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Uses of NonParsableException in de.jstacs |
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Methods in de.jstacs that throw NonParsableException | |
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protected abstract void |
AnnotatedEntity.extractFurtherInfos(StringBuffer buf)
This method can be used in the constructor with parameter StringBuffer to
extract the further information. |
Constructors in de.jstacs that throw NonParsableException | |
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AnnotatedEntity(StringBuffer rep)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.algorithms.optimization.termination |
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Uses of NonParsableException in de.jstacs.classifiers |
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Methods in de.jstacs.classifiers that throw NonParsableException | |
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protected void |
MappingClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)
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protected void |
AbstractScoreBasedClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)
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protected abstract void |
AbstractClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)
Extracts further information of a classifier from an XML representation. |
protected void |
AbstractScoreBasedClassifier.DoubleTableResult.extractFurtherInfos(StringBuffer xml)
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Constructors in de.jstacs.classifiers that throw NonParsableException | |
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AbstractClassifier(StringBuffer xml)
The standard constructor for the interface Storable . |
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AbstractScoreBasedClassifier.DoubleTableResult(StringBuffer representation)
The standard constructor for the interface Storable
. |
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AbstractScoreBasedClassifier(StringBuffer xml)
The standard constructor for the interface Storable . |
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MappingClassifier(StringBuffer representation)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.classifiers.assessment |
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Constructors in de.jstacs.classifiers.assessment that throw NonParsableException | |
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ClassifierAssessmentAssessParameterSet(StringBuffer representation)
The standard constructor for the interface Storable . |
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KFoldCrossValidationAssessParameterSet(StringBuffer representation)
The standard constructor for the interface Storable . |
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RepeatedHoldOutAssessParameterSet(StringBuffer representation)
The standard constructor for the interface Storable . |
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RepeatedSubSamplingAssessParameterSet(StringBuffer representation)
The standard constructor for the interface Storable . |
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Sampled_RepeatedHoldOutAssessParameterSet(StringBuffer representation)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.classifiers.differentiableSequenceScoreBased |
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Methods in de.jstacs.classifiers.differentiableSequenceScoreBased that throw NonParsableException | |
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protected void |
ScoreClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)
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Constructors in de.jstacs.classifiers.differentiableSequenceScoreBased that throw NonParsableException | |
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ScoreClassifier(StringBuffer xml)
The standard constructor for the interface Storable . |
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ScoreClassifierParameterSet(StringBuffer xml)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix |
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Methods in de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix that throw NonParsableException | |
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protected void |
GenDisMixClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)
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Constructors in de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix that throw NonParsableException | |
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GenDisMixClassifier(StringBuffer xml)
This is the constructor for Storable . |
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GenDisMixClassifierParameterSet(StringBuffer xml)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior |
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Constructors in de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior that throw NonParsableException | |
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SeparateGaussianLogPrior(StringBuffer xml)
The standard constructor for the interface Storable . |
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SeparateLaplaceLogPrior(StringBuffer xml)
The standard constructor for the interface Storable . |
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SeparateLogPrior(StringBuffer xml)
The standard constructor for the interface Storable . |
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SimpleGaussianSumLogPrior(StringBuffer xml)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.classifiers.differentiableSequenceScoreBased.msp |
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Constructors in de.jstacs.classifiers.differentiableSequenceScoreBased.msp that throw NonParsableException | |
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MSPClassifier(StringBuffer xml)
This is the constructor for Storable . |
Uses of NonParsableException in de.jstacs.classifiers.differentiableSequenceScoreBased.sampling |
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Methods in de.jstacs.classifiers.differentiableSequenceScoreBased.sampling that throw NonParsableException | |
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protected void |
SamplingScoreBasedClassifier.DiffSMSamplingComponent.createFiles(StringBuffer contents)
Creates files out of file contents saved as XML. |
protected void |
SamplingScoreBasedClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)
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protected void |
SamplingGenDisMixClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)
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Constructors in de.jstacs.classifiers.differentiableSequenceScoreBased.sampling that throw NonParsableException | |
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SamplingGenDisMixClassifier(StringBuffer xml)
Creates a new SamplingGenDisMixClassifier from its XML-representation |
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SamplingScoreBasedClassifier(StringBuffer xml)
This is the constructor for Storable . |
Uses of NonParsableException in de.jstacs.classifiers.performanceMeasures |
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Constructors in de.jstacs.classifiers.performanceMeasures that throw NonParsableException | |
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AbstractPerformanceMeasure(StringBuffer xml)
The standard constructor for the interface Storable . |
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AucPR(StringBuffer xml)
The standard constructor for the interface Storable . |
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AucROC(StringBuffer xml)
The standard constructor for the interface Storable . |
