Inheritance diagram for libsbmlcs.RenderLayoutPlugin:

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

SBasePlugin	clone ()
	Creates and returns a deep copy of this RenderLayoutPlugin object. More...

void	connectToParent (SBase sbase)
	Sets the parent SBML object of this plugin object to this object and child elements (if any). More...

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

SBase	createObject (XMLInputStream stream)
	Subclasses must override this method to create, store, and then return an SBML object corresponding to the next XMLToken in the XMLInputStream if they have their specific elements. More...

override void	Dispose ()

void	divideAssignmentsToSIdByFunction (string id, ASTNode function)
	If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function). More...

void	enablePackageInternal (string pkgURI, string pkgPrefix, bool flag)
	Enables/Disables the given package with child elements in this plugin object (if any). More...

long	getColumn ()
	Returns the column number on which this object first appears in the XML representation of the SBML document. More...

SBase	getElementByMetaId (string metaid)
	Returns the first child element it can find with the given `metaid`, or `null` if no such object is found. More...

SBase	getElementBySId (string id)
	Returns the first child element found that has the given `id` in the model-wide SId namespace, or `null` if no such object is found. More...

string	getElementNamespace ()
	Returns the XML namespace (URI) of the package extension of this plugin object. More...

long	getLevel ()
	Returns the SBML level of the package extension of this plugin object. More...

long	getLine ()
	Returns the line number on which this object first appears in the XML representation of the SBML document. More...

SBaseList	getListOfAllElements (ElementFilter filter)

SBaseList	getListOfAllElements ()

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

long	getNumLocalRenderInformationObjects ()
	Returns the number of local render information objects. More...

string	getPackageName ()
	Returns the package name of this plugin object. More...

long	getPackageVersion ()
	Returns the package version of the package extension of this plugin object. More...

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

string	getPrefix ()
	Returns the prefix of the package extension of this plugin object. More...

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

LocalRenderInformation	getRenderInformation (string id)
	Returns a pointer to the local render information object with the given id. More...

SBMLDocument	getSBMLDocument ()
	Returns the parent SBMLDocument of this plugin object. More...

SBMLNamespaces	getSBMLNamespaces ()

string	getURI ()
	Gets the URI to which this element belongs to. More...

long	getVersion ()
	Returns the SBML version of the package extension of this plugin object. More...

bool	hasIdentifierBeginningWith (string prefix)
	Check to see if the given prefix is used by any of the IDs defined by extension elements. More...

bool	hasRequiredElements ()
	Checks if this plugin object has all the required elements. More...

void	logUnknownElement (string element, long sbmlLevel, long sbmlVersion, long pkgVersion)
	Helper to log a common type of error for elements. More...

void	multiplyAssignmentsToSIdByFunction (string id, ASTNode function)
	If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function). More...

int	prependStringToAllIdentifiers (string prefix)
	Add the given string to all identifiers in the object. More...

LocalRenderInformation	removeLocalRenderInformation (long index)
	Removed the render information with the given index from the list. More...

LocalRenderInformation	removeLocalRenderInformation (string id)
	Removed the render information with the given `id` from the list. More...

	RenderLayoutPlugin (string uri, string prefix, RenderPkgNamespaces groupsns)
	Constructor. More...

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

void	replaceSIDWithFunction (string id, ASTNode function)
	If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function. More...

int	setElementNamespace (string uri)
	Sets the XML namespace to which this element belongs to. More...

bool	stripPackage (string pkgPrefix, bool flag)

int	transformIdentifiers (IdentifierTransformer sidTransformer)

void	writeAttributes (XMLOutputStream stream)
	Serialize the render information as L2 annotation. More...

Protected Attributes
bool	swigCMemOwn

Constructor & Destructor Documentation

libsbmlcs.RenderLayoutPlugin.RenderLayoutPlugin	(	string	uri,
		string	prefix,
		RenderPkgNamespaces	groupsns
	)

Constructor.

libsbmlcs.RenderLayoutPlugin.RenderLayoutPlugin ( RenderLayoutPlugin orig )

Copy constructor.

