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.forwardTransitionScores(MarkovModel model, State[] states, int[][] transitions, ScoreType scoreType)
           
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)
           
 

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
 CellCalculator CellCalculatorFactory.forwards(ScoreType scoreType)
           
 CellCalculator CellCalculatorFactory.backwards(ScoreType scoreType)
           
 CellCalculator CellCalculatorFactory.viterbi(ScoreType scoreType, BackPointer terminal)
           
 CellCalculator DPInterpreter.forwards(ScoreType scoreType)
           
 CellCalculator DPInterpreter.backwards(ScoreType scoreType)
           
 CellCalculator DPInterpreter.viterbi(ScoreType scoreType, BackPointer terminal)
           
 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)
           
 

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