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java.lang.Object de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.AbstractConditionalDiscreteEmission de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.DiscreteEmission
public class DiscreteEmission
This class implements a simple discrete emission without any condition.
Field Summary |
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Fields inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.AbstractConditionalDiscreteEmission |
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con, counter, ess, grad, hyperParams, logNorm, offset, params, paramsFile, probs, reader, samplingIndex, statistic, writer |
Constructor Summary | |
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DiscreteEmission(AlphabetContainer con,
double ess)
This is a simple constructor for a DiscreteEmission based on the equivalent sample size. |
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DiscreteEmission(AlphabetContainer con,
double[] hyperParams)
This is a simple constructor for a DiscreteEmission defining the individual hyper parameters. |
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DiscreteEmission(StringBuffer xml)
Creates a DiscreteEmission from its XML representation. |
Method Summary | |
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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 |
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acceptParameters, addGradientOfLogPriorTerm, addToStatistic, appendFurtherInformation, clone, drawParameters, drawParametersFromStatistic, estimateFromStatistic, extendSampling, extractFurtherInformation, fillCurrentParameter, fillSamplingGroups, finalize, fromXML, getAlphabetContainer, getHyperParams, 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 |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public DiscreteEmission(AlphabetContainer con, double ess)
DiscreteEmission
based on the equivalent sample size.
con
- the AlphabetContainer
of this emissioness
- the equivalent sample size (ess) of this emission that is equally distributed over all parametersDiscreteEmission(AlphabetContainer, double[])
public DiscreteEmission(AlphabetContainer con, double[] hyperParams)
DiscreteEmission
defining the individual hyper parameters.
con
- the AlphabetContainer
of this emissionhyperParams
- the individual hyper parameters for each parameterpublic DiscreteEmission(StringBuffer xml) throws NonParsableException
DiscreteEmission
from its XML representation.
xml
- the XML representation.
NonParsableException
- if the XML representation could not be parsedMethod Detail |
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protected int getConditionIndex(boolean forward, int seqPos, Sequence seq)
AbstractConditionalDiscreteEmission
getConditionIndex
in class AbstractConditionalDiscreteEmission
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
public String toString(NumberFormat nf)
Emission
String
representation of the instance.
nf
- the NumberFormat
for the String
representation of parameters or probabilities
String
representation of the instance
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