libSBML C++ API  5.11.0
Replacing Class Referenceabstract
Inheritance diagram for Replacing:
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Detailed Description

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.

Public Member Functions

virtual bool accept (SBMLVisitor &v) const
 Accepts the given SBMLVisitor. More...
 
virtual void clearReferencedElement ()
 Removes the saved referenced element, if it had been saved earlier. More...
 
virtual SBaseRefclone () const
 Creates and returns a deep copy of this SBaseRef object. More...
 
SBaseRefcreateSBaseRef ()
 Creates a new, empty SBaseRef, adds it to this SBaseRef and returns the created SBaseRef. More...
 
virtual ListgetAllElements (ElementFilter *filter=NULL)
 Returns a List of all child SBase* objects, including those nested to an arbitrary depth. More...
 
virtual SBasegetElementByMetaId (const std::string &metaid)
 Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or NULL if no such object is found. More...
 
virtual SBasegetElementBySId (const std::string &id)
 Returns the first child element found that has the given id in the model-wide SId namespace, or NULL if no such object is found. More...
 
virtual const std::string & getElementName () const
 Returns the XML element name of this SBML object. More...
 
virtual const std::string & getIdRef () const
 Returns the value of the "idRef" attribute of this SBaseRef. More...
 
virtual const std::string & getMetaIdRef () const
 Returns the value of the "metaIdRef" attribute of this SBaseRef. More...
 
virtual int getNumReferents () const
 Returns how many elements are being referred to by this SBaseRef. More...
 
virtual const std::string & getPortRef () const
 Returns the value of the "portRef" attribute of this SBaseRef. More...
 
virtual SBasegetReferencedElement ()
 Returns the object pointed to by this element. More...
 
virtual SBasegetReferencedElementFrom (Model *model)
 Examines the referenced Model for the referenced object, and returns it, if found. More...
 
const SBaseRefgetSBaseRef () const
 Get the child sBaseRef of this sBaseRef. More...
 
SBaseRefgetSBaseRef ()
 Get the child sBaseRef of this SBaseRef. More...
 
virtual const std::string & getSubmodelRef () const
 Returns the value of the "submodelRef" attribute of this SBaseRef. More...
 
virtual int getTypeCode () const
 Returns the libSBML type code of this object instance. More...
 
virtual const std::string & getUnitRef () const
 Returns the value of the "unitRef" attribute of this SBaseRef. More...
 
virtual bool hasRequiredAttributes () const
 Returns true if getNumReferents() is exactly 1 and if the submodelRef is set. More...
 
virtual bool isSetIdRef () const
 Predicate returning true or false depending on whether this SBaseRef's "idRef" attribute has been set. More...
 
virtual bool isSetMetaIdRef () const
 Predicate returning true or false depending on whether this SBaseRef's "metaIdRef" attribute has been set. More...
 
virtual bool isSetPortRef () const
 Predicate returning true or false depending on whether this SBaseRef's "portRef" attribute has been set. More...
 
bool isSetSBaseRef () const
 Predicate for testing whether the sBaseRef for this SBaseRef is set. More...
 
virtual bool isSetSubmodelRef () const
 Predicate returning true or false depending on whether this SBaseRef's "submodelRef" attribute has been set. More...
 
virtual bool isSetUnitRef () const
 Predicate returning true or false depending on whether this SBaseRef's "unitRef" attribute has been set. More...
 
Replacingoperator= (const Replacing &source)
 Assignment operator. More...
 
virtual int performDeletion ()
 DEPRECATED FUNCTION: DO NOT USE. More...
 
virtual int performReplacement ()
 DEPRECATED FUNCTION: DO NOT USE. More...
 
virtual int removeFromParentAndDelete ()
 Finds this SBaseRef's parent, which can either be a List or can be another SBaseRef, and tells it to remove this. More...
 
virtual void renameSIdRefs (const std::string &oldid, const std::string &newid)
 Replaces all uses of a given SIdRef type attribute value with another value. More...
 
 Replacing (unsigned int level=CompExtension::getDefaultLevel(), unsigned int version=CompExtension::getDefaultVersion(), unsigned int pkgVersion=CompExtension::getDefaultPackageVersion())
 Creates a new Replacing with the given level, version, and package version. More...
 
 Replacing (CompPkgNamespaces *compns)
 Creates a new Replacing with the given CompPkgNamespaces object. More...
 
