public class ReferenceSequenceDiscreteEmission extends AbstractConditionalDiscreteEmission
ReferenceSequenceAnnotation
at a certain reference position. This class can be used in so-called conditional profile HMM for
the match states.Modifier and Type | Field and Description |
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protected int |
refIdx
The index in the reference sequence
|
con, counter, ess, grad, hyperParams, logNorm, offset, params, paramsFile, probs, reader, samplingIndex, statistic, writer
Constructor and Description |
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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. |
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. |
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
public ReferenceSequenceDiscreteEmission(AlphabetContainer con, AlphabetContainer refCon, int refIdx, double ess)
ReferenceSequenceDiscreteEmission
based on the equivalent sample size.con
- the AlphabetContainer
of this emissionrefCon
- the AlphabetContainer
of the referencerefIdx
- the index in the reference sequenceess
- the equivalent sample size (ess) of this emission that is equally distributed over all parametersReferenceSequenceDiscreteEmission(AlphabetContainer, AlphabetContainer, int, double[][])
public ReferenceSequenceDiscreteEmission(AlphabetContainer con, AlphabetContainer refCon, int refIdx, double ess, double[][] initHyperParams)
ReferenceSequenceDiscreteEmission
based on the equivalent sample size.con
- the AlphabetContainer
of this emissionrefCon
- the AlphabetContainer
of the referencerefIdx
- the index in the reference sequenceess
- the equivalent sample size (ess) of this emission that is equally distributed over all parametersinitHyperParams
- the individual hyper parameters for each parameter used in AbstractConditionalDiscreteEmission.initializeFunctionRandomly()
ReferenceSequenceDiscreteEmission(AlphabetContainer, AlphabetContainer, int, double[][])
public ReferenceSequenceDiscreteEmission(AlphabetContainer con, AlphabetContainer refCon, int refIdx, double[][] hyperParams) throws IllegalArgumentException
ReferenceSequenceDiscreteEmission
defining the individual hyper parameters.con
- the AlphabetContainer
of this emissionrefCon
- the AlphabetContainer
of the referencerefIdx
- the index in the reference sequencehyperParams
- the individual hyper parameters for each parameterIllegalArgumentException
- if the dimension of the hyper parameters and the size of the alphabet defined by reference AlphabetContainer
do not matchpublic ReferenceSequenceDiscreteEmission(AlphabetContainer con, AlphabetContainer refCon, int refIdx, double[][] hyperParams, double[][] initHyperParams) throws IllegalArgumentException
ReferenceSequenceDiscreteEmission
defining the individual hyper parameters.con
- the AlphabetContainer
of this emissionrefCon
- the AlphabetContainer
of the referencerefIdx
- the index in the reference sequencehyperParams
- the individual hyper parameters for each parameterinitHyperParams
- the individual hyper parameters for each parameter used in AbstractConditionalDiscreteEmission.initializeFunctionRandomly()
IllegalArgumentException
- if the dimension of the hyper parameters and the size of the alphabet defined by reference AlphabetContainer
do not matchpublic ReferenceSequenceDiscreteEmission(StringBuffer xml) throws NonParsableException
ReferenceSequenceDiscreteEmission
from its XML representation.xml
- the XML representation.NonParsableException
- if the XML representation could not be parsedprotected static final Sequence getReferenceSequence(Sequence seq)
seq
.seq
- the sequenceReferenceSequenceAnnotation
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 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 instanceprotected void appendFurtherInformation(StringBuffer xml)
AbstractConditionalDiscreteEmission
appendFurtherInformation
in class AbstractConditionalDiscreteEmission
xml
- the XML representationprotected void extractFurtherInformation(StringBuffer xml) throws NonParsableException
AbstractConditionalDiscreteEmission
extractFurtherInformation
in class AbstractConditionalDiscreteEmission
xml
- the XML representationNonParsableException
- if the information could not be reconstructed out of the StringBuffer
xml