org.biojava.nbio.alignment.template.AbstractProfileProfileAligner 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 24, 2010
* Author: Mark Chapman
*/
package org.biojava.nbio.alignment.template;
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.alignment.template.GapPenalty.Type;
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 org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.ArrayList;
import java.util.List;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.Future;
/**
* Implements common code for an {@link Aligner} for a pair of {@link Profile}s.
*
* @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 abstract class AbstractProfileProfileAligner, C extends Compound>
extends AbstractMatrixAligner implements ProfileProfileAligner {
private final static Logger logger = LoggerFactory.getLogger(AbstractProfileProfileAligner.class);
// additional input fields
private Profile query, target;
// concurrent execution fields
private Future> queryFuture, targetFuture;
// cached fields
private List cslist;
private float[][] qfrac, tfrac;
// additional output field
protected ProfilePair pair;
/**
* 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)}.
*/
protected AbstractProfileProfileAligner() {
}
/**
* 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
*/
protected AbstractProfileProfileAligner(Profile query, Profile target, GapPenalty gapPenalty,
SubstitutionMatrix subMatrix) {
super(gapPenalty, subMatrix);
this.query = query;
this.target = target;
reset();
}
/**
* 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
*/
protected AbstractProfileProfileAligner(Future> query, Future> target,
GapPenalty gapPenalty, SubstitutionMatrix subMatrix) {
super(gapPenalty, subMatrix);
queryFuture = query;
targetFuture = target;
reset();
}
/**
* 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
*/
protected AbstractProfileProfileAligner(Profile query, Future> target,
GapPenalty gapPenalty, SubstitutionMatrix subMatrix) {
super(gapPenalty, subMatrix);
this.query = query;
targetFuture = target;
reset();
}
/**
* 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
*/
protected AbstractProfileProfileAligner(Future> query, Profile target,
GapPenalty gapPenalty, SubstitutionMatrix subMatrix) {
super(gapPenalty, subMatrix);
queryFuture = query;
this.target = target;
reset();
}
/**
* Sets the query {@link Profile}.
*
* @param query the first {@link Profile} of the pair to align
*/
public void setQuery(Profile query) {
this.query = query;
queryFuture = null;
reset();
}
/**
* Sets the target {@link Profile}.
*
* @param target the second {@link Profile} of the pair to align
*/
public void setTarget(Profile target) {
this.target = target;
targetFuture = null;
reset();
}
// method for ProfileProfileAligner
@Override
public ProfilePair getPair() {
if (pair == null) {
align();
}
return pair;
}
// methods for ProfileProfileScorer
@Override
public Profile getQuery() {
return query;
}
@Override
public Profile getTarget() {
return target;
}
// methods for AbstractMatrixAligner
@Override
protected CompoundSet getCompoundSet() {
return (query == null) ? null : query.getCompoundSet();
}
@Override
protected List getCompoundsOfQuery() {
// TODO replace with consensus sequence
return (query == null) ? new ArrayList() : query.getAlignedSequence(1).getAsList();
}
@Override
protected List getCompoundsOfTarget() {
// TODO replace with consensus sequence
return (target == null) ? new ArrayList() : target.getAlignedSequence(1).getAsList();
}
@Override
protected int[] getScoreMatrixDimensions() {
return new int[] { query.getLength() + 1, target.getLength() + 1, (getGapPenalty().getType() == Type.LINEAR) ?
1 : 3 };
}
@Override
protected int getSubstitutionScore(int queryColumn, int targetColumn) {
return getSubstitutionScore(qfrac[queryColumn - 1], tfrac[targetColumn - 1]);
}
@Override
protected boolean isReady() {
// TODO when added to ConcurrencyTools, log completions and exceptions instead of printing stack traces
try {
if (query == null && queryFuture != null) {
query = queryFuture.get();
}
if (target == null && targetFuture != null) {
target = targetFuture.get();
}
reset();
} catch (InterruptedException e) {
logger.error("Interrupted Exception: ", e);
} catch (ExecutionException e) {
logger.error("Execution Exception: ", e);
}
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;
cslist = query.getCompoundSet().getAllCompounds();
qfrac = new float[query.getLength()][];
for (int i = 0; i < qfrac.length; i++) {
qfrac[i] = query.getCompoundWeightsAt(i + 1, cslist);
maxq += getSubstitutionScore(qfrac[i], qfrac[i]);
}
tfrac = new float[target.getLength()][];
for (int i = 0; i < tfrac.length; i++) {
tfrac[i] = target.getCompoundWeightsAt(i + 1, cslist);
maxt += getSubstitutionScore(tfrac[i], tfrac[i]);
}
max = Math.max(maxq, maxt);
score = min = isLocal() ? 0 : (int) (2 * getGapPenalty().getOpenPenalty() + (query.getLength() +
target.getLength()) * getGapPenalty().getExtensionPenalty());
}
}
// helper method that scores alignment of two column vectors
private int getSubstitutionScore(float[] qv, float[] tv) {
float score = 0.0f;
for (int q = 0; q < qv.length; q++) {
if (qv[q] > 0.0f) {
for (int t = 0; t < tv.length; t++) {
if (tv[t] > 0.0f) {
score += qv[q]*tv[t]*getSubstitutionMatrix().getValue(cslist.get(q), cslist.get(t));
}
}
}
}
return Math.round(score);
}
}