de.jstacs.models.discrete.inhomogeneous
Class MEMConstraint

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

All Implemented Interfaces:

Storable, Cloneable

public class MEMConstraint
extends InhConstraint

The constraint can be used for any MEM application.

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

MEMConstraint(int[] pos, int[] alphabetLength)
Creates a MEMConstraint as part of a (whole) model

MEMConstraint(int[] pos, int[] alphabetLength, int[] corrected_positions)
Creates a MEMConstraint as part of a model

MEMConstraint(StringBuffer xml)
Creates a MEMConstraint from a StringBuffer

Method Summary

protected void	appendAdditionalInfo(StringBuffer xml) This method appends additional information that are not stored in the base class to the StringBuffer.
MEMConstraint	clone()
void	estimate(double ess) Estimates the (smoothed) relative frequencies using the ess.
protected void	extractAdditionalInfo(StringBuffer xml) This method parses additional information from the StringBuffer that are not parsed in the base class.
int	getCorrectedPosition(int index) Returns the value of the corrected position
double	getExpLambda(int index) Returns \exp(\lambda_{index}).
double	getFreq(int index) Returns the current frequency with index index
double	getLambda(int index) Returns \lambda_{index}.
protected String	getXMLTag() Returns the XML-tag that is used for the class to en- or decode.
void	multiplyExpLambdaWith(int index, double val) Multiplies \exp(\lambda_{index}) with val
void	reset() This method resets all member variables the are in someway counters, frequencies, ...
int	satisfiesSpecificConstraint(SequenceIterator sequence) Returns the index of that constraint that is satiesfied by sequence
void	setExpLambda(int index, double val) Sets the value of exp(\lambda_{index})
void	setLambda(int index, double val) Sets the value of \lambda_{index}
String	toString()

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

satisfiesSpecificConstraint

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

add, add, estimateUnConditional, getCount, getFreq, getMarginalOrder, getNumberOfSpecificConstraints, getPosition, getPositions, toXML

Methods inherited from class java.lang.Object

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

Constructor Detail

MEMConstraint

public MEMConstraint(int[] pos,
                     int[] alphabetLength)
              throws IllegalArgumentException

Creates a MEMConstraint as part of a (whole) model

Parameters:

pos - the used positions (have to be sorted)

alphabetLength - an array containing the length of the the alphabet for each position (of the whole model)

Throws:

IllegalArgumentException - if pos is not sorted

MEMConstraint

public MEMConstraint(int[] pos,
                     int[] alphabetLength,
                     int[] corrected_positions)
              throws IllegalArgumentException

Creates a MEMConstraint as part of a model

Parameters:

pos - the used positions (have to be sorted)

alphabetLength - an array containing the length of the the alphabet for each position (of the whole model)

corrected_positions - an array containing the corrected positions

Throws:

IllegalArgumentException - if pos is not sorted or pos.length!=corrected_positions.length

MEMConstraint

public MEMConstraint(StringBuffer xml)
              throws NonParsableException

Creates a MEMConstraint from a StringBuffer

Parameters:

xml - the buffer

Throws:

NonParsableException - if the buffer is not parsable

Method Detail

clone

public MEMConstraint clone()
                    throws CloneNotSupportedException

Overrides:

clone in class InhConstraint

Throws:

CloneNotSupportedException

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

getCorrectedPosition

public int getCorrectedPosition(int index)

Returns the value of the corrected position

Parameters:

index -

Returns:

the value of the corrected position

getExpLambda

public double getExpLambda(int index)

Returns \exp(\lambda_{index}).

Parameters:

index - the index

Returns:

\exp(\lambda_{index})

getLambda

public double getLambda(int index)

Returns \lambda_{index}.

Parameters:

index - the index

Returns:

\lambda_{index}

multiplyExpLambdaWith

public void multiplyExpLambdaWith(int index,
                                  double val)

Multiplies \exp(\lambda_{index}) with val

Parameters:

index - the index

val - the factor/value

reset

public void reset()

Description copied from class: Constraint

This method resets all member variables the are in someway counters, frequencies, ...

Overrides:

reset in class Constraint

satisfiesSpecificConstraint

public int satisfiesSpecificConstraint(SequenceIterator sequence)

Returns the index of that constraint that is satiesfied by sequence

Parameters:

sequence - the SequenceIterator

Returns:

the index of the fulfilled constraint

getFreq

public double getFreq(int index)

Description copied from class: Constraint

Returns the current frequency with index index

Overrides:

getFreq in class Constraint

Parameters:

index - the index

Returns:

the current frequency

setExpLambda

public void setExpLambda(int index,
                         double val)

Sets the value of exp(\lambda_{index})

Parameters:

index - the index

val - the value

setLambda

public void setLambda(int index,
                      double val)

Sets the value of \lambda_{index}

Parameters:

index - the index

val - the value

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.

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