public class ListOfLocalParameters extends ListOfParameters
LocalParameter
objects.
The various ListOf___ classes in SBML
are merely containers used for organizing the main components of an SBML
model. In libSBML's implementation, ListOf___
classes are derived from the
intermediate utility class ListOf
, which
is not defined by the SBML specifications but serves as a useful
programmatic construct. ListOf
is itself is in turn derived from SBase
,
which provides all of the various ListOf___
classes with common features
defined by the SBML specification, such as 'metaid' attributes and
annotations.
The relationship between the lists and the rest of an SBML model is illustrated by the following (for SBML Level 2 Version 4):
SBML Level 3 Version 1 has essentially the same structure as Level 2 Version 4, depicted above, but SBML Level 3 Version 2 allows containers to contain zero or more of the relevant object, instead of requiring at least one. As such, libsbml will write out an otherwise-empty ListOf___ element that has any optional attribute set (such as 'id' or 'metaid'), that has an optional child (such as a 'notes' or 'annotation'), or that has attributes or children set from any SBML Level 3 package, whether or not the ListOf___ has any other children.
Readers may wonder about the motivations for using the ListOf___
containers in SBML. A simpler approach in XML might be to place the
components all directly at the top level of the model definition. The
choice made in SBML is to group them within XML elements named after
ListOfClassname, in part because it helps organize the
components. More importantly, the fact that the container classes are
derived from SBase
means that software tools can add information about
the lists themselves into each list container's 'annotation'.
Constructor and Description |
---|
ListOfLocalParameters(long level,
long version)
Creates a new
ListOfLocalParameters object. |
ListOfLocalParameters(SBMLNamespaces sbmlns)
Creates a new
ListOfLocalParameters object. |
Modifier and Type | Method and Description |
---|---|
ListOfLocalParameters |
cloneObject()
Creates and returns a deep copy of this
ListOfLocalParameters object. |
void |
delete()
Explicitly deletes the underlying native object.
|
LocalParameter |
get(long n)
|
LocalParameter |
get(java.lang.String sid)
Returns the first
LocalParameter object matching the given identifier. |
SBase |
getElementBySId(java.lang.String id)
Returns the first child element found that has the given
id in the
model-wide SId namespace, or null if no such object is found. |
java.lang.String |
getElementName()
Returns the XML element name of this object.
|
int |
getItemTypeCode()
Returns the libSBML type code for the objects contained in this
ListOf
(i.e., LocalParameter objects, if the list is non-empty). |
LocalParameter |
remove(long n)
Removes the nth item from this
ListOfLocalParameters , and returns a
pointer to it. |
LocalParameter |
remove(java.lang.String sid)
Removes the first
LocalParameter object in this ListOfLocalParameters
matching the given identifier, and returns a pointer to it. |
append, appendAndOwn, appendFrom, clear, clear, connectToChild, getElementByMetaId, getTypeCode, insert, insertAndOwn, removeFromParentAndDelete, size
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, deleteDisabledPlugins, deleteDisabledPlugins, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getDisabledPlugin, getId, getIdAttribute, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getName, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumDisabledPlugins, getNumPlugins, getPackageCoreVersion, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetId, isSetIdAttribute, isSetMetaId, isSetModelHistory, isSetName, isSetNotes, isSetSBOTerm, isSetUserData, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setId, setIdAttribute, setMetaId, setModelHistory, setName, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetId, unsetIdAttribute, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm, unsetUserData
public ListOfLocalParameters(long level, long version) throws SBMLConstructorException
ListOfLocalParameters
object.
The object is constructed such that it is valid for the given SBML Level and Version combination.
level
- the SBML Level.
version
- the Version within the SBML Level.
SBMLConstructorException
- Thrown if the given level
and version
combination are invalid
or if this object is incompatible with the given level and version.
SBMLDocument
having a different
combination of SBML Level, Version and XML namespaces than the object
itself will result in an error at the time a caller attempts to make the
addition. A parent object must have compatible Level, Version and XML
namespaces. (Strictly speaking, a parent may also have more XML
namespaces than a child, but the reverse is not permitted.) The
restriction is necessary to ensure that an SBML model has a consistent
overall structure. This requires callers to manage their objects
carefully, but the benefit is increased flexibility in how models can be
created by permitting callers to create objects bottom-up if desired. In
situations where objects are not yet attached to parents (e.g.,
SBMLDocument
), knowledge of the intented SBML Level and Version help
libSBML determine such things as whether it is valid to assign a
particular value to an attribute.public ListOfLocalParameters(SBMLNamespaces sbmlns) throws SBMLConstructorException
ListOfLocalParameters
object.
The object is constructed such that it is valid for the SBML Level and
Version combination determined by the SBMLNamespaces
object in
sbmlns
.
sbmlns
- an SBMLNamespaces
object that is used to determine the
characteristics of the ListOfLocalParameters
object to be created.
SBMLConstructorException
- Thrown if the given sbmlns
is inconsistent or incompatible
with this object.
SBMLDocument
having a different
combination of SBML Level, Version and XML namespaces than the object
itself will result in an error at the time a caller attempts to make the
addition. A parent object must have compatible Level, Version and XML
namespaces. (Strictly speaking, a parent may also have more XML
namespaces than a child, but the reverse is not permitted.) The
restriction is necessary to ensure that an SBML model has a consistent
overall structure. This requires callers to manage their objects
carefully, but the benefit is increased flexibility in how models can be
created by permitting callers to create objects bottom-up if desired. In
situations where objects are not yet attached to parents (e.g.,
SBMLDocument
), knowledge of the intented SBML Level and Version help
libSBML determine such things as whether it is valid to assign a
particular value to an attribute.public void delete()
In general, application software will not need to call this method directly. The Java language binding for libSBML is implemented as a language wrapper that provides a Java interface to libSBML's underlying C++/C code. Some of the Java methods return objects that are linked to objects created not by Java code, but by C++ code. The Java objects wrapped around them will be deleted when the garbage collector invokes the corresponding C++ finalize()
methods for the objects. The finalize()
methods in turn call the ListOfLocalParameters.delete()
method on the libSBML object.
This method is exposed in case calling programs want to ensure that the underlying object is freed immediately, and not at some arbitrary time determined by the Java garbage collector. In normal usage, callers do not need to invoke ListOfLocalParameters.delete()
themselves.
delete
 in class ListOfParameters
public ListOfLocalParameters cloneObject()
ListOfLocalParameters
object.
cloneObject
 in class ListOfParameters
ListOfLocalParameters
object.public int getItemTypeCode()
ListOf
(i.e., LocalParameter
objects, if the list is non-empty).
LibSBML attaches an identifying code to every kind of SBML object. These
are integer constants known as SBML type codes. The names of all
the codes begin with the characters SBML_
.
In the Java language interface for libSBML, the
type codes are defined as static integer constants in the interface class
libsbmlConstants
. Note that different Level 3
package plug-ins may use overlapping type codes to identify the package
to which a given object belongs, call the
method on the object.
SBase.getPackageName()
getItemTypeCode
 in class ListOfParameters
SBML_LOCAL_PARAMETER
(default).
ListOfLocalParameters.getElementName()
,
SBase.getPackageName()
public java.lang.String getElementName()
For ListOfLocalParameters
, the XML element name is 'listOfLocalParameters'.
getElementName
 in class ListOfParameters
'listOfLocalParameters'.
public LocalParameter get(long n)
get
 in class ListOfParameters
n
- the index number of the LocalParameter
to get.
LocalParameter
in this ListOfLocalParameters
. If the
index n
is out of bounds for the length of the list, then null
is returned.
ListOf.size()
,
ListOfLocalParameters.get(String sid)
public LocalParameter get(java.lang.String sid)
LocalParameter
object matching the given identifier.
get
 in class ListOfParameters
sid
- a string, the identifier of the LocalParameter
to get.
LocalParameter
object found. The caller owns the returned
object and is responsible for deleting it. If none of the items have
an identifier matching sid
, then null
is returned.
ListOfLocalParameters.get(long n)
,
ListOf.size()
public SBase getElementBySId(java.lang.String id)
id
in the
model-wide SId namespace, or null
if no such object is found.
Note that LocalParameters, while they use the SId namespace, are not in
the model-wide SId namespace, so no LocalParameter
object will be
returned from this function (and is the reason we override the base
ListOf.getElementBySId function here).
getElementBySId
 in class ListOf
id
- string representing the id of the object to find.
id
.public LocalParameter remove(long n)
ListOfLocalParameters
, and returns a
pointer to it.
remove
 in class ListOfParameters
n
- the index of the item to remove.
n
is out of
bounds for the length of the list, then null
is returned.
ListOf.size()
,
ListOfLocalParameters.remove(String sid)
public LocalParameter remove(java.lang.String sid)
LocalParameter
object in this ListOfLocalParameters
matching the given identifier, and returns a pointer to it.
remove
 in class ListOfParameters
sid
- the identifier of the item to remove.
sid
, then null
is returned.