public abstract class AbstractVariableStructureModel
extends de.jstacs.sequenceScores.statisticalModels.trainable.AbstractTrainableStatisticalModel
Modifier and Type | Field and Description |
---|---|
int |
numberOfSamples |
protected java.io.BufferedReader |
reader |
protected java.lang.String |
sampleFilePath |
protected java.io.BufferedWriter |
writer |
Constructor and Description |
---|
AbstractVariableStructureModel(de.jstacs.data.AlphabetContainer alphabets,
int length)
Standard constructor.
|
AbstractVariableStructureModel(java.lang.StringBuffer sb)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
AbstractVariableStructureModel |
clone() |
abstract void |
drawParameters(de.jstacs.data.DataSet d) |
abstract double |
getLogScoreOfCurrentStructure()
The function returns the score (AIC, BIC, NML, Bayes) of the currently selected structure.
|
abstract java.lang.String |
getSparseParameterRepresentation() |
abstract void |
initForSampling(java.lang.String s) |
abstract void |
parse(java.lang.String rep) |
abstract void |
samplingStopped() |
abstract void |
saveCurrentParametersToFile() |
check, emitDataSet, fromXML, getAlphabetContainer, getCharacteristics, getLength, getLogProbFor, getLogProbFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, getMaximalMarkovOrder, toString, train
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
train
getLogPriorTerm, getLogProbFor
protected java.io.BufferedWriter writer
protected java.io.BufferedReader reader
protected java.lang.String sampleFilePath
public int numberOfSamples
public AbstractVariableStructureModel(de.jstacs.data.AlphabetContainer alphabets, int length)
alphabets
- The alphabet container.length
- The sequence length.public AbstractVariableStructureModel(java.lang.StringBuffer sb) throws de.jstacs.io.NonParsableException
Storable
.
Creates a new AbstractVariableStructureModel
out of a StringBuffer
.sb
- the StringBuffer
to be parsedde.jstacs.io.NonParsableException
- is thrown if the StringBuffer
could not be parsedpublic abstract double getLogScoreOfCurrentStructure()
public AbstractVariableStructureModel clone() throws java.lang.CloneNotSupportedException
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 abstract void parse(java.lang.String rep)
public abstract java.lang.String getSparseParameterRepresentation()
public abstract void saveCurrentParametersToFile() throws java.io.IOException
java.io.IOException
public abstract void initForSampling(java.lang.String s) throws java.io.IOException
java.io.IOException
public abstract void drawParameters(de.jstacs.data.DataSet d) throws java.lang.Exception
java.lang.Exception
public abstract void samplingStopped() throws java.io.IOException
java.io.IOException