Inheritance diagram for libsbmlcs.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 (SpeciesTypeComponentMapInProduct speciesTypeComponentMapInProduct)
	Adds a copy of the given SpeciesTypeComponentMapInProduct to the ListOfSpeciesTypeComponentMapInProducts. More...

new SBasePlugin	clone ()
	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...

override void	Dispose ()

long	getColumn ()

new string	getCompartmentReference ()
	Returns the value of the 'compartmentReference' attribute of this SimpleSpeciesReference. More...

new SBase	getElementByMetaId (string metaid)
	Return the first child object found with a given meta identifier. More...

new SBase	getElementBySId (string id)
	Return the first child object found with a given identifier. More...

string	getElementNamespace ()
	Returns the namespace URI of the package to which this plugin object belongs. More...

long	getLevel ()
	Returns the SBML Level of the package extension of this plugin object. More...

long	getLine ()

SBaseList	getListOfAllElements (ElementFilter filter)

SBaseList	getListOfAllElements ()

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

long	getNumSpeciesTypeComponentMapInProducts ()
	Returns the number of SpeciesTypeComponentMapInProduct objects. More...

string	getPackageName ()
	Returns the short-form name of the package to which this plugin object belongs. More...

long	getPackageVersion ()
	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...

string	getPrefix ()
	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...

SBMLExtension	getSBMLExtension ()

SpeciesTypeComponentMapInProduct	getSpeciesTypeComponentMapInProduct (long n)
	Returns the nth SpeciesTypeComponentMapInProduct object. More...

SpeciesTypeComponentMapInProduct	getSpeciesTypeComponentMapInProduct (string sid)
	Returns the SpeciesTypeComponentMapInProduct object with the given identifier `sid`. More...

string	getURI ()
	Returns the XML namespace URI for the package to which this object belongs. More...

long	getVersion ()
	Returns the Version within the SBML Level of the package extension of this plugin object. More...

new bool	hasRequiredElements ()
	Returns `true` if this object has all the required elements. More...

new bool	isSetCompartmentReference ()
	Returns `true` if this SimpleSpeciesReference's 'compartmentReference' attribute has been set. More...

new bool	isValidTypeForList (SBase item)

	MultiSpeciesReferencePlugin (string uri, string prefix, MultiPkgNamespaces multins)
	Creates a new MultiSpeciesReferencePlugin object. More...

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

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

SpeciesTypeComponentMapInProduct	removeSpeciesTypeComponentMapInProduct (string sid)
	Removes the SpeciesTypeComponentMapInProduct object with the given id and returns a pointer to it. More...

new void	renameMetaIdRefs (string oldid, string newid)
	Replaces all uses of a given meta identifier attribute value with another value. More...

new void	renameSIdRefs (string oldid, string newid)
	Replaces all uses of a given `SIdRef` type attribute value with another value. More...

new void	renameUnitSIdRefs (string oldid, string newid)
	Replaces all uses of a given `UnitSIdRef` type attribute value with another value. More...

new int	setCompartmentReference (string compartmentReference)
	Sets the value of the 'compartmentReference' attribute of this SimpleSpeciesReference. More...

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

new int	unsetCompartmentReference ()
	Unsets the value of the 'compartmentReference' attribute of this SimpleSpeciesReference. More...

Protected Attributes
bool	swigCMemOwn

Constructor & Destructor Documentation

libsbmlcs.MultiSpeciesReferencePlugin.MultiSpeciesReferencePlugin	(	string	uri,
		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.

libsbmlcs.MultiSpeciesReferencePlugin.MultiSpeciesReferencePlugin ( MultiSpeciesReferencePlugin orig )

Copy constructor for MultiSpeciesReferencePlugin.

Parameters

orig	the MultiSpeciesReferencePlugin instance to copy.

Member Function Documentation

int libsbmlcs.MultiSpeciesReferencePlugin.addSpeciesTypeComponentMapInProduct ( 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 possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

new SBasePlugin libsbmlcs.MultiSpeciesReferencePlugin.clone ( )

Creates and returns a deep copy of this MultiSpeciesReferencePlugin object.