Creates a copy of this SBase object.

Member Function Documentation

void libsbmlcs.RenderLayoutPlugin.addLocalRenderInformation ( 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.

SBasePlugin libsbmlcs.RenderLayoutPlugin.clone ( )

Creates and returns a deep copy of this RenderLayoutPlugin object.

Returns: a (deep) copy of this RenderLayoutPlugin object

void libsbmlcs.RenderLayoutPlugin.connectToParent ( SBase sbase )

Sets the parent SBML object of this plugin object to this object and child elements (if any).

(Creates a child-parent relationship by this plugin object)

This function is called when this object is created by the parent element. Subclasses must override this this function if they have one or more child elements.Also, SBasePlugin::connectToParent() must be called in the overridden function.

Parameters

sbase the SBase object to use

See also: setSBMLDocument; enablePackageInternal

LocalRenderInformation libsbmlcs.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.

SBase libsbmlcs.RenderLayoutPlugin.createObject ( XMLInputStream stream )

Subclasses must override this method to create, store, and then return an SBML object corresponding to the next XMLToken in the XMLInputStream if they have their specific elements.

Returns: the SBML object corresponding to next XMLToken in the XMLInputStream or null if the token was not recognized.

override void libsbmlcs.RenderLayoutPlugin.Dispose ( )

virtual

Reimplemented from libsbmlcs.SBasePlugin.

void libsbmlcs.SBasePlugin.divideAssignmentsToSIdByFunction	(	string	id,
		ASTNode	function
	)

inherited

If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function).

Note: This function does nothing itself–subclasses with ASTNode subelements must override this function.

void libsbmlcs.RenderLayoutPlugin.enablePackageInternal	(	string	pkgURI,
		string	pkgPrefix,
		bool	flag
	)

Enables/Disables the given package with child elements in this plugin object (if any).

(This is an internal implementation invoked from SBase::enablePakcageInternal() function)

Note: Subclasses in which one or more SBase derived elements are defined must override this function.

See also: setSBMLDocument; connectToParent

long libsbmlcs.SBasePlugin.getColumn ( )

inherited

Returns the column number on which this object first appears in the XML representation of the SBML document.

Returns: the column number of the underlying SBML object.

Note: The column number for each construct in an SBML model is set upon reading the model. The accuracy of the column number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real column number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)

See also: getLine()

SBase libsbmlcs.SBasePlugin.getElementByMetaId ( string metaid )

inherited

Returns the first child element it can find with the given metaid, or null if no such object is found.

Parameters

metaid string representing the metaid of objects to find

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

SBase libsbmlcs.SBasePlugin.getElementBySId ( string id )

inherited

Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.

Parameters

id	string representing the id of objects to find

Returns: pointer to the first element found with the given id.

string libsbmlcs.SBasePlugin.getElementNamespace ( )

inherited

Returns the XML namespace (URI) of the package extension of this plugin object.

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

long libsbmlcs.SBasePlugin.getLevel ( )

inherited

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

Returns: the SBML level of the package extension of this plugin object.

long libsbmlcs.SBasePlugin.getLine ( )

inherited

Returns the line number on which this object first appears in the XML representation of the SBML document.

Returns: the line number of the underlying SBML object.

Note: The line number for each construct in an SBML model is set upon reading the model. The accuracy of the line number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real line number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)

See also: getColumn()

SBaseList libsbmlcs.SBasePlugin.getListOfAllElements ( ElementFilter filter )

inherited

SBaseList libsbmlcs.SBasePlugin.getListOfAllElements ( )

inherited

ListOfLocalRenderInformation libsbmlcs.RenderLayoutPlugin.getListOfLocalRenderInformation ( )

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

long libsbmlcs.RenderLayoutPlugin.getNumLocalRenderInformationObjects ( )

Returns the number of local render information objects.

string libsbmlcs.SBasePlugin.getPackageName ( )

inherited

Returns the package name of this plugin object.

Returns: the package name of this plugin object.

long libsbmlcs.SBasePlugin.getPackageVersion ( )

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.

SBase libsbmlcs.SBasePlugin.getParentSBMLObject ( )

inherited

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

Returns: the parent SBase object to which this plugin object connected.

string libsbmlcs.SBasePlugin.getPrefix ( )

inherited

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

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

LocalRenderInformation libsbmlcs.RenderLayoutPlugin.getRenderInformation ( long index )

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

If the index is invalid, null is returned.

LocalRenderInformation libsbmlcs.RenderLayoutPlugin.getRenderInformation ( 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.

SBMLDocument libsbmlcs.SBasePlugin.getSBMLDocument ( )

inherited

Returns the parent SBMLDocument of this plugin object.

Returns: the parent SBMLDocument object of this plugin object.

SBMLNamespaces libsbmlcs.SBasePlugin.getSBMLNamespaces ( )

inherited

string libsbmlcs.SBasePlugin.getURI ( )

inherited

Gets the URI to which this element belongs to.

For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1/'

Unlike getElementNamespace, this function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. if not found it will return the result of getElementNamespace

Returns: the URI this elements

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

long libsbmlcs.SBasePlugin.getVersion ( )

inherited

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

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

bool libsbmlcs.SBasePlugin.hasIdentifierBeginningWith ( string prefix )

inherited

Check to see if the given prefix is used by any of the IDs defined by extension elements.

A package that defines its own 'id' attribute for a core element would check that attribute here.

bool libsbmlcs.RenderLayoutPlugin.hasRequiredElements ( )

Checks if this plugin object has all the required elements.

Subclasses should override this function if they have their specific elements.

Returns: true if this pugin object has all the required elements, otherwise false will be returned.

void libsbmlcs.SBasePlugin.logUnknownElement	(	string	element,
		long	sbmlLevel,
		long	sbmlVersion,
		long	pkgVersion
	)

inherited

Helper to log a common type of error for elements.

void libsbmlcs.SBasePlugin.multiplyAssignmentsToSIdByFunction	(	string	id,
		ASTNode	function
	)

inherited

If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function).

int libsbmlcs.SBasePlugin.prependStringToAllIdentifiers ( string prefix )

inherited

Add the given string to all identifiers in the object.

If the string is added to anything other than an id or a metaid, this code is responsible for tracking down and renaming all *idRefs in the package extention that identifier comes from.

LocalRenderInformation libsbmlcs.RenderLayoutPlugin.removeLocalRenderInformation ( long 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 libsbmlcs.RenderLayoutPlugin.removeLocalRenderInformation ( 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.

void libsbmlcs.SBasePlugin.replaceSIDWithFunction	(	string	id,
		ASTNode	function
	)

inherited

If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function.

Note: This function does nothing itself–subclasses with ASTNode subelements must override this function.

int libsbmlcs.SBasePlugin.setElementNamespace ( string uri )

inherited

Sets the XML namespace to which this element belongs to.

For example, all elements that belong to SBML Level 3 Version 1 Core must set the namespace to 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must set the namespace to 'http://www.sbml.org/sbml/level3/version1/layout/version1/'

Returns

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

bool libsbmlcs.SBasePlugin.stripPackage	(	string	pkgPrefix,
		bool	flag
	)

inherited

int libsbmlcs.SBasePlugin.transformIdentifiers ( IdentifierTransformer sidTransformer )

inherited

void libsbmlcs.RenderLayoutPlugin.writeAttributes ( XMLOutputStream stream )

Serialize the render information as L2 annotation.

Member Data Documentation

bool libsbmlcs.SBasePlugin.swigCMemOwn

protectedinherited

Public Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation