org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner<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

Direct Known Subclasses:: AnchoredPairwiseSequenceAligner, SmithWaterman

public abstract class AbstractPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> extends AbstractMatrixAligner<S,C> implements PairwiseSequenceAligner<S,C>

Implements common code for an Aligner for a pair of Sequences.

Author:: Mark Chapman

Field Summary

Fields

Modifier and Type

Field

Description

protected SequencePair<S,C>

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

Modifier

Constructor

Description

protected

AbstractPairwiseSequenceAligner()

Before running a pairwise global sequence alignment, data must be sent in via calls to setQuery(Sequence), setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).

protected

AbstractPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)

Prepares for a pairwise global sequence alignment.

protected

AbstractPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix, boolean local)

Prepares for a pairwise sequence alignment.
Method Summary

Modifier and Type

Method

Description

protected CompoundSet<C>

getCompoundSet()

protected List<C>

getCompoundsOfQuery()

protected List<C>

getCompoundsOfTarget()

SequencePair<S,C>

getPair()

Returns sequence alignment pair.

S

getQuery()

Returns the first sequence of the pair.

protected int[]

getScoreMatrixDimensions()

protected int

getSubstitutionScore(int queryColumn, int targetColumn)

S

getTarget()

Returns the second sequence of the pair.

protected boolean

isReady()

protected void

reset()

Resets output fields; should be overridden to set max and min

void

setQuery(S query)

Sets the query Sequence.

void

setTarget(S target)

Sets the target Sequence.

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, setProfile, 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

Field Details
- pair
  
  protected SequencePair<S extends Sequence<C>,C extends Compound> pair
Constructor Details
- AbstractPairwiseSequenceAligner
  
  protected AbstractPairwiseSequenceAligner()
  
  Before running a pairwise global sequence alignment, data must be sent in via calls to setQuery(Sequence), setTarget(Sequence), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
- AbstractPairwiseSequenceAligner
  
  protected AbstractPairwiseSequenceAligner(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
- AbstractPairwiseSequenceAligner
  
  protected AbstractPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix, boolean local)
  
  Prepares for a pairwise 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
  
  local - if true, find a region of similarity rather than aligning every compound
Method Details
- setQuery
  
  public void setQuery(S query)
  
  Sets the query Sequence.
  
  Parameters:
  
  query - the first Sequence of the pair to align
- setTarget
  
  public void setTarget(S target)
  
  Sets the target Sequence.
  
  Parameters:
  
  target - the second Sequence of the pair to align
- getPair
  
  public SequencePair<S,C> getPair()
  
  Description copied from interface: PairwiseSequenceAligner
  
  Returns sequence alignment pair.
  
  Specified by:
  
  getPair in interface PairwiseSequenceAligner<S extends Sequence<C>,C extends Compound>
  
  Returns:
  
  sequence alignment pair
- getQuery
  
  public S getQuery()
  
  Description copied from interface: PairwiseSequenceScorer
  
  Returns the first sequence of the pair.
  
  Specified by:
  
  getQuery in interface PairwiseSequenceScorer<S extends Sequence<C>,C extends Compound>
  
  Returns:
  
  the first sequence of the pair
- getTarget
  
  public S getTarget()
  
  Description copied from interface: PairwiseSequenceScorer
  
  Returns the second sequence of the pair.
  
  Specified by:
  
  getTarget in interface PairwiseSequenceScorer<S extends Sequence<C>,C extends Compound>
  
  Returns:
  
  the second sequence of the pair
- getCompoundSet
  
  protected CompoundSet<C> getCompoundSet()
  
  Specified by:
  
  getCompoundSet in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
- getCompoundsOfQuery
  
  protected List<C> getCompoundsOfQuery()
  
  Specified by:
  
  getCompoundsOfQuery in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
- getCompoundsOfTarget
  
  protected List<C> getCompoundsOfTarget()
  
  Specified by:
  
  getCompoundsOfTarget in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
- getScoreMatrixDimensions
  
  protected int[] getScoreMatrixDimensions()
  
  Specified by:
  
  getScoreMatrixDimensions in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
- getSubstitutionScore
  
  protected int getSubstitutionScore(int queryColumn, int targetColumn)
  
  Specified by:
  
  getSubstitutionScore in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
- isReady
  
  protected boolean isReady()
  
  Specified by:
  
  isReady in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
- reset
  
  protected void reset()
  
  Description copied from class: AbstractMatrixAligner
  
  Resets output fields; should be overridden to set max and min
  
  Overrides:
  
  reset in class AbstractMatrixAligner<S extends Sequence<C>,C extends Compound>

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

Field Summary

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

Constructor Summary

Method Summary

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

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

Methods inherited from class java.lang.Object

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

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

Field Details

pair

Constructor Details

AbstractPairwiseSequenceAligner

AbstractPairwiseSequenceAligner

AbstractPairwiseSequenceAligner

Method Details

setQuery

setTarget

getPair

getQuery

getTarget

getCompoundSet

getCompoundsOfQuery

getCompoundsOfTarget

getScoreMatrixDimensions

getSubstitutionScore

isReady

reset