de.jstacs.models.discrete.homogeneous
Class HomogeneousModel.HomCondProb

java.lang.Object
  de.jstacs.models.discrete.Constraint
      de.jstacs.models.discrete.homogeneous.HomogeneousModel.HomCondProb

All Implemented Interfaces:

Storable

Enclosing class:

HomogeneousModel

protected class HomogeneousModel.HomCondProb
extends Constraint

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

Author:

Jens Keilwagen

Field Summary

Fields inherited from class de.jstacs.models.discrete.Constraint

counts, freq, usedPositions

Constructor Summary

HomogeneousModel.HomCondProb(HomogeneousModel.HomCondProb old)
This constructor is used for cloning instances, since any instance is an inner instance of a HomogeneousModel.

HomogeneousModel.HomCondProb(int[] pos, int n)
The main constructor.

HomogeneousModel.HomCondProb(StringBuffer xml)
Creates an instance from a StringBuffer (see Storable).

Method Summary

protected void	appendAdditionalInfo(StringBuffer xml) This method appends additional information that are not stored in the base class to the StringBuffer.
void	estimate(double ess) Estimates the (smoothed) relative frequencies using the ess.
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 are not parsed in the base class.
double	getLnFreq(int index) Returns the logarithmic frequency.
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 fullfilled by the sequence beginning at start.
String	toString()

Methods inherited from class de.jstacs.models.discrete.Constraint

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

Methods inherited from class java.lang.Object

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

Constructor Detail

HomogeneousModel.HomCondProb

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

The main constructor. Checks that each position is used maximally once.

Parameters:

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

n - the number of specific constraints

HomogeneousModel.HomCondProb

public HomogeneousModel.HomCondProb(StringBuffer xml)
                             throws NonParsableException

Creates an instance from a StringBuffer (see Storable).

Parameters:

xml - the StringBuffer

Throws:

NonParsableException - if the buffer is not parsable

HomogeneousModel.HomCondProb

public HomogeneousModel.HomCondProb(HomogeneousModel.HomCondProb old)

This constructor is used for cloning instances, since any instance is an inner instance of a HomogeneousModel.

Parameters:

old - the old instance to be cloned

Method Detail

estimate

public void estimate(double ess)

Description copied from class: Constraint

Estimates the (smoothed) relative frequencies using the ess.

Specified by:

estimate in class Constraint

Parameters:

ess - the ESS

getLnFreq

public double getLnFreq(int index)

Returns the logarithmic frequency.

Parameters:

index - the index

Returns:

the logarithmic frequency

satisfiesSpecificConstraint

public int satisfiesSpecificConstraint(Sequence seq,
                                       int start)

Description copied from class: Constraint

This method returns the index of the specific constraint that is fullfilled by the sequence beginning at 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

appendAdditionalInfo

protected void appendAdditionalInfo(StringBuffer xml)

Description copied from class: Constraint

This method appends additional information that are 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 - if true 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 are not parsed in the base class.

Specified by:

extractAdditionalInfo in class Constraint

Parameters:

xml - the StringBuffer to parse

Throws:

NonParsableException - if something with the parsing went wrong