Package org.biojava.nbio.alignment

Class SimpleProfileProfileAligner<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.AbstractProfileProfileAligner<S,C>

org.biojava.nbio.alignment.SimpleProfileProfileAligner<S,C>

Type Parameters:

S - each Sequence in the pair of alignment Profiles 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>, ProfileProfileAligner<S,C>, ProfileProfileScorer<S,C>, Scorer

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

Implements a simple (naive) Aligner for a pair of Profiles. This is basically an extension of the NeedlemanWunsch pairwise sequence aligner to pairwise profile alignment using a sum-of-pairs score.

Author:

Mark Chapman

Field Summary

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

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
SimpleProfileProfileAligner()	Before running a profile-profile alignment, data must be sent in via calls to AbstractProfileProfileAligner.setQuery(Profile), AbstractProfileProfileAligner.setTarget(Profile), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).
SimpleProfileProfileAligner(Future<org.biojava.nbio.core.alignment.template.ProfilePair<S,C>> query, Future<org.biojava.nbio.core.alignment.template.ProfilePair<S,C>> target, GapPenalty gapPenalty, org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C> subMatrix)	Prepares for a profile-profile alignment run concurrently.
SimpleProfileProfileAligner(Future<org.biojava.nbio.core.alignment.template.ProfilePair<S,C>> query, org.biojava.nbio.core.alignment.template.Profile<S,C> target, GapPenalty gapPenalty, org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C> subMatrix)	Prepares for a profile-profile alignment run concurrently.
SimpleProfileProfileAligner(org.biojava.nbio.core.alignment.template.Profile<S,C> query, Future<org.biojava.nbio.core.alignment.template.ProfilePair<S,C>> target, GapPenalty gapPenalty, org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C> subMatrix)	Prepares for a profile-profile alignment run concurrently.
SimpleProfileProfileAligner(org.biojava.nbio.core.alignment.template.Profile<S,C> query, org.biojava.nbio.core.alignment.template.Profile<S,C> target, GapPenalty gapPenalty, org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C> subMatrix)	Prepares for a profile-profile alignment.

Method Summary

Modifier and Type	Method	Description
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.AbstractProfileProfileAligner

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

SimpleProfileProfileAligner

public SimpleProfileProfileAligner()

Before running a profile-profile alignment, data must be sent in via calls to AbstractProfileProfileAligner.setQuery(Profile), AbstractProfileProfileAligner.setTarget(Profile), AbstractMatrixAligner.setGapPenalty(GapPenalty), and AbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).

SimpleProfileProfileAligner

public SimpleProfileProfileAligner(org.biojava.nbio.core.alignment.template.Profile<S,C> query,
                                   org.biojava.nbio.core.alignment.template.Profile<S,C> target,
                                   GapPenalty gapPenalty,
                                   org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C> subMatrix)

Prepares for a profile-profile alignment.

Parameters:

query - the first Profile of the pair to align

target - the second Profile of the pair to align

gapPenalty - the gap penalties used during alignment

subMatrix - the set of substitution scores used during alignment

SimpleProfileProfileAligner

public SimpleProfileProfileAligner(Future<org.biojava.nbio.core.alignment.template.ProfilePair<S,C>> query,
                                   Future<org.biojava.nbio.core.alignment.template.ProfilePair<S,C>> target,
                                   GapPenalty gapPenalty,
                                   org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C> subMatrix)

Prepares for a profile-profile alignment run concurrently.

Parameters:

query - the first Profile of the pair to align, still to be calculated

target - the second Profile of the pair to align, still to be calculated

gapPenalty - the gap penalties used during alignment

subMatrix - the set of substitution scores used during alignment

SimpleProfileProfileAligner

public SimpleProfileProfileAligner(org.biojava.nbio.core.alignment.template.Profile<S,C> query,
                                   Future<org.biojava.nbio.core.alignment.template.ProfilePair<S,C>> target,
                                   GapPenalty gapPenalty,
                                   org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C> subMatrix)

Prepares for a profile-profile alignment run concurrently.

Parameters:

query - the first Profile of the pair to align

target - the second Profile of the pair to align, still to be calculated

gapPenalty - the gap penalties used during alignment

subMatrix - the set of substitution scores used during alignment

SimpleProfileProfileAligner

public SimpleProfileProfileAligner(Future<org.biojava.nbio.core.alignment.template.ProfilePair<S,C>> query,
                                   org.biojava.nbio.core.alignment.template.Profile<S,C> target,
                                   GapPenalty gapPenalty,
                                   org.biojava.nbio.core.alignment.template.SubstitutionMatrix<C> subMatrix)

Prepares for a profile-profile alignment run concurrently.

Parameters:

query - the first Profile of the pair to align, still to be calculated

target - the second Profile of the pair to align

gapPenalty - the gap penalties used during alignment

subMatrix - the set of substitution scores used during alignment

Method Detail

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>