T
- the type of the Alphabet.AlphabetParameterSet
public abstract static class Alphabet.AlphabetParameterSet<T extends Alphabet> extends InstanceParameterSet<T>
InstanceParameterSet
of any
Alphabet
.ParameterSet.ParameterList
errorMessage, parameters, parent
Constructor and Description |
---|
AlphabetParameterSet(Class<T> instanceClass)
Creates a new
Alphabet.AlphabetParameterSet from the class that can be
instantiated using this Alphabet.AlphabetParameterSet . |
AlphabetParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable
. |
Modifier and Type | Method and Description |
---|---|
Alphabet.AlphabetParameterSet |
clone()
Creates a full clone (deep copy) of this
ParameterSet . |
String |
getInstanceName()
Returns the name of an instance of the class that can be constructed
using this
ParameterSet . |
fromXML, getInstance, getInstanceClass, getInstanceComment, toXML
fromGalaxy, getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getNumberOfParameters, getParameterAt, getParameterForName, getParent, hasDefaultOrIsSet, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, reset, setParent, toGalaxy
public AlphabetParameterSet(Class<T> instanceClass)
Alphabet.AlphabetParameterSet
from the class that can be
instantiated using this Alphabet.AlphabetParameterSet
.instanceClass
- the classInstanceParameterSet.InstanceParameterSet(Class)
public AlphabetParameterSet(StringBuffer representation) throws NonParsableException
Storable
. Creates a new Alphabet.AlphabetParameterSet
out of its XML
representation.representation
- the XML representation as StringBuffer
NonParsableException
- if the Alphabet.AlphabetParameterSet
could not be
reconstructed out of the XML representation (the
StringBuffer
representation
could
not be parsed)InstanceParameterSet.InstanceParameterSet(StringBuffer)
,
Storable
public Alphabet.AlphabetParameterSet clone() throws CloneNotSupportedException
ParameterSet
ParameterSet
. As a
convenience-method the user can use
fillWithStandardFieldsForClone(ParameterSet)
on a newly
created instance of a subclass of ParameterSet
to obtain a
clone/copy of all standard member variables (those already defined in
ParameterSet
) in the passed ParameterSet
. Using this
method, the cloning process becomes merely three-step:ParameterSet
, most
likely with an empty constructor or the one taking just the instance
class.
this.fillWithStandardFieldsForClone
on this
instance.
Object
's method
Object.clone()
.clone
in class ParameterSet
ParameterSet
CloneNotSupportedException
public String getInstanceName()
InstanceParameterSet
ParameterSet
.getInstanceName
in class InstanceParameterSet<T extends Alphabet>