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ClassificationRate(StringBuffer xml)
The standard constructor for the interface Storable . |
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ConfusionMatrix(StringBuffer xml)
The standard constructor for the interface Storable . |
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FalsePositiveRateForFixedSensitivity(StringBuffer xml)
The standard constructor for the interface Storable . |
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MaximumCorrelationCoefficient(StringBuffer xml)
The standard constructor for the interface Storable . |
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MaximumFMeasure(StringBuffer xml)
The standard constructor for the interface Storable . |
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MaximumNumericalTwoClassMeasure(StringBuffer xml)
The standard constructor for the interface Storable . |
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NumericalPerformanceMeasureParameterSet(StringBuffer xml)
The standard constructor for the interface Storable . |
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PerformanceMeasureParameterSet(StringBuffer xml)
The standard constructor for the interface Storable . |
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PositivePredictiveValueForFixedSensitivity(StringBuffer xml)
The standard constructor for the interface Storable . |
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PRCurve(StringBuffer xml)
The standard constructor for the interface Storable . |
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ROCCurve(StringBuffer xml)
The standard constructor for the interface Storable . |
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SensitivityForFixedSpecificity(StringBuffer xml)
The standard constructor for the interface Storable . |
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TwoClassAbstractPerformanceMeasure(StringBuffer xml)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.classifiers.trainSMBased |
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Methods in de.jstacs.classifiers.trainSMBased that throw NonParsableException | |
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protected void |
TrainSMBasedClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)
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Constructors in de.jstacs.classifiers.trainSMBased that throw NonParsableException | |
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TrainSMBasedClassifier(StringBuffer xml)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.data |
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Methods in de.jstacs.data that throw NonParsableException | |
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protected void |
AlphabetContainerParameterSet.fromXML(StringBuffer representation)
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void |
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet.fromXML(StringBuffer representation)
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void |
AlphabetContainerParameterSet.AlphabetArrayParameterSet.fromXML(StringBuffer representation)
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Constructors in de.jstacs.data that throw NonParsableException | |
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AlphabetContainer.AbstractAlphabetContainerParameterSet(StringBuffer xml)
The standard constructor for the interface Storable . |
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AlphabetContainer(StringBuffer xml)
The standard constructor for the interface Storable . |
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AlphabetContainerParameterSet.AlphabetArrayParameterSet(StringBuffer representation)
The standard constructor for the interface Storable
. |
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AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(StringBuffer representation)
The standard constructor for the interface Storable
. |
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AlphabetContainerParameterSet(StringBuffer representation)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.data.alphabets |
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Constructors in de.jstacs.data.alphabets that throw NonParsableException | |
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Alphabet.AlphabetParameterSet(StringBuffer representation)
The standard constructor for the interface Storable
. |
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ComplementableDiscreteAlphabet(StringBuffer representation)
The standard constructor for the interface Storable . |
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ContinuousAlphabet.ContinuousAlphabetParameterSet(StringBuffer representation)
The standard constructor for the interface Storable
. |
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ContinuousAlphabet(StringBuffer xml)
The standard constructor for the interface Storable . |
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DiscreteAlphabet.DiscreteAlphabetParameterSet(StringBuffer representation)
The standard constructor for the interface Storable
. |
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DiscreteAlphabet(StringBuffer representation)
The standard constructor for the interface Storable . |
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DiscreteAlphabetMapping(StringBuffer xml)
The standard constructor for the interface Storable . |
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GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet(StringBuffer representation)
The standard constructor for the interface Storable . |
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GenericComplementableDiscreteAlphabet(StringBuffer representation)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.data.sequences.annotation |
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Methods in de.jstacs.data.sequences.annotation that throw NonParsableException | |
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protected void |
StrandedLocatedSequenceAnnotationWithLength.fromXML(StringBuffer representation)
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protected void |
SequenceAnnotation.fromXML(StringBuffer source)
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protected void |
LocatedSequenceAnnotationWithLength.fromXML(StringBuffer representation)
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protected void |
LocatedSequenceAnnotation.fromXML(StringBuffer representation)
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Constructors in de.jstacs.data.sequences.annotation that throw NonParsableException | |
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CisRegulatoryModuleAnnotation(StringBuffer representation)
The standard constructor for the interface Storable . |
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IntronAnnotation(StringBuffer representation)
The standard constructor for the interface Storable . |
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LocatedSequenceAnnotation(StringBuffer representation)
The standard constructor for the interface Storable . |
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LocatedSequenceAnnotationWithLength(StringBuffer representation)
The standard constructor for the interface Storable . |
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MotifAnnotation(StringBuffer representation)
The standard constructor for the interface Storable . |
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ReferenceSequenceAnnotation(StringBuffer representation)
The standard constructor for the interface Storable . |
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SequenceAnnotation(StringBuffer representation)
