de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training
Class BaumWelchParameterSet

java.lang.Object
  extended by de.jstacs.parameters.ParameterSet
      extended by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.HMMTrainingParameterSet
          extended by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.MaxHMMTrainingParameterSet
              extended by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.MultiThreadedTrainingParameterSet
                  extended by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.BaumWelchParameterSet
All Implemented Interfaces:
GalaxyConvertible, Storable, Cloneable

public class BaumWelchParameterSet
extends MultiThreadedTrainingParameterSet

This class implements an HMMTrainingParameterSet for the Baum-Welch training of an AbstractHMM.

Author:
Jens Keilwagen

Nested Class Summary
 
Nested classes/interfaces inherited from class de.jstacs.parameters.ParameterSet
ParameterSet.ParameterList
 
Field Summary
 
Fields inherited from class de.jstacs.parameters.ParameterSet
errorMessage, parameters, parent
 
Constructor Summary
BaumWelchParameterSet()
          This is the empty constructor that can be used to fill the parameters after creation.
BaumWelchParameterSet(int starts, AbstractTerminationCondition tc, int threads)
          This constructor can be used to create an instance with specified parameters.
BaumWelchParameterSet(StringBuffer xml)
          The standard constructor for the interface Storable.
 
Method Summary
 boolean hasDefaultOrIsSet()
          Returns true if all parameters in this ParameterSet are either set by the user or have default values.
 
Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.MultiThreadedTrainingParameterSet
getNumberOfThreads
 
Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.MaxHMMTrainingParameterSet
getTerminationCondition
 
Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.HMMTrainingParameterSet
getNumberOfStarts
 
Methods inherited from class de.jstacs.parameters.ParameterSet
clone, fromGalaxy, fromXML, getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getNumberOfParameters, getParameterAt, getParameterForName, getParent, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, reset, setParent, toGalaxy, toXML
 
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

BaumWelchParameterSet

public BaumWelchParameterSet()
This is the empty constructor that can be used to fill the parameters after creation.


BaumWelchParameterSet

public BaumWelchParameterSet(int starts,
                             AbstractTerminationCondition tc,
                             int threads)
                      throws Exception
This constructor can be used to create an instance with specified parameters.

Parameters:
starts - the number of different starts
tc - the termination condition for stopping the algorithm
threads - the number of threads that should be used during optimization
Throws:
Exception - if the BaumWelchParameterSet could not be created

BaumWelchParameterSet

public BaumWelchParameterSet(StringBuffer xml)
                      throws NonParsableException
The standard constructor for the interface Storable. Constructs a BaumWelchParameterSet out of an XML representation.

Parameters:
xml - the XML representation as StringBuffer
Throws:
NonParsableException - if the BaumWelchParameterSet could not be reconstructed out of the StringBuffer xml
Method Detail

hasDefaultOrIsSet

public boolean hasDefaultOrIsSet()
Description copied from class: ParameterSet
Returns true if all parameters in this ParameterSet are either set by the user or have default values. If any additional constraints are required on your parameters you should either specify some ParameterValidator on these parameters or implement these constraints by overriding this method in your implementation of ParameterSet. It is recommended to specify a useful remark which constraint failed in the member-variable errorMessage, which will be displayed to the user. In the overriding method super.ParameterSet.hasDefaultOrIsSet() should be called prior to checking specific constraints.

Overrides:
hasDefaultOrIsSet in class ParameterSet
Returns:
true if all parameters have some allowed value set, false otherwise