org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner Maven / Gradle / Ivy
/*
* 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 August 11, 2010
* Author: Mark Chapman
*/
package org.biojava.nbio.alignment.routines;
import org.biojava.nbio.core.alignment.SimpleSequencePair;
import org.biojava.nbio.alignment.routines.AlignerHelper.Anchor;
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.ArrayList;
import java.util.List;
/**
* This algorithm uses a divide-and-conquer approach to find optimal pairwise global sequence alignments (from the
* first until the last {@link Compound} of each {@link Sequence}) with the restriction that any alignment produced
* will connect the query sequence to the target sequence at the anchors. This class performs such global
* sequence comparisons efficiently by dynamic programming with a space requirement reduced from quadratic (a multiple
* of query sequence length times target sequence length) to only linear (a multiple of query sequence length). The
* counterpoint to this reduction in space complexity is a modest (a multiple < 2) increase in time.
*
* @author Mark Chapman
* @author Daniel Cameron
* @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 AnchoredPairwiseSequenceAligner, C extends Compound> extends
AbstractPairwiseSequenceAligner {
/**
* 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)}.
*/
public AnchoredPairwiseSequenceAligner() {
}
/**
* 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
* @param cutsPerSection the number of cuts added to each section during each pass
*/
public AnchoredPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix subMatrix) {
this(query, target, gapPenalty, subMatrix, null);
}
/**
* 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
* @param cutsPerSection the number of cuts added to each section during each pass
* @param anchors the initial list of anchors
*/
public AnchoredPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix subMatrix, int[] anchors) {
super(query, target, gapPenalty, subMatrix);
setAnchors(anchors);
}
/**
* Returns the list of anchors. The populated elements correspond to query compounds with a connection established
* to a target compound.
*
* @return the list of anchors
*/
public int[] getAnchors() {
int[] anchor = new int[getScoreMatrixDimensions()[0] - 1];
for (int i = 0; i < anchor.length; i++) {
anchor[i] = -1;
}
for (int i = 0; i < anchors.size(); i++) {
anchor[anchors.get(i).getQueryIndex()] = anchors.get(i).getTargetIndex();
}
return anchor;
}
/**
* Sets the starting list of anchors before running the alignment routine.
*
* @param anchors list of points that are tied to the given indices in the target
*/
public void setAnchors(int[] anchors) {
super.anchors = new ArrayList();
if (anchors != null) {
for (int i = 0; i < anchors.length; i++) {
if (anchors[i] >= 0) {
addAnchor(i, anchors[i]);
}
}
}
}
/**
* Adds an additional anchor to the set of anchored compounds
* @param queryIndex 0-based index of query sequence compound
* @param targetIndex 0-base index of target sequence compound to anchor to
*/
public void addAnchor(int queryIndex, int targetIndex) {
anchors.add(new Anchor(queryIndex, targetIndex));
}
// method for AbstractMatrixAligner
@Override
protected void setProfile(List sx, List sy) {
profile = pair = new SimpleSequencePair(getQuery(), getTarget(), sx, sy);
}
}