libSBML Python API  5.8.0
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libsbml.SBMLNamespaces Class Reference
Inheritance diagram for libsbml.SBMLNamespaces:
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Detailed Description

Class to store SBML level, version and namespace information.

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 addNamespace
 
def addNamespaces
 
def addPackageNamespace
 
def addPackageNamespaces
 
def clone
 
def getLevel
 
def getNamespaces
 
def getPackageName
 
def getSBMLNamespaceURI
 
def getSupportedNamespaces
 
def getURI
 
def getVersion
 
def isSBMLNamespace
 
def isValidCombination
 
def removeNamespace
 
def removePackageNamespace
 

Member Function Documentation

def libsbml.SBMLNamespaces.addNamespace (   self,
  args 
)

Python method signature(s):

addNamespace(SBMLNamespaces self, string uri, string prefix)   int

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

Parameters
urithe XML namespace to be added.
prefixthe prefix of the namespace to be added.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBMLNamespaces.addNamespaces (   self,
  args 
)

Python method signature(s):

addNamespaces(SBMLNamespaces self, XMLNamespaces xmlns)   int

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

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
xmlnsthe XML namespaces to be added.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBMLNamespaces.addPackageNamespace (   self,
  args 
)

Python method signature(s):

addPackageNamespace(SBMLNamespaces self, string pkgName, long pkgVersion, string prefix="")   int
addPackageNamespace(SBMLNamespaces self, string pkgName, long pkgVersion)   int

Add an XML namespace (a pair of URI and prefix) of a package extension to the set of namespaces within this SBMLNamespaces object. The SBML Level and SBML Version of this object is used.

Note
An XML namespace of a non-registered package extension can't be added by this function (LIBSBML_INVALID_ATTRIBUTE_VALUE will be returned).
Parameters
pkgNamethe string of package name (e.g. 'layout', 'multi')
pkgVersionthe package version
prefixthe 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:
See Also
addNamespace()
def libsbml.SBMLNamespaces.addPackageNamespaces (   self,
  args 
)

Python method signature(s):

addPackageNamespaces(SBMLNamespaces self, XMLNamespaces xmlns)   int

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).

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 null.
Parameters
xmlnsthe XML namespaces to be added.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBMLNamespaces.clone (   self)

Class to store SBML level, version and namespace information.

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. Python method signature(s):

clone(SBMLNamespaces self)   SBMLNamespaces

Creates and returns a deep copy of this SBMLNamespaces.

Returns
a (deep) copy of this SBMLNamespaces.
def libsbml.SBMLNamespaces.getLevel (   self,
  args 
)

Python method signature(s):

getLevel(SBMLNamespaces self)   long
getLevel(SBMLNamespaces self)   long

Get the SBML Level of this SBMLNamespaces object.

Returns
the SBML Level of this SBMLNamespaces object.
def libsbml.SBMLNamespaces.getNamespaces (   self,
  args 
)

Python method signature(s):

getNamespaces(SBMLNamespaces self)   XMLNamespaces
getNamespaces(SBMLNamespaces self)   XMLNamespaces

Get the XML namespaces list for this SBMLNamespaces object.

The plural 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 there may be multiple XML namespaces involved too. However, until the introduction of SBML Level 3, the SBMLNamespaces object only records one SBML Level/Version/namespace combination at a time, and so this method will also only return a list of one item.

Returns
the XML namespaces of this SBMLNamespaces object.
def libsbml.SBMLNamespaces.getPackageName (   self)

Python method signature(s):

getPackageName(SBMLNamespaces self)   string

Returns the name of the main package for this namespace.

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 (   args)

Python method signature(s):

getSBMLNamespaceURI(long level, long version)   string

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

Parameters
levelthe SBML level
versionthe SBML version
Returns
a string representing the SBML namespace that reflects the SBML Level and Version specified.
Note
Because this is a static method, the non-C++ language interfaces for libSBML will contain two variants. One will be a static method on the class (i.e., SBMLNamespaces), and the other will be a standalone top-level function with the name SBMLNamespaces_getSBMLNamespaceURI(). They are functionally identical.
def libsbml.SBMLNamespaces.getSupportedNamespaces ( )

getSupportedNamespaces() List *

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

Returns
a list with supported SBML namespaces.
Note
Because this is a static method, the non-C++ language interfaces for libSBML will contain two variants. One will be a static method on the class (i.e., SBMLNamespaces), and the other will be a standalone top-level function with the name SBMLNamespaces_getSupportedNamespaces(). They are functionally identical.
def libsbml.SBMLNamespaces.getURI (   self)

Python method signature(s):

getURI(SBMLNamespaces self)   string

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

Returns
a string representing the SBML namespace that reflects the SBML Level and Version of this object.
def libsbml.SBMLNamespaces.getVersion (   self,
  args 
)

Python method signature(s):

getVersion(SBMLNamespaces self)   long
getVersion(SBMLNamespaces self)   long

Get the SBML Version of this SBMLNamespaces object.

Returns
the SBML Version of this SBMLNamespaces object.
def libsbml.SBMLNamespaces.isSBMLNamespace (   args)

Python method signature(s):

isSBMLNamespace(string uri)   bool

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

Parameters
urithe URI of namespace
Returns
True if the 'uri' is one of SBML namespaces, False otherwise.
Note
Because this is a static method, the non-C++ language interfaces for libSBML will contain two variants. One will be a static method on the class (i.e., SBMLNamespaces), and the other will be a standalone top-level function with the name SBMLNamespaces_isSBMLNamespace(). They are functionally identical.
def libsbml.SBMLNamespaces.isValidCombination (   self)

Python method signature(s):

isValidCombination(SBMLNamespaces self)   bool

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

Returns
True if the set of namespaces is valid, False otherwise.
def libsbml.SBMLNamespaces.removeNamespace (   self,
  args 
)

Python method signature(s):

removeNamespace(SBMLNamespaces self, string uri)   int

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

Parameters
urithe XML namespace to be added.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.SBMLNamespaces.removePackageNamespace (   self,
  args 
)

Python method signature(s):

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

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

Parameters
levelthe SBML level
versionthe SBML version
pkgNamethe string of package name (e.g. 'layout', 'multi')
pkgVersionthe package version
Returns
integer value indicating success/failure of the function. The possible values returned by this function are: