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java.lang.Objectde.jstacs.parameters.ParameterSet
de.jstacs.parameters.InstanceParameterSet<T>
de.jstacs.parameters.SequenceScoringParameterSet
de.jstacs.classifiers.differentiableSequenceScoreBased.ScoreClassifierParameterSet
public abstract class ScoreClassifierParameterSet
A set of Parameter
s for any
ScoreClassifier
.
Nested Class Summary |
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Nested classes/interfaces inherited from class de.jstacs.parameters.ParameterSet |
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ParameterSet.ParameterList |
Field Summary |
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Fields inherited from class de.jstacs.parameters.SequenceScoringParameterSet |
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alphabet, length |
Fields inherited from class de.jstacs.parameters.ParameterSet |
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errorMessage, parameters, parent |
Constructor Summary | |
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ScoreClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass,
AlphabetContainer alphabet,
int length,
byte algo,
AbstractTerminationCondition tc,
double lineps,
double startD,
boolean free,
OptimizableFunction.KindOfParameter kind)
The constructor for a simple, instantiated parameter set. |
|
ScoreClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass,
AlphabetContainer alphabet,
int length,
byte algo,
double eps,
double lineps,
double startD,
boolean free,
OptimizableFunction.KindOfParameter kind)
The constructor for a simple, instantiated parameter set. |
|
ScoreClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass,
boolean simple,
AlphabetContainer.AlphabetContainerType type,
boolean variableLength)
Creates a new ScoreClassifierParameterSet with empty parameter
values. |
|
ScoreClassifierParameterSet(StringBuffer xml)
The standard constructor for the interface Storable . |
Method Summary | |
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String |
getInstanceComment()
Returns a comment (a textual description) of the class that can be constructed using this ParameterSet . |
String |
getInstanceName()
Returns the name of an instance of the class that can be constructed using this ParameterSet . |
AbstractTerminationCondition |
getTerminantionCondition()
This method returns the AbstractTerminationCondition for stopping the training, e.g., if the
difference of the scores between two iterations is smaller than a given
threshold the training is stopped. |
boolean |
useOnlyFreeParameter()
This method indicates if only the free parameters shall be used. |
Methods inherited from class de.jstacs.parameters.SequenceScoringParameterSet |
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clone, equals, fromXML, getAlphabetContainer, getLength, getNumberOfParameters, getParameterAt, hasDefaultOrIsSet, reset, toXML |
Methods inherited from class de.jstacs.parameters.InstanceParameterSet |
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getInstance, getInstanceClass |
Methods inherited from class de.jstacs.parameters.ParameterSet |
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fromGalaxy, getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getParameterForName, getParent, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, setParent, toGalaxy |
Methods inherited from class java.lang.Object |
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finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public ScoreClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass, boolean simple, AlphabetContainer.AlphabetContainerType type, boolean variableLength) throws Exception
ScoreClassifierParameterSet
with empty parameter
values.
instanceClass
- the class of the instancesimple
- indicates whether the AlphabetContainer
shall be
simpletype
- the type of the AlphabetContainer
variableLength
- indicates whether the corresponding classifier can handle
sequences of arbitrary length
Exception
- if the parameters could not be loadedSequenceScoringParameterSet.SequenceScoringParameterSet(Class,
de.jstacs.data.AlphabetContainer.AlphabetContainerType, boolean, boolean)
public ScoreClassifierParameterSet(StringBuffer xml) throws NonParsableException
Storable
.
Creates a new ScoreClassifierParameterSet
out of its XML
representation.
xml
- the XML representation as StringBuffer
NonParsableException
- if the ScoreClassifierParameterSet
could not be
reconstructed out of the XML representation (the
StringBuffer
could not be parsed)SequenceScoringParameterSet.SequenceScoringParameterSet(StringBuffer)
,
Storable
public ScoreClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass, AlphabetContainer alphabet, int length, byte algo, double eps, double lineps, double startD, boolean free, OptimizableFunction.KindOfParameter kind) throws Exception
instanceClass
- the class of the instancealphabet
- the alphabetlength
- the length of the sequences, 0 for homogeneousalgo
- the choice of algorithmeps
- the threshold for stopping the algorithmlineps
- the threshold for stopping the line search in the algorithmstartD
- the start distance for the line search in the algorithmfree
- indicates whether only the free parameters or all parameters
should be usedkind
- indicates the kind of class parameter initialization
Exception
- if something went wrongSequenceScoringParameterSet.SequenceScoringParameterSet(Class, AlphabetContainer, int, boolean)
,
ScoreClassifierParameterSet(Class, AlphabetContainer, int, byte, AbstractTerminationCondition, double, double, boolean, de.jstacs.classifiers.differentiableSequenceScoreBased.OptimizableFunction.KindOfParameter)
,
SmallDifferenceOfFunctionEvaluationsCondition
public ScoreClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass, AlphabetContainer alphabet, int length, byte algo, AbstractTerminationCondition tc, double lineps, double startD, boolean free, OptimizableFunction.KindOfParameter kind) throws Exception
instanceClass
- the class of the instancealphabet
- the alphabetlength
- the length of the sequences, 0 for homogeneousalgo
- the choice of algorithmtc
- the termination condition for stopping the algorithmlineps
- the threshold for stopping the line search in the algorithmstartD
- the start distance for the line search in the algorithmfree
- indicates whether only the free parameters or all parameters
should be usedkind
- indicates the kind of class parameter initialization
Exception
- if something went wrongSequenceScoringParameterSet.SequenceScoringParameterSet(Class,
AlphabetContainer, int, boolean)
Method Detail |
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public boolean useOnlyFreeParameter()
true
if only the free parameters shall be used,
false
otherwisepublic String getInstanceName()
InstanceParameterSet
ParameterSet
.
getInstanceName
in class InstanceParameterSet
public String getInstanceComment()
InstanceParameterSet
ParameterSet
.
getInstanceComment
in class InstanceParameterSet
public AbstractTerminationCondition getTerminantionCondition() throws ParameterSetParser.NotInstantiableException
AbstractTerminationCondition
for stopping the training, e.g., if the
difference of the scores between two iterations is smaller than a given
threshold the training is stopped.
AbstractTerminationCondition
for stopping the training
ParameterSetParser.NotInstantiableException
- if the AbstractTerminationCondition
could not be created from its ParameterSet
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