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threshold
Storable.
AbsoluteValueCondition.Storable.
BurnInTest to
alleviate the implementation of efficient and new burn-in tests.Storable interface.
AbstractBurnInTest.AbstractBurnInTestParameterSet with empty parameter values.
AbstractBurnInTestParameterSet with
pre-defined parameter values.
Storable.
Storable.
AbstractConditionalDiscreteEmission based on the equivalent sample size.
AbstractConditionalDiscreteEmission defining the individual hyper parameters.
AbstractConditionalDiscreteEmission defining the individual hyper parameters for the
prior used during training and initialization.
AbstractConditionalDiscreteEmission from its XML representation.
Storable.
AbstractMixtureModel.
Storable.
enum defines the different types of algorithms that can
be used in an AbstractMixtureModel.enum defines the different types of parameterization
for a probability that can be used in an AbstractMixtureModel.AbstractMixtureScoringFunction.
Storable.
length and
the AlphabetContainer to alphabets.
Storable.
ScoreClassifier.Storable.
OptimizableFunction and implements some common
methods.Storable.
Results given as a table of double
s.list
Storable
.
AbstractStringExtractor with the specified
character as start of each comment line.
TerminationConditions.Storable.
AbstractTerminationCondition.AbstractTerminationCondition.AbstractTerminationConditionParameterSet from the class that can be
instantiated using this AbstractTerminationCondition.AbstractTerminationConditionParameterSet.
Storable.
NormalizableScoringFunction based on the declaration
of methods in VariableLengthScoringFunction.VariableLengthScoringFunction that models sequences of arbitrary
length.
VariableLengthScoringFunction that models sequences of a given
length.
Storable.
identifier at position position
with length length and StrandedLocatedSequenceAnnotationWithLength.Strand strandedness
SequenceAnnotation to the internal list.
weight to the count with index
index.
Sequence seq and adds the 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.
weight to the counts corresponding to the
Sequence seq from start to the end
of the Sequence.
DoubleList list2 to the current list.
val to the list only if
it is not already contained in the list.
Constraint to the list of Constraints.
count2 to the counts of this parameter.
count to the parameter as returned by
ParameterTree.getParameterFor(Sequence, int).
Transition.getLogPriorTerm() for each
parameter of this transition.
BasicHigherOrderTransition.AbstractTransitionElement.getLogPriorTerm() for each
parameter of this transition element.
Emission.getLogPriorTerm() for each
parameter of this model.
NormalizableScoringFunction.getLogPriorTerm() for each
parameter of this model.
ParameterSetContainer containing a clone of the
ParameterSet-template to the set of Parameters.
MeanResultSets together.
NumericalResultSets to this MeanResultSet.
StringBuffer source with equal tags
"< tag>" and "</tag
>".
StringBuffer source with "<
tag attributes>" and "</tag
>".
term to the class parameter of the
class with index classIndex.
start to
end the value summand.
unparsed String in some way to
the SequenceAnnotation.
weight to the internal sufficient statistic.
weight to the sufficient statistic of the parameters that
are used for scoring the specific subsequence(s).
weight to the sufficient statistic of a specific transition.
start, and
the costs for elongating a gap by one position are given by elong.Alignment instance that aligns the sequences
s1 and s2 using the costs defined in
costs.
Alignment instance that aligns the sequences
s1 and s2 using the costs defined in
costs and a banded version of the alignment algorithm.
Alphabet.String array.
InstanceParameterSet of any
Alphabet.Alphabet.AlphabetParameterSet from the class that can be
instantiated using this Alphabet.AlphabetParameterSet.
Storable
.
Alphabets used in a Sequence,
Sample, AbstractModel or ... .AlphabetContainer.
AlphabetContainer with different Alphabets
for each position.
AlphabetContainer based on given
AlphabetContainers.
AlphabetContainer that uses different
Alphabets.
AlphabetContainer from an
AlphabetContainerParameterSet that contains all necessary
parameters.
Storable.
enum defines types of AlphabetContainers.AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet of an AlphabetContainer.AlphabetContainerParameterSet of an
AlphabetContainer with AlphabetContainer.AlphabetContainerType
type.
Storable.
AlphabetContainerParameterSet of a simple
AlphabetContainer from a single Alphabet.
AlphabetContainerParameterSet from an array of
Alphabets.
AlphabetContainerParameterSet from an array of
Alphabets and an array of ints defining the
Alphabet index i in alphabets
that is used for position i.
Alphabets of defined
length.AlphabetContainerParameterSet.AlphabetArrayParameterSet from the information
about the type of the Alphabets, e.g. if the
array shall contain only the parameters for discrete Alphabet
s.
Storable
.
AlphabetContainerParameterSet.AlphabetArrayParameterSet from an array of
Alphabets and the information about the type of
the Alphabets.
Alphabets where each
Alphabet may be used for one or more sections of positions.AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet for a set of
discrete or continuous Alphabets.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet from an
array of Alphabets and an array of indexes that define the
index of the Alphabet in alphabets belonging to
that position in indexes.
Storable
.
AlphabetContainer of this NormalizableScoringFunction
.
SequenceAnnotations.
Sequence.
Sample.
Sample starting in each sequence at startPos.
Sample.
Sample starting in each sequence at startPos.
Sequence.
ReferenceSequenceAnnotations.
str to the protocol.
StringBuffer.
ParameterSet in its XML representation (
ParameterSet.toXML()) to the StringBuffer
buf.
Storable.toXML() to append
the main information (name, comment, datatype).
Object with the tags to the StringBuffer xml.
Object with the tags and attributes to the StringBuffer xml.
Object with the tags and attributes to the StringBuffer xml.
ArbitrarySequence from an array of
double-encoded alphabet symbols.
ArbitrarySequence from a String
representation using the default delimiter.
ArbitrarySequence from a String
representation using the delimiter delim.
ArbitrarySequence from a SymbolExtractor.
ParameterSet that consists of a length-Parameter
that defines the length of the array and an array of
ParameterSetContainers of this length.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 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.
Storable.
Tensors which are not symmetric, as
opposed to the symmetry defined in SymmetricTensor.
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