Inheritance diagram for libsbml.LayoutModelPlugin:

Detailed Description

layout Extension of Model.

Public Member Functions
def	__init__ (self, args)
	layout Extension of Model. More...

def	addLayout (self, layout)
	Adds a copy of the layout object to the list of layouts. More...

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

def	createLayout (self)
	Creates a new layout object and adds it to the list of layout objects and returns it. 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)
	Base class for extending SBML objects in packages. More...

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

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

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

def	getListOfLayouts (self, args)
	Returns the ListOfLayouts object for this Model. More...

def	getNumLayouts (self)
	Returns the number of layout 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	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	removeLayout (self, n)
	Removes the nth Layout object from this Model object and returns a pointer to it. More...

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

Member Function Documentation

def libsbml.LayoutModelPlugin.addLayout	(	self,
		layout
	)

Adds a copy of the layout object to the list of layouts.

addLayout(Layout layout)   int

Parameters

layout the layout object 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.LayoutModelPlugin.clone ( self )

Creates and returns a deep copy of this LayoutModelPlugin object.

clone()   LayoutModelPlugin

Returns: a (deep) copy of this LayoutModelPlugin object

def libsbml.LayoutModelPlugin.createLayout ( self )

Creates a new layout object and adds it to the list of layout objects and returns it.

createLayout()   Layout

Returns: a new layout 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.LayoutModelPlugin.getLayout	(	self,
		args
	)

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

getLayout(long index)   Layout
getLayout(string sid)   Layout

Each variant is described separately below.

Method variant with the following signature:

getLayout(long index)

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

Parameters

index the index of list of layout objects.

Returns: the Layout object that belongs to the given index. None is returned if the index is invalid.

Method variant with the following signature:

getLayout(string sid)

Returns the layout object with the given sid attribute. If the id is invalid, None is returned.

Parameters

sid	the id attribute of the layout object.

Returns: the Layout object with the given sid attribute. None is returned if the given sid is invalid.

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=None)   SBaseList
getListOfAllElements()   SBaseList

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

def libsbml.LayoutModelPlugin.getListOfLayouts	(	self,
		args
	)

Returns the ListOfLayouts object for this Model.

getListOfLayouts()   ListOfLayouts

Returns: the ListOfLayouts object for this Model.

def libsbml.LayoutModelPlugin.getNumLayouts ( self )

Returns the number of layout objects.

getNumLayouts()   int

Returns: the number of layout 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.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(); SBMLDocument.getSBMLNamespaces(); 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.LayoutModelPlugin.removeLayout	(	self,
		n
	)

Removes the nth Layout object from this Model object and returns a pointer to it.

removeLayout(long n)   Layout

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

Parameters

n	the index of the Layout object to remove

Returns: the Layout 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.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. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

See also: getElementNamespace()

Detailed Description

Public Member Functions

Member Function Documentation