S
- each Sequence
of the alignment pair is of type SC
- each element of an AlignedSequence
is a Compound
of type CAligner<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>
Sequence
). This class performs such local sequence comparisons efficiently by dynamic programming.anchors, cutsPerSection, gapPenalty, max, min, profile, score, scores, time, xyMax, xyStart
pair
Constructor | Description |
---|---|
SmithWaterman() |
Before running a pairwise local sequence alignment, data must be sent in via calls to
AbstractPairwiseSequenceAligner.setQuery(Sequence) , AbstractPairwiseSequenceAligner.setTarget(Sequence) , AbstractMatrixAligner.setGapPenalty(GapPenalty) , and
AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix) . |
SmithWaterman(S query,
S target,
GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix) |
Prepares for a pairwise local sequence alignment.
|
Modifier and Type | Method | Description |
---|---|---|
protected void |
setProfile(java.util.List<AlignedSequence.Step> sx,
java.util.List<AlignedSequence.Step> sy) |
align, getComputationTime, getGapPenalty, getMaxScore, getMinScore, getProfile, getScore, getScoreMatrix, getScoreMatrixAsString, getSubstitutionMatrix, getSubstitutionScoreVector, getSubstitutionScoreVector, isLocal, isStoringScoreMatrix, setGapPenalty, setStoringScoreMatrix, setSubstitutionMatrix
getCompoundSet, getCompoundsOfQuery, getCompoundsOfTarget, getPair, getQuery, getScoreMatrixDimensions, getSubstitutionScore, getTarget, isReady, reset, setQuery, setTarget
getDistance, getDistance, getSimilarity, getSimilarity
getComputationTime, getProfile
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity
public SmithWaterman()
AbstractPairwiseSequenceAligner.setQuery(Sequence)
, AbstractPairwiseSequenceAligner.setTarget(Sequence)
, AbstractMatrixAligner.setGapPenalty(GapPenalty)
, and
AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix)
.public SmithWaterman(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
protected void setProfile(java.util.List<AlignedSequence.Step> sx, java.util.List<AlignedSequence.Step> sy)
setProfile
in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>