de.jstacs.scoringFunctions.mix.motifSearch
Class DurationScoringFunction

java.lang.Object
  de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
      de.jstacs.scoringFunctions.mix.motifSearch.PositionScoringFunction
          de.jstacs.scoringFunctions.mix.motifSearch.DurationScoringFunction

All Implemented Interfaces:

NormalizableScoringFunction, ScoringFunction, Storable, Cloneable

Direct Known Subclasses:

MixtureDuration, SkewNormalLikeScoringFunction, UniformDurationScoringFunction

public abstract class DurationScoringFunction
extends PositionScoringFunction

This class is the super class for all one dimensional position scoring functions that can be used as durations for semi Markov models.

Author:

Jens Keilwagen

See Also:

HiddenMotifsMixture

Field Summary

protected int	delta The difference of maximal and minimal value.
protected double	ess The equivalent sample size.
protected int	max The maximal value.
protected int	min The minimal value.

Fields inherited from class de.jstacs.scoringFunctions.mix.motifSearch.PositionScoringFunction

internal

Fields inherited from class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction

alphabets, length, r

Fields inherited from interface de.jstacs.scoringFunctions.ScoringFunction

UNKNOWN

Constructor Summary

protected	DurationScoringFunction(int min, int max, double ess) The default constructor.
protected	DurationScoringFunction(StringBuffer source) This is the constructor for Storable.

Method Summary

abstract void	adjust(int[] length, double[] weight) This method adjust the parameter based on the given statistic.
protected void	fromXML(StringBuffer xml) This method is called in the constructor for the Storable interface to create a scoring function from a StringBuffer.
double	getEss() Returns the equivalent sample size (ess) of this model, i.e. the equivalent sample size for the class or component that is represented by this model.
double	getLogNormalizationConstant() Returns the logarithm of the sum of the scores over all sequences of the event space.
double	getLogPartialNormalizationConstant(int parameterIndex) Returns the logarithm of the partial normalization constant for the parameter with index parameterIndex.
int	getMax() Returns the maximal value that can be scored.
int	getMin() Returns the minimal value that can be scored.
int	getNumberOfPossibilities() Returns the number of different possibilities that can be scored.
protected abstract String	getRNotation(String distributionName) This method returns the distribution in R notation.
int	getSizeOfEventSpaceForRandomVariablesOfParameter(int index) Returns the size of the event space of the random variables that are affected by parameter no.
abstract void	initializeUniformly() This method set special parameters that lead to an uniform distribution.
boolean	isPossible(int... positions) This method returns true if the given positions are in the domain of the PositionScoringFunction.
void	modify(int delta) This method modifies the underlying AlphabetContainer.
boolean	next() This method steps to the next reasonable outcome if possible.
void	reset() This method resets the iterator to the initial state (first reasonable output) so that it can be used again.
String	toString()
StringBuffer	toXML() This method returns an XML representation as StringBuffer of an instance of the implementing class.

Methods inherited from class de.jstacs.scoringFunctions.mix.motifSearch.PositionScoringFunction

clone, getInternalPosition, getLogScore, getLogScore, getLogScoreAndPartialDerivation, getLogScoreAndPartialDerivation, getLogScoreAndPartialDerivationForInternal, getLogScoreForInternal, getValuesFromSequence

Methods inherited from class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction

getAlphabetContainer, getInitialClassParam, getLength, getLogScore, getLogScoreAndPartialDerivation, getNumberOfRecommendedStarts, getNumberOfStarts, isNormalized, isNormalized

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.jstacs.scoringFunctions.NormalizableScoringFunction

addGradientOfLogPriorTerm, getLogPriorTerm

Methods inherited from interface de.jstacs.scoringFunctions.ScoringFunction

getCurrentParameterValues, getInstanceName, getNumberOfParameters, initializeFunction, initializeFunctionRandomly, isInitialized, setParameters

Field Detail

ess

protected double ess

The equivalent sample size.

min

protected int min

The minimal value.

max

protected int max

The maximal value.

delta

protected int delta

The difference of maximal and minimal value.

Constructor Detail

DurationScoringFunction

protected DurationScoringFunction(int min,
                                  int max,
                                  double ess)

The default constructor.

Parameters:

min - the minimal value

max - the maximal value

ess - the equivalent sample size

DurationScoringFunction

protected DurationScoringFunction(StringBuffer source)
                           throws NonParsableException

This is the constructor for Storable. Creates a new DurationScoringFunction out of a StringBuffer.

