Inheritance diagram for libsbml.MultiModelPlugin:

Detailed Description

multi Extension of Model.

This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.

The MultiModelPlugin object is used to extend the standard SBML Model object to allow a ListOfSpeciesTypes child.

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

def	addMultiSpeciesType (self, multiSpeciesType)
	Adds a copy of the given MultiSpeciesType to the ListOfMultiSpeciesTypes in this plugin object. More...

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

def	createBindingSiteSpeciesType (self)
	Creates a new BindingSiteSpeciesType object and adds it to the ListOfMultiSpeciesTypes in this plugin object. More...

def	createIntraSpeciesReaction (self)
	Creates a new IntraSpeciesReaction object and adds it to the ListOfReactions. More...

def	createMultiSpeciesType (self)
	Creates a new MultiSpeciesType object and adds it to the ListOfMultiSpeciesTypes in this plugin object. 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	getListOfMultiSpeciesTypes (self, args)
	Returns the ListOfMultiSpeciesTypes in this plugin object. More...

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

def	getNumMultiSpeciesTypes (self)
	Returns the number of MultiSpeciesType objects in this plugin object. 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	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	isValidTypeForList (self, item)

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

Constructor & Destructor Documentation

def libsbml.MultiModelPlugin.__init__	(	self,
		args
	)

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

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

Each variant is described separately below.

Method variant with the following signature:

MultiModelPlugin(MultiModelPlugin orig)

Copy constructor for MultiModelPlugin.

Parameters

orig	the MultiModelPlugin instance to copy.

Method variant with the following signature:

MultiModelPlugin(string uri, string prefix, MultiPkgNamespaces multins)

Creates a new MultiModelPlugin object using the given parameters.

: 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.MultiModelPlugin.addMultiSpeciesType	(	self,
		multiSpeciesType
	)

Adds a copy of the given MultiSpeciesType to the ListOfMultiSpeciesTypes in this plugin object.

addMultiSpeciesType(MultiSpeciesType multiSpeciesType)   int

Parameters

multiSpeciesType the multiSpeciesType 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.MultiModelPlugin.clone ( self )

Creates and returns a deep copy of this MultiModelPlugin object.

clone()   MultiModelPlugin

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

def libsbml.MultiModelPlugin.createBindingSiteSpeciesType ( self )

Creates a new BindingSiteSpeciesType object and adds it to the ListOfMultiSpeciesTypes in this plugin object.

createBindingSiteSpeciesType()   BindingSiteSpeciesType

Returns: the newly created BindingSiteSpeciesType object.

def libsbml.MultiModelPlugin.createIntraSpeciesReaction ( self )

Creates a new IntraSpeciesReaction object and adds it to the ListOfReactions.

createIntraSpeciesReaction()   IntraSpeciesReaction

Returns: the newly created IntraSpeciesReaction object.

def libsbml.MultiModelPlugin.createMultiSpeciesType ( self )

Creates a new MultiSpeciesType object and adds it to the ListOfMultiSpeciesTypes in this plugin object.

createMultiSpeciesType()   MultiSpeciesType

Returns: the newly created MultiSpeciesType object.

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.MultiModelPlugin.getListOfMultiSpeciesTypes	(	self,
		args
	)

Returns the ListOfMultiSpeciesTypes in this plugin object.

getListOfMultiSpeciesTypes()   ListOfMultiSpeciesTypes

Returns: ListOfMultiSpeciesTypes object in this plugin object.

def libsbml.MultiModelPlugin.getMultiSpeciesType	(	self,
		args
	)

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

getMultiSpeciesType(long  n)   MultiSpeciesType
getMultiSpeciesType(string sid)   MultiSpeciesType

Each variant is described separately below.

Method variant with the following signature:

getMultiSpeciesType(long n)

Returns the MultiSpeciesType object that belongs to the given index. If the index is invalid, None is returned.

Parameters

n	the index number of the MultiSpeciesType to get

Returns: the nth MultiSpeciesType in the ListOfMultiSpeciesTypes If the index n is invalid, None is returned.

Method variant with the following signature:

getMultiSpeciesType(string sid)

Returns the MultiSpeciesType object based on its identifier.

Parameters

sid	a string representing the id of the MultiSpeciesType to get

Returns: MultiSpeciesType in the ListOfMultiSpeciesTypes with the given id or None if no such MultiSpeciesType exists.

def libsbml.MultiModelPlugin.getNumMultiSpeciesTypes ( self )

Returns the number of MultiSpeciesType objects in this plugin object.

getNumMultiSpeciesTypes()   long

Returns: the number of MultiSpeciesType objects in this plugin object.

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.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.MultiModelPlugin.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.SBasePlugin.isValidTypeForList	(	self,
		item
	)

inherited

isValidTypeForList(SBase item)   bool

def libsbml.MultiModelPlugin.removeMultiSpeciesType	(	self,
		args
	)

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

removeMultiSpeciesType(long  n)   MultiSpeciesType
removeMultiSpeciesType(string sid)   MultiSpeciesType

Each variant is described separately below.

Method variant with the following signature:

removeMultiSpeciesType(long n)

Removes the nth MultiSpeciesType object from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters

n	the index of the MultiSpeciesType to remove

Returns: the MultiSpeciesType object removed or None index was out of range.

Method variant with the following signature:

removeMultiSpeciesType(string sid)

Removes the MultiSpeciesType object with the given id from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters

sid	a string representing the id of the MultiSpeciesType to remove

Returns: the MultiSpeciesType object removed or None if no such MultiSpeciesType exists.

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.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()

Detailed Description

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation