de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif

Class PositionDiffSM

java.lang.Object

de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore

de.jstacs.sequenceScores.statisticalModels.differentiable.AbstractDifferentiableStatisticalModel

de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.PositionDiffSM

All Implemented Interfaces:

DifferentiableSequenceScore, SequenceScore, DifferentiableStatisticalModel, StatisticalModel, Storable, Cloneable

Direct Known Subclasses:

DurationDiffSM

public abstract class PositionDiffSM
extends AbstractDifferentiableStatisticalModel

This class implements a position scoring function that enables the user to get a score without using a Sequence object. It furthermore implements a kind of iterator that allows the user to iterate over all reasonable possibilities.

Author:

Jens Keilwagen

See Also:

Sequence, reset(), next(), getLogScoreForInternal(), getLogScoreAndPartialDerivationForInternal(IntList, DoubleList)

Field Summary

Fields

Modifier and Type	Field and Description
protected int[]	internal This array is used for some method of DurationDiffSM that use an internal memory

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

Modifier	Constructor and Description
protected	PositionDiffSM(AlphabetContainer con, int length) This constructor allows create instance with more than one dimension.
protected	PositionDiffSM(int min, int max) This is the main constructor that creates the AlphabetContainer internally.
protected	PositionDiffSM(StringBuffer source) This is the constructor for Storable.

Method Summary

Methods

Modifier and Type	Method and Description
PositionDiffSM	clone() Creates a clone (deep copy) of the current DifferentiableSequenceScore instance.
protected void	fromXML(StringBuffer xml) This method is called in the constructor for the Storable interface to create a scoring function from a StringBuffer.
void	getInternalPosition(int[] positions) Copies the current value of the internal iterator in the given array.
abstract double	getLogScore(int... values) This method enables the user to get the log-score without using a sequence object.
abstract double	getLogScoreAndPartialDerivation(IntList indices, DoubleList partialDer, int... values) This method enables the user to get the log-score and the partial derivations without using a sequence object.
double	getLogScoreAndPartialDerivation(Sequence seq, int start, 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	getLogScoreAndPartialDerivationForInternal(IntList indices, DoubleList partialDer) This method enables the user to get the log-score and the partial derivations without using a sequence object by using the internal iterator.
double	getLogScoreFor(Sequence seq, int start) Returns the logarithmic score for the Sequence seq beginning at position start in the Sequence.
double	getLogScoreForInternal() This method enables the user to get the log-score without using a sequence object by using the internal iterator.
protected int[]	getValuesFromSequence(Sequence seq, int start) This method extracts the values form a sequence.
abstract boolean	isPossible(int... positions) This method returns true if the given positions are in the domain of the PositionDiffSM.
abstract boolean	next() This method steps to the next reasonable outcome if possible.
abstract void	reset() This method resets the iterator to the initial state (first reasonable output) so that it can be used again.
StringBuffer	toXML() This method returns an XML representation as StringBuffer of an instance of the implementing class.

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.differentiable.AbstractDifferentiableStatisticalModel

emitDataSet, getInitialClassParam, getLogProbFor, getLogProbFor, getLogProbFor, getLogScoreFor, getLogScoreFor, getMaximalMarkovOrder, isNormalized, isNormalized

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

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

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.jstacs.sequenceScores.statisticalModels.differentiable.DifferentiableStatisticalModel

addGradientOfLogPriorTerm, getESS, getLogNormalizationConstant, getLogPartialNormalizationConstant, getLogPriorTerm, getSizeOfEventSpaceForRandomVariablesOfParameter

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

getCurrentParameterValues, getLogScoreAndPartialDerivation, getLogScoreAndPartialDerivation, getNumberOfParameters, getNumberOfRecommendedStarts, initializeFunction, initializeFunctionRandomly, setParameters

Methods inherited from interface de.jstacs.sequenceScores.SequenceScore

getAlphabetContainer, getCharacteristics, getInstanceName, getLength, getLogScoreFor, getLogScoreFor, getNumericalCharacteristics, isInitialized, toString

Field Detail

internal

protected int[] internal

This array is used for some method of DurationDiffSM that use an internal memory

See Also:

DurationDiffSM.reset(), DurationDiffSM.next(), getInternalPosition(int[])

Constructor Detail

PositionDiffSM

protected PositionDiffSM(AlphabetContainer con,
              int length)

This constructor allows create instance with more than one dimension. This constructor can be used if the AlphabetContainer already exists.

Parameters:

con - the AlphabetContainer

length - the number of dimensions, e.g. the length of the modeled sequences

PositionDiffSM

protected PositionDiffSM(int min,
              int max)

This is the main constructor that creates the AlphabetContainer internally.

Parameters:

min - the minimal value

max - the maximal value

PositionDiffSM

protected PositionDiffSM(StringBuffer source)
                  throws NonParsableException

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

Parameters:

source - the XML representation as StringBuffer

Throws:

NonParsableException - if the XML representation could not be parsed

Method Detail

clone

public PositionDiffSM 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 AbstractDifferentiableStatisticalModel

Returns:

the cloned instance of the current DifferentiableSequenceScore

Throws:

CloneNotSupportedException - if something went wrong while cloning the DifferentiableSequenceScore

reset

public abstract void reset()

This method resets the iterator to the initial state (first reasonable output) so that it can be used again.

next

public abstract boolean next()

This method steps to the next reasonable outcome if possible.

Returns:

true if a next reasonable outcome could be set, otherwise false

getInternalPosition

public void getInternalPosition(int[] positions)

Copies the current value of the internal iterator in the given array.

Parameters:

positions - the array containing the internal positions after calling this method

getLogScoreForInternal

public double getLogScoreForInternal()

This method enables the user to get the log-score without using a sequence object by using the internal iterator.

Returns:

the score

getLogScoreAndPartialDerivationForInternal

public double getLogScoreAndPartialDerivationForInternal(IntList indices,
                                                DoubleList partialDer)

This method enables the user to get the log-score and the partial derivations without using a sequence object by using the internal iterator.

Parameters:

indices - a list for the indices of the parameters

partialDer - a list of the partial derivations

Returns:

the score

getLogScore

public abstract double getLogScore(int... values)

This method enables the user to get the log-score without using a sequence object.

Parameters:

values - the values

Returns:

the score

getLogScoreAndPartialDerivation

public abstract double getLogScoreAndPartialDerivation(IntList indices,
                                     DoubleList partialDer,
                                     int... values)

This method enables the user to get the log-score and the partial derivations without using a sequence object.

Parameters:

indices - a list for the indices of the parameters

partialDer - a list of the partial derivations

values - the values

Returns:

the score

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 partialDer)

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

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

getValuesFromSequence

protected int[] getValuesFromSequence(Sequence seq,
                          int start)

This method extracts the values form a sequence.

Parameters:

seq - the sequence

start - the index of the startposition

Returns:

the values of the sequence

isPossible

public abstract boolean isPossible(int... positions)

This method returns true if the given positions are in the domain of the PositionDiffSM.

Parameters:

positions - the positions to be tested

Returns:

true if the given positions are in the domain of the PositionDiffSM

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

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)