S
- each Sequence
of the alignment pair is of type SC
- each element of an AlignedSequence
is a Compound
of type Cpublic class GuanUberbacher<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 with a space requirement reduced from quadratic (a multiple of query sequence length times
target sequence length) to only linear (a multiple of query sequence length). The counterpoint to this reduction in
space complexity is a modest (a multiple < 2) increase in time.pair
anchors, cutsPerSection, gapPenalty, max, min, profile, score, scores, time, xyMax, xyStart
Constructor and Description |
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GuanUberbacher()
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) . |
GuanUberbacher(S query,
S target,
GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix)
Prepares for a pairwise global sequence alignment.
|
GuanUberbacher(S query,
S target,
GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix,
int cutsPerSection)
Prepares for a pairwise global sequence alignment.
|
getAnchors, getCutsPerSection, reset, setAnchors, setCutsPerSection, setDefaultCutsPerSection, setProfile
getCompoundSet, getCompoundsOfQuery, getCompoundsOfTarget, getPair, getQuery, getScoreMatrixDimensions, getSubstitutionScore, getTarget, isReady, 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 GuanUberbacher()
AbstractPairwiseSequenceAligner.setQuery(Sequence)
, AbstractPairwiseSequenceAligner.setTarget(Sequence)
, AbstractMatrixAligner.setGapPenalty(GapPenalty)
, and
AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix)
.public GuanUberbacher(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
public GuanUberbacher(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix, int cutsPerSection)