Package org.biojava.bio.dp
Class BaumWelchSampler
java.lang.Object
org.biojava.bio.dp.AbstractTrainer
org.biojava.bio.dp.BaumWelchSampler
- All Implemented Interfaces:
Serializable
,TrainingAlgorithm
Train a hidden markov model using a sampling algorithm.
Note: this class currently only works for one-head models.
- Since:
- 1.0
- Author:
- Matthew Pocock, Richard Holland
- See Also:
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected double
singleSequenceIteration
(ModelTrainer trainer, SymbolList symList) protected double
singleSequenceIteration
(ModelTrainer trainer, SymbolList symList, ScoreType scoreType) Methods inherited from class org.biojava.bio.dp.AbstractTrainer
getCurrentScore, getCycle, getDP, getLastScore, train
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Constructor Details
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BaumWelchSampler
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Method Details
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singleSequenceIteration
protected double singleSequenceIteration(ModelTrainer trainer, SymbolList symList) throws IllegalSymbolException, IllegalTransitionException, IllegalAlphabetException - Specified by:
singleSequenceIteration
in classAbstractTrainer
- Throws:
IllegalSymbolException
IllegalTransitionException
IllegalAlphabetException
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singleSequenceIteration
protected double singleSequenceIteration(ModelTrainer trainer, SymbolList symList, ScoreType scoreType) throws IllegalSymbolException, IllegalTransitionException, IllegalAlphabetException
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