public abstract class SamplingScoreBasedClassifierParameterSet extends SequenceScoringParameterSet
ParameterSet
to instantiate a SamplingScoreBasedClassifier
.ParameterSet.ParameterList
alphabet, length
errorMessage, parameters, parent
Constructor and Description |
---|
SamplingScoreBasedClassifierParameterSet(Class<? extends SamplingScoreBasedClassifier> instanceClass,
AlphabetContainer alphabet,
int length,
int numStarts,
int testSamplings,
int stationarySamplings,
String outfilePrefix)
Create a new
SamplingScoreBasedClassifierParameterSet with a grouped sampling scheme, sampling all parameters
(and not only the free ones), and adaption of the variance. |
SamplingScoreBasedClassifierParameterSet(Class<? extends SamplingScoreBasedClassifier> instanceClass,
AlphabetContainer alphabet,
int length,
int numStarts,
SamplingScoreBasedClassifier.SamplingScheme scheme,
int testSamplings,
int stationarySamplings,
boolean freeParameters,
boolean adaptVariance,
String outfilePrefix)
Create a new
SamplingScoreBasedClassifierParameterSet . |
Modifier and Type | Method and Description |
---|---|
SamplingScoreBasedClassifierParameterSet |
clone()
Creates a full clone (deep copy) of this
ParameterSet . |
boolean |
getAdaptVariance()
Returns true if the sampling variance shall be adapted to the size
of the event space of a random variable
|
boolean |
getFreeParameters()
Returns
true if only free parameters shall be used |
int |
getNumberOfStarts()
Returns the number of independent sampling starts
|
int |
getNumberOfStationarySamplings()
Returns the number of samplings steps in the stationary phase
|
int |
getNumberOfTestSamplings()
Returns the number of samplings between checks for the stationary phase
|
String |
getOutfilePrefix()
Returns the prefix of the temporary files for storing sampled
parameter values
|
SamplingScoreBasedClassifier.SamplingScheme |
getSamplingScheme()
Returns the sampling scheme
|
void |
setNumberOfStarts(int i)
Sets the number of starts to
i |
equals, fromXML, getAlphabetContainer, getLength, getNumberOfParameters, getParameterAt, hasDefaultOrIsSet, reset, toXML
getInstance, getInstanceClass, getInstanceComment, getInstanceName
fromGalaxy, getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getParameterForName, getParent, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, setParent, toGalaxy
public SamplingScoreBasedClassifierParameterSet(Class<? extends SamplingScoreBasedClassifier> instanceClass, AlphabetContainer alphabet, int length, int numStarts, SamplingScoreBasedClassifier.SamplingScheme scheme, int testSamplings, int stationarySamplings, boolean freeParameters, boolean adaptVariance, String outfilePrefix) throws Exception
SamplingScoreBasedClassifierParameterSet
.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 parametersException
- if the parameters could not be createdSamplingScoreBasedClassifier
public SamplingScoreBasedClassifierParameterSet(Class<? extends SamplingScoreBasedClassifier> instanceClass, AlphabetContainer alphabet, int length, int numStarts, int testSamplings, int stationarySamplings, String outfilePrefix) throws Exception
SamplingScoreBasedClassifierParameterSet
with a grouped sampling scheme, sampling all parameters
(and not only the free ones), and adaption of the variance.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 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 parametersException
- if the parameters could not be createdSamplingScoreBasedClassifier
public SamplingScoreBasedClassifierParameterSet clone() throws CloneNotSupportedException
ParameterSet
ParameterSet
. As a
convenience-method the user can use
fillWithStandardFieldsForClone(ParameterSet)
on a newly
created instance of a subclass of ParameterSet
to obtain a
clone/copy of all standard member variables (those already defined in
ParameterSet
) in the passed ParameterSet
. Using this
method, the cloning process becomes merely three-step:ParameterSet
, most
likely with an empty constructor or the one taking just the instance
class.
this.fillWithStandardFieldsForClone
on this
instance.
Object
's method
Object.clone()
.clone
in class SequenceScoringParameterSet
ParameterSet
CloneNotSupportedException
public int getNumberOfStarts()
public SamplingScoreBasedClassifier.SamplingScheme getSamplingScheme()
public int getNumberOfTestSamplings()
public int getNumberOfStationarySamplings()
public boolean getFreeParameters()
true
if only free parameters shall be usedpublic boolean getAdaptVariance()
SamplingScoreBasedClassifier
public String getOutfilePrefix()
public void setNumberOfStarts(int i) throws SimpleParameter.IllegalValueException
i
i
- the new number of startsSimpleParameter.IllegalValueException
- if this value is not allowed