de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters
Class FSMEMParameterSet
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
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.FSMEMParameterSet
- All Implemented Interfaces:
- GalaxyConvertible, Storable, Cloneable
public class FSMEMParameterSet
- extends MEManagerParameterSet
The ParameterSet for a FSMEManager.
- Author:
- Jens Keilwagen
- See Also:
FSMEManager
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 |
FSMEMParameterSet
public FSMEMParameterSet()
throws Exception
- The simple constructor.
- Throws:
Exception
- if some parameters templates could not be created properly
FSMEMParameterSet
public FSMEMParameterSet(StringBuffer s)
throws NonParsableException
- The constructor for the
Storable
interface.
- Parameters:
s
- the StringBuffer
- Throws:
NonParsableException
- if the StringBuffer is not parsable
FSMEMParameterSet
public FSMEMParameterSet(AlphabetContainer alphabet,
int length,
double ess,
String description,
ConstraintManager.Decomposition decomposition,
boolean reduce,
byte algorithm,
double epsilon,
String constraints)
throws Exception
- The fast constructor.
- Parameters:
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 used
There are two ways entering the constraints.
- Enter single constraints in the following way: node_1, node_2, ..., node_k.
- Enter groups of constraints in the following way: "m<number of
nodes>s<number of skipped nodes>". E.g. m2s1 is the set {0,2; 1,3; 2,4; ...}.
The "x" can be used to determine that each skip should be used (e.g. m2sx).
To separate the constraints use ";".
Additionally for each node a constraint is assumed (i.e. {0; 1; 2; ...}).
- Throws:
Exception
- if something went wrong- See Also:
ConstraintManager.Decomposition.DECOMPOSE_NOTHING
,
ConstraintManager.Decomposition.DECOMPOSE_UNCONNECTED
,
ConstraintManager.Decomposition.DECOMPOSE_LESS_CONNECTED
addParameters
protected void addParameters()
throws Exception
- Description copied from class:
MEManagerParameterSet
- Adds the parameter template in the constructor.
- Overrides:
addParameters
in class MEManagerParameterSet
- Throws:
Exception
- if some parameters could not be created properly
getInstanceComment
public String getInstanceComment()
- Description copied from class:
InstanceParameterSet
- Returns a comment (a textual description) of the class that can be
constructed using this
ParameterSet
.
- Specified by:
getInstanceComment
in class InstanceParameterSet
- Returns:
- the comment of the class