libsbml.SBMLNamespaces Class Reference

Inheritance diagram for libsbml.SBMLNamespaces:

Detailed Description

Set of SBML Level + Version + namespace triples.

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.

There are differences in the definitions of components between different SBML Levels, as well as Versions within Levels. For example, the 'sboTerm' attribute was not introduced until Level 2 Version 2, and then only on certain component classes; the SBML Level 2 Version 3 specification moved the 'sboTerm' attribute to the SBase class, thereby allowing nearly all components to have SBO annotations. As a result of differences such as those, libSBML needs to track the SBML Level and Version of every object created.

The purpose of the SBMLNamespaces object class is to make it easier to communicate SBML Level and Version data between libSBML constructors and other methods. The SBMLNamespaces object class tracks 3-tuples (triples) consisting of SBML Level, Version, and the corresponding SBML XML namespace.

The plural name (SBMLNamespaces) is not a mistake, because in SBML Level 3, objects may have extensions added by Level 3 packages used by a given model and therefore may have multiple namespaces associated with them; however, until the introduction of SBML Level 3, the SBMLNamespaces object only records one SBML Level/Version/namespace combination at a time. Most constructors for SBML objects in libSBML take a SBMLNamespaces object as an argument, thereby allowing the constructor to produce the proper combination of attributes and other internal data structures for the given SBML Level and Version.

Public Member Functions
def	__init__ (self, args)
	This method has multiple variants; they differ in the arguments they accept. More...
def	addNamespace (self, uri, prefix)
	Add an XML namespace (a pair of URI and prefix) to the set of namespaces within this SBMLNamespaces object. More...
def	addNamespaces (self, xmlns)
	Add the given XML namespaces list to the set of namespaces within this SBMLNamespaces object. More...
def	addPackageNamespace (self, args)
	Add an XML namespace (a pair of URI and prefix) of a package extension to the set of namespaces within this SBMLNamespaces object. More...
def	addPackageNamespaces (self, xmlns)
	Add the XML namespaces of package extensions in the given XMLNamespace object to the set of namespaces within this SBMLNamespaces object (Non-package XML namespaces are not added by this function). More...
def	clone (self)
	Creates and returns a deep copy of this SBMLNamespaces object. More...
def	freeSBMLNamespaces (supportedNS)
	Frees the list of supported namespaces as generated by getSupportedNamespaces(). More...
def	getLevel (self, args)
	Get the SBML Level of this SBMLNamespaces object. More...
def	getNamespaces (self, args)
	Get the XML namespaces list for this SBMLNamespaces object. More...
def	getPackageName (self)
	Returns the name of the main package for this namespace. More...
def	getSBMLNamespaceURI (level, version)
	Returns a string representing the SBML XML namespace for the given level and version of SBML. More...
def	getSupportedNamespaces ()
	Returns a list of all supported SBMLNamespaces in this version of libsbml. More...
def	getURI (self)
	Returns a string representing the SBML XML namespace of this object. More...
def	getVersion (self, args)
	Get the SBML Version of this SBMLNamespaces object. More...
def	isSBMLNamespace (uri)
	Predicate returning True if the given URL is one of SBML XML namespaces. More...
def	isValidCombination (self)
	Predicate returning True if the given set of namespaces represent a valid set. More...
def	removeNamespace (self, uri)
	Removes an XML namespace from the set of namespaces within this SBMLNamespaces object. More...
def	removePackageNamespace (self, level, version, pkgName, pkgVersion)
	Removes an XML namespace of a package extension from the set of namespaces within this SBMLNamespaces object. More...

Constructor & Destructor Documentation

def libsbml.SBMLNamespaces.__init__	(		self,
			args
	)

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

__init__(long  level, long  version)   SBMLNamespaces
__init__(long  level)   SBMLNamespaces
__init__()   SBMLNamespaces
__init__(long  level, long  version, string pkgName, long  pkgVersion, string pkgPrefix)   SBMLNamespaces
__init__(long  level, long  version, string pkgName, long  pkgVersion)   SBMLNamespaces
__init__(SBMLNamespaces orig)   SBMLNamespaces

Each variant is described separately below.

---

Method variant with the following signature:

SBMLNamespaces(SBMLNamespaces orig)

Copy constructor; creates a copy of a SBMLNamespaces.

Parameters

orig	the SBMLNamespaces instance to copy.

---

Method variant with the following signature:

SBMLNamespaces(long level, long version, string pkgName, long pkgVersion, string pkgPrefix = '')

(For extensions) Creates a new SBMLNamespaces object corresponding to the combination of (1) the given SBML level and version, and (2) the given package with the package version.

SBMLNamespaces objects are used in libSBML to communicate SBML Level and Version data between constructors and other methods. The SBMLNamespaces object class holds triples consisting of SBML Level, Version, and the corresponding SBML XML namespace. Most constructors for SBML objects in libSBML take a SBMLNamespaces object as an argument, thereby allowing the constructor to produce the proper combination of attributes and other internal data structures for the given SBML Level and Version.

