public class HomMMParameterSet extends HomogeneousTrainSMParameterSet
ParameterSet.ParameterListalphabet, lengtherrorMessage, 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. |
hasDefaultOrIsSetclone, getInstanceName, setEssequals, fromXML, getAlphabetContainer, getLength, getNumberOfParameters, getParameterAt, reset, toXMLgetInstance, getInstanceClassfromGalaxy, getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getParameterForName, getParent, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, setParent, toGalaxypublic HomMMParameterSet(StringBuffer s) throws NonParsableException
Storable.
Creates a new HomMMParameterSet out of its XML representation.s - the XML representation as StringBufferNonParsableException - 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 AlphabetContaineress - 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()
InstanceParameterSetParameterSet.getInstanceComment in class InstanceParameterSet