de.jstacs.classifier.scoringFunctionBased.gendismix
Class GenDisMixClassifierParameterSet
java.lang.Object
de.jstacs.parameters.ParameterSet
de.jstacs.parameters.InstanceParameterSet
de.jstacs.parameters.SequenceScoringParameterSet
de.jstacs.classifier.scoringFunctionBased.ScoreClassifierParameterSet
de.jstacs.classifier.scoringFunctionBased.gendismix.GenDisMixClassifierParameterSet
- All Implemented Interfaces:
- GalaxyConvertible, RangeIterator, Storable, Cloneable
public class GenDisMixClassifierParameterSet
- extends ScoreClassifierParameterSet
This class contains the parameters for the GenDisMixClassifier
.
- Author:
- Jan Grau, Jens Keilwagen
Constructor Summary |
|
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 . |
Method Summary |
int |
getNumberOfThreads()
This method returns the number of threads that should be used during optimization. |
protected void |
loadParameters()
Loads the parameters for this ParameterSet . |
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. |
Methods inherited from class de.jstacs.parameters.SequenceScoringParameterSet |
clone, equals, fromXML, getAlphabetContainer, getLength, getNumberOfParameters, getParameterAt, hasDefaultOrIsSet, replaceParametersWithRangedInstance, reset, toXML |
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 |
GenDisMixClassifierParameterSet
public GenDisMixClassifierParameterSet(StringBuffer xml)
throws NonParsableException
- The standard constructor for the interface
Storable
.
Constructs a GenDisMixClassifierParameterSet
out of its XML
representation.
- Parameters:
xml
- the XML representation as StringBuffer
- Throws:
NonParsableException
- if the GenDisMixClassifierParameterSet
could not be
reconstructed out of the XML representation (the
StringBuffer
could not be parsed)- See Also:
ScoreClassifierParameterSet.ScoreClassifierParameterSet(StringBuffer)
,
Storable
GenDisMixClassifierParameterSet
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
- The default constructor that constructs a new
GenDisMixClassifierParameterSet
.
- Parameters:
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
ScoringFunction
kind
- indicates the kind of class parameter initializationnorm
- the switch for using a normalization while optimizationthreads
- the NumberFormatException
of threads used during an optimization
- Throws:
Exception
- if something went wrong- See Also:
OptimizableFunction.KindOfParameter
,
GenDisMixClassifierParameterSet(Class,
de.jstacs.data.AlphabetContainer, int, byte, double, double, double, boolean,
de.jstacs.classifier.scoringFunctionBased.OptimizableFunction.KindOfParameter, boolean,int)
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)
throws Exception
- The default constructor that constructs a new
GenDisMixClassifierParameterSet
.
- Parameters:
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
ScoringFunction
kind
- indicates the kind of class parameter initializationnorm
- the switch for using a normalization while optimizationthreads
- the NumberFormatException
of threads used during an optimization
- Throws:
Exception
- if something went wrong- See Also:
OptimizableFunction.KindOfParameter
,
ScoreClassifierParameterSet.ScoreClassifierParameterSet(Class,
de.jstacs.data.AlphabetContainer, int, byte, double, double, double, boolean,
de.jstacs.classifier.scoringFunctionBased.OptimizableFunction.KindOfParameter)
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 ScoreClassifierParameterSet
- Throws:
Exception
- if the parameters could not be loaded- See Also:
Parameter
,
ParameterSet.parameters
,
ParameterSet.initParameterList()
,
ParameterSet.initParameterList(int)
shouldBeNormalized
public boolean shouldBeNormalized()
- This method indicates if a normalization shall be used while
optimization. The normalization is done through division by the number of
sequences.
- Returns:
true
if a normalization shall be used while
optimization, false
otherwise
getNumberOfThreads
public int getNumberOfThreads()
- This method returns the number of threads that should be used during optimization.
- Returns:
- the number of threads that should be used during optimization
setNumberOfThreads
public void setNumberOfThreads(int threads)
throws SimpleParameter.IllegalValueException
- This method set the number of threads used during optimization.
- Parameters:
threads
- the number of threads used during optimization
- Throws:
SimpleParameter.IllegalValueException
- if the value could not be set