The plural name (SBMLNamespaces) is not a mistake, because in SBML Level 3, objects may have extensions added by Level 3 packages used by a given model and therefore may have multiple namespaces associated with them. In SBML Levels below Level 3, the SBMLNamespaces object only records one SBML Level/Version/namespace combination at a time. Most constructors for SBML objects in libSBML take a SBMLNamespaces object as an argument, thereby allowing the constructor to produce the proper combination of attributes and other internal data structures for the given SBML Level and Version.

Parameters

level	the SBML Level.
version	the SBML Version.
pkgName	the string of package name (e.g. 'layout', 'multi').
pkgVersion	the package version.
pkgPrefix	the prefix of the package namespace (e.g. 'layout', 'multi') to be added. The package's name will be used if the given string is empty (default).

Exceptions

SBMLExtensionException

if the extension module that supports the combination of the given SBML Level, SBML Version, package name, and package version has not been registered with libSBML.

Note

Owing to the way that language interfaces are created in libSBML, this documentation may show methods that define default values for parameters with text that has the form parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.

---

Method variant with the following signature:

SBMLNamespaces(long level = SBML_DEFAULT_LEVEL, long version = SBML_DEFAULT_VERSION)

Creates a new SBMLNamespaces object corresponding to the given SBML level and version.

SBMLNamespaces objects are used in libSBML to communicate SBML Level and Version data between constructors and other methods. The SBMLNamespaces object class holds triples consisting of SBML Level, Version, and the corresponding SBML XML namespace. Most constructors for SBML objects in libSBML take a SBMLNamespaces object as an argument, thereby allowing the constructor to produce the proper combination of attributes and other internal data structures for the given SBML Level and Version.

The plural name (SBMLNamespaces) is not a mistake, because in SBML Level 3, objects may have extensions added by Level 3 packages used by a given model and therefore may have multiple namespaces associated with them. In SBML Levels below Level 3, the SBMLNamespaces object only records one SBML Level/Version/namespace combination at a time. Most constructors for SBML objects in libSBML take a SBMLNamespaces object as an argument, thereby allowing the constructor to produce the proper combination of attributes and other internal data structures for the given SBML Level and Version.

Parameters

level	the SBML level.
version	the SBML version.

Note

Owing to the way that language interfaces are created in libSBML, this documentation may show methods that define default values for parameters with text that has the form parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.

Member Function Documentation

def libsbml.SBMLNamespaces.addNamespace	(		self,
			uri,
			prefix
	)

Add an XML namespace (a pair of URI and prefix) to the set of namespaces within this SBMLNamespaces object.

addNamespace(string uri, string prefix)   int

Parameters

uri	the XML namespace to be added.
prefix	the prefix of the namespace to be added.

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED
• LIBSBML_INVALID_OBJECT

def libsbml.SBMLNamespaces.addNamespaces	(		self,
			xmlns
	)

Add the given XML namespaces list to the set of namespaces within this SBMLNamespaces object.

addNamespaces(XMLNamespaces xmlns)   int

The following code gives an example of how one could add the XHTML namespace to the list of namespaces recorded by the top-level <sbml> element of a model. It gives the new namespace a prefix of html.

sbmlDoc = None
try:
  sbmlDoc = SBMLDocument(3, 1)
except ValueError:
  # Do something to handle exceptional situation.  Candidate
  # causes include invalid combinations of SBML Level and Version
  # (impossible if hardwired as given here), running out of memory, and
  # unknown system exceptions.

namespaces = sbmlDoc.getNamespaces()
if namespaces == None:
  # Do something to handle case of no namespaces.

status = namespaces.add('http://www.w3.org/1999/xhtml', 'html')
if status != LIBSBML_OPERATION_SUCCESS:
  # Do something to handle failure.

Parameters

xmlns

the XML namespaces to be added.

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED
• LIBSBML_INVALID_OBJECT

def libsbml.SBMLNamespaces.addPackageNamespace	(		self,
			args
	)

Add an XML namespace (a pair of URI and prefix) of a package extension to the set of namespaces within this SBMLNamespaces object.

addPackageNamespace(string pkgName, long  pkgVersion, string prefix)   int
addPackageNamespace(string pkgName, long  pkgVersion)   int

The SBML Level and SBML Version of this object is used.

Parameters

pkgName	the string of package name (e.g. 'layout', 'multi').
pkgVersion	the package version.
prefix	the prefix of the package namespace to be added. The package's name will be used if the given string is empty (default).

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE

Note

An XML namespace of a non-registered package extension can't be added by this function (LIBSBML_INVALID_ATTRIBUTE_VALUE will be returned).

See also

addNamespace()

Note

Owing to the way that language interfaces are created in libSBML, this documentation may show methods that define default values for parameters with text that has the form parameter = value. This is not to be intepreted as a Python keyword argument; the use of a parameter name followed by an equals sign followed by a value is only meant to indicate a default value if the argument is not provided at all. It is not a keyword in the Python sense.

def libsbml.SBMLNamespaces.addPackageNamespaces	(		self,
			xmlns
	)

Add the XML namespaces of package extensions in the given XMLNamespace object to the set of namespaces within this SBMLNamespaces object (Non-package XML namespaces are not added by this function).

addPackageNamespaces(XMLNamespaces xmlns)   int

Parameters

xmlns

the XML namespaces to be added.

