de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters

Class MEManagerParameterSet

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.inhomogeneous.parameters.IDGTrainSMParameterSet

de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.MEManagerParameterSet

All Implemented Interfaces:

GalaxyConvertible, Storable, Cloneable

Direct Known Subclasses:

FSMEMParameterSet

public abstract class MEManagerParameterSet
extends IDGTrainSMParameterSet

The ParameterSet for any MEManager.

Author:

Jens Keilwagen

Nested Class Summary

Nested classes/interfaces inherited from class de.jstacs.parameters.ParameterSet

ParameterSet.ParameterList

Field Summary

Fields inherited from class de.jstacs.parameters.SequenceScoringParameterSet

alphabet, length

Fields inherited from class de.jstacs.parameters.ParameterSet

errorMessage, parameters, parent

Constructor Summary

Constructors

Constructor and Description
MEManagerParameterSet(Class<? extends MEManager> instanceClass) The constructor an empty constructor of extended class.
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.
MEManagerParameterSet(StringBuffer s) The constructor for the Storable interface.

Method Summary

Methods

Modifier and Type	Method and Description
protected void	addParameters() Adds the parameter template in the constructor.

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.IDGTrainSMParameterSet

getModelInstanceName

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.DGTrainSMParameterSet

clone, getInstanceName, hasDefaultOrIsSet, setEss

Methods inherited from class de.jstacs.parameters.SequenceScoringParameterSet

equals, fromXML, getAlphabetContainer, getLength, getNumberOfParameters, getParameterAt, reset, toXML

Methods inherited from class de.jstacs.parameters.InstanceParameterSet

getInstance, getInstanceClass, getInstanceComment

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

Methods inherited from class java.lang.Object

finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MEManagerParameterSet

public MEManagerParameterSet(StringBuffer s)
                      throws NonParsableException

The constructor for the Storable interface.

Parameters:

s - the StringBuffer

Throws:

NonParsableException - if the StringBuffer is not parsable

MEManagerParameterSet

public MEManagerParameterSet(Class<? extends MEManager> instanceClass)
                      throws Exception

The constructor an empty constructor of extended class.

Parameters:

instanceClass - the (sub-)class

Throws:

Exception - if some parameters template could not be created properly

MEManagerParameterSet

public MEManagerParameterSet(Class<? extends MEManager> instanceClass,
                     AlphabetContainer alphabet,
                     int length,
                     double ess,
                     String description,
                     ConstraintManager.Decomposition decomposition,
                     boolean reduce,
                     byte algorithm,
                     double epsilon)
                      throws Exception

The fast constructor.

Parameters:

instanceClass - the (sub-)class

alphabet - the alphabet

length - the length of the modeled sequences

ess - the ess

description - the description

decomposition - the kind of decomposition

reduce - whether the constraints should be reduced

algorithm - the choice of algorithm

epsilon - the threshold for stopping the numerical algorithms

Throws:

Exception - if something went wrong

See Also:

ConstraintManager.Decomposition.DECOMPOSE_NOTHING, ConstraintManager.Decomposition.DECOMPOSE_UNCONNECTED, ConstraintManager.Decomposition.DECOMPOSE_LESS_CONNECTED

Method Detail

addParameters

protected void addParameters()
                      throws Exception

Adds the parameter template in the constructor.

Throws:

Exception - if some parameters could not be created properly