 Replacing (const Replacing &source)
 Copy constructor. More...
 
virtual int saveReferencedElement ()
 Finds and stores the referenced object. More...
 
virtual int setIdRef (const std::string &id)
 Sets the value of the "idRef" attribute of this SBaseRef. More...
 
virtual int setMetaIdRef (const std::string &id)
 Sets the value of the "metaIdRef" attribute of this SBaseRef. More...
 
virtual int setPortRef (const std::string &id)
 Sets the value of the "portRef" attribute of this SBaseRef. More...
 
int setSBaseRef (const SBaseRef *sBaseRef)
 Sets the sBaseRef definition of this SBaseRef to a copy of the given SBaseRef object instance. More...
 
virtual int setSubmodelRef (const std::string &id)
 Sets the value of the "submodelRef" attribute of this SBaseRef. More...
 
virtual int setUnitRef (const std::string &id)
 Sets the value of the "unitRef" attribute of this SBaseRef. More...
 
virtual int unsetIdRef ()
 Unsets the value of the "idRef" attribute of this SBaseRef. More...
 
virtual int unsetMetaIdRef ()
 Unsets the value of the "metaIdRef" attribute of this SBaseRef. More...
 
virtual int unsetPortRef ()
 Unsets the value of the "portRef" attribute of this SBaseRef. More...
 
virtual int unsetSBaseRef ()
 Unsets the child SBaseRef of this SBaseRef. More...
 
virtual int unsetSubmodelRef ()
 Unsets the value of the "SubmodelRef" attribute of this SBaseRef. More...
 
virtual int unsetUnitRef ()
 Unsets the value of the "unitRef" attribute of this SBaseRef. More...
 
virtual ~Replacing ()
 Destructor. More...
 

Protected Member Functions

virtual int performReplacementAndCollect (std::set< SBase * > *removed, std::set< SBase * > *toremove)=0
 An internal flattening routine, necessarily overridden by any subclass, to rename the necessary elements, perform any conversions, and add the now-redundant element to the 'toremove' list. More...
 

Constructor & Destructor Documentation

Replacing::Replacing ( unsigned int  level = CompExtension::getDefaultLevel(),
unsigned int  version = CompExtension::getDefaultVersion(),
unsigned int  pkgVersion = CompExtension::getDefaultPackageVersion() 
)

Creates a new Replacing with the given level, version, and package version.

Parameters
levelthe SBML Level
versionthe Version within the SBML Level
pkgVersionthe version of the package
Replacing::Replacing ( CompPkgNamespaces compns)

Creates a new Replacing with the given CompPkgNamespaces object.

Parameters
compnsthe namespace to use
Replacing::Replacing ( const Replacing source)

Copy constructor.

Replacing::~Replacing ( )
virtual

Destructor.

Member Function Documentation

bool Replacing::accept ( SBMLVisitor v) const
virtual

Accepts the given SBMLVisitor.

Returns
the result of calling v.visit(), which indicates whether or not the Visitor would like to visit the SBML object's next sibling object (if available).

Reimplemented from SBaseRef.

void SBaseRef::clearReferencedElement ( )
virtualinherited

Removes the saved referenced element, if it had been saved earlier.

SBaseRef * SBaseRef::clone ( ) const
virtualinherited

Creates and returns a deep copy of this SBaseRef object.

Returns
a (deep) copy of this SBaseRef object

Reimplemented in ReplacedElement, Deletion, Port, and ReplacedBy.

SBaseRef * SBaseRef::createSBaseRef ( )
inherited

Creates a new, empty SBaseRef, adds it to this SBaseRef and returns the created SBaseRef.

Returns
the newly created SBaseRef object instance.
List * SBaseRef::getAllElements ( ElementFilter filter = NULL)
virtualinherited

Returns a List of all child SBase* objects, including those nested to an arbitrary depth.

Returns
a List* of pointers to all children objects.
SBase * SBaseRef::getElementByMetaId ( const std::string &  metaid)
virtualinherited

Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or NULL if no such object is found.

Parameters
metaidstring representing the metaid of objects to find
Returns
a pointer to the SBase element with the given metaid.
SBase * SBaseRef::getElementBySId ( const std::string &  id)
virtualinherited

Returns the first child element found that has the given id in the model-wide SId namespace, or NULL if no such object is found.

Parameters
idstring representing the id of objects to find
Returns
a pointer to the SBase element with the given id.
const std::string & SBaseRef::getElementName ( ) const
virtualinherited

Returns the XML element name of this SBML object.

Returns
the name of this element, as a text string.

Reimplemented in ReplacedElement, Deletion, Port, and ReplacedBy.

const string & SBaseRef::getIdRef ( ) const
virtualinherited

Returns the value of the "idRef" attribute of this SBaseRef.

