public class SamplingGenDisMixClassifierParameterSet extends SamplingScoreBasedClassifierParameterSet
ParameterSet
to instantiate a SamplingGenDisMixClassifier
.ParameterSet.ParameterList
alphabet, length
errorMessage, parameters, parent
Modifier | Constructor and Description |
---|---|
|
SamplingGenDisMixClassifierParameterSet(AlphabetContainer alphabet,
int length,
int numStarts,
int testSamplings,
int stationarySamplings,
String outfilePrefix,
int threads)
Create a new
SamplingGenDisMixClassifierParameterSet with a grouped sampling scheme, sampling all parameters
(and not only the free ones), and adaption of the variance. |
|
SamplingGenDisMixClassifierParameterSet(AlphabetContainer alphabet,
int length,
int numStarts,
SamplingScoreBasedClassifier.SamplingScheme scheme,
int testSamplings,
int stationarySamplings,
boolean freeParameters,
boolean adaptVariance,
String outfilePrefix,
int threads)
Create a new
SamplingGenDisMixClassifierParameterSet . |
protected |
SamplingGenDisMixClassifierParameterSet(Class<? extends SamplingScoreBasedClassifier> instanceClass,
AlphabetContainer alphabet,
int length,
int numStarts,
SamplingScoreBasedClassifier.SamplingScheme scheme,
int testSamplings,
int stationarySamplings,
boolean freeParameters,
boolean adaptVariance,
String outfilePrefix,
int threads)
Create a new
SamplingGenDisMixClassifierParameterSet . |
Modifier and Type | Method and Description |
---|---|
String |
getInstanceComment()
Returns a comment (a textual description) of the class that can be
constructed using this
ParameterSet . |
String |
getInstanceName()
Returns the name of an instance of the class that can be constructed
using this
ParameterSet . |
int |
getNumberOfThreads()
Returns the number of threads for evaluating the
LogGenDisMixFunction |
clone, getAdaptVariance, getFreeParameters, getNumberOfStarts, getNumberOfStationarySamplings, getNumberOfTestSamplings, getOutfilePrefix, getSamplingScheme, setNumberOfStarts
equals, fromXML, getAlphabetContainer, getLength, getNumberOfParameters, getParameterAt, hasDefaultOrIsSet, reset, toXML
getInstance, getInstanceClass
fromGalaxy, getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getParameterForName, getParent, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, setParent, toGalaxy
public SamplingGenDisMixClassifierParameterSet(AlphabetContainer alphabet, int length, int numStarts, SamplingScoreBasedClassifier.SamplingScheme scheme, int testSamplings, int stationarySamplings, boolean freeParameters, boolean adaptVariance, String outfilePrefix, int threads) throws Exception
SamplingGenDisMixClassifierParameterSet
.alphabet
- the alphabet of the classifierlength
- the length of the sequences that can be classifiednumStarts
- the number of independent samplingsscheme
- the sampling schemetestSamplings
- the number of samplings between checks for the length of the burn-in phasestationarySamplings
- the number of samplings in the stationary phasefreeParameters
- if only free parameters shall be usedadaptVariance
- if the variance shall be adapted to the size of the event space of a random variableoutfilePrefix
- the prefix of the temporary files for storing the parametersthreads
- the number of threads for evaluating the LogGenDisMixFunction
Exception
- if the parameters could not be createdprotected SamplingGenDisMixClassifierParameterSet(Class<? extends SamplingScoreBasedClassifier> instanceClass, AlphabetContainer alphabet, int length, int numStarts, SamplingScoreBasedClassifier.SamplingScheme scheme, int testSamplings, int stationarySamplings, boolean freeParameters, boolean adaptVariance, String outfilePrefix, int threads) throws Exception
SamplingGenDisMixClassifierParameterSet
.instanceClass
- the class, which must be a subclass of SamplingScoreBasedClassifier
alphabet
- the alphabet of the classifierlength
- the length of the sequences that can be classifiednumStarts
- the number of independent samplingsscheme
- the sampling schemetestSamplings
- the number of samplings between checks for the length of the burn-in phasestationarySamplings
- the number of samplings in the stationary phasefreeParameters
- if only free parameters shall be usedadaptVariance
- if the variance shall be adapted to the size of the event space of a random variableoutfilePrefix
- the prefix of the temporary files for storing the parametersthreads
- the number of threads for evaluating the LogGenDisMixFunction
Exception
- if the parameters could not be createdpublic SamplingGenDisMixClassifierParameterSet(AlphabetContainer alphabet, int length, int numStarts, int testSamplings, int stationarySamplings, String outfilePrefix, int threads) throws Exception
SamplingGenDisMixClassifierParameterSet
with a grouped sampling scheme, sampling all parameters
(and not only the free ones), and adaption of the variance.alphabet
- the alphabet of the classifierlength
- the length of the sequences that can be classifiednumStarts
- the number of independent samplingstestSamplings
- the number of samplings between checks for the length of the burn-in phasestationarySamplings
- the number of samplings in the stationary phaseoutfilePrefix
- the prefix of the temporary files for storing the parametersthreads
- the number of threads for evaluating the LogGenDisMixFunction
Exception
- if the parameters could not be createdpublic String getInstanceComment()
InstanceParameterSet
ParameterSet
.getInstanceComment
in class InstanceParameterSet
public String getInstanceName()
InstanceParameterSet
ParameterSet
.getInstanceName
in class InstanceParameterSet
public int getNumberOfThreads()
LogGenDisMixFunction