de.jstacs.sequenceScores.differentiable

Class UniformDiffSS

java.lang.Object

de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore

de.jstacs.sequenceScores.differentiable.UniformDiffSS

All Implemented Interfaces:

DifferentiableSequenceScore, SequenceScore, Storable, Cloneable

Direct Known Subclasses:

UniformDiffSM

public class UniformDiffSS
extends AbstractDifferentiableSequenceScore

This DifferentiableSequenceScore does nothing. So it is possible to save parameters in an optimization.

Author:

Jens Keilwagen, Jan Grau

Field Summary

Fields inherited from class de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore

alphabets, length, r

Fields inherited from interface de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore

UNKNOWN

Constructor Summary

Constructors

Constructor and Description
UniformDiffSS(AlphabetContainer alphabets, int length) This is the main constructor that creates an instance of a UniformDiffSS that models each sequence uniformly.
UniformDiffSS(StringBuffer xml) This is the constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
protected void	extractFurtherInformation(StringBuffer xml) This method is the opposite of getFurtherInformation().
protected void	fromXML(StringBuffer xml) This method is called in the constructor for the Storable interface to create a scoring function from a StringBuffer.
double[]	getCurrentParameterValues() Returns a double array of dimension DifferentiableSequenceScore.getNumberOfParameters() containing the current parameter values.
protected StringBuffer	getFurtherInformation() This method is used to append further information of the instance to the XML representation.
String	getInstanceName() Should return a short instance name such as iMM(0), BN(2), ...
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.
double	getLogScoreFor(Sequence seq, int start) Returns the logarithmic score for the Sequence seq beginning at position start in the Sequence.
int	getNumberOfParameters() Returns the number of parameters in this DifferentiableSequenceScore.
void	initializeFunction(int index, boolean meila, DataSet[] data, double[][] weights) This method creates the underlying structure of the DifferentiableSequenceScore.
void	initializeFunctionRandomly(boolean freeParams) This method initializes the DifferentiableSequenceScore randomly.
boolean	isInitialized() This method can be used to determine whether the instance is initialized.
void	setParameters(double[] params, int start) This method sets the internal parameters to the values of params between start and start + DifferentiableSequenceScore.getNumberOfParameters() - 1
String	toString(NumberFormat nf) This method returns a String representation of the instance.
StringBuffer	toXML() This method returns an XML representation as StringBuffer of an instance of the implementing class.

Methods inherited from class de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore

clone, getAlphabetContainer, getCharacteristics, getInitialClassParam, getLength, getLogScoreAndPartialDerivation, getLogScoreAndPartialDerivation, getLogScoreFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, getNumberOfRecommendedStarts, getNumberOfStarts, getNumericalCharacteristics, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

UniformDiffSS

public UniformDiffSS(AlphabetContainer alphabets,
                     int length)

This is the main constructor that creates an instance of a UniformDiffSS that models each sequence uniformly.

Parameters:

alphabets - the AlphabetContainer

length - the length of the modeled sequences

UniformDiffSS

public UniformDiffSS(StringBuffer xml)
              throws NonParsableException

This is the constructor for the interface Storable. Creates a new UniformDiffSS out of its XML representation as returned by fromXML(StringBuffer).

Parameters:

xml - the XML representation as StringBuffer

Throws:

NonParsableException - if the XML representation could not be parsed

Method Detail

getInstanceName

public String getInstanceName()

Description copied from interface: SequenceScore

Should return a short instance name such as iMM(0), BN(2), ...

Returns:

a short instance name

getLogScoreFor

public double getLogScoreFor(Sequence seq,
                             int start)

Description copied from interface: SequenceScore

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

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: DifferentiableSequenceScore

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

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

getNumberOfParameters

public int getNumberOfParameters()

Description copied from interface: DifferentiableSequenceScore

Returns the number of parameters in this DifferentiableSequenceScore. If the number of parameters is not known yet, the method returns DifferentiableSequenceScore.UNKNOWN.

Returns:

the number of parameters in this DifferentiableSequenceScore

See Also:

DifferentiableSequenceScore.UNKNOWN

setParameters

public void setParameters(double[] params,
                          int start)

Description copied from interface: DifferentiableSequenceScore

This method sets the internal parameters to the values of params between start and start + DifferentiableSequenceScore.getNumberOfParameters() - 1

Parameters:

params - the new parameters

start - the start index in params

getFurtherInformation

protected StringBuffer getFurtherInformation()

This method is used to append further information of the instance to the XML representation. This method is designed to allow subclasses to add information to the XML representation.

Returns:

the further information as XML code in a StringBuffer

See Also:

extractFurtherInformation(StringBuffer)

toXML

public StringBuffer toXML()

Description copied from interface: Storable

This method returns an XML representation as StringBuffer of an instance of the implementing class.

Returns:

the XML representation

extractFurtherInformation

protected void extractFurtherInformation(StringBuffer xml)
                                  throws NonParsableException

This method is the opposite of getFurtherInformation(). It extracts further information of the instance from a XML representation.

Parameters:

xml - the StringBuffer containing the information to be extracted as XML code

Throws:

NonParsableException - if the StringBuffer could not be parsed

See Also:

getFurtherInformation()

fromXML

protected void fromXML(StringBuffer xml)
                throws NonParsableException

Description copied from class: AbstractDifferentiableSequenceScore

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

Specified by:

fromXML in class AbstractDifferentiableSequenceScore

Parameters:

xml - the XML representation as StringBuffer

Throws:

NonParsableException - if the StringBuffer could not be parsed

See Also:

AbstractDifferentiableSequenceScore.AbstractDifferentiableSequenceScore(StringBuffer)

toString

public String toString(NumberFormat nf)

Description copied from interface: SequenceScore

This method returns a String representation of the instance.

Parameters:

nf - the NumberFormat for the String representation of parameters or probabilities

Returns:

a String representation of the instance

getCurrentParameterValues

public double[] getCurrentParameterValues()
                                   throws Exception

Description copied from interface: DifferentiableSequenceScore

Returns a double array of dimension DifferentiableSequenceScore.getNumberOfParameters() containing the current parameter values. If one likes to use these parameters to start an optimization it is highly recommended to invoke DifferentiableSequenceScore.initializeFunction(int, boolean, DataSet[], double[][]) before. After an optimization this method can be used to get the current parameter values.

Returns:

the current parameter values

Throws:

Exception - if no parameters exist (yet)

isInitialized

public boolean isInitialized()

Description copied from interface: SequenceScore

This method can be used to determine whether the instance is initialized. If the instance is initialized you should be able to invoke SequenceScore.getLogScoreFor(Sequence).

Returns:

true if the instance is initialized, false otherwise

initializeFunctionRandomly

public void initializeFunctionRandomly(boolean freeParams)
                                throws Exception

Description copied from interface: DifferentiableSequenceScore

This method initializes the DifferentiableSequenceScore randomly. It has to create the underlying structure of the DifferentiableSequenceScore.

Parameters:

freeParams - indicates whether the (reduced) parameterization is used

Throws:

Exception - if something went wrong

initializeFunction

public void initializeFunction(int index,
                               boolean meila,
                               DataSet[] data,
                               double[][] weights)

Description copied from interface: DifferentiableSequenceScore

This method creates the underlying structure of the DifferentiableSequenceScore.

Parameters:

index - the index of the class the DifferentiableSequenceScore models

meila - indicates whether the (reduced) parameterization is used

data - the data sets

weights - the weights of the sequences in the data sets