Package org.biojava.nbio.alignment
Class SmithWaterman<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.SmithWaterman<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 SmithWaterman<S extends Sequence<C>,C extends Compound>
extends AbstractPairwiseSequenceAligner<S,C>
Smith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from each
Sequence). This class performs such local sequence comparisons efficiently by dynamic programming.- 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 local sequence alignment, data must be sent in via calls toAbstractPairwiseSequenceAligner.setQuery(Sequence),AbstractPairwiseSequenceAligner.setTarget(Sequence),AbstractMatrixAligner.setGapPenalty(GapPenalty), andAbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).SmithWaterman(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) Prepares for a pairwise local sequence alignment. -
Method Summary
Modifier and TypeMethodDescriptionprotected voidMethods 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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SmithWaterman
public SmithWaterman()Before running a pairwise local sequence alignment, data must be sent in via calls toAbstractPairwiseSequenceAligner.setQuery(Sequence),AbstractPairwiseSequenceAligner.setTarget(Sequence),AbstractMatrixAligner.setGapPenalty(GapPenalty), andAbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix). -
SmithWaterman
Prepares for a pairwise local sequence alignment.
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Method Details
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setProfile
- Specified by:
setProfilein classAbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
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