de.jstacs.models.discrete.homogeneous.parameters
Class HomMMParameterSet

java.lang.Object
  de.jstacs.parameters.ParameterSet
      de.jstacs.parameters.InstanceParameterSet
          de.jstacs.parameters.SequenceScoringParameterSet
              de.jstacs.models.discrete.DGMParameterSet
                  de.jstacs.models.discrete.homogeneous.parameters.HomogeneousModelParameterSet
                      de.jstacs.models.discrete.homogeneous.parameters.HomMMParameterSet

All Implemented Interfaces:

RangeIterator, Storable, Cloneable

public class HomMMParameterSet
extends HomogeneousModelParameterSet

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, ranged

Constructor Summary

HomMMParameterSet()
An empty constructor.

HomMMParameterSet(AlphabetContainer alphabet, double ess, String description, byte order)
The constructor that sets already the ALphabetContainer, ESS, description and order.

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

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.models.discrete.homogeneous.parameters.HomogeneousModelParameterSet

hasDefaultOrIsSet, loadParameters

Methods inherited from class de.jstacs.models.discrete.DGMParameterSet

clone, getInstanceName, setEss

Methods inherited from class de.jstacs.parameters.SequenceScoringParameterSet

equals, fromXML, getAlphabet, getIndex, getLength, getNumberOfParameters, getParameterAt, replaceParametersWithRangedInstance, reset, toXML

Methods inherited from class de.jstacs.parameters.InstanceParameterSet

getInstance, getInstanceClass

Methods inherited from class de.jstacs.parameters.ParameterSet

getErrorMessage, getId, getNumberOfValues, getParent, initParameterList, initParameterList, isAtomic, isRanged, makeRanged, next, parametersLoaded, propagateId, recieveId, resetToFirst, setParent, simplify, valuesToString

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 constructor for the Storable interface.

Parameters:

s - the StringBuffer

Throws:

NonParsableException - if the StringBuffer is not parsable

HomMMParameterSet

public HomMMParameterSet()

An empty constructor.

HomMMParameterSet

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

The constructor that sets already the ALphabetContainer, ESS, description and order.

Parameters:

alphabet - the alphabet

ess - the ESS

description - the description

order - the Markov order of the model

Throws:

Exception - if something went wrong

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