libSBML C++ API  libSBML 5.12.0 C++ API
ReplacedBy Class Reference
Inheritance diagram for ReplacedBy:
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Detailed Description

{comp}

comp Indicates an object replaced by another.

The ReplacedBy class was introduced by the SBML Level 3 Hierarchical Model Composition

package (“comp”) to allow submodel elements to be 'canonical' versions of the element while still allowing the parent model to reference those elements. Whereas a ReplacedElement object indicates that the containing object replaces another, a ReplacedBy object indicates the converse: the parent object is to be replaced by another object.

As is the case with ReplacedElement, the ReplacedBy class inherits from SBaseRef. It additionally defines one required attribute ("submodelRef"), defined in libSBML in the Replacing class.

Examples:
spec_example3.cpp, and spec_example4.cpp.

Public Member Functions

virtual void clearReferencedElement ()
 Removes the saved referenced element, if it had been saved earlier. More...
 
virtual ReplacedByclone () const
 Creates and returns a deep copy of this ReplacedBy 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...
 
ReplacedByoperator= (const ReplacedBy &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 ReplacedBy's SBase parent, gets the “comp” plugin from it, and tells that to remove this. More...
 
virtual void renameSIdRefs (const std::string &oldid, const std::string &newid)
 
 ReplacedBy (unsigned int level=CompExtension::getDefaultLevel(), unsigned int version=CompExtension::getDefaultVersion(), unsigned int pkgVersion=CompExtension::getDefaultPackageVersion())
 Creates a new ReplacedBy with the given level, version, and package version. More...
 
 ReplacedBy (CompPkgNamespaces *compns)
 Creates a new ReplacedBy with the given CompPkgNamespaces object. More...
 
 ReplacedBy (const ReplacedBy &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 ~ReplacedBy ()
 Destructor. More...
 

Protected Member Functions

virtual int performReplacementAndCollect (std::set< SBase * > *removed, std::set< SBase * > *toremove)
 Updates all IDs and references to those IDs. More...
 

Friends

class CompModelPlugin
 

Constructor & Destructor Documentation

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

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

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

Creates a new ReplacedBy with the given CompPkgNamespaces object.

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

Copy constructor.

ReplacedBy::~ReplacedBy ( )
virtual

Destructor.

Member Function Documentation

void SBaseRef::clearReferencedElement ( )
virtualinherited

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

ReplacedBy * ReplacedBy::clone ( ) const
virtual

Creates and returns a deep copy of this ReplacedBy object.

Returns
a (deep) copy of this ReplacedBy object

Reimplemented from SBaseRef.

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 & ReplacedBy::getElementName ( ) const
virtual

Returns the XML element name of this SBML object.

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

Reimplemented from SBaseRef.

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
virtualinherited

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

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

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_REPLACEDBYendif

Reimplemented from SBaseRef.

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
virtualinherited

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
virtualinherited

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.
ReplacedBy & ReplacedBy::operator= ( const ReplacedBy 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 ( )
virtualinherited

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.

int ReplacedBy::performReplacementAndCollect ( std::set< SBase * > *  removed,
std::set< SBase * > *  toremove 
)
protectedvirtual

Updates all IDs and references to those IDs.

Does not actually remove the now-redundant element! The elements to be removed is instead added to 'toremove', allowing one to remove the element carefully to prevent double-deletion of elements, and to allow the correct interpretation of 'nested' replacements and deletions.

The 'removed' argument is present to ensure that the replaced element was not already removed, which would make it impossible to check it for its old IDs. In normal comp flattening, 'removed' will only contain comp elements, which should usually not be replaced, only deleted.

Implements Replacing.

int ReplacedBy::removeFromParentAndDelete ( )
virtual

Finds this ReplacedBy's SBase parent, gets the “comp” plugin from it, and tells that to remove this.

Reimplemented from SBaseRef.

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

Reimplemented from SBaseRef.

Reimplemented in ReplacedElement.

int Replacing::saveReferencedElement ( )
virtualinherited

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.

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_VALUEendif

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_VALUEendif

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_VALUEendif

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.
int Replacing::setSubmodelRef ( const std::string &  id)
virtualinherited

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

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

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_VALUEendif

int SBaseRef::unsetIdRef ( )
virtualinherited

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

Examples:
spec_example3.cpp, and spec_example4.cpp.
int SBaseRef::unsetMetaIdRef ( )
virtualinherited

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

int SBaseRef::unsetPortRef ( )
virtualinherited

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

int SBaseRef::unsetSBaseRef ( )
virtualinherited

Unsets the child SBaseRef of this SBaseRef.

Deletes the former SBaseRef child, if one existed.

int Replacing::unsetSubmodelRef ( )
virtualinherited

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

int SBaseRef::unsetUnitRef ( )
virtualinherited

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

Friends And Related Function Documentation

friend class CompModelPlugin
friend