public class DiscreteEmission extends AbstractConditionalDiscreteEmission
con, counter, ess, grad, hyperParams, logNorm, offset, params, paramsFile, probs, reader, samplingIndex, statistic, writer
Constructor and Description |
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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. |
Modifier and Type | Method and Description |
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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. |
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
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 parsedprotected 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 sequencepublic String toString(NumberFormat nf)
Emission
String
representation of the instance.nf
- the NumberFormat
for the String
representation of parameters or probabilitiesString
representation of the instance