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PREV NEXT | FRAMES NO FRAMES All Classes |
Packages that use DataSet | |
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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.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.trainSMBased | Provides the classes for Classifier s that are based on TrainableStatisticalModel s. |
de.jstacs.classifiers.utils | Provides some useful classes for working with classifiers. |
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.bioJava | Provides an adapter between the representation of data in BioJava and the representation used in Jstacs. |
de.jstacs.data.sequences | Provides classes for representing sequences. The implementations of sequences currently include DiscreteSequence s prepared for alphabets of different sizes, and ArbitrarySequence s that may
contain continuous values as well.As sub-package provides the facilities to annotate Sequence s. |
de.jstacs.motifDiscovery | This package provides the framework including the interface for any de novo motif discoverer. |
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 | Provides all SequenceScore s, which can be used to score a Sequence , typically using some model assumptions. |
de.jstacs.sequenceScores.differentiable | |
de.jstacs.sequenceScores.differentiable.logistic | |
de.jstacs.sequenceScores.statisticalModels | Provides all StatisticalModel s, which can compute a proper (i.e., normalized) likelihood over the input space of sequences.StatisticalModel s can be further differentiated into TrainableStatisticalModel s,
which can be learned from a single input DataSet , and DifferentiableStatisticalModel s,
which define a proper likelihood but can also compute gradients like DifferentiableSequenceScore s. |
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.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.inhomogeneous | This package contains various inhomogeneous models. |
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.mixture | This package is the super package for any mixture model. |
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif | |
de.jstacs.utils | This package contains a bundle of useful classes and interfaces like ... |
Uses of DataSet in de.jstacs.classifiers |
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Methods in de.jstacs.classifiers that return DataSet | |
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DataSet[] |
MappingClassifier.mapDataSet(DataSet[] s)
This method maps the given DataSet s to the internal classes. |
Methods in de.jstacs.classifiers with parameters of type DataSet | |
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protected void |
AbstractScoreBasedClassifier.check(DataSet s)
This method checks if the given DataSet can be used. |
byte[] |
AbstractClassifier.classify(DataSet s)
This method classifies all sequences of a data set and returns an array of indices of the classes to which the respective sequences are assigned with for each index i in the array
0 < i < getNumberOfClasses() . |
ResultSet |
AbstractClassifier.evaluate(AbstractPerformanceMeasureParameterSet<? extends PerformanceMeasure> params,
boolean exceptionIfNotComputeable,
DataSet... s)
This method evaluates the classifier and computes, for instance, the sensitivity for a given specificity, the area under the ROC curve and so on. |
ResultSet |
AbstractClassifier.evaluate(AbstractPerformanceMeasureParameterSet<? extends PerformanceMeasure> params,
boolean exceptionIfNotComputeable,
DataSet[] s,
double[][] weights)
This method evaluates the classifier and computes, for instance, the sensitivity for a given specificity, the area under the ROC curve and so on. |
protected double[][][] |
AbstractScoreBasedClassifier.getMultiClassScores(DataSet[] s)
|
protected double[][][] |
AbstractClassifier.getMultiClassScores(DataSet[] s)
This method returns a multidimensional array with class specific scores. |
double[] |
AbstractScoreBasedClassifier.getPValue(DataSet candidates,
DataSet bg)
Returns the p-values for all Sequence s in the DataSet
candidates with respect to a given background DataSet
. |
double |
AbstractScoreBasedClassifier.getPValue(Sequence candidate,
DataSet bg)
Returns the p-value for a Sequence candidate with
respect to a given background DataSet . |
protected boolean |
MappingClassifier.getResults(LinkedList list,
DataSet[] s,
double[][] weights,
AbstractPerformanceMeasureParameterSet<? extends PerformanceMeasure> params,
boolean exceptionIfNotComputeable)
|
protected boolean |
AbstractScoreBasedClassifier.getResults(LinkedList list,
DataSet[] s,
double[][] weights,
AbstractPerformanceMeasureParameterSet<? extends PerformanceMeasure> params,
boolean exceptionIfNotComputeable)
|
protected boolean |
AbstractClassifier.getResults(LinkedList list,
DataSet[] s,
double[][] weights,
AbstractPerformanceMeasureParameterSet<? extends PerformanceMeasure> params,
boolean exceptionIfNotComputeable)
This method computes the results for any evaluation of the classifier. |
double[] |
AbstractScoreBasedClassifier.getScores(DataSet s)
This method returns the scores of the classifier for any Sequence
in the DataSet . |
DataSet[] |
MappingClassifier.mapDataSet(DataSet[] s)
This method maps the given DataSet s to the internal classes. |
void |
AbstractClassifier.train(DataSet... s)
Trains the AbstractClassifier object given the data as
DataSet s.This method should work non-incrementally. |
void |
MappingClassifier.train(DataSet[] s,
double[][] weights)
|
abstract void |
AbstractClassifier.train(DataSet[] s,
double[][] weights)
This method trains a classifier over an array of weighted DataSet
s. |
Uses of DataSet in de.jstacs.classifiers.assessment |
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Methods in de.jstacs.classifiers.assessment with parameters of type DataSet | |
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ListResult |
ClassifierAssessment.assess(NumericalPerformanceMeasureParameterSet mp,
T assessPS,
DataSet... s)
Assesses the contained classifiers. |
ListResult |
ClassifierAssessment.assess(NumericalPerformanceMeasureParameterSet mp,
T assessPS,
ProgressUpdater pU,
DataSet[] s)
Assesses the contained classifiers. |
ListResult |
ClassifierAssessment.assess(NumericalPerformanceMeasureParameterSet mp,
T assessPS,
ProgressUpdater pU,
DataSet[][]... s)
Assesses the contained classifiers. |
ListResult |
ClassifierAssessment.assess(NumericalPerformanceMeasureParameterSet mp,
T assessPS,
ProgressUpdater pU,
DataSet[] s,
double[][] weights)
Assesses the contained classifiers. |
ListResult |
KFoldCrossValidation.assessWithPredefinedSplits(NumericalPerformanceMeasureParameterSet mp,
ClassifierAssessmentAssessParameterSet caaps,
ProgressUpdater pU,
DataSet[][] splitData,
double[][][] splitWeights)
This method implements a k-fold crossvalidation on previously split data. |
protected void |
KFoldCrossValidation.evaluateClassifier(NumericalPerformanceMeasureParameterSet mp,
KFoldCrossValidationAssessParameterSet assessPS,
DataSet[] s,
double[][] weights,
ProgressUpdater pU)
Evaluates a classifier. |
protected void |
RepeatedHoldOutExperiment.evaluateClassifier(NumericalPerformanceMeasureParameterSet mp,
RepeatedHoldOutAssessParameterSet assessPS,
DataSet[] s,
double[][] weights,
ProgressUpdater pU)
Evaluates the classifier. |
protected void |
RepeatedSubSamplingExperiment.evaluateClassifier(NumericalPerformanceMeasureParameterSet mp,
RepeatedSubSamplingAssessParameterSet assessPS,
DataSet[] s,
double[][] weights,
ProgressUpdater pU)
Evaluates the classifier. |
protected void |
Sampled_RepeatedHoldOutExperiment.evaluateClassifier(NumericalPerformanceMeasureParameterSet mp,
Sampled_RepeatedHoldOutAssessParameterSet assessPS,
DataSet[] s,
double[][] weights,
ProgressUpdater pU)
|
protected abstract void |
ClassifierAssessment.evaluateClassifier(NumericalPerformanceMeasureParameterSet mp,
T assessPS,
DataSet[] s,
double[][] weights,
ProgressUpdater pU)
This method must be implemented in all subclasses. |
protected void |
ClassifierAssessment.prepareAssessment(boolean storeAll,
DataSet... s)
Prepares an assessment. |
protected void |
ClassifierAssessment.test(NumericalPerformanceMeasureParameterSet mp,
boolean exception,
DataSet[] testS,
double[][] weights)
Uses the given test data sets to call the evaluate( ... |
protected void |
ClassifierAssessment.train(DataSet[] trainS,
double[][] weights)
Trains the local classifiers using the given training data sets. |
Uses of DataSet in de.jstacs.classifiers.differentiableSequenceScoreBased |
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Fields in de.jstacs.classifiers.differentiableSequenceScoreBased declared as DataSet | |
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protected DataSet[] |
AbstractOptimizableFunction.data
The data that is used to evaluate this function. |
Methods in de.jstacs.classifiers.differentiableSequenceScoreBased that return DataSet | |
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abstract DataSet[] |
OptimizableFunction.getData()
Returns the data for each class used in this OptimizableFunction . |
DataSet[] |
AbstractOptimizableFunction.getData()
|
Methods in de.jstacs.classifiers.differentiableSequenceScoreBased with parameters of type DataSet | |
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protected void |
ScoreClassifier.createStructure(DataSet[] data,
double[][] weights)
Creates the structure that will be used in the optimization. |
protected void |
ScoreClassifier.createStructure(DataSet[] data,
double[][] weights,
boolean initRandomly)
Creates the structure that will be used in the optimization. |
protected double |
ScoreClassifier.doOptimization(DataSet[] reduced,
double[][] newWeights)
This method does the optimization of the train -method |
protected abstract DiffSSBasedOptimizableFunction |
ScoreClassifier.getFunction(DataSet[] data,
double[][] weights)
Returns the function that should be optimized. |
abstract void |
OptimizableFunction.setDataAndWeights(DataSet[] data,
double[][] weights)
This method sets the data set and the sequence weights to be used. |
void |
AbstractOptimizableFunction.setDataAndWeights(DataSet[] data,
double[][] weights)
|
void |
AbstractMultiThreadedOptimizableFunction.setDataAndWeights(DataSet[] data,
double[][] weights)
|
void |
ScoreClassifier.train(DataSet[] data,
double[][] weights)
|
Constructors in de.jstacs.classifiers.differentiableSequenceScoreBased with parameters of type DataSet | |
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AbstractMultiThreadedOptimizableFunction(int threads,
DataSet[] data,
double[][] weights,
boolean norm,
boolean freeParams)
The constructor for an multi-threaded instance. |
|
AbstractOptimizableFunction(DataSet[] data,
double[][] weights,
boolean norm,
boolean freeParams)
The constructor creates an instance using the given weighted data. |
|
DiffSSBasedOptimizableFunction(int threads,
DifferentiableSequenceScore[] score,
DataSet[] data,
double[][] weights,
LogPrior prior,
boolean norm,
boolean freeParams)
Creates an instance with the underlying infrastructure. |
Uses of DataSet in de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix |
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Methods in de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix that return DataSet | |
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DataSet[] |
OneDataSetLogGenDisMixFunction.getData()
|
Methods in de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix with parameters of type DataSet | |
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protected LogGenDisMixFunction |
GenDisMixClassifier.getFunction(DataSet[] data,
double[][] weights)
|
void |
OneDataSetLogGenDisMixFunction.setDataAndWeights(DataSet[] data,
double[][] weights)
|
Constructors in de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix with parameters of type DataSet | |
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LogGenDisMixFunction(int threads,
DifferentiableSequenceScore[] score,
DataSet[] data,
double[][] weights,
LogPrior prior,
double[] beta,
boolean norm,
boolean freeParams)
The constructor for creating an instance that can be used in an Optimizer . |
|
OneDataSetLogGenDisMixFunction(int threads,
DifferentiableSequenceScore[] score,
DataSet data,
double[][] weights,
LogPrior prior,
double[] beta,
boolean norm,
boolean freeParams)
The constructor for creating an instance that can be used in an Optimizer . |
Uses of DataSet in de.jstacs.classifiers.differentiableSequenceScoreBased.sampling |
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Methods in de.jstacs.classifiers.differentiableSequenceScoreBased.sampling with parameters of type DataSet | |
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void |
SamplingScoreBasedClassifier.doSingleSampling(DataSet[] s,
double[][] weights,
int numSteps,
String outfilePrefix)
Does a single sampling run for a predefined number of steps. |
protected abstract DiffSSBasedOptimizableFunction |
SamplingScoreBasedClassifier.getFunction(DataSet[] data,
double[][] weights)
Returns the function that should be sampled from. |
protected DiffSSBasedOptimizableFunction |
SamplingGenDisMixClassifier.getFunction(DataSet[] data,
double[][] weights)
|
double[] |
SamplingScoreBasedClassifier.getScores(DataSet s)
|
void |
SamplingScoreBasedClassifier.train(DataSet[] s,
double[][] weights)
|
Uses of DataSet in de.jstacs.classifiers.trainSMBased |
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Methods in de.jstacs.classifiers.trainSMBased with parameters of type DataSet | |
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byte[] |
TrainSMBasedClassifier.classify(DataSet s)
|
double[] |
TrainSMBasedClassifier.getScores(DataSet s)
|
void |
TrainSMBasedClassifier.train(DataSet[] s,
double[][] weights)
|
Uses of DataSet in de.jstacs.classifiers.utils |
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Methods in de.jstacs.classifiers.utils with parameters of type DataSet | |
