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Uses of AlphabetContainer in de.jstacs.classifiers |
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Methods in de.jstacs.classifiers that return AlphabetContainer | |
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AlphabetContainer |
AbstractClassifier.getAlphabetContainer()
This method returns the container of alphabets that is used in the classifier. |
Constructors in de.jstacs.classifiers with parameters of type AlphabetContainer | |
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AbstractClassifier(AlphabetContainer abc)
The constructor for a homogeneous classifier. |
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AbstractClassifier(AlphabetContainer abc,
int length)
The constructor for an inhomogeneous classifier. |
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AbstractScoreBasedClassifier(AlphabetContainer abc,
int classes)
The constructor for a homogeneous classifier. |
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AbstractScoreBasedClassifier(AlphabetContainer abc,
int classes,
double classWeight)
The constructor for a homogeneous classifier. |
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AbstractScoreBasedClassifier(AlphabetContainer abc,
int length,
int classes)
The constructor for an inhomogeneous classifier. |
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AbstractScoreBasedClassifier(AlphabetContainer abc,
int length,
int classes,
double classWeight)
The constructor for an inhomogeneous classifier. |
Uses of AlphabetContainer in de.jstacs.classifiers.differentiableSequenceScoreBased |
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Constructors in de.jstacs.classifiers.differentiableSequenceScoreBased with parameters of type AlphabetContainer | |
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ScoreClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass,
AlphabetContainer alphabet,
int length,
byte algo,
AbstractTerminationCondition tc,
double lineps,
double startD,
boolean free,
OptimizableFunction.KindOfParameter kind)
The constructor for a simple, instantiated parameter set. |
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ScoreClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass,
AlphabetContainer alphabet,
int length,
byte algo,
double eps,
double lineps,
double startD,
boolean free,
OptimizableFunction.KindOfParameter kind)
The constructor for a simple, instantiated parameter set. |
Uses of AlphabetContainer in de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix |
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Constructors in de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix with parameters of type AlphabetContainer | |
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GenDisMixClassifierParameterSet(AlphabetContainer alphabet,
int length,
byte algo,
double eps,
double lineps,
double startD,
boolean free,
OptimizableFunction.KindOfParameter kind,
boolean norm,
int threads)
The default constructor that constructs a new GenDisMixClassifierParameterSet . |
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GenDisMixClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass,
AlphabetContainer alphabet,
int length,
byte algo,
double eps,
double lineps,
double startD,
boolean free,
OptimizableFunction.KindOfParameter kind,
boolean norm,
int threads)
The default constructor that constructs a new GenDisMixClassifierParameterSet . |
Uses of AlphabetContainer in de.jstacs.classifiers.differentiableSequenceScoreBased.sampling |
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Constructors in de.jstacs.classifiers.differentiableSequenceScoreBased.sampling with parameters of type AlphabetContainer | |
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SamplingGenDisMixClassifierParameterSet(AlphabetContainer alphabet,
int length,
int numStarts,
int testSamplings,
int stationarySamplings,
String outfilePrefix,
int threads)
Create a new SamplingGenDisMixClassifierParameterSet with a grouped sampling scheme, sampling all parameters
(and not only the free ones), and adaption of the variance. |
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SamplingGenDisMixClassifierParameterSet(AlphabetContainer alphabet,
int length,
int numStarts,
SamplingScoreBasedClassifier.SamplingScheme scheme,
int testSamplings,
int stationarySamplings,
boolean freeParameters,
boolean adaptVariance,
String outfilePrefix,
int threads)
Create a new SamplingGenDisMixClassifierParameterSet . |
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SamplingGenDisMixClassifierParameterSet(Class<? extends SamplingScoreBasedClassifier> instanceClass,
AlphabetContainer alphabet,
int length,
int numStarts,
SamplingScoreBasedClassifier.SamplingScheme scheme,
int testSamplings,
int stationarySamplings,
boolean freeParameters,
boolean adaptVariance,
String outfilePrefix,
int threads)
Create a new SamplingGenDisMixClassifierParameterSet . |
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SamplingScoreBasedClassifierParameterSet(Class<? extends SamplingScoreBasedClassifier> instanceClass,
AlphabetContainer alphabet,
int length,
int numStarts,
int testSamplings,
int stationarySamplings,
String outfilePrefix)
Create a new SamplingScoreBasedClassifierParameterSet with a grouped sampling scheme, sampling all parameters
(and not only the free ones), and adaption of the variance. |
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SamplingScoreBasedClassifierParameterSet(Class<? extends SamplingScoreBasedClassifier> instanceClass,
AlphabetContainer alphabet,
int length,
int numStarts,
SamplingScoreBasedClassifier.SamplingScheme scheme,
int testSamplings,
int stationarySamplings,
boolean freeParameters,
boolean adaptVariance,
String outfilePrefix)
