comp
Convenience class.
The Replacing class does not exist officialy in the the Hierarchical Model Composition package (“comp”), but is implemented here as a convenience subclass of the ReplacedElement and ReplacedBy classes, since both of those classes define a 'submodelRef' attribute.
The required attribute 'submodelRef' takes a value of type SIdRef, which must be the identifier of a Submodel object in the containing model. The model referenced by the Submodel object establishes the object namespaces for the 'portRef', 'idRef', 'unitRef' and 'metaIdRef' attributes: only objects within the Model object may be referenced by those attributes.
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def | clearReferencedElement (self) |
| Removes the saved referenced element, if it had been saved earlier. More...
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def | clone (self) |
| Creates and returns a deep copy of this SBaseRef object. More...
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def | connectToChild (self) |
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def | createSBaseRef (self) |
| Creates a new, empty SBaseRef, adds it to this SBaseRef and returns the created SBaseRef. More...
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def | getElementByMetaId (self, metaid) |
| Returns the first child element it can find with the given metaid , or itself if it 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 found 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 | getElementName (self) |
| Returns the XML element name of this SBML object. More...
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def | getIdRef (self) |
| Returns the value of the 'idRef' attribute of this SBaseRef. More...
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def | getMetaIdRef (self) |
| Returns the value of the 'metaIdRef' attribute of this SBaseRef. More...
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def | getNumReferents (self) |
| Returns how many elements are being referred to by this SBaseRef. More...
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def | getPortRef (self) |
| Returns the value of the 'portRef' attribute of this SBaseRef. More...
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def | getReferencedElement (self) |
| Returns the object pointed to by this element. More...
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def | getReferencedElementFrom (self, model) |
| Examines the referenced Model for the referenced object, and returns it, if found. More...
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def | getSBaseRef (self, args) |
| Get the child sBaseRef of this sBaseRef. More...
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def | getSubmodelRef (self) |
| comp
Convenience class. More...
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def | getTypeCode (self) |
| Returns the libSBML type code of this object instance. More...
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def | getUnitRef (self) |
| Returns the value of the 'unitRef' attribute of this SBaseRef. More...
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def | hasRequiredAttributes (self) |
| Returns true if getNumReferents() is exactly 1 and if the submodelRef is set. More...
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def | isSetIdRef (self) |
| Predicate returning True or False depending on whether this SBaseRef's 'idRef' attribute has been set. More...
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def | isSetMetaIdRef (self) |
| Predicate returning True or False depending on whether this SBaseRef's 'metaIdRef' attribute has been set. More...
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def | isSetPortRef (self) |
| Predicate returning True or False depending on whether this SBaseRef's 'portRef' attribute has been set. More...
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def | isSetSBaseRef (self) |
| Predicate for testing whether the sBaseRef for this SBaseRef is set. More...
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def | isSetSubmodelRef (self) |
| Predicate returning True or False depending on whether this SBaseRef's 'submodelRef' attribute has been set. More...
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def | isSetUnitRef (self) |
| Predicate returning True or False depending on whether this SBaseRef's 'unitRef' attribute has been set. More...
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def | performDeletion (self) |
| DEPRECATED FUNCTION: DO NOT USE. More...
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def | performReplacement (self) |
| DEPRECATED FUNCTION: DO NOT USE. More...
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def | removeFromParentAndDelete (self) |
| Finds this SBaseRef's parent, which can either be a List or can be another SBaseRef, and tells it to remove this. 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 | saveReferencedElement (self) |
| Finds and stores the referenced object. More...
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def | setIdRef (self, id) |
| Sets the value of the 'idRef' attribute of this SBaseRef. More...
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def | setMetaIdRef (self, id) |
| Sets the value of the 'metaIdRef' attribute of this SBaseRef. More...
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def | setPortRef (self, id) |
| Sets the value of the 'portRef' attribute of this SBaseRef. More...
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def | setSBaseRef (self, sBaseRef) |
| Sets the sBaseRef definition of this SBaseRef to a copy of the given SBaseRef object instance. More...
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def | setSubmodelRef (self, id) |
| Sets the value of the 'submodelRef' attribute of this SBaseRef. More...
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def | setUnitRef (self, id) |
| Sets the value of the 'unitRef' attribute of this SBaseRef. More...
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def | unsetIdRef (self) |
| Unsets the value of the 'idRef' attribute of this SBaseRef. More...
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def | unsetMetaIdRef (self) |
| Unsets the value of the 'metaIdRef' attribute of this SBaseRef. More...
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def | unsetPortRef (self) |
| Unsets the value of the 'portRef' attribute of this SBaseRef. More...
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def | unsetSBaseRef (self) |
| Unsets the child SBaseRef of this SBaseRef. More...
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def | unsetSubmodelRef (self) |
| Unsets the value of the 'SubmodelRef' attribute of this SBaseRef. More...
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def | unsetUnitRef (self) |
| Unsets the value of the 'unitRef' attribute of this SBaseRef. More...
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def libsbml.Replacing.performReplacement |
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self | ) |
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DEPRECATED FUNCTION: DO NOT USE.
To retain old functionality, this function calls performReplacementAndCollect, and then actually removes the now-redundant element.
performReplacement() int
However, this can lead to doubly-deleted elements, as well as the incorrect interpretation of some models. The replacement function performReplacementAndCollect has been marked protected, in the hopes that people will instead simply use CompModelPlugin::instantiateSubmodels, which hides all the complexity while still allowing access to a non-flattened version of a hierarchical model.
def libsbml.Replacing.renameSIdRefs |
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self, |
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oldid, |
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newid |
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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
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oldid | the old identifier |
newid | the new identifier |