de.jstacs.scoringFunctions.homogeneous
Class HomogeneousScoringFunction

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

All Implemented Interfaces:

NormalizableScoringFunction, ScoringFunction, Storable, Cloneable

Direct Known Subclasses:

HMM0ScoringFunction, HMMScoringFunction, UniformHomogeneousScoringFunction

public abstract class HomogeneousScoringFunction
extends VariableLengthScoringFunction

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 that models sequence s of arbitrary length.
protected	HomogeneousScoringFunction(AlphabetContainer alphabets, int length) This is the main constructor that creates an instance that models sequence s 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.

Methods inherited from class de.jstacs.scoringFunctions.VariableLengthScoringFunction

getAllConditionalStationaryDistributions, getLogScore, getLogScore, getLogScoreAndPartialDerivation, getLogScoreAndPartialDerivation, getNormalizationConstant, getNormalizationConstant, getPartialNormalizationConstant, getPartialNormalizationConstant, setStatisticForHyperparameters

Methods inherited from class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction

clone, fromXML, getAlphabetContainer, getInitialClassParam, getLength, getLogScore, getLogScoreAndPartialDerivation, getNumberOfRecommendedStarts, 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.NormalizableScoringFunction

addGradientOfLogPriorTerm, getEss, getLogPriorTerm, getSizeOfEventSpaceForRandomVariablesOfParameter

Methods inherited from interface de.jstacs.scoringFunctions.ScoringFunction

getCurrentParameterValues, getInstanceName, getNumberOfParameters, 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 that models sequence s of arbitrary length.

Parameters:

alphabets - the AlphabetContainer

HomogeneousScoringFunction

protected HomogeneousScoringFunction(AlphabetContainer alphabets,
                                     int length)

This is the main constructor that creates an instance that models sequence s 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.

Parameters:

source - the xml representation

Throws:

NonParsableException - if the representation could not be parsed.

Method Detail

getMaximalMarkovOrder

public abstract int getMaximalMarkovOrder()

Returns the maximal used markov oder.

Returns:

the maximal used markov oder