Inheritance diagram for CompSBasePlugin:

Detailed Description

comp Extension of SBase.

The CompSBasePlugin class inherits from the SBasePlugin class, and codifies the extensions to the SBase class defined in the Hierarchical Model Composition (“comp”) package. This extension allows the modeler to define one or more submodel elements which the parent SBase object replaces, and/or a single submodel element which replaces the parent SBase object.

This is accomplished through the addition of an optional ListOfReplacedElements child, which may contain one or more ReplacedElement objects, each of which references a submodel object to be replaced by the containing SBase object, and through the addition of a single optional ReplacedBy child, which references a submodel object which is to replace the containing SBase object.

If a single SBase element both contains a ListOfReplacedElements and has a ReplacedBy child, it and all the referenced ReplacedElement objects are to be replaced by the object referenced by the ReplacedBy element.

See also: ReplacedElement; ReplacedBy

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

Public Member Functions
int	addReplacedElement (const ReplacedElement *replacedElement)
	Adds a copy of the given ReplacedElement object to the list of ReplacedElements. More...

virtual void	clearReplacedElements ()
	Remove all ReplacedElements, if any exist. More...

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

	CompSBasePlugin (const std::string &uri, const std::string &prefix, CompPkgNamespaces *compns)
	Creates a new CompSBasePlugin object using the given parameters. More...

	CompSBasePlugin (const CompSBasePlugin &orig)
	Copy constructor. More...

ReplacedBy *	createReplacedBy ()
	Creates a new, empty ReplacedBy, adds it to this CompSBasePlugin and returns the created ReplacedBy. More...

ReplacedElement *	createReplacedElement ()
	Creates a ReplacedElement object, adds it to the end of the ReplacedElement objects list and returns a pointer to the newly created object. 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...

const std::string &	getElementNamespace () const
	Returns the namespace URI of the package to which this plugin object belongs. More...

unsigned int	getLevel () const
	Returns the SBML Level of the package extension of this plugin object. More...

const ListOfReplacedElements *	getListOfReplacedElements () const
	Returns the ListOf object that holds all replacedElements. More...

ListOfReplacedElements *	getListOfReplacedElements ()
	Returns the ListOf object that holds all replacedElements. More...

unsigned int	getNumReplacedElements () const
	Returns the number of ReplacedElements for this CompSBasePlugin. More...

const std::string &	getPackageName () const
	Returns the short-form name of the package to which this plugin object belongs. More...

unsigned int	getPackageVersion () const
	Returns the package version of the package extension of this plugin object. More...

SBase *	getParentSBMLObject ()
	Returns the parent object to which this plugin object is connected. More...

const SBase *	getParentSBMLObject () const
	Returns the parent object to which this plugin object is connected. More...

const std::string &	getPrefix () const
	Returns the XML namespace prefix of the package to which this plugin object belongs. More...

const ReplacedBy *	getReplacedBy () const
	Get the child ReplacedBy of this SBase. More...

ReplacedBy *	getReplacedBy ()
	Get the child ReplacedBy of this SBase. More...

ReplacedElement *	getReplacedElement (unsigned int n)
	Returns the ReplacedElement with the given index. More...

const ReplacedElement *	getReplacedElement (unsigned int n) const
	Returns the ReplacedElement with the given index. More...

SBMLDocument *	getSBMLDocument ()
	Returns the SBMLDocument object containing this object instance. More...

const SBMLDocument *	getSBMLDocument () const
	Returns the SBMLDocument object containing this object instance. More...

std::string	getURI () const
	Returns the XML namespace URI for the package to which this object belongs. More...

unsigned int	getVersion () const
	Returns the Version within the SBML Level of the package extension of this plugin object. More...

bool	isSetReplacedBy () const
	Predicate for testing whether the ReplacedBy for this SBase is set. More...

virtual bool	isValidTypeForList (SBase *item) const

virtual void	logInvalidId (const std::string &attribute, const std::string &wrongattribute)
	Helper to log a common type of error. More...

CompSBasePlugin &	operator= (const CompSBasePlugin &orig)
	Assignment operator for CompSBasePlugin. More...

ReplacedElement *	removeReplacedElement (unsigned int index)
	Removes the ReplacedElement with the given index. More...

virtual void	renameMetaIdRefs (const std::string &oldid, const std::string &newid)
	Replaces all uses of a given meta identifier attribute value with another value. 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...

virtual void	renameUnitSIdRefs (const std::string &oldid, const std::string &newid)
	Replaces all uses of a given `UnitSIdRef` type attribute value with another value. More...

int	setElementNamespace (const std::string &uri)
	Sets the XML namespace to which this object belongs. More...

int	setReplacedBy (const ReplacedBy *replacedBy)
	Sets the ReplacedBy definition of this SBase to a copy of the given ReplacedBy object instance. More...

virtual int	unsetReplacedBy ()
	Unsets the child ReplacedBy of this SBase. More...

virtual	~CompSBasePlugin ()
	Destroy this object. More...

