public class ZOOPSModel extends AbstractLatentVariableModel implements de.jstacs.motifDiscovery.MotifDiscoverer
expString, lagInStationaryPhase, lengthOfBurnIn, mode, numberOfIterations, numberOfRestarts, reader, sampleStorageDirectory, writer
Constructor and Description |
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ZOOPSModel(AbstractVariableStructureModel motifModel,
de.jstacs.sequenceScores.statisticalModels.trainable.AbstractTrainableStatisticalModel flankingModel,
int numberOfIterations,
int numberOfRestarts)
Creates ZOOPS model for learning via stochastic maximization algorithm
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ZOOPSModel(AbstractVariableStructureModel motifModel,
de.jstacs.sequenceScores.statisticalModels.trainable.AbstractTrainableStatisticalModel flankingModel,
int numberOfIterations,
int numberOfRestarts,
int lengthOfBurnIn,
int lagInStationaryPhase)
Creates ZOOPS model for learning via Gibbs sampling algorithm for model averaging
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ZOOPSModel(java.lang.StringBuffer sb)
Loads a ZOOPS model from XML
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Modifier and Type | Method and Description |
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ZOOPSModel |
clone() |
protected void |
fromXML(java.lang.StringBuffer xml) |
de.jstacs.sequenceScores.statisticalModels.trainable.AbstractTrainableStatisticalModel |
getFlankingModel() |
int |
getGlobalIndexOfMotifInComponent(int component,
int motif) |
int |
getIndexOfMaximalComponentFor(de.jstacs.data.sequences.Sequence sequence) |
java.lang.String |
getInstanceName() |
double |
getLogPriorTerm() |
double |
getLogProbFor(de.jstacs.data.DataSet data) |
double |
getLogProbFor(de.jstacs.data.sequences.Sequence sequence,
int startpos,
int endpos) |
int |
getMotifLength(int motif) |
de.jstacs.sequenceScores.statisticalModels.trainable.AbstractTrainableStatisticalModel |
getMotifModel() |
int |
getNumberOfComponents() |
int |
getNumberOfMotifs() |
int |
getNumberOfMotifsInComponent(int component) |
de.jstacs.results.NumericalResultSet |
getNumericalCharacteristics() |
double[] |
getProfileOfScoresFor(int component,
int motif,
de.jstacs.data.sequences.Sequence sequence,
int startpos,
de.jstacs.motifDiscovery.MotifDiscoverer.KindOfProfile kind) |
double[] |
getStrandProbabilitiesFor(int component,
int motif,
de.jstacs.data.sequences.Sequence sequence,
int startpos) |
boolean |
isInitialized() |
void |
setTextOutput(boolean out) |
java.lang.String |
toString(java.text.NumberFormat nf) |
java.lang.StringBuffer |
toXML()
Writes an XML representation of the ZOOPS model
|
void |
train(de.jstacs.data.DataSet data,
double[] weights) |
getSampleStorageDirectory, setSampleStorageDirectory
check, emitDataSet, getAlphabetContainer, getCharacteristics, getLength, getLogProbFor, getLogProbFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, getMaximalMarkovOrder, toString, train
public ZOOPSModel(AbstractVariableStructureModel motifModel, de.jstacs.sequenceScores.statisticalModels.trainable.AbstractTrainableStatisticalModel flankingModel, int numberOfIterations, int numberOfRestarts) throws java.lang.Exception
motifModel
- The model for the putative binding sitesflankingModel
- The model for the flanking regionsnumberOfIterations
- Number of iteration steps per restartnumberOfRestarts
- Number of restartsjava.lang.Exception
public ZOOPSModel(AbstractVariableStructureModel motifModel, de.jstacs.sequenceScores.statisticalModels.trainable.AbstractTrainableStatisticalModel flankingModel, int numberOfIterations, int numberOfRestarts, int lengthOfBurnIn, int lagInStationaryPhase) throws java.lang.Exception
motifModel
- The model for the putative binding sitesflankingModel
- The model for the flanking regionsnumberOfIterations
- Number of iteration steps per restartnumberOfRestarts
- Number of restartslengthOfBurnIn
