public abstract class HomogeneousTrainSMParameterSet extends DGTrainSMParameterSet
ParameterSet.ParameterList
alphabet, length
errorMessage, parameters, parent
Modifier | Constructor and Description |
---|---|
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 . |
protected |
HomogeneousTrainSMParameterSet(Class<? extends HomogeneousTrainSM> instanceClass,
AlphabetContainer alphabet,
double ess,
String description,
byte order)
Creates a new
HomogeneousTrainSMParameterSet with
AlphabetContainer , ess (equivalent sample
size), description and order of the homogeneous Markov model. |
protected |
HomogeneousTrainSMParameterSet(StringBuffer s)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
boolean |
hasDefaultOrIsSet()
Returns
true if all parameters in this ParameterSet
are either set by the user or have default values. |
clone, getInstanceName, setEss
equals, fromXML, getAlphabetContainer, getLength, getNumberOfParameters, getParameterAt, reset, toXML
getInstance, getInstanceClass, getInstanceComment
fromGalaxy, getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getParameterForName, getParent, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, setParent, toGalaxy
protected HomogeneousTrainSMParameterSet(StringBuffer s) throws NonParsableException
Storable
.
Creates a new HomogeneousTrainSMParameterSet
out of its XML
representation.s
- the XML representation as StringBuffer
NonParsableException
- if the HomogeneousTrainSMParameterSet
could not be
reconstructed out of the XML representation (the
StringBuffer
could not be parsed)Storable
,
DGTrainSMParameterSet.DGTrainSMParameterSet(StringBuffer)
protected HomogeneousTrainSMParameterSet(Class<? extends HomogeneousTrainSM> instanceClass)
HomogeneousTrainSMParameterSet
from the class that can be
instantiated using this HomogeneousTrainSMParameterSet
.instanceClass
- the (sub-)classHomogeneousMM
,
HomogeneousTrainSM
,
DGTrainSMParameterSet.DGTrainSMParameterSet(Class, boolean, boolean)
protected HomogeneousTrainSMParameterSet(Class<? extends HomogeneousTrainSM> instanceClass, AlphabetContainer alphabet, double ess, String description, byte order) throws Exception
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.instanceClass
- the (sub-)classalphabet
- the AlphabetContainer
ess
- the ess (equivalent sample size)description
- the descriptionorder
- the order of the modelException
- if something went wrongDGTrainSMParameterSet.DGTrainSMParameterSet(Class, AlphabetContainer, double,
String)
public boolean hasDefaultOrIsSet()
ParameterSet
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.hasDefaultOrIsSet
in class DGTrainSMParameterSet
true
if all parameters have some allowed value set,
false
otherwise