Package org.biojava.nbio.alignment
Class SimpleProfileProfileAligner<S extends Sequence<C>,C extends 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- eachSequencein the pair of alignmentProfiles is of type SC- each element of anAlignedSequenceis aCompoundof 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 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
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Field Summary
Fields inherited from class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
pairFields inherited from class org.biojava.nbio.alignment.template.AbstractMatrixAligner
anchors, cutsPerSection, gapPenalty, max, min, profile, score, scores, time, xyMax, xyStart -
Constructor Summary
ConstructorsConstructorDescriptionBefore 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. -
Method Summary
Modifier and TypeMethodDescriptionprotected voidMethods inherited from class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
getCompoundSet, getCompoundsOfQuery, getCompoundsOfTarget, getPair, getQuery, getScoreMatrixDimensions, getSubstitutionScore, getTarget, isReady, reset, setQuery, setTargetMethods 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, setSubstitutionMatrixMethods inherited from class org.biojava.nbio.alignment.template.AbstractScorer
getDistance, getDistance, getSimilarity, getSimilarityMethods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitMethods inherited from interface org.biojava.nbio.alignment.template.Aligner
getComputationTime, getProfileMethods inherited from interface org.biojava.nbio.alignment.template.Scorer
getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity
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Constructor Details
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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). -
SimpleProfileProfileAligner
public SimpleProfileProfileAligner(Profile<S, C> query, Profile<S, C> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) Prepares for a profile-profile alignment. -
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. -
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. -
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 Details
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setProfile
- Specified by:
setProfilein classAbstractMatrixAligner<S extends Sequence<C>,C extends Compound>
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