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 class
In this class, calculateScore returns the probability of a Symbol being emitted by the null model.static class
In this class, calculateScore returns the odds ratio of a symbol being emitted.static class
In this class, calculateScore returns the probability of a Symbol being emitted.Fields in org.biojava.bio.dp declared as ScoreTypeModifier and TypeFieldDescriptionstatic final ScoreType
ScoreType.NULL_MODEL
static final ScoreType
ScoreType.ODDS
static final ScoreType
ScoreType.PROBABILITY
Methods in org.biojava.bio.dp with parameters of type ScoreTypeModifier and TypeMethodDescriptionabstract double
DP.backward
(SymbolList[] symList, ScoreType scoreType) abstract DPMatrix
DP.backwardMatrix
(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType) abstract DPMatrix
DP.backwardMatrix
(SymbolList[] symList, ScoreType scoreType) static double[][]
DP.backwardTransitionScores
(MarkovModel model, State[] states, int[][] transitions, ScoreType scoreType) abstract double
DP.forward
(SymbolList[] symList, ScoreType scoreType) abstract DPMatrix
DP.forwardMatrix
(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType) abstract DPMatrix
DP.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 double
DP.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 double
BaumWelchSampler.singleSequenceIteration
(ModelTrainer trainer, SymbolList symList, ScoreType scoreType) abstract StatePath
DP.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 double
double
SingleDP.backward
(SymbolList[] seq, ScoreType scoreType) protected void
SingleDP.backward_initialize
(DPCursor dpCursor, ScoreType scoreType) protected void
SingleDP.backward_recurse
(DPCursor dpCursor, ScoreType scoreType) protected double
SingleDP.backward_termination
(DPCursor dpCursor, ScoreType scoreType) SingleDP.backwardMatrix
(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType) SingleDP.backwardMatrix
(SymbolList[] seq, ScoreType scoreType) protected double
double
SingleDP.forward
(SymbolList[] seq, ScoreType scoreType) protected void
SingleDP.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 TypeMethodDescriptiondouble
PairwiseDP.backward
(SymbolList[] seqs, ScoreType scoreType) PairwiseDP.backwardMatrix
(SymbolList[] seqs, DPMatrix d, ScoreType scoreType) PairwiseDP.backwardMatrix
(SymbolList[] seqs, ScoreType scoreType) double
PairwiseDP.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)