de.jstacs.scoringFunctions.homogeneous
Class HomogeneousScoringFunction

java.lang.Object
  de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
      de.jstacs.scoringFunctions.AbstractVariableLengthScoringFunction
          de.jstacs.scoringFunctions.homogeneous.HomogeneousScoringFunction

All Implemented Interfaces:

NormalizableScoringFunction, ScoringFunction, VariableLengthScoringFunction, Storable, Cloneable

Direct Known Subclasses:

HMM0ScoringFunction, HMMScoringFunction, UniformHomogeneousScoringFunction

public abstract class HomogeneousScoringFunction
extends AbstractVariableLengthScoringFunction

This is the main class for all homogeneous ScoringFunctions.

Author:

Jens Keilwagen

Field Summary

Fields inherited from class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction

alphabets, length, r

Fields inherited from interface de.jstacs.scoringFunctions.ScoringFunction

UNKNOWN

Constructor Summary

protected	HomogeneousScoringFunction(AlphabetContainer alphabets) This is the main constructor that creates an instance of a HomogeneousScoringFunction that models sequences of arbitrary length.
protected	HomogeneousScoringFunction(AlphabetContainer alphabets, int length) This is the main constructor that creates an instance of a HomogeneousScoringFunction that models sequences of a given length.
protected	HomogeneousScoringFunction(StringBuffer source) This is the constructor for Storable.

Method Summary

abstract int	getMaximalMarkovOrder() Returns the maximal used markov oder.
abstract void	initializeUniformly(boolean freeParams) This method allows to initialize the instance with an uniform distribution.

Methods inherited from class de.jstacs.scoringFunctions.AbstractVariableLengthScoringFunction

getLogNormalizationConstant, getLogPartialNormalizationConstant, getLogScore, getLogScoreAndPartialDerivation

Methods inherited from class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction

clone, fromXML, getAlphabetContainer, getInitialClassParam, getLength, getLogScore, getLogScoreAndPartialDerivation, getNumberOfRecommendedStarts, getNumberOfStarts, isNormalized, isNormalized

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.jstacs.scoringFunctions.VariableLengthScoringFunction

getLogNormalizationConstant, getLogPartialNormalizationConstant, getLogScore, getLogScoreAndPartialDerivation, setStatisticForHyperparameters

Methods inherited from interface de.jstacs.scoringFunctions.NormalizableScoringFunction

addGradientOfLogPriorTerm, getEss, getInitialClassParam, getLogPriorTerm, getSizeOfEventSpaceForRandomVariablesOfParameter, isNormalized

Methods inherited from interface de.jstacs.scoringFunctions.ScoringFunction

clone, getAlphabetContainer, getCurrentParameterValues, getInstanceName, getLength, getLogScore, getLogScoreAndPartialDerivation, getNumberOfParameters, getNumberOfRecommendedStarts, initializeFunction, initializeFunctionRandomly, isInitialized, setParameters

Methods inherited from interface de.jstacs.Storable

toXML

Constructor Detail

HomogeneousScoringFunction

protected HomogeneousScoringFunction(AlphabetContainer alphabets)

This is the main constructor that creates an instance of a HomogeneousScoringFunction that models sequences of arbitrary length.

Parameters:

alphabets - the AlphabetContainer

HomogeneousScoringFunction

protected HomogeneousScoringFunction(AlphabetContainer alphabets,
                                     int length)

This is the main constructor that creates an instance of a HomogeneousScoringFunction that models sequences of a given length.

Parameters:

alphabets - the AlphabetContainer

length - the length of the modeled sequences

HomogeneousScoringFunction

protected HomogeneousScoringFunction(StringBuffer source)
                              throws NonParsableException

This is the constructor for Storable. Creates a new HomogeneousScoringFunction out of its XML representation.

Parameters:

source - the XML representation as StringBuffer

Throws:

NonParsableException - if the XML representation could not be parsed

Method Detail

getMaximalMarkovOrder

public abstract int getMaximalMarkovOrder()

Returns the maximal used markov oder.

Returns:

the maximal used markov oder

initializeUniformly

public abstract void initializeUniformly(boolean freeParams)

This method allows to initialize the instance with an uniform distribution.

Parameters:

freeParams - a switch whether to take only free parameters or to take all