Inheritance diagram for MultiCompartmentPlugin:

Detailed Description

multi Extension of Compartment for the "multi" package.

The MultiCompartmentPlugin object is used to extend the standard SBML Compartment base object with an optional "compartmentType" attribute, a required "isType" Boolean attribute, and a child ListOfCompartmentReferences. The "isType" attribute flags whether this Compartment should be treated as a standard SBML Compartment (if false), or as a more generic rule-based "type" of Compartment (if true). A compartment "type" is a template (in the sense of prototype) for all Compartment objects referencing it (via "compartmentType" attributes). A Species object directly referencing a compartment type is not a "fully defined" species, but rather a "template" species. If the value of the "isType" attribute is false, the Compartment object is a "not-a-type" compartment, and it is similar to a SBML core Compartment except it can reference a compartment type and can have a ListOfCompartmentReferences child. Each child CompartmentReference in the ListOfCompartmentReferences defines a subcompartment of the parent Compartment. The "compartmentType" attribute identifies this Compartment as the CompartmentType defined elsewhere in the Model. If the "compartmentType" attribute is set, the "isType" attribute must be true.

Public Member Functions
int	addCompartmentReference (const CompartmentReference *compartmentReference)
	Adds a copy of the given CompartmentReference object to the ListOfCompartmentReferences. More...

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

CompartmentReference *	createCompartmentReference ()
	Creates a new CompartmentReference object and adds it to the ListOfCompartmentReferences. More...

virtual List *	getAllElements (ElementFilter *filter=NULL)
	Returns a List of all child SBase objects, including those nested to an arbitary depth. More...

const CompartmentReference *	getCompartmentReference (unsigned int n) const
	Returns the nth CompartmentReference object from the ListOfCompartmentReferences. More...

CompartmentReference *	getCompartmentReference (unsigned int n)
	Returns the nth CompartmentReference object from the ListOfCompartmentReferences. More...

const CompartmentReference *	getCompartmentReference (const std::string &sid) const
	Returns the CompartmentReference with the given identifier `sid`. More...

CompartmentReference *	getCompartmentReference (const std::string &sid)
	Returns the CompartmentReference with the given identifier `sid`. More...

virtual const std::string &	getCompartmentType () const
	Returns the value of the "compartmentType" attribute of this compartment. More...

virtual SBase *	getElementByMetaId (const std::string &metaid)
	Return the first child object found with a given meta identifier. More...

virtual SBase *	getElementBySId (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...

virtual bool	getIsType () const
	Returns the value of the "isType" attribute. More...

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

const ListOfCompartmentReferences *	getListOfCompartmentReferences () const
	Returns the ListOfCompartmentReferences object. More...

ListOfCompartmentReferences *	getListOfCompartmentReferences ()
	Returns the ListOfCompartmentReferences object. More...

unsigned int	getNumCompartmentReferences () const
	Returns the number of CompartmentReference objects in the ListOfCompartmentReferences. 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	hasRequiredElements () const
	Returns `true` if this object has all the required elements. More...

virtual bool	isSetCompartmentType () const
	Returns `true` if this compartment's "compartmentType" attribute has been set. More...

virtual bool	isSetIsType () const
	Returns `true` if this compartment's "isType" attribute has been set. More...

virtual bool	isValidTypeForList (SBase *item) const

	MultiCompartmentPlugin (const std::string &uri, const std::string &prefix, MultiPkgNamespaces *multins)
	Creates a new MultiCompartmentPlugin object. More...

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

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

CompartmentReference *	removeCompartmentReference (unsigned int n)
	Removes the nth CompartmentReference object from the ListOfCompartmentReferences. More...

CompartmentReference *	removeCompartmentReference (const std::string &sid)
	Removes the CompartmentReference object with the given identifier from the ListOfCompartmentReferences. 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...

virtual int	setCompartmentType (const std::string &compartmentType)
	Sets the value of the "compartmentType" attribute on this compartment. More...

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

virtual int	setIsType (bool isType)
	Sets the value of the "isType" attribute. More...

virtual int	unsetCompartmentType ()
	Unsets the value of the "compartmentType" attribute. More...

virtual int	unsetIsType ()
	Unsets the value of the "isType" attribute. More...

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

Constructor & Destructor Documentation

MultiCompartmentPlugin::MultiCompartmentPlugin	(	const std::string &	uri,
		const std::string &	prefix,
		MultiPkgNamespaces *	multins
	)

Creates a new MultiCompartmentPlugin object.

: 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.

Parameters

uri	the URI of the SBML Level 3 package implemented by this libSBML package extension.
prefix	the XML namespace prefix being used for the package.
multins	the namespaces object for the package.

MultiCompartmentPlugin::MultiCompartmentPlugin ( const MultiCompartmentPlugin & orig )

Copy constructor for MultiCompartmentPlugin.

Parameters

orig	the MultiCompartmentPlugin instance to copy.

MultiCompartmentPlugin::~MultiCompartmentPlugin ( )

virtual

Destructor for MultiCompartmentPlugin.

Member Function Documentation

int MultiCompartmentPlugin::addCompartmentReference ( const CompartmentReference * compartmentReference )

Adds a copy of the given CompartmentReference object to the ListOfCompartmentReferences.

Parameters

compartmentReference the CompartmentReference 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:

LIBSBML_OPERATION_SUCCESS

MultiCompartmentPlugin * MultiCompartmentPlugin::clone ( ) const

virtual

Creates and returns a deep copy of this MultiCompartmentPlugin object.

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

Reimplemented from SBasePlugin.

CompartmentReference * MultiCompartmentPlugin::createCompartmentReference ( )

Creates a new CompartmentReference object and adds it to the ListOfCompartmentReferences.

Returns: the newly created CompartmentReference object.

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

virtual

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

Parameters

filter a 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 child objects.

Reimplemented from SBasePlugin.

const CompartmentReference * MultiCompartmentPlugin::getCompartmentReference ( unsigned int n ) const

Returns the nth CompartmentReference object from the ListOfCompartmentReferences.

Parameters

n	the index number of the CompartmentReference to get.

Returns: the nth CompartmentReference, or NULL if the index n is out of range.

CompartmentReference * MultiCompartmentPlugin::getCompartmentReference ( unsigned int n )

Returns the nth CompartmentReference object from the ListOfCompartmentReferences.

Parameters

n	the index number of the CompartmentReference to get.

Returns: the nth CompartmentReference, or NULL if the index n is out of range.

const CompartmentReference * MultiCompartmentPlugin::getCompartmentReference ( const std::string & sid ) const

Returns the CompartmentReference with the given identifier sid.

Parameters

sid	the identifier of the CompartmentReference object to get from the ListOfCompartmentReferences.

Returns: the CompartmentReference object with the given identifier in the ListOfCompartmentReferences, or NULL if no such CompartmentReference exists.

CompartmentReference * MultiCompartmentPlugin::getCompartmentReference ( const std::string & sid )

Returns the CompartmentReference with the given identifier sid.

Parameters

sid	the identifier of the CompartmentReference object to get from the ListOfCompartmentReferences.

Returns: the CompartmentReference object with the given identifier in the ListOfCompartmentReferences, or NULL if no such CompartmentReference exists.

const std::string & MultiCompartmentPlugin::getCompartmentType ( ) const

virtual

Returns the value of the "compartmentType" attribute of this compartment.

Returns: the "compartmentType" attribute value.

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

metaid string, the metaid of the object to find.

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

Reimplemented in QualModelPlugin, GroupsModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.

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

id	string representing the identifier of the object to find.

Returns: pointer to the first object with the given id.

Reimplemented in QualModelPlugin, GroupsModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.

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.

bool MultiCompartmentPlugin::getIsType ( ) const

virtual

Returns the value of the "isType" attribute.

Returns: the value of the "isType" attribute.

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 ListOfCompartmentReferences * MultiCompartmentPlugin::getListOfCompartmentReferences ( ) const

Returns the ListOfCompartmentReferences object.

Returns: the ListOfCompartmentReferences object within this "multi" Compartment object.

ListOfCompartmentReferences * MultiCompartmentPlugin::getListOfCompartmentReferences ( )

Returns the ListOfCompartmentReferences object.

Returns: the ListOfCompartmentReferences object within this "multi" Compartment.

unsigned int MultiCompartmentPlugin::getNumCompartmentReferences ( ) const

Returns the number of CompartmentReference objects in the ListOfCompartmentReferences.

Returns: the number of CompartmentReference objects.

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()

bool MultiCompartmentPlugin::hasRequiredElements ( ) const

virtual

Returns true if this object has all the required elements.

Returns: true if this object has all the elements required by the package specification; otherwise, false will be returned.

bool MultiCompartmentPlugin::isSetCompartmentType ( ) const

virtual

Returns true if this compartment's "compartmentType" attribute has been set.

Returns: true if the "compartmentType" attribute has been set; otherwise, false is returned.

bool MultiCompartmentPlugin::isSetIsType ( ) const

virtual

Returns true if this compartment's "isType" attribute has been set.

Returns: true if the "isType" attribute has been set; otherwise, false is returned.

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

virtualinherited

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

Assignment operator for MultiCompartmentPlugin.

Parameters

rhs	the object whose values are used as the basis of the assignment

CompartmentReference * MultiCompartmentPlugin::removeCompartmentReference ( unsigned int n )

Removes the nth CompartmentReference object from the ListOfCompartmentReferences.

Parameters

n	the index of the CompartmentReference to remove.

Returns: the CompartmentReference object removed, or NULL if the given index n is out of range. Note that the caller owns the returned object and is responsible for deleting it.

CompartmentReference * MultiCompartmentPlugin::removeCompartmentReference ( const std::string & sid )

Removes the CompartmentReference object with the given identifier from the ListOfCompartmentReferences.

Parameters

sid	the id of the CompartmentReference to remove.

Returns: the CompartmentReference object removed, or NULL if no such CompartmentReference exists. Note that the caller owns the returned object and is responsible for deleting it.

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 MultiCompartmentPlugin::setCompartmentType ( const std::string & compartmentType )

virtual

Sets the value of the "compartmentType" attribute on this compartment.

Parameters

compartmentType the new value for the attribute.

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:

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.

int MultiCompartmentPlugin::setIsType ( bool isType )

virtual

Sets the value of the "isType" attribute.

Parameters

isType the new value of the attribute.

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:

int MultiCompartmentPlugin::unsetCompartmentType ( )

virtual

Unsets the value of the "compartmentType" attribute.

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:

int MultiCompartmentPlugin::unsetIsType ( )

virtual

Unsets the value of the "isType" attribute.

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:

Detailed Description

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation