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Storable.
AbstractMixtureModelAbstractMixtureModel.Storable.
length and the AlphabetContainer to
alphabets.
Storable.
Storable interface.
doubles.Storable.
weight to the count with index index.
weight
to the specific counter.
val at the end of the list.
val from fromIndex to toIndex (exclusive).
val at the end of the list.
Constraint to the list of Constraints.
count2 the the counts of this parameter.
count to the parameter as returned by ParameterTree.getParameterFor(Sequence, int).
getLogPriorTerm() for each parameter of this model.
ParameterSetContainer containing a clone of the ParameterSet-template
to the set of Parameters
MeanResultsSets.
source with "< tag
>" and "< /tag >"
source with "< startTag
>" and "< /endTag >"
Alignment.StringAlignment instance that aligns the sequences
s1 and s2 using the costs defined in
costs.
mismatch for a mismatch,
costs start to start a new gap, elong to
elongate a gap by one position, and costs of 0 for a matchmismatch for a mismatch, costs start to
start a new gap, elong to elongate a gap by one
position, and costs of 0 for a match
ParameterSet of any Alphabet.AlphabetParameterSet.
AlphabetParameterSet from its XML-representation.
AlphabetContainer from an AlphabetContainerParameterSet that contains
all necessary parameters
ParameterSet of an AlphabetContainer.AlphabetContainerParameterSet.
AlphabetContainerParameterSet from its XML-representation.
AlphabetContainerParameterSet from a single Alphabet.
AlphabetContainerParameterSet from an array of Alphabets.
AlphabetContainerParameterSet from an array of Alphabets and an
array of ints defining the number of the alphabet in alphabets that is used for
that position in indexes.
Alphabets of defined length.AlphabetArrayParameterSet from the information if the array shall contain only
the parameters for discrete Alphabets.
AlphabetArrayParameterSet from its XML-representation.
AlphabetArrayParameterSet from an array of Alphabets and the
information if all alphabets are discrete
Alphabets where each alphabet may be used for one or more
sections of positions.SectionDefinedAlphabetParameterSet for a set of discrete or continuous
alphabets.
SectionDefinedAlphabetParameterSet from an array of Alphabets,
an array of indexes that define the index of the Alphabet<>/code> in alphabets/code>
belonging to that position in indexes and a parameter if the alphabets may be discrete only.
- AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(StringBuffer) -
Constructor for class de.jstacs.data.AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
- Creates a new
SectionDefinedAlphabetParameterSet from its XML-representation.
- alphabets -
Variable in class de.jstacs.models.AbstractModel
- The underlying alphabets
- alphabets -
Variable in class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
- The AlphabetContainer of this
NormalizableScoringFunction
- alternativeInstanceClass -
Variable in class de.jstacs.parameters.ParameterSet
- The class that can be instantiated using this
ParameterSet
- alternativeModel -
Variable in class de.jstacs.models.mixture.AbstractMixtureModel
- The alternative models for the EM.
- annotate(boolean, SequenceAnnotation...) -
Method in class de.jstacs.data.Sequence
- This method allows to append annotation to a sequence.
- annotation -
Variable in class de.jstacs.data.Sequence
- The annotation of the sequence.
- appendAdditionalInfo(StringBuffer) -
Method in class de.jstacs.models.discrete.Constraint
- This method appends additional information that are not stored in the base class to the StringBuffer.
- appendAdditionalInfo(StringBuffer) -
Method in class de.jstacs.models.discrete.inhomogeneous.InhCondProb
-
- appendAdditionalInfo(StringBuffer) -
Method in class de.jstacs.models.discrete.inhomogeneous.InhConstraint
-
- appendAdditionalInfo(StringBuffer) -
Method in class de.jstacs.models.discrete.inhomogeneous.MEMConstraint
-
- appendBoolean2ArrayWithTags(StringBuffer, boolean[][], String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded two dimensional boolean array with equal tags to the StringBuffer
source.
- appendBoolean2ArrayWithTags(StringBuffer, boolean[][], String, String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded two dimensional boolean array with start and end tag to the StringBuffer
source.
- appendBooleanArrayWithTags(StringBuffer, boolean[], String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded boolean array with equal tags to the StringBuffer
source.
- appendBooleanArrayWithTags(StringBuffer, boolean[], String, String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded boolean array with start and end tag to the StringBuffer
source.
- appendBooleanWithTags(StringBuffer, boolean, String) -
Static method in class de.jstacs.io.XMLParser
- Appends a boolean value with equal tags to the StringBuffer
source in the following way: "< tag > b <
/tag >"
- appendBooleanWithTags(StringBuffer, boolean, String, String) -
Static method in class de.jstacs.io.XMLParser
- Appends a boolean value with start and end tag to the StringBuffer
source in the following way: "< startTag > b <
/endTag >"
- appendByte2ArrayWithTags(StringBuffer, byte[][], String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded two dimensional byte array with equal tags to the StringBuffer
source.
- appendByte2ArrayWithTags(StringBuffer, byte[][], String, String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded two dimensional byte array with start and end tag to the StringBuffer
source.
- appendByteArrayWithTags(StringBuffer, byte[], String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded byte array with equal tags to the StringBuffer
source.
- appendByteArrayWithTags(StringBuffer, byte[], String, String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded byte array with start and end tag to the StringBuffer
source.
- appendByteWithTags(StringBuffer, byte, String) -
Static method in class de.jstacs.io.XMLParser
- Appends a byte value with equal tags to the StringBuffer
source in the following way: "< tag > b <
/tag >"
- appendByteWithTags(StringBuffer, byte, String, String) -
Static method in class de.jstacs.io.XMLParser
- Appends a byte value with start and end tag to the StringBuffer
source in the following way: "< startTag > b <
/endTag >"
- appendCollection(StringBuffer) -
Method in class de.jstacs.parameters.CollectionParameter
- Appends the internal
ParameterSet in its XML-representation (ParameterSet.toXML()) to buf
- appendCollection(StringBuffer) -
Method in class de.jstacs.parameters.EnumParameter
-
- appendDouble2ArrayWithTags(StringBuffer, double[][], String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded two dimensional double array with equal tags to the StringBuffer
source.
- appendDouble2ArrayWithTags(StringBuffer, double[][], String, String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded two dimensional double array with start and end tag to the StringBuffer
source.
- appendDoubleArrayWithTags(StringBuffer, double[], String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded double array with equal tags to the StringBuffer
source.
- appendDoubleArrayWithTags(StringBuffer, double[], String, String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded double array with start and end tag to the StringBuffer
source.
- appendDoubleWithTags(StringBuffer, double, String) -
Static method in class de.jstacs.io.XMLParser
- Appends a double value with equal tags to the StringBuffer
source in the following way: "< tag > d <
/tag >"
- appendDoubleWithTags(StringBuffer, double, String, String) -
Static method in class de.jstacs.io.XMLParser
- Appends a double value with start and end tag to the StringBuffer
source in the following way: "< startTag > d <
/endTag >"
- appendEnumWithTags(StringBuffer, Enum<T>, String) -
Static method in class de.jstacs.io.XMLParser
- Appends an Enum object with equal tags to the StringBuffer
source.
- appendEnumWithTags(StringBuffer, Enum<T>, String, String) -
Static method in class de.jstacs.io.XMLParser
- Appends an Enum object with start and end tag to the StringBuffer
source.
- appendInt2ArrayWithTags(StringBuffer, int[][], String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded two dimensional int array with equal tags to the StringBuffer
source.
- appendInt2ArrayWithTags(StringBuffer, int[][], String, String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded two dimensional int array with start and end tag to the StringBuffer
source.
- appendIntArrayWithTags(StringBuffer, int[], String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded int array with equal tags to the StringBuffer
source.
- appendIntArrayWithTags(StringBuffer, int[], String, String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded int array with start and end tag to the StringBuffer
source.
- appendIntWithTags(StringBuffer, int, String) -
Static method in class de.jstacs.io.XMLParser
- Appends an int value with equal tags to the StringBuffer
source in the following way: "< tag > i <
/tag >"
- appendIntWithTags(StringBuffer, int, String, String) -
Static method in class de.jstacs.io.XMLParser
- Appends an int value with start and end tag to the StringBuffer
source in the following way: "< startTag > i <
/endTag >"
- appendLongWithTags(StringBuffer, long, String) -
Static method in class de.jstacs.io.XMLParser
- Appends a long value with equal tags to the StringBuffer
source in the following way: "< tag > i <
/tag >"
- appendLongWithTags(StringBuffer, long, String, String) -
Static method in class de.jstacs.io.XMLParser
- Appends a long value with start and end tag to the StringBuffer
source in the following way: "< startTag > i <
/endTag >"
- appendMainInfo(StringBuffer) -
Method in class de.jstacs.results.Result
- This method can be used in the toXML-method to append the main information (name, comment, datatype).
- appendStorable2ArrayWithTags(StringBuffer, Storable[][], String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded two dimensional
Storable array with equal tags to the StringBuffer source.
- appendStorable2ArrayWithTags(StringBuffer, Storable[][], String, String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded two dimensional
Storable array with start and end tag to the StringBuffer source.
- appendStorable3ArrayWithTags(StringBuffer, Storable[][][], String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded three dimensional
Storable array with equal tags to the StringBuffer source.
- appendStorable3ArrayWithTags(StringBuffer, Storable[][][], String, String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded three dimensional
Storable array with start and end tag to the StringBuffer source.
- appendStorableArrayWithTags(StringBuffer, Storable[], String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded Storable array with equal tags to the StringBuffer
source.
- appendStorableArrayWithTags(StringBuffer, Storable[], String, String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded Storable array with start and end tag to the StringBuffer
source.
- appendStorableOrNullWithTags(StringBuffer, Storable, String) -
Static method in class de.jstacs.io.XMLParser
- Appends a
Storable object or "null" with equal tags to the StringBuffer source.
- appendStorableOrNullWithTags(StringBuffer, Storable, String, String) -
Static method in class de.jstacs.io.XMLParser
- Appends a
Storable object or "null" with start and end tag to the StringBuffer source.
- appendStorableWithTags(StringBuffer, Storable, String) -
Static method in class de.jstacs.io.XMLParser
- Appends a
Storable object with equal tags to the StringBuffer source.
- appendStorableWithTags(StringBuffer, Storable, String, String) -
Static method in class de.jstacs.io.XMLParser
- Appends a
Storable object with start and end tag to the StringBuffer source.
- appendString2ArrayWithTags(StringBuffer, String[][], String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded two dimensional String array with equal tags to the StringBuffer
source.
- appendString2ArrayWithTags(StringBuffer, String[][], String, String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded two dimensional String array with start and end tag to the StringBuffer
source.
- appendStringArrayWithTags(StringBuffer, String[], String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded String array with equal tags to the StringBuffer
source.
- appendStringArrayWithTags(StringBuffer, String[], String, String) -
Static method in class de.jstacs.io.XMLParser
- Appends an encoded String array with start and end tag to the StringBuffer
source.
- appendStringWithTags(StringBuffer, String, String) -
Static method in class de.jstacs.io.XMLParser
- Appends a String with equal tags to the StringBuffer
source in the following way: "< tag > s <
/tag >"
- appendStringWithTags(StringBuffer, String, String, String) -
Static method in class de.jstacs.io.XMLParser
- Appends a String with start and end tag to the StringBuffer
source in the following way: "< startTag > s <
/endTag >"
- ArbitrarySequence - Class in de.jstacs.data.sequences
- The class for any continuous or hybrid sequence.
- ArbitrarySequence(AlphabetContainer, double[]) -
Constructor for class de.jstacs.data.sequences.ArbitrarySequence
- This constructor is designed for the
emitSample( int n ) of AbstractModel.
- ArbitrarySequence(AlphabetContainer, String) -
Constructor for class de.jstacs.data.sequences.ArbitrarySequence
- Creates a new sequence from a string representation using the default delimiter.
- ArbitrarySequence(AlphabetContainer, SequenceAnnotation[], String, String) -
Constructor for class de.jstacs.data.sequences.ArbitrarySequence
- Creates a new sequence from a string representation using the delimiter
delim.
- ArbitrarySequence(AlphabetContainer, SequenceAnnotation[], SymbolExtractor) -
Constructor for class de.jstacs.data.sequences.ArbitrarySequence
- Creates a new sequence from a SymbolExctractor.
- ArrayHandler - Class in de.jstacs.io
- This class enables the user to cast and clone arrays easily.
- ArrayHandler() -
Constructor for class de.jstacs.io.ArrayHandler
-
- ArrayParameterSet - Class in de.jstacs.parameters
- Class for a
ParameterSet that consists of a length-Parameter that defines the length
of the array and an array of ParameterSetContainers of this length. - ArrayParameterSet(Class, ParameterSet, String, String, String, String, NumberValidator<Integer>) -
Constructor for class de.jstacs.parameters.ArrayParameterSet
- Creates a new
ArrayParameterSet from a Class that can be instantiated using this
ArrayParameterSet and templates for the ParameterSet in each element of the array,
the name and the comment that are displayed for the ParameterSetContainers enclosing the ParameterSets.
- ArrayParameterSet(Class, ParameterSet, String, String) -
Constructor for class de.jstacs.parameters.ArrayParameterSet
- Creates a new
ArrayParameterSet from a Class that can be instantiated using this
ArrayParameterSet and templates for the ParameterSet in each element of the array,
the name and the comment that are displayed for the ParameterSetContainers enclosing the ParameterSets.
- ArrayParameterSet(StringBuffer) -
Constructor for class de.jstacs.parameters.ArrayParameterSet
- Creates a new
ArrayParameterSet from its XML-representation.
- assess(MeasureParameters, ClassifierAssessmentAssessParameterSet, Sample...) -
Method in class de.jstacs.classifier.assessment.ClassifierAssessment
- Assesses the contained classifiers.
- assess(MeasureParameters, ClassifierAssessmentAssessParameterSet, ProgressUpdater, Sample...) -
Method in class de.jstacs.classifier.assessment.ClassifierAssessment
- Assesses the contained classifiers.
- assess(MeasureParameters, ClassifierAssessmentAssessParameterSet, ProgressUpdater, Sample[][]...) -
Method in class de.jstacs.classifier.assessment.ClassifierAssessment
-
- AsymmetricTensor - Class in de.jstacs.algorithms.graphs.tensor
- This class can be used for Tensors which are not symmetric,
as opposed to the symmetry defined in
SymmetricTensor. - AsymmetricTensor(int, byte) -
Constructor for class de.jstacs.algorithms.graphs.tensor.AsymmetricTensor
-
- AsymmetricTensor(double[][][], int, byte) -
Constructor for class de.jstacs.algorithms.graphs.tensor.AsymmetricTensor
-
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