de.jstacs.scoringFunctions
Class AbstractVariableLengthScoringFunction

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

All Implemented Interfaces:

NormalizableScoringFunction, ScoringFunction, VariableLengthScoringFunction, Storable, Cloneable

Direct Known Subclasses:

CMMScoringFunction, HomogeneousScoringFunction

public abstract class AbstractVariableLengthScoringFunction
extends AbstractNormalizableScoringFunction
implements VariableLengthScoringFunction

This abstract class implements some methods declared in NormalizableScoringFunction based on the declaration of methods in VariableLengthScoringFunction. It allows to score subsequences of arbitrary length. This NormalizableScoringFunction should be the super class for non-motif NormalizableScoringFunctions like homogeneous Markov models, cyclic Markov models, ... etc.

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

Method Summary

double	getLogNormalizationConstant() Returns the logarithm of the sum of the scores over all sequences of the event space.
double	getLogPartialNormalizationConstant(int parameterIndex) Returns the logarithm of the partial normalization constant for the parameter with index parameterIndex.
double	getLogScore(Sequence seq, int start) Returns the logarithmic score for the Sequence seq beginning at position start in the Sequence.
double	getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList dList) Returns the logarithmic score for a Sequence beginning at position start in the Sequence and fills lists with the indices and the partial derivations.

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

AbstractVariableLengthScoringFunction

protected AbstractVariableLengthScoringFunction(AlphabetContainer alphabets)

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

Parameters:

alphabets - the AlphabetContainer of this VariableLengthScoringFunction

See Also:

AbstractVariableLengthScoringFunction(AlphabetContainer, int)

AbstractVariableLengthScoringFunction

protected AbstractVariableLengthScoringFunction(AlphabetContainer alphabets,
                                                int length)

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

Parameters:

alphabets - the AlphabetContainer of this VariableLengthScoringFunction

length - the length of the modeled sequences

AbstractVariableLengthScoringFunction

protected AbstractVariableLengthScoringFunction(StringBuffer source)
                                         throws NonParsableException

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

Parameters:

source - the XML representation as StringBuffer

Throws:

NonParsableException - if the XML representation could not be parsed.

Method Detail

getLogNormalizationConstant

public double getLogNormalizationConstant()

Description copied from interface: NormalizableScoringFunction

Returns the logarithm of the sum of the scores over all sequences of the event space.

Specified by:

getLogNormalizationConstant in interface NormalizableScoringFunction

Returns:

the logarithm of the normalization constant Z

getLogPartialNormalizationConstant

public double getLogPartialNormalizationConstant(int parameterIndex)
                                          throws Exception

Description copied from interface: NormalizableScoringFunction

Returns the logarithm of the partial normalization constant for the parameter with index parameterIndex. This is the logarithm of the partial derivation of the normalization constant for the parameter with index parameterIndex,

.

Specified by:

getLogPartialNormalizationConstant in interface NormalizableScoringFunction

Parameters:

parameterIndex - the index of the parameter

Returns:

the logarithm of the partial normalization constant

Throws:

Exception - if something went wrong with the normalization

See Also:

NormalizableScoringFunction.getLogNormalizationConstant()

getLogScore

public double getLogScore(Sequence seq,
                          int start)

Description copied from interface: ScoringFunction

Returns the logarithmic score for the Sequence seq beginning at position start in the Sequence.

Specified by:

getLogScore in interface ScoringFunction

Parameters:

seq - the Sequence

start - the start position in the Sequence

Returns:

the logarithmic score for the Sequence

getLogScoreAndPartialDerivation

public double getLogScoreAndPartialDerivation(Sequence seq,
                                              int start,
                                              IntList indices,
                                              DoubleList dList)

Description copied from interface: ScoringFunction

Returns the logarithmic score for a Sequence beginning at position start in the Sequence and fills lists with the indices and the partial derivations.

Specified by:

getLogScoreAndPartialDerivation in interface ScoringFunction

Parameters:

seq - the Sequence

start - the start position in the Sequence

indices - an IntList of indices, after method invocation the list should contain the indices i where is not zero

dList - a DoubleList of partial derivations, after method invocation the list should contain the corresponding that are not zero

Returns:

the logarithmic score for the Sequence