de.jstacs.models.discrete.inhomogeneous
Class InhCondProb

java.lang.Object
  de.jstacs.models.discrete.Constraint
      de.jstacs.models.discrete.inhomogeneous.InhConstraint
          de.jstacs.models.discrete.inhomogeneous.InhCondProb

All Implemented Interfaces:

Storable, Cloneable

public class InhCondProb
extends InhConstraint

This class handles the (conditional) probabilities.

Author:

Jens Keilwagen

Field Summary

Fields inherited from class de.jstacs.models.discrete.inhomogeneous.InhConstraint

offset

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

counts, freq, usedPositions

Constructor Summary

InhCondProb(int[] pos, int[] alphabetLength, boolean cond)

InhCondProb(int pos, int... alphabetLength)

InhCondProb(StringBuffer xml)
The constructor for saved objects.

Method Summary

protected void	appendAdditionalInfo(StringBuffer xml) This method appends additional information that are not stored in the base class to the StringBuffer.
InhCondProb	clone()
void	drawParameters(double ess) Draws the parameters using the counts and the given ESS as hyperparameters.
protected void	drawUnConditional(int start, int end, double pc) This method draws the parameters for a part of this constraint.
void	estimate(double ess) Estimates the (smoothed) relative frequencies using the ess.
void	estimateUnConditional(double ess, double all) Estimates the unconditional 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.
double	getLnFreq(Sequence s, int start) Returns the logarithmic frequency.
void	getOutput(byte[] content, double p) This method is used to create random sequences.
protected String	getXMLTag() Returns the XML-tag that is used for the class to en- or decode.
void	setFreqs(String[] array, int start) This method is used to restore the values of a Gibbs Sampling run.
String	toString()

Methods inherited from class de.jstacs.models.discrete.inhomogeneous.InhConstraint

satisfiesSpecificConstraint

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

add, add, 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

InhCondProb

public InhCondProb(int pos,
                   int... alphabetLength)

Parameters:

pos - the positions

alphabetLength - the length of each alphabet (not only the used positions)

InhCondProb

public InhCondProb(int[] pos,
                   int[] alphabetLength,
                   boolean cond)

Parameters:

pos - the positions

alphabetLength - the length of each alphabet (not only the used positions)

cond - true if the probabilties

InhCondProb

public InhCondProb(StringBuffer xml)
            throws NonParsableException

The constructor for saved objects.

Parameters:

xml - the representation

Throws:

NonParsableException - if the StringBuffer could not be parsed.

Method Detail

clone

public InhCondProb clone()
                  throws CloneNotSupportedException

Overrides:

clone in class InhConstraint

Throws:

CloneNotSupportedException

drawParameters

public void drawParameters(double ess)

Draws the parameters using the counts and the given ESS as hyperparameters.

Parameters:

ess - the given equivalent sample size

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

estimateUnConditional

public void estimateUnConditional(double ess,
                                  double all)

Estimates the unconditional frequencies using the ess.

Parameters:

ess - the ESS

all - the sum of all weights used to fill the counts

getLnFreq

public double getLnFreq(int index)

Returns the logarithmic frequency.

Parameters:

index - the index

Returns:

the logarithmic frequency

getLnFreq

public double getLnFreq(Sequence s,
                        int start)

Returns the logarithmic frequency.

Parameters:

s - the sequence

start - the index of the start position

Returns:

the logarithm of the frequency

getOutput

public void getOutput(byte[] content,
                      double p)
               throws OperationNotSupportedException

This method is used to create random sequences.

Parameters:

content - the content of the random sequence as far as it is known

p - the random number in (0,1)

Throws:

OperationNotSupportedException

See Also:

Model.emitSample(int, int...)

toString

public String toString()

Specified by:

toString in class Constraint

drawUnConditional

protected void drawUnConditional(int start,
                                 int end,
                                 double pc)

This method draws the parameters for a part of this constraint. It is used to draw a distribution with fixed context.

Parameters:

start - the start index

end - the end index

pc - the pseudo count respectively the hyperparameter

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

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.

Overrides:

appendAdditionalInfo in class InhConstraint

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

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.

Overrides:

extractAdditionalInfo in class InhConstraint

Parameters:

xml - the StringBuffer to parse

Throws:

NonParsableException - if something with the parsing went wrong

setFreqs

public void setFreqs(String[] array,
                     int start)
              throws IllegalArgumentException

This method is used to restore the values of a Gibbs Sampling run. The parameters are encoded in Strings. Each String is one frequency. The start index is used to begin at a specific position in the array.

Parameters:

array - the array of String chunks to be parsed

start - the start index

Throws:

IllegalArgumentException - if something with the frequencies is not okay