Uses of Interface
org.biojava.bio.dp.ScoreType
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Packages that use ScoreType Package Description org.biojava.bio.dp HMM and Dynamic Programming Algorithms.org.biojava.bio.dp.onehead org.biojava.bio.dp.twohead -
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Uses of ScoreType in org.biojava.bio.dp
Classes in org.biojava.bio.dp that implement ScoreType Modifier and Type Class Description static class
ScoreType.NullModel
In this class, calculateScore returns the probability of a Symbol being emitted by the null model.static class
ScoreType.Odds
In this class, calculateScore returns the odds ratio of a symbol being emitted.static class
ScoreType.Probability
In this class, calculateScore returns the probability of a Symbol being emitted.Fields in org.biojava.bio.dp declared as ScoreType Modifier and Type Field Description static ScoreType
ScoreType. NULL_MODEL
static ScoreType
ScoreType. ODDS
static ScoreType
ScoreType. PROBABILITY
Methods in org.biojava.bio.dp with parameters of type ScoreType Modifier and Type Method Description abstract 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)
DPMatrix
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 ScoreType Constructor Description WeightMatrixAnnotator(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 ScoreType Modifier and Type Method Description protected double
SingleDP. backward(DPCursor dpCursor, ScoreType scoreType)
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)
DPMatrix
SingleDP. backwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)
DPMatrix
SingleDP. backwardMatrix(SymbolList[] seq, ScoreType scoreType)
protected double
SingleDP. forward(DPCursor dpCursor, ScoreType scoreType)
double
SingleDP. forward(SymbolList[] seq, ScoreType scoreType)
protected void
SingleDP. forward_initialize(DPCursor dpCursor, ScoreType scoreType)
DPMatrix
SingleDP. forwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)
DPMatrix
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.StatePath
SingleDP. viterbi(SymbolList[] symList, ScoreType scoreType)
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Uses of ScoreType in org.biojava.bio.dp.twohead
Methods in org.biojava.bio.dp.twohead with parameters of type ScoreType Modifier and Type Method Description double
PairwiseDP. backward(SymbolList[] seqs, ScoreType scoreType)
DPMatrix
PairwiseDP. backwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)
DPMatrix
PairwiseDP. backwardMatrix(SymbolList[] seqs, ScoreType scoreType)
CellCalculator
CellCalculatorFactory. backwards(ScoreType scoreType)
CellCalculator
DPInterpreter. backwards(ScoreType scoreType)
double
PairwiseDP. forward(SymbolList[] seqs, ScoreType scoreType)
DPMatrix
PairwiseDP. forwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)
DPMatrix
PairwiseDP. forwardMatrix(SymbolList[] seqs, ScoreType scoreType)
CellCalculator
CellCalculatorFactory. forwards(ScoreType scoreType)
CellCalculator
DPInterpreter. forwards(ScoreType scoreType)
CellCalculator
CellCalculatorFactory. viterbi(ScoreType scoreType, BackPointer terminal)
CellCalculator
DPInterpreter. viterbi(ScoreType scoreType, BackPointer terminal)
StatePath
PairwiseDP. viterbi(SymbolList[] seqs, ScoreType scoreType)
Constructors in org.biojava.bio.dp.twohead with parameters of type ScoreType Constructor Description EmissionCache(Alphabet alpha, State[] states, int dsi, ScoreType scoreType)
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