Inheritance diagram for libsbmlcs.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

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

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

new SBasePlugin	clone ()
	Creates and returns a deep copy of this CompSBasePlugin object. More...

	CompSBasePlugin (string uri, string prefix, CompPkgNamespaces compns)
	Creates a new CompSBasePlugin object using the given parameters. More...

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

void	connectToParent (SBase parent)

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...

override void	Dispose ()

long	getColumn ()

new SBase	getElementByMetaId (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...

new SBase	getElementBySId (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...

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

long	getLevel ()
	Returns the SBML Level of the package extension of this plugin object. More...

long	getLine ()

SBaseList	getListOfAllElements (ElementFilter filter)

SBaseList	getListOfAllElements ()

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

long	getNumReplacedElements ()
	Returns the number of ReplacedElements for this CompSBasePlugin. More...

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

long	getPackageVersion ()
	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...

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

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

ReplacedElement	getReplacedElement (long n)
	Returns the ReplacedElement with the given index. More...

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

SBMLExtension	getSBMLExtension ()

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

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

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

new bool	isValidTypeForList (SBase item)

new void	logInvalidId (string attribute, string wrongattribute)
	Helper to log a common type of error. More...

ReplacedElement	removeReplacedElement (long index)
	Removes the ReplacedElement with the given index. More...

new void	renameMetaIdRefs (string oldid, string newid)
	Replaces all uses of a given meta identifier attribute value with another value. More...

new void	renameSIdRefs (string oldid, string newid)
	Replaces all uses of a given `SIdRef` type attribute value with another value. More...

new void	renameUnitSIdRefs (string oldid, string newid)
	Replaces all uses of a given `UnitSIdRef` type attribute value with another value. More...

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

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

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

Protected Attributes
bool	swigCMemOwn

Constructor & Destructor Documentation

libsbmlcs.CompSBasePlugin.CompSBasePlugin	(	string	uri,
		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.

libsbmlcs.CompSBasePlugin.CompSBasePlugin ( CompSBasePlugin orig )

Copy constructor.

Creates a copy of this CompSBasePlugin object.

Parameters

orig	the instance to copy.

Member Function Documentation

int libsbmlcs.CompSBasePlugin.addReplacedElement ( 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 possible values returned by this function are:

new void libsbmlcs.CompSBasePlugin.clearReplacedElements ( )

Remove all ReplacedElements, if any exist.

new SBasePlugin libsbmlcs.CompSBasePlugin.clone ( )

Creates and returns a deep copy of this CompSBasePlugin object.

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

void libsbmlcs.CompSBasePlugin.connectToParent ( SBase parent )

ReplacedBy libsbmlcs.CompSBasePlugin.createReplacedBy ( )

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

Returns: the newly created ReplacedBy object instance.

ReplacedElement libsbmlcs.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.

override void libsbmlcs.CompSBasePlugin.Dispose ( )

virtual

Reimplemented from libsbmlcs.SBasePlugin.

long libsbmlcs.SBasePlugin.getColumn ( )

inherited

new SBase libsbmlcs.CompSBasePlugin.getElementByMetaId ( 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.

Parameters

metaid string representing the metaid of the object to find.

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

new SBase libsbmlcs.CompSBasePlugin.getElementBySId ( 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.

Parameters

id	string representing the id of the object to find.

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

string libsbmlcs.SBasePlugin.getElementNamespace ( )

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.

long libsbmlcs.SBasePlugin.getLevel ( )

inherited

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

Returns: the SBML Level.

See also: getVersion()

long libsbmlcs.SBasePlugin.getLine ( )

inherited

SBaseList libsbmlcs.SBasePlugin.getListOfAllElements ( ElementFilter filter )

inherited

SBaseList libsbmlcs.SBasePlugin.getListOfAllElements ( )

inherited

ListOfReplacedElements libsbmlcs.CompSBasePlugin.getListOfReplacedElements ( )

Returns the ListOf object that holds all replacedElements.

Returns: the ListOf object that holds all replacedElements.

long libsbmlcs.CompSBasePlugin.getNumReplacedElements ( )

Returns the number of ReplacedElements for this CompSBasePlugin.

Returns: the number of ReplacedElements for this CompSBasePlugin.

string libsbmlcs.SBasePlugin.getPackageName ( )

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.

long libsbmlcs.SBasePlugin.getPackageVersion ( )

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 libsbmlcs.SBasePlugin.getParentSBMLObject ( )

inherited

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

Returns: the parent object of this object.

string libsbmlcs.SBasePlugin.getPrefix ( )

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.

ReplacedBy libsbmlcs.CompSBasePlugin.getReplacedBy ( )

Get the child ReplacedBy of this SBase.

Returns: the ReplacedBy child of this SBase.

ReplacedElement libsbmlcs.CompSBasePlugin.getReplacedElement ( long 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.

SBMLDocument libsbmlcs.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()

SBMLExtension libsbmlcs.SBasePlugin.getSBMLExtension ( )

inherited

string libsbmlcs.SBasePlugin.getURI ( )

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()

long libsbmlcs.SBasePlugin.getVersion ( )

inherited

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

Returns: the SBML Version.

See also: getLevel()

bool libsbmlcs.CompSBasePlugin.isSetReplacedBy ( )

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

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

new bool libsbmlcs.SBasePlugin.isValidTypeForList ( SBase item )

inherited

new void libsbmlcs.CompSBasePlugin.logInvalidId	(	string	attribute,
		string	wrongattribute
	)

Helper to log a common type of error.

ReplacedElement libsbmlcs.CompSBasePlugin.removeReplacedElement ( long 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.

new void libsbmlcs.SBasePlugin.renameMetaIdRefs	(	string	oldid,
		string	newid
	)

inherited

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.

new void libsbmlcs.SBasePlugin.renameSIdRefs	(	string	oldid,
		string	newid
	)

inherited

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.

new void libsbmlcs.SBasePlugin.renameUnitSIdRefs	(	string	oldid,
		string	newid
	)

inherited

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 libsbmlcs.SBasePlugin.setElementNamespace ( 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. 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()

int libsbmlcs.CompSBasePlugin.setReplacedBy ( 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 possible values returned by this function are:

new int libsbmlcs.CompSBasePlugin.unsetReplacedBy ( )

Unsets the child ReplacedBy of this SBase.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

Member Data Documentation

bool libsbmlcs.SBasePlugin.swigCMemOwn

protectedinherited

Detailed Description

Public Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation