Uses of Interface
org.biojava.bio.dp.ScoreType

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

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)

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)