de.jstacs.sequenceScores.differentiable

Class IndependentProductDiffSS

java.lang.Object

de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore

de.jstacs.sequenceScores.differentiable.IndependentProductDiffSS

All Implemented Interfaces:

DifferentiableSequenceScore, SequenceScore, Storable, Cloneable

Direct Known Subclasses:

IndependentProductDiffSM

public class IndependentProductDiffSS
extends AbstractDifferentiableSequenceScore

This class enables the user to model parts of a sequence independent of each other. For instance, the first part of the sequence is modeled by the first DifferentiableSequenceScore and has the length of the first DifferentiableSequenceScore, the second part starts directly after the first part, is modeled by the second DifferentiableSequenceScore ... etc. It is also possible to use a DifferentiableSequenceScore for more than one sequence part and in both orientations (if possible).

It is important to set the equivalent sample size (ESS) of each instance carefully, i.e., corresponding to the ESS of the parts.

Author:

Jens Keilwagen

Field Summary

Fields

Modifier and Type	Field and Description
protected int[]	index This index indicates which entry of the array score should be used for the specific parts.
protected boolean[]	isVariable This array specifies for each entry of score whether it is able to score sequences of variable length.
protected int[]	partialLength This array specifies the lengths of the specific parts.
protected boolean[]	reverse This array specifies whether the sequence or its reverse complement is used in the specific parts.
protected DifferentiableSequenceScore[]	score The internally used DifferentiableSequenceScores.
protected int[]	start This array specifies the start positions of the specific parts.
protected int[]	startIndexOfParams This array contains the start indices for DifferentiableSequenceScore.setParameters(double[], int) on score.

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
IndependentProductDiffSS(boolean plugIn, DifferentiableSequenceScore... functions) This constructor creates an instance of an IndependentProductDiffSS from a given series of independent DifferentiableSequenceScores.
IndependentProductDiffSS(boolean plugIn, DifferentiableSequenceScore[] functions, int[] length) This constructor creates an instance of an IndependentProductDiffSS from given series of independent DifferentiableSequenceScores and lengths.
IndependentProductDiffSS(boolean plugIn, DifferentiableSequenceScore[] functions, int[] index, int[] length, boolean[] reverse) This is the main constructor.
IndependentProductDiffSS(StringBuffer source) This is the constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
IndependentProductDiffSS	clone() Creates a clone (deep copy) of the current DifferentiableSequenceScore instance.
protected void	extractFurtherInformation(StringBuffer xml) This method is the opposite of getFurtherInformation().
int	extractSequenceParts(int scoringFunctionIndex, DataSet[] data, DataSet[] result) This method extracts the corresponding Sequence parts for a specific DifferentiableSequenceScore.
double[][]	extractWeights(int number, double[][] weights) This method creates the weights for extractSequenceParts(int, DataSet[], DataSet[]).
protected void	fromXML(StringBuffer rep) 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.
DifferentiableSequenceScore[]	getFunctions() This method returns a deep copy of the internally used DifferentiableSequenceScore.
protected StringBuffer	getFurtherInformation() This method is used to append further information of the instance to the XML representation.
int[]	getIndices() This method returns a deep copy of the internally used indices of the DifferentiableSequenceScore for the parts.
String	getInstanceName() Should return a short instance name such as iMM(0), BN(2), ...
protected static int[]	getLengthArray(DifferentiableSequenceScore... function) This method provides an array of lengths that can be used for instance as partialLength.
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	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.
int	getNumberOfRecommendedStarts() This method returns the number of recommended optimization starts.
int[]	getPartialLengths() This method returns a deep copy of the internally used partial lengths of the parts.
boolean[]	getReverseSwitches() This method returns a deep copy of the internally used switches for the parts whether to use the corresponding DifferentiableSequenceScore forward or as reverse complement.
void	initializeFunction(int index, boolean freeParams, 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
protected void	setParamsStarts() This method set the value of the array startIndexOfParams.
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

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

Methods inherited from class java.lang.Object

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

Field Detail

score

protected DifferentiableSequenceScore[] score

The internally used DifferentiableSequenceScores.

index

protected int[] index

This index indicates which entry of the array score should be used for the specific parts.

start

protected int[] start

This array specifies the start positions of the specific parts.

partialLength

protected int[] partialLength

This array specifies the lengths of the specific parts.

reverse

protected boolean[] reverse

This array specifies whether the sequence or its reverse complement is used in the specific parts.

isVariable

protected boolean[] isVariable

This array specifies for each entry of score whether it is able to score sequences of variable length.

startIndexOfParams

protected int[] startIndexOfParams

This array contains the start indices for DifferentiableSequenceScore.setParameters(double[], int) on score.

Constructor Detail

IndependentProductDiffSS

public IndependentProductDiffSS(boolean plugIn,
                                DifferentiableSequenceScore... functions)
                         throws CloneNotSupportedException,
                                WrongAlphabetException

This constructor creates an instance of an IndependentProductDiffSS from a given series of independent DifferentiableSequenceScores. The length that is modeled by each component is determined by SequenceScore.getLength(). So the length should not be 0.

Parameters:

plugIn - whether to use plugIn parameters for the parts, otherwise the last parameters are used for parts that are instance of HomogeneousDiffSM

functions - the components, i.e. the given series of independent DifferentiableSequenceScores

Throws:

CloneNotSupportedException - if at least one element of functions could not be cloned

WrongAlphabetException - if the user tries to use an alphabet for a reverse complement that can not be used for a reverse complement.

See Also:

IndependentProductDiffSS(boolean, DifferentiableSequenceScore[], int[])

IndependentProductDiffSS

public IndependentProductDiffSS(boolean plugIn,
                                DifferentiableSequenceScore[] functions,
                                int[] length)
                         throws CloneNotSupportedException,
                                WrongAlphabetException

This constructor creates an instance of an IndependentProductDiffSS from given series of independent DifferentiableSequenceScores and lengths.

Parameters:

plugIn - whether to use plugIn parameters for the parts, otherwise the last parameters are used for parts that are instance of HomogeneousDiffSM

functions - the components, i.e. the given series of independent DifferentiableSequenceScores

length - the lengths, one for each component

Throws:

CloneNotSupportedException - if at least one component could not be cloned

WrongAlphabetException - if the user tries to use an alphabet for a reverse complement that can not be used for a reverse complement.

See Also:

IndependentProductDiffSS(boolean, DifferentiableSequenceScore[], int[], int[], boolean[])

IndependentProductDiffSS

public IndependentProductDiffSS(boolean plugIn,
                                DifferentiableSequenceScore[] functions,
                                int[] index,
                                int[] length,
                                boolean[] reverse)
                         throws CloneNotSupportedException,
                                WrongAlphabetException

This is the main constructor.

Parameters:

plugIn - whether to use plugIn parameters for the parts, otherwise the last parameters are used for parts that are instance of HomogeneousDiffSM

functions - the DifferentiableSequenceScore

index - the index of the DifferentiableSequenceScore at each part

length - the length of each part

reverse - a switch whether to use it directly or the reverse complementary strand

Throws:

CloneNotSupportedException - if at least one component could not be cloned

WrongAlphabetException - if the user tries to use an alphabet for a reverse complement that can not be used for a reverse complement.

IndependentProductDiffSS

public IndependentProductDiffSS(StringBuffer source)
                         throws NonParsableException

This is the constructor for the interface Storable. Creates a new IndependentProductDiffSS out of a StringBuffer as returned by toXML().

Parameters:

source - the XML representation as StringBuffer

Throws:

NonParsableException - if the XML representation could not be parsed

Method Detail

getLengthArray

protected static final int[] getLengthArray(DifferentiableSequenceScore... function)
                                     throws IllegalArgumentException

This method provides an array of lengths that can be used for instance as partialLength.

Parameters:

function - the internally used DifferentiableSequenceScores

Returns:

an array of lengths that can be used for instance as partialLength

Throws:

IllegalArgumentException - if at least one function has length 0

See Also:

SequenceScore.getLength(), IndependentProductDiffSS(boolean, DifferentiableSequenceScore...)

setParamsStarts

protected void setParamsStarts()

This method set the value of the array startIndexOfParams.

clone

public IndependentProductDiffSS 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 AbstractDifferentiableSequenceScore

Returns:

the cloned instance of the current DifferentiableSequenceScore

Throws:

CloneNotSupportedException - if something went wrong while cloning the DifferentiableSequenceScore

initializeFunction

public void initializeFunction(int index,
                               boolean freeParams,
                               DataSet[] data,
                               double[][] weights)
                        throws Exception

Description copied from interface: DifferentiableSequenceScore

This method creates the underlying structure of the DifferentiableSequenceScore.

Parameters:

index - the index of the class the DifferentiableSequenceScore models

freeParams - indicates whether the (reduced) parameterization is used

data - the data sets

weights - the weights of the sequences in the data sets

Throws:

Exception - if something went wrong

extractSequenceParts

public int extractSequenceParts(int scoringFunctionIndex,
                                DataSet[] data,
                                DataSet[] result)
                         throws Exception

This method extracts the corresponding Sequence parts for a specific DifferentiableSequenceScore.

Parameters:

scoringFunctionIndex - the index of the DifferentiableSequenceScore

data - the original data

result - an array for the resulting DataSets of Sequences; has to have same length as data

Returns:

the number how often the DifferentiableSequenceScore was used

Throws:

Exception - if the DataSet can not be created

extractWeights

public double[][] extractWeights(int number,
                                 double[][] weights)

This method creates the weights for extractSequenceParts(int, DataSet[], DataSet[]).

Parameters:

number - the number how often the weights should be copied after each other.

weights - the original weights

Returns:

the new weights (might be null)

See Also:

extractSequenceParts(int, DataSet[], DataSet[])

fromXML

protected void fromXML(StringBuffer rep)
                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:

rep - the XML representation as StringBuffer

Throws:

NonParsableException - if the StringBuffer could not be parsed

See Also:

AbstractDifferentiableSequenceScore.AbstractDifferentiableSequenceScore(StringBuffer)

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

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

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

getFunctions

public DifferentiableSequenceScore[] getFunctions()
                                           throws Exception

This method returns a deep copy of the internally used DifferentiableSequenceScore.

Returns:

a deep copy of the internally used DifferentiableSequenceScore

Throws:

Exception - if at least one DifferentiableSequenceScore could not be cloned

See Also:

getIndices(), getPartialLengths(), getReverseSwitches()

getIndices

public int[] getIndices()

This method returns a deep copy of the internally used indices of the DifferentiableSequenceScore for the parts.

Returns:

a deep copy of the internally used indices of the DifferentiableSequenceScore for the parts

See Also:

getFunctions(), getPartialLengths(), getReverseSwitches()

getPartialLengths

public int[] getPartialLengths()

This method returns a deep copy of the internally used partial lengths of the parts.

Returns:

a deep copy of the internally used partial lengths of the parts

See Also:

getFunctions(), getIndices(), getReverseSwitches()

getReverseSwitches

public boolean[] getReverseSwitches()

This method returns a deep copy of the internally used switches for the parts whether to use the corresponding DifferentiableSequenceScore forward or as reverse complement.

Returns:

a deep copy of the internally used switches for the parts whether to use the corresponding DifferentiableSequenceScore forward or as reverse complement

See Also:

getFunctions(), getIndices(), getPartialLengths()

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)

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

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

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

Overrides:

getNumberOfRecommendedStarts in class AbstractDifferentiableSequenceScore

Returns:

the number of recommended optimization starts

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

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

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

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