Returns
the value of the "idRef" attribute of this SBaseRef.
const string & SBaseRef::getMetaIdRef ( ) const
virtualinherited

Returns the value of the "metaIdRef" attribute of this SBaseRef.

Returns
the value of the "metaIdRef" attribute of this SBaseRef.
int SBaseRef::getNumReferents ( ) const
virtualinherited

Returns how many elements are being referred to by this SBaseRef.

A valid SBaseRef will have exactly one. Possible referents are portRef, idRef, unitRef, and metaIdRef.

Returns
integer value between 0 and 4: the number of different ways this element points to its referent.

Reimplemented in ReplacedElement.

const string & SBaseRef::getPortRef ( ) const
virtualinherited

Returns the value of the "portRef" attribute of this SBaseRef.

Returns
the value of the "portRef" attribute of this SBaseRef.
SBase * SBaseRef::getReferencedElement ( )
virtualinherited

Returns the object pointed to by this element.

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.

SBase * SBaseRef::getReferencedElementFrom ( Model model)
virtualinherited

Examines the referenced Model for the referenced object, and returns it, if found.

Parameters
modelthe Model in which to look for the object referenced by this SBaseRef.
Returns
the element in the referenced Model to which this SBaseRef refers. If this object references an object in a Submodel, the returned object will be in the instantiated Model in that Submodel.

Reimplemented in ReplacedElement.

const SBaseRef * SBaseRef::getSBaseRef ( ) const
inherited

Get the child sBaseRef of this sBaseRef.

Returns
the const SBaseRef child of this SBaseRef, or NULL if none exists.
SBaseRef * SBaseRef::getSBaseRef ( )
inherited

Get the child sBaseRef of this SBaseRef.

Returns
the SBaseRef child of this SBaseRef, or NULL if none exists.
const string & Replacing::getSubmodelRef ( ) const
virtual

Returns the value of the "submodelRef" attribute of this SBaseRef.

Returns
the value of the "submodelRef" attribute of this SBaseRef.
int SBaseRef::getTypeCode ( ) const
virtualinherited

Returns the libSBML type code of this object instance.

LibSBML attaches an identifying code to every kind of SBML object. These are integer constants known as SBML type codes. The names of all the codes begin with the characters SBML_. The set of possible type codes for core elements is defined in the enumeration SBMLTypeCode_t, and in addition, libSBML plug-ins for SBML Level 3 packages define their own extra enumerations of type codes (e.g., SBMLLayoutTypeCode_t for the Level 3 Layout package). 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.
Returns
the SBML type code for this object: SBML_COMP_SBASEREF
Warning
The specific integer values of the possible type codes may be reused by different Level 3 package plug-ins. Thus, to identifiy the correct code, it is necessary to invoke both getTypeCode() and getPackageName().
See also
getElementName()
getPackageName()

Reimplemented in ReplacedElement, Deletion, Port, and ReplacedBy.

const string & SBaseRef::getUnitRef ( ) const
virtualinherited

Returns the value of the "unitRef" attribute of this SBaseRef.

Returns
the value of the "unitRef" attribute of this SBaseRef.
bool Replacing::hasRequiredAttributes ( ) const
virtual

Returns true if getNumReferents() is exactly 1 and if the submodelRef is set.

Returns
boolean: 'true' if the attributes are correctly set; 'false' if not.

Reimplemented from SBaseRef.

bool SBaseRef::isSetIdRef ( ) const
virtualinherited

Predicate returning true or false depending on whether this SBaseRef's "idRef" attribute has been set.

Returns
true if this SBaseRef's "idRef" attribute has been set, otherwise false is returned.
bool SBaseRef::isSetMetaIdRef ( ) const
virtualinherited

Predicate returning true or false depending on whether this SBaseRef's "metaIdRef" attribute has been set.

Returns
true if this SBaseRef's "metaIdRef" attribute has been set, otherwise false is returned.
bool SBaseRef::isSetPortRef ( ) const
virtualinherited

Predicate returning true or false depending on whether this SBaseRef's "portRef" attribute has been set.

Returns
true if this SBaseRef's "portRef" attribute has been set, otherwise false is returned.
bool SBaseRef::isSetSBaseRef ( ) const
inherited

Predicate for testing whether the sBaseRef for this SBaseRef is set.

Returns
true if the sBaseRef of this SBaseRef is set, false otherwise.
bool Replacing::isSetSubmodelRef ( ) const
virtual

Predicate returning true or false depending on whether this SBaseRef's "submodelRef" attribute has been set.

