org.biojava.nbio.alignment.SimpleProfileProfileAligner Maven / Gradle / Ivy
The newest version!
/*
* 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 30, 2010
* Author: Mark Chapman
*/
package org.biojava.nbio.alignment;
import org.biojava.nbio.core.alignment.template.ProfilePair;
import org.biojava.nbio.core.alignment.template.Profile;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.alignment.SimpleProfilePair;
import org.biojava.nbio.alignment.template.*;
import org.biojava.nbio.core.alignment.template.AlignedSequence.Step;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;
import java.util.List;
import java.util.concurrent.Future;
/**
* Implements a simple (naive) {@link Aligner} for a pair of {@link Profile}s. This is basically an extension of the
* {@link NeedlemanWunsch} pairwise sequence aligner to pairwise profile alignment using a sum-of-pairs score.
*
* @author Mark Chapman
* @param each {@link Sequence} in the pair of alignment {@link Profile}s is of type S
* @param each element of an {@link AlignedSequence} is a {@link Compound} of type C
*/
public class SimpleProfileProfileAligner, C extends Compound>
extends AbstractProfileProfileAligner {
/**
* Before running a profile-profile alignment, data must be sent in via calls to
* {@link #setQuery(Profile)}, {@link #setTarget(Profile)}, {@link #setGapPenalty(GapPenalty)}, and
* {@link #setSubstitutionMatrix(SubstitutionMatrix)}.
*/
public SimpleProfileProfileAligner() {
}
/**
* Prepares for a profile-profile alignment.
*
* @param query the first {@link Profile} of the pair to align
* @param target the second {@link Profile} of the pair to align
* @param gapPenalty the gap penalties used during alignment
* @param subMatrix the set of substitution scores used during alignment
*/
public SimpleProfileProfileAligner(Profile query, Profile target, GapPenalty gapPenalty,
SubstitutionMatrix subMatrix) {
super(query, target, gapPenalty, subMatrix);
}
/**
* Prepares for a profile-profile alignment run concurrently.
*
* @param query the first {@link Profile} of the pair to align, still to be calculated
* @param target the second {@link Profile} of the pair to align, still to be calculated
* @param gapPenalty the gap penalties used during alignment
* @param subMatrix the set of substitution scores used during alignment
*/
public SimpleProfileProfileAligner(Future> query, Future> target,
GapPenalty gapPenalty, SubstitutionMatrix subMatrix) {
super(query, target, gapPenalty, subMatrix);
}
/**
* Prepares for a profile-profile alignment run concurrently.
*
* @param query the first {@link Profile} of the pair to align
* @param target the second {@link Profile} of the pair to align, still to be calculated
* @param gapPenalty the gap penalties used during alignment
* @param subMatrix the set of substitution scores used during alignment
*/
public SimpleProfileProfileAligner(Profile query, Future> target, GapPenalty gapPenalty,
SubstitutionMatrix subMatrix) {
super(query, target, gapPenalty, subMatrix);
}
/**
* Prepares for a profile-profile alignment run concurrently.
*
* @param query the first {@link Profile} of the pair to align, still to be calculated
* @param target the second {@link Profile} of the pair to align
* @param gapPenalty the gap penalties used during alignment
* @param subMatrix the set of substitution scores used during alignment
*/
public SimpleProfileProfileAligner(Future> query, Profile target, GapPenalty gapPenalty,
SubstitutionMatrix subMatrix) {
super(query, target, gapPenalty, subMatrix);
}
// method for AbstractMatrixAligner
@Override
protected void setProfile(List sx, List sy) {
profile = pair = new SimpleProfilePair<>(getQuery(), getTarget(), sx, sy);
}
}