Create a new SamplingScoreBasedClassifierParameterSet . |
Uses of AlphabetContainer in de.jstacs.data |
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Classes in de.jstacs.data with type parameters of type AlphabetContainer | |
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static class |
AlphabetContainer.AbstractAlphabetContainerParameterSet<T extends AlphabetContainer>
This class is the super class of any InstanceParameterSet for AlphabetContainer . |
Methods in de.jstacs.data that return AlphabetContainer | |
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AlphabetContainer |
DataSet.getAlphabetContainer()
Returns the AlphabetContainer of this DataSet . |
AlphabetContainer |
AlphabetContainer.getCompositeContainer(int[] start,
int[] length)
Returns an AlphabetContainer of Alphabet s e.g. for
composite motifs/sequences. |
static AlphabetContainer |
AlphabetContainer.getSimplifiedAlphabetContainer(Alphabet[] abc,
int[] assignment)
This method creates a new AlphabetContainer that uses as less as
possible Alphabet s to describe the container. |
AlphabetContainer |
AlphabetContainer.getSubContainer(int start,
int length)
Returns a sub-container with the Alphabet s for the positions
starting at start and with length length . |
static AlphabetContainer |
AlphabetContainer.insertAlphabet(AlphabetContainer aC,
Alphabet a,
boolean[] useNewAlphabet)
This method may be used to construct a new AlphabetContainer by
incorporating additional Alphabet s into an existing
AlphabetContainer . |
Methods in de.jstacs.data that return types with arguments of type AlphabetContainer | |
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AlphabetContainer.AbstractAlphabetContainerParameterSet<? extends AlphabetContainer> |
AlphabetContainer.getCurrentParameterSet()
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Methods in de.jstacs.data with parameters of type AlphabetContainer | |
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boolean |
AlphabetContainer.checkConsistency(AlphabetContainer abc)
Checks if this AlphabetContainer is consistent consistent with
another AlphabetContainer . |
int |
AlphabetContainer.compareTo(AlphabetContainer abc)
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static AlphabetContainer |
AlphabetContainer.insertAlphabet(AlphabetContainer aC,
Alphabet a,
boolean[] useNewAlphabet)
This method may be used to construct a new AlphabetContainer by
incorporating additional Alphabet s into an existing
AlphabetContainer . |
Constructors in de.jstacs.data with parameters of type AlphabetContainer | |
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AlphabetContainer(AlphabetContainer[] cons,
int[] lengths)
Creates an new sparse AlphabetContainer based on given
AlphabetContainer s. |
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DataSet(AlphabetContainer abc,
AbstractStringExtractor se)
Creates a new DataSet from a StringExtractor
using the given AlphabetContainer . |
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DataSet(AlphabetContainer abc,
AbstractStringExtractor se,
int subsequenceLength)
Creates a new DataSet from a StringExtractor
using the given AlphabetContainer and all overlapping windows of
length subsequenceLength . |
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DataSet(AlphabetContainer abc,
AbstractStringExtractor se,
String delim)
Creates a new DataSet from a StringExtractor
using the given AlphabetContainer and a delimiter
delim . |
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DataSet(AlphabetContainer abc,
AbstractStringExtractor se,
String delim,
int subsequenceLength)
Creates a new DataSet from a StringExtractor
using the given AlphabetContainer , the given delimiter
delim and all overlapping windows of length
subsequenceLength . |
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DiscreteSequenceEnumerator(AlphabetContainer con,
int length,
boolean sparse)
Creates a new DiscreteSequenceEnumerator from a given
AlphabetContainer and a length. |
Constructor parameters in de.jstacs.data with type arguments of type AlphabetContainer | |
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AlphabetContainerParameterSet(Class<? extends AlphabetContainer> instanceClass,
Alphabet... alphabets)
/** Creates a new AlphabetContainerParameterSet from an array of
Alphabet s for a given sub-class of AlphabetContainer . |
Uses of AlphabetContainer in de.jstacs.data.alphabets |
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Subclasses of AlphabetContainer in de.jstacs.data.alphabets | |
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class |
DNAAlphabetContainer
This class implements a singleton for an AlphabetContainer that can be used for DNA. |
Uses of AlphabetContainer in de.jstacs.data.sequences |
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Fields in de.jstacs.data.sequences declared as AlphabetContainer | |
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protected AlphabetContainer |
Sequence.alphabetCon
The underlying alphabets. |
protected AlphabetContainer |
MappedDiscreteSequence.originalAlphabetContainer
The original AlphabetContainer . |
Methods in de.jstacs.data.sequences that return AlphabetContainer | |
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AlphabetContainer |
Sequence.getAlphabetContainer()
Return the alphabets, i.e. the AlphabetContainer , used in this
Sequence . |
static AlphabetContainer |
MappedDiscreteSequence.getNewAlphabetContainer(AlphabetContainer original,
DiscreteAlphabetMapping... transformation)
This method allows to create a new AlphabetContainer given an old AlphabetContainer and some DiscreteAlphabetMapping s. |
Methods in de.jstacs.data.sequences with parameters of type AlphabetContainer | |
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static Sequence |
Sequence.create(AlphabetContainer con,
SequenceAnnotation[] annotation,
String sequence,
String delim)
Creates a Sequence from a String based on the given
AlphabetContainer using the given delimiter delim
and some annotation for the Sequence . |
static Sequence |
Sequence.create(AlphabetContainer con,
String sequence)
Creates a Sequence from a String based on the given
AlphabetContainer using the standard delimiter for this
AlphabetContainer . |
static Sequence |
Sequence.create(AlphabetContainer con,
String sequence,
String delim)
Creates a Sequence from a String based on the given
AlphabetContainer using the given delimiter delim . |
Sequence<T> |
Sequence.getCompositeSequence(AlphabetContainer abc,
int[] starts,
int[] lengths)
This method should be used if one wants to create a DataSet of
Sequence.CompositeSequence s. |
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. |
static AlphabetContainer |
MappedDiscreteSequence.getNewAlphabetContainer(AlphabetContainer original,
DiscreteAlphabetMapping... transformation)
This method allows to create a new AlphabetContainer given an old AlphabetContainer and some DiscreteAlphabetMapping s. |
Sequence |
Sequence.getSubSequence(AlphabetContainer abc,
int start)
This method should be used if one wants to create a DataSet of
subsequences of defined length. |
Sequence |
Sequence.getSubSequence(AlphabetContainer abc,
int start,
int length)
This method should be used if one wants to create a DataSet of
subsequences of defined length. |
Constructors in de.jstacs.data.sequences with parameters of type AlphabetContainer | |
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ArbitraryFloatSequence(AlphabetContainer alphabetContainer,
float[] content)
Creates a new ArbitraryFloatSequence from an array of
float -encoded alphabet symbols. |
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ArbitraryFloatSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
Creates a new ArbitraryFloatSequence from a String
representation using the delimiter delim . |
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ArbitraryFloatSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new ArbitraryFloatSequence from a SymbolExtractor . |
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ArbitraryFloatSequence(AlphabetContainer alphabetContainer,
String sequence)
Creates a new ArbitraryFloatSequence from a String
representation using the default delimiter. |
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ArbitrarySequence(AlphabetContainer alphabetContainer,
double[] content)
Creates a new ArbitrarySequence from an array of
double -encoded alphabet symbols. |
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ArbitrarySequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
Creates a new ArbitrarySequence from a String
representation using the delimiter delim . |
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ArbitrarySequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new ArbitrarySequence from a SymbolExtractor . |
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ArbitrarySequence(AlphabetContainer alphabetContainer,
String sequence)
Creates a new ArbitrarySequence from a String
representation using the default delimiter. |
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ByteSequence(AlphabetContainer alphabetContainer,
byte[] content)
Creates a new ByteSequence from an array of byte -
encoded alphabet symbols. |
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ByteSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
Creates a new ByteSequence from a String representation
using the delimiter delim . |
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ByteSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new ByteSequence from a SymbolExtractor . |
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ByteSequence(AlphabetContainer alphabetContainer,
String sequence)
Creates a new ByteSequence from a String representation
using the default delimiter. |
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IntSequence(AlphabetContainer alphabetContainer,
int... content)
Creates a new IntSequence from an array of int -
encoded alphabet symbols. |
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IntSequence(AlphabetContainer alphabetContainer,
int[] content,
int start,
int length)
Creates a new IntSequence from a part of the array of
int - encoded alphabet symbols. |
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IntSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
Creates a new IntSequence from a String representation
using the delimiter delim . |
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IntSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new IntSequence from a SymbolExtractor . |
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IntSequence(AlphabetContainer alphabetContainer,
String sequence)
Creates a new IntSequence from a String representation
using the default delimiter. |
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MappedDiscreteSequence(AlphabetContainer originalAlphabetContainer,
SequenceAnnotation[] seqAn,
DiscreteAlphabetMapping... transformation)
This method allows to create an empty MappedDiscreteSequence . |
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Sequence.CompositeSequence(AlphabetContainer abc,
Sequence<T> seq,
int[] starts,
int[] lengths)
This constructor should be used if one wants to create a DataSet of Sequence.CompositeSequence s. |
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Sequence.RecursiveSequence(AlphabetContainer alphabet,
Sequence<T> seq)
Creates a new Sequence.RecursiveSequence on the Sequence
seq with the AlphabetContainer alphabet
using the annotation of the given Sequence . |
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Sequence.RecursiveSequence(AlphabetContainer alphabet,
SequenceAnnotation[] annotation,
Sequence<T> seq)
Creates a new Sequence.RecursiveSequence on the Sequence
seq with the AlphabetContainer alphabet
and the annotation annotation . |
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Sequence.SubSequence(AlphabetContainer abc,
Sequence seq,
int start,
int length)
This constructor should be used if one wants to create a DataSet of Sequence.SubSequence s of defined length. |
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Sequence(AlphabetContainer container,
SequenceAnnotation[] annotation)
Creates a new Sequence with the given AlphabetContainer
and the given annotation, but without the content. |
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ShortSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
Creates a new ShortSequence from a String representation
using the delimiter delim . |
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ShortSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new ShortSequence from a SymbolExtractor . |
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ShortSequence(AlphabetContainer alphabetContainer,
short[] content)
Creates a new ShortSequence from an array of short -
encoded alphabet symbols. |
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ShortSequence(AlphabetContainer alphabetContainer,
String sequence)
Creates a new ShortSequence from a String representation
using the default delimiter. |
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SimpleDiscreteSequence(AlphabetContainer container,
SequenceAnnotation[] annotation)
This constructor creates a new SimpleDiscreteSequence with the
AlphabetContainer container and the annotation
annotation but without the content. |
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SparseSequence(AlphabetContainer alphCon,
String seq)
Creates a new SparseSequence from a String
representation. |
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SparseSequence(AlphabetContainer alphCon,
SymbolExtractor se)
Creates a new SparseSequence from a SymbolExtractor . |
Uses of AlphabetContainer in de.jstacs.data.sequences.annotation |
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Constructors in de.jstacs.data.sequences.annotation with parameters of type AlphabetContainer | |
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ReferenceSequenceAnnotationParser(String key,
AlphabetContainer alphabet,
String keyValueDelimiter,
String annotationDelimiter)
Creates a new ReferenceSequenceAnnotationParser with user-specified delimiters. |
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ReferenceSequenceAnnotationParser(String key,
AlphabetContainer alphabet,
String keyValueDelimiter,
String annotationDelimiter,
String delim)
Creates a new ReferenceSequenceAnnotationParser with user-specified delimiters. |
Uses of AlphabetContainer in de.jstacs.io |
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Methods in de.jstacs.io with parameters of type AlphabetContainer | |
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static int |
SymbolExtractor.filter(String inFile,
char ignore,
AlphabetContainer con,
int minLength,
String outFile)
This method allows the user to filter the content of a File using a given AlphabetContainer and a
minimal sequence length. |
Uses of AlphabetContainer in de.jstacs.parameters |
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Methods in de.jstacs.parameters that return AlphabetContainer | |
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AlphabetContainer |
SequenceScoringParameterSet.getAlphabetContainer()
Returns the AlphabetContainer of the current instance. |
Constructors in de.jstacs.parameters with parameters of type AlphabetContainer | |
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SequenceScoringParameterSet(Class<T> instanceClass,
AlphabetContainer alphabet)
Constructs a SequenceScoringParameterSet for an object that can
handle sequences of variable length and with the
AlphabetContainer alphabet . |
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SequenceScoringParameterSet(Class<T> instanceClass,
AlphabetContainer alphabet,
int length,
boolean variableLength)
Constructs a SequenceScoringParameterSet from an
AlphabetContainer and the length of a sequence. |
Uses of AlphabetContainer in de.jstacs.sequenceScores |
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Methods in de.jstacs.sequenceScores that return AlphabetContainer | |
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AlphabetContainer |
SequenceScore.getAlphabetContainer()
Returns the container of alphabets that were used when constructing the instance. |
Uses of AlphabetContainer in de.jstacs.sequenceScores.differentiable |
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Fields in de.jstacs.sequenceScores.differentiable declared as AlphabetContainer | |
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protected AlphabetContainer |
AbstractDifferentiableSequenceScore.alphabets
The AlphabetContainer of this AbstractDifferentiableSequenceScore
. |
Methods in de.jstacs.sequenceScores.differentiable that return AlphabetContainer | |
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AlphabetContainer |
AbstractDifferentiableSequenceScore.getAlphabetContainer()
|
Constructors in de.jstacs.sequenceScores.differentiable with parameters of type AlphabetContainer | |
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AbstractDifferentiableSequenceScore(AlphabetContainer alphabets,
int length)
The main constructor. |
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UniformDiffSS(AlphabetContainer alphabets,
int length)
This is the main constructor that creates an instance of a UniformDiffSS that models each sequence uniformly. |
Uses of AlphabetContainer in de.jstacs.sequenceScores.differentiable.logistic |
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Constructors in de.jstacs.sequenceScores.differentiable.logistic with parameters of type AlphabetContainer | |
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LogisticDiffSS(AlphabetContainer con,
int length,
LogisticConstraint... constraint)
This is the main constructor to create LogisticDiffSS instance. |
Uses of AlphabetContainer in de.jstacs.sequenceScores.statisticalModels.differentiable |
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Methods in de.jstacs.sequenceScores.statisticalModels.differentiable with parameters of type AlphabetContainer | |
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static HomogeneousMMDiffSM |
DifferentiableStatisticalModelFactory.createHomogeneousMarkovModel(AlphabetContainer con,
double ess,
int order,
int priorLength)
This method returns a homogeneous Markov model with user-specified order. |
static BayesianNetworkDiffSM |
DifferentiableStatisticalModelFactory.createInhomogeneousMarkovModel(AlphabetContainer con,
int length,
double ess,
int order)
This method returns a inhomogeneous Markov model (IMM) with user-specified order. |
static MarkovRandomFieldDiffSM |
DifferentiableStatisticalModelFactory.createMarkovRandomField(AlphabetContainer con,
int length,
String constraintType)
This method allows to create a MarkovRandomFieldDiffSM of the specified length and with the given constraint type. |
static BayesianNetworkDiffSM |
DifferentiableStatisticalModelFactory.createPWM(AlphabetContainer con,
int length,
double ess)
This method returns a position weight matrix (PWM). |
Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable with parameters of type AlphabetContainer | |
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AbstractDifferentiableStatisticalModel(AlphabetContainer alphabets,
int length)
The main constructor. |
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AbstractVariableLengthDiffSM(AlphabetContainer alphabets)
This is the main constructor that creates an instance of a VariableLengthDiffSM that models sequences of arbitrary
length. |
|
AbstractVariableLengthDiffSM(AlphabetContainer alphabets,
int length)
This is the main constructor that creates an instance of a VariableLengthDiffSM that models sequences of a given
length. |
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CyclicMarkovModelDiffSM(AlphabetContainer alphabets,
double[] frameHyper,
double[][][] hyper,
boolean plugIn,
boolean optimize,
int starts,
int initFrame)
This constructor allows to create an instance with specific hyper-parameters for all conditional distributions. |
|
CyclicMarkovModelDiffSM(AlphabetContainer alphabets,
int order,
int period,
double classEss,
double[] sumOfHyperParams,
boolean plugIn,
boolean optimize,
int starts,
int initFrame)
The main constructor. |
|
MappingDiffSM(AlphabetContainer originalAlphabetContainer,
DifferentiableStatisticalModel nsf,
DiscreteAlphabetMapping... mapping)
The main constructor creating a MappingDiffSM . |
|
MarkovRandomFieldDiffSM(AlphabetContainer alphabets,
int length,
double ess,
String constr)
This is the main constructor that creates an instance of a MarkovRandomFieldDiffSM . |
|
MarkovRandomFieldDiffSM(AlphabetContainer alphabets,
int length,
String constr)
This constructor creates an instance of a MarkovRandomFieldDiffSM with
equivalent sample size (ess) 0. |
|
UniformDiffSM(AlphabetContainer alphabets,
int length,
double ess)
This is the main constructor that creates an instance of a UniformDiffSM that models each sequence uniformly. |
Uses of AlphabetContainer in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels |
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Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels with parameters of type AlphabetContainer | |
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BayesianNetworkDiffSM(AlphabetContainer alphabet,
int length,
double ess,
boolean plugInParameters,
Measure structureMeasure)
Creates a new BayesianNetworkDiffSM that has neither
been initialized nor trained. |
|
BayesianNetworkDiffSMParameterSet(AlphabetContainer alphabet,
int length,
double ess,
boolean plugInParameters,
Measure structureMeasure)
Creates a new BayesianNetworkDiffSMParameterSet with
pre-defined parameter values. |
|
BNDiffSMParameterTree(int pos,
int[] contextPoss,
AlphabetContainer alphabet,
int firstParent,
int[] firstChildren)
Creates a new BNDiffSMParameterTree for the parameters at position
pos using the parent positions in contextPoss . |
|
MarkovModelDiffSM(AlphabetContainer alphabet,
int length,
double ess,
boolean plugInParameters,
InhomogeneousMarkov structureMeasure)
This constructor creates an instance without any prior for the modeled length. |
|
MarkovModelDiffSM(AlphabetContainer alphabet,
int length,
double ess,
boolean plugInParameters,
InhomogeneousMarkov structureMeasure,
DurationDiffSM lengthPenalty)
This constructor creates an instance with an prior for the modeled length. |
|
MarkovModelDiffSM(AlphabetContainer alphabet,
int length,
double ess,
boolean plugInParameters,
int order,
DurationDiffSM lengthPenalty)
This constructor creates an instance with an prior for the modeled length. |
Uses of AlphabetContainer in de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous |
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Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous with parameters of type AlphabetContainer | |
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HomogeneousDiffSM(AlphabetContainer alphabets)
This is the main constructor that creates an instance of a HomogeneousDiffSM that models sequences of arbitrary
length. |
|
HomogeneousDiffSM(AlphabetContainer alphabets,
int length)
This is the main constructor that creates an instance of a HomogeneousDiffSM that models sequences of a given
length. |
|
HomogeneousMM0DiffSM(AlphabetContainer alphabets,
int length,
double ess,
boolean plugIn,
boolean optimize)
The main constructor that creates an instance of a homogeneous Markov model of order 0. |
|
HomogeneousMMDiffSM(AlphabetContainer alphabets,
int order,
double classEss,
double[] sumOfHyperParams,
boolean plugIn,
boolean optimize,
int starts)
This is the main constructor that creates an instance of a homogeneous Markov model of arbitrary order. |
|
HomogeneousMMDiffSM(AlphabetContainer alphabets,
int order,
double classEss,
int length)
This is a convenience constructor for creating an instance of a homogeneous Markov model of arbitrary order. |
|
UniformHomogeneousDiffSM(AlphabetContainer alphabets,
double ess)
This is the main constructor that creates an instance of a UniformHomogeneousDiffSM that models each sequence
uniformly. |
Uses of AlphabetContainer in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif |
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Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif with parameters of type AlphabetContainer | |
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PositionDiffSM(AlphabetContainer con,
int length)
This constructor allows create instance with more than one dimension. |
Uses of AlphabetContainer in de.jstacs.sequenceScores.statisticalModels.trainable |
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Fields in de.jstacs.sequenceScores.statisticalModels.trainable declared as AlphabetContainer | |
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protected AlphabetContainer |
AbstractTrainableStatisticalModel.alphabets
The underlying alphabets |
Methods in de.jstacs.sequenceScores.statisticalModels.trainable that return AlphabetContainer | |
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AlphabetContainer |
AbstractTrainableStatisticalModel.getAlphabetContainer()
|
Methods in de.jstacs.sequenceScores.statisticalModels.trainable with parameters of type AlphabetContainer | |
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static BayesianNetworkTrainSM |
TrainableStatisticalModelFactory.createBayesianNetworkModel(AlphabetContainer con,
int length,
double ess,
byte order)
This method returns a Bayesian network model (BN) with user-specified order. |
static HomogeneousMM |
TrainableStatisticalModelFactory.createHomogeneousMarkovModel(AlphabetContainer con,
double ess,
byte order)
This method returns a homogeneous Markov model with user-specified order. |
static FSDAGTrainSM |
TrainableStatisticalModelFactory.createInhomogeneousMarkovModel(AlphabetContainer con,
int length,
double ess,
byte order)
This method returns a inhomogeneous Markov model (IMM) with user-specified order. |
static BayesianNetworkTrainSM |
TrainableStatisticalModelFactory.createPermutedMarkovModel(AlphabetContainer con,
int length,
double ess,
byte order)
This method returns a permuted Markov model (PMM) with user-specified order. |
static FSDAGTrainSM |
TrainableStatisticalModelFactory.createPWM(AlphabetContainer con,
int length,
double ess)
This method returns a position weight matrix (PWM). |
Constructors in de.jstacs.sequenceScores.statisticalModels.trainable with parameters of type AlphabetContainer | |
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AbstractTrainableStatisticalModel(AlphabetContainer alphabets,
int length)
Constructor that sets the length of the model to length and
the AlphabetContainer to alphabets . |
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CompositeTrainSM(AlphabetContainer alphabets,
int[] assignment,
TrainableStatisticalModel... models)
Creates a new CompositeTrainSM . |
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UniformTrainSM(AlphabetContainer alphabet)
Creates a new UniformTrainSM using a given AlphabetContainer . |
Uses of AlphabetContainer in de.jstacs.sequenceScores.statisticalModels.trainable.discrete |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete with parameters of type AlphabetContainer | |
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static double |
ConstraintManager.countInhomogeneous(AlphabetContainer alphabets,
int length,
DataSet data,
double[] weights,
boolean reset,
Constraint... constr)
Fills the (inhomogeneous) Constraint constr with the
weighted absolute frequencies of the DataSet data . |
abstract String |
Constraint.getDescription(AlphabetContainer con,
int i)
Returns the decoded symbol for the encoded symbol i . |
String |
Constraint.getFreqInfo(AlphabetContainer con)
Returns an information about the stored frequencies. |
Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.discrete with parameters of type AlphabetContainer | |
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DGTrainSMParameterSet(Class<T> instanceClass,
AlphabetContainer alphabet,
double ess,
String description)
The constructor for models that can handle variable lengths. |
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DGTrainSMParameterSet(Class<T> instanceClass,
AlphabetContainer alphabet,
int length,
double ess,
String description)
The constructor for models that can handle only sequences of fixed length given by length . |
Uses of AlphabetContainer in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous with parameters of type AlphabetContainer | |
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String |
HomogeneousTrainSM.HomCondProb.getDescription(AlphabetContainer con,
int i)
|
Uses of AlphabetContainer in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters |
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Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters with parameters of type AlphabetContainer | |
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HomMMParameterSet(AlphabetContainer alphabet,
double ess,
String description,
byte order)
Creates a new HomMMParameterSet with AlphabetContainer ,
ess (equivalent sample size), description and order
of the homogeneous Markov model. |
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HomogeneousTrainSMParameterSet(Class<? extends HomogeneousTrainSM> instanceClass,
AlphabetContainer alphabet,
double ess,
String description,
byte order)
Creates a new HomogeneousTrainSMParameterSet with
AlphabetContainer , ess (equivalent sample
size), description and order of the homogeneous Markov model. |
Uses of AlphabetContainer in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous that return AlphabetContainer | |
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AlphabetContainer |
StructureLearner.getAlphabetContainer()
This method returns the AlphabetContainer of the
StructureLearner . |
Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous with parameters of type AlphabetContainer | |
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String |
InhConstraint.getDescription(AlphabetContainer con,
int i)
|
String |
InhCondProb.getDescription(AlphabetContainer con,
int i)
|
Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous with parameters of type AlphabetContainer | |
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StructureLearner(AlphabetContainer con,
int length)
Creates a StructureLearner with equivalent sample
size (ess) = 0. |
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StructureLearner(AlphabetContainer con,
int length,
double ess)
Creates a new StructureLearner for a given
AlphabetContainer , a given length and a given equivalent
sample size (ess). |
Uses of AlphabetContainer in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters |
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Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters with parameters of type AlphabetContainer | |
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BayesianNetworkTrainSMParameterSet(AlphabetContainer alphabet,
int length,
double ess,
String description,
StructureLearner.ModelType model,
byte order,
StructureLearner.LearningType method)
This is the constructor of a filled BayesianNetworkTrainSMParameterSet for a
BayesianNetworkTrainSM . |
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FSDAGModelForGibbsSamplingParameterSet(AlphabetContainer alphabet,
int length,
double ess,
String description,
String graph)
This is the constructor that creates a filled parameter set. |
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FSDAGTrainSMParameterSet(AlphabetContainer alphabet,
int length,
double ess,
String description,
String graph)
This constructor creates an FSDAGTrainSMParameterSet instance. |
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FSDAGTrainSMParameterSet(Class<? extends FSDAGTrainSM> clazz,
AlphabetContainer alphabet,
int length,
double ess,
String description,
String graph)
This constructor creates an FSDAGTrainSMParameterSet instance for the
specified class. |
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IDGTrainSMParameterSet(Class<? extends InhomogeneousDGTrainSM> instanceClass,
AlphabetContainer alphabet,
int length,
double ess,
String description)
This constructor creates an IDGTrainSMParameterSet instance for the
specified class. |
Uses of AlphabetContainer in de.jstacs.sequenceScores.statisticalModels.trainable.hmm |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm with parameters of type AlphabetContainer | |
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static AbstractHMM |
HMMFactory.createProfileHMM(MaxHMMTrainingParameterSet trainingParameterSet,
double[][] initFromTo,
boolean likelihood,
int order,
int numLayers,
AlphabetContainer con,
double ess,
boolean conditionalMain,
boolean closeCircle,
double[][] conditionInitProbs,
boolean insertUniform)
Creates a new profile HMM for a given architecture and number of layers. |
static AbstractHMM |
HMMFactory.createProfileHMM(MaxHMMTrainingParameterSet trainingParameterSet,
double[][] initFromTo,
boolean likelihood,
int order,
int numLayers,
AlphabetContainer con,
double ess,
boolean conditionalMain,
int joiningStates,
double[][] conditionInitProbs,
boolean insertUniform)
Creates a new profile HMM for a given architecture and number of layers. |
static AbstractHMM |
HMMFactory.createProfileHMM(MaxHMMTrainingParameterSet trainingParameterSet,
HMMFactory.HMMType type,
boolean likelihood,
int order,
int numLayers,
AlphabetContainer con,
double ess,
boolean conditionalMain,
boolean closeCircle,
double[][] conditionInitProbs)
Creates a new profile HMM for a given architecture and number of layers. |
static AbstractHMM |
HMMFactory.createPseudoErgodicHMM(HMMTrainingParameterSet pars,
double ess,
double selfTranistionPart,
double finalTranistionPart,
AlphabetContainer con,
int numStates,
boolean insertUniform)
Creates an HMM with numStates+1 states, where numStates emitting build a clique and each of those states is connected to the absorbing silent final state. |
static AbstractHMM |
HMMFactory.createSunflowerHMM(HMMTrainingParameterSet pars,
AlphabetContainer con,
double ess,
int expectedSequenceLength,
boolean startCentral,
int... motifLength)
This method creates a first order sunflower HMM. |
static AbstractHMM |
HMMFactory.createSunflowerHMM(HMMTrainingParameterSet pars,
AlphabetContainer con,
double ess,
int expectedSequenceLength,
boolean startCentral,
PhyloTree[] t,
double[] motifProb,
int[] motifLength)
This method creates a first order sunflower HMM allowing phylogenetic emissions. |
Uses of AlphabetContainer in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions that return AlphabetContainer | |
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AlphabetContainer |
UniformEmission.getAlphabetContainer()
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AlphabetContainer |
SilentEmission.getAlphabetContainer()
|
AlphabetContainer |
MixtureEmission.getAlphabetContainer()
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AlphabetContainer |
Emission.getAlphabetContainer()
This method returns the AlphabetContainer of this emission. |
Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions with parameters of type AlphabetContainer | |
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UniformEmission(AlphabetContainer con)
The main constructor for a UniformEmission . |
Uses of AlphabetContainer in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous that return AlphabetContainer | |
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AlphabetContainer |
GaussianEmission.getAlphabetContainer()
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Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous with parameters of type AlphabetContainer | |
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GaussianEmission(AlphabetContainer con)
Creates a GaussianEmission which can be used for maximum likelihood. |
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GaussianEmission(AlphabetContainer con,
double ess,
double priorMu,
double priorAlpha,
double priorBeta,
boolean transformed)
Creates a GaussianEmission with normal-gamma prior by directly defining the hyper-parameters of the prior. |
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GaussianEmission(double ess,
AlphabetContainer con,
double priorMu,
double expectedPrecision,
double sdPrecision,
boolean transformed)
Creates a GaussianEmission with normal-gamma prior by defining the expected precision and the expected standard deviation of the precision, i.e. via the
expectation and variance of the gamma part of the normal-gamma prior. |
Uses of AlphabetContainer in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete |
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Fields in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete declared as AlphabetContainer | |
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protected AlphabetContainer |
AbstractConditionalDiscreteEmission.con
The alphabet of the emissions |
Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete that return AlphabetContainer | |
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AlphabetContainer |
AbstractConditionalDiscreteEmission.getAlphabetContainer()
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Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete with parameters of type AlphabetContainer | |
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AbstractConditionalDiscreteEmission(AlphabetContainer con,
double[][] hyperParams)
This is a simple constructor for a AbstractConditionalDiscreteEmission defining the individual hyper parameters. |
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AbstractConditionalDiscreteEmission(AlphabetContainer con,
double[][] hyperParams,
double[][] initHyperParams)
This constructor creates a AbstractConditionalDiscreteEmission defining the individual hyper parameters for the
prior used during training and initialization. |
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AbstractConditionalDiscreteEmission(AlphabetContainer con,
int numberOfConditions,
double ess)
This is a simple constructor for a AbstractConditionalDiscreteEmission based on the equivalent sample size. |
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DiscreteEmission(AlphabetContainer con,
double ess)
This is a simple constructor for a DiscreteEmission based on the equivalent sample size. |
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DiscreteEmission(AlphabetContainer con,
double[] hyperParams)
This is a simple constructor for a DiscreteEmission defining the individual hyper parameters. |
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PhyloDiscreteEmission(AlphabetContainer con,
double[] hyperParams,
PhyloTree t)
This is a simple constructor for a DiscreteEmission defining the individual hyper parameters. |
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PhyloDiscreteEmission(AlphabetContainer con,
double ess,
PhyloTree t)
This is a simple constructor for a PhyloDiscreteEmission based on the equivalent sample size. |
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ReferenceSequenceDiscreteEmission(AlphabetContainer con,
AlphabetContainer refCon,
int refIdx,
double ess)
This is a simple constructor for a ReferenceSequenceDiscreteEmission based on the equivalent sample size. |
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ReferenceSequenceDiscreteEmission(AlphabetContainer con,
AlphabetContainer refCon,
int refIdx,
double[][] hyperParams)
This constructor creates a ReferenceSequenceDiscreteEmission defining the individual hyper parameters. |
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ReferenceSequenceDiscreteEmission(AlphabetContainer con,
AlphabetContainer refCon,
int refIdx,
double[][] hyperParams,
double[][] initHyperParams)
This constructor creates a ReferenceSequenceDiscreteEmission defining the individual hyper parameters. |
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ReferenceSequenceDiscreteEmission(AlphabetContainer con,
AlphabetContainer refCon,
int refIdx,
double ess,
double[][] initHyperParams)
This is a simple constructor for a ReferenceSequenceDiscreteEmission based on the equivalent sample size. |
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