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.pairanchors, 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.
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GuanUberbacher(S query,
S target,
GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix,
int cutsPerSection)
Prepares for a pairwise global sequence alignment.
|
| Modifier and Type | Method and Description |
|---|---|
int |
getCutsPerSection()
Returns the number of cuts added to each section during each pass.
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void |
setCutsPerSection(int cutsPerSection)
Sets the number of cuts added to each section during each pass.
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static void |
setDefaultCutsPerSection(int defaultCutsPerSection)
Sets the default number of cuts added to each section during each pass.
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addAnchor, getAnchors, setAnchors, setProfilegetCompoundSet, getCompoundsOfQuery, getCompoundsOfTarget, getPair, getQuery, getScoreMatrixDimensions, getSubstitutionScore, getTarget, isReady, reset, setQuery, setTargetalign, getComputationTime, getGapPenalty, getMaxScore, getMinScore, getProfile, getScore, getScoreMatrix, getScoreMatrixAsString, getSubstitutionMatrix, getSubstitutionScoreVector, getSubstitutionScoreVector, isLocal, isStoringScoreMatrix, setGapPenalty, setStoringScoreMatrix, setSubstitutionMatrixgetDistance, getDistance, getSimilarity, getSimilarityclone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitgetComputationTime, getProfilegetDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilaritypublic 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)
query - the first Sequence of the pair to aligntarget - the second Sequence of the pair to aligngapPenalty - the gap penalties used during alignmentsubMatrix - the set of substitution scores used during alignmentcutsPerSection - the number of cuts added to each section during each passpublic static void setDefaultCutsPerSection(int defaultCutsPerSection)
defaultCutsPerSection - the default number of cuts added to each section during each passpublic int getCutsPerSection()
public void setCutsPerSection(int cutsPerSection)
cutsPerSection - the number of cuts added to each section during each passCopyright © 2000–2018 BioJava. All rights reserved.