AbstractMatrixAligner (biojava 5.2.0 API)
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Field Summary
Fields Modifier and Type Field Description protected List<AlignerHelper.Anchor>anchorsprotected intcutsPerSectionprotected GapPenaltygapPenaltyprotected intmaxprotected intminprotected Profile<S,C>profileprotected intscoreprotected int[][][]scoresDynamic programming score matrix The first dimension has the length of the first (query) sequence + 1 The second has the length of the second (target) sequence + 1 The third has length 1 for linear gap penalty and 3 for affine/constant gap (one each for match/substitution, deletion, insertion)
protected longtimeprotected int[]xyMaxEnd position of the aligned sequence in the query and target respectively
protected int[]xyStartStart position of the aligned sequence in the query and target respectively
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Constructor Summary
Constructors Modifier Constructor Description protectedAbstractMatrixAligner()Before running an alignment, data must be sent in via calls to
setGapPenalty(GapPenalty)andsetSubstitutionMatrix(SubstitutionMatrix).protectedAbstractMatrixAligner(GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)Prepares for an alignment.
protectedAbstractMatrixAligner(GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix, boolean local)Prepares for an alignment.
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Method Summary
All Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description protected voidalign()Performs alignment
protected abstract CompoundSet<C>getCompoundSet()protected abstract List<C>getCompoundsOfQuery()protected abstract List<C>getCompoundsOfTarget()longgetComputationTime()Returns the computation time needed for an alignment computed in nanoseconds.
GapPenaltygetGapPenalty()Returns the gap penalties.
doublegetMaxScore()Returns maximum possible score.
doublegetMinScore()Returns minimum possible score.
Profile<S,C>getProfile()Returns the alignment
Profileproduced by this alignment algorithm.doublegetScore()Returns score resulting from algorithm.
int[][][]getScoreMatrix()Returns the entire score matrix built during alignment.
StringgetScoreMatrixAsString()Returns a depiction of the score matrix as a
String.protected abstract int[]getScoreMatrixDimensions()SubstitutionMatrix<C>getSubstitutionMatrix()Returns the substitution matrix.
protected abstract intgetSubstitutionScore(int queryColumn, int targetColumn)protected int[]getSubstitutionScoreVector(int queryColumn)Returns score for the alignment of the query column to all target columns
protected int[]getSubstitutionScoreVector(int queryColumn, AlignerHelper.Subproblem subproblem)Returns score for the alignment of the query column to all target columns
booleanisLocal()Returns whether alignment finds a region of similarity rather than aligning every compound.
protected abstract booleanisReady()booleanisStoringScoreMatrix()Returns choice to cache the score matrix or to save memory by deleting score matrix after alignment.
protected voidreset()Resets output fields; should be overridden to set max and min
voidsetGapPenalty(GapPenalty gapPenalty)Sets the gap penalties.
protected abstract voidsetProfile(List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)voidsetStoringScoreMatrix(boolean storingScoreMatrix)Sets choice to cache the score matrix or to save memory by deleting score matrix after alignment.
voidsetSubstitutionMatrix(SubstitutionMatrix<C> subMatrix)Sets the substitution matrix.
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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.Scorer
getDistance, getDistance, getSimilarity, getSimilarity
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