xyStart[1], getTarget().getLength() - xyMax[1]);
}
}