Inheritance diagram for libsbml.RenderPkgNamespaces:

Detailed Description

Set of SBML Level + Version + namespace triples.

This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.

SBMLExtensionNamespaces is a template class. It is extended from SBMLNamespaces and is meant to be used by package extensions to store the SBML Level, Version within a Level, and package version of the SBML Level 3 package implemented by a libSBML package extension.

Basic principles of SBML package extensions in libSBML

: SBML Level 3's package structure permits modular extensions to the core SBML format. In libSBML, support for SBML Level 3 packages is provided through optional package extensions that can be plugged into libSBML at the time it is built/compiled. Users of libSBML can thus choose which extensions are enabled in their software applications.

LibSBML defines a number of classes that developers of package extensions can use to implement support for an SBML Level 3 package. These classes make it easier to extend libSBML objects with new attributes and/or subobjects as needed by a particular Level 3 package. Three overall categories of classes make up libSBML's facilities for implementing package extensions. There are (1) classes that serve as base classes meant to be subclassed, (2) template classes meant to be instantiated rather than subclassed, and (3) support classes that provide utility features. A given package implementation for libSBML will take the form of code using these and other libSBML classes, placed in a subdirectory of src/sbml/packages/.

The basic libSBML distribution includes a number of package extensions implementing support for officially-endorsed SBML Level 3 packages; among these are Flux Balance Constraints ('fbc'), Hierarchical Model Composition ('comp'), Layout ('layout'), and Qualitative Models ('qual'). They can serve as working examples for developers working to implement other packages.

Extensions in libSBML can currently only be implemented in C++ or C; there is no mechanism to implement them first in languages such as Java or Python. However, once implemented in C++ or C, language interfaces can be generated semi-automatically using the framework in place in libSBML. (The approach is based on using SWIG and facilities in libSBML's build system.)

Public Member Functions
def	__init__ (self, args)

def	addNamespace (self, uri, prefix)
	Add an XML namespace (a pair of URI and prefix) to the set of namespaces within this SBMLNamespaces object. More...

def	addNamespaces (self, xmlns)
	Add the given XML namespaces list to the set of namespaces within this SBMLNamespaces object. More...

def	addPackageNamespace (self, args)
	Add an XML namespace (a pair of URI and prefix) of a package extension to the set of namespaces within this SBMLNamespaces object. More...

def	addPackageNamespaces (self, xmlns)
	Add the XML namespaces of package extensions in the given XMLNamespace object to the set of namespaces within this SBMLNamespaces object (Non-package XML namespaces are not added by this function). More...

def	clone (self)
	Creates and returns a deep copy of this SBMLNamespaces object. More...

def	freeSBMLNamespaces (supportedNS)
	Frees the list of supported namespaces as generated by getSupportedNamespaces(). More...

def	getLevel (self, args)
	Get the SBML Level of this SBMLNamespaces object. More...

def	getNamespaces (self, args)
	Get the XML namespaces list for this SBMLNamespaces object. More...

def	getPackageName (self)
	Returns the name of the main package for this namespace. More...

def	getPackageVersion (self)

def	getSBMLNamespaceURI (level, version)
	Returns a string representing the SBML XML namespace for the given `level` and `version` of SBML. More...

def	getSupportedNamespaces ()
	Returns a list of all supported SBMLNamespaces in this version of libsbml. More...

def	getURI (self)
	Returns a string representing the SBML XML namespace of this object. More...

def	getVersion (self, args)
	Get the SBML Version of this SBMLNamespaces object. More...

def	isSBMLNamespace (uri)
	Predicate returning `True` if the given URL is one of SBML XML namespaces. More...

def	isValidCombination (self)
	Predicate returning `True` if the given set of namespaces represent a valid set. More...

def	removeNamespace (self, uri)
	Removes an XML namespace from the set of namespaces within this SBMLNamespaces object. More...

def	removePackageNamespace (self, level, version, pkgName, pkgVersion)
	Removes an XML namespace of a package extension from the set of namespaces within this SBMLNamespaces object. More...

Member Function Documentation

def libsbml.SBMLNamespaces.addNamespace	(	self,
		uri,
		prefix
	)

inherited

Add an XML namespace (a pair of URI and prefix) to the set of namespaces within this SBMLNamespaces object.

addNamespace(string uri, string prefix)   int

Parameters

uri	the XML namespace to be added.
prefix	the prefix of the namespace to be added.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

def libsbml.SBMLNamespaces.addNamespaces	(	self,
		xmlns
	)

inherited

Add the given XML namespaces list to the set of namespaces within this SBMLNamespaces object.

addNamespaces(XMLNamespaces xmlns)   int

The following code gives an example of how one could add the XHTML namespace to the list of namespaces recorded by the top-level <sbml> element of a model. It gives the new namespace a prefix of html.

 sbmlDoc = None
 try:
   sbmlDoc = SBMLDocument(3, 1)
 except ValueError:
   # Do something to handle exceptional situation.  Candidate
   # causes include invalid combinations of SBML Level and Version
   # (impossible if hardwired as given here), running out of memory, and
   # unknown system exceptions.
 
 namespaces = sbmlDoc.getNamespaces()
 if namespaces == None:
   # Do something to handle case of no namespaces.
 
 status = namespaces.add('http://www.w3.org/1999/xhtml', 'html')
 if status != LIBSBML_OPERATION_SUCCESS:
   # Do something to handle failure.

Parameters

xmlns the XML namespaces to be added.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

def libsbml.SBMLNamespaces.addPackageNamespace	(	self,
		args
	)

inherited

Add an XML namespace (a pair of URI and prefix) of a package extension to the set of namespaces within this SBMLNamespaces object.

addPackageNamespace(string pkgName, long  pkgVersion, string prefix)   int
addPackageNamespace(string pkgName, long  pkgVersion)   int

The SBML Level and SBML Version of this object is used.

Parameters

pkgName	the string of package name (e.g. 'layout', 'multi').
pkgVersion	the package version.
prefix	the prefix of the package namespace to be added. The package's name will be used if the given string is empty (default).

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

Note: An XML namespace of a non-registered package extension can't be added by this function (LIBSBML_INVALID_ATTRIBUTE_VALUE will be returned).

See also: addNamespace()

Note: Owing to the way that language interfaces are created in libSBML, this documentation may show methods that define default values for parameters with text that has the form parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.

def libsbml.SBMLNamespaces.addPackageNamespaces	(	self,
		xmlns
	)

inherited

Add the XML namespaces of package extensions in the given XMLNamespace object to the set of namespaces within this SBMLNamespaces object (Non-package XML namespaces are not added by this function).

addPackageNamespaces(XMLNamespaces xmlns)   int

Parameters

xmlns the XML namespaces to be added.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

Note: XML namespaces of a non-registered package extensions are not added (just ignored) by this function. LIBSBML_INVALID_ATTRIBUTE_VALUE will be returned if the given xmlns is None.

def libsbml.RenderPkgNamespaces.clone ( self )

Creates and returns a deep copy of this SBMLNamespaces object.

clone()   ISBMLExtensionNamespaces

Returns: the (deep) copy of this SBMLNamespaces object.

def libsbml.SBMLNamespaces.freeSBMLNamespaces ( supportedNS )

inherited

Frees the list of supported namespaces as generated by getSupportedNamespaces().

freeSBMLNamespaces(List * supportedNS)

Parameters

supportedNS the list to be freed.

Note: Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.

def libsbml.SBMLNamespaces.getLevel	(	self,
		args
	)

inherited

Get the SBML Level of this SBMLNamespaces object.

getLevel()   long

Returns: the SBML Level of this SBMLNamespaces object.

def libsbml.SBMLNamespaces.getNamespaces	(	self,
		args
	)

inherited

Get the XML namespaces list for this SBMLNamespaces object.

getNamespaces()   XMLNamespaces

: SBMLNamespaces objects are used in libSBML to communicate SBML Level and Version data between constructors and other methods. The SBMLNamespaces object class holds triples consisting of SBML Level, Version, and the corresponding SBML XML namespace. Most constructors for SBML objects in libSBML take a SBMLNamespaces object as an argument, thereby allowing the constructor to produce the proper combination of attributes and other internal data structures for the given SBML Level and Version.

The plural name (SBMLNamespaces) is not a mistake, because in SBML Level 3, objects may have extensions added by Level 3 packages used by a given model and therefore may have multiple namespaces associated with them. In SBML Levels below Level 3, the SBMLNamespaces object only records one SBML Level/Version/namespace combination at a time. Most constructors for SBML objects in libSBML take a SBMLNamespaces object as an argument, thereby allowing the constructor to produce the proper combination of attributes and other internal data structures for the given SBML Level and Version.

Returns: the XML namespaces of this SBMLNamespaces object.

def libsbml.RenderPkgNamespaces.getPackageName ( self )

Returns the name of the main package for this namespace.

getPackageName()   string

Returns: the name of the main package for this namespace. 'core' will be returned if this namespace is defined in the SBML core.

def libsbml.RenderPkgNamespaces.getPackageVersion ( self )

getPackageVersion()   long

def libsbml.SBMLNamespaces.getSBMLNamespaceURI	(	level,
		version
	)

inherited

Returns a string representing the SBML XML namespace for the given level and version of SBML.

getSBMLNamespaceURI(long  level, long  version)   string

Parameters

level	the SBML level.
version	the SBML version.

Returns: a string representing the SBML namespace that reflects the SBML Level and Version specified.

Note: Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.

def libsbml.SBMLNamespaces.getSupportedNamespaces ( )

inherited

Returns a list of all supported SBMLNamespaces in this version of libsbml.

getSupportedNamespaces()   List  *

Returns: a list with supported SBML namespaces.

Note: Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.

def libsbml.RenderPkgNamespaces.getURI ( self )

Returns a string representing the SBML XML namespace of this object.

getURI()   string

Returns: a string representing the SBML namespace that reflects the SBML Level and Version of this object.

def libsbml.SBMLNamespaces.getVersion	(	self,
		args
	)

inherited

Get the SBML Version of this SBMLNamespaces object.

getVersion()   long

Returns: the SBML Version of this SBMLNamespaces object.

def libsbml.SBMLNamespaces.isSBMLNamespace ( uri )

inherited

Predicate returning True if the given URL is one of SBML XML namespaces.

isSBMLNamespace(string uri)   bool

Parameters

uri	the URI of namespace.

Returns: True if the 'uri' is one of SBML namespaces, False otherwise.

Note: Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.

def libsbml.SBMLNamespaces.isValidCombination ( self )

inherited

Predicate returning True if the given set of namespaces represent a valid set.

Returns: True if the set of namespaces is valid, False otherwise.

isValidCombination()   bool

def libsbml.SBMLNamespaces.removeNamespace	(	self,
		uri
	)

inherited

Removes an XML namespace from the set of namespaces within this SBMLNamespaces object.

removeNamespace(string uri)   int

Parameters

uri	the XML namespace to be added.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

def libsbml.SBMLNamespaces.removePackageNamespace	(	self,
		level,
		version,
		pkgName,
		pkgVersion
	)

inherited

Removes an XML namespace of a package extension from the set of namespaces within this SBMLNamespaces object.

removePackageNamespace(long  level, long  version, string pkgName, long  pkgVersion)   int

Parameters

level	the SBML level.
version	the SBML version.
pkgName	the string of package name (e.g. 'layout', 'multi').
pkgVersion	the package version.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

Detailed Description

Basic principles of SBML package extensions in libSBML

Public Member Functions

Member Function Documentation