org.biojava.nbio.alignment

Class SmithWaterman<S extends Sequence<C>,C extends Compound>

java.lang.Object

org.biojava.nbio.alignment.template.AbstractScorer

org.biojava.nbio.alignment.template.AbstractMatrixAligner<S,C>

org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner<S,C>

org.biojava.nbio.alignment.SmithWaterman<S,C>

Type Parameters:

S - each Sequence of the alignment pair is of type S

C - 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

Field Summary

Fields inherited from class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner

pair

Fields inherited from class org.biojava.nbio.alignment.template.AbstractMatrixAligner

anchors, cutsPerSection, gapPenalty, max, min, profile, score, scores, time, xyMax, xyStart

Constructor Summary

Constructors

Constructor and Description
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(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) Prepares for a pairwise local sequence alignment.

Method Summary

Modifier and Type	Method and Description
protected void	setProfile(List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)

Methods inherited from class org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner

getCompoundSet, getCompoundsOfQuery, getCompoundsOfTarget, getPair, getQuery, getScoreMatrixDimensions, getSubstitutionScore, getTarget, isReady, reset, setQuery, setTarget

Methods inherited from class org.biojava.nbio.alignment.template.AbstractMatrixAligner

align, getComputationTime, getGapPenalty, getMaxScore, getMinScore, getProfile, getScore, getScoreMatrix, getScoreMatrixAsString, getSubstitutionMatrix, getSubstitutionScoreVector, getSubstitutionScoreVector, isLocal, isStoringScoreMatrix, setGapPenalty, setStoringScoreMatrix, setSubstitutionMatrix

Methods inherited from class org.biojava.nbio.alignment.template.AbstractScorer

getDistance, getDistance, getSimilarity, getSimilarity

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biojava.nbio.alignment.template.Aligner

getComputationTime, getProfile

Methods inherited from interface org.biojava.nbio.alignment.template.Scorer

getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity

Constructor Detail

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 align

target - the second Sequence of the pair to align

gapPenalty - the gap penalties used during alignment

subMatrix - the set of substitution scores used during alignment

Method Detail

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>