Parameters:

source - the XML representation as StringBuffer

Throws:

NonParsableException - if the XML representation could not be parsed

Method Detail

toXML

public StringBuffer toXML()

Description copied from interface: Storable

This method returns an XML representation as StringBuffer of an instance of the implementing class.

Specified by:

toXML in interface Storable

Overrides:

toXML in class PositionScoringFunction

Returns:

the XML representation

fromXML

protected void fromXML(StringBuffer xml)
                throws NonParsableException

Description copied from class: AbstractNormalizableScoringFunction

This method is called in the constructor for the Storable interface to create a scoring function from a StringBuffer.

Overrides:

fromXML in class PositionScoringFunction

Parameters:

xml - the XML representation as StringBuffer

Throws:

NonParsableException - if the StringBuffer could not be parsed

See Also:

AbstractNormalizableScoringFunction.AbstractNormalizableScoringFunction(StringBuffer)

reset

public void reset()

Description copied from class: PositionScoringFunction

This method resets the iterator to the initial state (first reasonable output) so that it can be used again.

Specified by:

reset in class PositionScoringFunction

next

public boolean next()

Description copied from class: PositionScoringFunction

This method steps to the next reasonable outcome if possible.

Specified by:

next in class PositionScoringFunction

Returns:

true if a next reasonable outcome could be set, otherwise false

getSizeOfEventSpaceForRandomVariablesOfParameter

public int getSizeOfEventSpaceForRandomVariablesOfParameter(int index)

Description copied from interface: NormalizableScoringFunction

Returns the size of the event space of the random variables that are affected by parameter no. index, i.e. the product of the sizes of the alphabets at the position of each random variable affected by parameter index. For DNA alphabets this corresponds to 4 for a PWM, 16 for a WAM except position 0, ...

Parameters:

index - the index of the parameter

Returns:

the size of the event space

getEss

public final double getEss()

Description copied from interface: NormalizableScoringFunction

Returns the equivalent sample size (ess) of this model, i.e. the equivalent sample size for the class or component that is represented by this model.

Returns:

the equivalent sample size.

isPossible

public boolean isPossible(int... positions)

Description copied from class: PositionScoringFunction

This method returns true if the given positions are in the domain of the PositionScoringFunction.

Specified by:

isPossible in class PositionScoringFunction

Parameters:

positions - the positions to be tested

Returns:

true if the given positions are in the domain of the PositionScoringFunction

getMin

public final int getMin()

Returns the minimal value that can be scored.

Returns:

the minimal value that can be scored.

getMax

public final int getMax()

Returns the maximal value that can be scored.

Returns:

the maximal value that can be scored.

getNumberOfPossibilities

public int getNumberOfPossibilities()

Returns the number of different possibilities that can be scored.

Returns:

the number of different possibilities that can be scored.

initializeUniformly

public abstract void initializeUniformly()

This method set special parameters that lead to an uniform distribution.

adjust

public abstract void adjust(int[] length,
                            double[] weight)

This method adjust the parameter based on the given statistic.

Parameters:

length - an array containing length values

weight - an array containing corresponding weight values

modify

public void modify(int delta)

This method modifies the underlying AlphabetContainer. This might be necessary if the motif length changed.

Parameters:

delta - the change

See Also:

Mutable.modify(int, int), MutableMotifDiscoverer.modifyMotif(int, int, int)

getLogNormalizationConstant

public final double getLogNormalizationConstant()

Description copied from interface: NormalizableScoringFunction

Returns the logarithm of the sum of the scores over all sequences of the event space.

Returns:

the logarithm of the normalization constant Z

getLogPartialNormalizationConstant

public final double getLogPartialNormalizationConstant(int parameterIndex)
                                                throws Exception

Description copied from interface: NormalizableScoringFunction

Returns the logarithm of the partial normalization constant for the parameter with index parameterIndex. This is the logarithm of the partial derivation of the normalization constant for the parameter with index parameterIndex,

.

Parameters:

parameterIndex - the index of the parameter

Returns:

the logarithm of the partial normalization constant

Throws:

Exception - if something went wrong with the normalization

See Also:

NormalizableScoringFunction.getLogNormalizationConstant()

getRNotation

protected abstract String getRNotation(String distributionName)

This method returns the distribution in R notation.

Parameters:

distributionName - the name of the distribution, e.g., "p"

Returns:

the distribution in R notation

See Also:

REnvironment

toString

public String toString()

Overrides:

toString in class Object