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Files.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.
DinucleotidePropertys 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.ScoringFunctions that are used to
determine the score.
ScoringFunctions using the parameters that shall be
penalized.
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