Package org.biojava.bio.dist

Interface DistributionTrainer

All Known Implementing Classes:

IgnoreCountsTrainer, SimpleDistribution.Trainer, SimpleDistributionTrainer

public interface DistributionTrainer

An object that can be used to train a distribution up.

This lets the distribution implementation handle counts or distributions in the best way possible.

Since:

1.0

Author:

Matthew Pocock

Method Summary

Modifier and Type	Method	Description
void	addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times)	Registers that sym was counted in this state.
void	clearCounts(DistributionTrainerContext dtc)	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.

Method Detail

addCount

void addCount(DistributionTrainerContext dtc,
              AtomicSymbol sym,
              double times)
       throws IllegalSymbolException

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.

Parameters:

dtc - the DistributionTrainerContext within which the count was added

sym - the Symbol seen

times - the number of times to add

Throws:

IllegalSymbolException - if sym is not recognised

getCount

double getCount(DistributionTrainerContext dtc,
                AtomicSymbol sym)
         throws IllegalSymbolException

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.

Parameters:

dtc - the DistributionTrainerContext within which the count was added

sym - the Symbol seen

Returns:

the agregate of the counts

Throws:

IllegalSymbolException - if sym is not recognised

train

void train(DistributionTrainerContext dtc,
           double weight)
    throws ChangeVetoException

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.

Parameters:

dtc - the context to use

weight - how many lots of the null model to add

Throws:

ChangeVetoException - if the distribution could not have its weights modified

clearCounts

void clearCounts(DistributionTrainerContext dtc)

Clears all of the counts to zero.