Inheritance diagram for GroupsModelPlugin:

Detailed Description

groups Extension of Model.

Examples:: groups_example1.cpp, and groups_example2.cpp.

Public Member Functions
int	addGroup (const Group *g)
	Adds a copy of the given Group to this GroupsModelPlugin. More...

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

virtual void	copyInformationToNestedLists ()
	For nested groups (Member objects that reference a ListOfMembers object), SBO terms, Notes, and Annotation from the parent ListOfMembers applies to the child. More...

Group *	createGroup ()
	Creates a new Group object, adds it to this GroupsModelPlugin object and returns the Group object created. 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...

Group *	getGroup (unsigned int n)
	Get a Group from the GroupsModelPlugin. More...

const Group *	getGroup (unsigned int n) const
	Get a Group from the GroupsModelPlugin. More...

Group *	getGroup (const std::string &sid)
	Get a Group from the GroupsModelPlugin based on its identifier. More...

const Group *	getGroup (const std::string &sid) const
	Get a Group from the GroupsModelPlugin based on its identifier. More...

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

const ListOfGroups *	getListOfGroups () const
	Returns the ListOfGroups from this GroupsModelPlugin. More...

ListOfGroups *	getListOfGroups ()
	Returns the ListOfGroups from this GroupsModelPlugin. More...

unsigned int	getNumGroups () const
	Get the number of Group objects in this GroupsModelPlugin. 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...

	GroupsModelPlugin (const std::string &uri, const std::string &prefix, GroupsPkgNamespaces *groupsns)
	Creates a new GroupsModelPlugin using the given URI, prefix and package namespace. More...

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

virtual bool	isValidTypeForList (SBase *item) const

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

Group *	removeGroup (unsigned int n)
	Removes the nth Group from this GroupsModelPlugin and returns a pointer to it. More...

Group *	removeGroup (const std::string &sid)
	Removes the Group from this GroupsModelPlugin based on its identifier and returns a pointer to it. 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...

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

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

Constructor & Destructor Documentation

GroupsModelPlugin::GroupsModelPlugin	(	const std::string &	uri,
		const std::string &	prefix,
		GroupsPkgNamespaces *	groupsns
	)

Creates a new GroupsModelPlugin 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.
groupsns	a pointer to the namesspaces object (GroupsPkgNamespaces) 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.

GroupsModelPlugin::GroupsModelPlugin ( const GroupsModelPlugin & orig )

Copy constructor for GroupsModelPlugin.

Parameters

orig	the GroupsModelPlugin instance to copy.

GroupsModelPlugin::~GroupsModelPlugin ( )

virtual

Destructor for GroupsModelPlugin.

Member Function Documentation

int GroupsModelPlugin::addGroup ( const Group * g )

Adds a copy of the given Group to this GroupsModelPlugin.

Parameters

g	the Group object to add.

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:

Note: This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.

See also: createGroup(); getGroup(const std::string& sid); getGroup(unsigned int n); getNumGroups(); removeGroup(const std::string& sid); removeGroup(unsigned int n)

GroupsModelPlugin * GroupsModelPlugin::clone ( ) const

virtual

Creates and returns a deep copy of this GroupsModelPlugin object.

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

Reimplemented from SBasePlugin.

void GroupsModelPlugin::copyInformationToNestedLists ( )

virtual

For nested groups (Member objects that reference a ListOfMembers object), SBO terms, Notes, and Annotation from the parent ListOfMembers applies to the child.

This function copies any information from any of those three things to all child ListOfMembers, and if that information is not already set. After calling this function, it is sufficient to check any ListOfMembers to see if its SBO term, Notes, or Annotation is set, without further checking to see if that element was nested in another Group.

Group * GroupsModelPlugin::createGroup ( )

Creates a new Group object, adds it to this GroupsModelPlugin object and returns the Group object created.

Returns: a new Group object instance.

Note: The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

See also: addGroup(const Group* object); getGroup(const std::string& sid); getGroup(unsigned int n); getNumGroups(); removeGroup(const std::string& sid); removeGroup(unsigned int n)

Examples:: groups_example1.cpp, and groups_example2.cpp.

List * GroupsModelPlugin::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.

SBase * GroupsModelPlugin::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.

SBase * GroupsModelPlugin::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.

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.

Group * GroupsModelPlugin::getGroup ( unsigned int n )

Get a Group from the GroupsModelPlugin.

Parameters

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

Returns: the nth Group in the ListOfGroups within this GroupsModelPlugin or NULL if no such object exists..

Note: The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

See also: addGroup(const Group* object); createGroup(); getGroup(const std::string& sid); getNumGroups(); removeGroup(const std::string& sid); removeGroup(unsigned int n)

const Group * GroupsModelPlugin::getGroup ( unsigned int n ) const

Get a Group from the GroupsModelPlugin.

Parameters

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

Returns: the nth Group in the ListOfGroups within this GroupsModelPlugin or NULL if no such object exists..

Note: The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

See also: addGroup(const Group* object); createGroup(); getGroup(const std::string& sid); getNumGroups(); removeGroup(const std::string& sid); removeGroup(unsigned int n)

Group * GroupsModelPlugin::getGroup ( const std::string & sid )

Get a Group from the GroupsModelPlugin based on its identifier.

Parameters

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

Returns: the Group in the ListOfGroups within this GroupsModelPlugin with the given sid or NULL if no such Group exists.

Note: The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

See also: addGroup(const Group* object); createGroup(); getGroup(unsigned int n); getNumGroups(); removeGroup(const std::string& sid); removeGroup(unsigned int n)

const Group * GroupsModelPlugin::getGroup ( const std::string & sid ) const

Get a Group from the GroupsModelPlugin based on its identifier.

Parameters

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

Returns: the Group in the ListOfGroups within this GroupsModelPlugin with the given sid or NULL if no such Group exists.

Note: The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

See also: addGroup(const Group* object); createGroup(); getGroup(unsigned int n); getNumGroups(); removeGroup(const std::string& sid); removeGroup(unsigned int n)

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()

const ListOfGroups * GroupsModelPlugin::getListOfGroups ( ) const

Returns the ListOfGroups from this GroupsModelPlugin.

Returns: the ListOfGroups from this GroupsModelPlugin.

Note: The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

See also: addGroup(const Group* object); createGroup(); getGroup(const std::string& sid); getGroup(unsigned int n); getNumGroups(); removeGroup(const std::string& sid); removeGroup(unsigned int n)

ListOfGroups * GroupsModelPlugin::getListOfGroups ( )

Returns the ListOfGroups from this GroupsModelPlugin.

Returns: the ListOfGroups from this GroupsModelPlugin.

Note: The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

See also: addGroup(const Group* object); createGroup(); getGroup(const std::string& sid); getGroup(unsigned int n); getNumGroups(); removeGroup(const std::string& sid); removeGroup(unsigned int n)

unsigned int GroupsModelPlugin::getNumGroups ( ) const

Get the number of Group objects in this GroupsModelPlugin.

Returns: the number of Group objects in this GroupsModelPlugin.

See also: addGroup(const Group* object); createGroup(); getGroup(const std::string& sid); getGroup(unsigned int n); removeGroup(const std::string& sid); removeGroup(unsigned int n)

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.

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

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

Assignment operator for GroupsModelPlugin.

Parameters

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

Group * GroupsModelPlugin::removeGroup ( unsigned int n )

Removes the nth Group from this GroupsModelPlugin and returns a pointer to it.

Parameters

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

Returns: a pointer to the nth Group in this GroupsModelPlugin.

Warning: The pointer that is returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the element will not be reflected in any resulting SBML document unless the element is added to an SBML Document. Even in this case, the element's deletion is still the responsibility of the caller with two exceptions: if it is used as the "disownedItem" in the ListOf::appendAndOwn() or ListOf::insertAndOwn() functions. All other functions in libsbml add a copy of the element, and do not transfer ownership of the pointer.

See also: addGroup(const Group* object); createGroup(); getGroup(const std::string& sid); getGroup(unsigned int n); getNumGroups(); removeGroup(const std::string& sid)

Group * GroupsModelPlugin::removeGroup ( const std::string & sid )

Removes the Group from this GroupsModelPlugin based on its identifier and returns a pointer to it.

Parameters

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

Returns: the Group in this GroupsModelPlugin based on the identifier or NULL if no such Group exists.

Warning: The pointer that is returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the element will not be reflected in any resulting SBML document unless the element is added to an SBML Document. Even in this case, the element's deletion is still the responsibility of the caller with two exceptions: if it is used as the "disownedItem" in the ListOf::appendAndOwn() or ListOf::insertAndOwn() functions. All other functions in libsbml add a copy of the element, and do not transfer ownership of the pointer.

See also: addGroup(const Group* object); createGroup(); getGroup(const std::string& sid); getGroup(unsigned int n); getNumGroups(); removeGroup(unsigned int n)

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