Package org.biojava.nbio.alignment.routines

Class GuanUberbacher<S extends Sequence<C>,C extends Compound>

java.lang.Object

org.biojava.nbio.alignment.template.AbstractScorer

org.biojava.nbio.alignment.template.AbstractMatrixAligner<S,C>

org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner<S,C>

org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner<S,C>

org.biojava.nbio.alignment.routines.GuanUberbacher<S,C>

Type Parameters:

S - each Sequence of the alignment pair is of type S

C - each element of an AlignedSequence is a Compound of type C

All Implemented Interfaces:

Aligner<S,C>, MatrixAligner<S,C>, PairwiseSequenceAligner<S,C>, PairwiseSequenceScorer<S,C>, Scorer

public class GuanUberbacher<S extends Sequence<C>,C extends Compound>
extends AnchoredPairwiseSequenceAligner<S,C>

Guan and Uberbacher defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each 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

Field Summary

Fields inherited from class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner

pair

Fields inherited from class org.biojava.nbio.alignment.template.AbstractMatrixAligner

anchors, cutsPerSection, gapPenalty, max, min, profile, score, scores, time, xyMax, xyStart

Constructor Summary

Constructors

Constructor	Description
GuanUberbacher()	Before running a pairwise global sequence alignment, data must be sent in via calls to AbstractPairwiseSequenceAligner.setQuery(Sequence), AbstractPairwiseSequenceAligner.setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
GuanUberbacher(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)	Prepares for a pairwise global sequence alignment.
GuanUberbacher(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix, int cutsPerSection)	Prepares for a pairwise global sequence alignment.

Method Summary

Modifier and Type	Method	Description
int	getCutsPerSection()	Returns the number of cuts added to each section during each pass.
void	setCutsPerSection(int cutsPerSection)	Sets the number of cuts added to each section during each pass.
static void	setDefaultCutsPerSection(int defaultCutsPerSection)	Sets the default number of cuts added to each section during each pass.

Methods inherited from class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner

addAnchor, getAnchors, setAnchors, setProfile

Methods inherited from class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner

getCompoundSet, getCompoundsOfQuery, getCompoundsOfTarget, getPair, getQuery, getScoreMatrixDimensions, getSubstitutionScore, getTarget, isReady, reset, setQuery, setTarget

Methods inherited from class org.biojava.nbio.alignment.template.AbstractMatrixAligner

align, getComputationTime, getGapPenalty, getMaxScore, getMinScore, getProfile, getScore, getScoreMatrix, getScoreMatrixAsString, getSubstitutionMatrix, getSubstitutionScoreVector, getSubstitutionScoreVector, isLocal, isStoringScoreMatrix, setGapPenalty, setStoringScoreMatrix, setSubstitutionMatrix

Methods inherited from class org.biojava.nbio.alignment.template.AbstractScorer

getDistance, getDistance, getSimilarity, getSimilarity

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biojava.nbio.alignment.template.Aligner

getComputationTime, getProfile

Methods inherited from interface org.biojava.nbio.alignment.template.Scorer

getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity

Constructor Details

GuanUberbacher

public GuanUberbacher()

Before running a pairwise global sequence alignment, data must be sent in via calls to AbstractPairwiseSequenceAligner.setQuery(Sequence), AbstractPairwiseSequenceAligner.setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).

GuanUberbacher

public GuanUberbacher(S query,
 S target,
 GapPenalty gapPenalty,
 SubstitutionMatrix<C> subMatrix)

Prepares for a pairwise global sequence alignment.

Parameters:

query - the first Sequence of the pair to align

target - the second Sequence of the pair to align

gapPenalty - the gap penalties used during alignment

subMatrix - the set of substitution scores used during alignment

GuanUberbacher

public GuanUberbacher(S query,
 S target,
 GapPenalty gapPenalty,
 SubstitutionMatrix<C> subMatrix,
 int cutsPerSection)

Prepares for a pairwise global sequence alignment.

Parameters:

query - the first Sequence of the pair to align

target - the second Sequence of the pair to align

gapPenalty - the gap penalties used during alignment

subMatrix - the set of substitution scores used during alignment

cutsPerSection - the number of cuts added to each section during each pass

Method Details

setDefaultCutsPerSection

public static void setDefaultCutsPerSection(int defaultCutsPerSection)

Sets the default number of cuts added to each section during each pass.

Parameters:

defaultCutsPerSection - the default number of cuts added to each section during each pass

getCutsPerSection

public int getCutsPerSection()

Returns the number of cuts added to each section during each pass.

Returns:

the number of cuts added to each section during each pass

setCutsPerSection

public void setCutsPerSection(int cutsPerSection)

Sets the number of cuts added to each section during each pass.

Parameters:

cutsPerSection - the number of cuts added to each section during each pass