public class ListOfModelDefinitions extends ListOf
The ListOfModelDefinitions
is a container for the extended
SBMLDocument
that allows one to define multiple Models in a single file
for use in Submodel
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):
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'.
ListOfFunctionDefinitions
,
ListOfUnitDefinitions
,
ListOfCompartmentTypes
,
ListOfSpeciesTypes
,
ListOfCompartments
,
ListOfSpecies
,
ListOfParameters
,
ListOfInitialAssignments
,
ListOfRules
,
ListOfConstraints
,
ListOfReactions
,
,
ModelDefinition
,
ListOfDeletions
,
ListOfExternalModelDefinitions
,
ListOfPorts
,
ListOfReplacedElements
,
ListOfSubmodels
Constructor and Description |
---|
ListOfModelDefinitions()
Creates a new
ListOfModelDefinitions with the given level, version, and
package version. |
ListOfModelDefinitions(CompPkgNamespaces compns)
Creates a new
ListOfModelDefinitions with the given CompPkgNamespaces
object. |
ListOfModelDefinitions(long level)
Creates a new
ListOfModelDefinitions with the given level, version, and
package version. |
ListOfModelDefinitions(long level,
long version)
Creates a new
ListOfModelDefinitions with the given level, version, and
package version. |
ListOfModelDefinitions(long level,
long version,
long pkgVersion)
Creates a new
ListOfModelDefinitions with the given level, version, and
package version. |
Modifier and Type | Method and Description |
---|---|
ListOfModelDefinitions |
cloneObject()
Creates and returns a deep copy of this
ListOfModelDefinitions object. |
void |
delete()
Explicitly deletes the underlying native object.
|
SBase |
get(long n)
Get a
ModelDefinition from the ListOfModelDefinitions . |
ModelDefinition |
get(java.lang.String sid)
Get a
Model from the ListOfModelDefinitions
based on its identifier. |
java.lang.String |
getElementName()
Returns the XML element name of
this SBML object.
|
int |
getItemTypeCode()
Returns the libSBML type code for the objects contained in this
ListOf
(i.e., ModelDefinition objects, if the list is non-empty). |
SBase |
remove(long n)
Removes the nth item from this
ListOfModelDefinitions items and returns
a pointer to it. |
ModelDefinition |
remove(java.lang.String sid)
Removes the item with given identifer from this
ListOfModelDefinitions
items and returns a pointer to it. |
append, appendAndOwn, appendFrom, clear, clear, getElementByMetaId, getElementBySId, getTypeCode, insert, insertAndOwn, removeFromParentAndDelete, size
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isSetAnnotation, isSetMetaId, isSetModelHistory, isSetNotes, isSetSBOTerm, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetId, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm
public ListOfModelDefinitions() throws SBMLConstructorException
ListOfModelDefinitions
with the given level, version, and
package version.
level
- the SBML Levelversion
- the Version within the SBML LevelpkgVersion
- the version of the packageSBMLConstructorException
public ListOfModelDefinitions(CompPkgNamespaces compns) throws SBMLConstructorException
ListOfModelDefinitions
with the given CompPkgNamespaces
object.SBMLConstructorException
public ListOfModelDefinitions(long level) throws SBMLConstructorException
ListOfModelDefinitions
with the given level, version, and
package version.
level
- the SBML Levelversion
- the Version within the SBML LevelpkgVersion
- the version of the packageSBMLConstructorException
public ListOfModelDefinitions(long level, long version) throws SBMLConstructorException
ListOfModelDefinitions
with the given level, version, and
package version.
level
- the SBML Levelversion
- the Version within the SBML LevelpkgVersion
- the version of the packageSBMLConstructorException
public ListOfModelDefinitions(long level, long version, long pkgVersion) throws SBMLConstructorException
ListOfModelDefinitions
with the given level, version, and
package version.
level
- the SBML Levelversion
- the Version within the SBML LevelpkgVersion
- the version of the packageSBMLConstructorException
public ListOfModelDefinitions cloneObject()
ListOfModelDefinitions
object.
cloneObject
 in class ListOf
ListOfModelDefinitions
.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 ListOfModelDefinitions.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 ListOfModelDefinitions.delete()
themselves.
public SBase get(long n)
ModelDefinition
from the ListOfModelDefinitions
.
get
 in class ListOf
n
- the index number of the ModelDefinition
to get.
ModelDefinition
in this ListOfModelDefinitions
.
ListOf.size()
public ModelDefinition get(java.lang.String sid)
Model
from the ListOfModelDefinitions
based on its identifier.
sid
- a string representing the identifier
of the Model
to get.
Model
in this ListOfModelDefinitions
with the given sid
or null
if no such
Member exists.
ListOfModelDefinitions.get(long n)
,
ListOf.size()
public java.lang.String getElementName()
getElementName
 in class ListOf
public int getItemTypeCode()
ListOf
(i.e., ModelDefinition
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 &ldquoSBML_
&rdquo.
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 getPackageName()
method on the object.
getItemTypeCode
 in class ListOf
SBML_COMP_MODELDEFINITION
(default).
ListOfModelDefinitions.getElementName()
,
SBase.getPackageName()
public SBase remove(long n)
ListOfModelDefinitions
items and returns
a pointer to it.
The caller owns the returned item and is responsible for deleting it.
remove
 in class ListOf
n
- the index of the item to remove
ListOf.size()
public ModelDefinition remove(java.lang.String sid)
ListOfModelDefinitions
items and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
sid
- the id of the item to remove
ListOf.size()