The standard constructor for the interface Storable . |
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SinglePositionSequenceAnnotation(StringBuffer representation)
The standard constructor for the interface Storable . |
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StrandedLocatedSequenceAnnotationWithLength(StringBuffer representation)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.io |
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Methods in de.jstacs.io that throw NonParsableException | ||
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static StringBuffer |
XMLParser.extractForTag(StringBuffer source,
String tag)
Extracts the contents of source between tag start and end tags. |
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static StringBuffer |
XMLParser.extractForTag(StringBuffer source,
String tag,
Map<String,String> attributes,
Map<String,String> filterAttributes)
Extracts the contents of source between tag start and end tags. |
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static Object |
XMLParser.extractObjectAndAttributesForTags(StringBuffer xml,
String tag,
Map<String,String> attributes,
Map<String,String> filterAttributes)
Returns the parsed value between the tags. |
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static
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XMLParser.extractObjectAndAttributesForTags(StringBuffer xml,
String tag,
Map<String,String> attributes,
Map<String,String> filterAttributes,
Class<T> k)
Returns the parsed value between the tags. |
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static
|
XMLParser.extractObjectAndAttributesForTags(StringBuffer xml,
String tag,
Map<String,String> attributes,
Map<String,String> filterAttributes,
Class<T> k,
Class<S> outerClass,
S outerInstance)
Returns the parsed value between the tags as an inner instance of the object outerInstance . |
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static Object |
XMLParser.extractObjectForTags(StringBuffer xml,
String tag)
Returns the parsed value between the tags. |
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static
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XMLParser.extractObjectForTags(StringBuffer xml,
String tag,
Class<T> k)
Returns the parsed value between the tags. |
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static boolean |
XMLParser.hasTag(StringBuffer source,
String tag,
Map<String,String> attributes,
Map<String,String> filterAttributes)
This method allows to check whether an XML contains a tagged entry. |
Uses of NonParsableException in de.jstacs.motifDiscovery.history |
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Constructors in de.jstacs.motifDiscovery.history that throw NonParsableException | |
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CappedHistory(StringBuffer xml)
This is the constructor for the interface Storable . |
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NoRevertHistory(StringBuffer xml)
This is the constructor for the interface Storable . |
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RestrictedRepeatHistory(StringBuffer xml)
This is the constructor for the interface Storable . |
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SimpleHistory(StringBuffer xml)
This is the constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.parameters |
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Methods in de.jstacs.parameters that throw NonParsableException | |
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protected void |
SimpleParameter.extractFurtherInfos(StringBuffer representation)
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protected void |
SelectionParameter.extractFurtherInfos(StringBuffer representation)
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protected void |
RangeParameter.extractFurtherInfos(StringBuffer buf)
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protected void |
ParameterSetContainer.extractFurtherInfos(StringBuffer representation)
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protected void |
Parameter.extractFurtherInfos(StringBuffer source)
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protected void |
MultiSelectionParameter.extractFurtherInfos(StringBuffer representation)
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protected void |
FileParameter.extractFurtherInfos(StringBuffer buf)
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protected void |
EnumParameter.extractFurtherInfos(StringBuffer buf)
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protected void |
AbstractSelectionParameter.extractFurtherInfos(StringBuffer representation)
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protected void |
SequenceScoringParameterSet.fromXML(StringBuffer representation)
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protected void |
ParameterSet.fromXML(StringBuffer representation)
Parses the instance fields of a ParameterSet from the XML
representation as returned by ParameterSet.toXML() . |
protected void |
InstanceParameterSet.fromXML(StringBuffer representation)
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protected void |
ExpandableParameterSet.fromXML(StringBuffer representation)
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protected void |
ArrayParameterSet.fromXML(StringBuffer representation)
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Constructors in de.jstacs.parameters that throw NonParsableException | |
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AbstractSelectionParameter(StringBuffer representation)
The standard constructor for the interface Storable . |
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ArrayParameterSet(StringBuffer representation)
The standard constructor for the interface Storable . |
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EnumParameter(StringBuffer representation)
The standard constructor for the interface Storable . |
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ExpandableParameterSet(StringBuffer representation)
The standard constructor for the interface Storable . |
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FileParameter.FileRepresentation(StringBuffer buf)
The standard constructor for the interface Storable
. |
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FileParameter(StringBuffer buf)
The standard constructor for the interface Storable . |
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InstanceParameterSet(StringBuffer representation)
The standard constructor for the interface Storable . |
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MultiSelectionParameter(StringBuffer representation)
The standard constructor for the interface Storable . |
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Parameter(StringBuffer xml)
The standard constructor for the interface Storable . |
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ParameterSet(StringBuffer representation)
The standard constructor for the interface Storable . |
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ParameterSetContainer(StringBuffer representation)
The standard constructor for the interface Storable . |
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RangeParameter(StringBuffer representation)
The standard constructor for the interface Storable . |
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SelectionParameter(StringBuffer representation)
The standard constructor for the interface Storable . |
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SequenceScoringParameterSet(StringBuffer representation)
The standard constructor for the interface Storable . |
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SimpleParameter(StringBuffer representation)
The standard constructor for the interface Storable . |
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SimpleParameterSet(StringBuffer representation)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.parameters.validation |
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Methods in de.jstacs.parameters.validation that throw NonParsableException | |
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void |
StorableValidator.fromXML(StringBuffer representation)
Parses a StorableValidator from the XML representation as
returned by StorableValidator.toXML() . |
void |
SimpleStaticConstraint.fromXML(StringBuffer representation)
Parses a SimpleStaticConstraint from the XML representation as
returned by SimpleStaticConstraint.toXML() . |
void |
NumberValidator.fromXML(StringBuffer representation)
Parses a NumberValidator from the XML representation as returned
by NumberValidator.toXML() . |
void |
ConstraintValidator.fromXML(StringBuffer representation)
Parses a ConstraintValidator from the XML representation as
returned by ConstraintValidator.toXML() . |
Constructors in de.jstacs.parameters.validation that throw NonParsableException | |
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ConstraintValidator(StringBuffer representation)
The standard constructor for the interface Storable . |
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NumberValidator(StringBuffer representation)
The standard constructor for the interface Storable . |
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SimpleStaticConstraint(StringBuffer representation)
The standard constructor for the interface Storable . |
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StorableValidator(StringBuffer buf)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.results |
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Methods in de.jstacs.results that throw NonParsableException | |
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protected void |
StorableResult.extractFurtherInfos(StringBuffer representation)
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protected void |
SimpleResult.extractFurtherInfos(StringBuffer representation)
|
protected void |
ListResult.extractFurtherInfos(StringBuffer representation)
|
protected void |
ImageResult.extractFurtherInfos(StringBuffer representation)
|
protected void |
DataSetResult.extractFurtherInfos(StringBuffer rep)
|
protected void |
ResultSet.fromXML(StringBuffer representation)
Parses the contents of a ResultSet from its XML representation as
returned by ResultSet.toXML() . |
protected void |
MeanResultSet.fromXML(StringBuffer representation)
|
Constructors in de.jstacs.results that throw NonParsableException | |
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CategoricalResult(StringBuffer representation)
The standard constructor for the interface Storable . |
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DataSetResult(StringBuffer source)
The standard constructor for the interface Storable . |
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ImageResult(StringBuffer xml)
The standard constructor for the interface Storable . |
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ListResult(StringBuffer representation)
The standard constructor for the interface Storable . |
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MeanResultSet(StringBuffer representation)
The standard constructor for the interface Storable . |
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NumericalResult(StringBuffer representation)
The standard constructor for the interface Storable . |
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NumericalResultSet(StringBuffer representation)
The standard constructor for the interface Storable . |
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Result(StringBuffer rep)
The standard constructor for the interface Storable . |
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ResultSet(StringBuffer representation)
The standard constructor for the interface Storable . |
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SimpleResult(StringBuffer rep)
This is the constructor for Storable . |
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StorableResult(StringBuffer buf)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sampling |
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Methods in de.jstacs.sampling that throw NonParsableException | |
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protected void |
VarianceRatioBurnInTest.setFurtherInformation(StringBuffer xml)
|
protected abstract void |
AbstractBurnInTest.setFurtherInformation(StringBuffer xml)
This method sets further information for the AbstractBurnInTest . |
Constructors in de.jstacs.sampling that throw NonParsableException | |
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AbstractBurnInTest(StringBuffer rep)
This is the constructor for the Storable interface. |
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AbstractBurnInTestParameterSet(StringBuffer representation)
The standard constructor for the interface Storable . |
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SimpleBurnInTest(StringBuffer xml)
Deprecated. The standard constructor for the interface Storable . |
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VarianceRatioBurnInTest(StringBuffer rep)
The standard constructor for the Storable interface. |
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VarianceRatioBurnInTestParameterSet(StringBuffer representation)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.differentiable |
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Methods in de.jstacs.sequenceScores.differentiable that throw NonParsableException | |
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protected void |
UniformDiffSS.extractFurtherInformation(StringBuffer xml)
This method is the opposite of UniformDiffSS.getFurtherInformation() . |
protected void |
IndependentProductDiffSS.extractFurtherInformation(StringBuffer xml)
This method is the opposite of IndependentProductDiffSS.getFurtherInformation() . |
protected void |
UniformDiffSS.fromXML(StringBuffer xml)
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protected void |
IndependentProductDiffSS.fromXML(StringBuffer rep)
|
protected abstract void |
AbstractDifferentiableSequenceScore.fromXML(StringBuffer xml)
This method is called in the constructor for the Storable
interface to create a scoring function from a StringBuffer . |
Constructors in de.jstacs.sequenceScores.differentiable that throw NonParsableException | |
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AbstractDifferentiableSequenceScore(StringBuffer xml)
This is the constructor for Storable . |
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IndependentProductDiffSS(StringBuffer source)
This is the constructor for the interface Storable . |
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UniformDiffSS(StringBuffer xml)
This is the constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.differentiable.logistic |
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Methods in de.jstacs.sequenceScores.differentiable.logistic that throw NonParsableException | |
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protected void |
LogisticDiffSS.fromXML(StringBuffer xml)
|
Constructors in de.jstacs.sequenceScores.differentiable.logistic that throw NonParsableException | |
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LogisticDiffSS(StringBuffer xml)
This is the constructor for Storable . |
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ProductConstraint(StringBuffer xml)
This is the constructor for Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.differentiable |
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Methods in de.jstacs.sequenceScores.statisticalModels.differentiable that throw NonParsableException | |
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protected void |
UniformDiffSM.extractFurtherInformation(StringBuffer xml)
|
protected void |
IndependentProductDiffSM.extractFurtherInformation(StringBuffer rep)
|
protected void |
NormalizedDiffSM.fromXML(StringBuffer xml)
|
protected void |
MultiDimensionalSequenceWrapperDiffSM.fromXML(StringBuffer xml)
|
protected void |
MarkovRandomFieldDiffSM.fromXML(StringBuffer representation)
|
protected void |
MappingDiffSM.fromXML(StringBuffer xml)
|
protected void |
CyclicMarkovModelDiffSM.fromXML(StringBuffer xml)
|
Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable that throw NonParsableException | |
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AbstractDifferentiableStatisticalModel(StringBuffer xml)
This is the constructor for Storable . |
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AbstractVariableLengthDiffSM(StringBuffer source)
This is the constructor for the interface Storable . |
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CyclicMarkovModelDiffSM(StringBuffer source)
This is the constructor for Storable . |
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IndependentProductDiffSM(StringBuffer source)
This is the constructor for the interface Storable . |
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MappingDiffSM(StringBuffer xml)
This is the constructor for Storable . |
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MarkovRandomFieldDiffSM(StringBuffer source)
This is the constructor for the interface Storable . |
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MultiDimensionalSequenceWrapperDiffSM(StringBuffer xml)
This is the constructor for Storable . |
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NormalizedDiffSM(StringBuffer xml)
This is the constructor for Storable . |
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UniformDiffSM(StringBuffer xml)
This is the constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels |
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Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels that throw NonParsableException | |
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protected void |
MarkovModelDiffSM.fromXML(StringBuffer source)
|
protected void |
BayesianNetworkDiffSM.fromXML(StringBuffer source)
|
Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels that throw NonParsableException | |
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BayesianNetworkDiffSM(StringBuffer xml)
The standard constructor for the interface Storable . |
|
BayesianNetworkDiffSMParameterSet(StringBuffer representation)
Creates a new BayesianNetworkDiffSMParameterSet from its
XML representation as defined by the Storable
interface. |
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BNDiffSMParameter(StringBuffer representation)
The standard constructor for the interface Storable . |
|
BNDiffSMParameterTree.TreeElement(StringBuffer representation)
Constructor for the Storable interface. |
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BNDiffSMParameterTree(StringBuffer source)
Recreates a BNDiffSMParameterTree from its XML representation as
returned by BNDiffSMParameterTree.toXML() . |
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MarkovModelDiffSM(StringBuffer xml)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures |
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Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures that throw NonParsableException | |
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InhomogeneousMarkov.InhomogeneousMarkovParameterSet(StringBuffer representation)
Creates a new InhomogeneousMarkov.InhomogeneousMarkovParameterSet from its XML
representation as defined by the Storable
interface. |
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InhomogeneousMarkov(StringBuffer buf)
The standard constructor for the interface Storable . |
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Measure.MeasureParameterSet(StringBuffer xml)
The standard constructor for the interface Storable . |
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Measure(StringBuffer xml)
Creates a new Measure from its XML-representation. |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures |
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Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures that throw NonParsableException | |
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BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet(StringBuffer representation)
The standard constructor for the interface Storable
. |
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BTExplainingAwayResidual(StringBuffer buf)
The standard constructor for the interface Storable . |
|
BTMutualInformation.BTMutualInformationParameterSet(StringBuffer representation)
The standard constructor for the interface Storable
. |
|
BTMutualInformation(StringBuffer buf)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures |
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Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures that throw NonParsableException | |
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PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet(StringBuffer representation)
Creates a new PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet from its
XML representation as defined by the Storable
interface. |
|
PMMExplainingAwayResidual(StringBuffer buf)
The standard constructor for the interface Storable . |
|
PMMMutualInformation.PMMMutualInformationParameterSet(StringBuffer representation)
Creates a new PMMMutualInformation.PMMMutualInformationParameterSet from its
XML representation as defined by the Storable
interface. |
|
PMMMutualInformation(StringBuffer buf)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous |
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Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous that throw NonParsableException | |
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protected void |
UniformHomogeneousDiffSM.fromXML(StringBuffer xml)
|
protected void |
HomogeneousMMDiffSM.fromXML(StringBuffer xml)
|
protected void |
HomogeneousMM0DiffSM.fromXML(StringBuffer xml)
|
Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous that throw NonParsableException | |
---|---|
HomogeneousDiffSM(StringBuffer source)
This is the constructor for Storable . |
|
HomogeneousMM0DiffSM(StringBuffer xml)
This is the constructor for Storable . |
|
HomogeneousMMDiffSM(StringBuffer xml)
This is the constructor for Storable . |
|
UniformHomogeneousDiffSM(StringBuffer xml)
This is the constructor for Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture |
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Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture that throw NonParsableException | |
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protected void |
StrandDiffSM.extractFurtherInformation(StringBuffer xml)
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protected void |
AbstractMixtureDiffSM.extractFurtherInformation(StringBuffer xml)
This method is the opposite of AbstractMixtureDiffSM.getFurtherInformation() . |
protected void |
AbstractMixtureDiffSM.fromXML(StringBuffer b)
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Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture that throw NonParsableException | |
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AbstractMixtureDiffSM(StringBuffer xml)
This is the constructor for the interface Storable . |
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MixtureDiffSM(StringBuffer xml)
This is the constructor for the interface Storable . |
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StrandDiffSM(StringBuffer xml)
This is the constructor for Storable . |
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VariableLengthMixtureDiffSM(StringBuffer xml)
This is the constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif |
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Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif that throw NonParsableException | |
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protected void |
ExtendedZOOPSDiffSM.extractFurtherInformation(StringBuffer xml)
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protected void |
SkewNormalLikeDurationDiffSM.fromXML(StringBuffer rep)
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protected void |
PositionDiffSM.fromXML(StringBuffer xml)
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protected void |
MixtureDurationDiffSM.fromXML(StringBuffer rep)
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protected void |
DurationDiffSM.fromXML(StringBuffer xml)
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Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif that throw NonParsableException | |
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DurationDiffSM(StringBuffer source)
This is the constructor for Storable . |
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ExtendedZOOPSDiffSM(StringBuffer source)
This is the constructor for the interface Storable . |
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MixtureDurationDiffSM(StringBuffer source)
This is the constructor for Storable . |
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PositionDiffSM(StringBuffer source)
This is the constructor for Storable . |
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SkewNormalLikeDurationDiffSM(StringBuffer source)
This is the constructor for Storable . |
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UniformDurationDiffSM(StringBuffer b)
This is the constructor for Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable that throw NonParsableException | |
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protected void |
VariableLengthWrapperTrainSM.fromXML(StringBuffer xml)
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void |
UniformTrainSM.fromXML(StringBuffer representation)
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protected void |
DifferentiableStatisticalModelWrapperTrainSM.fromXML(StringBuffer xml)
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void |
CompositeTrainSM.fromXML(StringBuffer representation)
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protected abstract void |
AbstractTrainableStatisticalModel.fromXML(StringBuffer xml)
This method should only be used by the constructor that works on a StringBuffer . |
Constructors in de.jstacs.sequenceScores.statisticalModels.trainable that throw NonParsableException | |
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AbstractTrainableStatisticalModel(StringBuffer stringBuff)
The standard constructor for the interface Storable . |
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CompositeTrainSM(StringBuffer stringBuff)
The standard constructor for the interface Storable . |
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DifferentiableStatisticalModelWrapperTrainSM(StringBuffer stringBuff)
The standard constructor for the interface Storable . |
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UniformTrainSM(StringBuffer stringBuff)
The standard constructor for the interface Storable . |
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VariableLengthWrapperTrainSM(StringBuffer stringBuff)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.discrete |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete that throw NonParsableException | |
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protected abstract void |
Constraint.extractAdditionalInfo(StringBuffer xml)
This method parses additional information from the StringBuffer
that is not parsed in the base class. |
protected void |
DiscreteGraphicalTrainSM.fromXML(StringBuffer representation)
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protected void |
DiscreteGraphicalTrainSM.set(DGTrainSMParameterSet params,
boolean trained)
Sets the parameters as internal parameters and does some essential computations. |
protected abstract void |
DiscreteGraphicalTrainSM.setFurtherModelInfos(StringBuffer xml)
This method replaces the internal model information with those from a StringBuffer . |
Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.discrete that throw NonParsableException | |
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Constraint(StringBuffer xml)
The standard constructor for the interface Storable . |
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DGTrainSMParameterSet(StringBuffer s)
The standard constructor for the interface Storable . |
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DiscreteGraphicalTrainSM(DGTrainSMParameterSet params)
The default constructor. |
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DiscreteGraphicalTrainSM(StringBuffer representation)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous that throw NonParsableException | |
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protected void |
HomogeneousTrainSM.HomCondProb.extractAdditionalInfo(StringBuffer xml)
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protected void |
HomogeneousTrainSM.set(DGTrainSMParameterSet params,
boolean trained)
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protected void |
HomogeneousMM.set(DGTrainSMParameterSet params,
boolean trained)
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protected void |
HomogeneousMM.setFurtherModelInfos(StringBuffer xml)
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Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous that throw NonParsableException | |
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HomogeneousMM(HomMMParameterSet params)
Creates a new homogeneous Markov model from a parameter set. |
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HomogeneousMM(StringBuffer stringBuff)
The standard constructor for the interface Storable . |
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HomogeneousTrainSM.HomCondProb(StringBuffer xml)
The standard constructor for the interface Storable
. |
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HomogeneousTrainSM(HomogeneousTrainSMParameterSet params)
Creates a homogeneous model from a parameter set. |
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HomogeneousTrainSM(StringBuffer stringBuff)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters |
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Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters that throw NonParsableException | |
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HomMMParameterSet(StringBuffer s)
The standard constructor for the interface Storable . |
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HomogeneousTrainSMParameterSet(StringBuffer s)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous that throw NonParsableException | |
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protected void |
MEMConstraint.extractAdditionalInfo(StringBuffer xml)
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protected void |
InhConstraint.extractAdditionalInfo(StringBuffer xml)
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protected void |
InhCondProb.extractAdditionalInfo(StringBuffer xml)
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protected void |
InhomogeneousDGTrainSM.set(DGTrainSMParameterSet parameter,
boolean trained)
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protected void |
FSDAGTrainSM.set(DGTrainSMParameterSet params,
boolean trained)
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protected void |
BayesianNetworkTrainSM.set(DGTrainSMParameterSet parameter,
boolean trained)
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protected void |
FSDAGModelForGibbsSampling.setFurtherModelInfos(StringBuffer xml)
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protected void |
DAGTrainSM.setFurtherModelInfos(StringBuffer xml)
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Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters |
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Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters that throw NonParsableException | |
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BayesianNetworkTrainSMParameterSet(StringBuffer s)
The standard constructor for the interface Storable . |
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FSDAGModelForGibbsSamplingParameterSet(StringBuffer s)
The constructor for the Storable interface. |
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FSDAGTrainSMParameterSet(StringBuffer s)
The standard constructor for the interface Storable . |
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IDGTrainSMParameterSet(StringBuffer s)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared that throw NonParsableException | |
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protected void |
SharedStructureClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)
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protected void |
SharedStructureMixture.fromXML(StringBuffer representation)
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Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared that throw NonParsableException | |
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SharedStructureClassifier(StringBuffer xml)
The standard constructor for the interface Storable . |
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SharedStructureMixture(StringBuffer xml)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.hmm |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm that throw NonParsableException | |
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protected abstract void |
AbstractHMM.extractFurtherInformation(StringBuffer xml)
This method extracts further information from the XML representation. |
protected void |
AbstractHMM.fromXML(StringBuffer xml)
This method is used by the AbstractHMM.AbstractHMM(StringBuffer) constructor for creating an instance from an XML representation. |
Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm that throw NonParsableException | |
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AbstractHMM(StringBuffer xml)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models that throw NonParsableException | |
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protected void |
SamplingHigherOrderHMM.extractFurtherInformation(StringBuffer xml)
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protected void |
HigherOrderHMM.extractFurtherInformation(StringBuffer xml)
This method extracts further information from the XML representation. |
protected void |
DifferentiableHigherOrderHMM.extractFurtherInformation(StringBuffer xml)
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Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models that throw NonParsableException | |
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DifferentiableHigherOrderHMM(StringBuffer xml)
The standard constructor for the interface Storable . |
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HigherOrderHMM(StringBuffer xml)
The standard constructor for the interface Storable . |
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SamplingHigherOrderHMM(StringBuffer xml)
The standard constructor for the interface Storable . |
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SamplingPhyloHMM(StringBuffer xml)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions |
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Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions that throw NonParsableException | |
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MixtureEmission(StringBuffer xml)
The standard constructor for the interface Storable . |
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UniformEmission(StringBuffer xml)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous that throw NonParsableException | |
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protected void |
PluginGaussianEmission.fromXML(StringBuffer xml)
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protected void |
GaussianEmission.fromXML(StringBuffer xml)
This method is internally used by the constructor GaussianEmission.GaussianEmission(StringBuffer) . |
Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous that throw NonParsableException | |
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GaussianEmission(StringBuffer xml)
Creates a GaussianEmission from its XML representation. |
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PluginGaussianEmission(StringBuffer xml)
Creates a PluginGaussianEmission from its XML representation. |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete that throw NonParsableException | |
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protected void |
ReferenceSequenceDiscreteEmission.extractFurtherInformation(StringBuffer xml)
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protected void |
PhyloDiscreteEmission.extractFurtherInformation(StringBuffer xml)
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protected void |
AbstractConditionalDiscreteEmission.extractFurtherInformation(StringBuffer xml)
This method extracts further information from the XML representation. |
protected void |
AbstractConditionalDiscreteEmission.fromXML(StringBuffer xml)
This method is internally used by the constructor AbstractConditionalDiscreteEmission.AbstractConditionalDiscreteEmission(StringBuffer) . |
Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete that throw NonParsableException | |
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AbstractConditionalDiscreteEmission(StringBuffer xml)
Creates a AbstractConditionalDiscreteEmission from its XML representation. |
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DiscreteEmission(StringBuffer xml)
Creates a DiscreteEmission from its XML representation. |
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ReferenceSequenceDiscreteEmission(StringBuffer xml)
Creates a ReferenceSequenceDiscreteEmission from its XML representation. |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training |
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Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training that throw NonParsableException | |
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BaumWelchParameterSet(StringBuffer xml)
The standard constructor for the interface Storable . |
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HMMTrainingParameterSet(StringBuffer xml)
The standard constructor for the interface Storable . |
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MaxHMMTrainingParameterSet(StringBuffer xml)
The standard constructor for the interface Storable . |
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MultiThreadedTrainingParameterSet(StringBuffer xml)
The standard constructor for the interface Storable . |
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NumericalHMMTrainingParameterSet(StringBuffer xml)
The standard constructor for the interface Storable . |
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SamplingHMMTrainingParameterSet(StringBuffer xml)
The standard constructor for the interface Storable . |
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ViterbiParameterSet(StringBuffer xml)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions that throw NonParsableException | |
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protected void |
HigherOrderTransition.extractFurtherInformation(StringBuffer xml)
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protected void |
BasicHigherOrderTransition.extractFurtherInformation(StringBuffer xml)
This method extracts further information from the XML representation. |
protected abstract void |
BasicHigherOrderTransition.AbstractTransitionElement.extractFurtherInformation(StringBuffer xml)
This method extracts further information from the XML representation. |
Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions that throw NonParsableException | |
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BasicHigherOrderTransition.AbstractTransitionElement(StringBuffer xml)
The standard constructor for the interface Storable . |
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BasicHigherOrderTransition(StringBuffer xml)
The standard constructor for the interface Storable . |
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HigherOrderTransition(StringBuffer xml)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements that throw NonParsableException | |
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protected void |
ScaledTransitionElement.extractFurtherInformation(StringBuffer xml)
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protected void |
ReferenceBasedTransitionElement.extractFurtherInformation(StringBuffer xml)
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protected void |
DistanceBasedScaledTransitionElement.extractFurtherInformation(StringBuffer xml)
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protected void |
BasicTransitionElement.extractFurtherInformation(StringBuffer xml)
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protected void |
BasicPluginTransitionElement.extractFurtherInformation(StringBuffer xml)
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Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements that throw NonParsableException | |
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BasicPluginTransitionElement(StringBuffer xml)
The standard constructor for the interface Storable . |
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BasicTransitionElement(StringBuffer xml)
The standard constructor for the interface Storable . |
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DistanceBasedScaledTransitionElement(StringBuffer xml)
Extracts a distance-base scaled transition element from XML. |
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ReferenceBasedTransitionElement(StringBuffer xml)
The standard constructor for the interface Storable . |
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ScaledTransitionElement(StringBuffer xml)
The standard constructor for the interface Storable . |
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TransitionElement(StringBuffer xml)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.mixture |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.mixture that throw NonParsableException | |
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protected void |
AbstractMixtureTrainSM.extractFurtherInformation(StringBuffer xml)
This method is used in the subclasses to extract further information from the XML representation and to set these as values of the instance. |
protected void |
AbstractMixtureTrainSM.fromXML(StringBuffer representation)
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Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.mixture that throw NonParsableException | |
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AbstractMixtureTrainSM(StringBuffer xml)
The standard constructor for the interface Storable . |
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MixtureTrainSM(StringBuffer xml)
The constructor for the interface Storable . |
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StrandTrainSM(StringBuffer stringBuff)
The constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif that throw NonParsableException | |
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protected void |
HiddenMotifMixture.extractFurtherInformation(StringBuffer xml)
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Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif that throw NonParsableException | |
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HiddenMotifMixture(StringBuffer xml)
The standard constructor for the interface Storable . |
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ZOOPSTrainSM(StringBuffer xml)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior that throw NonParsableException | |
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protected abstract void |
PositionPrior.extractAdditionalInformation(StringBuffer xml)
This method extracts additional information from a StringBuffer . |
protected void |
GaussianLikePositionPrior.extractAdditionalInformation(StringBuffer xml)
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Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior that throw NonParsableException | |
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GaussianLikePositionPrior(StringBuffer rep)
The standard constructor for the interface Storable . |
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PositionPrior(StringBuffer rep)
The standard constructor for the interface Storable . |
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UniformPositionPrior(StringBuffer xml)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.phylo |
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Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.phylo that throw NonParsableException | |
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PhyloNode(StringBuffer xml)
The standard constructor for the interface Storable . |
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PhyloTree(StringBuffer xml)
The standard constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.phylo.parser |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.phylo.parser that throw NonParsableException | |
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PhyloTree |
NewickParser.tokenize()
This method construct a PhyloTree from the given input stream |
Uses of NonParsableException in de.jstacs.utils |
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Constructors in de.jstacs.utils that throw NonParsableException | |
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DoubleList(StringBuffer rep)
This is the constructor for the interface Storable . |
Uses of NonParsableException in de.jstacs.utils.galaxy |
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Methods in de.jstacs.utils.galaxy that throw NonParsableException | |
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protected void |
GalaxyAdaptor.LinkedImageResult.extractFurtherInfos(StringBuffer representation)
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protected void |
GalaxyAdaptor.FileResult.extractFurtherInfos(StringBuffer rep)
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Constructors in de.jstacs.utils.galaxy that throw NonParsableException | |
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GalaxyAdaptor.FileResult(StringBuffer rep)
Creates a new GalaxyAdaptor.FileResult from its XML-representation |
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GalaxyAdaptor.LinkedImageResult(StringBuffer xml)
Creates a new GalaxyAdaptor.LinkedImageResult from its XML-representation |
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