Inheritance diagram for libsbml.CompSBasePlugin:

Detailed Description

comp Extension of SBase.

The CompSBasePlugin class inherits from the SBasePlugin class, and codifies the extensions to the SBase class defined in the Hierarchical Model Composition (“comp”) package. This extension allows the modeler to define one or more submodel elements which the parent SBase object replaces, and/or a single submodel element which replaces the parent SBase object. This is accomplished through the addition of an optional ListOfReplacedElements child, which may contain one or more ReplacedElement objects, each of which references a submodel object to be replaced by the containing SBase object, and through the addition of a single optional ReplacedBy child, which references a submodel object which is to replace the containing SBase object. If a single SBase element both contains a ListOfReplacedElements and has a ReplacedBy child, it and all the referenced ReplacedElement objects are to be replaced by the object referenced by the ReplacedBy element.

See also: ReplacedElement; ReplacedBy

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

def	addReplacedElement (self, replacedElement)
	Adds a copy of the given ReplacedElement object to the list of ReplacedElements. More...

def	clearReplacedElements (self)
	Remove all ReplacedElements, if any exist. More...

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

def	createReplacedBy (self)
	Creates a new, empty ReplacedBy, adds it to this CompSBasePlugin and returns the created ReplacedBy. More...

def	createReplacedElement (self)
	Creates a ReplacedElement object, adds it to the end of the ReplacedElement objects list and returns a pointer to the newly created object. More...

def	getElementByMetaId (self, metaid)
	Returns the first child element it can find with the given `metaid`, or itself if it has the given `metaid`, or `None` if no such object is found. More...

def	getElementBySId (self, id)
	Returns the first child element found that has the given `id` in the model-wide SId namespace, or `None` if no such object is found. 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	getListOfReplacedElements (self, args)
	Returns the ListOf object that holds all replacedElements. More...

def	getNumReplacedElements (self)
	Returns the number of ReplacedElements for this CompSBasePlugin. 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	getReplacedBy (self, args)
	Get the child ReplacedBy of this SBase. More...

def	getReplacedElement (self, args)
	Returns the ReplacedElement with the given index. 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	isSetReplacedBy (self)
	Predicate for testing whether the ReplacedBy for this SBase is set. More...

def	isValidTypeForList (self, item)

def	logInvalidId (self, attribute, wrongattribute)
	Helper to log a common type of error. More...

def	removeReplacedElement (self, index)
	Removes the ReplacedElement with the given index. 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...

def	setReplacedBy (self, replacedBy)
	Sets the ReplacedBy definition of this SBase to a copy of the given ReplacedBy object instance. More...

def	unsetReplacedBy (self)
	Unsets the child ReplacedBy of this SBase. More...

Constructor & Destructor Documentation

def libsbml.CompSBasePlugin.__init__	(	self,
		args
	)

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

__init__(string uri, string prefix, CompPkgNamespaces compns)   CompSBasePlugin
__init__(CompSBasePlugin orig)   CompSBasePlugin

Each variant is described separately below.

Method variant with the following signature:

CompSBasePlugin(string uri, string prefix, CompPkgNamespaces compns)

Creates a new CompSBasePlugin 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.
compns	the namespaces object for the package.

Method variant with the following signature:

CompSBasePlugin(CompSBasePlugin orig)

Copy constructor. Creates a copy of this CompSBasePlugin object.

Parameters

orig	the instance to copy.

Member Function Documentation

def libsbml.CompSBasePlugin.addReplacedElement	(	self,
		replacedElement
	)

Adds a copy of the given ReplacedElement object to the list of ReplacedElements.

addReplacedElement(ReplacedElement replacedElement)   int

Parameters

replacedElement the ReplacedElement object to be added to the list of ReplacedElements. Fails if the added ReplacedElement is None, does not match the level/version/package of the parent object, or cannot be added to the list of replaced elements.

Returns

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

def libsbml.CompSBasePlugin.clearReplacedElements ( self )

Remove all ReplacedElements, if any exist.

clearReplacedElements()

def libsbml.CompSBasePlugin.clone ( self )

Creates and returns a deep copy of this CompSBasePlugin object.

clone()   CompSBasePlugin

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

def libsbml.CompSBasePlugin.createReplacedBy ( self )

Creates a new, empty ReplacedBy, adds it to this CompSBasePlugin and returns the created ReplacedBy.

createReplacedBy()   ReplacedBy

Returns: the newly created ReplacedBy object instance.

def libsbml.CompSBasePlugin.createReplacedElement ( self )

Creates a ReplacedElement object, adds it to the end of the ReplacedElement objects list and returns a pointer to the newly created object.

createReplacedElement()   ReplacedElement

Returns: a newly created ReplacedElement object.

def libsbml.CompSBasePlugin.getElementByMetaId	(	self,
		metaid
	)

Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or None if no such object is found.

getElementByMetaId(string metaid)   SBase

Parameters

metaid string representing the metaid of the object to find.

Returns: a pointer to the SBase element with the given metaid.

def libsbml.CompSBasePlugin.getElementBySId	(	self,
		id
	)

Returns the first child element found that has the given id in the model-wide SId namespace, or None if no such object is found.

getElementBySId(string id)   SBase

Parameters

id	string representing the id of the object to find.

Returns: a pointer to the SBase element 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.CompSBasePlugin.getListOfReplacedElements	(	self,
		args
	)

Returns the ListOf object that holds all replacedElements.

getListOfReplacedElements()   ListOfReplacedElements

Returns: the ListOf object that holds all replacedElements.

def libsbml.CompSBasePlugin.getNumReplacedElements ( self )

Returns the number of ReplacedElements for this CompSBasePlugin.

getNumReplacedElements()   long

Returns: the number of ReplacedElements for this CompSBasePlugin.

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.CompSBasePlugin.getReplacedBy	(	self,
		args
	)

Get the child ReplacedBy of this SBase.

getReplacedBy()   ReplacedBy

Returns: the ReplacedBy child of this SBase.

def libsbml.CompSBasePlugin.getReplacedElement	(	self,
		args
	)

Returns the ReplacedElement with the given index.

getReplacedElement(long  n)   ReplacedElement

Parameters

n	the index number of the ReplacedElement to get.

Returns: the nth ReplacedElement in the ListOfReplacedElements. If the index is invalid, None is returned.

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.CompSBasePlugin.isSetReplacedBy ( self )

Predicate for testing whether the ReplacedBy for this SBase is set.

isSetReplacedBy()   bool

Returns: True if the ReplacedBy of this SBase is set, False otherwise.

def libsbml.SBasePlugin.isValidTypeForList	(	self,
		item
	)

inherited

isValidTypeForList(SBase item)   bool

def libsbml.CompSBasePlugin.logInvalidId	(	self,
		attribute,
		wrongattribute
	)

Helper to log a common type of error.

logInvalidId(string attribute, string wrongattribute)

def libsbml.CompSBasePlugin.removeReplacedElement	(	self,
		index
	)

Removes the ReplacedElement with the given index.

removeReplacedElement(long  index)   ReplacedElement

A pointer to the ReplacedElement that was removed is returned. If no ReplacedElement has been removed, None is returned.

Parameters

index the index of the ReplacedElement object to remove.

Returns: the ReplacedElement object removed. As mentioned above, the caller owns the returned object. None is returned if the given index is out of range.

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()

def libsbml.CompSBasePlugin.setReplacedBy	(	self,
		replacedBy
	)

Sets the ReplacedBy definition of this SBase to a copy of the given ReplacedBy object instance.

setReplacedBy(ReplacedBy replacedBy)   int

This method fails if the added ReplacedBy does not match the level/version/package of the parent object or if the added ReplacedBy cannot be copied.

Parameters

replacedBy the ReplacedBy object instance to use.

Returns

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

def libsbml.CompSBasePlugin.unsetReplacedBy ( self )

Unsets the child ReplacedBy of this SBase.

unsetReplacedBy()   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