## 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.NULL_MODEL`
`static ScoreType` `ScoreType.ODDS`
`static ScoreType` `ScoreType.PROBABILITY`

Methods in org.biojava.bio.dp with parameters of type ScoreType
`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
`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
`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)`
`protected double` `SingleDP.backward(DPCursor dpCursor, ScoreType scoreType)`
`double` `SingleDP.backward(SymbolList[] seq, ScoreType scoreType)`
`DPMatrix` `SingleDP.backwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)`
`DPMatrix` `SingleDP.backwardMatrix(SymbolList[] seq, ScoreType scoreType)`
`protected void` `SingleDP.forward_initialize(DPCursor dpCursor, ScoreType scoreType)`
`protected double` `SingleDP.forward(DPCursor dpCursor, ScoreType scoreType)`
`double` `SingleDP.forward(SymbolList[] seq, 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
`double` `PairwiseDP.backward(SymbolList[] seqs, ScoreType scoreType)`
`DPMatrix` `PairwiseDP.backwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)`
`DPMatrix` `PairwiseDP.backwardMatrix(SymbolList[] seqs, ScoreType scoreType)`
`CellCalculator` `DPInterpreter.backwards(ScoreType scoreType)`
`CellCalculator` `CellCalculatorFactory.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` `DPInterpreter.forwards(ScoreType scoreType)`
`CellCalculator` `CellCalculatorFactory.forwards(ScoreType scoreType)`
`CellCalculator` `DPInterpreter.viterbi(ScoreType scoreType, BackPointer terminal)`
`CellCalculator` `CellCalculatorFactory.viterbi(ScoreType scoreType, BackPointer terminal)`
`StatePath` `PairwiseDP.viterbi(SymbolList[] seqs, ScoreType scoreType)`

Constructors in org.biojava.bio.dp.twohead with parameters of type ScoreType
`EmissionCache(Alphabet alpha, State[] states, int dsi, ScoreType scoreType)`