- The number of iteration steps until parameter samples are storedlagInStationaryPhase
- The number of iteration steps between two stored parameter samplesjava.lang.Exception
public ZOOPSModel(java.lang.StringBuffer sb) throws de.jstacs.io.NonParsableException
sb
- XML representationde.jstacs.io.NonParsableException
protected void fromXML(java.lang.StringBuffer xml) throws de.jstacs.io.NonParsableException
fromXML
in class de.jstacs.sequenceScores.statisticalModels.trainable.AbstractTrainableStatisticalModel
de.jstacs.io.NonParsableException
public java.lang.StringBuffer toXML()
toXML
in interface de.jstacs.Storable
de.jstacs.io.NonParsableException
public ZOOPSModel clone() throws java.lang.CloneNotSupportedException
clone
in interface de.jstacs.motifDiscovery.MotifDiscoverer
clone
in interface de.jstacs.sequenceScores.SequenceScore
clone
in interface de.jstacs.sequenceScores.statisticalModels.trainable.TrainableStatisticalModel
clone
in class de.jstacs.sequenceScores.statisticalModels.trainable.AbstractTrainableStatisticalModel
java.lang.CloneNotSupportedException
public void train(de.jstacs.data.DataSet data, double[] weights) throws java.lang.Exception
train
in interface de.jstacs.sequenceScores.statisticalModels.trainable.TrainableStatisticalModel
java.lang.Exception
public double getLogPriorTerm() throws java.lang.Exception
getLogPriorTerm
in interface de.jstacs.sequenceScores.statisticalModels.StatisticalModel
java.lang.Exception
public double getLogProbFor(de.jstacs.data.sequences.Sequence sequence, int startpos, int endpos) throws java.lang.Exception
getLogProbFor
in interface de.jstacs.sequenceScores.statisticalModels.StatisticalModel
java.lang.Exception
public double getLogProbFor(de.jstacs.data.DataSet data) throws java.lang.Exception
java.lang.Exception
public java.lang.String getInstanceName()
getInstanceName
in interface de.jstacs.sequenceScores.SequenceScore
public de.jstacs.results.NumericalResultSet getNumericalCharacteristics() throws java.lang.Exception
getNumericalCharacteristics
in interface de.jstacs.sequenceScores.SequenceScore
java.lang.Exception
public boolean isInitialized()
isInitialized
in interface de.jstacs.sequenceScores.SequenceScore
public int getMotifLength(int motif)
getMotifLength
in interface de.jstacs.motifDiscovery.MotifDiscoverer
public int getNumberOfComponents()
getNumberOfComponents
in interface de.jstacs.motifDiscovery.MotifDiscoverer
public int getNumberOfMotifs()
getNumberOfMotifs
in interface de.jstacs.motifDiscovery.MotifDiscoverer
public int getNumberOfMotifsInComponent(int component)
getNumberOfMotifsInComponent
in interface de.jstacs.motifDiscovery.MotifDiscoverer
public int getGlobalIndexOfMotifInComponent(int component, int motif)
getGlobalIndexOfMotifInComponent
in interface de.jstacs.motifDiscovery.MotifDiscoverer
public double[] getProfileOfScoresFor(int component, int motif, de.jstacs.data.sequences.Sequence sequence, int startpos, de.jstacs.motifDiscovery.MotifDiscoverer.KindOfProfile kind) throws java.lang.Exception
getProfileOfScoresFor
in interface de.jstacs.motifDiscovery.MotifDiscoverer
java.lang.Exception
public double[] getStrandProbabilitiesFor(int component, int motif, de.jstacs.data.sequences.Sequence sequence, int startpos) throws java.lang.Exception
getStrandProbabilitiesFor
in interface de.jstacs.motifDiscovery.MotifDiscoverer
java.lang.Exception
public de.jstacs.sequenceScores.statisticalModels.trainable.AbstractTrainableStatisticalModel getMotifModel()
public de.jstacs.sequenceScores.statisticalModels.trainable.AbstractTrainableStatisticalModel getFlankingModel()
public java.lang.String toString(java.text.NumberFormat nf)
toString
in interface de.jstacs.sequenceScores.SequenceScore
public int getIndexOfMaximalComponentFor(de.jstacs.data.sequences.Sequence sequence) throws java.lang.Exception
getIndexOfMaximalComponentFor
in interface de.jstacs.motifDiscovery.MotifDiscoverer
java.lang.Exception
public void setTextOutput(boolean out)