Package | Description |
---|---|
de.jstacs |
This package is the root package for the most and important packages.
|
de.jstacs.algorithms.alignment |
Provides classes for alignments.
|
de.jstacs.algorithms.alignment.cost |
Provides classes for cost functions used in alignments.
|
de.jstacs.algorithms.optimization.termination |
Provides classes for termination conditions that can be used in algorithms.
|
de.jstacs.classifiers |
This package provides the framework for any classifier.
|
de.jstacs.classifiers.assessment |
This package allows to assess classifiers.
It contains the class ClassifierAssessment that
is used as a super-class of all implemented methodologies of
an assessment to assess classifiers. |
de.jstacs.classifiers.differentiableSequenceScoreBased |
Provides the classes for
Classifier s that are based on SequenceScore s.It includes a sub-package for discriminative objective functions, namely conditional likelihood and supervised posterior, and a separate sub-package for the parameter priors, that can be used for the supervised posterior. |
de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix |
Provides an implementation of a classifier that allows to train the parameters of a set of
DifferentiableStatisticalModel s by
a unified generative-discriminative learning principle. |
de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior |
Provides a general definition of a parameter log-prior and a number of implementations of Laplace and Gaussian priors.
|
de.jstacs.classifiers.differentiableSequenceScoreBased.msp |
Provides an implementation of a classifier that allows to train the parameters of a set of
DifferentiableStatisticalModel s either
by maximum supervised posterior (MSP) or by maximum conditional likelihood (MCL). |
de.jstacs.classifiers.differentiableSequenceScoreBased.sampling |
Provides the classes for
AbstractScoreBasedClassifier s that are based on
SamplingDifferentiableStatisticalModel s
and that sample parameters using the Metropolis-Hastings algorithm. |
de.jstacs.classifiers.performanceMeasures |
This package provides the implementations of performance measures that can be used to assess any classifier.
|
de.jstacs.classifiers.trainSMBased |
Provides the classes for
Classifier s that are based on TrainableStatisticalModel s. |
de.jstacs.clustering.hierachical | |
de.jstacs.data |
Provides classes for the representation of data.
The base classes to represent data are Alphabet and AlphabetContainer for representing alphabets,
Sequence and its sub-classes to represent continuous and discrete sequences, and
DataSet to represent data sets comprising a set of sequences. |
de.jstacs.data.alphabets |
Provides classes for the representation of discrete and continuous alphabets, including a
DNAAlphabet for the most common case of DNA-sequences. |
de.jstacs.data.sequences.annotation |
Provides the facilities to annotate
Sequence s using a number of pre-defined annotation types, or additional
implementations of the SequenceAnnotation class. |
de.jstacs.io |
Provides classes for reading data from and writing to a file and storing a number of datatypes, including all primitives, arrays of primitives, and
Storable s to an XML-representation. |
de.jstacs.motifDiscovery.history | |
de.jstacs.parameters |
This package provides classes for parameters that establish a general convention for the description of parameters
as defined in the
Parameter -interface. |
de.jstacs.parameters.validation |
Provides classes for the validation of
Parameter values. |
de.jstacs.results |
This package provides classes for results and sets of results.
|
de.jstacs.sampling |
This package contains many classes that can be used while a sampling.
|
de.jstacs.sequenceScores.differentiable | |
de.jstacs.sequenceScores.differentiable.logistic | |
de.jstacs.sequenceScores.statisticalModels.differentiable |
Provides all
DifferentiableStatisticalModel s, which can compute the gradient with
respect to their parameters for a given input Sequence . |
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels |
Provides
DifferentiableStatisticalModel s that are directed graphical models. |
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures |
Provides the facilities to learn the structure of a
BayesianNetworkDiffSM . |
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures |
Provides the facilities to learn the structure of a
BayesianNetworkDiffSM as
a Bayesian tree using a number of measures to define a rating of structures. |
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures |
Provides the facilities to learn the structure of a
BayesianNetworkDiffSM as
a permuted Markov model using a number of measures to define a rating of structures. |
de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous |
Provides
DifferentiableStatisticalModel s that are homogeneous, i.e. |
de.jstacs.sequenceScores.statisticalModels.differentiable.localMixture | |
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture |
Provides
DifferentiableSequenceScore s that are mixtures of other DifferentiableSequenceScore s. |
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif | |
de.jstacs.sequenceScores.statisticalModels.trainable |
Provides all
TrainableStatisticalModel s, which can
be learned from a single DataSet . |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete | |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous | |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters | |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous |
This package contains various inhomogeneous models.
|
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters | |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared | |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm |
The package provides all interfaces and classes for a hidden Markov model (HMM).
|
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models |
The package provides different implementations of hidden Markov models based on
AbstractHMM . |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions | |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous | |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete | |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training |
The package provides all classes used to determine the training algorithm of a hidden Markov model.
|
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions |
The package provides all interfaces and classes for transitions used in hidden Markov models.
|
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements | |
de.jstacs.sequenceScores.statisticalModels.trainable.mixture |
This package is the super package for any mixture model.
|
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif | |
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior | |
de.jstacs.sequenceScores.statisticalModels.trainable.phylo | |
de.jstacs.sequenceScores.statisticalModels.trainable.phylo.parser | |
de.jstacs.tools | |
de.jstacs.tools.ui.galaxy | |
de.jstacs.utils |
This package contains a bundle of useful classes and interfaces like ...
|
Modifier and Type | Method and Description |
---|---|
protected abstract void |
AnnotatedEntity.extractFurtherInfos(StringBuffer buf)
This method can be used in the constructor with parameter
StringBuffer to
extract the further information. |
Constructor and Description |
---|
AnnotatedEntity(StringBuffer rep)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
protected void |
StringAlignment.fromXML(StringBuffer xml)
Parses the XML representation.
|
protected void |
PairwiseStringAlignment.fromXML(StringBuffer xml) |
Constructor and Description |
---|
PairwiseStringAlignment(StringBuffer xml)
The standard constructor for the interface
Storable . |
StringAlignment(StringBuffer xml)
Restores
StringAlignment object from its XML representation. |
Constructor and Description |
---|
AffineCosts(StringBuffer xml)
Restores
AffineCosts object from its XML representation. |
MatrixCosts(StringBuffer xml)
Restores
MatrixCosts object from its XML representation. |
SimpleCosts(StringBuffer xml)
Restores
SimpleCosts object from its XML representation. |
Constructor and Description |
---|
AbsoluteValueCondition(StringBuffer xml)
Deprecated.
The standard constructor for the interface
Storable . |
AbsoluteValueConditionParameterSet(StringBuffer xml)
The standard constructor for the interface
Storable . |
AbstractTerminationCondition(StringBuffer xml)
The standard constructor for the interface
Storable . |
AbstractTerminationConditionParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable . |
CombinedCondition(StringBuffer xml)
The standard constructor for the interface
Storable . |
CombinedConditionParameterSet(StringBuffer xml)
The standard constructor for the interface
Storable . |
IterationCondition(StringBuffer xml)
The standard constructor for the interface
Storable . |
IterationConditionParameterSet(StringBuffer xml)
The standard constructor for the interface
Storable . |
MultipleIterationsCondition(StringBuffer xml)
The standard constructor for the interface
Storable . |
MultipleIterationsConditionParameterSet(StringBuffer xml)
The standard constructor for the interface
Storable . |
SmallDifferenceOfFunctionEvaluationsCondition(StringBuffer xml)
The standard constructor for the interface
Storable . |
SmallDifferenceOfFunctionEvaluationsConditionParameterSet(StringBuffer xml)
The standard constructor for the interface
Storable . |
SmallGradientConditon(StringBuffer xml)
The standard constructor for the interface
Storable . |
SmallGradientConditonParameterSet(StringBuffer xml)
The standard constructor for the interface
Storable . |
SmallStepCondition(StringBuffer xml)
The standard constructor for the interface
Storable . |
SmallStepConditionParameterSet(StringBuffer xml)
The standard constructor for the interface
Storable . |
TimeCondition(StringBuffer xml)
The standard constructor for the interface
Storable . |
TimeConditionParameterSet(StringBuffer xml)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
protected void |
MappingClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml) |
protected void |
AbstractScoreBasedClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml) |
protected abstract void |
AbstractClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)
Extracts further information of a classifier from an XML representation.
|
protected void |
AbstractScoreBasedClassifier.DoubleTableResult.extractFurtherInfos(StringBuffer xml) |
Constructor and Description |
---|
AbstractClassifier(StringBuffer xml)
The standard constructor for the interface
Storable . |
AbstractScoreBasedClassifier(StringBuffer xml)
The standard constructor for the interface
Storable . |
DoubleTableResult(StringBuffer representation)
The standard constructor for the interface
Storable
. |
MappingClassifier(StringBuffer representation)
The standard constructor for the interface
Storable . |
Constructor and Description |
---|
ClassifierAssessmentAssessParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable . |
KFoldCrossValidationAssessParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable . |
RepeatedHoldOutAssessParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable . |
RepeatedSubSamplingAssessParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable . |
Sampled_RepeatedHoldOutAssessParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
protected void |
ScoreClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml) |
Constructor and Description |
---|
ScoreClassifier(StringBuffer xml)
The standard constructor for the interface
Storable . |
ScoreClassifierParameterSet(StringBuffer xml)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
protected void |
GenDisMixClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml) |
Constructor and Description |
---|
GenDisMixClassifier(StringBuffer xml)
This is the constructor for
Storable . |
GenDisMixClassifierParameterSet(StringBuffer xml)
The standard constructor for the interface
Storable . |
Constructor and Description |
---|
SeparateGaussianLogPrior(StringBuffer xml)
The standard constructor for the interface
Storable . |
SeparateLaplaceLogPrior(StringBuffer xml)
The standard constructor for the interface
Storable . |
SeparateLogPrior(StringBuffer xml)
The standard constructor for the interface
Storable . |
SimpleGaussianSumLogPrior(StringBuffer xml)
The standard constructor for the interface
Storable . |
Constructor and Description |
---|
MSPClassifier(StringBuffer xml)
This is the constructor for
Storable . |
Modifier and Type | Method and Description |
---|---|
protected void |
SamplingScoreBasedClassifier.DiffSMSamplingComponent.createFiles(StringBuffer contents)
Creates files out of file contents saved as XML.
