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| def | __init__ (self, args) |
| | This method has multiple variants; they differ in the arguments they accept. More...
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| def | addGroup (self, g) |
| | Adds a copy of the given Group to this GroupsModelPlugin. More...
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| def | clone (self) |
| | Creates and returns a deep copy of this GroupsModelPlugin object. More...
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| def | copyInformationToNestedLists (self) |
| | For nested groups (Member objects that reference a ListOfMembers object), SBO terms, Notes, and Annotation from the parent ListOfMembers applies to the child. More...
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| def | createGroup (self) |
| | Creates a new Group object, adds it to this GroupsModelPlugin object and returns the Group object created. More...
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| def | getElementByMetaId (self, metaid) |
| | Returns the first child element that has the given metaid, or None if no such object is found. More...
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| def | getElementBySId (self, id) |
| | Returns the first child element that has the given id in the model-wide SId namespace, or None if no such object is found. More...
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| def | getElementNamespace (self) |
| | Returns the namespace URI of the package to which this plugin object belongs. More...
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| def | getGroup (self, args) |
| | This method has multiple variants; they differ in the arguments they accept. More...
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| def | getLevel (self) |
| | Returns the SBML Level of the package extension of this plugin object. More...
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| def | getListOfAllElements (self, filter=None) |
| | Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth. More...
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| def | getListOfGroups (self, args) |
| | Returns the ListOfGroups from this GroupsModelPlugin. More...
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| def | getNumGroups (self) |
| | Get the number of Group objects in this GroupsModelPlugin. More...
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| def | getPackageName (self) |
| | Returns the short-form name of the package to which this plugin object belongs. More...
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| def | getPackageVersion (self) |
| | Returns the package version of the package extension of this plugin object. More...
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| def | getParentSBMLObject (self, args) |
| | Returns the parent object to which this plugin object is connected. More...
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| def | getPrefix (self) |
| | Returns the XML namespace prefix of the package to which this plugin object belongs. More...
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| def | getSBMLDocument (self, args) |
| | Returns the SBMLDocument object containing this object instance. More...
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| def | getURI (self) |
| | Returns the XML namespace URI for the package to which this object belongs. More...
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| def | getVersion (self) |
| | Returns the Version within the SBML Level of the package extension of this plugin object. More...
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| def | isValidTypeForList (self, item) |
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| def | removeGroup (self, args) |
| | This method has multiple variants; they differ in the arguments they accept. More...
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| def | renameMetaIdRefs (self, oldid, newid) |
| | Replaces all uses of a given meta identifier attribute value with another value. More...
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| def | renameSIdRefs (self, oldid, newid) |
| | Replaces all uses of a given SIdRef type attribute value with another value. More...
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| def | renameUnitSIdRefs (self, oldid, newid) |
| | Replaces all uses of a given UnitSIdRef type attribute value with another value. More...
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| def | setElementNamespace (self, uri) |
| | Sets the XML namespace to which this object belongs. More...
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| def libsbml.GroupsModelPlugin.__init__ |
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self, |
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args |
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This method has multiple variants; they differ in the arguments they accept.
__init__(string uri, string prefix, GroupsPkgNamespaces groupsns) GroupsModelPlugin
__init__(GroupsModelPlugin orig) GroupsModelPlugin
Each variant is described separately below.
Method variant with the following signature: GroupsModelPlugin(GroupsModelPlugin orig)
Copy constructor for GroupsModelPlugin.
- Parameters
-
Method variant with the following signature: GroupsModelPlugin(string uri, string prefix, GroupsPkgNamespaces groupsns)
Creates a new GroupsModelPlugin using the given URI, prefix and package namespace.
- Parameters
-
| uri | a string, representing the URI of the SBML Level 3 package implemented by this libSBML package extension. |
| prefix | a string, the XML namespace prefix being used for this package. |
| groupsns | a pointer to the namesspaces object (GroupsPkgNamespaces) for this package. |
- 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/'.
- The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
| def libsbml.GroupsModelPlugin.copyInformationToNestedLists |
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self | ) |
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For nested groups (Member objects that reference a ListOfMembers object), SBO terms, Notes, and Annotation from the parent ListOfMembers applies to the child.
copyInformationToNestedLists()
This function copies any information from any of those three things to all child ListOfMembers, and if that information is not already set. After calling this function, it is sufficient to check any ListOfMembers to see if its SBO term, Notes, or Annotation is set, without further checking to see if that element was nested in another Group.
| def libsbml.GroupsModelPlugin.removeGroup |
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self, |
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args |
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This method has multiple variants; they differ in the arguments they accept.
removeGroup(long n) Group
removeGroup(string sid) Group
Each variant is described separately below.
Method variant with the following signature: removeGroup(long n)
Removes the nth Group from this GroupsModelPlugin and returns a pointer to it.
- Parameters
-
| n | a long integer representing the index of the Group to remove. |
- Returns
- a pointer to the nth Group in this GroupsModelPlugin.
- Warning
- The pointer that is returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the element will not be reflected in any resulting SBML document unless the element is added to an SBML Document. Even in this case, the element's deletion is still the responsibility of the caller with two exceptions: if it is used as the 'disownedItem' in theListOf.appendAndOwn() or ListOf.insertAndOwn() functions. All other functions in libsbml add a copy of the element, and do not transfer ownership of the pointer.
- See also
- addGroup()
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createGroup()
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getGroup()
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getGroup()
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getNumGroups()
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removeGroup()
Method variant with the following signature: removeGroup(string sid)
Removes the Group from this GroupsModelPlugin based on its identifier and returns a pointer to it.
- Parameters
-
| sid | a string representing the identifier of the Group to remove. |
- Returns
- the Group in this GroupsModelPlugin based on the identifier or None if no such Group exists.
- Warning
- The pointer that is returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the element will not be reflected in any resulting SBML document unless the element is added to an SBML Document. Even in this case, the element's deletion is still the responsibility of the caller with two exceptions: if it is used as the 'disownedItem' in theListOf.appendAndOwn() or ListOf.insertAndOwn() functions. All other functions in libsbml add a copy of the element, and do not transfer ownership of the pointer.
- See also
- addGroup()
-
createGroup()
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getGroup()
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getGroup()
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getNumGroups()
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removeGroup()
| def libsbml.SBasePlugin.renameMetaIdRefs |
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self, |
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oldid, |
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newid |
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inherited |
Replaces all uses of a given meta identifier attribute value with another value.
renameMetaIdRefs(string oldid, string newid)
- In SBML, object 'meta' identifiers are of the XML data type
ID; the SBML object attribute itself is typically named metaid. All attributes that hold values referring to values of type ID are of the XML data type IDREF. They are also sometimes informally referred to as 'metaid refs', in analogy to the SBML-defined type SIdRef.
This method works by looking at all meta-identifier attribute values, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.
- Parameters
-
| oldid | the old identifier. |
| newid | the new identifier. |
| def libsbml.SBasePlugin.renameSIdRefs |
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self, |
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oldid, |
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newid |
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) |
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inherited |
Replaces all uses of a given SIdRef type attribute value with another value.
renameSIdRefs(string oldid, string newid)
- In SBML, object identifiers are of a data type called
SId. In SBML Level 3, an explicit data type called SIdRef was introduced for attribute values that refer to SId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to an identifier', but the effective data type was the same as SIdRef in Level 3. These and other methods of libSBML refer to the type SIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.
This method works by looking at all attributes and (if appropriate) mathematical formulas in MathML content, comparing the referenced identifiers to the value of oldid. If any matches are found, the matching values are replaced with newid. The method does not descend into child elements.
- Parameters
-
| oldid | the old identifier. |
| newid | the new identifier. |
| def libsbml.SBasePlugin.renameUnitSIdRefs |
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self, |
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oldid, |
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newid |
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) |
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inherited |
Replaces all uses of a given UnitSIdRef type attribute value with another value.
renameUnitSIdRefs(string oldid, string newid)
- In SBML, unit definitions have identifiers of type
UnitSId. In SBML Level 3, an explicit data type called UnitSIdRef was introduced for attribute values that refer to UnitSId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to a unit identifier', but the effective data type was the same as UnitSIdRef in Level 3. These and other methods of libSBML refer to the type UnitSIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.
This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the referenced unit identifiers to the value of oldid. If any matches are found, the matching values are replaced with newid. The method does not descend into child elements.
- Parameters
-
| oldid | the old identifier. |
| newid | the new identifier. |
