de.jstacs.sequenceScores.differentiable

Class AbstractDifferentiableSequenceScore

java.lang.Object

de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore

All Implemented Interfaces:

DifferentiableSequenceScore, SequenceScore, Storable, Cloneable

Direct Known Subclasses:

AbstractDifferentiableStatisticalModel, IndependentProductDiffSS, LogisticDiffSS, MultiDimensionalSequenceWrapperDiffSS, UniformDiffSS

public abstract class AbstractDifferentiableSequenceScore
extends Object
implements DifferentiableSequenceScore

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

Author:

Jens Keilwagen, Jan Grau

Field Summary

Fields

Modifier and Type	Field and Description
protected AlphabetContainer	alphabets The AlphabetContainer of this AbstractDifferentiableSequenceScore .
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.sequenceScores.differentiable.DifferentiableSequenceScore

UNKNOWN

Constructor Summary

Constructors

Constructor and Description
AbstractDifferentiableSequenceScore(AlphabetContainer alphabets, int length) The main constructor.
AbstractDifferentiableSequenceScore(StringBuffer xml) This is the constructor for Storable.

Method Summary

Modifier and Type	Method and Description
AbstractDifferentiableSequenceScore	clone() Creates a clone (deep copy) of the current DifferentiableSequenceScore 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 container of alphabets that were used when constructing the instance.
ResultSet	getCharacteristics() Returns some information characterizing or describing the current instance.
double	getInitialClassParam(double classProb) Returns the initial class parameter for the class this DifferentiableSequenceScore is responsible for, based on the class probability classProb.
int	getLength() Returns the length of sequences this instance can score.
double	getLogScoreAndPartialDerivation(Sequence seq, int startpos, int endpos, IntList indices, DoubleList partialDer) 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	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.
double[]	getLogScoreFor(DataSet data) This method computes the logarithm of the scores of all sequences in the given data set.
void	getLogScoreFor(DataSet data, double[] res) This method computes and stores the logarithm of the scores for any sequence in the data set in the given double-array.
double	getLogScoreFor(Sequence seq) Returns the logarithmic score for the Sequence seq.
double	getLogScoreFor(Sequence seq, int startpos, int endpos) Returns the logarithmic score for the Sequence seq beginning at position start in the Sequence.
int	getNumberOfRecommendedStarts() This method returns the number of recommended optimization starts.
static int	getNumberOfStarts(DifferentiableSequenceScore[] score) Returns the number of recommended starts in a numerical optimization.
NumericalResultSet	getNumericalCharacteristics() Returns the subset of numerical values that are also returned by SequenceScore.getCharacteristics().
String	toString()

Methods inherited from class java.lang.Object

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

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

getCurrentParameterValues, getLogScoreAndPartialDerivation, getNumberOfParameters, initializeFunction, initializeFunctionRandomly, setParameters

Methods inherited from interface de.jstacs.sequenceScores.SequenceScore

getInstanceName, getLogScoreFor, isInitialized, toString

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:

DifferentiableSequenceScore.getCurrentParameterValues()

alphabets

protected AlphabetContainer alphabets

The AlphabetContainer of this AbstractDifferentiableSequenceScore .

length

protected int length

The length of the modeled sequences.

Constructor Detail

AbstractDifferentiableSequenceScore

public AbstractDifferentiableSequenceScore(AlphabetContainer alphabets,
                                           int length)
                                    throws IllegalArgumentException

The main constructor.

Parameters:

alphabets - the AlphabetContainer of this DifferentiableSequenceScore

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

Throws:

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

AbstractDifferentiableSequenceScore

public AbstractDifferentiableSequenceScore(StringBuffer xml)
                                    throws NonParsableException

This is the constructor for Storable. Creates a new AbstractDifferentiableSequenceScore 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(DifferentiableSequenceScore[] score)

Returns the number of recommended starts in a numerical optimization.

Parameters:

score - the scoring functions

Returns:

the number of recommended starts

See Also:

DifferentiableSequenceScore.getNumberOfRecommendedStarts()

clone

public AbstractDifferentiableSequenceScore clone()
                                          throws CloneNotSupportedException

Description copied from interface: DifferentiableSequenceScore

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

Specified by:

clone in interface DifferentiableSequenceScore

Specified by:

clone in interface SequenceScore

Overrides:

clone in class Object

Returns:

the cloned instance of the current DifferentiableSequenceScore

Throws:

CloneNotSupportedException - if something went wrong while cloning the DifferentiableSequenceScore

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:

AbstractDifferentiableSequenceScore(StringBuffer)

getAlphabetContainer

public final AlphabetContainer getAlphabetContainer()

Description copied from interface: SequenceScore

Returns the container of alphabets that were used when constructing the instance.

Specified by:

getAlphabetContainer in interface SequenceScore

Returns:

the container of alphabets that were used when constructing the instance

getLength

public int getLength()

Description copied from interface: SequenceScore

Returns the length of sequences this instance can score. Instances that can only score sequences of defined length are e.g. PWM or inhomogeneous Markov models. If the instance can score sequences of arbitrary length, e.g. homogeneous Markov models, this method returns 0 (zero).

Specified by:

getLength in interface SequenceScore

Returns:

the length of sequences the instance can score

getLogScoreFor

public final double getLogScoreFor(Sequence seq)

Description copied from interface: SequenceScore

Returns the logarithmic score for the Sequence seq.

Specified by:

getLogScoreFor in interface SequenceScore

Parameters:

seq - the sequence

Returns:

the logarithmic score for the sequence

getLogScoreFor

public double getLogScoreFor(Sequence seq,
                             int startpos,
                             int endpos)
                      throws WrongLengthException

Description copied from interface: SequenceScore

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

Specified by:

getLogScoreFor in interface SequenceScore

Parameters:

seq - the Sequence

startpos - the start position in the Sequence

endpos - the end position (inclusive) in the Sequence

Returns:

the logarithmic score for the Sequence

Throws:

WrongLengthException

getLogScoreAndPartialDerivation

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

Description copied from interface: DifferentiableSequenceScore

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

Specified by:

getLogScoreAndPartialDerivation in interface DifferentiableSequenceScore

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

getLogScoreAndPartialDerivation

public double getLogScoreAndPartialDerivation(Sequence seq,
                                              int startpos,
                                              int endpos,
                                              IntList indices,
                                              DoubleList partialDer)
                                       throws WrongLengthException

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.

Specified by:

getLogScoreAndPartialDerivation in interface DifferentiableSequenceScore

Parameters:

seq - the Sequence

startpos - the start position in the Sequence

endpos - the end position (inclusive) in 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

Throws:

WrongLengthException

getNumberOfRecommendedStarts

public int getNumberOfRecommendedStarts()

Description copied from interface: DifferentiableSequenceScore

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

Specified by:

getNumberOfRecommendedStarts in interface DifferentiableSequenceScore

Returns:

the number of recommended optimization starts

getInitialClassParam

public double getInitialClassParam(double classProb)

Description copied from interface: DifferentiableSequenceScore

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

Specified by:

getInitialClassParam in interface DifferentiableSequenceScore

Parameters:

classProb - the class probability

Returns:

the initial class parameter

getLogScoreFor

public double[] getLogScoreFor(DataSet data)
                        throws Exception

Description copied from interface: SequenceScore

This method computes the logarithm of the scores of all sequences in the given data set. The values are stored in an array according to the index of the respective sequence in the data set.

The score for any sequence shall be computed independent of all other sequences in the data set. So the result should be exactly the same as for the method SequenceScore.getLogScoreFor(Sequence).

Specified by:

getLogScoreFor in interface SequenceScore

Parameters:

data - the data set of sequences

Returns:

an array containing the logarithm of the score of all sequences of the data set

Throws:

Exception - if something went wrong

See Also:

SequenceScore.getLogScoreFor(Sequence)

getLogScoreFor

public void getLogScoreFor(DataSet data,
                           double[] res)
                    throws Exception

Description copied from interface: SequenceScore

This method computes and stores the logarithm of the scores for any sequence in the data set in the given double-array.

The score for any sequence shall be computed independent of all other sequences in the data set. So the result should be exactly the same as for the method SequenceScore.getLogScoreFor(Sequence).

Specified by:

getLogScoreFor in interface SequenceScore

Parameters:

data - the data set of sequences

res - the array for the results, has to have length data.getNumberOfElements() (which returns the number of sequences in the data set)

Throws:

Exception - if something went wrong

See Also:

SequenceScore.getLogScoreFor(Sequence), SequenceScore.getLogScoreFor(DataSet)

getCharacteristics

public ResultSet getCharacteristics()
                             throws Exception

Description copied from interface: SequenceScore

Returns some information characterizing or describing the current instance. This could be e.g. the number of edges for a Bayesian network or an image showing some representation of the instance. The set of characteristics should always include the XML-representation of the instance. The corresponding result type is StorableResult.

Specified by:

getCharacteristics in interface SequenceScore

Returns:

the characteristics of the current instance

Throws:

Exception - if some of the characteristics could not be defined

See Also:

StorableResult

getNumericalCharacteristics

public NumericalResultSet getNumericalCharacteristics()
                                               throws Exception

Description copied from interface: SequenceScore

Returns the subset of numerical values that are also returned by SequenceScore.getCharacteristics().

Specified by:

getNumericalCharacteristics in interface SequenceScore

Returns:

the numerical characteristics of the current instance

Throws:

Exception - if some of the characteristics could not be defined

toString

public final String toString()

Overrides:

toString in class Object