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE

Note

XML namespaces of a non-registered package extensions are not added (just ignored) by this function. LIBSBML_INVALID_ATTRIBUTE_VALUE will be returned if the given xmlns is None.

def libsbml.SBMLNamespaces.clone

(

self

)

Creates and returns a deep copy of this SBMLNamespaces object.

clone()   SBMLNamespaces

Returns

the (deep) copy of this SBMLNamespaces object.

def libsbml.SBMLNamespaces.freeSBMLNamespaces

(

supportedNS

)

Frees the list of supported namespaces as generated by getSupportedNamespaces().

freeSBMLNamespaces(List * supportedNS)

Parameters

supportedNS

the list to be freed.

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.SBMLNamespaces.getLevel	(		self,
			args
	)

Get the SBML Level of this SBMLNamespaces object.

getLevel()   long

Returns

the SBML Level of this SBMLNamespaces object.

def libsbml.SBMLNamespaces.getNamespaces	(		self,
			args
	)

Get the XML namespaces list for this SBMLNamespaces object.

getNamespaces()   XMLNamespaces

SBMLNamespaces objects are used in libSBML to communicate SBML Level and Version data between constructors and other methods. The SBMLNamespaces object class holds triples consisting of SBML Level, Version, and the corresponding SBML XML namespace. Most constructors for SBML objects in libSBML take a SBMLNamespaces object as an argument, thereby allowing the constructor to produce the proper combination of attributes and other internal data structures for the given SBML Level and Version.

The plural name (SBMLNamespaces) is not a mistake, because in SBML Level 3, objects may have extensions added by Level 3 packages used by a given model and therefore may have multiple namespaces associated with them. In SBML Levels below Level 3, the SBMLNamespaces object only records one SBML Level/Version/namespace combination at a time. Most constructors for SBML objects in libSBML take a SBMLNamespaces object as an argument, thereby allowing the constructor to produce the proper combination of attributes and other internal data structures for the given SBML Level and Version.

Returns

the XML namespaces of this SBMLNamespaces object.

def libsbml.SBMLNamespaces.getPackageName

(

self

)

Returns the name of the main package for this namespace.

getPackageName()   string

Returns

the name of the main package for this namespace. 'core' will be returned if this namespace is defined in the SBML core.

def libsbml.SBMLNamespaces.getSBMLNamespaceURI	(		level,
			version
	)

Returns a string representing the SBML XML namespace for the given level and version of SBML.

getSBMLNamespaceURI(long  level, long  version)   string

Parameters

level	the SBML level.
version	the SBML version.

Returns

a string representing the SBML namespace that reflects the SBML Level and Version specified.

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.SBMLNamespaces.getSupportedNamespaces

(

)

Returns a list of all supported SBMLNamespaces in this version of libsbml.

getSupportedNamespaces()   List  *

Returns

a list with supported SBML namespaces.

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.SBMLNamespaces.getURI

(

self

)

Returns a string representing the SBML XML namespace of this object.

getURI()   string

Returns

a string representing the SBML namespace that reflects the SBML Level and Version of this object.

def libsbml.SBMLNamespaces.getVersion	(		self,
			args
	)

Get the SBML Version of this SBMLNamespaces object.

getVersion()   long

Returns

the SBML Version of this SBMLNamespaces object.

def libsbml.SBMLNamespaces.isSBMLNamespace

(

uri

)

Predicate returning True if the given URL is one of SBML XML namespaces.

isSBMLNamespace(string uri)   bool

Parameters

uri	the URI of namespace.

Returns

True if the 'uri' is one of SBML namespaces, False otherwise.

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.SBMLNamespaces.isValidCombination

(

self

)

Predicate returning True if the given set of namespaces represent a valid set.

Returns

True if the set of namespaces is valid, False otherwise.

isValidCombination()   bool

def libsbml.SBMLNamespaces.removeNamespace	(		self,
			uri
	)

Removes an XML namespace from the set of namespaces within this SBMLNamespaces object.

removeNamespace(string uri)   int

Parameters

uri	the XML namespace to be added.

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INDEX_EXCEEDS_SIZE

def libsbml.SBMLNamespaces.removePackageNamespace	(		self,
			level,
			version,
			pkgName,
			pkgVersion
	)

Removes an XML namespace of a package extension from the set of namespaces within this SBMLNamespaces object.

removePackageNamespace(long  level, long  version, string pkgName, long  pkgVersion)   int

Parameters

level	the SBML level.
version	the SBML version.
pkgName	the string of package name (e.g. 'layout', 'multi').
pkgVersion	the package version.

Returns

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

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE
• LIBSBML_INDEX_EXCEEDS_SIZE