Inheritance diagram for libsbml.LayoutExtension:

Detailed Description

layout Base extension class for the package.

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.

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

def	addL2Namespaces (self, xmlns)
	adds all L2 Extension namespaces to the namespace list. More...

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

def	enableL2NamespaceForDocument (self, doc)
	Adds the L2 Namespace to the document and enables the extension. More...

def	getDefaultLevel ()
	Returns the default SBML Level used by this libSBML package extension. More...

def	getDefaultPackageVersion ()
	Returns the default version of the SBML Level 3 package implemented by this libSBML extension. More...

def	getDefaultVersion ()
	Returns the default SBML Version used by this libSBML package extension. More...

def	getLevel (self, uri)
	Returns the SBML Level for the given URI of this package. More...

def	getName (self)
	Returns the name of this package ('layout') More...

def	getNumOfSBasePlugins (self)
	Returns the number of SBasePluginCreatorBase objects stored in this object. More...

def	getNumOfSupportedPackageURI (self)
	Returns the number of supported package namespace URIs. More...

def	getPackageName ()
	Returns the nickname of the SBML Level 3 package implemented by this libSBML extension. More...

def	getPackageVersion (self, uri)
	Returns the SBML Level 3 package version for the given URI of this package. More...

def	getSBMLExtensionNamespaces (self, uri)
	Returns a LayoutPkgNamespaces object. More...

def	getStringFromTypeCode (self, typeCode)
	Takes a type code of the “layout” package and returns a string describing the code. More...

def	getSupportedPackageURI (self, n)
	Returns the nth XML namespace URI. More...

def	getURI (self, sbmlLevel, sbmlVersion, pkgVersion)
	Returns a string representing the SBML XML namespace of this SBML Level 3 package. More...

def	getVersion (self, uri)
	Returns the Version within the SBML Level for the given URI of this package. More...

def	getXmlnsL2 ()
	Returns the XML namespace URI of the SBML Level 2 version of the package implemented by this libSBML Extension. More...

def	getXmlnsL3V1V1 ()
	Returns the XML namespace URI of the SBML Level 3 package implemented by this libSBML extension. More...

def	getXmlnsXSI ()
	Returns the XML namespace URI of any additional XML namespaces needed or used by this SBML Level 3 package. More...

def	isEnabled (self)
	Returns `True` if this package is enabled. More...

def	isInUse (self, doc)
	Determines whether this extension is being used by the given SBMLDocument. More...

def	isSupported (self, uri)
	Returns `True` if the given XML namespace URI is supported by this package extension. More...

def	removeL2Namespaces (self, xmlns)
	Removes the L2 Namespace from a document. More...

def	setEnabled (self, isEnabled)
	Enable or disable this package. More...

Constructor & Destructor Documentation

def libsbml.LayoutExtension.__init__	(	self,
		args
	)

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

__init__()   LayoutExtension
__init__(LayoutExtension orig)   LayoutExtension

Each variant is described separately below.

Method variant with the following signature:

LayoutExtension(LayoutExtension orig)

Copy constructor.

Parameters

orig	the instance to copy.

Method variant with the following signature:

LayoutExtension()

Creates a new LayoutExtension instance.

Member Function Documentation

def libsbml.LayoutExtension.addL2Namespaces	(	self,
		xmlns
	)

adds all L2 Extension namespaces to the namespace list.

addL2Namespaces(XMLNamespaces xmlns)

This method is overridden here since Layout does serialize to an L2 annotation.

def libsbml.LayoutExtension.clone ( self )

Creates and returns a deep copy of this LayoutExtension object.

clone()   LayoutExtension

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

def libsbml.LayoutExtension.enableL2NamespaceForDocument	(	self,
		doc
	)

Adds the L2 Namespace to the document and enables the extension.

enableL2NamespaceForDocument(SBMLDocument doc)

This method is overridden here since Layout does serialize to an L2 annotation.

def libsbml.LayoutExtension.getDefaultLevel ( )

Returns the default SBML Level used by this libSBML package extension.

getDefaultLevel()   long

Returns: the SBML Level.

Note: Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.

def libsbml.LayoutExtension.getDefaultPackageVersion ( )

Returns the default version of the SBML Level 3 package implemented by this libSBML extension.

getDefaultPackageVersion()   long

Returns: the default version number of the SBML Level 3 package definition.

Note: Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.

def libsbml.LayoutExtension.getDefaultVersion ( )

Returns the default SBML Version used by this libSBML package extension.

getDefaultVersion()   long

Returns: the Version within the default SBML Level.

Note: Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.

def libsbml.LayoutExtension.getLevel	(	self,
		uri
	)

Returns the SBML Level for the given URI of this package.

getLevel(string uri)   long

Parameters

uri	a URI that represents a version of this package.

Returns: the SBML Level for the given URI of this package, or 0 if the given URI is invalid, or for a different package.

def libsbml.LayoutExtension.getName ( self )

Returns the name of this package ('layout')

Returns: the name of this package ('layout').

getName()   string

def libsbml.SBMLExtension.getNumOfSBasePlugins ( self )

inherited

Returns the number of SBasePluginCreatorBase objects stored in this object.

getNumOfSBasePlugins()   int

Returns: the total number of SBasePluginCreatorBase objects stored in this SBMLExtension-derived object.

def libsbml.SBMLExtension.getNumOfSupportedPackageURI ( self )

inherited

Returns the number of supported package namespace URIs.

getNumOfSupportedPackageURI()   long

Returns: the number of supported package XML namespace URIs of this package extension.

def libsbml.LayoutExtension.getPackageName ( )

Returns the nickname of the SBML Level 3 package implemented by this libSBML extension.

getPackageName()   string

Returns: the package nickname, as a string.

