libSBML Python API
5.11.0
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The Port class was introduced by the SBML Level 3 Hierarchical Model Composition package (“comp”) to allow a Model to define a standard interface between it and other models that might use it as a submodel. It derives from the SBaseRef class, and the elements defined there refer to elements in the same parent Model as the Port object. A Port object instance therefore uses those attributes to define a port for a component in a model. When other SBaseRef or SBaseRef-derived classes refer to a Port object using a 'portRef' attribute, the element being referenced is the element the Port object itself points to.
In the present formulation of the Hierarchical Model Composition package, the use of ports is not enforced, nor is there any mechanism to restrict which ports may be used in what ways—they are only an advisory construct. Future versions of this SBML package may provide additional functionality to support explicit restrictions on port use. For the present definition of Hierarchical Model Composition, users of models containing ports are encouraged to respect the modeler's intention in defining ports, and use the port definitions to interact with components through their ports (when they have ports defined) rather than interact directly with the components.
The required attribute 'id' is used to give an identifier to a Port object so that other objects can refer to it. The attribute has type PortSId and is essentially identical to the SBML primitive type SId, except that its namespace is limited to the identifiers of Port objects defined within a Model object. In parallel, the PortSId type has a companion type, PortSIdRef, that corresponds to the SBML primitive type SIdRef; the value space of PortSIdRef is limited to PortSId values.
Public Member Functions | |
def | __init__ (self, args) |
comp
An interface to be used in composition. More... | |
def | clearReferencedElement (self) |
Removes the saved referenced element, if it had been saved earlier. More... | |
def | clone (self) |
Creates and returns a deep copy of this Port object. More... | |
def | connectToChild (self) |
def | createSBaseRef (self) |
Creates a new, empty SBaseRef, adds it to this SBaseRef and returns the created SBaseRef. More... | |
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... | |
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... | |
def | getElementName (self) |
Returns the XML element name of this SBML object. More... | |
def | getId (self) |
Returns the value of the 'id' attribute of this Port. More... | |
def | getIdRef (self) |
Returns the value of the 'idRef' attribute of this SBaseRef. More... | |
def | getMetaIdRef (self) |
Returns the value of the 'metaIdRef' attribute of this SBaseRef. More... | |
def | getName (self) |
Returns the value of the 'name' attribute of this Port. More... | |
def | getNumReferents (self) |
Returns how many elements are being referred to by this SBaseRef. More... | |
def | getPortRef (self) |
Returns the value of the 'portRef' attribute of this SBaseRef. More... | |
def | getReferencedElement (self) |
Returns the object pointed to by this element. More... | |
def | getReferencedElementFrom (self, model) |
Examines the referenced Model for the referenced object, and returns it, if found. More... | |
def | getSBaseRef (self, args) |
Get the child sBaseRef of this sBaseRef. More... | |
def | getTypeCode (self) |
Returns the libSBML type code of this object instance. More... | |
def | getUnitRef (self) |
Returns the value of the 'unitRef' attribute of this SBaseRef. More... | |
def | hasRequiredAttributes (self) |
Returns true if the 'id' attribute is set, and if exactly one of the optional attributes of SBaseRef (portRef, idRef, metaIdRef, and unitRef)are set. More... | |
def | isSetId (self) |
Predicate returning True or False depending on whether this Port's 'id' attribute has been set. More... | |
def | isSetIdRef (self) |
Predicate returning True or False depending on whether this SBaseRef's 'idRef' attribute has been set. More... | |
def | isSetMetaIdRef (self) |
Predicate returning True or False depending on whether this SBaseRef's 'metaIdRef' attribute has been set. More... | |
def | isSetName (self) |
Predicate returning True or False depending on whether this Port's 'name' attribute has been set. More... | |
def | isSetPortRef (self) |
Predicate returning True or False depending on whether this SBaseRef's 'portRef' attribute has been set. More... | |
def | isSetSBaseRef (self) |
Predicate for testing whether the sBaseRef for this SBaseRef is set. More... | |
def | isSetUnitRef (self) |
