Inheritance diagram for libsbml.SBMLDocumentPlugin:

Detailed Description

Base class for extending SBMLDocument in packages.

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 SBMLDocumentPlugin class is a specialization of SBasePlugin designed specifically for extending SBMLDocument. All package extensions must extend SBMLDocument to implement support for SBML Level 3 packages; these extensions can be subclasses of this class or from a derived class of this class.

All packages must additionally define a required flag named required, which indicates whether that package's constructs can be used to change the core mathematics of the <model> child of the <sbml> element. If they can, this attribute must be set True, and if they cannot, this attribute must be set False.

Basic principles of SBML package extensions in libSBML

: SBML Level 3's package structure permits modular extensions to the core SBML format. In libSBML, support for SBML Level 3 packages is provided through optional package extensions that can be plugged into libSBML at the time it is built/compiled. Users of libSBML can thus choose which extensions are enabled in their software applications.

LibSBML defines a number of classes that developers of package extensions can use to implement support for an SBML Level 3 package. These classes make it easier to extend libSBML objects with new attributes and/or subobjects as needed by a particular Level 3 package. Three overall categories of classes make up libSBML's facilities for implementing package extensions. There are (1) classes that serve as base classes meant to be subclassed, (2) template classes meant to be instantiated rather than subclassed, and (3) support classes that provide utility features. A given package implementation for libSBML will take the form of code using these and other libSBML classes, placed in a subdirectory of src/sbml/packages/.

The basic libSBML distribution includes a number of package extensions implementing support for officially-endorsed SBML Level 3 packages; among these are Flux Balance Constraints ('fbc'), Hierarchical Model Composition ('comp'), Layout ('layout'), and Qualitative Models ('qual'). They can serve as working examples for developers working to implement other packages.

Extensions in libSBML can currently only be implemented in C++ or C; there is no mechanism to implement them first in languages such as Java or Python. However, once implemented in C++ or C, language interfaces can be generated semi-automatically using the framework in place in libSBML. (The approach is based on using SWIG and facilities in libSBML's build system.)

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

def	clone (self)
	Creates and returns a deep copy of this SBMLDocumentPlugin 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	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	getRequired (self)
	Returns the value of the 'required' attribute. 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	isSetRequired (self)
	Returns the value of the 'required' attribute. More...

def	isValidTypeForList (self, item)

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	setRequired (self, value)
	Sets the SBML 'required' attribute value. More...

def	unsetRequired (self)
	Unsets the value of the 'required' attribute of this SBMLDocumentPlugin. More...

Constructor & Destructor Documentation

def libsbml.SBMLDocumentPlugin.__init__	(	self,
		args
	)

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

__init__(string uri, string prefix, SBMLNamespaces sbmlns)   SBMLDocumentPlugin
__init__(SBMLDocumentPlugin orig)   SBMLDocumentPlugin

Each variant is described separately below.

Method variant with the following signature:

SBMLDocumentPlugin(string uri, string prefix, SBMLNamespaces sbmlns)

Creates a new SBMLDocumentPlugin 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.
sbmlns	the SBMLNamespaces object for the package.

Method variant with the following signature:

SBMLDocumentPlugin(SBMLDocumentPlugin orig)

Copy constructor.

This creates a copy of this object.

Parameters

orig	the SBMLDocumentPlugin instance to copy.

Member Function Documentation

def libsbml.SBMLDocumentPlugin.clone ( self )

Creates and returns a deep copy of this SBMLDocumentPlugin object.

clone()   SBMLDocumentPlugin

Returns: the (deep) copy of this SBMLDocumentPlugin 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.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.SBMLDocumentPlugin.getRequired ( self )

Returns the value of the 'required' attribute.

getRequired()   bool

: SBML Level 3 requires that every package defines an attribute named 'required' on the root <sbml> element in an SBML file or data stream. The attribute, being in the namespace of the Level 3 package in question, must be prefixed by the XML namespace prefix associated with the package. The value of the 'required' attribute indicates whether constructs in that package may change the mathematical interpretation of constructs defined in SBML Level 3 Core. A 'required' value of True indicates that the package may do so. The value of the attribute is set by the Level 3 package specification, and does not depend on the actual presence or absence of particular package constructs in a given SBML document: in other words, if the package specification defines any construct that can change the model's meaning, the value of the 'required' attribute must always be set to True in any SBML document that uses the package.

The XML namespace declaration for an SBML Level 3 package is an indication that a model makes use of features defined by that package, while the 'required' attribute indicates whether the features may be ignored without compromising the mathematical meaning of the model. Both are necessary for a complete reference to an SBML Level 3 package.

Returns: the bool value of 'required' attribute for the SBML package.

See also: setRequired(); isSetRequired(); unsetRequired()

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.SBMLDocumentPlugin.isSetRequired ( self )

Returns the value of the 'required' attribute.

isSetRequired()   bool

: SBML Level 3 requires that every package defines an attribute named 'required' on the root <sbml> element in an SBML file or data stream. The attribute, being in the namespace of the Level 3 package in question, must be prefixed by the XML namespace prefix associated with the package. The value of the 'required' attribute indicates whether constructs in that package may change the mathematical interpretation of constructs defined in SBML Level 3 Core. A 'required' value of True indicates that the package may do so. The value of the attribute is set by the Level 3 package specification, and does not depend on the actual presence or absence of particular package constructs in a given SBML document: in other words, if the package specification defines any construct that can change the model's meaning, the value of the 'required' attribute must always be set to True in any SBML document that uses the package.

The XML namespace declaration for an SBML Level 3 package is an indication that a model makes use of features defined by that package, while the 'required' attribute indicates whether the features may be ignored without compromising the mathematical meaning of the model. Both are necessary for a complete reference to an SBML Level 3 package.

Returns: True if the 'required' attribute of this SBMLDocument has been set to True, False otherwise.

def libsbml.SBasePlugin.isValidTypeForList	(	self,
		item
	)

inherited

isValidTypeForList(SBase item)   bool

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.SBMLDocumentPlugin.setRequired	(	self,
		value
	)

Sets the SBML 'required' attribute value.

setRequired(bool value)   int

: SBML Level 3 requires that every package defines an attribute named 'required' on the root <sbml> element in an SBML file or data stream. The attribute, being in the namespace of the Level 3 package in question, must be prefixed by the XML namespace prefix associated with the package. The value of the 'required' attribute indicates whether constructs in that package may change the mathematical interpretation of constructs defined in SBML Level 3 Core. A 'required' value of True indicates that the package may do so. The value of the attribute is set by the Level 3 package specification, and does not depend on the actual presence or absence of particular package constructs in a given SBML document: in other words, if the package specification defines any construct that can change the model's meaning, the value of the 'required' attribute must always be set to True in any SBML document that uses the package.

The XML namespace declaration for an SBML Level 3 package is an indication that a model makes use of features defined by that package, while the 'required' attribute indicates whether the features may be ignored without compromising the mathematical meaning of the model. Both are necessary for a complete reference to an SBML Level 3 package.

Parameters

value the value to be assigned to the 'required' attribute. The 'required' attribute takes a Boolean value, either True or False.

Returns

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

See also: getRequired(); isSetRequired(); unsetRequired()

def libsbml.SBMLDocumentPlugin.unsetRequired ( self )

Unsets the value of the 'required' attribute of this SBMLDocumentPlugin.

unsetRequired()   int

Returns

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

LIBSBML_OPERATION_SUCCESS

Detailed Description

Basic principles of SBML package extensions in libSBML

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation