public class FbcSBMLDocumentPlugin extends SBMLDocumentPlugin
SBMLDocument
for the &ldquofbc&rdquo package.
The FbcSBMLDocumentPlugin
class inherits from the SBMLDocumentPlugin
class, and codifies the extensions to the SBMLDocument
class defined in
the SBML Level 3 Flux Balance Constraints (&ldquofbc&rdquo) package. This
extension defines a required flag named 'required', which indicates
whether &ldquofbc&rdquo constructs can be used to change the core
mathematical interpretation of the Model
defined in the SBML input. Since
&ldquofbc&rdquo constructs cannot, this attribute must be set to the
value 'false'.
Constructor and Description |
---|
FbcSBMLDocumentPlugin(FbcSBMLDocumentPlugin orig)
Copy constructor for
FbcSBMLDocumentPlugin . |
FbcSBMLDocumentPlugin(java.lang.String uri,
java.lang.String prefix,
FbcPkgNamespaces fbcns)
Creates a new
FbcSBMLDocumentPlugin object using the given parameters. |
Modifier and Type | Method and Description |
---|---|
SBasePlugin |
cloneObject()
Creates and returns a deep copy of this
FbcSBMLDocumentPlugin object. |
void |
delete()
Explicitly deletes the underlying native object.
|
getRequired, isSetRequired, setRequired, unsetRequired
getElementByMetaId, getElementBySId, getElementNamespace, getLevel, getListOfAllElements, getListOfAllElements, getPackageName, getPackageVersion, getParentSBMLObject, getPrefix, getSBMLDocument, getURI, getVersion, isValidTypeForList, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, setElementNamespace
public FbcSBMLDocumentPlugin(java.lang.String uri, java.lang.String prefix, FbcPkgNamespaces fbcns)
FbcSBMLDocumentPlugin
object using the given parameters.
In the XML representation of an SBML document, XML namespaces are used to
identify the origin of each XML construct used. XML namespaces are
identified by their unique resource identifiers (URIs). The core SBML
specifications stipulate the namespaces that must be used for core SBML
constructs for example, all XML elements that belong to SBML Level 3
Version 1 Core must be placed in the XML namespace identified by the URI
'http://www.sbml.org/sbml/level3/version1/core'
. Individual
SBML Level 3 packages define their own XML namespaces for example,
all elements belonging to the SBML Level 3 Layout Version 1
package must be placed in the XML namespace
'http://www.sbml.org/sbml/level3/version1/layout/version1/'
.
The SBMLNamespaces
object encapsulates SBML Level/Version/namespaces
information. It is used to communicate the SBML Level, Version, and (in
Level 3) packages used in addition to SBML Level 3 Core. A
common approach to using libSBML's SBMLNamespaces
facilities is to create an
SBMLNamespaces
object somewhere in a program once, then hand that object
as needed to object constructors that accept SBMLNamespaces
as arguments.
uri
- the URI of the SBML Level 3 package implemented by
this libSBML package extension.
prefix
- the XML namespace prefix being used for the package.
fbcns
- the namespaces object for the package.public FbcSBMLDocumentPlugin(FbcSBMLDocumentPlugin orig)
FbcSBMLDocumentPlugin
.
orig
- the FbcSBMLDocumentPlugin
instance to copy.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 FbcSBMLDocumentPlugin.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 FbcSBMLDocumentPlugin.delete()
themselves.
delete
 in class SBMLDocumentPlugin
public SBasePlugin cloneObject()
FbcSBMLDocumentPlugin
object.
cloneObject
 in class SBMLDocumentPlugin
FbcSBMLDocumentPlugin
object.