Predicate returning True or False depending on whether this SBaseRef's 'unitRef' attribute has been set. More... | |
def | performDeletion (self) |
DEPRECATED FUNCTION: DO NOT USE. More... | |
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... | |
def | renameMetaIdRefs (self, oldid, newid) |
Replaces all uses of a given meta identifier attribute value with another value. More... | |
def | renameSIdRefs (self, oldid, newid) |
Replaces all uses of a given SIdRef type attribute value with another value. More... | |
def | renameUnitSIdRefs (self, oldid, newid) |
Replaces all uses of a given UnitSIdRef type attribute value with another value. More... | |
def | saveReferencedElement (self) |
Finds and stores the referenced object by finding its Model parent, calling 'getReferencedElementFrom()' on that model, and storing the result. More... | |
def | setId (self, id) |
Sets the value of the 'id' attribute of this Port. More... | |
def | setIdRef (self, id) |
Sets the value of the 'idRef' attribute of this SBaseRef. More... | |
def | setMetaIdRef (self, id) |
Sets the value of the 'metaIdRef' attribute of this SBaseRef. More... | |
def | setName (self, name) |
Sets the value of the 'name' attribute of this Port. More... | |
def | setPortRef (self, id) |
Overrides SBaseRef::setPortRef to always fail, because Port objects themselves cannot refer to model elements by PortSId. More... | |
def | setSBaseRef (self, sBaseRef) |
Sets the sBaseRef definition of this SBaseRef to a copy of the given SBaseRef object instance. More... | |
def | setUnitRef (self, id) |
Sets the value of the 'unitRef' attribute of this SBaseRef. More... | |
def | unsetId (self) |
Unsets the value of the 'id' attribute of this Port. More... | |
def | unsetIdRef (self) |
Unsets the value of the 'idRef' attribute of this SBaseRef. More... | |
def | unsetMetaIdRef (self) |
Unsets the value of the 'metaIdRef' attribute of this SBaseRef. More... | |
def | unsetName (self) |
Unsets the value of the 'name' attribute of this Port. More... | |
def | unsetPortRef (self) |
Unsets the value of the 'portRef' attribute of this SBaseRef. More... | |
def | unsetSBaseRef (self) |
Unsets the child SBaseRef of this SBaseRef. More... | |
def | unsetUnitRef (self) |
Unsets the value of the 'unitRef' attribute of this SBaseRef. More... | |
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inherited |
Removes the saved referenced element, if it had been saved earlier.
clearReferencedElement()
def libsbml.Port.clone | ( | self | ) |
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connectToChild()
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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.
getElementByMetaId(string metaid) SBase
metaid | string representing the metaid of objects to find |
metaid
.
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def libsbml.Port.getElementName | ( | self | ) |
Returns the XML element name of this SBML object.
getElementName() string
def libsbml.Port.getId | ( | self | ) |
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def libsbml.Port.getName | ( | self | ) |
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Returns the object pointed to by this element.
getReferencedElement() SBase
If that element was previously found and set with 'saveReferencedElement', that element is returned; otherwise, 'saveReferencedElement' is called first, and the found element is returned.
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def libsbml.Port.getTypeCode | ( | self | ) |
Returns the libSBML type code of this object instance.
getTypeCode() int
SBML_
. In the Python language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbml. Note that different Level 3 package plug-ins may use overlapping type codes; to identify the package to which a given object belongs, call the getPackageName()
method on the object.
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def libsbml.Port.hasRequiredAttributes | ( | self | ) |
Returns true if the 'id' attribute is set, and if exactly one of the optional attributes of SBaseRef (portRef, idRef, metaIdRef, and unitRef)are set.
hasRequiredAttributes() bool
def libsbml.Port.isSetId | ( | self | ) |
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def libsbml.Port.isSetName | ( | self | ) |
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DEPRECATED FUNCTION: DO NOT USE.
Deletes the referenced object, plus any other elements that element points to through ReplacedElement or ReplacedBy children.
performDeletion() int
Instead of calling this function directly, use 'CompModelPlugin::instantiateSubmodels' instead, which deals with all the intricacies of replacements and deletions, and gives you access to the non-flattened hierarchical form of the model.
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def libsbml.Port.renameMetaIdRefs | ( | self, | |
oldid, | |||
newid | |||
) |
Replaces all uses of a given meta identifier attribute value with another value.
renameMetaIdRefs(string oldid, string newid)
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.
oldid | the old identifier |
newid | the new identifier |
def libsbml.Port.renameSIdRefs | ( | self, | |
oldid, | |||
newid | |||
) |
Replaces all uses of a given SIdRef
type attribute value with another value.
renameSIdRefs(string oldid, string newid)
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.
oldid | the old identifier |
newid | the new identifier |
def libsbml.Port.renameUnitSIdRefs | ( | self, | |
oldid, | |||
newid | |||
) |
Replaces all uses of a given UnitSIdRef
type attribute value with another value.
renameUnitSIdRefs(string oldid, string newid)
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.
oldid | the old identifier |
newid | the new identifier |
def libsbml.Port.saveReferencedElement | ( | self | ) |
Finds and stores the referenced object by finding its Model parent, calling 'getReferencedElementFrom()' on that model, and storing the result.
saveReferencedElement() int
def libsbml.Port.setId | ( | self, | |
id | |||
) |
Sets the value of the 'id' attribute of this Port.
setId(string id) int
This method fails if the id
is not a valid syntax for an SId.
id | the identifier for the port |
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Sets the value of the 'idRef' attribute of this SBaseRef.
setIdRef(string id) int
This method fails if the id is not a valid syntax for an SIdRef (LIBSBML_INVALID_ATTRIBUTE_VALUE), or if the SBaseRef already points to an element of the submodel using a different interface (LIBSBML_OPERATION_FAILED). A sBaseRef must use exactly one method to point to a submodel element.
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Sets the value of the 'metaIdRef' attribute of this SBaseRef.
setMetaIdRef(string id) int
This method fails if the id is not a valid syntax for an IDREF (LIBSBML_INVALID_ATTRIBUTE_VALUE), or if the SBaseRef already points to an element of the submodel using a different interface (LIBSBML_OPERATION_FAILED). An sBaseRef must use exactly one method to point to a submodel element.
def libsbml.Port.setName | ( | self, | |
name | |||
) |
Sets the value of the 'name' attribute of this Port.
setName(string name) int
def libsbml.Port.setPortRef | ( | self, | |
id | |||
) |
Overrides SBaseRef::setPortRef to always fail, because Port objects themselves cannot refer to model elements by PortSId.
setPortRef(string id) int
id | the identifier to set for the port reference |
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Sets the sBaseRef definition of this SBaseRef to a copy of the given SBaseRef object instance.
setSBaseRef(SBaseRef sBaseRef) int
This method fails if the added sBaseRef does not match the level/version/package of the parent object or if the added sBaseRef cannot be copied.
sBaseRef | the SBaseRef object instance to use. |
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Sets the value of the 'unitRef' attribute of this SBaseRef.
setUnitRef(string id) int
This method fails if the id is not a valid syntax for a UnitSIdRef (LIBSBML_INVALID_ATTRIBUTE_VALUE), or if the SBaseRef already points to an element of the submodel using a different interface (LIBSBML_OPERATION_FAILED). A sBaseRef must use exactly one method to point to a submodel element.
def libsbml.Port.unsetId | ( | self | ) |
Unsets the value of the 'id' attribute of this Port.
unsetId() int
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Unsets the value of the 'idRef' attribute of this SBaseRef.
unsetIdRef() int
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Unsets the value of the 'metaIdRef' attribute of this SBaseRef.
unsetMetaIdRef() int
def libsbml.Port.unsetName | ( | self | ) |
Unsets the value of the 'name' attribute of this Port.
unsetName() int
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Unsets the value of the 'portRef' attribute of this SBaseRef.
unsetPortRef() int
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Unsets the value of the 'unitRef' attribute of this SBaseRef.
unsetUnitRef() int