de.jstacs.classifier.scoringFunctionBased.sampling
Class SamplingGenDisMixClassifierParameterSet
java.lang.Object
de.jstacs.parameters.ParameterSet
de.jstacs.parameters.InstanceParameterSet
de.jstacs.parameters.SequenceScoringParameterSet
de.jstacs.classifier.scoringFunctionBased.sampling.SamplingScoreBasedClassifierParameterSet
de.jstacs.classifier.scoringFunctionBased.sampling.SamplingGenDisMixClassifierParameterSet
- All Implemented Interfaces:
- GalaxyConvertible, RangeIterator, Storable, Cloneable
public class SamplingGenDisMixClassifierParameterSet
- extends SamplingScoreBasedClassifierParameterSet
ParameterSet
to instantiate a SamplingGenDisMixClassifier
.
- Author:
- Jan Grau
Constructor Summary |
|
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 . |
Methods inherited from class de.jstacs.parameters.ParameterSet |
fromGalaxy, getErrorMessage, getId, getIndex, getNumberOfValues, getParent, initParameterList, initParameterList, isAtomic, isRanged, makeRanged, next, parametersLoaded, propagateId, recieveId, resetToFirst, setParent, simplify, toGalaxy, valuesToString |
SamplingGenDisMixClassifierParameterSet
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
- Create a new
SamplingGenDisMixClassifierParameterSet
.
- Parameters:
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 lenght 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
- Throws:
Exception
- if the parameters could not be created
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)
throws Exception
- Create a new
SamplingGenDisMixClassifierParameterSet
.
- Parameters:
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 lenght 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
- Throws:
Exception
- if the parameters could not be created
SamplingGenDisMixClassifierParameterSet
public SamplingGenDisMixClassifierParameterSet(AlphabetContainer alphabet,
int length,
int numStarts,
int testSamplings,
int stationarySamplings,
String outfilePrefix,
int threads)
throws Exception
- Create a new
SamplingGenDisMixClassifierParameterSet
with a grouped sampling scheme, sampling all parameters
(and not only the free ones), and adaption of the variance.
- Parameters:
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 lenght 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
- Throws:
Exception
- if the parameters could not be created
getInstanceComment
public String getInstanceComment()
- Description copied from class:
InstanceParameterSet
- Returns a comment (a textual description) of the class that can be
constructed using this
ParameterSet
.
- Specified by:
getInstanceComment
in class InstanceParameterSet
- Returns:
- the comment of the class
getInstanceName
public String getInstanceName()
- Description copied from class:
InstanceParameterSet
- Returns the name of an instance of the class that can be constructed
using this
ParameterSet
.
- Specified by:
getInstanceName
in class InstanceParameterSet
- Returns:
- the name of the class
loadParameters
protected void loadParameters()
throws Exception
- Description copied from class:
ParameterSet
- Loads the parameters for this
ParameterSet
. This is in most cases
done by calling ParameterSet.initParameterList()
or
ParameterSet.initParameterList(int)
to initialize
ParameterSet.parameters
and afterwards filling
ParameterSet.parameters
with instances of subclasses of
Parameter
.
- Overrides:
loadParameters
in class SamplingScoreBasedClassifierParameterSet
- Throws:
Exception
- if the parameters could not be loaded- See Also:
Parameter
,
ParameterSet.parameters
,
ParameterSet.initParameterList()
,
ParameterSet.initParameterList(int)
getNumberOfThreads
public int getNumberOfThreads()
- Returns the number of threads for evaluating the
LogGenDisMixFunction
- Returns:
- the number of threads