Inheritance diagram for RenderLayoutPlugin:

Detailed Description

render LibSBML implementation for the extension to the Layout class by the Render extension.

The Render package extends the Layout object from the Layout package with the addition of an optional ListOfLocalRenderInformation object.

Examples:: convertLayout.cpp.

Public Member Functions
void	addLocalRenderInformation (const LocalRenderInformation *pLRI)
	Adds a copy of the given local render information object to the list of local render information objects. More...

virtual RenderLayoutPlugin *	clone () const
	Creates and returns a deep copy of this RenderLayoutPlugin object. More...

LocalRenderInformation *	createLocalRenderInformation ()
	Creates a new local render information object and adds it to the list. More...

virtual List *	getAllElements (ElementFilter *filter=NULL)
	Returns a List of all child SBase objects, including those nested to an arbitrary depth. More...

virtual SBase *	getElementByMetaId (const std::string &metaid)
	Return the first child object found with a given meta identifier. More...

virtual SBase *	getElementBySId (const std::string &id)
	Return the first child object found with a given identifier. More...

const std::string &	getElementNamespace () const
	Returns the namespace URI of the package to which this plugin object belongs. More...

unsigned int	getLevel () const
	Returns the SBML Level of the package extension of this plugin object. More...

ListOfLocalRenderInformation *	getListOfLocalRenderInformation ()
	Returns a pointer to the list object that contains local render information. More...

const ListOfLocalRenderInformation *	getListOfLocalRenderInformation () const
	Returns a const pointer to the list object that contains local render information. More...

unsigned int	getNumLocalRenderInformationObjects () const
	Returns the number of local render information objects. More...

const std::string &	getPackageName () const
	Returns the short-form name of the package to which this plugin object belongs. More...

unsigned int	getPackageVersion () const
	Returns the package version of the package extension of this plugin object. More...

SBase *	getParentSBMLObject ()
	Returns the parent object to which this plugin object is connected. More...

const SBase *	getParentSBMLObject () const
	Returns the parent object to which this plugin object is connected. More...

const std::string &	getPrefix () const
	Returns the XML namespace prefix of the package to which this plugin object belongs. More...

LocalRenderInformation *	getRenderInformation (unsigned int index)
	Returns a pointer to the local render information object with the given index. More...

const LocalRenderInformation *	getRenderInformation (unsigned int index) const
	Returns a const pointer to the local render information object with the given index. More...

LocalRenderInformation *	getRenderInformation (const std::string &id)
	Returns a pointer to the local render information object with the given id. More...

const LocalRenderInformation *	getRenderInformation (const std::string &id) const
	Returns a const pointer to the local render information object with the given id. More...

SBMLDocument *	getSBMLDocument ()
	Returns the SBMLDocument object containing this object instance. More...

const SBMLDocument *	getSBMLDocument () const
	Returns the SBMLDocument object containing this object instance. More...

std::string	getURI () const
	Returns the XML namespace URI for the package to which this object belongs. More...

unsigned int	getVersion () const
	Returns the Version within the SBML Level of the package extension of this plugin object. More...

virtual bool	isValidTypeForList (SBase *item) const

RenderLayoutPlugin &	operator= (const RenderLayoutPlugin &orig)
	Assignment operator for RenderLayoutPlugin . More...

LocalRenderInformation *	removeLocalRenderInformation (unsigned int index)
	Removed the render information with the given index from the list. More...

LocalRenderInformation *	removeLocalRenderInformation (const std::string &id)
	Removed the render information with the given `id` from the list. More...

virtual void	renameMetaIdRefs (const std::string &oldid, const std::string &newid)
	Replaces all uses of a given meta identifier attribute value with another value. More...

virtual void	renameSIdRefs (const std::string &oldid, const std::string &newid)
	Replaces all uses of a given `SIdRef` type attribute value with another value. More...

virtual void	renameUnitSIdRefs (const std::string &oldid, const std::string &newid)
	Replaces all uses of a given `UnitSIdRef` type attribute value with another value. More...

	RenderLayoutPlugin (const std::string &uri, const std::string &prefix, RenderPkgNamespaces *groupsns)
	Constructor. More...

	RenderLayoutPlugin (const RenderLayoutPlugin &orig)
	Copy constructor. More...

int	setElementNamespace (const std::string &uri)
	Sets the XML namespace to which this object belongs. More...

virtual	~RenderLayoutPlugin ()
	Destroy this object. More...

Constructor & Destructor Documentation

RenderLayoutPlugin::RenderLayoutPlugin	(	const std::string &	uri,
		const std::string &	prefix,
		RenderPkgNamespaces *	groupsns
	)

Constructor.

RenderLayoutPlugin::RenderLayoutPlugin ( const RenderLayoutPlugin & orig )

Copy constructor.

Creates a copy of this SBase object.

RenderLayoutPlugin::~RenderLayoutPlugin ( )

virtual

Destroy this object.

Member Function Documentation

void RenderLayoutPlugin::addLocalRenderInformation ( const LocalRenderInformation * pLRI )

Adds a copy of the given local render information object to the list of local render information objects.

If an object with the same id exists, it is replaced.

RenderLayoutPlugin * RenderLayoutPlugin::clone ( ) const

virtual

Creates and returns a deep copy of this RenderLayoutPlugin object.

Returns: a (deep) copy of this RenderLayoutPlugin object

Reimplemented from SBasePlugin.

LocalRenderInformation * RenderLayoutPlugin::createLocalRenderInformation ( )

Creates a new local render information object and adds it to the list.

The created object does not have a id and it is the responsibility of the calling code to ensure that it gets one. For constraints on the id, please consult the render information document.

List * RenderLayoutPlugin::getAllElements ( ElementFilter * filter = NULL )

virtual

Returns a List of all child SBase objects, including those nested to an arbitrary depth.

Returns: a List of pointers to all children objects.

Reimplemented from SBasePlugin.

SBase * SBasePlugin::getElementByMetaId ( const std::string & metaid )

virtualinherited

Return the first child object found with a given meta identifier.

This method searches all the subobjects under this one, compares their meta identifiers to metaid, and returns the first one that machines.

Parameters

metaid string, the metaid of the object to find.

Returns: pointer to the first object found with the given metaid.

Reimplemented in QualModelPlugin, GroupsModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.

SBase * SBasePlugin::getElementBySId ( const std::string & id )

virtualinherited

Return the first child object found with a given identifier.

This method searches all the subobjects under this one, compares their identifiers to id, and returns the first one that machines. It uses SBasePlugin::getAllElements(ElementFilter* filter) to get the list of identifiers, so the order in which identifiers are searched is the order in which they appear in the results returned by that method.

Normally, SId type identifier values are unique across a model in SBML. However, in some circumstances they may not be, such as if a model is invalid because of multiple objects having the same identifier.

Parameters

id	string representing the identifier of the object to find.

Returns: pointer to the first object with the given id.

Reimplemented in QualModelPlugin, GroupsModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.

const std::string & SBasePlugin::getElementNamespace ( ) const

inherited

Returns the namespace URI of the package to which this plugin object belongs.

Returns: the XML namespace URI of the SBML Level 3 package implemented by this libSBML package extension.

unsigned int SBasePlugin::getLevel ( ) const

inherited

Returns the SBML Level of the package extension of this plugin object.

Returns: the SBML Level.

See also: getVersion()

ListOfLocalRenderInformation * RenderLayoutPlugin::getListOfLocalRenderInformation ( )

Returns a pointer to the list object that contains local render information.

const ListOfLocalRenderInformation * RenderLayoutPlugin::getListOfLocalRenderInformation ( ) const

Returns a const pointer to the list object that contains local render information.

unsigned int RenderLayoutPlugin::getNumLocalRenderInformationObjects ( ) const

Returns the number of local render information objects.

const std::string & SBasePlugin::getPackageName ( ) const

inherited

Returns the short-form name of the package to which this plugin object belongs.

Returns: the short-form package name (or nickname) of the SBML package implemented by this package extension.

unsigned int SBasePlugin::getPackageVersion ( ) const

inherited

Returns the package version of the package extension of this plugin object.

Returns: the package version of the package extension of this plugin object.

See also: getLevel(); getVersion()

SBase * SBasePlugin::getParentSBMLObject ( )

inherited

Returns the parent object to which this plugin object is connected.

Returns: the parent object of this object.

const SBase * SBasePlugin::getParentSBMLObject ( ) const

inherited

Returns the parent object to which this plugin object is connected.

Returns: the parent object of this object.

const std::string & SBasePlugin::getPrefix ( ) const

inherited

Returns the XML namespace prefix of the package to which this plugin object belongs.

Returns: the XML namespace prefix of the SBML Level 3 package implemented by this libSBML package extension.

LocalRenderInformation * RenderLayoutPlugin::getRenderInformation ( unsigned int index )

Returns a pointer to the local render information object with the given index.

If the index is invalid, NULL is returned.

const LocalRenderInformation * RenderLayoutPlugin::getRenderInformation ( unsigned int index ) const

Returns a const pointer to the local render information object with the given index.

If the index is invalid, NULL is returned.

LocalRenderInformation * RenderLayoutPlugin::getRenderInformation ( const std::string & id )

Returns a pointer to the local render information object with the given id.

If no object with the given id exists, NULL is returned.

const LocalRenderInformation * RenderLayoutPlugin::getRenderInformation ( const std::string & id ) const

Returns a const pointer to the local render information object with the given id.

If no object with the given id exists, NULL is returned.

SBMLDocument * SBasePlugin::getSBMLDocument ( )

inherited

Returns the SBMLDocument object containing this object instance.

: LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns: the parent SBMLDocument object of this plugin object.

See also: getParentSBMLObject()

const SBMLDocument * SBasePlugin::getSBMLDocument ( ) const

inherited

Returns the SBMLDocument object containing this object instance.

: LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns: the parent SBMLDocument object of this plugin object.

See also: getParentSBMLObject()

std::string SBasePlugin::getURI ( ) const

inherited

Returns the XML namespace URI for the package to which this object belongs.

: 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/".

This method first looks into the SBMLNamespaces object possessed by the parent SBMLDocument object of the current object. If this cannot be found, this method returns the result of getElementNamespace().

Returns: a string, the URI of the XML namespace to which this object belongs.

See also: getPackageName(); getElementNamespace(); getSBMLDocument()

unsigned int SBasePlugin::getVersion ( ) const

inherited

Returns the Version within the SBML Level of the package extension of this plugin object.

Returns: the SBML Version.

See also: getLevel()

virtual bool SBasePlugin::isValidTypeForList ( SBase * item ) const

virtualinherited

RenderLayoutPlugin & RenderLayoutPlugin::operator= ( const RenderLayoutPlugin & orig )

Assignment operator for RenderLayoutPlugin .

LocalRenderInformation * RenderLayoutPlugin::removeLocalRenderInformation ( unsigned int index )

Removed the render information with the given index from the list.

The removed object is returned. It is the responsibility of the calling code to delete the object. If the index is not valid, NULL is returned.

LocalRenderInformation * RenderLayoutPlugin::removeLocalRenderInformation ( const std::string & id )

Removed the render information with the given id from the list.

The removed object is returned. It is the responsibility of the calling code to delete the object. If an object with the given id does not exist, NULL is returned.

virtual void SBasePlugin::renameMetaIdRefs	(	const std::string &	oldid,
		const std::string &	newid
	)

virtualinherited

Replaces all uses of a given meta identifier attribute value with another value.

: In SBML, object "meta" identifiers are of the XML data type ID; the SBML object attribute itself is typically named metaid. All attributes that hold values referring to values of type ID are of the XML data type IDREF. They are also sometimes informally referred to as "metaid refs", in analogy to the SBML-defined type SIdRef.

This method works by looking at all meta-identifier attribute values, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters

oldid	the old identifier.
newid	the new identifier.

virtual void SBasePlugin::renameSIdRefs	(	const std::string &	oldid,
		const std::string &	newid
	)

virtualinherited

Replaces all uses of a given SIdRef type attribute value with another value.

In SBML, object identifiers are of a data type called SId. In SBML Level 3, an explicit data type called SIdRef was introduced for attribute values that refer to SId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as "referring to an identifier", but the effective data type was the same as SIdRef in Level 3. These and other methods of libSBML refer to the type SIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

This method works by looking at all attributes and (if appropriate) mathematical formulas in MathML content, comparing the referenced identifiers to the value of oldid. If any matches are found, the matching values are replaced with newid. The method does not descend into child elements.

Parameters

oldid	the old identifier.
newid	the new identifier.

Reimplemented in FbcReactionPlugin.

virtual void SBasePlugin::renameUnitSIdRefs	(	const std::string &	oldid,
		const std::string &	newid
	)

virtualinherited

Replaces all uses of a given UnitSIdRef type attribute value with another value.

: In SBML, unit definitions have identifiers of type UnitSId. In SBML Level 3, an explicit data type called UnitSIdRef was introduced for attribute values that refer to UnitSId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as "referring to a unit identifier", but the effective data type was the same as UnitSIdRef in Level 3. These and other methods of libSBML refer to the type UnitSIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the referenced unit identifiers to the value of oldid. If any matches are found, the matching values are replaced with newid. The method does not descend into child elements.

Parameters

oldid	the old identifier.
newid	the new identifier.

int SBasePlugin::setElementNamespace ( const std::string & uri )

inherited

Sets the XML namespace to which this object belongs.

: 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/".

Parameters

uri	the URI to assign to this object.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:

LIBSBML_OPERATION_SUCCESS

See also: getElementNamespace()

Examples:: convertLayout.cpp.

Detailed Description

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation