java.lang.Object

org.biojava.bio.dist.SimpleDistributionTrainerContext

All Implemented Interfaces:: Serializable, DistributionTrainerContext

Direct Known Subclasses:: SimpleModelTrainer

public class SimpleDistributionTrainerContext extends Object implements DistributionTrainerContext, Serializable

A no-frills implementation of DistributionTrainerContext.

Since:

1.0

Author:

Matthew Pocock

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor

Description

SimpleDistributionTrainerContext()

Create a new context with no initial distributions or trainers.
Method Summary

Modifier and Type

Method

Description

void

addCount(Distribution dist, Symbol sym, double times)

Registers that sym was counted in this state.

void

clearCounts()

Clears all of the counts to zero.

double

getCount(Distribution dist, Symbol sym)

Return the number of counts of a particular symbol which will be used to train the specified distribution.

double

getNullModelWeight()

Return the number of pseudocounts added to the distribution when training.

DistributionTrainer

getTrainer(Distribution dist)

Return the Distribution trainer object from the current context.

void

registerDistribution(Distribution dist)

Register a distribution object with this context.

void

registerTrainer(Distribution dist, DistributionTrainer trainer)

Register a Distribution and an associated DistributionTrainer object.

void

setNullModelWeight(double nullModelWeight)

Set the number of pseudocounts to add when training the distribution.

void

train()

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 Details
- SimpleDistributionTrainerContext
  
  public SimpleDistributionTrainerContext()
  
  Create a new context with no initial distributions or trainers.
Method Details
- getNullModelWeight
  
  public double getNullModelWeight()
  
  Description copied from interface: DistributionTrainerContext
  
  Return the number of pseudocounts added to the distribution when training.
  
  Specified by:
  
  getNullModelWeight in interface DistributionTrainerContext
  
  Returns:
  
  the null model weight
- setNullModelWeight
  
  public void setNullModelWeight(double nullModelWeight)
  
  Description copied from interface: DistributionTrainerContext
  
  Set the number of pseudocounts to add when training the distribution. These counts are added in proportion to the null model of the distribution being trained.
  
  Specified by:
  
  setNullModelWeight in interface DistributionTrainerContext
  
  Parameters:
  
  nullModelWeight - the new null model weight
- registerDistribution
  
  public void registerDistribution(Distribution dist)
  
  Description copied from interface: DistributionTrainerContext
  
  Register a distribution object with this context.
  
  This method is a request to the context to register dist. If dist is already registered then this method should do nothing. If it is not registered, then it should invoke dist.registerWithTrainer
  
  Specified by:
  
  registerDistribution in interface DistributionTrainerContext
  
  Parameters:
  
  dist - the Distribution to register
- registerTrainer
  
  public void registerTrainer(Distribution dist, DistributionTrainer trainer)
  
  Description copied from interface: DistributionTrainerContext
  
  Register a Distribution and an associated DistributionTrainer object.
  
  In the registerWithTrainer method of a Distribution, it should associate itself with a trainer using this method.
  
  Specified by:
  
  registerTrainer in interface DistributionTrainerContext
  
  Parameters:
  
  dist - the distribution to be registered.
  
  trainer - the distribution's trainer object to be registered.
- getTrainer
  
  public DistributionTrainer getTrainer(Distribution dist)
  
  Description copied from interface: DistributionTrainerContext
  
  Return the Distribution trainer object from the current context.
  
  Specified by:
  
  getTrainer in interface DistributionTrainerContext
  
  Parameters:
  
  dist - the Distribution whose trainer is required
  
  Returns:
  
  the DistributionTrainer for the distribution
- 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
  
  Parameters:
  
  dist - the Distribution that the symbol was associated with
  
  sym - the Symbol seen
  
  times - the number of times to add
  
  Throws:
  
  IllegalSymbolException - if sym is not recognised by dist
- getCount
  
  public double getCount(Distribution dist, Symbol sym) throws IllegalSymbolException
  
  Description copied from interface: DistributionTrainerContext
  
  Return the number of counts of a particular symbol which will be used to train the specified distribution.
  
  Specified by:
  
  getCount in interface DistributionTrainerContext
  
  Parameters:
  
  dist - the Distribution to return counts for
  
  sym - the symbol to get the count for
  
  Returns:
  
  the number of counts
  
  Throws:
  
  IllegalSymbolException - if the symbol is not accepted by the distribution
- train
  
  public void train() throws ChangeVetoException
  
  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:
  
  train in interface DistributionTrainerContext
  
  Throws:
  
  ChangeVetoException - if any of the distributions can't be trained
- clearCounts
  
  public void clearCounts()
  
  Description copied from interface: DistributionTrainerContext
  
  Clears all of the counts to zero.
  
  Specified by:
  
  clearCounts in interface DistributionTrainerContext

Class SimpleDistributionTrainerContext

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

SimpleDistributionTrainerContext

Method Details

getNullModelWeight

setNullModelWeight

registerDistribution

registerTrainer

getTrainer

addCount

getCount

train

clearCounts