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BurnInTest to
alleviate the implementation of efficient and new burn-in tests.Storable.
Storable interface.
Storable.
AbstractMixtureModelAbstractMixtureModel.Storable.
length and the AlphabetContainer to
alphabets.
Storable.
OptimizableFunction and implements some common
methods.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 >"
term to the class parameter.
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
Alphabet.InstanceParameterSet of any
Alphabet.Alphabet.AlphabetParameterSet.
Alphabet.AlphabetParameterSet from its XML
representation.
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.
AlphabetContainerParameterSet from a
StringBuffer.
AlphabetContainers are discrete alphabets,
continuous alphabets, or alphabets mixed of discrete and continuous
symbols at different positions.AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet 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.AlphabetContainerParameterSet.AlphabetArrayParameterSet from the information
if the array shall contain only the parameters for discrete
Alphabets.
AlphabetContainerParameterSet.AlphabetArrayParameterSet from its XML
representation.
AlphabetContainerParameterSet.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.AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet for a set of
discrete or continuous alphabets.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet from an
array of Alphabets, an array of indexes that define the index
of the Alphabet in alphabets belonging to that
position in indexes and a parameter if the alphabets may
be discrete only.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet from its XML
representation.
NormalizableScoringFunction
source.
source.
source.
source.
source in the following way: "< tag > b <
/tag >"
source in the following way: "< startTag > b <
/endTag >"
source.
source.
source.
source.
source in the following way: "< tag > b <
/tag >"
source in the following way: "< startTag > b <
/endTag >"
ParameterSet in its XML-representation (ParameterSet.toXML()) to buf
source.
source.
source.
source.
source in the following way: "< tag > d <
/tag >"
source in the following way: "< startTag > d <
/endTag >"
source.
source.
source.
source.
source.
source.
source in the following way: "< tag > i <
/tag >"
source in the following way: "< startTag > i <
/endTag >"
source in the following way: "< tag > i <
/tag >"
source in the following way: "< startTag > i <
/endTag >"
Storable array with equal tags to the StringBuffer source.
Storable array with start and end tag to the StringBuffer source.
Storable array with equal tags to the StringBuffer source.
Storable array with start and end tag to the StringBuffer source.
source.
source.
Storable object or "null" with equal tags to the StringBuffer source.
Storable object or "null" with start and end tag to the StringBuffer source.
Storable object with equal tags to the StringBuffer source.
Storable object with start and end tag to the StringBuffer source.
source.
source.
source.
source.
source in the following way: "< tag > s <
/tag >"
source in the following way: "< startTag > s <
/endTag >"
AbstractModel.emitSample(int, int...).
delim.
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.
ArrayParameterSet from its XML-representation.
Tensors which are not symmetric, as
opposed to the symmetry defined in SymmetricTensor.
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