Package org.biojava.nbio.alignment
Class NeedlemanWunsch<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.NeedlemanWunsch<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 NeedlemanWunsch<S extends Sequence<C>,C extends Compound>
extends AnchoredPairwiseSequenceAligner<S,C>
Needleman and Wunsch 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.- 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).NeedlemanWunsch(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) Prepares for a pairwise global sequence alignment. -
Method Summary
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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NeedlemanWunsch
public NeedlemanWunsch()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). -
NeedlemanWunsch
Prepares for a pairwise global sequence alignment.
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