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java.lang.Objectde.jstacs.parameters.ParameterSet
de.jstacs.parameters.InstanceParameterSet
de.jstacs.models.discrete.DGMParameterSet
public abstract class DGMParameterSet
The super ParameterSet for any ParameterSet of a DiscreteGraphicalModel
.
Nested Class Summary |
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Nested classes/interfaces inherited from class de.jstacs.parameters.ParameterSet |
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ParameterSet.ParameterList |
Field Summary |
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Fields inherited from class de.jstacs.parameters.InstanceParameterSet |
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alphabet, length |
Fields inherited from class de.jstacs.parameters.ParameterSet |
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alternativeInstanceClass, errorMessage, parameters, parent, ranged |
Constructor Summary | |
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protected |
DGMParameterSet(Class<? extends DiscreteGraphicalModel> instanceClass,
AlphabetContainer alphabet,
double ess,
String description)
The constructor for models, that can handle variable lengths. |
protected |
DGMParameterSet(Class<? extends DiscreteGraphicalModel> instanceClass,
AlphabetContainer alphabet,
int length,
double ess,
String description)
The constructor for models that can handle only sequences of fixed length. |
protected |
DGMParameterSet(Class<? extends DiscreteGraphicalModel> instanceClass,
boolean simple,
boolean variableLength)
An empty constructor of extended classes. |
protected |
DGMParameterSet(StringBuffer s)
The constructor for the Storable interface. |
Method Summary | |
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DGMParameterSet |
clone()
Creates a full clone (deep copy) of this ParameterSet . |
String |
getInstanceName()
Returns the name of an instance of the class that can be constructed using this ParameterSet . |
boolean |
hasDefaultOrIsSet()
Returns true if all parameters in this ParameterSet are
either set by the user or have default values. |
protected void |
loadParameters()
Loads the parameters for this ParameterSet . |
void |
setEss(double ess)
This method can be used to set the ess of this parameter set. |
Methods inherited from class de.jstacs.parameters.InstanceParameterSet |
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equals, fromXML, getAlphabet, getIndex, getLength, getNumberOfParameters, getParameterAt, replaceParametersWithRangedInstance, reset, toXML |
Methods inherited from class de.jstacs.parameters.ParameterSet |
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getErrorMessage, getId, getInstance, getInstanceClass, getInstanceComment, getNumberOfValues, getParent, initParameterList, initParameterList, isAtomic, isRanged, makeRanged, next, parametersLoaded, propagateId, recieveId, resetToFirst, setAlternativeInstanceClass, setParent, simplify, valuesToString |
Methods inherited from class java.lang.Object |
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finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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protected DGMParameterSet(StringBuffer s) throws NonParsableException
Storable
interface.
s
- the StringBuffer
NonParsableException
- if the StringBuffer is not parsableprotected DGMParameterSet(Class<? extends DiscreteGraphicalModel> instanceClass, boolean simple, boolean variableLength)
instanceClass
- the (sub-)classsimple
- whether the alphabet should be simple or notvariableLength
- whether the model can handle sequences of variable lengthprotected DGMParameterSet(Class<? extends DiscreteGraphicalModel> instanceClass, AlphabetContainer alphabet, double ess, String description) throws Exception
instanceClass
- the (sub-)classalphabet
- the alphabetess
- the ESSdescription
- the description
Exception
- if something went wrongprotected DGMParameterSet(Class<? extends DiscreteGraphicalModel> instanceClass, AlphabetContainer alphabet, int length, double ess, String description) throws Exception
instanceClass
- the (sub-)classalphabet
- the alphabetlength
- the length of the modeled sequencesess
- the ESSdescription
- the description
Exception
- if something went wrongMethod Detail |
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protected void loadParameters() throws Exception
ParameterSet
ParameterSet
. This is in
most cases done by simply creating a new ArrayList<Parameter>
for the
field parameters/code>
and filling it with instances of subclasses of Parameter
- Specified by:
loadParameters
in class ParameterSet
- Throws:
Exception
- an Exception
is thrown if the parameters could not be loaded- See Also:
ParameterSet.parameters
,
Parameter
public boolean hasDefaultOrIsSet()
ParameterSet
ParameterSet
are
either set by the user or have default values. If any additional
constraints are required on your parameters you should either specifiy
some ParameterValidator
on these parameters or implement
these contraints 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.hasDefaultOrIsSet() should be called prior to
checking specific constraints.
hasDefaultOrIsSet
in class InstanceParameterSet
public String getInstanceName()
ParameterSet
ParameterSet
.
getInstanceName
in class ParameterSet
public DGMParameterSet clone() throws CloneNotSupportedException
ParameterSet
ParameterSet
. As
a convenience-method the user can use
fillWithStandardFieldsForClone(ParameterSet)
on a newly
created instance of a subclass of ParameterSet
to obtain a
clone/copy of all standard member variables (those already defined in
ParameterSet
) in the passed ParameterSet
.
Using this method, the cloning-process becomes merely three-step:ParameterSet
,
most likely with an empty constructor or the one taking just the
instance-class
this.fillWithStandardFieldsForClone
on this
instance
Object
's method clone()
clone
in class InstanceParameterSet
ParameterSet
CloneNotSupportedException
public void setEss(double ess) throws SimpleParameter.IllegalValueException
ess
- the ESS
SimpleParameter.IllegalValueException
- if ess is negative
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