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

Packages that use ScoreType

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

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

static ScoreType	ScoreType.PROBABILITY
static ScoreType	ScoreType.ODDS
static ScoreType	ScoreType.NULL_MODEL

Methods in org.biojava.bio.dp with parameters of type 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.
static double[][]	DP.forwardTransitionScores(MarkovModel model, State[] states, int[][] transitions, ScoreType scoreType) Compute the log(score) of all transitions between the specified States.
static double[][]	DP.backwardTransitionScores(MarkovModel model, State[] states, int[][] transitions, ScoreType scoreType)
double[][]	DP.getForwardTransitionScores(ScoreType scoreType)
double[][]	DP.getBackwardTransitionScores(ScoreType scoreType)
abstract double	DP.forward(SymbolList[] symList, ScoreType scoreType)
abstract double	DP.backward(SymbolList[] symList, ScoreType scoreType)
abstract DPMatrix	DP.forwardMatrix(SymbolList[] symList, ScoreType scoreType)
abstract DPMatrix	DP.backwardMatrix(SymbolList[] symList, ScoreType scoreType)
abstract DPMatrix	DP.forwardMatrix(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType)
abstract DPMatrix	DP.backwardMatrix(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType)
abstract StatePath	DP.viterbi(SymbolList[] symList, ScoreType scoreType)
DPMatrix	DP.forwardsBackwards(SymbolList[] symList, ScoreType scoreType)

Constructors in org.biojava.bio.dp with parameters of type ScoreType

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.

WeightMatrixAnnotator(WeightMatrix wm, ScoreType scoreType, double threshold)
Create a new annotator that uses a specific score type.

Uses of ScoreType in org.biojava.bio.dp.onehead

Methods in org.biojava.bio.dp.onehead with parameters of type 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.
double	SingleDP.forward(SymbolList[] seq, ScoreType scoreType)
double	SingleDP.backward(SymbolList[] seq, ScoreType scoreType)
DPMatrix	SingleDP.forwardMatrix(SymbolList[] seq, ScoreType scoreType)
DPMatrix	SingleDP.backwardMatrix(SymbolList[] seq, ScoreType scoreType)
DPMatrix	SingleDP.forwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)
DPMatrix	SingleDP.backwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)
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

double	PairwiseDP.backward(SymbolList[] seqs, ScoreType scoreType)
DPMatrix	PairwiseDP.backwardMatrix(SymbolList[] seqs, ScoreType scoreType)
DPMatrix	PairwiseDP.backwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)
double	PairwiseDP.forward(SymbolList[] seqs, ScoreType scoreType)
DPMatrix	PairwiseDP.forwardMatrix(SymbolList[] seqs, ScoreType scoreType)
DPMatrix	PairwiseDP.forwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)
StatePath	PairwiseDP.viterbi(SymbolList[] seqs, ScoreType scoreType)
CellCalculator	DPInterpreter.forwards(ScoreType scoreType)
CellCalculator	DPInterpreter.backwards(ScoreType scoreType)
CellCalculator	DPInterpreter.viterbi(ScoreType scoreType, BackPointer terminal)
CellCalculator	CellCalculatorFactory.forwards(ScoreType scoreType)
CellCalculator	CellCalculatorFactory.backwards(ScoreType scoreType)
CellCalculator	CellCalculatorFactory.viterbi(ScoreType scoreType, BackPointer terminal)

Constructors in org.biojava.bio.dp.twohead with parameters of type ScoreType

EmissionCache(Alphabet alpha, State[] states, int dsi, ScoreType scoreType)