libSBML C++ API  5.20.4
GroupsSBMLDocumentPlugin Class Reference
Inheritance diagram for GroupsSBMLDocumentPlugin:
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Detailed Description

groups Extension of SBMLDocument.

This class extends SBMLDocumentPlugin, a class that is used by libSBML plugins as part of their implementation of SBML Level 3 packages.

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.)

Public Member Functions

virtual GroupsSBMLDocumentPluginclone () const
 Creates and returns a deep copy of this GroupsSBMLDocumentPlugin object. More...
 
virtual ListgetAllElements (ElementFilter *filter=NULL)
 Returns all child objects of this object. More...
 
virtual SBasegetElementByMetaId (const std::string &metaid)
 Return the first child object found with a given meta identifier. More...
 
virtual SBasegetElementBySId (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...
 
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...
 
virtual bool getRequired () const
 Returns the value of the "required" attribute. 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...
 
 GroupsSBMLDocumentPlugin (const GroupsSBMLDocumentPlugin &orig)
 Copy constructor for GroupsSBMLDocumentPlugin. More...
 
 GroupsSBMLDocumentPlugin (const std::string &uri, const std::string &prefix, GroupsPkgNamespaces *groupsns)
 Creates a new GroupsSBMLDocumentPlugin using the given URI, prefix and package namespace. More...
 
virtual bool isSetRequired () const
 Returns the value of the "required" attribute. More...
 
virtual bool isValidTypeForList (SBase *item) const
 
GroupsSBMLDocumentPluginoperator= (const GroupsSBMLDocumentPlugin &rhs)
 Assignment operator for GroupsSBMLDocumentPlugin. 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 int setRequired (bool value)
 Sets the SBML "required" attribute value. More...
 
virtual int unsetRequired ()
 Unsets the value of the "required" attribute of this SBMLDocumentPlugin. More...
 
virtual ~GroupsSBMLDocumentPlugin ()
 Destructor for GroupsSBMLDocumentPlugin. More...
 

Constructor & Destructor Documentation

◆ GroupsSBMLDocumentPlugin() [1/2]

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

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

Parameters
uria string, representing the URI of the SBML Level 3 package implemented by this libSBML package extension.
prefixa string, the XML namespace prefix being used for this package.
groupsnsa 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.

◆ GroupsSBMLDocumentPlugin() [2/2]

GroupsSBMLDocumentPlugin::GroupsSBMLDocumentPlugin ( const GroupsSBMLDocumentPlugin orig)

Copy constructor for GroupsSBMLDocumentPlugin.

Parameters
origthe GroupsSBMLDocumentPlugin instance to copy.

◆ ~GroupsSBMLDocumentPlugin()

GroupsSBMLDocumentPlugin::~GroupsSBMLDocumentPlugin ( )
virtual

Destructor for GroupsSBMLDocumentPlugin.

Member Function Documentation

◆ clone()

GroupsSBMLDocumentPlugin * GroupsSBMLDocumentPlugin::clone ( ) const
virtual

Creates and returns a deep copy of this GroupsSBMLDocumentPlugin object.

Returns
a (deep) copy of this GroupsSBMLDocumentPlugin object.

Reimplemented from SBMLDocumentPlugin.

◆ getAllElements()

List * SBasePlugin::getAllElements ( ElementFilter filter = NULL)
virtualinherited

Returns all child objects of this object.

This returns a List object containing all child SBase objects of this one, at any nesting depth. Optionally, callers can supply a filter that will establish the search criteria for matching objects.

Parameters
filtera pointer to an ElementFilter, which causes the function to return only elements that match a particular set of constraints. If NULL (the default), the function will return all child objects.
Returns
a List of pointers to all children objects.

Reimplemented in SpatialParameterPlugin, SpatialModelPlugin, SpatialCompartmentPlugin, RenderListOfLayoutsPlugin, RenderLayoutPlugin, QualModelPlugin, MultiSpeciesReferencePlugin, MultiSpeciesPlugin, MultiSimpleSpeciesReferencePlugin, MultiModelPlugin, MultiCompartmentPlugin, LayoutModelPlugin, GroupsModelPlugin, FbcSBasePlugin, FbcReactionPlugin, FbcModelPlugin, DistribSBasePlugin, CompSBMLDocumentPlugin, CompSBasePlugin, and CompModelPlugin.

◆ getElementByMetaId()

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
metaidstring, the metaid of the object to find.
Returns
pointer to the first object found with the given metaid.

Reimplemented in SpatialParameterPlugin, SpatialModelPlugin, SpatialCompartmentPlugin, QualModelPlugin, GroupsModelPlugin, FbcSBasePlugin, FbcModelPlugin, DistribSBasePlugin, CompSBMLDocumentPlugin, CompSBasePlugin, and CompModelPlugin.

◆ getElementBySId()

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
idstring representing the identifier of the object to find.
Returns
pointer to the first object with the given id.

Reimplemented in SpatialParameterPlugin, SpatialModelPlugin, SpatialCompartmentPlugin, QualModelPlugin, GroupsModelPlugin, FbcSBasePlugin, FbcModelPlugin, DistribSBasePlugin, CompSBMLDocumentPlugin, CompSBasePlugin, and CompModelPlugin.

◆ 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.

◆ 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()

◆ 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.

◆ getRequired()

bool SBMLDocumentPlugin::getRequired ( ) const
virtualinherited

Returns the value of the "required" attribute.

SBML Level 3 requires that every package defines an attribute named "required" on the root <sbml> element in an SBML file or data stream. The attribute, being in the namespace of the Level 3 package in question, must be prefixed by the XML namespace prefix associated with the package. The value of the "required" attribute indicates whether constructs in that package may change the mathematical interpretation of constructs defined in SBML Level 3 Core. A "required" value of true indicates that the package may do so. The value of the attribute is set by the Level 3 package specification, and does not depend on the actual presence or absence of particular package constructs in a given SBML document: in other words, if the package specification defines any construct that can change the model's meaning, the value of the "required" attribute must always be set to true in any SBML document that uses the package.

The XML namespace declaration for an SBML Level 3 package is an indication that a model makes use of features defined by that package, while the "required" attribute indicates whether the features may be ignored without compromising the mathematical meaning of the model. Both are necessary for a complete reference to an SBML Level 3 package.

Returns
the bool value of "required" attribute for the SBML package.
See also
setRequired(bool value)
isSetRequired()
unsetRequired()

◆ 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()

◆ isSetRequired()

bool SBMLDocumentPlugin::isSetRequired ( ) const
virtualinherited

Returns the value of the "required" attribute.

SBML Level 3 requires that every package defines an attribute named "required" on the root <sbml> element in an SBML file or data stream. The attribute, being in the namespace of the Level 3 package in question, must be prefixed by the XML namespace prefix associated with the package. The value of the "required" attribute indicates whether constructs in that package may change the mathematical interpretation of constructs defined in SBML Level 3 Core. A "required" value of true indicates that the package may do so. The value of the attribute is set by the Level 3 package specification, and does not depend on the actual presence or absence of particular package constructs in a given SBML document: in other words, if the package specification defines any construct that can change the model's meaning, the value of the "required" attribute must always be set to true in any SBML document that uses the package.

The XML namespace declaration for an SBML Level 3 package is an indication that a model makes use of features defined by that package, while the "required" attribute indicates whether the features may be ignored without compromising the mathematical meaning of the model. Both are necessary for a complete reference to an SBML Level 3 package.

Returns
true if the "required" attribute of this SBMLDocument has been set to true, false otherwise.

◆ isValidTypeForList()

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

◆ operator=()

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

Assignment operator for GroupsSBMLDocumentPlugin.

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

◆ renameMetaIdRefs()

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
oldidthe old identifier.
newidthe new identifier.

◆ renameSIdRefs()

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
oldidthe old identifier.
newidthe new identifier.

Reimplemented in FbcReactionPlugin.

◆ renameUnitSIdRefs()

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
oldidthe old identifier.
newidthe new identifier.

◆ 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.
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:
See also
getElementNamespace()
Examples
convertLayout.cpp.

◆ setRequired()

int SBMLDocumentPlugin::setRequired ( bool  value)
virtualinherited

Sets the SBML "required" attribute value.

SBML Level 3 requires that every package defines an attribute named "required" on the root <sbml> element in an SBML file or data stream. The attribute, being in the namespace of the Level 3 package in question, must be prefixed by the XML namespace prefix associated with the package. The value of the "required" attribute indicates whether constructs in that package may change the mathematical interpretation of constructs defined in SBML Level 3 Core. A "required" value of true indicates that the package may do so. The value of the attribute is set by the Level 3 package specification, and does not depend on the actual presence or absence of particular package constructs in a given SBML document: in other words, if the package specification defines any construct that can change the model's meaning, the value of the "required" attribute must always be set to true in any SBML document that uses the package.

The XML namespace declaration for an SBML Level 3 package is an indication that a model makes use of features defined by that package, while the "required" attribute indicates whether the features may be ignored without compromising the mathematical meaning of the model. Both are necessary for a complete reference to an SBML Level 3 package.

Parameters
valuethe value to be assigned to the "required" attribute. The "required" attribute takes a Boolean value, either true or false.
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:
See also
getRequired()
isSetRequired()
unsetRequired()

Reimplemented in CompSBMLDocumentPlugin.

◆ unsetRequired()

int SBMLDocumentPlugin::unsetRequired ( )
virtualinherited

Unsets the value of the "required" attribute of this SBMLDocumentPlugin.

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: