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 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 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
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 |
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 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>