org.biojava3.alignment.routines
Class GuanUberbacher<S extends Sequence<C>,C extends Compound>
java.lang.Object
org.biojava3.alignment.template.AbstractScorer
org.biojava3.alignment.template.AbstractMatrixAligner<S,C>
org.biojava3.alignment.template.AbstractPairwiseSequenceAligner<S,C>
org.biojava3.alignment.routines.AnchoredPairwiseSequenceAligner<S,C>
org.biojava3.alignment.routines.GuanUberbacher<S,C>
- Type Parameters:
S
- each Sequence
of the alignment pair is of type SC
- each element of an AlignedSequence
is a Compound
of type C
- All Implemented Interfaces:
- Aligner<S,C>, MatrixAligner<S,C>, PairwiseSequenceAligner<S,C>, PairwiseSequenceScorer<S,C>, Scorer
public class GuanUberbacher<S extends Sequence<C>,C extends Compound>
- extends AnchoredPairwiseSequenceAligner<S,C>
Guan and Uberbacher defined an algorithm for pairwise global sequence alignments (from the first until the last
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.
- Author:
- Mark Chapman
Fields inherited from class org.biojava3.alignment.template.AbstractMatrixAligner |
anchors, cutsPerSection, gapPenalty, max, min, profile, score, scores, time, xyMax, xyStart |
Constructor Summary |
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. |
Methods inherited from class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner |
getCompoundSet, getCompoundsOfQuery, getCompoundsOfTarget, getPair, getQuery, getScoreMatrixDimensions, getSubstitutionScore, getTarget, isReady, setQuery, setTarget |
Methods inherited from class org.biojava3.alignment.template.AbstractMatrixAligner |
align, getComputationTime, getGapPenalty, getMaxScore, getMinScore, getProfile, getScore, getScoreMatrix, getScoreMatrixAsString, getSubstitutionMatrix, getSubstitutionScoreVector, getSubstitutionScoreVector, isLocal, isStoringScoreMatrix, resetAnchors, setGapPenalty, setStoringScoreMatrix, setSubstitutionMatrix |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
GuanUberbacher
public 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
public GuanUberbacher(S query,
S target,
GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix)
- Prepares for a pairwise global sequence alignment.
- Parameters:
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 alignment
GuanUberbacher
public GuanUberbacher(S query,
S target,
GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix,
int cutsPerSection)
- Prepares for a pairwise global sequence alignment.
- Parameters:
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 pass