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
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 |
Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.AbstractConditionalDiscreteEmission |
acceptParameters, addGradientOfLogPriorTerm, addToStatistic, appendFurtherInformation, clone, 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 |
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 emissioness
- 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 emissionhyperParams
- 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
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()
- Specified by:
toString
in class AbstractConditionalDiscreteEmission