|
protected void |
SamplingScoreBasedClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml) |
protected void |
SamplingGenDisMixClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml) |
Constructor and Description |
---|
SamplingGenDisMixClassifier(StringBuffer xml)
Creates a new
SamplingGenDisMixClassifier from its XML-representation |
SamplingScoreBasedClassifier(StringBuffer xml)
This is the constructor for
Storable . |
Constructor and Description |
---|
AbstractNumericalTwoClassPerformanceMeasure(StringBuffer xml)
The standard constructor for the interface
Storable . |
AbstractPerformanceMeasure(StringBuffer xml)
The standard constructor for the interface
Storable . |
AbstractPerformanceMeasureParameterSet(StringBuffer xml)
The standard constructor for the interface
Storable . |
AbstractTwoClassPerformanceMeasure(StringBuffer xml)
The standard constructor for the interface
Storable . |
AucPR(StringBuffer xml)
The standard constructor for the interface
Storable . |
AucROC(StringBuffer xml)
The standard constructor for the interface
Storable . |
ClassificationRate(StringBuffer xml)
The standard constructor for the interface
Storable . |
ConfusionMatrix(StringBuffer xml)
The standard constructor for the interface
Storable . |
FalsePositiveRateForFixedSensitivity(StringBuffer xml)
The standard constructor for the interface
Storable . |
MaximumCorrelationCoefficient(StringBuffer xml)
The standard constructor for the interface
Storable . |
MaximumFMeasure(StringBuffer xml)
The standard constructor for the interface
Storable . |
MaximumNumericalTwoClassMeasure(StringBuffer xml)
The standard constructor for the interface
Storable . |
NumericalPerformanceMeasureParameterSet(StringBuffer xml)
The standard constructor for the interface
Storable . |
PerformanceMeasureParameterSet(StringBuffer xml)
The standard constructor for the interface
Storable . |
PositivePredictiveValueForFixedSensitivity(StringBuffer xml)
The standard constructor for the interface
Storable . |
PRCurve(StringBuffer xml)
The standard constructor for the interface
Storable . |
ROCCurve(StringBuffer xml)
The standard constructor for the interface
Storable . |
SensitivityForFixedSpecificity(StringBuffer xml)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
protected void |
TrainSMBasedClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml) |
Constructor and Description |
---|
TrainSMBasedClassifier(StringBuffer xml)
The standard constructor for the interface
Storable . |
Constructor and Description |
---|
ClusterTree(StringBuffer xml)
Creates a cluster tree from its XML representation
|
Modifier and Type | Method and Description |
---|---|
protected void |
AlphabetContainerParameterSet.fromXML(StringBuffer representation) |
void |
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet.fromXML(StringBuffer representation) |
void |
AlphabetContainerParameterSet.AlphabetArrayParameterSet.fromXML(StringBuffer representation) |
Constructor and Description |
---|
AbstractAlphabetContainerParameterSet(StringBuffer xml)
The standard constructor for the interface
Storable . |
AlphabetArrayParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable
. |
AlphabetContainer(StringBuffer xml)
The standard constructor for the interface
Storable . |
AlphabetContainerParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable . |
SectionDefinedAlphabetParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable
. |
Constructor and Description |
---|
AlphabetParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable
. |
ComplementableDiscreteAlphabet(StringBuffer representation)
The standard constructor for the interface
Storable . |
ContinuousAlphabet(StringBuffer xml)
The standard constructor for the interface
Storable . |
ContinuousAlphabetParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable
. |
DiscreteAlphabet(StringBuffer representation)
The standard constructor for the interface
Storable . |
DiscreteAlphabetMapping(StringBuffer xml)
The standard constructor for the interface
Storable . |
DiscreteAlphabetParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable
. |
GenericComplementableDiscreteAlphabet(StringBuffer representation)
The standard constructor for the interface
Storable . |
GenericComplementableDiscreteAlphabetParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
protected void |
StrandedLocatedSequenceAnnotationWithLength.fromXML(StringBuffer representation) |
protected void |
SequenceAnnotation.fromXML(StringBuffer source) |
protected void |
LocatedSequenceAnnotationWithLength.fromXML(StringBuffer representation) |
protected void |
LocatedSequenceAnnotation.fromXML(StringBuffer representation) |
Constructor and Description |
---|
CisRegulatoryModuleAnnotation(StringBuffer representation)
The standard constructor for the interface
Storable . |
IntronAnnotation(StringBuffer representation)
The standard constructor for the interface
Storable . |
LocatedSequenceAnnotation(StringBuffer representation)
The standard constructor for the interface
Storable . |
LocatedSequenceAnnotationWithLength(StringBuffer representation)
The standard constructor for the interface
Storable . |
MotifAnnotation(StringBuffer representation)
The standard constructor for the interface
Storable . |
ReferenceSequenceAnnotation(StringBuffer representation)
The standard constructor for the interface
Storable . |
SequenceAnnotation(StringBuffer representation)
The standard constructor for the interface
Storable . |
SinglePositionSequenceAnnotation(StringBuffer representation)
The standard constructor for the interface
Storable . |
StrandedLocatedSequenceAnnotationWithLength(StringBuffer representation)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
static StringBuffer |
XMLParser.extractForTag(StringBuffer source,
String tag)
Extracts the contents of
source between tag start and end tags. |
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. |
static Object |
XMLParser.extractObjectAndAttributesForTags(StringBuffer xml,
String tag,
Map<String,String> attributes,
Map<String,String> filterAttributes)
Returns the parsed value between the tags.
|
static <T> T |
XMLParser.extractObjectAndAttributesForTags(StringBuffer xml,
String tag,
Map<String,String> attributes,
Map<String,String> filterAttributes,
Class<T> k)
Returns the parsed value between the tags.
|
static <T,S> T |
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 . |
static Object |
XMLParser.extractObjectForTags(StringBuffer xml,
String tag)
Returns the parsed value between the tags.
|
static <T> T |
XMLParser.extractObjectForTags(StringBuffer xml,
String tag,
Class<T> k)
Returns the parsed value between the tags.
|
static Sequence[] |
XMLParser.extractSequencesWithTags(StringBuffer xml,
String tag)
Extracts a set of sequences from their XML representation.
|
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.
|
Constructor and Description |
---|
CappedHistory(StringBuffer xml)
This is the constructor for the interface
Storable . |
NoRevertHistory(StringBuffer xml)
This is the constructor for the interface
Storable . |
RestrictedRepeatHistory(StringBuffer xml)
This is the constructor for the interface
Storable . |
SimpleHistory(StringBuffer xml)
This is the constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
protected void |
SimpleParameter.extractFurtherInfos(StringBuffer representation) |
protected void |
SelectionParameter.extractFurtherInfos(StringBuffer representation) |
protected void |
RangeParameter.extractFurtherInfos(StringBuffer buf) |
protected void |
ParameterSetContainer.extractFurtherInfos(StringBuffer representation) |
protected void |
Parameter.extractFurtherInfos(StringBuffer source) |
protected void |
MultiSelectionParameter.extractFurtherInfos(StringBuffer representation) |
protected void |
FileParameter.extractFurtherInfos(StringBuffer buf) |
protected void |
EnumParameter.extractFurtherInfos(StringBuffer buf) |
protected void |
AbstractSelectionParameter.extractFurtherInfos(StringBuffer representation) |
protected void |
SequenceScoringParameterSet.fromXML(StringBuffer representation) |
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) |
protected void |
ExpandableParameterSet.fromXML(StringBuffer representation) |
protected void |
ArrayParameterSet.fromXML(StringBuffer representation) |
Constructor and Description |
---|
AbstractSelectionParameter(StringBuffer representation)
The standard constructor for the interface
Storable . |
ArrayParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable . |
EnumParameter(StringBuffer representation)
The standard constructor for the interface
Storable . |
ExpandableParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable . |
FileParameter(StringBuffer buf)
The standard constructor for the interface
Storable . |
FileRepresentation(StringBuffer buf)
The standard constructor for the interface
Storable
. |
InstanceParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable . |
MultiSelectionParameter(StringBuffer representation)
The standard constructor for the interface
Storable . |
Parameter(StringBuffer xml)
The standard constructor for the interface
Storable . |
ParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable . |
ParameterSetContainer(StringBuffer representation)
The standard constructor for the interface
Storable . |
RangeParameter(StringBuffer representation)
The standard constructor for the interface
Storable . |
SelectionParameter(StringBuffer representation)
The standard constructor for the interface
Storable . |
SequenceScoringParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable . |
SimpleParameter(StringBuffer representation)
The standard constructor for the interface
Storable . |
SimpleParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
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() . |
Constructor and Description |
---|
ConstraintValidator(StringBuffer representation)
The standard constructor for the interface
Storable . |
NumberValidator(StringBuffer representation)
The standard constructor for the interface
Storable . |
RegExpValidator(StringBuffer xml)
Creates a
RegExpValidator from its XML representation. |
SimpleStaticConstraint(StringBuffer representation)
The standard constructor for the interface
Storable . |
StorableValidator(StringBuffer buf)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
protected void |
TextResult.extractFurtherInfos(StringBuffer buf) |
protected void |
StorableResult.extractFurtherInfos(StringBuffer representation) |
protected void |
SimpleResult.extractFurtherInfos(StringBuffer representation) |
protected void |
Result.extractFurtherInfos(StringBuffer buf) |
protected void |
PlotGeneratorResult.extractFurtherInfos(StringBuffer buf) |
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) |
Constructor and Description |
---|
CategoricalResult(StringBuffer representation)
The standard constructor for the interface
Storable . |
DataSetResult(StringBuffer source)
The standard constructor for the interface
Storable . |
ImageResult(StringBuffer xml)
The standard constructor for the interface
Storable . |
ListResult(StringBuffer representation)
The standard constructor for the interface
Storable . |
MeanResultSet(StringBuffer representation)
The standard constructor for the interface
Storable . |
NumericalResult(StringBuffer representation)
The standard constructor for the interface
Storable . |
NumericalResultSet(StringBuffer representation)
The standard constructor for the interface
Storable . |
PlotGeneratorResult(StringBuffer rep)
Creates a new
PlotGeneratorResult from its XML representation. |
Result(StringBuffer rep)
The standard constructor for the interface
Storable . |
ResultSet(StringBuffer representation)
The standard constructor for the interface
Storable . |
ResultSetResult(StringBuffer representation)
Creates a
ResultSetResult from its XML representation. |
SimpleResult(StringBuffer rep)
This is the constructor for
Storable . |
StorableResult(StringBuffer buf)
The standard constructor for the interface
Storable . |
TextResult(StringBuffer xml)
Creates a
TextResult from its XML representation. |
Modifier and Type | Method and Description |
---|---|
protected void |
VarianceRatioBurnInTest.setFurtherInformation(StringBuffer xml) |
protected abstract void |
AbstractBurnInTest.setFurtherInformation(StringBuffer xml)
This method sets further information for the
AbstractBurnInTest . |
Constructor and Description |
---|
AbstractBurnInTest(StringBuffer rep)
This is the constructor for the
Storable interface. |
AbstractBurnInTestParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable . |
SimpleBurnInTest(StringBuffer xml)
Deprecated.
