de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions
Class MixtureEmission

java.lang.Object
  de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.MixtureEmission

All Implemented Interfaces:

Emission, Storable, Cloneable

public final class MixtureEmission
extends Object
implements Emission

This class implements a mixture of Emissions.

Author:

Jens Keilwagen

Constructor Summary

MixtureEmission(Emission[] emission, double[] hyperParameters)
The main constructor creating a MixtureEmission from a set of emissions.

MixtureEmission(StringBuffer xml)
The standard constructor for the interface Storable.

Method Summary

void	addToStatistic(boolean forward, int startPos, int endPos, double weight, Sequence seq) This method adds the weight to the internal sufficient statistic.
MixtureEmission	clone()
void	estimateFromStatistic() This method estimates the parameters from the internal sufficient statistic.
AlphabetContainer	getAlphabetContainer() This method returns the AlphabetContainer of this emission.
double	getLogPriorTerm() Returns a value that is proportional to the log of the prior.
double	getLogProbFor(boolean forward, int startPos, int endPos, Sequence seq) This method computes the logarithm of the likelihood.
String	getNodeLabel(double weight, String name, NumberFormat nf) Returns the graphviz label of the node containing this emission.
String	getNodeShape(boolean forward) Returns the graphviz string for the shape of the node.
void	initializeFunctionRandomly() This method initializes the emission randomly.
void	joinStatistics(Emission... emissions) This method joins the statistics of different instances and sets this joined statistic as statistic of each instance.
void	resetStatistic() This method resets the internal sufficient statistic.
void	setParameters(Emission t) Set values of parameters of the instance to the value of the parameters of the given instance.
String	toString(NumberFormat nf) This method returns a String representation of the instance.
StringBuffer	toXML() This method returns an XML representation as StringBuffer of an instance of the implementing class.

Methods inherited from class java.lang.Object

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

Constructor Detail

MixtureEmission

public MixtureEmission(Emission[] emission,
                       double[] hyperParameters)
                throws CloneNotSupportedException

The main constructor creating a MixtureEmission from a set of emissions.

Parameters:

emission - the individual emissions

hyperParameters - the hyper parameters for each component

Throws:

CloneNotSupportedException - if the emission could not be cloned

MixtureEmission

public MixtureEmission(StringBuffer xml)
                throws NonParsableException

The standard constructor for the interface Storable. Constructs an MixtureEmission out of an XML representation.

Parameters:

xml - the XML representation as StringBuffer

Throws:

NonParsableException - if the MixtureEmission could not be reconstructed out of the StringBuffer xml

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

Returns:

the XML representation

clone

public MixtureEmission clone()
                      throws CloneNotSupportedException

Overrides:

clone in class Object

Throws:

CloneNotSupportedException

joinStatistics

public void joinStatistics(Emission... emissions)

Description copied from interface: Emission

This method joins the statistics of different instances and sets this joined statistic as statistic of each instance. This method might be used for instance in a multi-threaded optimization to join partial statistics.

Specified by:

joinStatistics in interface Emission

Parameters:

emissions - the emissions to be joined

addToStatistic

public void addToStatistic(boolean forward,
                           int startPos,
                           int endPos,
                           double weight,
                           Sequence seq)
                    throws OperationNotSupportedException

Description copied from interface: Emission

This method adds the weight to the internal sufficient statistic.

Specified by:

addToStatistic in interface Emission

Parameters:

forward - whether to use the forward or the reverse strand

startPos - the start position

endPos - the end position

weight - the weight of the sequence

seq - the sequence

Throws:

OperationNotSupportedException - if forward=false and the reverse complement of the sequence seq is not defined

estimateFromStatistic

public void estimateFromStatistic()

Description copied from interface: Emission

This method estimates the parameters from the internal sufficient statistic.

Specified by:

estimateFromStatistic in interface Emission

getAlphabetContainer

public AlphabetContainer getAlphabetContainer()

Description copied from interface: Emission

This method returns the AlphabetContainer of this emission.

Specified by:

getAlphabetContainer in interface Emission

Returns:

the AlphabetContainer of this emission

getLogPriorTerm

public double getLogPriorTerm()

Description copied from interface: Emission

Returns a value that is proportional to the log of the prior. For maximum likelihood (ML) 0 should be returned.

Specified by:

getLogPriorTerm in interface Emission

Returns:

a value that is proportional to the log of the prior

See Also:

StatisticalModel.getLogPriorTerm()

getLogProbFor

public double getLogProbFor(boolean forward,
                            int startPos,
                            int endPos,
                            Sequence seq)
                     throws OperationNotSupportedException

Description copied from interface: Emission

This method computes the logarithm of the likelihood.

Specified by:

getLogProbFor in interface Emission

Parameters:

forward - whether to use the forward or the reverse strand

startPos - the start position

endPos - the end position

seq - the sequence

Returns:

the logarithm of the probability

Throws:

OperationNotSupportedException - if forward=false and the reverse complement of the sequence seq is not defined

initializeFunctionRandomly

public void initializeFunctionRandomly()

Description copied from interface: Emission

This method initializes the emission randomly.

Specified by:

initializeFunctionRandomly in interface Emission

resetStatistic

public void resetStatistic()

Description copied from interface: Emission

This method resets the internal sufficient statistic.

Specified by:

resetStatistic in interface Emission

getNodeShape

public String getNodeShape(boolean forward)

Description copied from interface: Emission

Returns the graphviz string for the shape of the node.

Specified by:

getNodeShape in interface Emission

Parameters:

forward - if this emission is used on the forward strand

Returns:

the shape

getNodeLabel

public String getNodeLabel(double weight,
                           String name,
                           NumberFormat nf)

Description copied from interface: Emission

Returns the graphviz label of the node containing this emission.

Specified by:

getNodeLabel in interface Emission

Parameters:

weight - the weight of the node which is represented by the color of the node, or -1 for no representation, i.e., white background

name - the name of the state using this emission

nf - the NumberFormat for formatting the textual representation of this emission

Returns:

the label

setParameters

public void setParameters(Emission t)
                   throws IllegalArgumentException

Description copied from interface: Emission

Set values of parameters of the instance to the value of the parameters of the given instance. It can be assumed that the given instance and the current instance are from the same class. This method might be used for instance in a multi-threaded optimization to broadcast the parameters.

Specified by:

setParameters in interface Emission

Parameters:

t - the emission with the parameters to be set

Throws:

IllegalArgumentException - if the assumption about the same class for given and current instance is wrong

toString

public String toString(NumberFormat nf)

Description copied from interface: Emission

This method returns a String representation of the instance.

Specified by:

toString in interface Emission

Parameters:

nf - the NumberFormat for the String representation of parameters or probabilities

Returns:

a String representation of the instance