Inheritance diagram for MultiSpeciesReferencePlugin:

Detailed Description

multi Extension of SpeciesReference for the "multi" package.

The MultiSpeciesReferencePlugin class inherits from the MultiSimpleSpeciesReferencePlugin class, and extends the SpeciesReference class to establish component mappings between the reactant species and the product species when the mappings cannot be inferred from the ids of the SpeciesTypeInstance objects. A MultiSpeciesReferencePlugin object defines an optional ListOfSpeciesTypeComponentMapInProducts child. Only a reaction product can contain the ListOfSpeciesTypeComponentMapInProducts child and it is not necessary to store the mappings again in the reactants.

Public Member Functions
int	addSpeciesTypeComponentMapInProduct (const SpeciesTypeComponentMapInProduct *speciesTypeComponentMapInProduct)
	Adds a copy of the given SpeciesTypeComponentMapInProduct to the ListOfSpeciesTypeComponentMapInProducts. More...

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

SpeciesTypeComponentMapInProduct *	createSpeciesTypeComponentMapInProduct ()
	Creates a new SpeciesTypeComponentMapInProduct object and adds it to the ListOfSpeciesTypeComponentMapInProducts. More...

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

virtual const std::string &	getCompartmentReference () const
	Returns the value of the "compartmentReference" attribute of this SimpleSpeciesReference. 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...

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

const ListOfSpeciesTypeComponentMapInProducts *	getListOfSpeciesTypeComponentMapInProducts () const
	Returns the ListOfSpeciesTypeComponentMapInProducts object. More...

ListOfSpeciesTypeComponentMapInProducts *	getListOfSpeciesTypeComponentMapInProducts ()
	Returns the ListOfSpeciesTypeComponentMapInProducts object. More...

unsigned int	getNumSpeciesTypeComponentMapInProducts () const
	Returns the number of SpeciesTypeComponentMapInProduct objects. 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...

const SpeciesTypeComponentMapInProduct *	getSpeciesTypeComponentMapInProduct (unsigned int n) const
	Returns the nth SpeciesTypeComponentMapInProduct object. More...

SpeciesTypeComponentMapInProduct *	getSpeciesTypeComponentMapInProduct (unsigned int n)
	Returns the nth SpeciesTypeComponentMapInProduct object. More...

const SpeciesTypeComponentMapInProduct *	getSpeciesTypeComponentMapInProduct (const std::string &sid) const
	Returns the SpeciesTypeComponentMapInProduct object with the given identifier `sid`. More...

SpeciesTypeComponentMapInProduct *	getSpeciesTypeComponentMapInProduct (const std::string &sid)
	Returns the SpeciesTypeComponentMapInProduct object with the given identifier `sid`. 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	isSetCompartmentReference () const
	Returns `true` if this SimpleSpeciesReference's "compartmentReference" attribute has been set. More...

virtual bool	isValidTypeForList (SBase *item) const

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

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

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

SpeciesTypeComponentMapInProduct *	removeSpeciesTypeComponentMapInProduct (unsigned int n)
	Removes the nth SpeciesTypeComponentMapInProduct object and returns a pointer to it. More...

SpeciesTypeComponentMapInProduct *	removeSpeciesTypeComponentMapInProduct (const std::string &sid)
	Removes the SpeciesTypeComponentMapInProduct object with the given id 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...

virtual int	setCompartmentReference (const std::string &compartmentReference)
	Sets the value of the "compartmentReference" attribute of this SimpleSpeciesReference. More...

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

virtual int	unsetCompartmentReference ()
	Unsets the value of the "compartmentReference" attribute of this SimpleSpeciesReference. More...

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

Constructor & Destructor Documentation

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

Creates a new MultiSpeciesReferencePlugin 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.

MultiSpeciesReferencePlugin::MultiSpeciesReferencePlugin ( const MultiSpeciesReferencePlugin & orig )

Copy constructor for MultiSpeciesReferencePlugin.

Parameters

orig	the MultiSpeciesReferencePlugin instance to copy.

MultiSpeciesReferencePlugin::~MultiSpeciesReferencePlugin ( )

virtual

Destructor for MultiSpeciesReferencePlugin.

Member Function Documentation

int MultiSpeciesReferencePlugin::addSpeciesTypeComponentMapInProduct ( const SpeciesTypeComponentMapInProduct * speciesTypeComponentMapInProduct )

Adds a copy of the given SpeciesTypeComponentMapInProduct to the ListOfSpeciesTypeComponentMapInProducts.

Parameters

speciesTypeComponentMapInProduct the speciesTypeComponentMapInProduct to be added.

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

MultiSpeciesReferencePlugin * MultiSpeciesReferencePlugin::clone ( ) const

virtual

Creates and returns a deep copy of this MultiSpeciesReferencePlugin object.

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

Reimplemented from MultiSimpleSpeciesReferencePlugin.

SpeciesTypeComponentMapInProduct * MultiSpeciesReferencePlugin::createSpeciesTypeComponentMapInProduct ( )

Creates a new SpeciesTypeComponentMapInProduct object and adds it to the ListOfSpeciesTypeComponentMapInProducts.

Returns: the newly created SpeciesTypeComponentMapInProduct object. Note that the caller owns the returned object and is responsible for deleting it.

