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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
.
Result
s 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 Constraint
s.
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 Parameter
s.
MeanResultSet
s together.
NumericalResultSet
s 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.
String
s.String
s and the
edit-costs.
Alphabet
.InstanceParameterSet
of any
Alphabet
.Alphabet.AlphabetParameterSet
from the class that can be
instantiated using this Alphabet.AlphabetParameterSet
.
Storable
.
Alphabet
s used in a Sequence
,
Sample
, AbstractModel
or ... .AlphabetContainer
.
AlphabetContainer
with different Alphabet
s
for each position.
AlphabetContainer
based on given
AlphabetContainer
s.
AlphabetContainer
that uses different
Alphabet
s.
AlphabetContainer
from an
AlphabetContainerParameterSet
that contains all necessary
parameters.
Storable
.
enum
defines types of AlphabetContainer
s.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
Alphabet
s.
AlphabetContainerParameterSet
from an array of
Alphabet
s and an array of int
s defining the
Alphabet
index i
in alphabets
that is used for position i
.
Alphabet
s of defined
length.AlphabetContainerParameterSet.AlphabetArrayParameterSet
from the information
about the type
of the Alphabet
s, e.g. if the
array shall contain only the parameters for discrete Alphabet
s.
Storable
.
AlphabetContainerParameterSet.AlphabetArrayParameterSet
from an array of
Alphabet
s and the information about the type
of
the Alphabet
s.
Alphabet
s where each
Alphabet
may be used for one or more sections of positions.AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
for a set of
discrete or continuous Alphabet
s.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
from an
array of Alphabet
s 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
ParameterSetContainer
s 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 ParameterSetContainer
s
enclosing the ParameterSet
s.
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 ParameterSetContainer
s
enclosing the ParameterSet
s.
Storable
.
Tensor
s which are not symmetric, as
opposed to the symmetry defined in SymmetricTensor
.
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