de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters
Class HomogeneousTrainSMParameterSet
java.lang.Object
de.jstacs.parameters.ParameterSet
de.jstacs.parameters.InstanceParameterSet<T>
de.jstacs.parameters.SequenceScoringParameterSet<T>
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.DGTrainSMParameterSet
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters.HomogeneousTrainSMParameterSet
- All Implemented Interfaces:
- GalaxyConvertible, Storable, Cloneable
- Direct Known Subclasses:
- HomMMParameterSet
public abstract class HomogeneousTrainSMParameterSet
- extends DGTrainSMParameterSet
This class implements a container for all parameters of any homogeneous
model.
- Author:
- Jens Keilwagen
Method Summary |
boolean |
hasDefaultOrIsSet()
Returns true if all parameters in this ParameterSet
are either set by the user or have default values. |
Methods inherited from class de.jstacs.parameters.ParameterSet |
fromGalaxy, getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getParameterForName, getParent, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, setParent, toGalaxy |
HomogeneousTrainSMParameterSet
protected HomogeneousTrainSMParameterSet(StringBuffer s)
throws NonParsableException
- The standard constructor for the interface
Storable
.
Creates a new HomogeneousTrainSMParameterSet
out of its XML
representation.
- Parameters:
s
- the XML representation as StringBuffer
- Throws:
NonParsableException
- if the HomogeneousTrainSMParameterSet
could not be
reconstructed out of the XML representation (the
StringBuffer
could not be parsed)- See Also:
Storable
,
DGTrainSMParameterSet.DGTrainSMParameterSet(StringBuffer)
HomogeneousTrainSMParameterSet
protected HomogeneousTrainSMParameterSet(Class<? extends HomogeneousTrainSM> instanceClass)
- This is the constructor that creates an empty
HomogeneousTrainSMParameterSet
from the class that can be
instantiated using this HomogeneousTrainSMParameterSet
.
- Parameters:
instanceClass
- the (sub-)class- See Also:
HomogeneousMM
,
HomogeneousTrainSM
,
DGTrainSMParameterSet.DGTrainSMParameterSet(Class, boolean, boolean)
HomogeneousTrainSMParameterSet
protected HomogeneousTrainSMParameterSet(Class<? extends HomogeneousTrainSM> instanceClass,
AlphabetContainer alphabet,
double ess,
String description,
byte order)
throws Exception
- Creates a new
HomogeneousTrainSMParameterSet
with
AlphabetContainer
, ess (equivalent sample
size), description and order of the homogeneous Markov model. This
constructor is for models that can handle variable lengths.
- Parameters:
instanceClass
- the (sub-)classalphabet
- the AlphabetContainer
ess
- the ess (equivalent sample size)description
- the descriptionorder
- the order of the model
- Throws:
Exception
- if something went wrong- See Also:
DGTrainSMParameterSet.DGTrainSMParameterSet(Class, AlphabetContainer, double,
String)
hasDefaultOrIsSet
public boolean hasDefaultOrIsSet()
- Description copied from class:
ParameterSet
- Returns
true
if all parameters in this ParameterSet
are either set by the user or have default values. If any additional
constraints are required on your parameters you should either specify
some ParameterValidator
on these parameters or implement these
constraints by overriding this method in your implementation of
ParameterSet
. It is recommended to specify a useful remark which
constraint failed in the member-variable errorMessage
, which
will be displayed to the user. In the overriding method
super.
ParameterSet.hasDefaultOrIsSet()
should be called prior to
checking specific constraints.
- Overrides:
hasDefaultOrIsSet
in class DGTrainSMParameterSet
- Returns:
true
if all parameters have some allowed value set,
false
otherwise