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

SpeciesTypeComponentMapInProduct libsbmlcs.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.

override void libsbmlcs.MultiSpeciesReferencePlugin.Dispose ( )

virtual

Reimplemented from libsbmlcs.MultiSimpleSpeciesReferencePlugin.

long libsbmlcs.SBasePlugin.getColumn ( )

inherited

new string libsbmlcs.MultiSimpleSpeciesReferencePlugin.getCompartmentReference ( )

inherited

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

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

new SBase libsbmlcs.SBasePlugin.getElementByMetaId ( string metaid )

inherited

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.

new SBase libsbmlcs.SBasePlugin.getElementBySId ( string id )

inherited

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.

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.

string libsbmlcs.SBasePlugin.getElementNamespace ( )

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.

long libsbmlcs.SBasePlugin.getLevel ( )

inherited

Returns the SBML Level of the package extension of this plugin object.

Returns: the SBML Level.

See also: getVersion()

long libsbmlcs.SBasePlugin.getLine ( )

inherited

SBaseList libsbmlcs.SBasePlugin.getListOfAllElements ( ElementFilter filter )

inherited

SBaseList libsbmlcs.SBasePlugin.getListOfAllElements ( )

inherited

ListOfSpeciesTypeComponentMapInProducts libsbmlcs.MultiSpeciesReferencePlugin.getListOfSpeciesTypeComponentMapInProducts ( )

Returns the ListOfSpeciesTypeComponentMapInProducts object.

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

long libsbmlcs.MultiSpeciesReferencePlugin.getNumSpeciesTypeComponentMapInProducts ( )

Returns the number of SpeciesTypeComponentMapInProduct objects.

Returns: the number of SpeciesTypeComponentMapInProduct objects.

string libsbmlcs.SBasePlugin.getPackageName ( )

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.

long libsbmlcs.SBasePlugin.getPackageVersion ( )

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 libsbmlcs.SBasePlugin.getParentSBMLObject ( )

inherited

Returns the parent object to which this plugin object is connected.

Returns: the parent object of this object.

string libsbmlcs.SBasePlugin.getPrefix ( )

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 libsbmlcs.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()

SBMLExtension libsbmlcs.SBasePlugin.getSBMLExtension ( )

inherited

SpeciesTypeComponentMapInProduct libsbmlcs.MultiSpeciesReferencePlugin.getSpeciesTypeComponentMapInProduct ( long 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.

SpeciesTypeComponentMapInProduct libsbmlcs.MultiSpeciesReferencePlugin.getSpeciesTypeComponentMapInProduct ( 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.

string libsbmlcs.SBasePlugin.getURI ( )

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()

long libsbmlcs.SBasePlugin.getVersion ( )

inherited

Returns the Version within the SBML Level of the package extension of this plugin object.

Returns: the SBML Version.

See also: getLevel()

new bool libsbmlcs.MultiSpeciesReferencePlugin.hasRequiredElements ( )

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.

new bool libsbmlcs.MultiSimpleSpeciesReferencePlugin.isSetCompartmentReference ( )

inherited

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.

new bool libsbmlcs.SBasePlugin.isValidTypeForList ( SBase item )

inherited

SpeciesTypeComponentMapInProduct libsbmlcs.MultiSpeciesReferencePlugin.removeSpeciesTypeComponentMapInProduct ( long 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 libsbmlcs.MultiSpeciesReferencePlugin.removeSpeciesTypeComponentMapInProduct ( 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.

new void libsbmlcs.SBasePlugin.renameMetaIdRefs	(	string	oldid,
		string	newid
	)

inherited

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.

new void libsbmlcs.SBasePlugin.renameSIdRefs	(	string	oldid,
		string	newid
	)

inherited

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.

new void libsbmlcs.SBasePlugin.renameUnitSIdRefs	(	string	oldid,
		string	newid
	)

inherited

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.

new int libsbmlcs.MultiSimpleSpeciesReferencePlugin.setCompartmentReference ( string compartmentReference )

inherited

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 possible values returned by this function are:

int libsbmlcs.SBasePlugin.setElementNamespace ( 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. 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()

new int libsbmlcs.MultiSimpleSpeciesReferencePlugin.unsetCompartmentReference ( )

inherited

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

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

Member Data Documentation

bool libsbmlcs.SBasePlugin.swigCMemOwn

protectedinherited

Detailed Description

Public Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation