de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete

Class DiscreteEmission

java.lang.Object

de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.AbstractConditionalDiscreteEmission

de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.DiscreteEmission

All Implemented Interfaces:

SamplingComponent, SamplingFromStatistic, DifferentiableEmission, Emission, SamplingEmission, Storable, Cloneable

Direct Known Subclasses:

PhyloDiscreteEmission

public class DiscreteEmission
extends AbstractConditionalDiscreteEmission

This class implements a simple discrete emission without any condition.

Author:

Jens Keilwagen, Michael Scharfe, Jan Grau

Field Summary

Fields inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.AbstractConditionalDiscreteEmission

con, counter, ess, grad, hyperParams, logNorm, offset, params, paramsFile, probs, reader, samplingIndex, statistic, writer

Constructor Summary

Constructors

Constructor and Description
DiscreteEmission(AlphabetContainer con, double ess) This is a simple constructor for a DiscreteEmission based on the equivalent sample size.
DiscreteEmission(AlphabetContainer con, double[] hyperParams) This is a simple constructor for a DiscreteEmission defining the individual hyper parameters.
DiscreteEmission(StringBuffer xml) Creates a DiscreteEmission from its XML representation.

Method Summary

Modifier and Type	Method and Description
protected int	getConditionIndex(boolean forward, int seqPos, Sequence seq) This method returns an index encoding the condition.
String	toString(NumberFormat nf) This method returns a String representation of the instance.

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.AbstractConditionalDiscreteEmission

acceptParameters, addGradientOfLogPriorTerm, addToStatistic, appendFurtherInformation, clone, drawParameters, drawParametersFromStatistic, estimateFromStatistic, extendSampling, extractFurtherInformation, fillCurrentParameter, fillSamplingGroups, finalize, fromXML, getAlphabetContainer, getHyperParams, getIndex, getLogGammaScoreFromStatistic, getLogPosteriorFromStatistic, getLogPriorTerm, getLogProbAndPartialDerivationFor, getLogProbFor, getNodeLabel, getNodeShape, getNumberOfParameters, getSizeOfEventSpace, initForSampling, initializeFunctionRandomly, isInSamplingMode, joinStatistics, parseNextParameterSet, parseParameterSet, precompute, resetStatistic, samplingStopped, setLinear, setParameter, setParameterOffset, setParameters, setShape, toXML

Methods inherited from class java.lang.Object

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

Constructor Detail

DiscreteEmission

public DiscreteEmission(AlphabetContainer con,
                        double ess)

This is a simple constructor for a DiscreteEmission based on the equivalent sample size.

Parameters:

con - the AlphabetContainer of this emission

ess - the equivalent sample size (ess) of this emission that is equally distributed over all parameters

See Also:

DiscreteEmission(AlphabetContainer, double[])

DiscreteEmission

public DiscreteEmission(AlphabetContainer con,
                        double[] hyperParams)

This is a simple constructor for a DiscreteEmission defining the individual hyper parameters.

Parameters:

con - the AlphabetContainer of this emission

hyperParams - the individual hyper parameters for each parameter

DiscreteEmission

public DiscreteEmission(StringBuffer xml)
                 throws NonParsableException

Creates a DiscreteEmission from its XML representation.

Parameters:

xml - the XML representation.

Throws:

NonParsableException - if the XML representation could not be parsed

Method Detail

getConditionIndex

protected int getConditionIndex(boolean forward,
                                int seqPos,
                                Sequence seq)

Description copied from class: AbstractConditionalDiscreteEmission

This method returns an index encoding the condition.

Specified by:

getConditionIndex in class AbstractConditionalDiscreteEmission

Parameters:

forward - a switch to decide whether to use the forward or the reverse complementary strand (e.g. for DNA sequences)

seqPos - the position in the sequence seq

seq - the sequence

Returns:

the index encoding the condition

toString

public String toString(NumberFormat nf)

Description copied from interface: Emission

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