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libSBML Python API
5.5.0
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libSBML Python API
5.5.0
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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 |
| 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.
| uri | the XML namespace to be added. |
| prefix | the prefix of the namespace to be added. |
| def libsbml.SBMLNamespaces.addNamespaces | ( | self, | |
| args | |||
| ) |
Python method signature(s):
addNamespaces(SBMLNamespaces self, XMLNamespaces xmlns)
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.| xmlns | the XML namespaces to be added. |
| def libsbml.SBMLNamespaces.addPackageNamespace | ( | self, | |
| args | |||
| ) |
Python method signature(s):
addPackageNamespace(SBMLNamespaces self, string pkgName, long pkgVersion, string prefix="")
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.
| 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). |
| def libsbml.SBMLNamespaces.addPackageNamespaces | ( | self, | |
| args | |||
| ) |
Python method signature(s):
addPackageNamespaces(SBMLNamespaces self, XMLNamespaces 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).
| xmlns | the XML namespaces to be added. |
| 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)
Creates and returns a deep copy of this SBMLNamespaces.
| def libsbml.SBMLNamespaces.getLevel | ( | self, | |
| args | |||
| ) |
Python method signature(s):
getLevel(SBMLNamespaces self)
Get the SBML Level of this SBMLNamespaces object.
| def libsbml.SBMLNamespaces.getNamespaces | ( | self, | |
| args | |||
| ) |
Python method signature(s):
getNamespaces(SBMLNamespaces self)
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.
| def libsbml.SBMLNamespaces.getPackageName | ( | self | ) |
Python method signature(s):
getPackageName(SBMLNamespaces self)
Returns the name of the main package for this namespace.
| def libsbml.SBMLNamespaces.getSBMLNamespaceURI | ( | args | ) |
Python method signature(s):
getSBMLNamespaceURI(long level, long version)
Returns a string representing the SBML XML namespace for the given level and version of SBML.
| level | the SBML level |
| version | the SBML version |
getSupportedNamespaces() List *
Returns a list of all supported SBMLNamespaces in this version of libsbml.
| def libsbml.SBMLNamespaces.getURI | ( | self | ) |
Python method signature(s):
getURI(SBMLNamespaces self)
Returns a string representing the SBML XML namespace of this object.
| def libsbml.SBMLNamespaces.getVersion | ( | self, | |
| args | |||
| ) |
Python method signature(s):
getVersion(SBMLNamespaces self)
Get the SBML Version of this SBMLNamespaces object.
| def libsbml.SBMLNamespaces.isSBMLNamespace | ( | args | ) |
Python method signature(s):
isSBMLNamespace(string uri)
Predicate returning True if the given URL is one of SBML XML namespaces.
| uri | the URI of namespace |
True if the 'uri' is one of SBML namespaces, False otherwise.| def libsbml.SBMLNamespaces.isValidCombination | ( | self | ) |
Python method signature(s):
isValidCombination(SBMLNamespaces self)
Predicate returning True if the given set of namespaces represent a valid set
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)
Removes an XML namespace from the set of namespaces within this SBMLNamespaces object.
| uri | the XML namespace to be added. |
| def libsbml.SBMLNamespaces.removePackageNamespace | ( | self, | |
| args | |||
| ) |
Python method signature(s):
removePackageNamespace(SBMLNamespaces self, long level, long version, string pkgName, long pkgVersion)
Removes an XML namespace of a package extension from the set of namespaces within this SBMLNamespaces object.
| level | the SBML level |
| version | the SBML version |
| pkgName | the string of package name (e.g. 'layout', 'multi') |
| pkgVersion | the package version |