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Packages that use IllegalTransitionException | |
org.biojava.bio.dp | HMM and Dynamic Programming Algorithms. |
org.biojava.bio.dp.onehead | |
org.biojava.bio.dp.twohead | |
org.biojava.bio.program.hmmer | Tools for working with profile Hidden Markov Models from the HMMer package. |
Uses of IllegalTransitionException in org.biojava.bio.dp |
Methods in org.biojava.bio.dp that throw IllegalTransitionException | |
protected double |
BaumWelchTrainer.singleSequenceIteration(ModelTrainer trainer,
SymbolList symList)
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protected abstract double |
AbstractTrainer.singleSequenceIteration(ModelTrainer trainer,
SymbolList symList)
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protected void |
ProfileHMM.connectModel()
This is called by constructor in setting up the allowed transitions in the model |
protected double |
BaumWelchSampler.singleSequenceIteration(ModelTrainer trainer,
SymbolList symList)
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void |
SimpleMarkovModel.removeState(State toGo)
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static State[] |
DP.stateList(MarkovModel mm)
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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)
|
void |
MarkovModel.removeState(State toGo)
Remove a state from the model. |
void |
TransitionTrainer.addCount(State from,
State to,
double count)
Add 'count' to the transition from->to. |
Constructors in org.biojava.bio.dp that throw IllegalTransitionException | |
ProfileHMM(Alphabet alpha,
int columns,
DistributionFactory matchFactory,
DistributionFactory insertFactory)
Deprecated. |
|
ProfileHMM(Alphabet alpha,
int columns,
DistributionFactory matchFactory,
DistributionFactory insertFactory,
java.lang.String name)
Create a new ProfileHMM. |
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DP(MarkovModel model)
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Uses of IllegalTransitionException in org.biojava.bio.dp.onehead |
Constructors in org.biojava.bio.dp.onehead that throw IllegalTransitionException | |
SingleDP(MarkovModel model)
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Uses of IllegalTransitionException in org.biojava.bio.dp.twohead |
Methods in org.biojava.bio.dp.twohead that throw IllegalTransitionException | |
CellCalculator |
DPInterpreter.forwards(ScoreType scoreType)
|
CellCalculator |
DPInterpreter.backwards(ScoreType scoreType)
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CellCalculator |
DPInterpreter.viterbi(ScoreType scoreType,
BackPointer terminal)
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void |
CellCalculator.initialize(Cell[][] cells)
Initialize the cell at [0][0] to the recursion initial parameters. |
void |
CellCalculator.calcCell(Cell[][] cells)
Calculate the 'scores' array in the cell at cells[0][0]. |
CellCalculator |
CellCalculatorFactory.forwards(ScoreType scoreType)
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CellCalculator |
CellCalculatorFactory.backwards(ScoreType scoreType)
|
CellCalculator |
CellCalculatorFactory.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)
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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 that throw IllegalTransitionException | |
PairwiseDP(MarkovModel mm,
CellCalculatorFactoryMaker ccfm)
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Uses of IllegalTransitionException in org.biojava.bio.program.hmmer |
Methods in org.biojava.bio.program.hmmer that throw IllegalTransitionException | |
protected void |
HmmerProfileHMM.connectModel()
This is called by constructor in setting up the allowed transitions in the model |
Constructors in org.biojava.bio.program.hmmer that throw IllegalTransitionException | |
HmmerProfileHMM(Alphabet alpha,
int columns,
DistributionFactory matchFactory,
DistributionFactory insertFactory,
java.lang.String name)
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