Package org.biojava.nbio.alignment.template

Class AbstractPairwiseSequenceAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.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>

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 org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.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 org.biojava.nbio.core.alignment.template.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, org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C> subMatrix)	Prepares for a pairwise global sequence alignment.
protected	AbstractPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty, org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C> subMatrix, boolean local)	Prepares for a pairwise sequence alignment.

Method Summary

Modifier and Type	Method	Description
protected org.biojava.nbio.core.sequence.template.CompoundSet<C>	getCompoundSet()
protected List<C>	getCompoundsOfQuery()
protected List<C>	getCompoundsOfTarget()
org.biojava.nbio.core.alignment.template.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 Detail

pair

protected org.biojava.nbio.core.alignment.template.SequencePair<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound> pair

Constructor Detail

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,
                                          org.biojava.nbio.core.alignment.template.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,
                                          org.biojava.nbio.core.alignment.template.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 Detail

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 org.biojava.nbio.core.alignment.template.SequencePair<S,C> getPair()

Description copied from interface: PairwiseSequenceAligner

Returns sequence alignment pair.

Specified by:

getPair in interface PairwiseSequenceAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.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 org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.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 org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>

Returns:

the second sequence of the pair

getCompoundSet

protected org.biojava.nbio.core.sequence.template.CompoundSet<C> getCompoundSet()

Specified by:

getCompoundSet in class AbstractMatrixAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>

getCompoundsOfQuery

protected List<C> getCompoundsOfQuery()

Specified by:

getCompoundsOfQuery in class AbstractMatrixAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>

getCompoundsOfTarget

protected List<C> getCompoundsOfTarget()

Specified by:

getCompoundsOfTarget in class AbstractMatrixAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>

getScoreMatrixDimensions

protected int[] getScoreMatrixDimensions()

Specified by:

getScoreMatrixDimensions in class AbstractMatrixAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>

getSubstitutionScore

protected int getSubstitutionScore(int queryColumn,
                                   int targetColumn)

Specified by:

getSubstitutionScore in class AbstractMatrixAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>

isReady

protected boolean isReady()

Specified by:

isReady in class AbstractMatrixAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.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 org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>