Package org.biojava.nbio.alignment.routines

Class AnchoredPairwiseSequenceAligner<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>

org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner<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:

GuanUberbacher, NeedlemanWunsch

public class AnchoredPairwiseSequenceAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>
extends AbstractPairwiseSequenceAligner<S,C>

This algorithm uses a divide-and-conquer approach to find optimal pairwise global sequence alignments (from the first until the last Compound of each Sequence) with the restriction that any alignment produced will connect the query sequence to the target sequence at the anchors. This class performs such global sequence comparisons efficiently by dynamic programming with a space requirement reduced from quadratic (a multiple of query sequence length times target sequence length) to only linear (a multiple of query sequence length). The counterpoint to this reduction in space complexity is a modest (a multiple < 2) increase in time.

Author:

Mark Chapman, Daniel Cameron

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
AnchoredPairwiseSequenceAligner()	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).
AnchoredPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty, org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C> subMatrix)	Prepares for a pairwise global sequence alignment.
AnchoredPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty, org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C> subMatrix, int[] anchors)	Prepares for a pairwise global sequence alignment.

Method Summary

Modifier and Type	Method	Description
void	addAnchor(int queryIndex, int targetIndex)	Adds an additional anchor to the set of anchored compounds
int[]	getAnchors()	Returns the list of anchors.
void	setAnchors(int[] anchors)	Sets the starting list of anchors before running the alignment routine.
protected void	setProfile(List<org.biojava.nbio.core.alignment.template.AlignedSequence.Step> sx, List<org.biojava.nbio.core.alignment.template.AlignedSequence.Step> sy)

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

AnchoredPairwiseSequenceAligner

public AnchoredPairwiseSequenceAligner()

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).

AnchoredPairwiseSequenceAligner

public AnchoredPairwiseSequenceAligner(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

cutsPerSection - the number of cuts added to each section during each pass

AnchoredPairwiseSequenceAligner

public AnchoredPairwiseSequenceAligner(S query,
                                       S target,
                                       GapPenalty gapPenalty,
                                       org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C> subMatrix,
                                       int[] anchors)

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

cutsPerSection - the number of cuts added to each section during each pass

anchors - the initial list of anchors

Method Detail

getAnchors

public int[] getAnchors()

Returns the list of anchors. The populated elements correspond to query compounds with a connection established to a target compound.

Returns:

the list of anchors

setAnchors

public void setAnchors(int[] anchors)

Sets the starting list of anchors before running the alignment routine.

Parameters:

anchors - list of points that are tied to the given indices in the target

addAnchor

public void addAnchor(int queryIndex,
                      int targetIndex)

Adds an additional anchor to the set of anchored compounds

Parameters:

queryIndex - 0-based index of query sequence compound

targetIndex - 0-base index of target sequence compound to anchor to

setProfile

protected void setProfile(List<org.biojava.nbio.core.alignment.template.AlignedSequence.Step> sx,
                          List<org.biojava.nbio.core.alignment.template.AlignedSequence.Step> sy)

Specified by:

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