public abstract class MEManagerParameterSet extends IDGTrainSMParameterSet
ParameterSet.ParameterList
alphabet, length
errorMessage, parameters, parent
Constructor and Description |
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MEManagerParameterSet(Class<? extends MEManager> instanceClass)
The constructor an empty constructor of extended class.
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MEManagerParameterSet(Class<? extends MEManager> instanceClass,
AlphabetContainer alphabet,
int length,
double ess,
String description,
ConstraintManager.Decomposition decomposition,
boolean reduce,
byte algorithm,
double epsilon)
The fast constructor.
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MEManagerParameterSet(StringBuffer s)
The constructor for the
Storable interface. |
Modifier and Type | Method and Description |
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protected void |
addParameters()
Adds the parameter template in the constructor.
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getModelInstanceName
clone, getInstanceName, hasDefaultOrIsSet, 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
public MEManagerParameterSet(StringBuffer s) throws NonParsableException
Storable
interface.s
- the StringBufferNonParsableException
- if the StringBuffer is not parsablepublic MEManagerParameterSet(Class<? extends MEManager> instanceClass) throws Exception
instanceClass
- the (sub-)classException
- if some parameters template could not be created properlypublic MEManagerParameterSet(Class<? extends MEManager> instanceClass, AlphabetContainer alphabet, int length, double ess, String description, ConstraintManager.Decomposition decomposition, boolean reduce, byte algorithm, double epsilon) throws Exception
instanceClass
- the (sub-)classalphabet
- the alphabetlength
- the length of the modeled sequencesess
- the essdescription
- the descriptiondecomposition
- the kind of decompositionreduce
- whether the constraints should be reducedalgorithm
- the choice of algorithmepsilon
- the threshold for stopping the numerical algorithmsException
- if something went wrongConstraintManager.Decomposition.DECOMPOSE_NOTHING
,
ConstraintManager.Decomposition.DECOMPOSE_UNCONNECTED
,
ConstraintManager.Decomposition.DECOMPOSE_LESS_CONNECTED