Package org.biojava.nbio.alignment
Class SimpleProfileProfileAligner<S extends Sequence<C>,C extends Compound>
- java.lang.Object
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- org.biojava.nbio.alignment.template.AbstractScorer
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- org.biojava.nbio.alignment.template.AbstractMatrixAligner<S,C>
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- org.biojava.nbio.alignment.template.AbstractProfileProfileAligner<S,C>
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- org.biojava.nbio.alignment.SimpleProfileProfileAligner<S,C>
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- Type Parameters:
S
- eachSequence
in the pair of alignmentProfile
s is of type SC
- each element of anAlignedSequence
is aCompound
of type C
- All Implemented Interfaces:
Aligner<S,C>
,MatrixAligner<S,C>
,ProfileProfileAligner<S,C>
,ProfileProfileScorer<S,C>
,Scorer
public class SimpleProfileProfileAligner<S extends Sequence<C>,C extends Compound> extends AbstractProfileProfileAligner<S,C>
Implements a simple (naive)Aligner
for a pair ofProfile
s. This is basically an extension of theNeedlemanWunsch
pairwise sequence aligner to pairwise profile alignment using a sum-of-pairs score.- Author:
- Mark Chapman
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Field Summary
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Fields inherited from class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
pair
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Fields inherited from class org.biojava.nbio.alignment.template.AbstractMatrixAligner
anchors, cutsPerSection, gapPenalty, max, min, profile, score, scores, time, xyMax, xyStart
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Constructor Summary
Constructors Constructor Description SimpleProfileProfileAligner()
Before running a profile-profile alignment, data must be sent in via calls toAbstractProfileProfileAligner.setQuery(Profile)
,AbstractProfileProfileAligner.setTarget(Profile)
,AbstractMatrixAligner.setGapPenalty(GapPenalty)
, andAbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix)
.SimpleProfileProfileAligner(Future<ProfilePair<S,C>> query, Future<ProfilePair<S,C>> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
Prepares for a profile-profile alignment run concurrently.SimpleProfileProfileAligner(Future<ProfilePair<S,C>> query, Profile<S,C> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
Prepares for a profile-profile alignment run concurrently.SimpleProfileProfileAligner(Profile<S,C> query, Future<ProfilePair<S,C>> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
Prepares for a profile-profile alignment run concurrently.SimpleProfileProfileAligner(Profile<S,C> query, Profile<S,C> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
Prepares for a profile-profile alignment.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
setProfile(List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
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Methods inherited from class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
getCompoundSet, getCompoundsOfQuery, getCompoundsOfTarget, getPair, getQuery, getScoreMatrixDimensions, getSubstitutionScore, getTarget, isReady, reset, setQuery, setTarget
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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
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Methods inherited from class org.biojava.nbio.alignment.template.AbstractScorer
getDistance, getDistance, getSimilarity, getSimilarity
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.biojava.nbio.alignment.template.Aligner
getComputationTime, getProfile
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Methods inherited from interface org.biojava.nbio.alignment.template.Scorer
getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity
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Constructor Detail
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SimpleProfileProfileAligner
public SimpleProfileProfileAligner()
Before running a profile-profile alignment, data must be sent in via calls toAbstractProfileProfileAligner.setQuery(Profile)
,AbstractProfileProfileAligner.setTarget(Profile)
,AbstractMatrixAligner.setGapPenalty(GapPenalty)
, andAbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix)
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SimpleProfileProfileAligner
public SimpleProfileProfileAligner(Profile<S,C> query, Profile<S,C> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
Prepares for a profile-profile alignment.
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SimpleProfileProfileAligner
public SimpleProfileProfileAligner(Future<ProfilePair<S,C>> query, Future<ProfilePair<S,C>> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
Prepares for a profile-profile alignment run concurrently.
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SimpleProfileProfileAligner
public SimpleProfileProfileAligner(Profile<S,C> query, Future<ProfilePair<S,C>> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
Prepares for a profile-profile alignment run concurrently.
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SimpleProfileProfileAligner
public SimpleProfileProfileAligner(Future<ProfilePair<S,C>> query, Profile<S,C> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)
Prepares for a profile-profile alignment run concurrently.
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Method Detail
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setProfile
protected void setProfile(List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
- Specified by:
setProfile
in classAbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
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