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 NeedlemanWunsch<S extends Sequence<C>,C extends Compound> extends AnchoredPairwiseSequenceAligner<S,C>
Compound
of each Sequence
). This class performs such global sequence comparisons efficiently by
dynamic programming.anchors, cutsPerSection, gapPenalty, max, min, profile, score, scores, time, xyMax, xyStart
pair
Constructor | 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.
|
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
addAnchor, getAnchors, setAnchors, setProfile
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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)