public class GenDisMixClassifierParameterSet extends ScoreClassifierParameterSet
GenDisMixClassifier
.ParameterSet.ParameterList
alphabet, length
errorMessage, parameters, parent
Modifier | Constructor and Description |
---|---|
|
GenDisMixClassifierParameterSet(AlphabetContainer alphabet,
int length,
byte algo,
double eps,
double lineps,
double startD,
boolean free,
OptimizableFunction.KindOfParameter kind,
boolean norm,
int threads)
The default constructor that constructs a new
GenDisMixClassifierParameterSet . |
protected |
GenDisMixClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass,
AlphabetContainer alphabet,
int length,
byte algo,
double eps,
double lineps,
double startD,
boolean free,
OptimizableFunction.KindOfParameter kind,
boolean norm,
int threads)
The default constructor that constructs a new
GenDisMixClassifierParameterSet . |
|
GenDisMixClassifierParameterSet(StringBuffer xml)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
int |
getNumberOfThreads()
This method returns the number of threads that should be used during optimization.
|
void |
setNumberOfThreads(int threads)
This method set the number of threads used during optimization.
|
boolean |
shouldBeNormalized()
This method indicates if a normalization shall be used while
optimization.
|
getInstanceComment, getInstanceName, getTerminantionCondition, useOnlyFreeParameter
clone, 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 GenDisMixClassifierParameterSet(StringBuffer xml) throws NonParsableException
Storable
.
Constructs a GenDisMixClassifierParameterSet
out of its XML
representation.xml
- the XML representation as StringBuffer
NonParsableException
- if the GenDisMixClassifierParameterSet
could not be
reconstructed out of the XML representation (the
StringBuffer
could not be parsed)ScoreClassifierParameterSet.ScoreClassifierParameterSet(StringBuffer)
,
Storable
public GenDisMixClassifierParameterSet(AlphabetContainer alphabet, int length, byte algo, double eps, double lineps, double startD, boolean free, OptimizableFunction.KindOfParameter kind, boolean norm, int threads) throws Exception
GenDisMixClassifierParameterSet
.alphabet
- the AlphabetContainer
length
- the length of the sequencesalgo
- the algorithm that shall be used for optimizationeps
- the epsilon for stopping the optimizationlineps
- the epsilon for stopping the line searchstartD
- the start distance for the line searchfree
- the switch for using only the free or all parameters in a
DifferentiableSequenceScore
kind
- indicates the kind of class parameter initializationnorm
- the switch for using a normalization while optimizationthreads
- the number of threads used during an optimizationException
- if something went wrongOptimizableFunction.KindOfParameter
,
GenDisMixClassifierParameterSet(Class,
de.jstacs.data.AlphabetContainer, int, byte, double, double, double, boolean,
de.jstacs.classifiers.differentiableSequenceScoreBased.OptimizableFunction.KindOfParameter, boolean,int)
protected GenDisMixClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass, AlphabetContainer alphabet, int length, byte algo, double eps, double lineps, double startD, boolean free, OptimizableFunction.KindOfParameter kind, boolean norm, int threads) throws Exception
GenDisMixClassifierParameterSet
.instanceClass
- the class of the instancealphabet
- the AlphabetContainer
length
- the length of the sequencesalgo
- the algorithm that shall be used for optimizationeps
- the epsilon for stopping the optimizationlineps
- the epsilon for stopping the line searchstartD
- the start distance for the line searchfree
- the switch for using only the free or all parameters in a
DifferentiableSequenceScore
kind
- indicates the kind of class parameter initializationnorm
- the switch for using a normalization while optimizationthreads
- the number of threads used during an optimizationException
- if something went wrongOptimizableFunction.KindOfParameter
,
ScoreClassifierParameterSet.ScoreClassifierParameterSet(Class,
de.jstacs.data.AlphabetContainer, int, byte, double, double, double, boolean,
de.jstacs.classifiers.differentiableSequenceScoreBased.OptimizableFunction.KindOfParameter)
public boolean shouldBeNormalized()
true
if a normalization shall be used while
optimization, false
otherwisepublic int getNumberOfThreads()
public void setNumberOfThreads(int threads) throws SimpleParameter.IllegalValueException
threads
- the number of threads used during optimizationSimpleParameter.IllegalValueException
- if the value could not be set