public class SamplingPhyloHMM extends SamplingHigherOrderHMM
SamplingHigherOrderHMM.ViterbiComputation
HigherOrderHMM.Type
burnInTest, hasSampled
backwardIntermediate, container, logEmission, numberOfSummands, skipInit, stateList
bwdMatrix, emission, emissionIdx, finalState, forward, fwdMatrix, name, sostream, START_NODE, states, threads, trainingParameter, transition
alphabets, length
Constructor and Description |
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SamplingPhyloHMM(SamplingHMMTrainingParameterSet trainingParameterSet,
String[] name,
int[] emissionIdx,
boolean[] forward,
PhyloDiscreteEmission[] emission,
TransitionElement... te)
This is the main constructor for a hidden markov model with phylogenetic emission(s)
This model can be trained using a metropolis hastings algorithm
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SamplingPhyloHMM(StringBuffer xml)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
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String |
getInstanceName()
Should return a short instance name such as iMM(0), BN(2), ...
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protected void |
getNewParameters()
This method set all parameters for the next sampling step
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acceptParameters, appendFurtherInformation, clone, createStates, drawFromStatistics, extractFurtherInformation, furtherInits, getLogPosteriorFromStatistic, getLogProbForPath, getLogStatePosteriorMatrixFor, getViterbiPath, getViterbiPathFor, getXMLTag, gibbsSampling, gibbsSamplingStep, initTraining, isInitialized, logProb, parseNextParameterSet, parseParameterSet, train
baumWelch, createHelperVariables, estimateFromStatistics, fillBwdMatrix, fillBwdOrViterbiMatrix, fillFwdMatrix, fillLogStatePosteriorMatrix, finalize, getCharacteristics, getEmissionIndexes, getEmissions, getLogPriorTerm, getLogScoreFor, getLogScoreFor, getMaximalMarkovOrder, getNames, getNumericalCharacteristics, getTrainingParams, getTransisionElements, initialize, initializeRandomly, resetStatistics, samplePath, setSkiptInit, viterbi
createMatrixForStatePosterior, decodePath, decodeStatePosterior, determineFinalStates, fromXML, getFinalStatePosterioriMatrix, getGraphvizRepresentation, getGraphvizRepresentation, getGraphvizRepresentation, getGraphvizRepresentation, getLogProbFor, getLogStatePosteriorMatrixFor, getNumberOfStates, getNumberOfThreads, getRunTimeException, getStatePosteriorMatrixFor, getStatePosteriorMatrixFor, getViterbiPathFor, getViterbiPathsFor, initTransition, provideMatrix, setOutputStream, toString, toXML, train
check, emitDataSet, getAlphabetContainer, getLength, getLogProbFor, getLogProbFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, toString
public SamplingPhyloHMM(SamplingHMMTrainingParameterSet trainingParameterSet, String[] name, int[] emissionIdx, boolean[] forward, PhyloDiscreteEmission[] emission, TransitionElement... te) throws CloneNotSupportedException, IllegalArgumentException, WrongAlphabetException, Exception
trainingParameterSet
- the ParameterSet
that determines the training algorithm and contains the necessary Parameter
sname
- the names of the statesemissionIdx
- the indices of the emissions that should be used for each stateforward
- a boolean array that indicates whether the symbol on the forward or the reverse complementary strand should be usedemission
- the emissionste
- the TransitionElement
s building a transitionCloneNotSupportedException
- if the parameters or the emissions or transition elements could not be clonedIllegalArgumentException
- if one of the parameters is not allowedWrongAlphabetException
- if the alphabet does not fit the modelException
- if something else went wrongpublic SamplingPhyloHMM(StringBuffer xml) throws NonParsableException
Storable
.
Constructs an SamplingPhyloHMM
out of an XML representation.xml
- the XML representation as StringBuffer
NonParsableException
- if the SamplingPhyloHMM
could not be reconstructed out of
the StringBuffer
xml
public String getInstanceName()
SequenceScore
getInstanceName
in interface SequenceScore
getInstanceName
in class SamplingHigherOrderHMM
protected void getNewParameters() throws Exception
SamplingHigherOrderHMM
getNewParameters
in class SamplingHigherOrderHMM
Exception
- if something went wrong