org.biojava.nbio.alignment.routines.GuanUberbacher 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
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*
* http://www.biojava.org/
*
* Created on August 11, 2010
* Author: Mark Chapman
*/
package org.biojava.nbio.alignment.routines;
import org.biojava.nbio.core.alignment.template.AlignedSequence;
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;
/**
* Guan and Uberbacher defined an algorithm for pairwise global sequence alignments (from the first until the last
* {@link Compound} of each {@link Sequence}). 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
* @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 GuanUberbacher, C extends Compound> extends AnchoredPairwiseSequenceAligner {
private static int defaultCutsPerSection = 10;
/**
* Sets the default number of cuts added to each section during each pass.
* @param defaultCutsPerSection the default number of cuts added to each section during each pass
*/
public static void setDefaultCutsPerSection(int defaultCutsPerSection) {
defaultCutsPerSection = Math.max(1, defaultCutsPerSection);
}
/**
* 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 GuanUberbacher() {
setDefaultCutsPerSection(defaultCutsPerSection);
}
/**
* 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
*/
public GuanUberbacher(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix subMatrix) {
super(query, target, gapPenalty, subMatrix);
setDefaultCutsPerSection(defaultCutsPerSection);
}
/**
* 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 GuanUberbacher(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix subMatrix,
int cutsPerSection) {
super(query, target, gapPenalty, subMatrix);
setCutsPerSection(cutsPerSection);
}
/**
* Returns the number of cuts added to each section during each pass.
*
* @return the number of cuts added to each section during each pass
*/
public int getCutsPerSection() {
return cutsPerSection;
}
/**
* Sets the number of cuts added to each section during each pass.
*
* @param cutsPerSection the number of cuts added to each section during each pass
*/
public void setCutsPerSection(int cutsPerSection) {
this.cutsPerSection = Math.max(1, cutsPerSection);
}
}