Inheritance diagram for FbcSBasePlugin:

Detailed Description

@sbmlpackage{fbc}

fbc Extension of SBase.

Public Member Functions
int	addKeyValuePair (const KeyValuePair *kvp)
	Adds a copy of the given KeyValuePair to this FbcSBasePlugin. More...

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

KeyValuePair *	createKeyValuePair ()
	Creates a new KeyValuePair object, adds it to this FbcSBasePlugin object and returns the KeyValuePair object created. More...

	FbcSBasePlugin (const FbcSBasePlugin &orig)
	Copy constructor for FbcSBasePlugin. More...

	FbcSBasePlugin (const std::string &uri, const std::string &prefix, FbcPkgNamespaces *fbcns)
	Creates a new FbcSBasePlugin using the given URI, prefix and package namespace. 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)
	Returns the first child element that has the given `metaid`, or `NULL` if no such object is found. More...

virtual SBase *	getElementBySId (const std::string &id)
	Returns the first child element that has the given `id` in the model-wide SId namespace, or `NULL` if no such object is found. More...

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

KeyValuePair *	getKeyValuePair (const std::string &sid)
	Get a KeyValuePair from the FbcSBasePlugin based on its identifier. More...

const KeyValuePair *	getKeyValuePair (const std::string &sid) const
	Get a KeyValuePair from the FbcSBasePlugin based on its identifier. More...

KeyValuePair *	getKeyValuePair (unsigned int n)
	Get a KeyValuePair from the FbcSBasePlugin. More...

const KeyValuePair *	getKeyValuePair (unsigned int n) const
	Get a KeyValuePair from the FbcSBasePlugin. More...

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

ListOfKeyValuePairs *	getListOfKeyValuePairs ()
	Returns the ListOfKeyValuePairs from this FbcSBasePlugin. More...

const ListOfKeyValuePairs *	getListOfKeyValuePairs () const
	Returns the ListOfKeyValuePairs from this FbcSBasePlugin. More...

unsigned int	getNumKeyValuePairs () const
	Get the number of KeyValuePair objects in this FbcSBasePlugin. 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...

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

FbcSBasePlugin &	operator= (const FbcSBasePlugin &rhs)
	Assignment operator for FbcSBasePlugin. More...

KeyValuePair *	removeKeyValuePair (const std::string &sid)
	Removes the KeyValuePair from this FbcSBasePlugin based on its identifier and returns a pointer to it. More...

KeyValuePair *	removeKeyValuePair (unsigned int n)
	Removes the nth KeyValuePair from this FbcSBasePlugin and returns a pointer to it. More...

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

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

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

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

virtual	~FbcSBasePlugin ()
	Destructor for FbcSBasePlugin. More...

Constructor & Destructor Documentation

◆ FbcSBasePlugin() [1/2]

FbcSBasePlugin::FbcSBasePlugin	(	const std::string &	uri,
		const std::string &	prefix,
		FbcPkgNamespaces *	fbcns
	)

Creates a new FbcSBasePlugin using the given URI, prefix and package namespace.

Parameters

uri	a string, representing the URI of the SBML Level 3 package implemented by this libSBML package extension.
prefix	a string, the XML namespace prefix being used for this package.
fbcns	a pointer to the namesspaces object (FbcPkgNamespaces) for this package.

: 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/".

: The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.

◆ FbcSBasePlugin() [2/2]

FbcSBasePlugin::FbcSBasePlugin ( const FbcSBasePlugin & orig )

Copy constructor for FbcSBasePlugin.

Parameters

orig	the FbcSBasePlugin instance to copy.

◆ ~FbcSBasePlugin()

FbcSBasePlugin::~FbcSBasePlugin ( )

virtual

Destructor for FbcSBasePlugin.

Member Function Documentation

◆ addKeyValuePair()

int FbcSBasePlugin::addKeyValuePair ( const KeyValuePair * kvp )

Adds a copy of the given KeyValuePair to this FbcSBasePlugin.

Parameters

kvp	the KeyValuePair object to add.

LIBSBML_OPERATION_SUCCESSendif

◆ clone()

FbcSBasePlugin * FbcSBasePlugin::clone ( ) const

virtual

Creates and returns a deep copy of this FbcSBasePlugin object.

Returns: a (deep) copy of this FbcSBasePlugin object.

Reimplemented from SBasePlugin.

Reimplemented in FbcModelPlugin, FbcReactionPlugin, and FbcSpeciesPlugin.

◆ createKeyValuePair()

KeyValuePair * FbcSBasePlugin::createKeyValuePair ( )

Creates a new KeyValuePair object, adds it to this FbcSBasePlugin object and returns the KeyValuePair object created.

Returns: a new KeyValuePair object instance.

See also: addKeyValuePair(const KeyValuePair* object); getKeyValuePair(const std::string& sid); getKeyValuePair(unsigned int n); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getAllElements()

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

virtual

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

Parameters

filter an ElementFilter that may impose restrictions on the objects to be retrieved.

Returns: a List pointer of pointers to all SBase child objects with any restriction imposed.

Reimplemented from SBasePlugin.

Reimplemented in FbcModelPlugin, and FbcReactionPlugin.

◆ getElementByMetaId()

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

virtual

Returns the first child element that has the given metaid, or NULL if no such object is found.

Parameters

metaid a string representing the metaid attribute of the object to retrieve.

Returns: a pointer to the SBase element with the given metaid. If no such object is found this method returns NULL.

Reimplemented from SBasePlugin.

Reimplemented in FbcModelPlugin.

◆ getElementBySId()

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

virtual

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

Parameters

id	a string representing the id attribute of the object to retrieve.

Returns: a pointer to the SBase element with the given id. If no such object is found, this method returns NULL.

Reimplemented from SBasePlugin.

Reimplemented in FbcModelPlugin.

◆ getElementNamespace()

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.

◆ getKeyValuePair() [1/4]

KeyValuePair * FbcSBasePlugin::getKeyValuePair ( const std::string & sid )

Get a KeyValuePair from the FbcSBasePlugin based on its identifier.

Parameters

sid	a string representing the identifier of the KeyValuePair to retrieve.

Returns: the KeyValuePair in the ListOfKeyValuePairs within this FbcSBasePlugin with the given sid or NULL if no such KeyValuePair exists.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(unsigned int n); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getKeyValuePair() [2/4]

const KeyValuePair * FbcSBasePlugin::getKeyValuePair ( const std::string & sid ) const

Get a KeyValuePair from the FbcSBasePlugin based on its identifier.

Parameters

sid	a string representing the identifier of the KeyValuePair to retrieve.

Returns: the KeyValuePair in the ListOfKeyValuePairs within this FbcSBasePlugin with the given sid or NULL if no such KeyValuePair exists.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(unsigned int n); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getKeyValuePair() [3/4]

KeyValuePair * FbcSBasePlugin::getKeyValuePair ( unsigned int n )

Get a KeyValuePair from the FbcSBasePlugin.

Parameters

n	an unsigned int representing the index of the KeyValuePair to retrieve.

Returns: the nth KeyValuePair in the ListOfKeyValuePairs within this FbcSBasePlugin or NULL if no such object exists.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(const std::string& sid); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getKeyValuePair() [4/4]

const KeyValuePair * FbcSBasePlugin::getKeyValuePair ( unsigned int n ) const

Get a KeyValuePair from the FbcSBasePlugin.

Parameters

n	an unsigned int representing the index of the KeyValuePair to retrieve.

Returns: the nth KeyValuePair in the ListOfKeyValuePairs within this FbcSBasePlugin or NULL if no such object exists.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(const std::string& sid); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getLevel()

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()

◆ getListOfKeyValuePairs() [1/2]

ListOfKeyValuePairs * FbcSBasePlugin::getListOfKeyValuePairs ( )

Returns the ListOfKeyValuePairs from this FbcSBasePlugin.

Returns: the ListOfKeyValuePairs from this FbcSBasePlugin.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(const std::string& sid); getKeyValuePair(unsigned int n); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getListOfKeyValuePairs() [2/2]

const ListOfKeyValuePairs * FbcSBasePlugin::getListOfKeyValuePairs ( ) const

Returns the ListOfKeyValuePairs from this FbcSBasePlugin.

Returns: the ListOfKeyValuePairs from this FbcSBasePlugin.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(const std::string& sid); getKeyValuePair(unsigned int n); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getNumKeyValuePairs()

unsigned int FbcSBasePlugin::getNumKeyValuePairs ( ) const

Get the number of KeyValuePair objects in this FbcSBasePlugin.

Returns: the number of KeyValuePair objects in this FbcSBasePlugin.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(const std::string& sid); getKeyValuePair(unsigned int n); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getPackageName()

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.

◆ getPackageVersion()

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()

◆ getParentSBMLObject() [1/2]

SBase * SBasePlugin::getParentSBMLObject ( )

inherited

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

Returns: the parent object of this object.

◆ getParentSBMLObject() [2/2]

const SBase * SBasePlugin::getParentSBMLObject ( ) const

inherited

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

Returns: the parent object of this object.

◆ getPrefix()

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.

◆ getSBMLDocument() [1/2]

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()

◆ getSBMLDocument() [2/2]

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()

◆ getURI()

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()

◆ getVersion()

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()

◆ isValidTypeForList()

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

virtualinherited

◆ operator=()

FbcSBasePlugin & FbcSBasePlugin::operator= ( const FbcSBasePlugin & rhs )

Assignment operator for FbcSBasePlugin.

Parameters

rhs	the FbcSBasePlugin object whose values are to be used as the basis of the assignment.

◆ removeKeyValuePair() [1/2]

KeyValuePair * FbcSBasePlugin::removeKeyValuePair ( const std::string & sid )

Removes the KeyValuePair from this FbcSBasePlugin based on its identifier and returns a pointer to it.

Parameters

sid	a string representing the identifier of the KeyValuePair to remove.

Returns: the KeyValuePair in this FbcSBasePlugin based on the identifier or NULL if no such KeyValuePair exists.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(const std::string& sid); getKeyValuePair(unsigned int n); getNumKeyValuePairs(); removeKeyValuePair(unsigned int n)

◆ removeKeyValuePair() [2/2]

KeyValuePair * FbcSBasePlugin::removeKeyValuePair ( unsigned int n )

Removes the nth KeyValuePair from this FbcSBasePlugin and returns a pointer to it.

Parameters

n	an unsigned int representing the index of the KeyValuePair to remove.

Returns: a pointer to the nth KeyValuePair in this FbcSBasePlugin.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(const std::string& sid); getKeyValuePair(unsigned int n); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid)

◆ renameMetaIdRefs()

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

virtualinherited

◆ renameSIdRefs()

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

virtualinherited

Reimplemented in FbcReactionPlugin.

◆ renameUnitSIdRefs()

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

virtualinherited

◆ setElementNamespace()

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.

LIBSBML_OPERATION_SUCCESSendif

Examples: convertLayout.cpp.

Detailed Description

Public Member Functions

Constructor & Destructor Documentation

◆ FbcSBasePlugin() [1/2]

◆ FbcSBasePlugin() [2/2]

◆ ~FbcSBasePlugin()

Member Function Documentation

◆ addKeyValuePair()

◆ clone()

◆ createKeyValuePair()

◆ getAllElements()

◆ getElementByMetaId()

◆ getElementBySId()

◆ getElementNamespace()

◆ getKeyValuePair() [1/4]

◆ getKeyValuePair() [2/4]

◆ getKeyValuePair() [3/4]

◆ getKeyValuePair() [4/4]

◆ getLevel()

◆ getListOfKeyValuePairs() [1/2]

◆ getListOfKeyValuePairs() [2/2]

◆ getNumKeyValuePairs()

◆ getPackageName()

◆ getPackageVersion()

◆ getParentSBMLObject() [1/2]

◆ getParentSBMLObject() [2/2]

◆ getPrefix()

◆ getSBMLDocument() [1/2]

◆ getSBMLDocument() [2/2]

◆ getURI()

◆ getVersion()

◆ isValidTypeForList()

◆ operator=()

◆ removeKeyValuePair() [1/2]

◆ removeKeyValuePair() [2/2]

◆ renameMetaIdRefs()

◆ renameSIdRefs()

◆ renameUnitSIdRefs()

◆ setElementNamespace()