de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters
Class HomMMParameterSet

java.lang.Object
  de.jstacs.parameters.ParameterSet
      de.jstacs.parameters.InstanceParameterSet<T>
          de.jstacs.parameters.SequenceScoringParameterSet<T>
              de.jstacs.sequenceScores.statisticalModels.trainable.discrete.DGTrainSMParameterSet
                  de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters.HomogeneousTrainSMParameterSet
                      de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters.HomMMParameterSet

All Implemented Interfaces:

GalaxyConvertible, Storable, Cloneable

public class HomMMParameterSet
extends HomogeneousTrainSMParameterSet

This class implements a container for all parameters of a homogeneous Markov model.

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.SequenceScoringParameterSet

alphabet, length

Fields inherited from class de.jstacs.parameters.ParameterSet

errorMessage, parameters, parent

Constructor Summary

HomMMParameterSet()
An empty constructor.

HomMMParameterSet(AlphabetContainer alphabet, double ess, String description, byte order)
Creates a new HomMMParameterSet with AlphabetContainer, ess (equivalent sample size), description and order of the homogeneous Markov model.

HomMMParameterSet(StringBuffer s)
The standard constructor for the interface Storable.

Method Summary

String

getInstanceComment() Returns a comment (a textual description) of the class that can be constructed using this ParameterSet.

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters.HomogeneousTrainSMParameterSet

hasDefaultOrIsSet

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.DGTrainSMParameterSet

clone, getInstanceName, setEss

Methods inherited from class de.jstacs.parameters.SequenceScoringParameterSet

equals, fromXML, getAlphabetContainer, getLength, getNumberOfParameters, getParameterAt, reset, toXML

Methods inherited from class de.jstacs.parameters.InstanceParameterSet

getInstance, getInstanceClass

Methods inherited from class de.jstacs.parameters.ParameterSet

fromGalaxy, getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getParameterForName, getParent, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, setParent, toGalaxy

Methods inherited from class java.lang.Object

finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

HomMMParameterSet

public HomMMParameterSet(StringBuffer s)
                  throws NonParsableException

The standard constructor for the interface Storable. Creates a new HomMMParameterSet out of its XML representation.

Parameters:

s - the XML representation as StringBuffer

Throws:

NonParsableException - if the HomMMParameterSet could not be reconstructed out of the XML representation (the StringBuffer could not be parsed)

See Also:

Storable, HomogeneousTrainSMParameterSet.HomogeneousTrainSMParameterSet(StringBuffer)

HomMMParameterSet

public HomMMParameterSet()

An empty constructor. Creates a new HomMMParameterSet.

HomMMParameterSet

public HomMMParameterSet(AlphabetContainer alphabet,
                         double ess,
                         String description,
                         byte order)
                  throws Exception

Creates a new HomMMParameterSet with AlphabetContainer, ess (equivalent sample size), description and order of the homogeneous Markov model.

Parameters:

alphabet - the AlphabetContainer

ess - the ess (equivalent sample size)

description - the description

order - the order of the Markov model

Throws:

Exception - if something went wrong

See Also:

HomogeneousTrainSMParameterSet.HomogeneousTrainSMParameterSet(Class, AlphabetContainer, double, String, byte)

Method Detail

getInstanceComment

public String getInstanceComment()

Description copied from class: InstanceParameterSet

Returns a comment (a textual description) of the class that can be constructed using this ParameterSet.

Specified by:

getInstanceComment in class InstanceParameterSet

Returns:

the comment of the class