org.biojava.bio.dist
Interface DistributionTrainerContext

All Known Subinterfaces:
ModelTrainer
All Known Implementing Classes:
SimpleDistributionTrainerContext

public interface DistributionTrainerContext

A context within a group of DistributionTrainers can be trained together.

Author:
Matthew Pocock

Method Summary
 void addCount(Distribution dist, Symbol sym, double times)
          Registers that sym was counted in this state.
 void clearDistributionCounts()
          Clears all of the counts to zero.
 DistributionTrainer getDistributionTrainer(Distribution dist)
          Return the Distribution trainer object from the current context.
 void registerDistribution(Distribution dist)
          Register a distribution object
 void registerDistributionTrainer(Distribution dist, DistributionTrainer trainer)
          Register a distribution and an associated distributiontrainer object
 void trainDistributions()
          Trains the Distribution, given a null model.
 

Method Detail

registerDistribution

public void registerDistribution(Distribution dist)
Register a distribution object

registerDistributionTrainer

public void registerDistributionTrainer(Distribution dist,
                                        DistributionTrainer trainer)
Register a distribution and an associated distributiontrainer object
Parameters:
dist - the distribution to be registered.
trainer - the distribution's trainer object to be registered.

getDistributionTrainer

public DistributionTrainer getDistributionTrainer(Distribution dist)
Return the Distribution trainer object from the current context.
Parameters:
dist - the Distribution whose trainer is required.

addCount

public void addCount(Distribution dist,
                     Symbol 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:
dist - the Distribution that the symbol was associated with
sym - the Symbol seen
times - the number of times to add

trainDistributions

public void trainDistributions()
                        throws IllegalSymbolException
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.

Parameters:
nullModel - the null model Distribution
weight - how many lots of the null model to add

clearDistributionCounts

public void clearDistributionCounts()
Clears all of the counts to zero.