Returns
true if this SBaseRef's "submodelRef" attribute has been set, otherwise false is returned.
bool SBaseRef::isSetUnitRef ( ) const
virtualinherited

Predicate returning true or false depending on whether this SBaseRef's "unitRef" attribute has been set.

Returns
true if this SBaseRef's "unitRef" attribute has been set, otherwise false is returned.
Replacing & Replacing::operator= ( const Replacing source)

Assignment operator.

int SBaseRef::performDeletion ( )
virtualinherited

DEPRECATED FUNCTION: DO NOT USE.

Deletes the referenced object, plus any other elements that element points to through ReplacedElement or ReplacedBy children. 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.

int Replacing::performReplacement ( )
virtual

DEPRECATED FUNCTION: DO NOT USE.

To retain old functionality, this function calls performReplacementAndCollect, and then actually removes the now-redundant element. 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.

virtual int Replacing::performReplacementAndCollect ( std::set< SBase * > *  removed,
std::set< SBase * > *  toremove 
)
protectedpure virtual

An internal flattening routine, necessarily overridden by any subclass, to rename the necessary elements, perform any conversions, and add the now-redundant element to the 'toremove' list.

Implemented in ReplacedElement, and ReplacedBy.

int SBaseRef::removeFromParentAndDelete ( )
virtualinherited

Finds this SBaseRef's parent, which can either be a List or can be another SBaseRef, and tells it to remove this.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

Reimplemented in ReplacedBy.

void Replacing::renameSIdRefs ( const std::string &  oldid,
const std::string &  newid 
)
virtual

Replaces all uses of a given SIdRef type attribute value with another value.

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 SIdRefin 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
oldidthe old identifier
newidthe new identifier

Reimplemented from SBaseRef.

Reimplemented in ReplacedElement.

int Replacing::saveReferencedElement ( )
virtual

Finds and stores the referenced object.

Finds the Submodel to which it refers, getting the instantiated Model inside that Submodel, calling 'getReferencedElementFrom' on that model, and storing the result.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

Reimplemented from SBaseRef.

int SBaseRef::setIdRef ( const std::string &  id)
virtualinherited

Sets the value of the "idRef" attribute of this SBaseRef.

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.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Examples:
spec_example2.cpp, spec_example3.cpp, and spec_example4.cpp.
int SBaseRef::setMetaIdRef ( const std::string &  id)
virtualinherited

Sets the value of the "metaIdRef" attribute of this SBaseRef.

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.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int SBaseRef::setPortRef ( const std::string &  id)
virtualinherited

Sets the value of the "portRef" attribute of this SBaseRef.

Fails if the id is not a valid syntax for a PortSIdRef (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.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

Reimplemented in Port.

Examples:
spec_example3.cpp, and spec_example4.cpp.
int SBaseRef::setSBaseRef ( const SBaseRef sBaseRef)
inherited

Sets the sBaseRef definition of this SBaseRef to a copy of the given SBaseRef object instance.

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.

Parameters
sBaseRefthe SBaseRef object instance to use.
Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int Replacing::setSubmodelRef ( const std::string &  id)
virtual

Sets the value of the "submodelRef" attribute of this SBaseRef.

Fails if the id is not a valid syntax for an SIdRef.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Examples:
spec_example2.cpp, spec_example3.cpp, and spec_example4.cpp.
int SBaseRef::setUnitRef ( const std::string &  id)
virtualinherited

Sets the value of the "unitRef" attribute of this SBaseRef.

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.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int SBaseRef::unsetIdRef ( )
virtualinherited

Unsets the value of the "idRef" attribute of this SBaseRef.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
Examples:
spec_example3.cpp, and spec_example4.cpp.
int SBaseRef::unsetMetaIdRef ( )
virtualinherited

Unsets the value of the "metaIdRef" attribute of this SBaseRef.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int SBaseRef::unsetPortRef ( )
virtualinherited

Unsets the value of the "portRef" attribute of this SBaseRef.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int SBaseRef::unsetSBaseRef ( )
virtualinherited

Unsets the child SBaseRef of this SBaseRef.

Deletes the former SBaseRef child, if one existed.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int Replacing::unsetSubmodelRef ( )
virtual

Unsets the value of the "SubmodelRef" attribute of this SBaseRef.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:
int SBaseRef::unsetUnitRef ( )
virtualinherited

Unsets the value of the "unitRef" attribute of this SBaseRef.

Returns
integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are: