Uses of Interface
org.biojava.bio.dp.ScoreType
Packages that use ScoreType
Package
Description
HMM and Dynamic Programming Algorithms.
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Uses of ScoreType in org.biojava.bio.dp
Classes in org.biojava.bio.dp that implement ScoreTypeModifier and TypeClassDescriptionstatic classIn this class, calculateScore returns the probability of a Symbol being emitted by the null model.static classIn this class, calculateScore returns the odds ratio of a symbol being emitted.static classIn this class, calculateScore returns the probability of a Symbol being emitted.Fields in org.biojava.bio.dp declared as ScoreTypeModifier and TypeFieldDescriptionstatic final ScoreTypeScoreType.NULL_MODELstatic final ScoreTypeScoreType.ODDSstatic final ScoreTypeScoreType.PROBABILITYMethods in org.biojava.bio.dp with parameters of type ScoreTypeModifier and TypeMethodDescriptionabstract doubleDP.backward(SymbolList[] symList, ScoreType scoreType) abstract DPMatrixDP.backwardMatrix(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType) abstract DPMatrixDP.backwardMatrix(SymbolList[] symList, ScoreType scoreType) static double[][]DP.backwardTransitionScores(MarkovModel model, State[] states, int[][] transitions, ScoreType scoreType) abstract doubleDP.forward(SymbolList[] symList, ScoreType scoreType) abstract DPMatrixDP.forwardMatrix(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType) abstract DPMatrixDP.forwardMatrix(SymbolList[] symList, ScoreType scoreType) DP.forwardsBackwards(SymbolList[] symList, ScoreType scoreType) static double[][]DP.forwardTransitionScores(MarkovModel model, State[] states, int[][] transitions, ScoreType scoreType) Compute the log(score) of all transitions between the specified States.double[][]DP.getBackwardTransitionScores(ScoreType scoreType) double[][]DP.getForwardTransitionScores(ScoreType scoreType) static doubleDP.scoreWeightMatrix(WeightMatrix matrix, SymbolList symList, ScoreType scoreType, int start) Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix using a particular ScoreType.protected doubleBaumWelchSampler.singleSequenceIteration(ModelTrainer trainer, SymbolList symList, ScoreType scoreType) abstract StatePathDP.viterbi(SymbolList[] symList, ScoreType scoreType) Constructors in org.biojava.bio.dp with parameters of type ScoreTypeModifierConstructorDescriptionWeightMatrixAnnotator(WeightMatrix wm, ScoreType scoreType, double threshold) Create a new annotator that uses a specific score type.WeightMatrixAnnotator(WeightMatrix wm, ScoreType scoreType, double threshold, String wmID) Create a new annotator that uses the PROBABILITY score type and an ID for the weight matrix. -
Uses of ScoreType in org.biojava.bio.dp.onehead
Methods in org.biojava.bio.dp.onehead with parameters of type ScoreTypeModifier and TypeMethodDescriptionprotected doubledoubleSingleDP.backward(SymbolList[] seq, ScoreType scoreType) protected voidSingleDP.backward_initialize(DPCursor dpCursor, ScoreType scoreType) protected voidSingleDP.backward_recurse(DPCursor dpCursor, ScoreType scoreType) protected doubleSingleDP.backward_termination(DPCursor dpCursor, ScoreType scoreType) SingleDP.backwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType) SingleDP.backwardMatrix(SymbolList[] seq, ScoreType scoreType) protected doubledoubleSingleDP.forward(SymbolList[] seq, ScoreType scoreType) protected voidSingleDP.forward_initialize(DPCursor dpCursor, ScoreType scoreType) SingleDP.forwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType) SingleDP.forwardMatrix(SymbolList[] seq, ScoreType scoreType) double[]SingleDP.getEmission(Symbol sym, ScoreType scoreType) This method is public for the benefit of training algorithms, and in the future we should look at a better way of exposing the emissions cache.SingleDP.viterbi(SymbolList[] symList, ScoreType scoreType) -
Uses of ScoreType in org.biojava.bio.dp.twohead
Methods in org.biojava.bio.dp.twohead with parameters of type ScoreTypeModifier and TypeMethodDescriptiondoublePairwiseDP.backward(SymbolList[] seqs, ScoreType scoreType) PairwiseDP.backwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType) PairwiseDP.backwardMatrix(SymbolList[] seqs, ScoreType scoreType) doublePairwiseDP.forward(SymbolList[] seqs, ScoreType scoreType) PairwiseDP.forwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType) PairwiseDP.forwardMatrix(SymbolList[] seqs, ScoreType scoreType) CellCalculatorFactory.viterbi(ScoreType scoreType, BackPointer terminal) DPInterpreter.viterbi(ScoreType scoreType, BackPointer terminal) PairwiseDP.viterbi(SymbolList[] seqs, ScoreType scoreType) Constructors in org.biojava.bio.dp.twohead with parameters of type ScoreTypeModifierConstructorDescriptionEmissionCache(Alphabet alpha, State[] states, int dsi, ScoreType scoreType)