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static ImageResult |
ClassificationVisualizer.getScatterplot(AbstractScoreBasedClassifier cl1,
AbstractScoreBasedClassifier cl2,
DataSet class0,
DataSet class1,
REnvironment e,
boolean drawThreshold)
This method returns an ImageResult containing a scatter plot of
the scores for the given classifiers cl1 and
cl2 . |
static ImageResult |
ClassificationVisualizer.plotScores(AbstractScoreBasedClassifier cl,
DataSet class0,
DataSet class1,
REnvironment e,
int bins,
double density,
String plotOptions)
This method returns an ImageResult containing a plot of the
histograms of the scores. |
static void |
ClassificationVisualizer.plotScores(AbstractScoreBasedClassifier cl,
DataSet class0,
DataSet class1,
REnvironment e,
int bins,
double density,
String plotOptions,
String fName)
This method creates a pdf containing a plot of the histograms of the scores. |
Uses of DataSet in de.jstacs.data |
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Subclasses of DataSet in de.jstacs.data | |
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class |
DNADataSet
This class exist for convenience to allow the user an easy creation of DataSet s of DNA Sequence s. |
Methods in de.jstacs.data that return DataSet | |
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static DataSet |
DataSet.diff(DataSet data,
DataSet... samples)
This method computes the difference between the DataSet data and
the DataSet s samples . |
DataSet |
DataSet.getCompositeDataSet(int[] starts,
int[] lengths)
This method enables you to use only composite Sequence s of all
elements in the current DataSet . |
DataSet |
DataSet.WeightedDataSetFactory.getDataSet()
Returns the DataSet , where each Sequence occurs only
once. |
static DataSet |
DinucleotideProperty.getDataSetForProperty(DataSet original,
DinucleotideProperty... properties)
Creates a new DataSet by converting each Sequence in original to the DinucleotideProperty s properties and setting these as ReferenceSequenceAnnotation of each original sequence. |
static DataSet |
DinucleotideProperty.getDataSetForProperty(DataSet original,
DinucleotideProperty.Smoothing smoothing,
boolean addToAnnotation,
DinucleotideProperty... properties)
Creates a new DataSet by converting each Sequence in original to the DinucleotideProperty s properties and adding or setting these as ReferenceSequenceAnnotation of each original sequence. |
static DataSet |
DinucleotideProperty.getDataSetForProperty(DataSet original,
DinucleotideProperty.Smoothing smoothing,
boolean originalAsAnnotation,
DinucleotideProperty property)
Creates a new DataSet by converting each Sequence in original to the DinucleotideProperty property using the DinucleotideProperty.Smoothing smoothing. |
static DataSet |
DinucleotideProperty.getDataSetForProperty(DataSet original,
DinucleotideProperty property)
Creates a new DataSet by converting each Sequence in original to the DinucleotideProperty property . |
DataSet |
DataSet.getInfixDataSet(int start,
int length)
This method enables you to use only an infix of all elements, i.e. |
DataSet |
DataSet.getPartialDataSet(int[]... indexes)
Returns a new DataSet that contains all elements of this DataSet that are specified
by the supplied pairs of start and end indexes in indexes . |
DataSet |
DataSet.getPartialDataSet(int start,
int end)
Returns a new DataSet that contains all elements of this DataSet that are specified
by the supplied start (inclusive) and end (exclusive) indexes. |
DataSet |
DataSet.getReverseComplementaryDataSet()
Returns a DataSet that contains the reverse complement of all Sequence s in
this DataSet . |
DataSet |
DataSet.getSuffixDataSet(int start)
This method enables you to use only a suffix of all elements, i.e. |
static DataSet |
DataSet.intersection(DataSet... samples)
This method computes the intersection between all elements/ DataSet
s of the array, i.e. |
DataSet[] |
DataSet.partition(DataSet.PartitionMethod method,
double... percentage)
This method partitions the elements, i.e. |
DataSet[] |
DataSet.partition(DataSet.PartitionMethod method,
int k)
This method partitions the elements, i.e. |
DataSet |
DataSet.subSampling(double number)
Randomly samples elements, i.e. |
static DataSet |
DataSet.union(DataSet... s)
Unites all DataSet s of the array s . |
static DataSet |
DataSet.union(DataSet[] s,
boolean[] in)
This method unites all DataSet s of the array s
regarding the array in . |
Methods in de.jstacs.data that return types with arguments of type DataSet | |
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Pair<DataSet,double[]> |
DataSet.resize(double[] weights,
int subsequenceLength)
|
Pair<DataSet,double[]> |
DataSet.subSampling(double number,
double[] weights)
|
static Pair<DataSet,double[]> |
DataSet.union(DataSet[] s,
double[][] weights,
boolean[] in)
This method unites all DataSet s of the array s
regarding the array in and sets the element length in the
united DataSet to subsequenceLength . |
Methods in de.jstacs.data with parameters of type DataSet | |
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static DataSet |
DataSet.diff(DataSet data,
DataSet... samples)
This method computes the difference between the DataSet data and
the DataSet s samples . |
static DataSet |
DataSet.diff(DataSet data,
DataSet... samples)
This method computes the difference between the DataSet data and
the DataSet s samples . |
static String |
DataSet.getAnnotation(DataSet... s)
Returns the annotation for an array of DataSet s. |
static DataSet |
DinucleotideProperty.getDataSetForProperty(DataSet original,
DinucleotideProperty... properties)
Creates a new DataSet by converting each Sequence in original to the DinucleotideProperty s properties and setting these as ReferenceSequenceAnnotation of each original sequence. |
static DataSet |
DinucleotideProperty.getDataSetForProperty(DataSet original,
DinucleotideProperty.Smoothing smoothing,
boolean addToAnnotation,
DinucleotideProperty... properties)
Creates a new DataSet by converting each Sequence in original to the DinucleotideProperty s properties and adding or setting these as ReferenceSequenceAnnotation of each original sequence. |
static DataSet |
DinucleotideProperty.getDataSetForProperty(DataSet original,
DinucleotideProperty.Smoothing smoothing,
boolean originalAsAnnotation,
DinucleotideProperty property)
Creates a new DataSet by converting each Sequence in original to the DinucleotideProperty property using the DinucleotideProperty.Smoothing smoothing. |
static DataSet |
DinucleotideProperty.getDataSetForProperty(DataSet original,
DinucleotideProperty property)
Creates a new DataSet by converting each Sequence in original to the DinucleotideProperty property . |
static ImageResult |
DinucleotideProperty.getPropertyImage(DataSet original,
DinucleotideProperty prop,
DinucleotideProperty.Smoothing smoothing,
REnvironment re,
int xLeft,
String pltOptions,
int width,
int height)
|
static DataSet |
DataSet.intersection(DataSet... samples)
This method computes the intersection between all elements/ DataSet
s of the array, i.e. |
static DataSet |
DataSet.union(DataSet... s)
Unites all DataSet s of the array s . |
static DataSet |
DataSet.union(DataSet[] s,
boolean[] in)
This method unites all DataSet s of the array s
regarding the array in . |
static Pair<DataSet,double[]> |
DataSet.union(DataSet[] s,
double[][] weights,
boolean[] in)
This method unites all DataSet s of the array s
regarding the array in and sets the element length in the
united DataSet to subsequenceLength . |
Uses of DataSet in de.jstacs.data.bioJava |
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Methods in de.jstacs.data.bioJava that return DataSet | |
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static DataSet |
BioJavaAdapter.sequenceIteratorToDataSet(SequenceIterator it,
FeatureFilter filter)
This method creates a new DataSet from a SequenceIterator . |
Methods in de.jstacs.data.bioJava with parameters of type DataSet | |
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static SequenceIterator |
BioJavaAdapter.dataSetToSequenceIterator(DataSet sample,
boolean flat)
Creates a SequenceIterator from the DataSet
sample preserving as much annotation as possible. |
Uses of DataSet in de.jstacs.data.sequences |
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Methods in de.jstacs.data.sequences that return DataSet | |
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static DataSet |
SparseSequence.getDataSet(AlphabetContainer con,
AbstractStringExtractor... se)
This method allows to create a DataSet containing SparseSequence s. |
static DataSet |
ArbitraryFloatSequence.getDataSet(AlphabetContainer con,
AbstractStringExtractor... se)
This method allows to create a DataSet containing ArbitraryFloatSequence s. |
static DataSet |
SparseSequence.getDataSet(AlphabetContainer con,
String filename)
This method allows to create a DataSet containing SparseSequence s using
a file name. |
static DataSet |
ArbitraryFloatSequence.getDataSet(AlphabetContainer con,
String filename)
This method allows to create a DataSet containing ArbitraryFloatSequence s using
a file name. |
static DataSet |
SparseSequence.getDataSet(AlphabetContainer con,
String filename,
SequenceAnnotationParser parser)
This method allows to create a DataSet containing SparseSequence s using
a file name. |
static DataSet |
ArbitraryFloatSequence.getDataSet(AlphabetContainer con,
String filename,
SequenceAnnotationParser parser)
This method allows to create a DataSet containing ArbitraryFloatSequence s using
a file name. |
Uses of DataSet in de.jstacs.motifDiscovery |
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Methods in de.jstacs.motifDiscovery that return DataSet | |
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DataSet |
SignificantMotifOccurrencesFinder.annotateMotif(DataSet data,
int motifIndex)
This method annotates a DataSet . |
DataSet |
SignificantMotifOccurrencesFinder.annotateMotif(DataSet data,
int motifIndex,
int addMax)
This method annotates a DataSet . |
DataSet |
SignificantMotifOccurrencesFinder.annotateMotif(int startPos,
DataSet data,
int motifIndex)
This method annotates a DataSet starting in each sequence at startPos . |
DataSet |
SignificantMotifOccurrencesFinder.annotateMotif(int startPos,
DataSet data,
int motifIndex,
int addMax,
boolean addAnnotation)
This method annotates a DataSet starting in each sequence at startPos . |
DataSet |
SignificantMotifOccurrencesFinder.getBindingSites(DataSet data,
int motifIndex)
This method returns a DataSet containing the predicted binding sites. |
DataSet |
SignificantMotifOccurrencesFinder.getBindingSites(int startPos,
DataSet data,
int motifIndex,
int addMax,
int addLeft,
int addRight)
This method returns a DataSet containing the predicted binding sites. |
Methods in de.jstacs.motifDiscovery with parameters of type DataSet | |
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void |
MutableMotifDiscoverer.adjustHiddenParameters(int index,
DataSet[] data,
double[][] weights)
Adjusts all hidden parameters including duration and mixture parameters according to the current values of the remaining parameters. |
DataSet |
SignificantMotifOccurrencesFinder.annotateMotif(DataSet data,
int motifIndex)
This method annotates a DataSet . |
DataSet |
SignificantMotifOccurrencesFinder.annotateMotif(DataSet data,
int motifIndex,
int addMax)
This method annotates a DataSet . |
DataSet |
SignificantMotifOccurrencesFinder.annotateMotif(int startPos,
DataSet data,
int motifIndex)
This method annotates a DataSet starting in each sequence at startPos . |
DataSet |
SignificantMotifOccurrencesFinder.annotateMotif(int startPos,
DataSet data,
int motifIndex,
int addMax,
boolean addAnnotation)
This method annotates a DataSet starting in each sequence at startPos . |
static ListResult |
MotifDiscoveryAssessment.assess(DataSet truth,
DataSet prediction,
int maxDiff)
This method computes the nucleotide and site measures. |
static boolean |
MutableMotifDiscovererToolbox.doHeuristicSteps(DifferentiableSequenceScore[] funs,
DataSet[] data,
double[][] weights,
DiffSSBasedOptimizableFunction opt,
DifferentiableFunction neg,
byte algorithm,
double linEps,
StartDistanceForecaster startDistance,
SafeOutputStream out,
boolean breakOnChanged,
History[][] hist,
int[][] minimalNewLength,
boolean maxPos)
This method tries to make some heuristic step if at least one DifferentiableSequenceScore is a MutableMotifDiscoverer . |
static boolean |
MutableMotifDiscovererToolbox.findModification(int clazz,
int motif,
MutableMotifDiscoverer mmd,
DifferentiableSequenceScore[] score,
DataSet[] data,
double[][] weights,
DiffSSBasedOptimizableFunction opt,
DifferentiableFunction neg,
byte algo,
double linEps,
StartDistanceForecaster startDistance,
SafeOutputStream out,
History hist,
int minimalNewLength,
boolean maxPos)
This method tries to find a modification, i.e. |
static DataSet.WeightedDataSetFactory |
KMereStatistic.getAbsoluteKMereFrequencies(DataSet data,
int k,
boolean bothStrands)
This method enables the user to get a statistic over all k -mers
in the data . |
static DataSet.WeightedDataSetFactory |
KMereStatistic.getAbsoluteKMereFrequencies(DataSet data,
int k,
boolean bothStrands,
DataSet.WeightedDataSetFactory.SortOperation sortOp)
This method enables the user to get a statistic over all k -mers
in the data . |
DataSet |
SignificantMotifOccurrencesFinder.getBindingSites(DataSet data,
int motifIndex)
This method returns a DataSet containing the predicted binding sites. |
DataSet |
SignificantMotifOccurrencesFinder.getBindingSites(int startPos,
DataSet data,
int motifIndex,
int addMax,
int addLeft,
int addRight)
This method returns a DataSet containing the predicted binding sites. |
static Sequence[] |
KMereStatistic.getCommonString(DataSet data,
int motifLength,
boolean bothStrands)
This method returns an array of sequences of length motifLength so that each string is contained in all
sequences of the data set, more precisely in the data set or the reverse
complementary data set. |
static Pair<Sequence,BitSet[]>[] |
KMereStatistic.getKmereSequenceStatistic(boolean bothStrands,
int maxMismatch,
HashSet<Sequence> filter,
DataSet... data)
This method enables the user to get a statistic for a set of k -mers. |
static Hashtable<Sequence,BitSet[]> |
KMereStatistic.getKmereSequenceStatistic(int k,
boolean bothStrands,
int addIndex,
DataSet... data)
This method enables the user to get a statistic over all k -mers
in the sequences. |
double |
SignificantMotifOccurrencesFinder.getNumberOfBoundSequences(DataSet data,
double[] weights,
int motifIndex)
Returns the number of sequences in data that are predicted to be bound at least once by motif no. |
double[][] |
SignificantMotifOccurrencesFinder.getPWM(int motif,
DataSet data,
double[] weights,
int addLeft,
int addRight)
Returns the Position weight matrix (PWM) of the binding sites of motif motif
in the data set data of the MotifDiscoverer of this SignificantMotifOccurrencesFinder . |
Pair<double[][],double[]> |
SignificantMotifOccurrencesFinder.getPWMAndPosDist(int motif,
DataSet data,
double[] weights,
double[] mean,
int addLeft,
int addRight)
Returns the Position weight matrix (PWM) of the binding sites of motif motif
in the data set data of the MotifDiscoverer of this SignificantMotifOccurrencesFinder
together with standard deviation of binding site positions computed using the provided mean values for each sequence. |
Pair<double[][][],int[][]> |
SignificantMotifOccurrencesFinder.getPWMAndPositions(int motif,
DataSet data,
double[] weights,
int addLeft,
int addRight)
Returns the Position weight matrix (PWM) of the binding sites of motif motif
in the data set data of the MotifDiscoverer of this SignificantMotifOccurrencesFinder
together with the positions of the binding sites within the sequences of data and the corresponding p-values. |
protected double[][] |
SignificantMotifOccurrencesFinder.getPWMAndPositions(int motif,
DataSet data,
double[] weights,
int addLeft,
int addRight,
int[][] positions,
double[][] pvals,
double[] mean,
double[] sd)
Returns the Position weight matrix (PWM) of the binding sites of motif motif
in the data set data of the MotifDiscoverer of this SignificantMotifOccurrencesFinder
and fills with the positions of the binding sites within the sequences of data and the corresponding p-values into the corresponding arrays. |
static double[][] |
MotifDiscoveryAssessment.getSortedScoresForMotifAndFlanking(DataSet data,
DataSet pred,
String identifier)
Returns the scores read from the prediction pred for the motif with identifier identifier and flanking sequences as annotated in
the DataSet data. |
static double[][] |
MotifDiscoveryAssessment.getSortedValuesForMotifAndFlanking(DataSet data,
double[][] values,
double offset,
double factor,
String identifier)
This method provides some score arrays that can be used in AbstractPerformanceMeasure to determine some
curves or area under curves based on the values of the predictions. |
IntList |
SignificantMotifOccurrencesFinder.getStartPositions(int startPos,
DataSet data,
int motifIndex,
int addMax)
This method returns a list of start positions of binding sites. |
double[][] |
SignificantMotifOccurrencesFinder.getValuesForEachNucleotide(DataSet data,
int motif,
boolean addOnlyBest)
This method determines a score for each possible starting position in each of the sequences in data
that this position is covered by at least one motif occurrence of the
motif with index index . |
void |
MutableMotifDiscoverer.initializeMotif(int motifIndex,
DataSet data,
double[] weights)
This method allows to initialize the model of a motif manually using a weighted data set. |
static void |
MutableMotifDiscovererToolbox.initMotif(int idx,
int[] classIndex,
int[] motifIndex,
DataSet[] s,
double[][] seqWeights,
boolean[] adjust,
MutableMotifDiscoverer[] mmd,
int[] len,
DataSet[] data,
double[][] dataWeights)
This method allows to initialize a number of motifs. |
static void |
MutableMotifDiscovererToolbox.initMotif(int idx,
int[] classIndex,
int[] motifIndex,
DataSet[] s,
double[][] seqWeights,
boolean[] adjust,
MutableMotifDiscoverer[] mmd,
int[] len,
DataSet[] data,
double[][] dataWeights)
This method allows to initialize a number of motifs. |
Constructors in de.jstacs.motifDiscovery with parameters of type DataSet | |
---|---|
KMereStatistic(DataSet data,
int k)
This constructor creates an internal statistic counting all k -mers in the data . |
|
SignificantMotifOccurrencesFinder(MotifDiscoverer disc,
DataSet bg,
double[] weights,
double sign)
This constructor creates an instance of SignificantMotifOccurrencesFinder that uses a DataSet to determine the siginificance level. |
|
SignificantMotifOccurrencesFinder(MotifDiscoverer disc,
SignificantMotifOccurrencesFinder.JoinMethod joiner,
DataSet bg,
double[] weights,
double sign)
This constructor creates an instance of SignificantMotifOccurrencesFinder that uses a DataSet to determine the siginificance level. |
Uses of DataSet in de.jstacs.results |
---|
Methods in de.jstacs.results that return DataSet | |
---|---|
DataSet |
DataSetResult.getValue()
|
Constructors in de.jstacs.results with parameters of type DataSet | |
---|---|
DataSetResult(String name,
String comment,
DataSet data)
Creates a new DataSetResult from a DataSet with the
annotation name and comment . |
Uses of DataSet in de.jstacs.sampling |
---|
Methods in de.jstacs.sampling with parameters of type DataSet | |
---|---|
void |
GibbsSamplingModel.drawParameters(DataSet data,
double[] weights)
This method draws the parameters of the model from the a posteriori density. |
Uses of DataSet in de.jstacs.sequenceScores |
---|
Methods in de.jstacs.sequenceScores with parameters of type DataSet | |
---|---|
double[] |
SequenceScore.getLogScoreFor(DataSet data)
This method computes the logarithm of the scores of all sequences in the given data set. |
void |
SequenceScore.getLogScoreFor(DataSet data,
double[] res)
This method computes and stores the logarithm of the scores for any sequence in the data set in the given double -array. |
Uses of DataSet in de.jstacs.sequenceScores.differentiable |
---|
Methods in de.jstacs.sequenceScores.differentiable with parameters of type DataSet | |
---|---|
int |
IndependentProductDiffSS.extractSequenceParts(int scoringFunctionIndex,
DataSet[] data,
DataSet[] result)
This method extracts the corresponding Sequence parts for a specific DifferentiableSequenceScore . |
int |
IndependentProductDiffSS.extractSequenceParts(int scoringFunctionIndex,
DataSet[] data,
DataSet[] result)
This method extracts the corresponding Sequence parts for a specific DifferentiableSequenceScore . |
double[] |
AbstractDifferentiableSequenceScore.getLogScoreFor(DataSet data)
|
void |
AbstractDifferentiableSequenceScore.getLogScoreFor(DataSet data,
double[] res)
|
void |
UniformDiffSS.initializeFunction(int index,
boolean meila,
DataSet[] data,
double[][] weights)
|
void |
MultiDimensionalSequenceWrapperDiffSS.initializeFunction(int index,
boolean freeParams,
DataSet[] data,
double[][] weights)
|
void |
IndependentProductDiffSS.initializeFunction(int index,
boolean freeParams,
DataSet[] data,
double[][] weights)
|
void |
DifferentiableSequenceScore.initializeFunction(int index,
boolean freeParams,
DataSet[] data,
double[][] weights)
This method creates the underlying structure of the DifferentiableSequenceScore . |
Uses of DataSet in de.jstacs.sequenceScores.differentiable.logistic |
---|
Methods in de.jstacs.sequenceScores.differentiable.logistic with parameters of type DataSet | |
---|---|
void |
LogisticDiffSS.initializeFunction(int index,
boolean freeParams,
DataSet[] data,
double[][] weights)
|
Uses of DataSet in de.jstacs.sequenceScores.statisticalModels |
---|
Methods in de.jstacs.sequenceScores.statisticalModels that return DataSet | |
---|---|
DataSet |
StatisticalModel.emitDataSet(int numberOfSequences,
int... seqLength)
This method returns a DataSet object containing artificial
sequence(s). |
Uses of DataSet in de.jstacs.sequenceScores.statisticalModels.differentiable |
---|
Methods in de.jstacs.sequenceScores.statisticalModels.differentiable that return DataSet | |
---|---|
DataSet |
UniformDiffSM.emitDataSet(int numberOfSequences,
int... seqLength)
|
DataSet |
MarkovRandomFieldDiffSM.emitDataSet(int numberOfSequences,
int... seqLength)
|
DataSet |
IndependentProductDiffSM.emitDataSet(int numberOfSequences,
int... seqLength)
|
DataSet |
AbstractDifferentiableStatisticalModel.emitDataSet(int numberOfSequences,
int... seqLength)
|
Methods in de.jstacs.sequenceScores.statisticalModels.differentiable with parameters of type DataSet | |
---|---|
void |
MappingDiffSM.adjustHiddenParameters(int index,
DataSet[] data,
double[][] weights)
|
void |
IndependentProductDiffSM.adjustHiddenParameters(int index,
DataSet[] data,
double[][] weights)
|
double[] |
AbstractDifferentiableStatisticalModel.getLogScoreFor(DataSet data)
|
void |
AbstractDifferentiableStatisticalModel.getLogScoreFor(DataSet data,
double[] res)
|
void |
UniformDiffSM.initializeFunction(int index,
boolean meila,
DataSet[] data,
double[][] weights)
|
void |
NormalizedDiffSM.initializeFunction(int index,
boolean freeParams,
DataSet[] data,
double[][] weights)
|
void |
MarkovRandomFieldDiffSM.initializeFunction(int index,
boolean freeParams,
DataSet[] data,
double[][] weights)
|
void |
MappingDiffSM.initializeFunction(int index,
boolean freeParams,
DataSet[] data,
double[][] weights)
|
void |
CyclicMarkovModelDiffSM.initializeFunction(int index,
boolean freeParams,
DataSet[] data,
double[][] weights)
|
void |
MappingDiffSM.initializeMotif(int motifIndex,
DataSet data,
double[] weights)
|
void |
IndependentProductDiffSM.initializeMotif(int motifIndex,
DataSet data,
double[] weights)
|
Uses of DataSet in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels |
---|
Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels that return DataSet | |
---|---|
DataSet |
BayesianNetworkDiffSM.emitDataSet(int numberOfSequences,
int... seqLength)
|
Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels with parameters of type DataSet | |
---|---|
protected void |
BayesianNetworkDiffSM.createTrees(DataSet[] data2,
double[][] weights2)
Creates the tree structures that represent the context (array BayesianNetworkDiffSM.trees ) and the parameter objects BayesianNetworkDiffSM.parameters using the
given Measure BayesianNetworkDiffSM.structureMeasure . |
void |
BayesianNetworkDiffSM.initializeFunction(int index,
boolean freeParams,
DataSet[] data,
double[][] weights)
|
protected void |
BayesianNetworkDiffSM.setPlugInParameters(int index,
boolean freeParameters,
DataSet[] data,
double[][] weights)
Computes and sets the plug-in parameters (MAP estimated parameters) from data using weights . |
Uses of DataSet in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures |
---|
Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures with parameters of type DataSet | |
---|---|
abstract int[][] |
Measure.getParents(DataSet fg,
DataSet bg,
double[] weightsFg,
double[] weightsBg,
int length)
Returns the optimal parents for the given data and weights. |
int[][] |
InhomogeneousMarkov.getParents(DataSet fg,
DataSet bg,
double[] weightsFg,
double[] weightsBg,
int length)
|
protected static double[][][][] |
Measure.getStatistics(DataSet s,
double[] weights,
int length,
double ess)
Counts the occurrences of symbols of the AlphabetContainer of
DataSet s using weights . |
protected static double[][][][][][] |
Measure.getStatisticsOrderTwo(DataSet s,
double[] weights,
int length,
double ess)
Counts the occurrences of symbols of the AlphabetContainer of
DataSet s using weights . |
Uses of DataSet in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures |
---|
Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures with parameters of type DataSet | |
---|---|
int[][] |
BTMutualInformation.getParents(DataSet fg,
DataSet bg,
double[] weightsFg,
double[] weightsBg,
int length)
|
int[][] |
BTExplainingAwayResidual.getParents(DataSet fg,
DataSet bg,
double[] weightsFg,
double[] weightsBg,
int length)
|
Uses of DataSet in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures |
---|
Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures with parameters of type DataSet | |
---|---|
int[][] |
PMMMutualInformation.getParents(DataSet fg,
DataSet bg,
double[] weightsFg,
double[] weightsBg,
int length)
|
int[][] |
PMMExplainingAwayResidual.getParents(DataSet fg,
DataSet bg,
double[] weightsFg,
double[] weightsBg,
int length)
|
Uses of DataSet in de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous |
---|
Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous that return DataSet | |
---|---|
DataSet |
HomogeneousMMDiffSM.emit(int numberOfSequences,
int... seqLength)
This method returns a DataSet object containing artificial
sequence(s). |
Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous with parameters of type DataSet | |
---|---|
void |
UniformHomogeneousDiffSM.initializeFunction(int index,
boolean meila,
DataSet[] data,
double[][] weights)
|
void |
HomogeneousMMDiffSM.initializeFunction(int index,
boolean freeParams,
DataSet[] data,
double[][] weights)
|
void |
HomogeneousMM0DiffSM.initializeFunction(int index,
boolean freeParams,
DataSet[] data,
double[][] weights)
|
Uses of DataSet in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture |
---|
Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture with parameters of type DataSet | |
---|---|
void |
MixtureDiffSM.adjustHiddenParameters(int index,
DataSet[] data,
double[][] weights)
Adjusts all hidden parameters including duration and mixture parameters according to the current values of the remaining parameters. |
void |
AbstractMixtureDiffSM.initializeFunction(int index,
boolean freeParams,
DataSet[] data,
double[][] weights)
|
void |
MixtureDiffSM.initializeMotif(int motifIndex,
DataSet data,
double[] weights)
|
protected void |
StrandDiffSM.initializeUsingPlugIn(int index,
boolean freeParams,
DataSet[] data,
double[][] weights)
|
protected void |
MixtureDiffSM.initializeUsingPlugIn(int index,
boolean freeParams,
DataSet[] data,
double[][] weights)
|
protected abstract void |
AbstractMixtureDiffSM.initializeUsingPlugIn(int index,
boolean freeParams,
DataSet[] data,
double[][] weights)
This method initializes the functions using the data in some way. |
Uses of DataSet in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif |
---|
Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif with parameters of type DataSet | |
---|---|
void |
ExtendedZOOPSDiffSM.adjustHiddenParameters(int classIndex,
DataSet[] data,
double[][] dataWeights)
|
void |
UniformDurationDiffSM.initializeFunction(int index,
boolean meila,
DataSet[] data,
double[][] weights)
|
void |
SkewNormalLikeDurationDiffSM.initializeFunction(int index,
boolean freeParams,
DataSet[] data,
double[][] weights)
|
void |
MixtureDurationDiffSM.initializeFunction(int index,
boolean freeParams,
DataSet[] data,
double[][] weights)
|
void |
ExtendedZOOPSDiffSM.initializeMotif(int motif,
DataSet data,
double[] weights)
|
protected void |
ExtendedZOOPSDiffSM.initializeUsingPlugIn(int index,
boolean freeParams,
DataSet[] data,
double[][] weights)
|
Uses of DataSet in de.jstacs.sequenceScores.statisticalModels.trainable |
---|
Methods in de.jstacs.sequenceScores.statisticalModels.trainable that return DataSet | |
---|---|
DataSet |
UniformTrainSM.emitDataSet(int n,
int... lengths)
|
DataSet |
AbstractTrainableStatisticalModel.emitDataSet(int numberOfSequences,
int... seqLength)
|
Methods in de.jstacs.sequenceScores.statisticalModels.trainable with parameters of type DataSet | |
---|---|
double[] |
AbstractTrainableStatisticalModel.getLogScoreFor(DataSet data)
|
void |
AbstractTrainableStatisticalModel.getLogScoreFor(DataSet data,
double[] res)
|
void |
TrainableStatisticalModel.train(DataSet data)
Trains the TrainableStatisticalModel object given the data as DataSet . |
void |
AbstractTrainableStatisticalModel.train(DataSet data)
|
void |
VariableLengthWrapperTrainSM.train(DataSet data,
double[] weights)
|
void |
UniformTrainSM.train(DataSet data,
double[] weights)
Deprecated. |
void |
TrainableStatisticalModel.train(DataSet data,
double[] weights)
Trains the TrainableStatisticalModel object given the data as DataSet using
the specified weights. |
void |
DifferentiableStatisticalModelWrapperTrainSM.train(DataSet data,
double[] weights)
|
void |
CompositeTrainSM.train(DataSet data,
double[] weights)
|
Uses of DataSet in de.jstacs.sequenceScores.statisticalModels.trainable.discrete |
---|
Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete with parameters of type DataSet | |
---|---|
static double |
ConstraintManager.countInhomogeneous(AlphabetContainer alphabets,
int length,
DataSet data,
double[] weights,
boolean reset,
Constraint... constr)
Fills the (inhomogeneous) constr with the weighted absolute frequency of the DataSet
data and computes the frequencies will not be computed. |
Uses of DataSet in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous |
---|
Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous that return DataSet | |
---|---|
DataSet |
HomogeneousTrainSM.emitDataSet(int no,
int... length)
Creates a DataSet of a given number of Sequence s from a
trained homogeneous model. |
Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous with parameters of type DataSet | |
---|---|
void |
HomogeneousTrainSM.train(DataSet[] data)
Trains the homogeneous model on all given DataSet s. |
abstract void |
HomogeneousTrainSM.train(DataSet[] data,
double[][] weights)
Trains the homogeneous model using an array of weighted DataSet s. |
void |
HomogeneousMM.train(DataSet[] data,
double[][] weights)
|
void |
HomogeneousMM.train(DataSet data,
double[] weights)
|
Uses of DataSet in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous |
---|
Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous that return DataSet | |
---|---|
DataSet |
MEManager.emitDataSet(int n,
int... lengths)
|
DataSet |
DAGTrainSM.emitDataSet(int n,
int... lengths)
|
Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous with parameters of type DataSet | |
---|---|
void |
FSDAGModelForGibbsSampling.drawParameters(DataSet data,
double[] weights)
|
protected void |
DAGTrainSM.drawParameters(DataSet data,
double[] weights)
This method draws the parameter of the model from the likelihood or the posterior, respectively. |
void |
FSDAGTrainSM.drawParameters(DataSet data,
double[] weights,
int[][] graph)
This method draws the parameters of the model from the a posteriori density. |
void |
FSDAGModelForGibbsSampling.drawParameters(DataSet data,
double[] weights,
int[][] graph)
|
protected void |
DAGTrainSM.estimateParameters(DataSet data,
double[] weights)
This method estimates the parameter of the model from the likelihood or the posterior, respectively. |
static BufferedImage |
TwoPointEvaluater.getImage(DataSet d,
double[] weights,
REnvironment r,
double alpha,
int... borders)
|
static double[][] |
TwoPointEvaluater.getMI(DataSet s,
double[] weights)
This method computes the pairwise mutual information between the sequence positions. |
static double[][] |
TwoPointEvaluater.getMIInBits(DataSet s,
double[] weights)
This method computes the pairwise mutual information (in bits) between the sequence positions. |
int[][] |
StructureLearner.getStructure(DataSet data,
double[] weights,
StructureLearner.ModelType model,
byte order,
StructureLearner.LearningType method)
This method finds the optimal structure of a model by using a given learning method (in some sense). |
SymmetricTensor |
StructureLearner.getTensor(DataSet data,
double[] weights,
byte order,
StructureLearner.LearningType method)
This method can be used to compute a Tensor that can be used to
determine the optimal structure. |
void |
FSMEManager.train(DataSet data,
double[] weights)
|
void |
FSDAGTrainSM.train(DataSet data,
double[] weights)
|
void |
FSDAGModelForGibbsSampling.train(DataSet data,
double[] weights)
|
void |
BayesianNetworkTrainSM.train(DataSet data,
double[] weights)
|
void |
FSDAGTrainSM.train(DataSet data,
double[] weights,
int[][] graph)
Computes the model with structure graph . |
void |
FSDAGModelForGibbsSampling.train(DataSet data,
double[] weights,
int[][] graph)
|
static void |
FSDAGTrainSM.train(TrainableStatisticalModel[] models,
int[][] graph,
double[][] weights,
DataSet... data)
Computes the models with structure graph . |
protected void |
MEManager.trainFactors(DataSet data,
double[] weights)
This method trains the internal MEM array,
i.e., it optimizes the parameters of the underlying MEMConstraint s. |
Uses of DataSet in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared |
---|
Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared with parameters of type DataSet | |
---|---|
void |
SharedStructureClassifier.train(DataSet[] data,
double[][] weights)
|
Uses of DataSet in de.jstacs.sequenceScores.statisticalModels.trainable.hmm |
---|
Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm with parameters of type DataSet | |
---|---|
String |
AbstractHMM.getGraphvizRepresentation(NumberFormat nf,
DataSet data,
double[] weight,
boolean sameTypeSameRank)
This method returns a String representation of the structure that
can be used in Graphviz to create an image. |
String |
AbstractHMM.getGraphvizRepresentation(NumberFormat nf,
DataSet data,
double[] weight,
HashMap<String,String> rankPatterns)
This method returns a String representation of the structure that
can be used in Graphviz to create an image. |
double[][][] |
AbstractHMM.getLogStatePosteriorMatrixFor(DataSet data)
This method returns the log state posteriors for all sequences of the data set data . |
double[][][] |
AbstractHMM.getStatePosteriorMatrixFor(DataSet data)
This method returns the state posteriors for all sequences of the data set data . |
Pair<IntList,Double>[] |
AbstractHMM.getViterbiPathsFor(DataSet data)
This method returns the viterbi paths and scores for all sequences of the data set data . |
void |
AbstractHMM.train(DataSet data)
|
Uses of DataSet in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models |
---|
Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models with parameters of type DataSet | |
---|---|
protected void |
SamplingHigherOrderHMM.furtherInits(DataSet data,
double[] weights)
This method allows the implementation of further initializations |
double[] |
HigherOrderHMM.getLogScoreFor(DataSet data)
|
void |
HigherOrderHMM.getLogScoreFor(DataSet data,
double[] res)
|
protected void |
SamplingHigherOrderHMM.gibbsSamplingStep(int sampling,
int steps,
boolean append,
DataSet data,
double[] weights)
This method implements the next step(s) in the sampling procedure |
protected void |
HigherOrderHMM.initialize(DataSet data,
double[] weight)
This method initializes all emissions and the transition. |
void |
DifferentiableHigherOrderHMM.initializeFunction(int index,
boolean freeParams,
DataSet[] data,
double[][] weights)
|
protected void |
SamplingHigherOrderHMM.initTraining(DataSet data,
double[] weights)
This methods initialize the training procedure with the given training data |
void |
SamplingHigherOrderHMM.train(DataSet data,
double[] weights)
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void |
HigherOrderHMM.train(DataSet data,
double[] weights)
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void |
DifferentiableHigherOrderHMM.train(DataSet data,
double[] weights)
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Uses of DataSet in de.jstacs.sequenceScores.statisticalModels.trainable.mixture |
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Fields in de.jstacs.sequenceScores.statisticalModels.trainable.mixture declared as DataSet | |
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protected DataSet[] |
AbstractMixtureTrainSM.sample
The data set that was used in the last training. |
Methods in de.jstacs.sequenceScores.statisticalModels.trainable.mixture that return DataSet | |
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DataSet |
AbstractMixtureTrainSM.emitDataSet(int n,
int... lengths)
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.mixture with parameters of type DataSet | |
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protected double[][] |
AbstractMixtureTrainSM.doFirstIteration(DataSet data,
double[] dataWeights)
This method will do the first step in the train algorithm for the current model. |
double[][] |
MixtureTrainSM.doFirstIteration(DataSet data,
double[] dataWeights,
double[][] partitioning)
This method enables you to train a mixture model with a fixed start partitioning. |
protected double[][] |
AbstractMixtureTrainSM.doFirstIteration(DataSet data,
double[] dataWeights,
MultivariateRandomGenerator m,
MRGParams[] params)
This method will do the first step in the train algorithm for the current model. |
double[] |
AbstractMixtureTrainSM.getLogScoreFor(DataSet data)
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double |
AbstractMixtureTrainSM.iterate(DataSet data,
double[] dataWeights,
MultivariateRandomGenerator m,
MRGParams[] params)
This method runs the train algorithm for the current model. |
void |
StrandTrainSM.setTrainData(DataSet s)
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protected void |
MixtureTrainSM.setTrainData(DataSet data)
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protected abstract void |
AbstractMixtureTrainSM.setTrainData(DataSet data)
This method is invoked by the train -method and sets for a
given data set the data set that should be used for train . |
void |
AbstractMixtureTrainSM.train(DataSet data,
double[] dataWeights)
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Uses of DataSet in de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif with parameters of type DataSet | |
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protected void |
ZOOPSTrainSM.setTrainData(DataSet data)
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void |
HiddenMotifMixture.train(DataSet data,
double[] weights)
|
void |
ZOOPSTrainSM.trainBgModel(DataSet data,
double[] weights)
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abstract void |
HiddenMotifMixture.trainBgModel(DataSet data,
double[] weights)
This method trains the background model. |
Uses of DataSet in de.jstacs.utils |
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Methods in de.jstacs.utils that return DataSet | |
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static DataSet |
DiscreteInhomogenousDataSetEmitter.emitDataSet(StatisticalModel m,
int n)
This method emits a data set with n |
Methods in de.jstacs.utils with parameters of type DataSet | |
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static double[] |
PFMComparator.getCounts(DataSet... data)
This method counts the occurrences of symbols in the given data sets. |
static double |
StatisticalModelTester.getLogLikelihood(StatisticalModel m,
DataSet data)
Returns the log-likelihood of a DataSet data for a
given model m . |
static double |
StatisticalModelTester.getLogLikelihood(StatisticalModel m,
DataSet data,
double[] weights)
Returns the log-likelihood of a DataSet data for a
given model m . |
static double[][] |
PFMComparator.getPFM(DataSet data)
This method creates a PFM from a DataSet of Sequence s. |
static double[][] |
PFMComparator.getPFM(DataSet data,
double[] weights)
This method creates a PFM from a DataSet of Sequence s. |
static double |
StatisticalModelTester.getValueOfAIC(StatisticalModel m,
DataSet s,
int k)
This method computes the value of Akaikes Information Criterion (AIC). |
static double |
StatisticalModelTester.getValueOfBIC(StatisticalModel m,
DataSet s,
int k)
This method computes the value of the Bayesian Information Criterion (BIC). |
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