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