de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous

Class HomogeneousTrainSM.HomCondProb

java.lang.Object

de.jstacs.sequenceScores.statisticalModels.trainable.discrete.Constraint

de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.HomogeneousTrainSM.HomCondProb

All Implemented Interfaces:

Storable

Enclosing class:

HomogeneousTrainSM

protected class HomogeneousTrainSM.HomCondProb
extends Constraint

This class handles the (conditional) probabilities of a homogeneous model in a fast way.

Author:

Jens Keilwagen

Field Summary

Fields inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.Constraint

counts, freq, usedPositions

Constructor Summary

Constructors

Constructor and Description
HomogeneousTrainSM.HomCondProb(HomogeneousTrainSM.HomCondProb old) Creates a new HomogeneousTrainSM.HomCondProb instance from a given one.
HomogeneousTrainSM.HomCondProb(int[] pos, int n) The main constructor.
HomogeneousTrainSM.HomCondProb(StringBuffer xml) The standard constructor for the interface Storable .

Method Summary

Methods

Modifier and Type	Method and Description
void	addAll(Sequence seq, double weight, int start, int prevIndex) Adds the given weight to the counts corresponding to the Sequence seq from start to the end of the Sequence.
protected void	appendAdditionalInfo(StringBuffer xml) This method appends additional information that is not stored in the base class to the StringBuffer.
void	estimate(double ess) Estimates the (smoothed) relative frequencies using the ess (equivalent sample size).
protected void	estimateUnConditional(int start, int end, double pc, boolean exceptionWhenNoData) Estimates unconditionally.
protected void	extractAdditionalInfo(StringBuffer xml) This method parses additional information from the StringBuffer that is not parsed in the base class.
String	getDescription(AlphabetContainer con, int i) Returns the decoded symbol for the encoded symbol i.
double	getLnFreq(int index) Returns the logarithmic frequency at a given position index.
protected String	getXMLTag() Returns the XML tag that is used for the class to en- or decode.
int	satisfiesSpecificConstraint(Sequence seq, int start) This method returns the index of the specific constraint that is fulfilled by the Sequence seq beginning at position start.
String	toString()

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.Constraint

add, add, clone, getCount, getFreq, getFreq, getFreqInfo, getMarginalOrder, getNumberOfSpecificConstraints, getPosition, getPositions, reset, resetCounts, toXML

Methods inherited from class java.lang.Object

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

Constructor Detail

HomogeneousTrainSM.HomCondProb

public HomogeneousTrainSM.HomCondProb(int[] pos,
                              int n)

The main constructor. Creates a new HomogeneousTrainSM.HomCondProb instance and checks that each position is used maximally once. In all/most cases pos is new int[]{0,1,2...} and n is Math.pow(Alphabet.length(),pos.length).

Parameters:

pos - the used positions (will be cloned), have to be non-negative

n - the number of specific constraints

See Also:

Constraint.Constraint(int[], int)

HomogeneousTrainSM.HomCondProb

public HomogeneousTrainSM.HomCondProb(StringBuffer xml)
                               throws NonParsableException

The standard constructor for the interface Storable . Creates a new HomogeneousTrainSM.HomCondProb instance out of its XML representation.

Parameters:

xml - the XML representation as StringBuffer

Throws:

NonParsableException - if the StringBuffer could not be parsed

See Also:

Storable, Constraint.Constraint(StringBuffer)

HomogeneousTrainSM.HomCondProb

public HomogeneousTrainSM.HomCondProb(HomogeneousTrainSM.HomCondProb old)

Creates a new HomogeneousTrainSM.HomCondProb instance from a given one. This constructor is used for cloning instances, since any instance is an inner instance of a HomogeneousTrainSM.

Parameters:

old - the old instance to be cloned

See Also:

HomogeneousTrainSM.HomCondProb#HomCondProb(int[],int)

Method Detail

estimate

public void estimate(double ess)

Description copied from class: Constraint

Estimates the (smoothed) relative frequencies using the ess (equivalent sample size).

Specified by:

estimate in class Constraint

Parameters:

ess - the ess

getLnFreq

public double getLnFreq(int index)

Returns the logarithmic frequency at a given position index.

Parameters:

index - the given index

Returns:

the logarithmic frequency at index

satisfiesSpecificConstraint

public int satisfiesSpecificConstraint(Sequence seq,
                              int start)

Description copied from class: Constraint

This method returns the index of the specific constraint that is fulfilled by the Sequence seq beginning at position start.

Specified by:

satisfiesSpecificConstraint in class Constraint

Parameters:

seq - the sequence

start - the start position

Returns:

the index of the fulfilled, specific constraint

toString

public String toString()

Specified by:

toString in class Constraint

addAll

public final void addAll(Sequence seq,
          double weight,
          int start,
          int prevIndex)

Adds the given weight to the counts corresponding to the Sequence seq from start to the end of the Sequence.

Parameters:

seq - the Sequence

weight - the given weight

start - the first index within the Sequence

prevIndex - the previous index used for adding a count

appendAdditionalInfo

protected void appendAdditionalInfo(StringBuffer xml)

Description copied from class: Constraint

This method appends additional information that is not stored in the base class to the StringBuffer.

Specified by:

appendAdditionalInfo in class Constraint

Parameters:

xml - the StringBuffer that is used for appending additional information

getXMLTag

protected String getXMLTag()

Description copied from class: Constraint

Returns the XML tag that is used for the class to en- or decode.

Specified by:

getXMLTag in class Constraint

Returns:

the XML tag that is used for the class to en- or decode

estimateUnConditional

protected void estimateUnConditional(int start,
                         int end,
                         double pc,
                         boolean exceptionWhenNoData)

Description copied from class: Constraint

Estimates unconditionally.

Overrides:

estimateUnConditional in class Constraint

Parameters:

start - the start index

end - the end index

pc - the pseudocount for each parameter

exceptionWhenNoData - indicates if an (runtime) exception is thrown if no data was available to estimate the parameters

extractAdditionalInfo

protected void extractAdditionalInfo(StringBuffer xml)
                              throws NonParsableException

Description copied from class: Constraint

This method parses additional information from the StringBuffer that is not parsed in the base class.

Specified by:

extractAdditionalInfo in class Constraint

Parameters:

xml - the StringBuffer to be parsed

Throws:

NonParsableException - if something with the parsing went wrong

getDescription

public String getDescription(AlphabetContainer con,
                    int i)

Description copied from class: Constraint

Returns the decoded symbol for the encoded symbol i.

Specified by:

getDescription in class Constraint

Parameters:

con - the AlphabetContainer

i - the encoded symbol

Returns:

the decoded symbol for the encoded symbol i