SBMLExtensionNamespaces< SBMLExtensionType > Class Template Reference

Inheritance diagram for SBMLExtensionNamespaces< SBMLExtensionType >:

Detailed Description

template<class SBMLExtensionType>
class SBMLExtensionNamespaces< SBMLExtensionType >

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.

How to use SBMLExtensionNamespaces for a package implementation

Each package extension in libSBML needs to extend and instantiate the template class SBMLExtensionNamespaces, as well as declare a specific typedef. The following sections explain these steps in detail.

1. Define the typedef

Each package needs to declare a package-specific version of the SBMLExtensionNamespaces class using a typedef. The following example code demonstrates how this is done in the case of the Layout package:

typedef SBMLExtensionNamespaces<LayoutExtension> LayoutPkgNamespaces;

This creates a new type called LayoutPkgNamespaces. The code above is usually placed in the same file that contains the SBMLExtension-derived definition of the package extension base class. In the case of the Layout package, this is in the file src/packages/layout/extension/LayoutExtension.h in the libSBML source distribution.

2. Instantiate a template instance

Each package needs to instantiate a template instance of the SBMLExtensionNamespaces class. The following example code demonstrates how this is done in the case of the Layout package:

template class LIBSBML_EXTERN SBMLExtensionNamespaces<LayoutExtension>;

In the case of the Layout package, the code above is located in the file src/packages/layout/extension/LayoutExtension.cpp in the libSBML source distribution.

3. Create constructors that accept the class

Each SBase-derived class in the package extension should implement a constructor that accepts the SBMLExtensionNamespaces-derived class as an argument. For example, in the Layout package, the class BoundBox has a constructor declared as follows

BoundingBox(LayoutPkgNamespaces* layoutns);

The implementation of this constructor must, among other things, take the argument namespace object and use it to set the XML namespace URI for the object. Again, for the BoundingBox example:

BoundingBox::BoundingBox(LayoutPkgNamespaces* layoutns)
 : SBase(layoutns)
  ,mPosition(layoutns)
  ,mDimensions(layoutns)
  ,mPositionExplicitlySet (false)
  ,mDimensionsExplicitlySet (false)
{
  // Standard extension actions.
  setElementNamespace(layoutns->getURI());
  connectToChild();
 
  // Package-specific actions.
  mPosition.setElementName("position");
 
  // Load package extensions bound with this object (if any).
  loadPlugins(layoutns);
}

Public Member Functions
int	addNamespace (const std::string &uri, const std::string &prefix)
	Add an XML namespace (a pair of URI and prefix) to the set of namespaces within this SBMLNamespaces object. More...
int	addNamespaces (const XMLNamespaces *xmlns)
	Add the given XML namespaces list to the set of namespaces within this SBMLNamespaces object. More...
int	addPackageNamespace (const std::string &pkgName, unsigned int pkgVersion, const std::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	addPackageNamespaces (const 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...
virtual ISBMLExtensionNamespaces *	clone () const
	Creates and returns a deep copy of this SBMLExtensionNamespaces object. More...
unsigned int	getLevel ()
	Get the SBML Level of this SBMLNamespaces object. More...
unsigned int	getLevel () const
	Get the SBML Level of this SBMLNamespaces object. More...
XMLNamespaces *	getNamespaces ()
	Get the XML namespaces list for this SBMLNamespaces object. More...
const XMLNamespaces *	getNamespaces () const
	Get the XML namespaces list for this SBMLNamespaces object. More...
virtual const std::string &	getPackageName () const
	Returns the name of the SBML package represented by this namespace object. More...
unsigned int	getPackageVersion () const
	Returns the version of the SBML package represented by this namespace object. More...
virtual std::string	getURI () const
	Returns a string representing the SBML XML namespace of this package. More...
unsigned int	getVersion ()
	Get the SBML Version of this SBMLNamespaces object. More...
unsigned int	getVersion () const
	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...
SBMLExtensionNamespaces &	operator= (const SBMLExtensionNamespaces &rhs)
	Assignment operator for SBMLExtensionNamespaces. More...
int	removeNamespace (const std::string &uri)
	Removes an XML namespace from the set of namespaces within this SBMLNamespaces object. More...
int	removePackageNamespace (unsigned int level, unsigned version, const std::string &pkgName, unsigned int pkgVersion)
	Removes an XML namespace of a package extension from the set of namespaces within this SBMLNamespaces object. More...
	SBMLExtensionNamespaces (const SBMLExtensionNamespaces &orig)
	Copy constructor; creates a copy of a SBMLExtensionNamespaces. More...
	SBMLExtensionNamespaces (unsigned int level=SBMLExtensionType::getDefaultLevel(), unsigned int version=SBMLExtensionType::getDefaultVersion(), unsigned int pkgVersion=SBMLExtensionType::getDefaultPackageVersion(), const std::string &prefix=SBMLExtensionType::getPackageName())
	Creates a new SBMLExtensionNamespaces object corresponding to the given SBML level, version and package version. More...
virtual	~SBMLExtensionNamespaces ()
	Destroys this SBMLExtensionNamespaces object. More...

Static Public Member Functions
static void	freeSBMLNamespaces (List *supportedNS)
	Frees the list of supported namespaces as generated by getSupportedNamespaces(). More...
static std::string	getSBMLNamespaceURI (unsigned int level, unsigned int version)
	Returns a string representing the SBML XML namespace for the given level and version of SBML. More...
static const List *	getSupportedNamespaces ()
	Returns a list of all supported SBMLNamespaces in this version of libsbml. More...
static bool	isSBMLNamespace (const std::string &uri)
	Predicate returning true if the given URL is one of SBML XML namespaces. More...

Constructor & Destructor Documentation

SBMLExtensionNamespaces() [1/2]

template<class SBMLExtensionType >

SBMLExtensionNamespaces< SBMLExtensionType >::SBMLExtensionNamespaces	(	unsigned int	level = SBMLExtensionType::getDefaultLevel(),
		unsigned int	version = SBMLExtensionType::getDefaultVersion(),
		unsigned int	pkgVersion = SBMLExtensionType::getDefaultPackageVersion(),
		const std::string &	prefix = SBMLExtensionType::getPackageName()
	)

Creates a new SBMLExtensionNamespaces object corresponding to the given SBML level, version and package version.

Parameters

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

Exceptions

SBMLExtensionException

if the extension module that supports the combination of the given SBML Level, SBML Version, package name, and package version has not been registered.

~SBMLExtensionNamespaces()

template<class SBMLExtensionType >

virtual SBMLExtensionNamespaces< SBMLExtensionType >::~SBMLExtensionNamespaces ( )

virtual

Destroys this SBMLExtensionNamespaces object.

SBMLExtensionNamespaces() [2/2]

template<class SBMLExtensionType >

SBMLExtensionNamespaces< SBMLExtensionType >::SBMLExtensionNamespaces

(

const SBMLExtensionNamespaces< SBMLExtensionType > &

orig

)

Copy constructor; creates a copy of a SBMLExtensionNamespaces.

Parameters

orig	the SBMLExtensionNamespaces instance to copy.

Member Function Documentation

addNamespace()

int SBMLNamespaces::addNamespace ( const std::string &  uri, const std::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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED
• LIBSBML_INVALID_OBJECT

Examples

example1.cpp, and example3.cpp.

addNamespaces()

int SBMLNamespaces::addNamespaces ( const 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;
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.
}
 
SBMLNamespaces 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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED
• LIBSBML_INVALID_OBJECT

addPackageNamespace()

int SBMLNamespaces::addPackageNamespace ( const std::string &  pkgName, unsigned int  pkgVersion, const std::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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE

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()

addPackageNamespaces()

int SBMLNamespaces::addPackageNamespaces ( const 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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE

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.

clone()

template<class SBMLExtensionType >

virtual ISBMLExtensionNamespaces* SBMLExtensionNamespaces< SBMLExtensionType >::clone ( ) const

virtual

Creates and returns a deep copy of this SBMLExtensionNamespaces object.

Returns

a (deep) copy of this SBMLExtensionNamespaces object.

Reimplemented from SBMLNamespaces.

freeSBMLNamespaces()

void SBMLNamespaces::freeSBMLNamespaces ( List *  supportedNS )

staticinherited

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

Parameters

supportedNS

the list to be freed.

Examples

printSupported.cpp.

getLevel() [1/2]

unsigned int SBMLNamespaces::getLevel ( )

inherited

Get the SBML Level of this SBMLNamespaces object.

Returns

the SBML Level of this SBMLNamespaces object.

Examples

printSupported.cpp.

getLevel() [2/2]

unsigned int SBMLNamespaces::getLevel ( ) const

inherited

Get the SBML Level of this SBMLNamespaces object.

Returns

the SBML Level of this SBMLNamespaces object.

getNamespaces() [1/2]

XMLNamespaces * 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.

getNamespaces() [2/2]

const XMLNamespaces * SBMLNamespaces::getNamespaces ( ) const

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.

getPackageName()

template<class SBMLExtensionType >

virtual const std::string& SBMLExtensionNamespaces< SBMLExtensionType >::getPackageName ( ) const

virtual

Returns the name of the SBML package represented by this namespace object.

Returns

a string, the name of package.

Reimplemented from SBMLNamespaces.

getPackageVersion()

template<class SBMLExtensionType >

unsigned int SBMLExtensionNamespaces< SBMLExtensionType >::getPackageVersion

(

)

const

Returns the version of the SBML package represented by this namespace object.

Returns

the SBML Package Version of this SBMLExtensionNamespaces object.

getSBMLNamespaceURI()

std::string SBMLNamespaces::getSBMLNamespaceURI ( unsigned int  level, unsigned int  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.

getSupportedNamespaces()

const List * SBMLNamespaces::getSupportedNamespaces ( )

staticinherited

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

Returns

a list with supported SBML namespaces.

Examples

printSupported.cpp.

getURI()

template<class SBMLExtensionType >

virtual std::string SBMLExtensionNamespaces< SBMLExtensionType >::getURI ( ) const

virtual

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

Returns

a string representing the SBML namespace that reflects the SBML Level and Version, and package version, of this package.

Reimplemented from SBMLNamespaces.

getVersion() [1/2]

unsigned int SBMLNamespaces::getVersion ( )

inherited

Get the SBML Version of this SBMLNamespaces object.

Returns

the SBML Version of this SBMLNamespaces object.

Examples

printSupported.cpp.

getVersion() [2/2]

unsigned int SBMLNamespaces::getVersion ( ) const

inherited

Get the SBML Version of this SBMLNamespaces object.

Returns

the SBML Version of this SBMLNamespaces object.

isSBMLNamespace()

bool SBMLNamespaces::isSBMLNamespace ( const std::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.

isValidCombination()

bool 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.

operator=()

template<class SBMLExtensionType >

SBMLExtensionNamespaces& SBMLExtensionNamespaces< SBMLExtensionType >::operator=

(

const SBMLExtensionNamespaces< SBMLExtensionType > &

rhs

)

Assignment operator for SBMLExtensionNamespaces.

Parameters

rhs	the SBMLExtensionNamespaces instance to assign from.

removeNamespace()

int SBMLNamespaces::removeNamespace ( const std::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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INDEX_EXCEEDS_SIZE

removePackageNamespace()

int SBMLNamespaces::removePackageNamespace ( unsigned int  level, unsigned  version, const std::string &  pkgName, unsigned int  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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE
• LIBSBML_INDEX_EXCEEDS_SIZE