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threshold
BurnInTest to
alleviate the implementation of efficient and new burn-in tests.Storable interface.
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.
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.
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.
Constraint to the list of Constraints.
count2 to the counts of this parameter.
count to the parameter as returned by
ParameterTree.getParameterFor(Sequence, int).
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.
unparsed String in some way to
the SequenceAnnotation.
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, costs elong to
elongate a gap by one position and costs of 0 for a match.mismatch for a mismatch, costs start to
start a new gap, costs elong to elongate a gap by one
position and costs of 0 for a match.
Strings.Strings and the
edit-costs.
Alphabet.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
.
Sequence.CompositeSequence.
Sample.
Sample starting in each sequence at startPos.
Sample.
Sample starting in each sequence at startPos.
Sequence.CompositeSequence.
StringBuffer.
boolean array with equal
tags to the StringBuffer source.
boolean array with the
tags to the StringBuffer source.
boolean array with equal tags to the
StringBuffer source.
boolean array with the tags to
the StringBuffer source.
boolean value with equal tags to the
StringBuffer source in the following way: "<
tag>b</tag>".
boolean value with the tags to the
StringBuffer source in the following way: "<
tag attributes>b</tag
>".
byte array with equal
tags to the StringBuffer source.
byte array with the
tags to the StringBuffer source.
byte array with equal tags to the
StringBuffer source.
byte array with the tags to the
StringBuffer source.
byte value with equal tags to the
StringBuffer source in the following way: "<
tag>b</tag>".
byte value with the tags to the
StringBuffer source in the following way: "<
tag attributes>b</tag
>".
ParameterSet in its XML representation (
ParameterSet.toXML()) to the StringBuffer
buf.
double array with equal
tags to the StringBuffer source.
double array with the
tags to the StringBuffer source.
double array with equal tags to the
StringBuffer source.
double array with the tags to
the StringBuffer source.
double value with equal tags to the
StringBuffer source in the following way: "<
tag>d</tag>".
double value with the tags to the
StringBuffer source in the following way: "<
tag attributes>d</tag
>".
Enum object with equal tags to the
StringBuffer source.
Enum object with the tags to the
StringBuffer source.
int array with equal tags
to the StringBuffer source.
int array with the
tags to the StringBuffer source.
int array with equal tags to the
StringBuffer source.
int array with the tags to the
StringBuffer source.
int value with equal tags to the
StringBuffer source in the following way: "<
tag>i</tag>"
int value with the tags to the
StringBuffer source in the following way: "<
tag attributes>i</tag
>".
long value with equal tags to the
StringBuffer source in the following way: "<
tag>i</tag>".
long value with the tags to the
StringBuffer source in the following way: "<
tag attributes>i</tag
>".
Storable.toXML() to append
the main information (name, comment, datatype).
Storable array with equal tags
to the StringBuffer source.
Storable array with the
tags to the StringBuffer source.
Storable array with equal
tags to the StringBuffer source.
Storable array with the
tags to the StringBuffer source.
Storable array with equal tags to the
StringBuffer source.
Storable array with the tags to the
StringBuffer source.
Storable object or "null" with equal tags to
the StringBuffer source.
Storable object or "null" with the
tags to the StringBuffer source.
String array with equal tags
to the StringBuffer source.
String array with the
tags to the StringBuffer source.
String array with equal tags to the
StringBuffer source.
String array with the tags to the
StringBuffer source.
String with equal tags to the StringBuffer
source in the following way: "<tag>
s</tag >".
String with the tags to the
StringBuffer source in the following way: "<
tag attributes>s</tag
>".
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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