de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions
Interface Emission

All Superinterfaces:

Cloneable, Storable

All Known Subinterfaces:

DifferentiableEmission, SamplingEmission

All Known Implementing Classes:

AbstractConditionalDiscreteEmission, DiscreteEmission, GaussianEmission, MixtureEmission, MultivariateGaussianEmission, PhyloDiscreteEmission, PluginGaussianEmission, ReferenceSequenceDiscreteEmission, SilentEmission, UniformEmission

public interface Emission
extends Storable, Cloneable

This interface declares all method for an emission of a state.

Author:

Jens Keilwagen

See Also:

State

Method Summary

void	addToStatistic(boolean forward, int startPos, int endPos, double weight, Sequence seq) This method adds the weight to the internal sufficient statistic.
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.

Methods inherited from interface de.jstacs.Storable

toXML

Method Detail

getAlphabetContainer

AlphabetContainer getAlphabetContainer()

This method returns the AlphabetContainer of this emission.

Returns:

the AlphabetContainer of this emission

initializeFunctionRandomly

void initializeFunctionRandomly()

This method initializes the emission randomly.

getLogProbFor

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

This method computes the logarithm of the likelihood.

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

getLogPriorTerm

double getLogPriorTerm()

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

Returns:

a value that is proportional to the log of the prior

See Also:

StatisticalModel.getLogPriorTerm()

resetStatistic

void resetStatistic()

This method resets the internal sufficient statistic.

addToStatistic

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

This method adds the weight to the internal sufficient statistic.

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

joinStatistics

void joinStatistics(Emission... emissions)

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.

Parameters:

emissions - the emissions to be joined

estimateFromStatistic

void estimateFromStatistic()

This method estimates the parameters from the internal sufficient statistic.

getNodeShape

String getNodeShape(boolean forward)

Returns the graphviz string for the shape of the node.

Parameters:

forward - if this emission is used on the forward strand

Returns:

the shape

getNodeLabel

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

Returns the graphviz label of the node containing this 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

void setParameters(Emission t)
                   throws IllegalArgumentException

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.

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

String toString(NumberFormat nf)

This method returns a String representation of the instance.

Parameters:

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

Returns:

a String representation of the instance