public static final class DNAAlphabetContainer.DNAAlphabetContainerParameterSet extends AlphabetContainer.AbstractAlphabetContainerParameterSet<DNAAlphabetContainer> implements Singleton
ParameterSet
of a DNAAlphabetContainer
.ParameterSet.ParameterList
Singleton.SingletonHandler
Modifier and Type | Field and Description |
---|---|
static DNAAlphabetContainer.DNAAlphabetContainerParameterSet |
SINGLETON
The only instance of this class.
|
errorMessage, parameters, parent
Modifier and Type | Method and Description |
---|---|
DNAAlphabetContainer.DNAAlphabetContainerParameterSet |
clone()
Creates a full clone (deep copy) of this
ParameterSet . |
String |
getInstanceComment()
Returns a comment (a textual description) of the class that can be
constructed using this
ParameterSet . |
String |
getInstanceName()
Returns the name of an instance of the class that can be constructed
using this
ParameterSet . |
int |
getPossibleLength()
Returns the length of the
AlphabetContainer that can be instantiated using
this ParameterSet . |
boolean |
isDiscrete()
Indicates if all positions use
DiscreteAlphabet.DiscreteAlphabetParameterSet , i.e. |
boolean |
isSimple()
Indicates if all positions use the same
Alphabet , i.e. |
fromXML, getInstance, getInstanceClass, toXML
fromGalaxy, getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getNumberOfParameters, getParameterAt, getParameterForName, getParent, hasDefaultOrIsSet, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, reset, setParent, toGalaxy
public static final DNAAlphabetContainer.DNAAlphabetContainerParameterSet SINGLETON
Singleton
public DNAAlphabetContainer.DNAAlphabetContainerParameterSet clone()
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 AlphabetContainer.AbstractAlphabetContainerParameterSet<DNAAlphabetContainer>
ParameterSet
public String getInstanceComment()
InstanceParameterSet
ParameterSet
.getInstanceComment
in class InstanceParameterSet<DNAAlphabetContainer>
public String getInstanceName()
InstanceParameterSet
ParameterSet
.getInstanceName
in class InstanceParameterSet<DNAAlphabetContainer>
public int getPossibleLength()
AlphabetContainer.AbstractAlphabetContainerParameterSet
AlphabetContainer
that can be instantiated using
this ParameterSet
.getPossibleLength
in class AlphabetContainer.AbstractAlphabetContainerParameterSet<DNAAlphabetContainer>
AlphabetContainer.getPossibleLength()
public boolean isDiscrete()
AlphabetContainer.AbstractAlphabetContainerParameterSet
DiscreteAlphabet.DiscreteAlphabetParameterSet
, i.e.
if all Alphabet
s of the corresponding AlphabetContainer
are discrete.isDiscrete
in class AlphabetContainer.AbstractAlphabetContainerParameterSet<DNAAlphabetContainer>
true
if all positions are discrete,
false
otherwiseAlphabetContainer.isDiscrete()
public boolean isSimple()
AlphabetContainer.AbstractAlphabetContainerParameterSet
Alphabet
, i.e. if the
corresponding AlphabetContainer
is simple.isSimple
in class AlphabetContainer.AbstractAlphabetContainerParameterSet<DNAAlphabetContainer>
true
if all positions use the same Alphabet
,
false
otherwise