Note: Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.

def libsbml.LayoutExtension.getPackageVersion	(	self,
		uri
	)

Returns the SBML Level 3 package version for the given URI of this package.

getPackageVersion(string uri)   long

Parameters

uri	a URI that represents one of the valid versions of this package.

Returns: the version of the SBML Level 3 package with the given URI, or 0 if the given URI is invalid, or for a different package.

def libsbml.LayoutExtension.getSBMLExtensionNamespaces	(	self,
		uri
	)

Returns a LayoutPkgNamespaces object.

getSBMLExtensionNamespaces(string uri)   SBMLNamespaces

Parameters

uri	a URI that represents one of the valid versions of the “layout” package.

Returns: a LayoutPkgNamespaces object corresponding to the given uri, or None if the URI is not defined in the Layout package.

def libsbml.LayoutExtension.getStringFromTypeCode	(	self,
		typeCode
	)

Takes a type code of the “layout” package and returns a string describing the code.

getStringFromTypeCode(int typeCode)   string  *

Parameters

typeCode a libSBML type code defined by the libSBML extension. implementing support for the SBML Level 3 “layout” package.

Returns: a text string representing the type code given by typeCode. If the type code is unrecognized for this implementation of the libSBML “layout” package, the string returned will be '(Unknown SBML Layout Type)'.

def libsbml.SBMLExtension.getSupportedPackageURI	(	self,
		n
	)

inherited

Returns the nth XML namespace URI.

getSupportedPackageURI(long  n)   string

Parameters

n	the index number of the namespace URI being sought.

Returns: a string representing the XML namespace URI understood to be supported by this package. An empty string will be returned if there is no nth URI.

def libsbml.LayoutExtension.getURI	(	self,
		sbmlLevel,
		sbmlVersion,
		pkgVersion
	)

Returns a string representing the SBML XML namespace of this SBML Level 3 package.

getURI(long  sbmlLevel, long  sbmlVersion, long  pkgVersion)   string

The namespace URI constructed by this method corresponds to the combination of the Level and Version of SBML, and the Version of the SBML Level 3 package. (At the time of this writing, the only SBML Level that supports packages is Level 3, so the value of sbmlLevel must necessarily always be 3.)

Parameters

sbmlLevel	the level of SBML.
sbmlVersion	the version of SBML.
pkgVersion	the version of the package.

Returns: a string of the package URI, or an empty string if no corresponding URI exists.

def libsbml.LayoutExtension.getVersion	(	self,
		uri
	)

Returns the Version within the SBML Level for the given URI of this package.

getVersion(string uri)   long

Parameters

uri	a URI that represents a version of this package.

Returns: the SBML Version within the SBML Level for the given URI of this package, or 0 if the given URI is invalid, or for a different package.

def libsbml.LayoutExtension.getXmlnsL2 ( )

Returns the XML namespace URI of the SBML Level 2 version of the package implemented by this libSBML Extension.

getXmlnsL2()   string

Unique among the SBML Level 3 packages, the Layout package existed and was in widespread use prior to the introduction of SBML Level 3. The Layout package was used as model annotations in SBML Level 2. This method returns the SBML annotation XML namespace used for Level 2.

Returns: the XML namespace as a string.

Note: Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.

def libsbml.LayoutExtension.getXmlnsL3V1V1 ( )

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

getXmlnsL3V1V1()   string

Returns: the XML namespace as a string.

Note: Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.

def libsbml.LayoutExtension.getXmlnsXSI ( )

Returns the XML namespace URI of any additional XML namespaces needed or used by this SBML Level 3 package.

getXmlnsXSI()   string

Returns: the XML namespace as a string.

Note: Because this is a static method on a class, the Python language interface for libSBML will contain two variants. One will be the expected, normal static method on the class (i.e., a regular methodName), and the other will be a standalone top-level function with the name ClassName_methodName(). This is merely an artifact of how the language interfaces are created in libSBML. The methods are functionally identical.

def libsbml.SBMLExtension.isEnabled ( self )

inherited

Returns True if this package is enabled.

isEnabled()   bool

Returns: True if this package is enabled, False otherwise.

def libsbml.LayoutExtension.isInUse	(	self,
		doc
	)

Determines whether this extension is being used by the given SBMLDocument.

The implementation returns true if the model object contains one or more layouts.

isInUse(SBMLDocument doc)   bool

Parameters

doc	the sbml document to test.

Returns: a boolean indicating whether the extension is actually being used by the document.

def libsbml.SBMLExtension.isSupported	(	self,
		uri
	)

inherited

Returns True if the given XML namespace URI is supported by this package extension.

isSupported(string uri)   bool

Returns: True if the given XML namespace URI (equivalent to a package version) is supported by this package extension, False otherwise.

def libsbml.LayoutExtension.removeL2Namespaces	(	self,
		xmlns
	)

Removes the L2 Namespace from a document.

removeL2Namespaces(XMLNamespaces xmlns)

This method is overridden here since Layout does serialize to an L2 annotation.

def libsbml.SBMLExtension.setEnabled	(	self,
		isEnabled
	)

inherited

Enable or disable this package.

setEnabled(bool isEnabled)   bool

Parameters

isEnabled flag indicating whether to enable (if True) or disable (False) this package extension.

Returns: True if this call succeeded; False otherwise.

Detailed Description

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation