public static class AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet extends ExpandableParameterSet
Alphabet
s where each
Alphabet
may be used for one or more sections of positions.ParameterSet.ParameterList
commentTemplate, nameTemplate, template
errorMessage, parameters, parent
Constructor and Description |
---|
SectionDefinedAlphabetParameterSet()
Creates a new
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet for a set of
discrete and continuous Alphabet s. |
SectionDefinedAlphabetParameterSet(Alphabet[] alphabets,
int[] indexes)
Creates a new
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet from an
array of Alphabet s and an array of indexes that define the
index of the Alphabet in alphabets belonging to
that position in indexes . |
SectionDefinedAlphabetParameterSet(AlphabetContainer.AlphabetContainerType type)
Creates a new
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet for a set of
discrete or continuous Alphabet s. |
SectionDefinedAlphabetParameterSet(StringBuffer representation)
The standard constructor for the interface
Storable
. |
Modifier and Type | Method and Description |
---|---|
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet |
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.SectionDefinedAlphabetParameterSet . |
String |
getInstanceName()
Returns a descriptive name for this
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet . |
boolean |
hasDefaultOrIsSet()
Returns
true if all parameters in this ParameterSet
are either set by the user or have default values. |
static LinkedList<Integer> |
parseSections(String sections)
|
StringBuffer |
toXML()
This method returns an XML representation as
StringBuffer of an
instance of the implementing class. |
addParameterToSet, fromGalaxy, parameterRemovable, removeParameterFromSet, replaceContentWith, toGalaxy
getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getNumberOfParameters, getParameterAt, getParameterForName, getParent, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, reset, setParent
public SectionDefinedAlphabetParameterSet(AlphabetContainer.AlphabetContainerType type) throws Exception
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
for a set of
discrete or continuous Alphabet
s.type
- the type of the Alphabet
(s)Exception
- if the AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
could
not be createdExpandableParameterSet.ExpandableParameterSet(ParameterSet,
String, String)
public SectionDefinedAlphabetParameterSet() throws Exception
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
for a set of
discrete and continuous Alphabet
s.Exception
- if the AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
could
not be createdpublic SectionDefinedAlphabetParameterSet(Alphabet[] alphabets, int[] indexes) throws Exception
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
from an
array of Alphabet
s and an array of indexes that define the
index of the Alphabet
in alphabets
belonging to
that position in indexes
.alphabets
- the array of Alphabet
sindexes
- the array of indexes of the Alphabet
s belonging to
the positionsException
- if the AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
could
not be createdpublic SectionDefinedAlphabetParameterSet(StringBuffer representation) throws NonParsableException
Storable
. Creates a new AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
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)ExpandableParameterSet.ExpandableParameterSet(StringBuffer)
,
Storable
public StringBuffer toXML()
Storable
StringBuffer
of an
instance of the implementing class.toXML
in interface Storable
toXML
in class ExpandableParameterSet
public void fromXML(StringBuffer representation) throws NonParsableException
ParameterSet
ParameterSet
from the XML
representation as returned by ParameterSet.toXML()
.fromXML
in class ExpandableParameterSet
representation
- the XML representation as StringBuffer
NonParsableException
- if the XML code could not be parsedParameterSet.toXML()
public boolean hasDefaultOrIsSet()
ParameterSet
true
if all parameters in this ParameterSet
are either set by the user or have default values. If any additional
constraints are required on your parameters you should either specify
some ParameterValidator
on these parameters or implement these
constraints by overriding this method in your implementation of
ParameterSet
. It is recommended to specify a useful remark which
constraint failed in the member-variable errorMessage
, which
will be displayed to the user. In the overriding method
super.
ParameterSet.hasDefaultOrIsSet()
should be called prior to
checking specific constraints.hasDefaultOrIsSet
in class ParameterSet
true
if all parameters have some allowed value set,
false
otherwisepublic static LinkedList<Integer> parseSections(String sections) throws Exception
sections
to a
LinkedList
of Integer
s. Sections may be defined
as ranges (e.g. "3-6"), as lists (e.g. "3,4,5,6")
or as combinations of both (e.g. "3-5,6").sections
- the sectionsLinkedList
of positionsException
- if sections
could not be parsed, contains a
position more than once or contains positions that are
out of rangepublic AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet 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 String getInstanceName()
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
.public String getInstanceComment()
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
.