public static class AlphabetContainerParameterSet.AlphabetArrayParameterSet extends ArrayParameterSet
Alphabet
s of defined
length.ParameterSet.ParameterList
commentTemplate, nameTemplate, template
errorMessage, parameters, parent
Constructor and Description |
---|
AlphabetArrayParameterSet()
Creates a new
AlphabetContainerParameterSet.AlphabetArrayParameterSet with type AlphabetContainer.AlphabetContainerType.BOTH . |
AlphabetArrayParameterSet(Alphabet[] alphabets,
AlphabetContainer.AlphabetContainerType type)
Creates a new
AlphabetContainerParameterSet.AlphabetArrayParameterSet from an array of
Alphabet s and the information about the type of
the Alphabet s. |
AlphabetArrayParameterSet(AlphabetContainer.AlphabetContainerType type)
Creates a new
AlphabetContainerParameterSet.AlphabetArrayParameterSet from the information
about the type of the Alphabet s, e.g. |
AlphabetArrayParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable
. |
Modifier and Type | Method and Description |
---|---|
AlphabetContainerParameterSet.AlphabetArrayParameterSet |
clone()
Creates a full clone (deep copy) of this
ParameterSet . |
void |
fromXML(StringBuffer representation)
Parses the instance fields of a
ParameterSet from the XML
representation as returned by ParameterSet.toXML() . |
String |
getInstanceComment()
Returns a descriptive comment on this
AlphabetContainerParameterSet.AlphabetArrayParameterSet . |
String |
getInstanceName()
Returns a descriptive name for this
AlphabetContainerParameterSet.AlphabetArrayParameterSet
. |
StringBuffer |
toXML()
This method returns an XML representation as
StringBuffer of an
instance of the implementing class. |
getNumberOfParameters, getParameterAt, hasDefaultOrIsSet, setLength
addParameterToSet, fromGalaxy, parameterRemovable, removeParameterFromSet, replaceContentWith, toGalaxy
getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getParameterForName, getParent, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, reset, setParent
public AlphabetArrayParameterSet(AlphabetContainer.AlphabetContainerType type) throws Exception
AlphabetContainerParameterSet.AlphabetArrayParameterSet
from the information
about the type
of the Alphabet
s, e.g. if the
array shall contain only the parameters for discrete Alphabet
s.type
- the type of the Alphabet
(s)Exception
- if the AlphabetContainerParameterSet.AlphabetArrayParameterSet
could not be
createdArrayParameterSet.ArrayParameterSet(ParameterSet, String,
String)
public AlphabetArrayParameterSet() throws Exception
AlphabetContainerParameterSet.AlphabetArrayParameterSet
with type
AlphabetContainer.AlphabetContainerType.BOTH
.Exception
- if the AlphabetContainerParameterSet.AlphabetArrayParameterSet
could not be
createdpublic AlphabetArrayParameterSet(StringBuffer representation) throws NonParsableException
Storable
. Creates a new AlphabetContainerParameterSet.AlphabetArrayParameterSet
out of its XML
representation.representation
- the XML representation as StringBuffer
NonParsableException
- if the AlphabetContainerParameterSet.AlphabetArrayParameterSet
could not be
reconstructed out of the XML representation (the
StringBuffer
representation
could
not be parsed)ArrayParameterSet.ArrayParameterSet(StringBuffer)
,
Storable
public AlphabetArrayParameterSet(Alphabet[] alphabets, AlphabetContainer.AlphabetContainerType type) throws Exception
AlphabetContainerParameterSet.AlphabetArrayParameterSet
from an array of
Alphabet
s and the information about the type
of
the Alphabet
s.alphabets
- the Alphabet
stype
- the type of the AlphabetContainer
Exception
- if the AlphabetContainerParameterSet.AlphabetArrayParameterSet
could not be
createdpublic AlphabetContainerParameterSet.AlphabetArrayParameterSet 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 ExpandableParameterSet
ParameterSet
CloneNotSupportedException
public StringBuffer toXML()
Storable
StringBuffer
of an
instance of the implementing class.toXML
in interface Storable
toXML
in class ArrayParameterSet
public void fromXML(StringBuffer representation) throws NonParsableException
ParameterSet
ParameterSet
from the XML
representation as returned by ParameterSet.toXML()
.fromXML
in class ArrayParameterSet
representation
- the XML representation as StringBuffer
NonParsableException
- if the XML code could not be parsedParameterSet.toXML()
public String getInstanceName()
AlphabetContainerParameterSet.AlphabetArrayParameterSet
.public String getInstanceComment()
AlphabetContainerParameterSet.AlphabetArrayParameterSet
.