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- eachSequenceof the alignment pair is of type SC- each element of anAlignedSequenceis aCompoundof 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
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Field Summary
Fields inherited from class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
pairFields inherited from class org.biojava.nbio.alignment.template.AbstractMatrixAligner
anchors, cutsPerSection, gapPenalty, max, min, profile, score, scores, time, xyMax, xyStart -
Constructor Summary
ConstructorsConstructorDescriptionBefore running a pairwise global sequence alignment, data must be sent in via calls toAbstractPairwiseSequenceAligner.setQuery(Sequence),AbstractPairwiseSequenceAligner.setTarget(Sequence),AbstractMatrixAligner.setGapPenalty(GapPenalty), andAbstractMatrixAligner.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 TypeMethodDescriptionintReturns the number of cuts added to each section during each pass.voidsetCutsPerSection(int cutsPerSection) Sets the number of cuts added to each section during each pass.static voidsetDefaultCutsPerSection(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, setProfileMethods inherited from class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
getCompoundSet, getCompoundsOfQuery, getCompoundsOfTarget, getPair, getQuery, getScoreMatrixDimensions, getSubstitutionScore, getTarget, isReady, reset, setQuery, setTargetMethods 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, setSubstitutionMatrixMethods inherited from class org.biojava.nbio.alignment.template.AbstractScorer
getDistance, getDistance, getSimilarity, getSimilarityMethods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitMethods inherited from interface org.biojava.nbio.alignment.template.Aligner
getComputationTime, getProfileMethods inherited from interface org.biojava.nbio.alignment.template.Scorer
getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity
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Constructor Details
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GuanUberbacher
public GuanUberbacher()Before running a pairwise global sequence alignment, data must be sent in via calls toAbstractPairwiseSequenceAligner.setQuery(Sequence),AbstractPairwiseSequenceAligner.setTarget(Sequence),AbstractMatrixAligner.setGapPenalty(GapPenalty), andAbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix). -
GuanUberbacher
Prepares for a pairwise global sequence 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 firstSequenceof the pair to aligntarget- the secondSequenceof the pair to aligngapPenalty- the gap penalties used during alignmentsubMatrix- the set of substitution scores used during alignmentcutsPerSection- the number of cuts added to each section during each pass
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Method Details
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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
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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
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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
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