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

Class ReferenceSequenceDiscreteEmission

java.lang.Object

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

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

All Implemented Interfaces:

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

public class ReferenceSequenceDiscreteEmission
extends AbstractConditionalDiscreteEmission

This class implements a discrete emission that depends on some ReferenceSequenceAnnotation at a certain reference position. This class can be used in so-called conditional profile HMM for the match states.

Author:

Jan Grau, Jens Keilwagen

Field Summary

Fields

Modifier and Type	Field and Description
protected int	refIdx The index in the reference sequence

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
ReferenceSequenceDiscreteEmission(AlphabetContainer con, AlphabetContainer refCon, int refIdx, double ess) This is a simple constructor for a ReferenceSequenceDiscreteEmission based on the equivalent sample size.
ReferenceSequenceDiscreteEmission(AlphabetContainer con, AlphabetContainer refCon, int refIdx, double[][] hyperParams) This constructor creates a ReferenceSequenceDiscreteEmission defining the individual hyper parameters.
ReferenceSequenceDiscreteEmission(AlphabetContainer con, AlphabetContainer refCon, int refIdx, double[][] hyperParams, double[][] initHyperParams) This constructor creates a ReferenceSequenceDiscreteEmission defining the individual hyper parameters.
ReferenceSequenceDiscreteEmission(AlphabetContainer con, AlphabetContainer refCon, int refIdx, double ess, double[][] initHyperParams) This is a simple constructor for a ReferenceSequenceDiscreteEmission based on the equivalent sample size.
ReferenceSequenceDiscreteEmission(StringBuffer xml) Creates a ReferenceSequenceDiscreteEmission from its XML representation.

Method Summary

Modifier and Type	Method and Description
protected void	appendFurtherInformation(StringBuffer xml) This method appends further information to the XML representation.
protected void	extractFurtherInformation(StringBuffer xml) This method extracts further information from the XML representation.
protected int	getConditionIndex(boolean forward, int seqPos, Sequence seq) This method returns an index encoding the condition.
protected static Sequence	getReferenceSequence(Sequence seq) Returns the reference sequence annotated to seq.
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, clone, drawParameters, drawParametersFromStatistic, estimateFromStatistic, extendSampling, 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

Field Detail

refIdx

protected int refIdx

The index in the reference sequence

Constructor Detail

ReferenceSequenceDiscreteEmission

public ReferenceSequenceDiscreteEmission(AlphabetContainer con,
                                         AlphabetContainer refCon,
                                         int refIdx,
                                         double ess)

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

Parameters:

con - the AlphabetContainer of this emission

refCon - the AlphabetContainer of the reference

refIdx - the index in the reference sequence

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

See Also:

ReferenceSequenceDiscreteEmission(AlphabetContainer, AlphabetContainer, int, double[][])

ReferenceSequenceDiscreteEmission

public ReferenceSequenceDiscreteEmission(AlphabetContainer con,
                                         AlphabetContainer refCon,
                                         int refIdx,
                                         double ess,
                                         double[][] initHyperParams)

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

Parameters:

con - the AlphabetContainer of this emission

refCon - the AlphabetContainer of the reference

refIdx - the index in the reference sequence

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

initHyperParams - the individual hyper parameters for each parameter used in AbstractConditionalDiscreteEmission.initializeFunctionRandomly()

See Also:

ReferenceSequenceDiscreteEmission(AlphabetContainer, AlphabetContainer, int, double[][])

ReferenceSequenceDiscreteEmission

public ReferenceSequenceDiscreteEmission(AlphabetContainer con,
                                         AlphabetContainer refCon,
                                         int refIdx,
                                         double[][] hyperParams)
                                  throws IllegalArgumentException

This constructor creates a ReferenceSequenceDiscreteEmission defining the individual hyper parameters.

Parameters:

con - the AlphabetContainer of this emission

refCon - the AlphabetContainer of the reference

refIdx - the index in the reference sequence

hyperParams - the individual hyper parameters for each parameter

Throws:

IllegalArgumentException - if the dimension of the hyper parameters and the size of the alphabet defined by reference AlphabetContainer do not match

ReferenceSequenceDiscreteEmission

public ReferenceSequenceDiscreteEmission(AlphabetContainer con,
                                         AlphabetContainer refCon,
                                         int refIdx,
                                         double[][] hyperParams,
                                         double[][] initHyperParams)
                                  throws IllegalArgumentException

This constructor creates a ReferenceSequenceDiscreteEmission defining the individual hyper parameters.

Parameters:

con - the AlphabetContainer of this emission

refCon - the AlphabetContainer of the reference

refIdx - the index in the reference sequence

hyperParams - the individual hyper parameters for each parameter

initHyperParams - the individual hyper parameters for each parameter used in AbstractConditionalDiscreteEmission.initializeFunctionRandomly()

Throws:

IllegalArgumentException - if the dimension of the hyper parameters and the size of the alphabet defined by reference AlphabetContainer do not match

ReferenceSequenceDiscreteEmission

public ReferenceSequenceDiscreteEmission(StringBuffer xml)
                                  throws NonParsableException

Creates a ReferenceSequenceDiscreteEmission from its XML representation.

Parameters:

xml - the XML representation.

Throws:

NonParsableException - if the XML representation could not be parsed

Method Detail

getReferenceSequence

protected static final Sequence getReferenceSequence(Sequence seq)

Returns the reference sequence annotated to seq.

Parameters:

seq - the sequence

Returns:

the reference sequence

See Also:

ReferenceSequenceAnnotation

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

appendFurtherInformation

protected void appendFurtherInformation(StringBuffer xml)

Description copied from class: AbstractConditionalDiscreteEmission

This method appends further information to the XML representation. It allows subclasses to save further parameters that are not defined in the superclass.

Overrides:

appendFurtherInformation in class AbstractConditionalDiscreteEmission

Parameters:

xml - the XML representation

extractFurtherInformation

protected void extractFurtherInformation(StringBuffer xml)
                                  throws NonParsableException

Description copied from class: AbstractConditionalDiscreteEmission

This method extracts further information from the XML representation. It allows subclasses to cast further parameters that are not defined in the superclass.

Overrides:

extractFurtherInformation in class AbstractConditionalDiscreteEmission

Parameters:

xml - the XML representation

Throws:

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