de.jstacs.classifier.scoringFunctionBased.cll
Class CLLClassifierParameterSet
java.lang.Object
de.jstacs.parameters.ParameterSet
de.jstacs.parameters.InstanceParameterSet
de.jstacs.classifier.scoringFunctionBased.ScoreClassifierParameterSet
de.jstacs.classifier.scoringFunctionBased.cll.CLLClassifierParameterSet
- All Implemented Interfaces:
- RangeIterator, Storable, Cloneable
public class CLLClassifierParameterSet
- extends ScoreClassifierParameterSet
This class contains the parameters for the CLLClassifier
.
- Author:
- Jan Grau, Jens Keilwagen
Method Summary |
protected void |
loadParameters()
Loads the parameters for this ParameterSet . |
boolean |
shouldBeNormalized()
This method true if a normalization shall be used while optimization. |
Methods inherited from class de.jstacs.parameters.InstanceParameterSet |
clone, equals, fromXML, getAlphabet, getIndex, getLength, getNumberOfParameters, getParameterAt, hasDefaultOrIsSet, replaceParametersWithRangedInstance, reset, toXML |
Methods inherited from class de.jstacs.parameters.ParameterSet |
getErrorMessage, getId, getInstance, getInstanceClass, getNumberOfValues, getParent, initParameterList, initParameterList, isAtomic, isRanged, makeRanged, next, parametersLoaded, propagateId, recieveId, resetToFirst, setAlternativeInstanceClass, setParent, simplify, valuesToString |
CLLClassifierParameterSet
public CLLClassifierParameterSet(StringBuffer xml)
throws NonParsableException
- This is the constructor for
Storable
.
- Parameters:
xml
- the xml representation
- Throws:
NonParsableException
- if the representation could not be parsed.
CLLClassifierParameterSet
public CLLClassifierParameterSet(AlphabetContainer alphabet,
int length,
byte algo,
double eps,
double lineps,
double startD,
boolean free,
boolean plugIn,
boolean norm)
throws Exception
- The default constructor.
- Parameters:
alphabet
- the AlphabetContainerlength
- 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 the free or all parameters in a ScoringFunctionplugIn
- the switch for using plug-in parameters in a ScoringFunctonnorm
- the switch for using a normalization while optimization
- Throws:
Exception
- if something went wrong
loadParameters
protected void loadParameters()
throws Exception
- Description copied from class:
ParameterSet
- Loads the parameters for this
ParameterSet
. This is in
most cases done by simply creating a new ArrayList<Parameter>
for the
field parameters/code>
and filling it with instances of subclasses of Parameter
- Overrides:
loadParameters
in class ScoreClassifierParameterSet
- Throws:
Exception
- an Exception
is thrown if the parameters could not be loaded- See Also:
ParameterSet.parameters
,
Parameter
shouldBeNormalized
public boolean shouldBeNormalized()
- This method
true
if a normalization shall be used while optimization.
The normalization is done by division with the number of sequences.
- Returns:
true
if a normalization shall be used while optimization