Inheritance diagram for libsbmlcs.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 (CompartmentReference compartmentReference)
	Adds a copy of the given CompartmentReference object to the ListOfCompartmentReferences. More...

new SBasePlugin	clone ()
	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...

override void	Dispose ()

long	getColumn ()

CompartmentReference	getCompartmentReference (long n)
	Returns the nth CompartmentReference object from the ListOfCompartmentReferences. More...

CompartmentReference	getCompartmentReference (string sid)
	Returns the CompartmentReference with the given identifier `sid`. More...

new string	getCompartmentType ()
	Returns the value of the 'compartmentType' attribute of this compartment. 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...

new bool	getIsType ()
	Returns the value of the 'isType' attribute. More...

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

long	getLine ()

SBaseList	getListOfAllElements (ElementFilter filter)

SBaseList	getListOfAllElements ()

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

long	getNumCompartmentReferences ()
	Returns the number of CompartmentReference objects in the ListOfCompartmentReferences. 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 ()

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

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

new bool	isValidTypeForList (SBase item)

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

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

CompartmentReference	removeCompartmentReference (long n)
	Removes the nth CompartmentReference object from the ListOfCompartmentReferences. More...

CompartmentReference	removeCompartmentReference (string sid)
	Removes the CompartmentReference object with the given identifier from the ListOfCompartmentReferences. 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	setCompartmentType (string compartmentType)
	Sets the value of the 'compartmentType' attribute on this compartment. More...

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

new int	setIsType (bool isType)
	Sets the value of the 'isType' attribute. More...

new int	unsetCompartmentType ()
	Unsets the value of the 'compartmentType' attribute. More...

new int	unsetIsType ()
	Unsets the value of the 'isType' attribute. More...

Protected Attributes
bool	swigCMemOwn

Constructor & Destructor Documentation

libsbmlcs.MultiCompartmentPlugin.MultiCompartmentPlugin	(	string	uri,
		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.

libsbmlcs.MultiCompartmentPlugin.MultiCompartmentPlugin ( MultiCompartmentPlugin orig )

Copy constructor for MultiCompartmentPlugin.

Parameters

orig	the MultiCompartmentPlugin instance to copy.

Member Function Documentation

int libsbmlcs.MultiCompartmentPlugin.addCompartmentReference ( 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 possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

new SBasePlugin libsbmlcs.MultiCompartmentPlugin.clone ( )

Creates and returns a deep copy of this MultiCompartmentPlugin object.

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

CompartmentReference libsbmlcs.MultiCompartmentPlugin.createCompartmentReference ( )

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

Returns: the newly created CompartmentReference object.

override void libsbmlcs.MultiCompartmentPlugin.Dispose ( )

virtual

Reimplemented from libsbmlcs.SBasePlugin.

long libsbmlcs.SBasePlugin.getColumn ( )

inherited

CompartmentReference libsbmlcs.MultiCompartmentPlugin.getCompartmentReference ( long 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.

CompartmentReference libsbmlcs.MultiCompartmentPlugin.getCompartmentReference ( 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.

new string libsbmlcs.MultiCompartmentPlugin.getCompartmentType ( )

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

Returns: the 'compartmentType' attribute value.

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.

new bool libsbmlcs.MultiCompartmentPlugin.getIsType ( )

Returns the value of the 'isType' attribute.

Returns: the value of the 'isType' attribute.

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

ListOfCompartmentReferences libsbmlcs.MultiCompartmentPlugin.getListOfCompartmentReferences ( )

Returns the ListOfCompartmentReferences object.

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

long libsbmlcs.MultiCompartmentPlugin.getNumCompartmentReferences ( )

Returns the number of CompartmentReference objects in the ListOfCompartmentReferences.

Returns: the number of CompartmentReference 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

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.MultiCompartmentPlugin.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.MultiCompartmentPlugin.isSetCompartmentType ( )

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

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

new bool libsbmlcs.MultiCompartmentPlugin.isSetIsType ( )

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

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

new bool libsbmlcs.SBasePlugin.isValidTypeForList ( SBase item )

inherited

CompartmentReference libsbmlcs.MultiCompartmentPlugin.removeCompartmentReference ( long 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 libsbmlcs.MultiCompartmentPlugin.removeCompartmentReference ( 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.

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.MultiCompartmentPlugin.setCompartmentType ( string compartmentType )

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 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.MultiCompartmentPlugin.setIsType ( bool isType )

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 possible values returned by this function are:

new int libsbmlcs.MultiCompartmentPlugin.unsetCompartmentType ( )

Unsets the value of the 'compartmentType' attribute.

Returns

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

new int libsbmlcs.MultiCompartmentPlugin.unsetIsType ( )

Unsets the value of the 'isType' attribute.

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