List * MultiSpeciesReferencePlugin::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 MultiSimpleSpeciesReferencePlugin.

const std::string & MultiSimpleSpeciesReferencePlugin::getCompartmentReference ( ) const

virtualinherited

Returns the value of the "compartmentReference" attribute of this SimpleSpeciesReference.

Returns: the value of the "compartmentReference" attribute of this SimpleSpeciesReference, as a string.

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.

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 ListOfSpeciesTypeComponentMapInProducts * MultiSpeciesReferencePlugin::getListOfSpeciesTypeComponentMapInProducts ( ) const

Returns the ListOfSpeciesTypeComponentMapInProducts object.

Returns: ListOfSpeciesTypeComponentMapInProducts object within this "multi" SpeciesReference object.

ListOfSpeciesTypeComponentMapInProducts * MultiSpeciesReferencePlugin::getListOfSpeciesTypeComponentMapInProducts ( )

Returns the ListOfSpeciesTypeComponentMapInProducts object.

Returns: ListOfSpeciesTypeComponentMapInProducts object within this "multi" SpeciesReference object.

unsigned int MultiSpeciesReferencePlugin::getNumSpeciesTypeComponentMapInProducts ( ) const

Returns the number of SpeciesTypeComponentMapInProduct objects.

Returns: the number of SpeciesTypeComponentMapInProduct 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()

const SpeciesTypeComponentMapInProduct * MultiSpeciesReferencePlugin::getSpeciesTypeComponentMapInProduct ( unsigned int n ) const

Returns the nth SpeciesTypeComponentMapInProduct object.

Parameters

n	the index number of the SpeciesTypeComponentMapInProduct to get.

Returns: the nth SpeciesTypeComponentMapInProduct in the ListOfSpeciesTypeComponentMapInProducts. If the index is invalid, NULL is returned.

SpeciesTypeComponentMapInProduct * MultiSpeciesReferencePlugin::getSpeciesTypeComponentMapInProduct ( unsigned int n )

Returns the nth SpeciesTypeComponentMapInProduct object.

Parameters

n	the index number of the SpeciesTypeComponentMapInProduct to get.

Returns: the nth SpeciesTypeComponentMapInProduct in the ListOfSpeciesTypeComponentMapInProducts. If the index is invalid, NULL is returned.

const SpeciesTypeComponentMapInProduct * MultiSpeciesReferencePlugin::getSpeciesTypeComponentMapInProduct ( const std::string & sid ) const

Returns the SpeciesTypeComponentMapInProduct object with the given identifier sid.

Parameters

sid	a string representing the id of the SpeciesTypeComponentMapInProduct to get.

Returns: the SpeciesTypeComponentMapInProduct object within the ListOfSpeciesTypeComponentMapInProducts with the given id, or NULL if no such SpeciesTypeComponentMapInProduct exists.

SpeciesTypeComponentMapInProduct * MultiSpeciesReferencePlugin::getSpeciesTypeComponentMapInProduct ( const std::string & sid )

Returns the SpeciesTypeComponentMapInProduct object with the given identifier sid.

Parameters

sid	a string representing the id of the SpeciesTypeComponentMapInProduct to get.

Returns: the SpeciesTypeComponentMapInProduct object within the ListOfSpeciesTypeComponentMapInProducts with the given id, or NULL if no such SpeciesTypeComponentMapInProduct exists.

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 MultiSpeciesReferencePlugin::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.

Reimplemented from MultiSimpleSpeciesReferencePlugin.

bool MultiSimpleSpeciesReferencePlugin::isSetCompartmentReference ( ) const

virtualinherited

Returns true if this SimpleSpeciesReference's "compartmentReference" attribute has been set.

Returns: true if this SimpleSpeciesReference's "compartmentReference" attribute has been set; otherwise, false is returned.

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

virtualinherited

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

Assignment operator for MultiSpeciesReferencePlugin.

Parameters

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

SpeciesTypeComponentMapInProduct * MultiSpeciesReferencePlugin::removeSpeciesTypeComponentMapInProduct ( unsigned int n )

Removes the nth SpeciesTypeComponentMapInProduct object and returns a pointer to it.

Parameters

n	the index of the SpeciesTypeComponentMapInProduct to remove.

Returns: the SpeciesTypeComponentMapInProduct object removed or NULL index was out of range. Note that the caller owns the returned object and is responsible for deleting it.

SpeciesTypeComponentMapInProduct * MultiSpeciesReferencePlugin::removeSpeciesTypeComponentMapInProduct ( const std::string & sid )

Removes the SpeciesTypeComponentMapInProduct object with the given id and returns a pointer to it.

Parameters

sid	a string representing the id of the SpeciesTypeComponentMapInProduct to remove.

Returns: the SpeciesTypeComponentMapInProduct object removed or NULL if no such SpeciesTypeComponentMapInProduct 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 MultiSimpleSpeciesReferencePlugin::setCompartmentReference ( const std::string & compartmentReference )

virtualinherited

Sets the value of the "compartmentReference" attribute of this SimpleSpeciesReference.

Parameters

compartmentReference the new value of the "compartmentReference" 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 MultiSimpleSpeciesReferencePlugin::unsetCompartmentReference ( )

virtualinherited

Unsets the value of the "compartmentReference" attribute of this SimpleSpeciesReference.

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