org.biojava3.alignment
Class NeedlemanWunsch<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.NeedlemanWunsch<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 NeedlemanWunsch<S extends Sequence<C>,C extends Compound>
extends AbstractPairwiseSequenceAligner<S,C>

Needleman and Wunsch 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.

Author:

Mark Chapman

Field Summary

Fields inherited from class org.biojava3.alignment.template.AbstractPairwiseSequenceAligner

pair

Fields inherited from class org.biojava3.alignment.template.AbstractMatrixAligner

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

Constructor Summary

NeedlemanWunsch()
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).

NeedlemanWunsch(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
Prepares for a pairwise global sequence alignment.

Method Summary

protected void

setProfile(java.util.List<AlignedSequence.Step> sx, java.util.List<AlignedSequence.Step> sy)

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 org.biojava3.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.biojava3.alignment.template.Aligner

getComputationTime, getProfile

Methods inherited from interface org.biojava3.alignment.template.Scorer

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

Constructor Detail

NeedlemanWunsch

public NeedlemanWunsch()

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).

NeedlemanWunsch

public NeedlemanWunsch(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 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(java.util.List<AlignedSequence.Step> sx,
                          java.util.List<AlignedSequence.Step> sy)

Specified by:

setProfile in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>