Inheritance diagram for libsbmlcs.LayoutPkgNamespaces:

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

int	addNamespaces (XMLNamespaces xmlns)
	Add the given XML namespaces list to the set of namespaces within this SBMLNamespaces object. More...

int	addPackageNamespace (string pkgName, long pkgVersion, string prefix)
	Add an XML namespace (a pair of URI and prefix) of a package extension to the set of namespaces within this SBMLNamespaces object. More...

int	addPackageNamespace (string pkgName, long pkgVersion)
	Add an XML namespace (a pair of URI and prefix) of a package extension to the set of namespaces within this SBMLNamespaces object. More...

int	addPackageNamespaces (XMLNamespaces 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...

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

int	addPkgNamespace (string pkgName, long pkgVersion)

int	addPkgNamespaces (XMLNamespaces xmlns)

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

override void	Dispose ()

override bool	Equals (Object sb)

override int	GetHashCode ()

long	getLevel ()
	Get the SBML Level of this SBMLNamespaces object. More...

XMLNamespaces	getNamespaces ()
	Get the XML namespaces list for this SBMLNamespaces object. More...

new string	getPackageName ()
	Returns the name of the main package for this namespace. More...

long	getPackageVersion ()

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

long	getVersion ()
	Get the SBML Version of this SBMLNamespaces object. More...

bool	isValidCombination ()
	Predicate returning `true` if the given set of namespaces represent a valid set. More...

	LayoutPkgNamespaces (long level, long version, long pkgVersion, string prefix)

	LayoutPkgNamespaces (long level, long version, long pkgVersion)

	LayoutPkgNamespaces (long level, long version)

	LayoutPkgNamespaces (long level)

	LayoutPkgNamespaces ()

	LayoutPkgNamespaces (LayoutPkgNamespaces orig)

int	removeNamespace (string uri)
	Removes an XML namespace from the set of namespaces within this SBMLNamespaces object. More...

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

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

Static Public Member Functions
static void	freeSBMLNamespaces (SWIGTYPE_p_List supportedNS)
	Frees the list of supported namespaces as generated by getSupportedNamespaces(). More...

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

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

static bool	isSBMLNamespace (string uri)
	Predicate returning `true` if the given URL is one of SBML XML namespaces. More...

static bool	operator!= (SBMLNamespaces lhs, SBMLNamespaces rhs)

static bool	operator== (SBMLNamespaces lhs, SBMLNamespaces rhs)

Protected Attributes
bool	swigCMemOwn

Constructor & Destructor Documentation

libsbmlcs.LayoutPkgNamespaces.LayoutPkgNamespaces	(	long	level,
		long	version,
		long	pkgVersion,
		string	prefix
	)

libsbmlcs.LayoutPkgNamespaces.LayoutPkgNamespaces	(	long	level,
		long	version,
		long	pkgVersion
	)

libsbmlcs.LayoutPkgNamespaces.LayoutPkgNamespaces	(	long	level,
		long	version
	)

libsbmlcs.LayoutPkgNamespaces.LayoutPkgNamespaces ( long level )

libsbmlcs.LayoutPkgNamespaces.LayoutPkgNamespaces ( )

libsbmlcs.LayoutPkgNamespaces.LayoutPkgNamespaces ( LayoutPkgNamespaces orig )

Member Function Documentation

int libsbmlcs.SBMLNamespaces.addNamespace	(	string	uri,
		string	prefix
	)

inherited

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

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:

int libsbmlcs.SBMLNamespaces.addNamespaces ( XMLNamespaces xmlns )

inherited

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

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.

SBMLDocument sd = null;
try
{
    sd = new SBMLDocument(3, 1);
}
catch (SBMLConstructorException e)
{
    // Here, have code to handle a truly 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.
}
XMLNamespaces sn = sd.getNamespaces();
if (sn != null)
{
    sn.add('http://www.w3.org/1999/xhtml', 'html');
}
else
{
    // Handle another truly exceptional situation.
}

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:

int libsbmlcs.SBMLNamespaces.addPackageNamespace	(	string	pkgName,
		long	pkgVersion,
		string	prefix
	)

inherited

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

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()

int libsbmlcs.SBMLNamespaces.addPackageNamespace	(	string	pkgName,
		long	pkgVersion
	)

inherited

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

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()

int libsbmlcs.SBMLNamespaces.addPackageNamespaces ( XMLNamespaces 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).

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 null.

int libsbmlcs.SBMLNamespaces.addPkgNamespace	(	string	pkgName,
		long	pkgVersion,
		string	prefix
	)

inherited

int libsbmlcs.SBMLNamespaces.addPkgNamespace	(	string	pkgName,
		long	pkgVersion
	)

inherited

int libsbmlcs.SBMLNamespaces.addPkgNamespaces ( XMLNamespaces xmlns )

inherited

new SBMLNamespaces libsbmlcs.LayoutPkgNamespaces.clone ( )

Creates and returns a deep copy of this SBMLNamespaces object.

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

override void libsbmlcs.LayoutPkgNamespaces.Dispose ( )

virtual

Reimplemented from libsbmlcs.SBMLNamespaces.

override bool libsbmlcs.SBMLNamespaces.Equals ( Object sb )

inherited

static void libsbmlcs.SBMLNamespaces.freeSBMLNamespaces ( SWIGTYPE_p_List supportedNS )

staticinherited

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

Parameters

supportedNS the list to be freed.

override int libsbmlcs.SBMLNamespaces.GetHashCode ( )

inherited

long libsbmlcs.SBMLNamespaces.getLevel ( )

inherited

Get the SBML Level of this SBMLNamespaces object.

Returns: the SBML Level of this SBMLNamespaces object.

XMLNamespaces libsbmlcs.SBMLNamespaces.getNamespaces ( )

inherited

Get the XML namespaces list for this SBMLNamespaces object.

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.

new string libsbmlcs.LayoutPkgNamespaces.getPackageName ( )

Returns the name of the main package for this namespace.

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

long libsbmlcs.LayoutPkgNamespaces.getPackageVersion ( )

static string libsbmlcs.SBMLNamespaces.getSBMLNamespaceURI	(	long	level,
		long	version
	)

staticinherited

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

Parameters

level	the SBML level.
version	the SBML version.

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

static SBMLNamespacesList libsbmlcs.SBMLNamespaces.getSupportedNamespaces ( )

staticinherited

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

Returns: a list with supported SBML namespaces.

new string libsbmlcs.LayoutPkgNamespaces.getURI ( )

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

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

long libsbmlcs.SBMLNamespaces.getVersion ( )

inherited

Get the SBML Version of this SBMLNamespaces object.

Returns: the SBML Version of this SBMLNamespaces object.

static bool libsbmlcs.SBMLNamespaces.isSBMLNamespace ( string uri )

staticinherited

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

Parameters

uri	the URI of namespace.

Returns: true if the 'uri' is one of SBML namespaces, false otherwise.

bool libsbmlcs.SBMLNamespaces.isValidCombination ( )

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.

static bool libsbmlcs.SBMLNamespaces.operator!=	(	SBMLNamespaces	lhs,
		SBMLNamespaces	rhs
	)

staticinherited

static bool libsbmlcs.SBMLNamespaces.operator==	(	SBMLNamespaces	lhs,
		SBMLNamespaces	rhs
	)

staticinherited

int libsbmlcs.SBMLNamespaces.removeNamespace ( string uri )

inherited

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

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:

int libsbmlcs.SBMLNamespaces.removePackageNamespace	(	long	level,
		long	version,
		string	pkgName,
		long	pkgVersion
	)

inherited

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

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:

int libsbmlcs.SBMLNamespaces.removePkgNamespace	(	long	level,
		long	version,
		string	pkgName,
		long	pkgVersion
	)

inherited

Member Data Documentation

bool libsbmlcs.SBMLNamespaces.swigCMemOwn

protectedinherited

Detailed Description

Basic principles of SBML package extensions in libSBML

Public Member Functions

Static Public Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation