NeedlemanWunsch (biojava 5.2.0 API)

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Package org.biojava.nbio.alignment

Class NeedlemanWunsch<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.routines.AnchoredPairwiseSequenceAligner<S,C>
      - org.biojava.nbio.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 AnchoredPairwiseSequenceAligner<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.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	Description
`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
- Methods inherited from class org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner
  addAnchor, getAnchors, setAnchors, setProfile
- 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
  - 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