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File
s.Parameter
that represents a local file.Storable
.
FileParameter
.
FileParameter
.
FileParameter.FileRepresentation
out of the filename and the
file's contents.
FileParameter.FileRepresentation
from a filename.
Storable
.
distribution
.
AbstractMixtureScoringFunction.componentScore
with the logarithmic
scores of the components given a Sequence
.
seq
in a given matrix.
TransitionElement
into the given array params
starting at position offset
.
int[]
, into list
.
int[]
, into list
.
Tensor
t
with the weights defined in
weights
.
Tensor
t
with the weights defined in
weights
.
clone
to the values (or clones
of them) of this instance.
File
using a given AlphabetContainer
and a
minimal sequence length.
LinkedList
of the Class
objects for all classes
in listToFilter
that are sub-classes of
superClass
.
DinucleotideProperty
s by some of their annotations.
n
and does path
contraction.
T
that can be instantiated, i.e.
QuadraticFunction
.
x
and the value
f(x)
, starting the search at lower
.
QuadraticFunction
.
T
including interfaces and
abstract classes that are located in a package below
startPackage
.
Object.clone()
, but does not clone the
annotation.
ParameterTree
.
boolean
indicates whether free parameterization or all
parameters are used.
command
in the format defined by configBuffer
of GalaxyConvertible.toGalaxy(String, String, int, StringBuffer, StringBuffer)
and sets the values of the Parameter
or ParameterSet
accordingly.
StringBuffer
.
AbstractHMM.AbstractHMM(StringBuffer)
constructor for creating an instance from an XML representation.
GaussianEmission.GaussianEmission(StringBuffer)
.
AbstractConditionalDiscreteEmission.AbstractConditionalDiscreteEmission(StringBuffer)
.
Parameter
from a XML representation as returned by
Parameter.toXML()
.
ParameterSet
from the XML
representation as returned by ParameterSet.toXML()
.
ConstraintValidator
from the XML representation as
returned by ConstraintValidator.toXML()
.
NumberValidator
from the XML representation as returned
by NumberValidator.toXML()
.
ReferenceConstraint
from the XML representation as
returned by ReferenceConstraint.toXML()
.
SimpleStaticConstraint
from the XML representation as
returned by SimpleStaticConstraint.toXML()
.
StorableValidator
from the XML representation as
returned by StorableValidator.toXML()
.
Result.Result(StringBuffer)
to extract the
information.
ResultSet
from its XML representation as
returned by ResultSet.toXML()
.
Storable
interface to create a scoring function from a StringBuffer
.
FSDAGModel
).Storable
.
FSDAGModel
) that can be used in a Gibbs sampling.Storable
interface.
FSDAGModelForGibbsSampling
.Storable
interface.
FSDAGModelForGibbsSampling
.
FSDAGModel
(fixed
structure directed acyclic graphical
model).Storable
.
FSDAGMParameterSet
set for a
FSDAGModel
.
FSDAGMParameterSet
instance.
FSDAGMParameterSet
from the
class that can be instantiated using this FSDAGMParameterSet
.
FSDAGMParameterSet
instance for the
specified class.
f: R^n -> R
.ScoringFunction
s that are used to
determine the score.
ScoringFunction
s using the parameters that shall be
penalized.
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