public class FSMEMParameterSet extends MEManagerParameterSet
FSMEManager
ParameterSet.ParameterList
alphabet, length
errorMessage, parameters, parent
Constructor and Description |
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FSMEMParameterSet()
The simple constructor.
|
FSMEMParameterSet(AlphabetContainer alphabet,
int length,
double ess,
String description,
ConstraintManager.Decomposition decomposition,
boolean reduce,
byte algorithm,
double epsilon,
String constraints)
The fast constructor.
|
FSMEMParameterSet(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.
|
String |
getInstanceComment()
Returns a comment (a textual description) of the class that can be
constructed using this
ParameterSet . |
getModelInstanceName
clone, getInstanceName, hasDefaultOrIsSet, setEss
equals, fromXML, getAlphabetContainer, getLength, getNumberOfParameters, getParameterAt, reset, toXML
getInstance, getInstanceClass
fromGalaxy, getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getParameterForName, getParent, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, setParent, toGalaxy
public FSMEMParameterSet() throws Exception
Exception
- if some parameters templates could not be created properlypublic FSMEMParameterSet(StringBuffer s) throws NonParsableException
Storable
interface.s
- the StringBufferNonParsableException
- if the StringBuffer is not parsablepublic FSMEMParameterSet(AlphabetContainer alphabet, int length, double ess, String description, ConstraintManager.Decomposition decomposition, boolean reduce, byte algorithm, double epsilon, String constraints) throws Exception
alphabet
- 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 algorithmsconstraints
- the constraints to be usedException
- if something went wrongConstraintManager.Decomposition.DECOMPOSE_NOTHING
,
ConstraintManager.Decomposition.DECOMPOSE_UNCONNECTED
,
ConstraintManager.Decomposition.DECOMPOSE_LESS_CONNECTED
protected void addParameters() throws Exception
MEManagerParameterSet
addParameters
in class MEManagerParameterSet
Exception
- if some parameters could not be created properlypublic String getInstanceComment()
InstanceParameterSet
ParameterSet
.getInstanceComment
in class InstanceParameterSet