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.
|
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...
|
|
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.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(long n)
Returns the Transition object that belongs to the given index. If the index is invalid, None is returned.
- Parameters
-
- Returns
- the nth Transition in the ListOfTransitions.
Method variant with the following signature: getTransition(string sid)
Returns the qualitativeSpecies object based on its identifier.
- Parameters
-
sid | a 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()
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(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
-
- 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(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
-
- 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(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
-
- 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(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
-
sid | the 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.