Constructor & Destructor Documentation

CompSBasePlugin::CompSBasePlugin	(	const std::string &	uri,
		const std::string &	prefix,
		CompPkgNamespaces *	compns
	)

Creates a new CompSBasePlugin object using the given parameters.

: In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs; for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI "http://www.sbml.org/sbml/level3/version1/core". Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace "http://www.sbml.org/sbml/level3/version1/layout/version1/".

: The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.

Parameters

uri	the URI of the SBML Level 3 package implemented by this libSBML package extension.
prefix	the XML namespace prefix being used for the package.
compns	the namespaces object for the package.

CompSBasePlugin::CompSBasePlugin ( const CompSBasePlugin & orig )

Copy constructor.

Creates a copy of this CompSBasePlugin object.

Parameters

orig	the instance to copy.

CompSBasePlugin::~CompSBasePlugin ( )

virtual

Destroy this object.

Member Function Documentation

int CompSBasePlugin::addReplacedElement ( const ReplacedElement * replacedElement )

Adds a copy of the given ReplacedElement object to the list of ReplacedElements.

Parameters

replacedElement the ReplacedElement object to be added to the list of ReplacedElements. Fails if the added ReplacedElement is NULL, does not match the level/version/package of the parent object, or cannot be added to the list of replaced elements.

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.

void CompSBasePlugin::clearReplacedElements ( )

virtual

Remove all ReplacedElements, if any exist.

CompSBasePlugin * CompSBasePlugin::clone ( ) const

virtual

Creates and returns a deep copy of this CompSBasePlugin object.

Returns: a (deep) copy of this CompSBasePlugin object.

Reimplemented from SBasePlugin.

Reimplemented in CompModelPlugin.

ReplacedBy * CompSBasePlugin::createReplacedBy ( )

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

Returns: the newly created ReplacedBy object instance.

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

ReplacedElement * CompSBasePlugin::createReplacedElement ( )

Creates a ReplacedElement object, adds it to the end of the ReplacedElement objects list and returns a pointer to the newly created object.

Returns: a newly created ReplacedElement object.

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

List * CompSBasePlugin::getAllElements ( ElementFilter * filter = NULL )

virtual

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

Parameters

filter a pointer to an ElementFilter, which causes the function to return only elements that match a particular set of constraints. If NULL (the default), the function will return all child objects.

Returns: a List of pointers to all children objects.

Reimplemented from SBasePlugin.

Reimplemented in CompModelPlugin.

SBase * CompSBasePlugin::getElementByMetaId ( const std::string & metaid )

virtual

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 the object to find.

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

Reimplemented from SBasePlugin.

Reimplemented in CompModelPlugin.

SBase * CompSBasePlugin::getElementBySId ( const std::string & id )

virtual

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 the object to find.

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

Reimplemented from SBasePlugin.

Reimplemented in CompModelPlugin.

const std::string & SBasePlugin::getElementNamespace ( ) const

inherited

Returns the namespace URI of the package to which this plugin object belongs.

Returns: the XML namespace URI of the SBML Level 3 package implemented by this libSBML package extension.

unsigned int SBasePlugin::getLevel ( ) const

inherited

Returns the SBML Level of the package extension of this plugin object.

Returns: the SBML Level.

See also: getVersion()

const ListOfReplacedElements * CompSBasePlugin::getListOfReplacedElements ( ) const

Returns the ListOf object that holds all replacedElements.

Returns: the ListOf object that holds all replacedElements.

ListOfReplacedElements * CompSBasePlugin::getListOfReplacedElements ( )

Returns the ListOf object that holds all replacedElements.

Returns: the ListOf object that holds all replacedElements.

unsigned int CompSBasePlugin::getNumReplacedElements ( ) const

Returns the number of ReplacedElements for this CompSBasePlugin.

Returns: the number of ReplacedElements for this CompSBasePlugin.

const std::string & SBasePlugin::getPackageName ( ) const

inherited

Returns the short-form name of the package to which this plugin object belongs.

Returns: the short-form package name (or nickname) of the SBML package implemented by this package extension.

unsigned int SBasePlugin::getPackageVersion ( ) const

inherited

Returns the package version of the package extension of this plugin object.

Returns: the package version of the package extension of this plugin object.

See also: getLevel(); getVersion()

SBase * SBasePlugin::getParentSBMLObject ( )

inherited

Returns the parent object to which this plugin object is connected.

Returns: the parent object of this object.

const SBase * SBasePlugin::getParentSBMLObject ( ) const

inherited

Returns the parent object to which this plugin object is connected.

Returns: the parent object of this object.

const std::string & SBasePlugin::getPrefix ( ) const

inherited

Returns the XML namespace prefix of the package to which this plugin object belongs.

Returns: the XML namespace prefix of the SBML Level 3 package implemented by this libSBML package extension.

const ReplacedBy * CompSBasePlugin::getReplacedBy ( ) const

Get the child ReplacedBy of this SBase.

Returns: the const ReplacedBy child of this SBase.

ReplacedBy * CompSBasePlugin::getReplacedBy ( )

Get the child ReplacedBy of this SBase.

Returns: the ReplacedBy child of this SBase.

ReplacedElement * CompSBasePlugin::getReplacedElement ( unsigned int n )

Returns the ReplacedElement with the given index.

Parameters

n	the index number of the ReplacedElement to get.

Returns: the nth ReplacedElement in the ListOfReplacedElements. If the index is invalid, NULL is returned.

const ReplacedElement * CompSBasePlugin::getReplacedElement ( unsigned int n ) const

Returns the ReplacedElement with the given index.

Parameters

n	the index number of the ReplacedElement to get.

Returns: the nth ReplacedElement in the ListOfReplacedElements. If the index is invalid, NULL is returned.

SBMLDocument * SBasePlugin::getSBMLDocument ( )

inherited

Returns the SBMLDocument object containing this object instance.

: LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns: the parent SBMLDocument object of this plugin object.

See also: getParentSBMLObject()

const SBMLDocument * SBasePlugin::getSBMLDocument ( ) const

inherited

Returns the SBMLDocument object containing this object instance.

: LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns: the parent SBMLDocument object of this plugin object.

See also: getParentSBMLObject()

std::string SBasePlugin::getURI ( ) const

inherited

Returns the XML namespace URI for the package to which this object belongs.

: In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs; for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI "http://www.sbml.org/sbml/level3/version1/core". Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace "http://www.sbml.org/sbml/level3/version1/layout/version1/".

This method first looks into the SBMLNamespaces object possessed by the parent SBMLDocument object of the current object. If this cannot be found, this method returns the result of getElementNamespace().

Returns: a string, the URI of the XML namespace to which this object belongs.

See also: getPackageName(); getElementNamespace(); getSBMLDocument()

unsigned int SBasePlugin::getVersion ( ) const

inherited

Returns the Version within the SBML Level of the package extension of this plugin object.

Returns: the SBML Version.

See also: getLevel()

bool CompSBasePlugin::isSetReplacedBy ( ) const

Predicate for testing whether the ReplacedBy for this SBase is set.

Returns: true if the ReplacedBy of this SBase is set, false otherwise.

virtual bool SBasePlugin::isValidTypeForList ( SBase * item ) const

virtualinherited

void CompSBasePlugin::logInvalidId	(	const std::string &	attribute,
		const std::string &	wrongattribute
	)

virtual

Helper to log a common type of error.

CompSBasePlugin & CompSBasePlugin::operator= ( const CompSBasePlugin & orig )

Assignment operator for CompSBasePlugin.

Parameters

orig	the object whose values are used as the basis of the assignment.

ReplacedElement * CompSBasePlugin::removeReplacedElement ( unsigned int index )

Removes the ReplacedElement with the given index.

A pointer to the ReplacedElement that was removed is returned. If no ReplacedElement has been removed, NULL is returned.

Parameters

index the index of the ReplacedElement object to remove.

Returns: the ReplacedElement object removed. As mentioned above, the caller owns the returned object. NULL is returned if the given index is out of range.

virtual void SBasePlugin::renameMetaIdRefs	(	const std::string &	oldid,
		const std::string &	newid
	)

virtualinherited

Replaces all uses of a given meta identifier attribute value with another value.

: In SBML, object "meta" identifiers are of the XML data type 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.

Parameters

oldid	the old identifier.
newid	the new identifier.

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

virtualinherited

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 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

oldid	the old identifier.
newid	the new identifier.

Reimplemented in FbcReactionPlugin.

virtual void SBasePlugin::renameUnitSIdRefs	(	const std::string &	oldid,
		const std::string &	newid
	)

virtualinherited

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

: In SBML, unit definitions have identifiers of type 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.

Parameters

oldid	the old identifier.
newid	the new identifier.

int SBasePlugin::setElementNamespace ( const std::string & uri )

inherited

Sets the XML namespace to which this object belongs.

: In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs; for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI "http://www.sbml.org/sbml/level3/version1/core". Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace "http://www.sbml.org/sbml/level3/version1/layout/version1/".

Parameters

uri	the URI to assign to this object.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:

LIBSBML_OPERATION_SUCCESS

See also: getElementNamespace()

Examples:: convertLayout.cpp.

int CompSBasePlugin::setReplacedBy ( const ReplacedBy * replacedBy )

Sets the ReplacedBy definition of this SBase to a copy of the given ReplacedBy object instance.

This method fails if the added ReplacedBy does not match the level/version/package of the parent object or if the added ReplacedBy cannot be copied.

Parameters

replacedBy the ReplacedBy 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 CompSBasePlugin::unsetReplacedBy ( )

virtual

Unsets the child ReplacedBy of this SBase.

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:

Detailed Description

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation