Methods in org.biojava.bio.dp with parameters of type ScoreType |
static double[][] |
DP.forwardTransitionScores(MarkovModel model,
State[] states,
int[][] transitions,
ScoreType scoreType)
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static double[][] |
DP.backwardTransitionScores(MarkovModel model,
State[] states,
int[][] transitions,
ScoreType scoreType)
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double[][] |
DP.getForwardTransitionScores(ScoreType scoreType)
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double[][] |
DP.getBackwardTransitionScores(ScoreType scoreType)
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abstract double |
DP.forward(SymbolList[] symList,
ScoreType scoreType)
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abstract double |
DP.backward(SymbolList[] symList,
ScoreType scoreType)
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abstract DPMatrix |
DP.forwardMatrix(SymbolList[] symList,
ScoreType scoreType)
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abstract DPMatrix |
DP.backwardMatrix(SymbolList[] symList,
ScoreType scoreType)
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abstract DPMatrix |
DP.forwardMatrix(SymbolList[] symList,
DPMatrix matrix,
ScoreType scoreType)
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abstract DPMatrix |
DP.backwardMatrix(SymbolList[] symList,
DPMatrix matrix,
ScoreType scoreType)
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abstract StatePath |
DP.viterbi(SymbolList[] symList,
ScoreType scoreType)
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DPMatrix |
DP.forwardsBackwards(SymbolList[] symList,
ScoreType scoreType)
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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)
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double |
SingleDP.backward(SymbolList[] seq,
ScoreType scoreType)
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DPMatrix |
SingleDP.forwardMatrix(SymbolList[] seq,
ScoreType scoreType)
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DPMatrix |
SingleDP.backwardMatrix(SymbolList[] seq,
ScoreType scoreType)
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DPMatrix |
SingleDP.forwardMatrix(SymbolList[] seq,
DPMatrix matrix,
ScoreType scoreType)
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DPMatrix |
SingleDP.backwardMatrix(SymbolList[] seq,
DPMatrix matrix,
ScoreType scoreType)
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StatePath |
SingleDP.viterbi(SymbolList[] symList,
ScoreType scoreType)
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Methods in org.biojava.bio.dp.twohead with parameters of type ScoreType |
CellCalculator |
CellCalculatorFactory.forwards(ScoreType scoreType)
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CellCalculator |
CellCalculatorFactory.backwards(ScoreType scoreType)
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CellCalculator |
CellCalculatorFactory.viterbi(ScoreType scoreType,
BackPointer terminal)
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CellCalculator |
DPInterpreter.forwards(ScoreType scoreType)
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CellCalculator |
DPInterpreter.backwards(ScoreType scoreType)
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CellCalculator |
DPInterpreter.viterbi(ScoreType scoreType,
BackPointer terminal)
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double |
PairwiseDP.backward(SymbolList[] seqs,
ScoreType scoreType)
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DPMatrix |
PairwiseDP.backwardMatrix(SymbolList[] seqs,
ScoreType scoreType)
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DPMatrix |
PairwiseDP.backwardMatrix(SymbolList[] seqs,
DPMatrix d,
ScoreType scoreType)
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double |
PairwiseDP.forward(SymbolList[] seqs,
ScoreType scoreType)
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DPMatrix |
PairwiseDP.forwardMatrix(SymbolList[] seqs,
ScoreType scoreType)
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DPMatrix |
PairwiseDP.forwardMatrix(SymbolList[] seqs,
DPMatrix d,
ScoreType scoreType)
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StatePath |
PairwiseDP.viterbi(SymbolList[] seqs,
ScoreType scoreType)
|