libSBML C++ API  libSBML 5.13.0 C++ API
GroupsModelPlugin Class Reference
Inheritance diagram for GroupsModelPlugin:
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Detailed Description

{groups}

groups Extension of Model.

The GroupsModelPlugin class inherits from the SBMLSBasePlugin class, and codifies the extensions to the Model class defined in the SBML Level 3 Groups (“groups”) package. This extension allows a Model to contain an optional ListOfGroups object inside a new element called <listOfGroups>. This list holds the definition of optional groups defined in the model.

A "group" in SBML Level 3 provides a mechanism for indicating that components of an SBML model are related in some way. Groups may contain either the same or different types of SBML objects, and groups may be nested if desired. There are no predefined behavioral semantics associated with groups. All groups in a given model have to be defined as Group objects and included in the ListOfGroups object attached to the Model object containing them.

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 GroupsModelPluginclone () 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...
 
GroupcreateGroup ()
 Creates a new Group object. More...
 
virtual ListgetAllElements (ElementFilter *filter=NULL)
 Returns a List of all child SBase objects, including those nested to an arbitrary depth. More...
 
virtual SBasegetElementByMetaId (const std::string &metaid)
 Returns the first child element that has the given metaid. More...
 
virtual SBasegetElementBySId (const std::string &id)
 Returns the first child element that has the given id. More...
 
const std::string & getElementNamespace () const
 Returns the namespace URI of the package to which this plugin object belongs. More...
 
GroupgetGroup (unsigned int n)
 Returns the nth Group. More...
 
const GroupgetGroup (unsigned int n) const
 Get a Group from the GroupsModelPlugin. More...
 
GroupgetGroup (const std::string &sid)
 Get a Group from the GroupsModelPlugin based on its identifier. More...
 
const GroupgetGroup (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 ListOfGroupsgetListOfGroups () const
 Returns the ListOfGroups from this GroupsModelPlugin. More...
 
ListOfGroupsgetListOfGroups ()
 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...
 
SBasegetParentSBMLObject ()
 Returns the parent object to which this plugin object is connected. More...
 
const SBasegetParentSBMLObject () 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...
 
SBMLDocumentgetSBMLDocument ()
 Returns the SBMLDocument object containing this object instance. More...
 
const SBMLDocumentgetSBMLDocument () 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
 
GroupsModelPluginoperator= (const GroupsModelPlugin &rhs)
 Assignment operator for GroupsModelPlugin. More...
 
GroupremoveGroup (unsigned int n)
 Removes the nth Group. More...
 
GroupremoveGroup (const std::string &sid)
 Removes the Group from this GroupsModelPlugin based on its identifier. 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 ~GroupsModelPlugin ()
 Destructor for GroupsModelPlugin. More...
 

Constructor & Destructor Documentation

§ GroupsModelPlugin() [1/2]

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
uria string, representing the URI of the package.
prefixa string, the prefix to be used.
groupsnsa pointer to the GroupsPkgNamespaces object to be used.

§ GroupsModelPlugin() [2/2]

GroupsModelPlugin::GroupsModelPlugin ( const GroupsModelPlugin orig)

Copy constructor for GroupsModelPlugin.

Parameters
origthe GroupsModelPlugin instance to copy.

§ ~GroupsModelPlugin()

GroupsModelPlugin::~GroupsModelPlugin ( )
virtual

Destructor for GroupsModelPlugin.

Member Function Documentation

§ addGroup()

int GroupsModelPlugin::addGroup ( const Group g)

Adds a copy of the given Group to this GroupsModelPlugin.

Parameters
gthe Group object to add.

§ clone()

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.

§ copyInformationToNestedLists()

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.

§ createGroup()

Group * GroupsModelPlugin::createGroup ( )

Creates a new Group object.

This method creates a new Group object, adds it to this GroupsModelPlugin object, and returns the Group object created.

Returns
a new Group object instance.
See also
addGroup(const Group* g)
getGroup(const std::string& sid)
getGroup(unsigned int n)
removeGroup(unsigned int n)
removeGroup(const std::string& sid)
Examples:
groups_example1.cpp, and groups_example2.cpp.

§ getAllElements()

List * GroupsModelPlugin::getAllElements ( ElementFilter filter = NULL)
virtual

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

Parameters
filteran 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.

§ getElementByMetaId()

SBase * GroupsModelPlugin::getElementByMetaId ( const std::string &  metaid)
virtual

Returns the first child element that has the given metaid.

Parameters
metaida 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.

§ getElementBySId()

SBase * GroupsModelPlugin::getElementBySId ( const std::string &  id)
virtual

Returns the first child element that has the given id.

This method searches the model-wide SId namespace for the id.

Parameters
ida 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.

§ 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.

§ getGroup() [1/4]

Group * GroupsModelPlugin::getGroup ( unsigned int  n)

Returns the nth Group.

Parameters
nan unsigned int representing the index of the Group to retrieve.
Returns
the nth Group in the ListOfGroups within this GroupsModelPlugin.
See also
addGroup(const Group* g)
createGroup()
getGroup(const std::string& sid)
getGroup(unsigned int n)
getNumGroups()
removeGroup(unsigned int n)
removeGroup(const std::string& sid)

§ getGroup() [2/4]

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

§ getGroup() [3/4]

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

Get a Group from the GroupsModelPlugin based on its identifier.

Parameters
sida string representing the identifier of the Group to retrieve.
Returns
the Group in the ListOfGroups within this GroupsModelPlugin with the given identifier sid, or NULL if no such Group exists.
See also
addGroup(const Group* g)
createGroup()
getGroup(const std::string& sid)
getGroup(unsigned int n)
getNumGroups()
removeGroup(unsigned int n)
removeGroup(const std::string& sid)

§ getGroup() [4/4]

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

Get a Group from the GroupsModelPlugin based on its identifier.

Parameters
sida string representing the identifier of the Group to retrieve.
Returns
the Group in the ListOfGroups within this GroupsModelPlugin with the given identifier sid, or NULL if no such Group exists.
See also
addGroup(const Group* g)
createGroup()
getGroup(unsigned int n)
getNumGroups()
removeGroup(unsigned int n)
removeGroup(const std::string& sid)

§ 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()

§ getListOfGroups() [1/2]

§ getListOfGroups() [2/2]

§ getNumGroups()

unsigned int GroupsModelPlugin::getNumGroups ( ) const

§ 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=()

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

Assignment operator for GroupsModelPlugin.

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

§ removeGroup() [1/2]

Group * GroupsModelPlugin::removeGroup ( unsigned int  n)

Removes the nth Group.

This removes the nth Group from this GroupsModelPlugin object and returns a pointer to it.

Parameters
nan unsigned int representing the index of the Group to remove.
Returns
a pointer to the nth Group in this GroupsModelPlugin.
Note
The caller owns the returned object and is responsible for deleting it.
See also
addGroup(const Group* g)
createGroup()
getGroup(const std::string& sid)
getGroup(unsigned int n)
getNumGroups()
removeGroup(const std::string& sid)

§ removeGroup() [2/2]

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

Removes the Group from this GroupsModelPlugin based on its identifier.

This method removes the Group from this GroupsModelPlugin based on its identifier, and returns a pointer to it.

Parameters
sida 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.
Note
The caller owns the returned object and is responsible for deleting it.
See also
addGroup(const Group* g)
createGroup()
getGroup(const std::string& sid)
getGroup(unsigned int n)
getNumGroups()

§ 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
urithe URI to assign to this object.
Examples:
convertLayout.cpp.