Inheritance diagram for Replacing:

Detailed Description

{comp}

comp Convenience class.

The Replacing class does not exist officialy in the the Hierarchical Model Composition (“comp”) package, 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 void	clearReferencedElement ()
	Removes the saved referenced element, if it had been saved earlier. More...

virtual SBaseRef *	clone () const
	Creates and returns a deep copy of this SBaseRef object. More...

SBaseRef *	createSBaseRef ()
	Creates a new, empty SBaseRef, adds it to this SBaseRef and returns the created SBaseRef. More...

virtual List *	getAllElements (ElementFilter *filter=NULL)
	Returns a List of all child SBase* objects, including those nested to an arbitrary depth. More...

virtual SBase *	getElementByMetaId (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 SBase *	getElementBySId (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 SBase *	getReferencedElement ()
	Returns the object pointed to by this element. More...

virtual SBase *	getReferencedElementFrom (Model *model)
	Examines the referenced Model for the referenced object, and returns it, if found. More...

const SBaseRef *	getSBaseRef () const
	Get the child sBaseRef of this sBaseRef. More...

SBaseRef *	getSBaseRef ()
	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...

Replacing &	operator= (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)

	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() [1/3]

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

level	the SBML Level
version	the Version within the SBML Level
pkgVersion	the version of the package

§ Replacing() [2/3]

Replacing::Replacing ( CompPkgNamespaces * compns )

Creates a new Replacing with the given CompPkgNamespaces object.

Parameters

compns the namespace to use

§ Replacing() [3/3]

Replacing::Replacing ( const Replacing & source )

Copy constructor.

§ ~Replacing()

Replacing::~Replacing ( )

virtual

Destructor.

Member Function Documentation

§ clearReferencedElement()

void SBaseRef::clearReferencedElement ( )

virtualinherited

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

§ clone()

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.

§ createSBaseRef()

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.

§ getAllElements()

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.

§ getElementByMetaId()

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

metaid string representing the metaid of objects to find

Returns: a pointer to the SBase element with the given metaid.

§ getElementBySId()

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

id	string representing the id of objects to find

Returns: a pointer to the SBase element with the given id.

§ getElementName()

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.

§ getIdRef()

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.

§ getMetaIdRef()

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.

§ getNumReferents()

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.

§ getPortRef()

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.

§ getReferencedElement()

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.

§ getReferencedElementFrom()

SBase * SBaseRef::getReferencedElementFrom ( Model * model )

virtualinherited

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

Parameters

model the 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.

§ getSBaseRef() [1/2]

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.

§ getSBaseRef() [2/2]

SBaseRef * SBaseRef::getSBaseRef ( )

inherited

Get the child sBaseRef of this SBaseRef.

Returns: the SBaseRef child of this SBaseRef, or NULL if none exists.

§ getSubmodelRef()

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.

§ getTypeCode()

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_SBASEREFendif

Reimplemented in ReplacedElement, Deletion, Port, and ReplacedBy.

§ getUnitRef()

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.

§ hasRequiredAttributes()

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.

§ isSetIdRef()

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.

§ isSetMetaIdRef()

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.

§ isSetPortRef()

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.

§ isSetSBaseRef()

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.

§ isSetSubmodelRef()

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.

§ isSetUnitRef()

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.

§ operator=()

Replacing & Replacing::operator= ( const Replacing & source )

Assignment operator.

§ performDeletion()

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.

§ performReplacement()

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.

§ performReplacementAndCollect()

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.

§ removeFromParentAndDelete()

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.

LIBSBML_OPERATION_SUCCESSendif

Reimplemented in ReplacedBy.

§ renameSIdRefs()

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

virtual

Reimplemented from SBaseRef.

Reimplemented in ReplacedElement.

§ saveReferencedElement()

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.

LIBSBML_OPERATION_SUCCESSendif

Reimplemented from SBaseRef.

§ setIdRef()

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.

§ setMetaIdRef()

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

§ setPortRef()

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.

§ setSBaseRef()

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

sBaseRef the SBaseRef object instance to use.

LIBSBML_OPERATION_SUCCESSendif

§ setSubmodelRef()

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.

LIBSBML_OPERATION_SUCCESSendif

Examples:: spec_example2.cpp, spec_example3.cpp, and spec_example4.cpp.

§ setUnitRef()

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

§ unsetIdRef()

int SBaseRef::unsetIdRef ( )

virtualinherited

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

LIBSBML_OPERATION_SUCCESSendif

Examples:: spec_example3.cpp, and spec_example4.cpp.

§ unsetMetaIdRef()

int SBaseRef::unsetMetaIdRef ( )

virtualinherited

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

LIBSBML_OPERATION_SUCCESSendif

§ unsetPortRef()

int SBaseRef::unsetPortRef ( )

virtualinherited

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

LIBSBML_OPERATION_SUCCESSendif

§ unsetSBaseRef()

int SBaseRef::unsetSBaseRef ( )

virtualinherited

Unsets the child SBaseRef of this SBaseRef.

Deletes the former SBaseRef child, if one existed.

LIBSBML_OPERATION_SUCCESSendif

§ unsetSubmodelRef()

int Replacing::unsetSubmodelRef ( )

virtual

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

LIBSBML_OPERATION_SUCCESSendif

§ unsetUnitRef()

int SBaseRef::unsetUnitRef ( )

virtualinherited

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

LIBSBML_OPERATION_SUCCESSendif

Detailed Description

Public Member Functions

Protected Member Functions

Constructor & Destructor Documentation

§ Replacing() [1/3]

§ Replacing() [2/3]

§ Replacing() [3/3]

§ ~Replacing()

Member Function Documentation

§ clearReferencedElement()

§ clone()

§ createSBaseRef()

§ getAllElements()

§ getElementByMetaId()

§ getElementBySId()

§ getElementName()

§ getIdRef()

§ getMetaIdRef()

§ getNumReferents()

§ getPortRef()

§ getReferencedElement()

§ getReferencedElementFrom()

§ getSBaseRef() [1/2]

§ getSBaseRef() [2/2]

§ getSubmodelRef()

§ getTypeCode()

§ getUnitRef()

§ hasRequiredAttributes()

§ isSetIdRef()

§ isSetMetaIdRef()

§ isSetPortRef()

§ isSetSBaseRef()

§ isSetSubmodelRef()

§ isSetUnitRef()

§ operator=()

§ performDeletion()

§ performReplacement()

§ performReplacementAndCollect()

§ removeFromParentAndDelete()

§ renameSIdRefs()

§ saveReferencedElement()

§ setIdRef()

§ setMetaIdRef()

§ setPortRef()

§ setSBaseRef()

§ setSubmodelRef()

§ setUnitRef()

§ unsetIdRef()

§ unsetMetaIdRef()

§ unsetPortRef()

§ unsetSBaseRef()

§ unsetSubmodelRef()

§ unsetUnitRef()