Inheritance diagram for libsbml.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
def	__init__ (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...

def	addSpeciesTypeComponentMapInProduct (self, speciesTypeComponentMapInProduct)
	Adds a copy of the given SpeciesTypeComponentMapInProduct to the ListOfSpeciesTypeComponentMapInProducts. More...

def	clone (self)
	Creates and returns a deep copy of this MultiSpeciesReferencePlugin object. More...

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

def	getCompartmentReference (self)
	Returns the value of the 'compartmentReference' attribute of this SimpleSpeciesReference. More...

def	getElementByMetaId (self, metaid)
	Return the first child object found with a given meta identifier. More...

def	getElementBySId (self, id)
	Return the first child object found with a given identifier. More...

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

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

def	getListOfAllElements (self, filter=None)
	Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth. More...

def	getListOfSpeciesTypeComponentMapInProducts (self, args)
	Returns the ListOfSpeciesTypeComponentMapInProducts object. More...

def	getNumSpeciesTypeComponentMapInProducts (self)
	Returns the number of SpeciesTypeComponentMapInProduct objects. More...

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

def	getPackageVersion (self)
	Returns the package version of the package extension of this plugin object. More...

def	getParentSBMLObject (self, args)
	Returns the parent object to which this plugin object is connected. More...

def	getPrefix (self)
	Returns the XML namespace prefix of the package to which this plugin object belongs. More...

def	getSBMLDocument (self, args)
	Returns the SBMLDocument object containing this object instance. More...

def	getSpeciesTypeComponentMapInProduct (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...

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

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

def	hasRequiredElements (self)
	Returns `True` if this object has all the required elements. More...

def	isSetCompartmentReference (self)
	Returns `True` if this SimpleSpeciesReference's 'compartmentReference' attribute has been set. More...

def	isValidTypeForList (self, item)

def	removeSpeciesTypeComponentMapInProduct (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...

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

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

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

def	setCompartmentReference (self, compartmentReference)
	Sets the value of the 'compartmentReference' attribute of this SimpleSpeciesReference. More...

def	setElementNamespace (self, uri)
	Sets the XML namespace to which this object belongs. More...

def	unsetCompartmentReference (self)
	Unsets the value of the 'compartmentReference' attribute of this SimpleSpeciesReference. More...

Constructor & Destructor Documentation

def libsbml.MultiSpeciesReferencePlugin.__init__	(	self,
		args
	)

This method has multiple variants; they differ in the arguments they accept.

__init__(string uri, string prefix, MultiPkgNamespaces multins)   MultiSpeciesReferencePlugin
__init__(MultiSpeciesReferencePlugin orig)   MultiSpeciesReferencePlugin

Each variant is described separately below.

Method variant with the following signature:

MultiSpeciesReferencePlugin(MultiSpeciesReferencePlugin orig)

Copy constructor for MultiSpeciesReferencePlugin.

Parameters

orig	the MultiSpeciesReferencePlugin instance to copy.

Method variant with the following signature:

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.

Member Function Documentation

def libsbml.MultiSpeciesReferencePlugin.addSpeciesTypeComponentMapInProduct	(	self,
		speciesTypeComponentMapInProduct
	)

Adds a copy of the given SpeciesTypeComponentMapInProduct to the ListOfSpeciesTypeComponentMapInProducts.

addSpeciesTypeComponentMapInProduct(SpeciesTypeComponentMapInProduct speciesTypeComponentMapInProduct)   int

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

def libsbml.MultiSpeciesReferencePlugin.clone ( self )

Creates and returns a deep copy of this MultiSpeciesReferencePlugin object.

clone()   MultiSpeciesReferencePlugin

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

def libsbml.MultiSpeciesReferencePlugin.createSpeciesTypeComponentMapInProduct ( self )

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

createSpeciesTypeComponentMapInProduct()   SpeciesTypeComponentMapInProduct

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

def libsbml.MultiSimpleSpeciesReferencePlugin.getCompartmentReference ( self )

inherited

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

getCompartmentReference()   string

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

def libsbml.SBasePlugin.getElementByMetaId	(	self,
		metaid
	)

inherited

Return the first child object found with a given meta identifier.

getElementByMetaId(string metaid)   SBase

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.

def libsbml.SBasePlugin.getElementBySId	(	self,
		id
	)

inherited

Return the first child object found with a given identifier.

getElementBySId(string id)   SBase

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.

def libsbml.SBasePlugin.getElementNamespace ( self )

inherited

Returns the namespace URI of the package to which this plugin object belongs.

getElementNamespace()   string

Returns: the XML namespace URI of the SBML Level 3 package implemented by this libSBML package extension.

def libsbml.SBasePlugin.getLevel ( self )

inherited

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

getLevel()   long

Returns: the SBML Level.

See also: getVersion()

def libsbml.SBasePlugin.getListOfAllElements	(	self,
		filter = `None`
	)

inherited

Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth.

getListOfAllElements(ElementFilter filter)   SBaseList
getListOfAllElements()   SBaseList

Returns: a list of all objects that are children of this object.

def libsbml.MultiSpeciesReferencePlugin.getListOfSpeciesTypeComponentMapInProducts	(	self,
		args
	)

Returns the ListOfSpeciesTypeComponentMapInProducts object.

getListOfSpeciesTypeComponentMapInProducts()   ListOfSpeciesTypeComponentMapInProducts

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

def libsbml.MultiSpeciesReferencePlugin.getNumSpeciesTypeComponentMapInProducts ( self )

Returns the number of SpeciesTypeComponentMapInProduct objects.

getNumSpeciesTypeComponentMapInProducts()   long

Returns: the number of SpeciesTypeComponentMapInProduct objects.

def libsbml.SBasePlugin.getPackageName ( self )

inherited

Returns the short-form name of the package to which this plugin object belongs.

getPackageName()   string

Returns: the short-form package name (or nickname) of the SBML package implemented by this package extension.

def libsbml.SBasePlugin.getPackageVersion ( self )

inherited

Returns the package version of the package extension of this plugin object.

getPackageVersion()   long

Returns: the package version of the package extension of this plugin object.

See also: getLevel(); getVersion()

def libsbml.SBasePlugin.getParentSBMLObject	(	self,
		args
	)

inherited

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

getParentSBMLObject()   SBase

Returns: the parent object of this object.

def libsbml.SBasePlugin.getPrefix ( self )

inherited

Returns the XML namespace prefix of the package to which this plugin object belongs.

getPrefix()   string

Returns: the XML namespace prefix of the SBML Level 3 package implemented by this libSBML package extension.

def libsbml.SBasePlugin.getSBMLDocument	(	self,
		args
	)

inherited

Returns the SBMLDocument object containing this object instance.

getSBMLDocument()   SBMLDocument

: 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()

def libsbml.MultiSpeciesReferencePlugin.getSpeciesTypeComponentMapInProduct	(	self,
		args
	)

This method has multiple variants; they differ in the arguments they accept.

getSpeciesTypeComponentMapInProduct(long  n)   SpeciesTypeComponentMapInProduct
getSpeciesTypeComponentMapInProduct(string sid)   SpeciesTypeComponentMapInProduct

Each variant is described separately below.

Method variant with the following signature:

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, None is returned.

Method variant with the following signature:

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 None if no such SpeciesTypeComponentMapInProduct exists.

def libsbml.SBasePlugin.getURI ( self )

inherited

Returns the XML namespace URI for the package to which this object belongs.

getURI()   string

: 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()

def libsbml.SBasePlugin.getVersion ( self )

inherited

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

getVersion()   long

Returns: the SBML Version.

See also: getLevel()

def libsbml.MultiSpeciesReferencePlugin.hasRequiredElements ( self )

Returns True if this object has all the required elements.

hasRequiredElements()   bool

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

def libsbml.MultiSimpleSpeciesReferencePlugin.isSetCompartmentReference ( self )

inherited

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

isSetCompartmentReference()   bool

Returns: True if this SimpleSpeciesReference's 'compartmentReference' attribute has been set; otherwise, False is returned.

def libsbml.SBasePlugin.isValidTypeForList	(	self,
		item
	)

inherited

isValidTypeForList(SBase item)   bool

def libsbml.MultiSpeciesReferencePlugin.removeSpeciesTypeComponentMapInProduct	(	self,
		args
	)

This method has multiple variants; they differ in the arguments they accept.

removeSpeciesTypeComponentMapInProduct(long  n)   SpeciesTypeComponentMapInProduct
removeSpeciesTypeComponentMapInProduct(string sid)   SpeciesTypeComponentMapInProduct

Each variant is described separately below.

Method variant with the following signature:

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 None index was out of range. Note that the caller owns the returned object and is responsible for deleting it.

Method variant with the following signature:

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 None if no such SpeciesTypeComponentMapInProduct exists. Note that the caller owns the returned object and is responsible for deleting it.

def libsbml.SBasePlugin.renameMetaIdRefs	(	self,
		oldid,
		newid
	)

inherited

Replaces all uses of a given meta identifier attribute value with another value.

renameMetaIdRefs(string oldid, string newid)

: 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.

def libsbml.SBasePlugin.renameSIdRefs	(	self,
		oldid,
		newid
	)

inherited

Replaces all uses of a given SIdRef type attribute value with another value.

renameSIdRefs(string oldid, string newid)

: 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.

def libsbml.SBasePlugin.renameUnitSIdRefs	(	self,
		oldid,
		newid
	)

inherited

Replaces all uses of a given UnitSIdRef type attribute value with another value.

renameUnitSIdRefs(string oldid, string newid)

: 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.

def libsbml.MultiSimpleSpeciesReferencePlugin.setCompartmentReference	(	self,
		compartmentReference
	)

inherited

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

setCompartmentReference(string compartmentReference)   int

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:

def libsbml.SBasePlugin.setElementNamespace	(	self,
		uri
	)

inherited

Sets the XML namespace to which this object belongs.

setElementNamespace(string uri)   int

: 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()

def libsbml.MultiSimpleSpeciesReferencePlugin.unsetCompartmentReference ( self )

inherited

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

unsetCompartmentReference()   int

Returns

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

Detailed Description

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation