public class CompSBMLDocumentPlugin extends SBMLDocumentPlugin
The CompSBMLDocumentPlugin
class inherits from the SBMLDocumentPlugin
class, and codifies the extentions to the SBMLDocument
class defined in
the SBML Level 3
'Hierarchical Model Composition'
package (&ldquocomp&rdquo). This extention allows multiple Model
objects to be defined in a single SBMLDocument
, stored in an optional
child ListOfModelDefinitions
object, as well as define references to Model
objects in other files, stored in the optional child
ListOfExternalModelDefinitions
object. These model definitions, if
present, allow Submodel
objects to reference other Models to instantiate.
The presence of ModelDefinitions and ExternalModelDefinitions in an
SBMLDocument
does not change the default Model
in the file. If a
SBMLDocument
is submitted somewhere to be simulated, it is still the
<model>
child of the <sbml>
element
that should be simulated.
In addition, as all packages do, the CompSBMLDocumentPlugin
defines a
required flag named required
, which indicates whether
&ldquocomp&rdquo constructs can be used to change the core mathematics of the
<model>
child of the <sbml>
element.
Because they can, this attribute must be set true.
Constructor and Description |
---|
CompSBMLDocumentPlugin(CompSBMLDocumentPlugin orig)
Copy constructor.
|
CompSBMLDocumentPlugin(java.lang.String uri,
java.lang.String prefix,
CompPkgNamespaces compns)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
int |
addExternalModelDefinition(ExternalModelDefinition externalModelDefinition)
Adds a copy of the given
ExternalModelDefinition object to the list of
ExternalModelDefinitions. |
int |
addModelDefinition(ModelDefinition modelDefinition)
Adds a copy of the given
ModelDefinition object to the list of
ModelDefinitions. |
SBasePlugin |
cloneObject()
Creates and returns a deep copy of this
CompSBMLDocumentPlugin object. |
ExternalModelDefinition |
createExternalModelDefinition()
Creates a
ExternalModelDefinition object, adds it to the end of the
ExternalModelDefinition objects list and returns a pointer to the newly
created object. |
ModelDefinition |
createModelDefinition()
Creates a
ModelDefinition object, adds it to the end of the
ModelDefinition objects list and returns a pointer to the newly
created object. |
void |
delete()
Explicitly deletes the underlying native object.
|
SBase |
getElementByMetaId(java.lang.String metaid)
Returns the first child element it can find with the given
metaid , or
itself if it has the given metaid , or null if no such object is
found. |
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. |
ExternalModelDefinition |
getExternalModelDefinition(long n)
Returns the
ExternalModelDefinition with the given index. |
ExternalModelDefinition |
getExternalModelDefinition(java.lang.String sid)
Returns the model definition object based on its identifier.
|
ListOfExternalModelDefinitions |
getListOfExternalModelDefinitions()
Returns the
ListOf object that holds all ExternalModelDefinitions. |
ListOfModelDefinitions |
getListOfModelDefinitions()
Returns the
ListOf object that holds all ModelDefinitions. |
SBase |
getModel(java.lang.String sid)
Searches the model namespace of the document and returns the
Model ,
ModelDefinition , or ExternalModelDefintion object with the given
identifier. |
ModelDefinition |
getModelDefinition(long n)
Returns the
ModelDefinition with the given index. |
ModelDefinition |
getModelDefinition(java.lang.String sid)
Returns the model definition object based on its identifier.
|
long |
getNumExternalModelDefinitions()
Returns the number of ExternalModelDefinitions for this
SBMLDocumentPlugin . |
long |
getNumModelDefinitions()
Returns the number of ModelDefinitions for this
SBMLDocumentPlugin . |
ExternalModelDefinition |
removeExternalModelDefinition(long index)
Removes the
ExternalModelDefinition with the given index. |
ExternalModelDefinition |
removeExternalModelDefinition(java.lang.String id)
Removes the
ExternalModelDefinition with the given id . |
ModelDefinition |
removeModelDefinition(long index)
Removes the
ModelDefinition with the given index from the CompSBMLDocumentPlugin . |
ModelDefinition |
removeModelDefinition(java.lang.String id)
|
int |
setRequired(boolean value)
Sets the boolean value of 'required' attribute of corresponding package
in
SBMLDocument element. |
getRequired, isSetRequired, unsetRequired
getElementNamespace, getLevel, getListOfAllElements, getListOfAllElements, getPackageName, getPackageVersion, getParentSBMLObject, getPrefix, getSBMLDocument, getURI, getVersion, setElementNamespace
public CompSBMLDocumentPlugin(CompSBMLDocumentPlugin orig)
CompSBMLDocumentPlugin
object.public CompSBMLDocumentPlugin(java.lang.String uri, java.lang.String prefix, CompPkgNamespaces compns)
public int addExternalModelDefinition(ExternalModelDefinition externalModelDefinition)
ExternalModelDefinition
object to the list of
ExternalModelDefinitions.
externalModelDefinition
- the ExternalModelDefinition
object to be
added to the list of ExternalModelDefinitions. Fails if the added
ExternalModelDefinition
is null
, does not match the
level/version/package of the parent object, or cannot be added to the
list of external model definitions.
public int addModelDefinition(ModelDefinition modelDefinition)
ModelDefinition
object to the list of
ModelDefinitions.
modelDefinition
- the ModelDefinition
object to be added to the
list of ModelDefinitions. Fails if the added ModelDefinition
is null
,
does not match the level/version/package of the parent object, or cannot
be added to the list of replaced elements.
public SBasePlugin cloneObject()
CompSBMLDocumentPlugin
object.
cloneObject
 in class SBMLDocumentPlugin
CompSBMLDocumentPlugin
objectpublic ExternalModelDefinition createExternalModelDefinition()
ExternalModelDefinition
object, adds it to the end of the
ExternalModelDefinition
objects list and returns a pointer to the newly
created object.
ExternalModelDefinition
objectpublic ModelDefinition createModelDefinition()
ModelDefinition
object, adds it to the end of the
ModelDefinition
objects list and returns a pointer to the newly
created object.
ModelDefinition
objectpublic 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 CompSBMLDocumentPlugin.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 CompSBMLDocumentPlugin.delete()
themselves.
delete
 in class SBMLDocumentPlugin
public SBase getElementByMetaId(java.lang.String metaid)
metaid
, or
itself if it has the given metaid
, or null
if no such object is
found.
getElementByMetaId
 in class SBasePlugin
metaid
- string representing the meta identifier of objects to find
SBase
element with the given metaid
.public SBase getElementBySId(java.lang.String id)
id
in the
model-wide SId namespace, or null
if no such object is found.
getElementBySId
 in class SBasePlugin
id
- string representing the identifier of objects to find
SBase
element with the given id
.
ModelDefinition
objects.public ExternalModelDefinition getExternalModelDefinition(long n)
ExternalModelDefinition
with the given index.
n
- the index number of the ExternalModelDefinition
to get.
ExternalModelDefinition
in the
ListOfExternalModelDefinitions
. If the index is invalid, null
is
returned.public ExternalModelDefinition getExternalModelDefinition(java.lang.String sid)
sid
- a string representing the identifier
of the model definition to get.
ExternalModelDefinition
in the ListOfExternalModelDefinitions
with the given sid
or null
if no such ExternalModelDefinition
exists.
CompSBMLDocumentPlugin.getExternalModelDefinition(long n)
,
CompSBMLDocumentPlugin.getListOfExternalModelDefinitions()
public ListOfExternalModelDefinitions getListOfExternalModelDefinitions()
ListOf
object that holds all ExternalModelDefinitions.
ListOf
object that holds all ExternalModelDefinitions.public ListOfModelDefinitions getListOfModelDefinitions()
ListOf
object that holds all ModelDefinitions.
ListOf
object that holds all ModelDefinitions.public SBase getModel(java.lang.String sid)
Model
,
ModelDefinition
, or ExternalModelDefintion object with the given
identifier.
sid
- a string representing the identifier of the model definition to get.
SBase
corresponding to the given sid
or null
if no such
model exists. If no such model exists, this will return null.
public ModelDefinition getModelDefinition(long n)
ModelDefinition
with the given index.
n
- the index number of the ModelDefinition
to get.
ModelDefinition
in the ListOfModelDefinitions
. If the
index is invalid, null
is returned.public ModelDefinition getModelDefinition(java.lang.String sid)
sid
- a string representing the identifier
of the model definition to get.
ModelDefinition
in the ListOfModelDefinitions
with the given sid
or null
if no such ModelDefinition
exists.
CompSBMLDocumentPlugin.getModelDefinition(long n)
,
CompSBMLDocumentPlugin.getListOfModelDefinitions()
public long getNumExternalModelDefinitions()
SBMLDocumentPlugin
.
SBMLDocumentPlugin
.public long getNumModelDefinitions()
SBMLDocumentPlugin
.
public ExternalModelDefinition removeExternalModelDefinition(long index)
ExternalModelDefinition
with the given index.
A pointer to the ExternalModelDefinition
that was removed is returned.
If no ExternalModelDefinition
has been removed, null
is returned.
index
- the index of the ExternalModelDefinition
object to remove
ExternalModelDefinition
object removed. As mentioned above,
the caller owns the returned object. null
is returned if
the given index is out of range.public ExternalModelDefinition removeExternalModelDefinition(java.lang.String id)
ExternalModelDefinition
with the given id
.
A pointer to the ExternalModelDefinition
that was removed is returned.
If no ExternalModelDefinition
has been removed, null
is returned.
id
- the id of the ExternalModelDefinition
object to remove
ExternalModelDefinition
object removed. As mentioned above,
the caller owns the returned object. null
is returned if
the given index is out of range.public ModelDefinition removeModelDefinition(long index)
ModelDefinition
with the given index from the CompSBMLDocumentPlugin
.
A pointer to the ModelDefinition
that was removed is returned.
If no ModelDefinition
has been removed, null
is returned.
index
- the index of the ModelDefinition
object to remove
ModelDefinition
object removed. As mentioned above,
the caller owns the returned object. null
is returned if
the given index is out of range.public ModelDefinition removeModelDefinition(java.lang.String id)
ModelDefinition
with the given id
from the CompSBMLDocumentPlugin
.
A pointer to the ModelDefinition
that was removed is returned.
If no ModelDefinition
has been removed, null
is returned.
id
- the id of the ModelDefinition
object to remove
ModelDefinition
object removed. As mentioned above,
the caller owns the returned object. null
is returned if
the given index is out of range.public int setRequired(boolean value)
Sets the boolean value of 'required' attribute of corresponding package
in SBMLDocument
element. The only legal value is 'true' for the
Hierarchical Model
Composition package.
setRequired
 in class SBMLDocumentPlugin
value
- the boolean value of 'required' attribute of corresponding
package in SBMLDocument
element.