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