public class HomMMParameterSet extends HomogeneousTrainSMParameterSet
ParameterSet.ParameterList
alphabet, length
errorMessage, parameters, parent
Constructor and Description |
---|
HomMMParameterSet()
An empty constructor.
|
HomMMParameterSet(AlphabetContainer alphabet,
double ess,
String description,
byte order)
Creates a new
HomMMParameterSet with AlphabetContainer ,
ess (equivalent sample size), description and order
of the homogeneous Markov model. |
HomMMParameterSet(StringBuffer s)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
String |
getInstanceComment()
Returns a comment (a textual description) of the class that can be
constructed using this
ParameterSet . |
hasDefaultOrIsSet
clone, getInstanceName, 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 HomMMParameterSet(StringBuffer s) throws NonParsableException
Storable
.
Creates a new HomMMParameterSet
out of its XML representation.s
- the XML representation as StringBuffer
NonParsableException
- if the HomMMParameterSet
could not be reconstructed
out of the XML representation (the StringBuffer
could
not be parsed)Storable
,
HomogeneousTrainSMParameterSet.HomogeneousTrainSMParameterSet(StringBuffer)
public HomMMParameterSet()
HomMMParameterSet
.public HomMMParameterSet(AlphabetContainer alphabet, double ess, String description, byte order) throws Exception
HomMMParameterSet
with AlphabetContainer
,
ess (equivalent sample size), description and order
of the homogeneous Markov model.alphabet
- the AlphabetContainer
ess
- the ess (equivalent sample size)description
- the descriptionorder
- the order of the Markov modelException
- if something went wrongHomogeneousTrainSMParameterSet.HomogeneousTrainSMParameterSet(Class,
AlphabetContainer, double, String, byte)
public String getInstanceComment()
InstanceParameterSet
ParameterSet
.getInstanceComment
in class InstanceParameterSet