org.biojava3.alignment
Class SmithWaterman<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.SmithWaterman<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 SmithWaterman<S extends Sequence<C>,C extends Compound>
- extends AbstractPairwiseSequenceAligner<S,C>
Smith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from each
Sequence
). This class performs such local sequence comparisons efficiently by dynamic programming.
- Author:
- Mark Chapman
Fields inherited from class org.biojava3.alignment.template.AbstractMatrixAligner |
anchors, cutsPerSection, gapPenalty, max, min, profile, score, scores, time, xyMax, xyStart |
Methods inherited from class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner |
getCompoundSet, getCompoundsOfQuery, getCompoundsOfTarget, getPair, getQuery, getScoreMatrixDimensions, getSubstitutionScore, getTarget, isReady, reset, 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 |
SmithWaterman
public SmithWaterman()
- Before running a pairwise local sequence alignment, data must be sent in via calls to
AbstractPairwiseSequenceAligner.setQuery(Sequence)
, AbstractPairwiseSequenceAligner.setTarget(Sequence)
, AbstractMatrixAligner.setGapPenalty(GapPenalty)
, and
AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix)
.
SmithWaterman
public SmithWaterman(S query,
S target,
GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix)
- Prepares for a pairwise local 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
setProfile
protected void setProfile(List<AlignedSequence.Step> sx,
List<AlignedSequence.Step> sy)
- Specified by:
setProfile
in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>