org.biojava.bio.dist
Class SimpleDistributionTrainerContext

java.lang.Object
  |
  +--org.biojava.bio.dist.SimpleDistributionTrainerContext
Direct Known Subclasses:
SimpleModelTrainer

public class SimpleDistributionTrainerContext
extends java.lang.Object
implements DistributionTrainerContext, java.io.Serializable

A no-frills implementation of DistributionTrainerContext.

Author:
Matthew Pocock
See Also:
Serialized Form

Constructor Summary
SimpleDistributionTrainerContext()
           
 
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.
 Distribution getNullModel()
          Retrieve the background distribution
 double getNullModelWeight()
          Retrieve the weight of the background distribution
 void registerDistribution(Distribution dist)
          Register a distribution object
 void registerDistributionTrainer(Distribution dist, DistributionTrainer trainer)
          Register a distribution and an associated distributiontrainer object
 void setNullModel(Distribution nullModel)
          Assign a background distribution
 void setNullModelWeight(double nullModelWeight)
          Assign a weight to the background distribution
 void trainDistributions()
          Trains the Distribution, given a null model.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SimpleDistributionTrainerContext

public SimpleDistributionTrainerContext()
Method Detail

getNullModel

public Distribution getNullModel()
Retrieve the background distribution

setNullModel

public void setNullModel(Distribution nullModel)
Assign a background distribution
Parameters:
nullModel - the background distribution to assign

getNullModelWeight

public double getNullModelWeight()
Retrieve the weight of the background distribution

setNullModelWeight

public void setNullModelWeight(double nullModelWeight)
Assign a weight to the background distribution
Parameters:
nullModelWeight - the weight of the null model to assign.

registerDistribution

public void registerDistribution(Distribution dist)
Description copied from interface: DistributionTrainerContext
Register a distribution object
Specified by:
registerDistribution in interface DistributionTrainerContext

registerDistributionTrainer

public void registerDistributionTrainer(Distribution dist,
                                        DistributionTrainer trainer)
Description copied from interface: DistributionTrainerContext
Register a distribution and an associated distributiontrainer object
Specified by:
registerDistributionTrainer in interface DistributionTrainerContext
Tags copied from interface: DistributionTrainerContext
Parameters:
dist - the distribution to be registered.
trainer - the distribution's trainer object to be registered.

getDistributionTrainer

public DistributionTrainer getDistributionTrainer(Distribution dist)
Description copied from interface: DistributionTrainerContext
Return the Distribution trainer object from the current context.
Specified by:
getDistributionTrainer in interface DistributionTrainerContext
Tags copied from interface: DistributionTrainerContext
Parameters:
dist - the Distribution whose trainer is required.

addCount

public void addCount(Distribution dist,
                     Symbol sym,
                     double times)
              throws IllegalSymbolException
Description copied from interface: DistributionTrainerContext
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 interface DistributionTrainerContext
Tags copied from interface: DistributionTrainerContext
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
Description copied from interface: DistributionTrainerContext
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.

Specified by:
trainDistributions in interface DistributionTrainerContext
Tags copied from interface: DistributionTrainerContext
Parameters:
nullModel - the null model Distribution
weight - how many lots of the null model to add

clearDistributionCounts

public void clearDistributionCounts()
Description copied from interface: DistributionTrainerContext
Clears all of the counts to zero.
Specified by:
clearDistributionCounts in interface DistributionTrainerContext