The standard constructor for the interface
Storable . |
VarianceRatioBurnInTest(StringBuffer rep)
The standard constructor for the
Storable interface. |
VarianceRatioBurnInTestParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
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) |
protected void |
MultiDimensionalSequenceWrapperDiffSS.fromXML(StringBuffer xml) |
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 . |
Constructor and Description |
---|
AbstractDifferentiableSequenceScore(StringBuffer xml)
This is the constructor for
Storable . |
IndependentProductDiffSS(StringBuffer source)
This is the constructor for the interface
Storable . |
MultiDimensionalSequenceWrapperDiffSS(StringBuffer xml)
This is the constructor for
Storable . |
UniformDiffSS(StringBuffer xml)
This is the constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
protected void |
LogisticDiffSS.fromXML(StringBuffer xml) |
Constructor and Description |
---|
LogisticDiffSS(StringBuffer xml)
This is the constructor for
Storable . |
ProductConstraint(StringBuffer xml)
This is the constructor for
Storable . |
Modifier and Type | Method and Description |
---|---|
protected void |
UniformDiffSM.extractFurtherInformation(StringBuffer xml) |
protected void |
IndependentProductDiffSM.extractFurtherInformation(StringBuffer rep) |
protected void |
NormalizedDiffSM.fromXML(StringBuffer xml) |
protected void |
MarkovRandomFieldDiffSM.fromXML(StringBuffer representation) |
protected void |
MappingDiffSM.fromXML(StringBuffer xml) |
protected void |
CyclicMarkovModelDiffSM.fromXML(StringBuffer xml) |
Constructor and Description |
---|
AbstractDifferentiableStatisticalModel(StringBuffer xml)
This is the constructor for
Storable . |
AbstractVariableLengthDiffSM(StringBuffer source)
This is the constructor for the interface
Storable . |
CyclicMarkovModelDiffSM(StringBuffer source)
This is the constructor for
Storable . |
IndependentProductDiffSM(StringBuffer source)
This is the constructor for the interface
Storable . |
MappingDiffSM(StringBuffer xml)
This is the constructor for
Storable . |
MarkovRandomFieldDiffSM(StringBuffer source)
This is the constructor for the interface
Storable . |
NormalizedDiffSM(StringBuffer xml)
This is the constructor for
Storable . |
UniformDiffSM(StringBuffer xml)
This is the constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
protected void |
MarkovModelDiffSM.fromXML(StringBuffer source) |
protected void |
BayesianNetworkDiffSM.fromXML(StringBuffer source) |
Constructor and Description |
---|
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. |
BNDiffSMParameter(StringBuffer representation)
The standard constructor for the interface
Storable . |
BNDiffSMParameterTree(StringBuffer source)
Recreates a
BNDiffSMParameterTree from its XML representation as
returned by BNDiffSMParameterTree.toXML() . |
MarkovModelDiffSM(StringBuffer xml)
The standard constructor for the interface
Storable . |
TreeElement(StringBuffer representation)
Constructor for the
Storable interface. |
Modifier and Type | Method and Description |
---|---|
protected void |
Measure.fromXML(StringBuffer xml)
Parses this
Measure from its XML representation. |
Constructor and Description |
---|
InhomogeneousMarkov(StringBuffer buf)
The standard constructor for the interface
Storable . |
InhomogeneousMarkovParameterSet(StringBuffer representation)
Creates a new
InhomogeneousMarkov.InhomogeneousMarkovParameterSet from its XML
representation as defined by the Storable
interface. |
Measure(StringBuffer xml)
Creates a new
Measure from its XML-representation. |
MeasureParameterSet(StringBuffer xml)
The standard constructor for the interface
Storable . |
Constructor and Description |
---|
BTExplainingAwayResidual(StringBuffer buf)
The standard constructor for the interface
Storable . |
BTExplainingAwayResidualParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable
. |
BTMutualInformation(StringBuffer buf)
The standard constructor for the interface
Storable . |
BTMutualInformationParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable
. |
Constructor and Description |
---|
PMMExplainingAwayResidual(StringBuffer buf)
The standard constructor for the interface
Storable . |
PMMExplainingAwayResidualParameterSet(StringBuffer representation)
Creates a new
PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet from its
XML representation as defined by the Storable
interface. |
PMMMutualInformation(StringBuffer buf)
The standard constructor for the interface
Storable . |
PMMMutualInformationParameterSet(StringBuffer representation)
Creates a new
PMMMutualInformation.PMMMutualInformationParameterSet from its
XML representation as defined by the Storable
interface. |
Modifier and Type | Method and Description |
---|---|
protected void |
UniformHomogeneousDiffSM.fromXML(StringBuffer xml) |
protected void |
HomogeneousMMDiffSM.fromXML(StringBuffer xml) |
protected void |
HomogeneousMM0DiffSM.fromXML(StringBuffer xml) |
Constructor and Description |
---|
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 . |
Modifier and Type | Method and Description |
---|---|
protected void |
LimitedSparseLocalInhomogeneousMixtureDiffSM_higherOrder.fromXML(StringBuffer xml) |
Constructor and Description |
---|
LimitedSparseLocalInhomogeneousMixtureDiffSM_higherOrder(StringBuffer xml)
Creates a
LimitedSparseLocalInhomogeneousMixtureDiffSM_higherOrder model from its XML representation |
Modifier and Type | Method and Description |
---|---|
protected void |
StrandDiffSM.extractFurtherInformation(StringBuffer xml) |
protected void |
AbstractMixtureDiffSM.extractFurtherInformation(StringBuffer xml)
This method is the opposite of
AbstractMixtureDiffSM.getFurtherInformation() . |
protected void |
AbstractMixtureDiffSM.fromXML(StringBuffer b) |
Constructor and Description |
---|
AbstractMixtureDiffSM(StringBuffer xml)
This is the constructor for the interface
Storable . |
MixtureDiffSM(StringBuffer xml)
This is the constructor for the interface
Storable . |
StrandDiffSM(StringBuffer xml)
This is the constructor for
Storable . |
VariableLengthMixtureDiffSM(StringBuffer xml)
This is the constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
protected void |
ExtendedZOOPSDiffSM.extractFurtherInformation(StringBuffer xml) |
protected void |
SkewNormalLikeDurationDiffSM.fromXML(StringBuffer rep) |
protected void |
PositionDiffSM.fromXML(StringBuffer xml) |
protected void |
MixtureDurationDiffSM.fromXML(StringBuffer rep) |
protected void |
DurationDiffSM.fromXML(StringBuffer xml) |
Constructor and Description |
---|
DurationDiffSM(StringBuffer source)
This is the constructor for
Storable . |
ExtendedZOOPSDiffSM(StringBuffer source)
This is the constructor for the interface
Storable . |
MixtureDurationDiffSM(StringBuffer source)
This is the constructor for
Storable . |
PositionDiffSM(StringBuffer source)
This is the constructor for
Storable . |
SkewNormalLikeDurationDiffSM(StringBuffer source)
This is the constructor for
Storable . |
UniformDurationDiffSM(StringBuffer b)
This is the constructor for
Storable . |
Modifier and Type | Method and Description |
---|---|
protected void |
VariableLengthWrapperTrainSM.fromXML(StringBuffer xml) |
void |
UniformTrainSM.fromXML(StringBuffer representation) |
protected void |
PFMWrapperTrainSM.fromXML(StringBuffer xml) |
protected void |
DifferentiableStatisticalModelWrapperTrainSM.fromXML(StringBuffer xml) |
void |
CompositeTrainSM.fromXML(StringBuffer representation) |
protected abstract void |
AbstractTrainableStatisticalModel.fromXML(StringBuffer xml)
This method should only be used by the constructor that works on a
StringBuffer . |
Constructor and Description |
---|
AbstractTrainableStatisticalModel(StringBuffer stringBuff)
The standard constructor for the interface
Storable . |
CompositeTrainSM(StringBuffer stringBuff)
The standard constructor for the interface
Storable . |
DifferentiableStatisticalModelWrapperTrainSM(StringBuffer stringBuff)
The standard constructor for the interface
Storable . |
PFMWrapperTrainSM(StringBuffer stringBuff)
Creates a wrapper from its XML representation
|
UniformTrainSM(StringBuffer stringBuff)
The standard constructor for the interface
Storable . |
VariableLengthWrapperTrainSM(StringBuffer stringBuff)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
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) |
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 . |
Constructor and Description |
---|
Constraint(StringBuffer xml)
The standard constructor for the interface
Storable . |
DGTrainSMParameterSet(StringBuffer s)
The standard constructor for the interface
Storable . |
DiscreteGraphicalTrainSM(DGTrainSMParameterSet params)
The default constructor.
|
DiscreteGraphicalTrainSM(StringBuffer representation)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
protected void |
HomogeneousTrainSM.HomCondProb.extractAdditionalInfo(StringBuffer xml) |
protected void |
HomogeneousTrainSM.set(DGTrainSMParameterSet params,
boolean trained) |
protected void |
HomogeneousMM.set(DGTrainSMParameterSet params,
boolean trained) |
protected void |
HomogeneousMM.setFurtherModelInfos(StringBuffer xml) |
Constructor and Description |
---|
HomCondProb(StringBuffer xml)
The standard constructor for the interface
Storable
. |
HomogeneousMM(HomMMParameterSet params)
Creates a new homogeneous Markov model from a parameter set.
|
HomogeneousMM(StringBuffer stringBuff)
The standard constructor for the interface
Storable . |
HomogeneousTrainSM(HomogeneousTrainSMParameterSet params)
Creates a homogeneous model from a parameter set.
|
HomogeneousTrainSM(StringBuffer stringBuff)
The standard constructor for the interface
Storable . |
Constructor and Description |
---|
HomMMParameterSet(StringBuffer s)
The standard constructor for the interface
Storable . |
HomogeneousTrainSMParameterSet(StringBuffer s)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
protected void |
MEMConstraint.extractAdditionalInfo(StringBuffer xml) |
protected void |
InhConstraint.extractAdditionalInfo(StringBuffer xml) |
protected void |
InhCondProb.extractAdditionalInfo(StringBuffer xml) |
protected void |
InhomogeneousDGTrainSM.set(DGTrainSMParameterSet parameter,
boolean trained) |
protected void |
FSMEManager.set(DGTrainSMParameterSet params,
boolean trained) |
protected void |
FSDAGTrainSM.set(DGTrainSMParameterSet params,
boolean trained) |
protected void |
BayesianNetworkTrainSM.set(DGTrainSMParameterSet parameter,
boolean trained) |
protected void |
MEManager.setFurtherModelInfos(StringBuffer xml) |
protected void |
FSDAGModelForGibbsSampling.setFurtherModelInfos(StringBuffer xml) |
protected void |
DAGTrainSM.setFurtherModelInfos(StringBuffer xml) |
Constructor and Description |
---|
BayesianNetworkTrainSM(BayesianNetworkTrainSMParameterSet params)
Creates a new
BayesianNetworkTrainSM from a given
BayesianNetworkTrainSMParameterSet . |
BayesianNetworkTrainSM(StringBuffer representation)
The standard constructor for the interface
Storable . |
DAGTrainSM(IDGTrainSMParameterSet params)
This is the main constructor.
|
DAGTrainSM(StringBuffer xml)
The standard constructor for the interface
Storable . |
FSDAGModelForGibbsSampling(FSDAGModelForGibbsSamplingParameterSet params)
The default constructor.
|
FSDAGModelForGibbsSampling(StringBuffer representation)
This is the constructor for the
Storable interface. |
FSDAGTrainSM(FSDAGTrainSMParameterSet params)
This is the main constructor.
|
FSDAGTrainSM(StringBuffer xml)
The standard constructor for the interface
Storable . |
FSMEManager(FSMEMParameterSet params)
Creates a new
MEManager from a given
MEManagerParameterSet . |
FSMEManager(StringBuffer stringBuff)
The standard constructor for the interface
Storable . |
InhCondProb(StringBuffer xml)
The standard constructor for the interface
Storable . |
InhConstraint(StringBuffer xml)
The standard constructor for the interface
Storable . |
InhomogeneousDGTrainSM(IDGTrainSMParameterSet params)
Creates a new
InhomogeneousDGTrainSM from a given
IDGTrainSMParameterSet . |
InhomogeneousDGTrainSM(StringBuffer representation)
The standard constructor for the interface
Storable . |
MEM(StringBuffer representation)
The constructor for the
Storable interface. |
MEManager(MEManagerParameterSet params)
Creates a new
MEManager from a given
MEManagerParameterSet . |
MEManager(StringBuffer stringBuff)
The standard constructor for the interface
Storable . |
MEMConstraint(StringBuffer xml)
The standard constructor for the interface
Storable . |
Constructor and Description |
---|
BayesianNetworkTrainSMParameterSet(StringBuffer s)
The standard constructor for the interface
Storable . |
ConstraintParameterSet(StringBuffer xml)
The constructor for the
Storable interface. |
FSDAGModelForGibbsSamplingParameterSet(StringBuffer s)
The constructor for the
Storable interface. |
FSDAGTrainSMParameterSet(StringBuffer s)
The standard constructor for the interface
Storable . |
FSMEMParameterSet(StringBuffer s)
The constructor for the
Storable interface. |
IDGTrainSMParameterSet(StringBuffer s)
The standard constructor for the interface
Storable . |
MEManagerParameterSet(StringBuffer s)
The constructor for the
Storable interface. |
Modifier and Type | Method and Description |
---|---|
protected void |
SharedStructureClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml) |
protected void |
SharedStructureMixture.fromXML(StringBuffer representation) |
Constructor and Description |
---|
SharedStructureClassifier(StringBuffer xml)
The standard constructor for the interface
Storable . |
SharedStructureMixture(StringBuffer xml)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
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. |
Constructor and Description |
---|
AbstractHMM(StringBuffer xml)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
protected void |
SamplingHigherOrderHMM.extractFurtherInformation(StringBuffer xml) |
protected void |
HigherOrderHMM.extractFurtherInformation(StringBuffer xml)
This method extracts further information from the XML representation.
|
protected void |
DifferentiableHigherOrderHMM.extractFurtherInformation(StringBuffer xml) |
Constructor and Description |
---|
DifferentiableHigherOrderHMM(StringBuffer xml)
The standard constructor for the interface
Storable . |
HigherOrderHMM(StringBuffer xml)
The standard constructor for the interface
Storable . |
SamplingHigherOrderHMM(StringBuffer xml)
The standard constructor for the interface
Storable . |
SamplingPhyloHMM(StringBuffer xml)
The standard constructor for the interface
Storable . |
Constructor and Description |
---|
MixtureEmission(StringBuffer xml)
The standard constructor for the interface
Storable . |
UniformEmission(StringBuffer xml)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
protected void |
PluginGaussianEmission.fromXML(StringBuffer xml) |
protected void |
MultivariateGaussianEmission.fromXML(StringBuffer xml)
Parses the XML representation.
|
protected void |
GaussianEmission.fromXML(StringBuffer xml)
This method is internally used by the constructor
GaussianEmission.GaussianEmission(StringBuffer) . |
Constructor and Description |
---|
GaussianEmission(StringBuffer xml)
Creates a
GaussianEmission from its XML representation. |
MultivariateGaussianEmission(StringBuffer xml)
Creates a
MultivariateGaussianEmission from its XML representation. |
PluginGaussianEmission(StringBuffer xml)
Creates a
PluginGaussianEmission from its XML representation. |
Modifier and Type | Method and Description |
---|---|
protected void |
ReferenceSequenceDiscreteEmission.extractFurtherInformation(StringBuffer xml) |
protected void |
PhyloDiscreteEmission.extractFurtherInformation(StringBuffer xml) |
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) . |
Constructor and Description |
---|
AbstractConditionalDiscreteEmission(StringBuffer xml)
Creates a
AbstractConditionalDiscreteEmission from its XML representation. |
DiscreteEmission(StringBuffer xml)
Creates a
DiscreteEmission from its XML representation. |
ReferenceSequenceDiscreteEmission(StringBuffer xml)
Creates a
ReferenceSequenceDiscreteEmission from its XML representation. |
Constructor and Description |
---|
BaumWelchParameterSet(StringBuffer xml)
The standard constructor for the interface
Storable . |
HMMTrainingParameterSet(StringBuffer xml)
The standard constructor for the interface
Storable . |
MaxHMMTrainingParameterSet(StringBuffer xml)
The standard constructor for the interface
Storable . |
MultiThreadedTrainingParameterSet(StringBuffer xml)
The standard constructor for the interface
Storable . |
NumericalHMMTrainingParameterSet(StringBuffer xml)
The standard constructor for the interface
Storable . |
SamplingHMMTrainingParameterSet(StringBuffer xml)
The standard constructor for the interface
Storable . |
ViterbiParameterSet(StringBuffer xml)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
protected void |
HigherOrderTransition.extractFurtherInformation(StringBuffer xml) |
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.
|
Constructor and Description |
---|
AbstractTransitionElement(StringBuffer xml)
The standard constructor for the interface
Storable . |
BasicHigherOrderTransition(StringBuffer xml)
The standard constructor for the interface
Storable . |
HigherOrderTransition(StringBuffer xml)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
protected void |
ScaledTransitionElement.extractFurtherInformation(StringBuffer xml) |
protected void |
ReferenceBasedTransitionElement.extractFurtherInformation(StringBuffer xml) |
protected void |
DistanceBasedScaledTransitionElement.extractFurtherInformation(StringBuffer xml) |
protected void |
BasicTransitionElement.extractFurtherInformation(StringBuffer xml) |
protected void |
BasicPluginTransitionElement.extractFurtherInformation(StringBuffer xml) |
Constructor and Description |
---|
BasicPluginTransitionElement(StringBuffer xml)
The standard constructor for the interface
Storable . |
BasicTransitionElement(StringBuffer xml)
The standard constructor for the interface
Storable . |
DistanceBasedScaledTransitionElement(StringBuffer xml)
Extracts a distance-base scaled transition element from XML.
|
ReferenceBasedTransitionElement(StringBuffer xml)
The standard constructor for the interface
Storable . |
ScaledTransitionElement(StringBuffer xml)
The standard constructor for the interface
Storable . |
TransitionElement(StringBuffer xml)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
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) |
Constructor and Description |
---|
AbstractMixtureTrainSM(StringBuffer xml)
The standard constructor for the interface
Storable . |
MixtureTrainSM(StringBuffer xml)
The constructor for the interface
Storable . |
StrandTrainSM(StringBuffer stringBuff)
The constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
protected void |
HiddenMotifMixture.extractFurtherInformation(StringBuffer xml) |
Constructor and Description |
---|
HiddenMotifMixture(StringBuffer xml)
The standard constructor for the interface
Storable . |
ZOOPSTrainSM(StringBuffer xml)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
protected abstract void |
PositionPrior.extractAdditionalInformation(StringBuffer xml)
This method extracts additional information from a
StringBuffer . |
protected void |
GaussianLikePositionPrior.extractAdditionalInformation(StringBuffer xml) |
Constructor and Description |
---|
GaussianLikePositionPrior(StringBuffer rep)
The standard constructor for the interface
Storable . |
PositionPrior(StringBuffer rep)
The standard constructor for the interface
Storable . |
UniformPositionPrior(StringBuffer xml)
The standard constructor for the interface
Storable . |
Constructor and Description |
---|
PhyloNode(StringBuffer xml)
The standard constructor for the interface
Storable . |
PhyloTree(StringBuffer xml)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
PhyloTree |
NewickParser.tokenize()
This method construct a
PhyloTree from the given input stream |
Modifier and Type | Method and Description |
---|---|
protected void |
ToolResult.extractFurtherInfos(StringBuffer representation) |
protected void |
DataColumnParameter.extractFurtherInfos(StringBuffer representation) |
Constructor and Description |
---|
DataColumnParameter(StringBuffer representation)
The standard constructor for the interface
Storable . |
ToolResult(StringBuffer representation)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
protected void |
GalaxyAdaptor.LinkedImageResult.extractFurtherInfos(StringBuffer representation) |
protected void |
GalaxyAdaptor.FileResult.extractFurtherInfos(StringBuffer rep) |
Constructor and Description |
---|
FileResult(StringBuffer rep)
Creates a new
TextResult from its XML-representation |
LinkedImageResult(StringBuffer xml)
Creates a new
GalaxyAdaptor.LinkedImageResult from its XML-representation |
MultilineSimpleParameter(StringBuffer representation)
The standard constructor for the interface
Storable . |
Constructor and Description |
---|
DoubleList(StringBuffer rep)
This is the constructor for the interface
Storable . |
SeqLogoPlotGenerator(StringBuffer xml)
Creates a
SeqLogoPlotter.SeqLogoPlotGenerator from its XML representation. |