Package org.biojava.bio.dist
Class SimpleDistribution.Trainer
java.lang.Object
org.biojava.bio.dist.SimpleDistribution.Trainer
- All Implemented Interfaces:
DistributionTrainer
- Enclosing class:
SimpleDistribution
A simple implementation of a trainer for this class.
- Since:
- 1.0
- Author:
- Matthew Pocock
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
addCount
(DistributionTrainerContext dtc, AtomicSymbol sym, double times) Registers that sym was counted in this state.void
Clears all of the counts to zero.double
getCount
(DistributionTrainerContext dtc, AtomicSymbol sym) Get the current count for this state.void
train
(DistributionTrainerContext dtc, double weight) Trains the Distribution, given a null model.protected void
trainImpl
(DistributionTrainerContext dtc, double weight)
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Constructor Details
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Trainer
public Trainer()Create a new trainer.
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Method Details
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addCount
public void addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times) throws IllegalSymbolException Description copied from interface:DistributionTrainer
Registers that sym was counted in this state.
This method may be called multiple times with the same symbol. In this case, the times should be summed.
- Specified by:
addCount
in interfaceDistributionTrainer
- Parameters:
dtc
- the DistributionTrainerContext within which the count was addedsym
- the Symbol seentimes
- the number of times to add- Throws:
IllegalSymbolException
- if sym is not recognised
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getCount
public double getCount(DistributionTrainerContext dtc, AtomicSymbol sym) throws IllegalSymbolException Description copied from interface:DistributionTrainer
Get the current count for this state.
This method may be called multiple times with the same symbol. Each time it should return the agregate of the counts added with addCount since the last invocation of clearCounts.
- Specified by:
getCount
in interfaceDistributionTrainer
- Parameters:
dtc
- the DistributionTrainerContext within which the count was addedsym
- the Symbol seen- Returns:
- the agregate of the counts
- Throws:
IllegalSymbolException
- if sym is not recognised
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clearCounts
Description copied from interface:DistributionTrainer
Clears all of the counts to zero.- Specified by:
clearCounts
in interfaceDistributionTrainer
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train
Description copied from interface:DistributionTrainer
Trains the Distribution, given a null model.
This will use the information collected with multiple addCount calls, and the null model to generate the new weights.
This method should not modify the underlying counts.
- Specified by:
train
in interfaceDistributionTrainer
- Parameters:
dtc
- the context to useweight
- how many lots of the null model to add- Throws:
ChangeVetoException
- if the distribution could not have its weights modified
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trainImpl
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