libSBML Python API  5.11.0
libsbml.QualModelPlugin Class Reference
Inheritance diagram for libsbml.QualModelPlugin:
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Detailed Description

qual Extension of Model.

The extension of SBML Level 3 Core's Model class is relatively straightforward: the Qualitative Models Package adds two lists, one for holding qualitativeSpecies (ListOfQualitativeSpecies), and the other for holding transitions (ListOfTransitions). The Model element may contain at most one ListOfQualitativeSpecies, which must contain at least one QualitativeSpecies. It may also contain at most one ListOfTransitions which must contain at least one Transition.

Public Member Functions

def __init__ (self, args)
 qual Extension of Model. More...
 
def addQualitativeSpecies (self, qualitativeSpecies)
 Adds a copy of the given QualitativeSpecies object to the list of qual. More...
 
def addTransition (self, transition)
 Adds a copy of the given Transition object to the list of qual. More...
 
def clone (self)
 Creates and returns a deep copy of this QualModelPlugin object. More...
 
def createQualitativeSpecies (self)
 Creates a new qual object and adds it to the list of qual objects and returns it. More...
 
def createTransition (self)
 Creates a new qual object and adds it to the list of qual 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 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 getListOfQualitativeSpecies (self, args)
 Returns the ListOfQualitativeSpecies in this plugin object. More...
 
def getListOfTransitions (self, args)
 Returns the ListOfTransitions in this plugin object. More...
 
def getNumQualitativeSpecies (self)
 Returns the number of QualitativeSpecies object in this plugin object. More...
 
def getNumTransitions (self)
 Returns the number of Transition object in this plugin object. 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 getQualitativeSpecies (self, args)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def getSBMLDocument (self, args)
 Returns the SBMLDocument object containing this object instance. More...
 
def getTransition (self, args)
 This method has multiple variants; they differ in the arguments they accept. 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 removeQualitativeSpecies (self, args)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def removeTransition (self, args)
 This method has multiple variants; they differ in the arguments they accept. More...
 
def setElementNamespace (self, uri)
 Sets the XML namespace to which this object belongs. More...
 

Member Function Documentation

def libsbml.QualModelPlugin.addQualitativeSpecies (   self,
  qualitativeSpecies 
)

Adds a copy of the given QualitativeSpecies object to the list of qual.

addQualitativeSpecies(QualitativeSpecies qualitativeSpecies)   int
Parameters
qualitativeSpeciesthe QualitativeSpecies object to be added to the list of qual.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.QualModelPlugin.addTransition (   self,
  transition 
)

Adds a copy of the given Transition object to the list of qual.

addTransition(Transition transition)   int
Parameters
transitionthe Transition object to be added to the list of qual.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.QualModelPlugin.clone (   self)

Creates and returns a deep copy of this QualModelPlugin object.

clone()   QualModelPlugin
Returns
a (deep) copy of this SBase object
def libsbml.QualModelPlugin.createQualitativeSpecies (   self)

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

createQualitativeSpecies()   QualitativeSpecies
Returns
a newly created QualitativeSpecies object
def libsbml.QualModelPlugin.createTransition (   self)

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

createTransition()   Transition
Returns
a newly created Transition 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
metaidstring, 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
idstring representing the identifier of the object to find
Returns
pointer to the first object with the given id.
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.QualModelPlugin.getListOfQualitativeSpecies (   self,
  args 
)

Returns the ListOfQualitativeSpecies in this plugin object.

getListOfQualitativeSpecies()   ListOfQualitativeSpecies
Returns
ListOfQualitativeSpecies object in this plugin object.
def libsbml.QualModelPlugin.getListOfTransitions (   self,
  args 
)

Returns the ListOfTransitions in this plugin object.

getListOfTransitions()   ListOfTransitions
Returns
ListOfTransitions object in this plugin object.
def libsbml.QualModelPlugin.getNumQualitativeSpecies (   self)

Returns the number of QualitativeSpecies object in this plugin object.

getNumQualitativeSpecies()   long
Returns
the number of QualitativeSpecies object in this plugin object.
def libsbml.QualModelPlugin.getNumTransitions (   self)

Returns the number of Transition object in this plugin object.

getNumTransitions()   long
Returns
the number of Transition object in this plugin object.
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.QualModelPlugin.getQualitativeSpecies (   self,
  args 
)

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

getQualitativeSpecies(long n)   QualitativeSpecies
getQualitativeSpecies(string sid)   QualitativeSpecies

Each variant is described separately below.


Method variant with the following signature:
getQualitativeSpecies(string sid)

Returns the qualitativeSpecies object based on its identifier.

Parameters
sida string representing the identifier of the QualitativeSpecies to get.
Returns
QualitativeSpecies in the ListOfQualitativeSpecies with the given id or None if no such QualitativeSpecies exists.
See also
getQualitativeSpecies()
getListOfQualitativeSpecies()

Method variant with the following signature:
getQualitativeSpecies(long n)

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

Parameters
nthe index number of the QualitativeSpecies to get.
Returns
the nth QualitativeSpecies in the ListOfQualitativeSpecies.
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.QualModelPlugin.getTransition (   self,
  args 
)

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

getTransition(long n)   Transition
getTransition(string sid)   Transition

Each variant is described separately below.


Method variant with the following signature:
getTransition(string sid)

Returns the qualitativeSpecies object based on its identifier.

Parameters
sida string representing the identifier of the Transition to get.
Returns
Transition in the ListOfTransitions with the given id or None if no such Transition exists.
See also
getTransition()
getListOfTransitions()

Method variant with the following signature:
getTransition(long n)

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

Parameters
nthe index number of the Transition to get.
Returns
the nth Transition in the ListOfTransitions.
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.QualModelPlugin.removeQualitativeSpecies (   self,
  args 
)

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

removeQualitativeSpecies(long n)   QualitativeSpecies
removeQualitativeSpecies(string sid)   QualitativeSpecies

Each variant is described separately below.


Method variant with the following signature:
removeQualitativeSpecies(string sid)

Removes the QualitativeSpecies object with the given id attribute from this plugin object and returns a pointer to it.

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

Parameters
sidthe id attribute of the QualitativeSpecies object to remove
Returns
the QualitativeSpecies object removed. As mentioned above, the caller owns the returned object. None is returned if the given index is out of range.

Method variant with the following signature:
removeQualitativeSpecies(long n)

Removes the nth QualitativeSpecies object from this plugin object and returns a pointer to it.

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

Parameters
nthe index of the QualitativeSpecies object to remove
Returns
the QualitativeSpecies object removed. As mentioned above, the caller owns the returned object. None is returned if the given index is out of range.
def libsbml.QualModelPlugin.removeTransition (   self,
  args 
)

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

removeTransition(long n)   Transition
removeTransition(string sid)   Transition

Each variant is described separately below.


Method variant with the following signature:
removeTransition(string sid)

Removes the Transition object with the given id attribute from this plugin object and returns a pointer to it.

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

Parameters
sidthe id attribute of the Transition object to remove
Returns
the Transition object removed. As mentioned above, the caller owns the returned object. None is returned if the given index is out of range.

Method variant with the following signature:
removeTransition(long n)

Removes the nth Transition object from this plugin object and returns a pointer to it.

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

Parameters
nthe index of the Transition object to remove
Returns
the Transition 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
urithe URI to assign to this object.
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
See also
getElementNamespace()