de.jstacs.scoringFunctions
Class AbstractNormalizableScoringFunction

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

All Implemented Interfaces:

NormalizableScoringFunction, ScoringFunction, Storable, Cloneable

Direct Known Subclasses:

AbstractMixtureScoringFunction, AbstractVariableLengthScoringFunction, BayesianNetworkScoringFunction, IndependentProductScoringFunction, MappingScoringFunction, MRFScoringFunction, NormalizedScoringFunction, PositionScoringFunction, UniformScoringFunction

public abstract class AbstractNormalizableScoringFunction
extends Object
implements NormalizableScoringFunction

This class is the main part of any ScoreClassifier. It implements many methods of the interface NormalizableScoringFunction.

Author:

Jens Keilwagen, Jan Grau

Field Summary

protected AlphabetContainer	alphabets The AlphabetContainer of this NormalizableScoringFunction .
protected int	length The length of the modeled sequences.
protected static Random	r This object can be used for drawing initial parameters.

Fields inherited from interface de.jstacs.scoringFunctions.ScoringFunction

UNKNOWN

Constructor Summary

AbstractNormalizableScoringFunction(AlphabetContainer alphabets, int length)
The main constructor.

AbstractNormalizableScoringFunction(StringBuffer xml)
This is the constructor for Storable.

Method Summary

AbstractNormalizableScoringFunction	clone() Creates a clone (deep copy) of the current ScoringFunction instance.
protected abstract void	fromXML(StringBuffer xml) This method is called in the constructor for the Storable interface to create a scoring function from a StringBuffer.
AlphabetContainer	getAlphabetContainer() Returns the AlphabetContainer for this ScoringFunction.
double	getInitialClassParam(double classProb) Returns the initial class parameter for the class this ScoringFunction is responsible for, based on the class probability classProb.
int	getLength() Returns the length of this ScoringFunction, i.e. the length of the Sequences this ScoringFunction can handle.
double	getLogScore(Sequence seq) Returns the logarithmic score for a given Sequence.
double	getLogScoreAndPartialDerivation(Sequence seq, IntList indices, DoubleList partialDer) Returns the logarithmic score for a Sequence seq and fills lists with the indices and the partial derivations.
int	getNumberOfRecommendedStarts() This method returns the number of recommended optimization starts.
static int	getNumberOfStarts(ScoringFunction[] score) Returns the number of recommended starts in a numerical optimization.
boolean	isNormalized() This method indicates whether the implemented score is already normalized to 1 or not.
static boolean	isNormalized(NormalizableScoringFunction... function) This method checks whether all given NormalizableScoringFunctions are normalized.

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, getLogNormalizationConstant, getLogPartialNormalizationConstant, getLogPriorTerm, getSizeOfEventSpaceForRandomVariablesOfParameter

Methods inherited from interface de.jstacs.scoringFunctions.ScoringFunction

getCurrentParameterValues, getInstanceName, getLogScore, getLogScoreAndPartialDerivation, getNumberOfParameters, initializeFunction, initializeFunctionRandomly, isInitialized, setParameters

Methods inherited from interface de.jstacs.Storable

toXML

Field Detail

r

protected static final Random r

This object can be used for drawing initial parameters.

See Also:

ScoringFunction.getCurrentParameterValues()

alphabets

protected AlphabetContainer alphabets

The AlphabetContainer of this NormalizableScoringFunction .

length

protected int length

The length of the modeled sequences.

Constructor Detail

AbstractNormalizableScoringFunction

public AbstractNormalizableScoringFunction(AlphabetContainer alphabets,
                                           int length)
                                    throws IllegalArgumentException

The main constructor.

Parameters:

alphabets - the AlphabetContainer of this ScoringFunction

length - the length of this ScoringFunction, i.e. the length of the modeled sequences

Throws:

IllegalArgumentException - if the length is negative or does not match with AlphabetContainer.getPossibleLength()

AbstractNormalizableScoringFunction

public AbstractNormalizableScoringFunction(StringBuffer xml)
                                    throws NonParsableException

This is the constructor for Storable. Creates a new AbstractNormalizableScoringFunction out of a StringBuffer .

Parameters:

xml - the XML representation as StringBuffer

Throws:

NonParsableException - if the XML representation could not be parsed

Method Detail

getNumberOfStarts

public static final int getNumberOfStarts(ScoringFunction[] score)

Returns the number of recommended starts in a numerical optimization.

Parameters:

score - the scoring functions

Returns:

the number of recommended starts

See Also:

ScoringFunction.getNumberOfRecommendedStarts()

clone

public AbstractNormalizableScoringFunction clone()
                                          throws CloneNotSupportedException

Description copied from interface: ScoringFunction

Creates a clone (deep copy) of the current ScoringFunction instance.

Specified by:

clone in interface ScoringFunction

Overrides:

clone in class Object

Returns:

the cloned instance of the current ScoringFunction

Throws:

CloneNotSupportedException - if something went wrong while cloning the ScoringFunction

fromXML

protected abstract void fromXML(StringBuffer xml)
                         throws NonParsableException

This method is called in the constructor for the Storable interface to create a scoring function from a StringBuffer.

Parameters:

xml - the XML representation as StringBuffer

Throws:

NonParsableException - if the StringBuffer could not be parsed

See Also:

AbstractNormalizableScoringFunction(StringBuffer)

getAlphabetContainer

public final AlphabetContainer getAlphabetContainer()

Description copied from interface: ScoringFunction

Returns the AlphabetContainer for this ScoringFunction. Only Sequences with a comparable AlphabetContainer can be modeled.

Specified by:

getAlphabetContainer in interface ScoringFunction

Returns:

the AlphabetContainer

getLength

public int getLength()

Description copied from interface: ScoringFunction

Returns the length of this ScoringFunction, i.e. the length of the Sequences this ScoringFunction can handle. For homogeneous ScoringFunctions, i.e. ScoringFunctions that support Sequences of different lengths, the method should return 0.

Specified by:

getLength in interface ScoringFunction

Returns:

the length of this ScoringFunction

getLogScore

public final double getLogScore(Sequence seq)

Returns the logarithmic score for a given Sequence.

Specified by:

getLogScore in interface ScoringFunction

Parameters:

seq - the Sequence

Returns:

the log score for the Sequence

getLogScoreAndPartialDerivation

public final double getLogScoreAndPartialDerivation(Sequence seq,
                                                    IntList indices,
                                                    DoubleList partialDer)

Description copied from interface: ScoringFunction

Returns the logarithmic score for a Sequence seq and fills lists with the indices and the partial derivations.

Specified by:

getLogScoreAndPartialDerivation in interface ScoringFunction

Parameters:

seq - the Sequence

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

partialDer - 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

getNumberOfRecommendedStarts

public int getNumberOfRecommendedStarts()

Description copied from interface: ScoringFunction

This method returns the number of recommended optimization starts. The standard implementation returns 1.

Specified by:

getNumberOfRecommendedStarts in interface ScoringFunction

Returns:

the number of recommended optimization starts

isNormalized

public boolean isNormalized()

Description copied from interface: NormalizableScoringFunction

This method indicates whether the implemented score is already normalized to 1 or not. The standard implementation returns false.

Specified by:

isNormalized in interface NormalizableScoringFunction

Returns:

true if the implemented score is already normalized to 1, false otherwise

isNormalized

public static boolean isNormalized(NormalizableScoringFunction... function)

This method checks whether all given NormalizableScoringFunctions are normalized.

Parameters:

function - the NormalizableScoringFunctions to be checked

Returns:

true if all NormalizableScoringFunctions are already normalized, otherwise false

See Also:

NormalizableScoringFunction.isNormalized()

getInitialClassParam

public double getInitialClassParam(double classProb)

Description copied from interface: ScoringFunction

Returns the initial class parameter for the class this ScoringFunction is responsible for, based on the class probability classProb.

Specified by:

getInitialClassParam in interface NormalizableScoringFunction

Specified by:

getInitialClassParam in interface ScoringFunction

Parameters:

classProb - the class probability

Returns:

the initial class parameter