Package org.biojava.nbio.alignment
Class SmithWaterman<S extends Sequence<C>,C extends Compound>
- java.lang.Object
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- org.biojava.nbio.alignment.template.AbstractScorer
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- org.biojava.nbio.alignment.template.AbstractMatrixAligner<S,C>
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- org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner<S,C>
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- org.biojava.nbio.alignment.SmithWaterman<S,C>
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- Type Parameters:
S
- eachSequence
of the alignment pair is of type SC
- each element of anAlignedSequence
is aCompound
of 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 eachSequence
). This class performs such local sequence comparisons efficiently by dynamic programming.- Author:
- Mark Chapman
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Field Summary
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Fields inherited from class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
pair
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Fields inherited from class org.biojava.nbio.alignment.template.AbstractMatrixAligner
anchors, cutsPerSection, gapPenalty, max, min, profile, score, scores, time, xyMax, xyStart
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Constructor Summary
Constructors Constructor Description 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(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
Prepares for a pairwise local sequence alignment.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
setProfile(List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
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Methods inherited from class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner
getCompoundSet, getCompoundsOfQuery, getCompoundsOfTarget, getPair, getQuery, getScoreMatrixDimensions, getSubstitutionScore, getTarget, isReady, reset, setQuery, setTarget
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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
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Methods inherited from class org.biojava.nbio.alignment.template.AbstractScorer
getDistance, getDistance, getSimilarity, getSimilarity
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.biojava.nbio.alignment.template.Aligner
getComputationTime, getProfile
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Methods inherited from interface org.biojava.nbio.alignment.template.Scorer
getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity
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Constructor Detail
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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)
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SmithWaterman
public SmithWaterman(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
Prepares for a pairwise local sequence alignment.
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Method Detail
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setProfile
protected void setProfile(List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
- Specified by:
setProfile
in classAbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
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