Inheritance diagram for libsbmlcs.CompSBasePlugin:

Detailed Description

{comp}

comp Implementation of the “comp” package extention to the SBase construct.

The CompSBasePlugin class inherits from the SBasePlugin class, and codifies the extentions to the SBase class defined in the comp package (“comp”). This extention 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...

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

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

	CompSBasePlugin (string uri, string prefix, CompPkgNamespaces compns)
	Constructor. More...

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

void	connectToChild ()
	Sets the parent of this SBML object to child SBML objects (if any). More...

void	connectToParent (SBase parent)
	Sets the parent SBML object of this SBML object. More...

SBase	createObject (XMLInputStream stream)
	Create and return an SBML object of this class, if present. 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...

override void	Dispose ()

void	divideAssignmentsToSIdByFunction (string id, ASTNode function)
	If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function). More...

void	enablePackageInternal (string pkgURI, string pkgPrefix, bool flag)
	Enables/Disables the given package with child elements in this plugin object (if any). More...

long	getColumn ()
	Returns the column number on which this object first appears in the XML representation of the SBML document. More...

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...

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 XML namespace (URI) of the package extension of this plugin object. More...

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

long	getLine ()
	Returns the line number on which this object first appears in the XML representation of the SBML document. More...

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 package name of this plugin object. More...

long	getPackageVersion ()
	Returns the package version of the package extension of this plugin object. More...

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

string	getPrefix ()
	Returns the prefix of the package extension of this plugin object. 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 parent SBMLDocument of this plugin object. More...

SBMLNamespaces	getSBMLNamespaces ()

string	getURI ()
	Gets the URI to which this element belongs to. More...

long	getVersion ()
	Returns the SBML version of the package extension of this plugin object. More...

bool	hasIdentifierBeginningWith (string prefix)
	Check to see if the given prefix is used by any of the IDs defined by extension elements. More...

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

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

void	logUnknownElement (string element, long sbmlLevel, long sbmlVersion, long pkgVersion)
	Helper to log a common type of error for elements. More...

void	multiplyAssignmentsToSIdByFunction (string id, ASTNode function)
	If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function). More...

int	prependStringToAllIdentifiers (string prefix)
	Add the given string to all identifiers in the object. More...

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

void	replaceSIDWithFunction (string id, ASTNode function)
	If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function. More...

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

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

bool	stripPackage (string pkgPrefix, bool flag)

int	transformIdentifiers (IdentifierTransformer sidTransformer)

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
	)

Constructor.

libsbmlcs.CompSBasePlugin.CompSBasePlugin ( CompSBasePlugin orig )

Copy constructor.

Creates a copy of this CompSBasePlugin object.

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 operation. The possible return values are:

void libsbmlcs.CompSBasePlugin.clearReplacedElements ( )

Remove all ReplacedElements, if any exist.

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.connectToChild ( )

Sets the *parent* of this SBML object to child SBML objects (if any).

(Creates a child-parent relationship by the parent)

See also: setSBMLDocument; enablePackageInternal

void libsbmlcs.CompSBasePlugin.connectToParent ( SBase parent )

Sets the parent SBML object of this SBML object.

(Creates a child-parent relationship by the child) This function is called when a child element is set/added/created by its parent element (e.g. by setXXX, addXXX, createXXX, and connectToChild functions of the parent element).

Parameters

parent the SBML object to use

SBase libsbmlcs.CompSBasePlugin.createObject ( XMLInputStream stream )

Create and return an SBML object of this class, if present.

Returns: the SBML object corresponding to next XMLToken in the XMLInputStream or null if the token was not recognized.

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.

void libsbmlcs.SBasePlugin.divideAssignmentsToSIdByFunction	(	string	id,
		ASTNode	function
	)

inherited

If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function).

Note: This function does nothing itself–subclasses with ASTNode subelements must override this function.

void libsbmlcs.CompSBasePlugin.enablePackageInternal	(	string	pkgURI,
		string	pkgPrefix,
		bool	flag
	)

Enables/Disables the given package with child elements in this plugin object (if any).

(This is an internal implementation invoked from SBase::enablePackageInternal() function)

Note: Subclasses in which one or more SBase derived elements are defined must override this function.

See also: setSBMLDocument; connectToParent

long libsbmlcs.SBasePlugin.getColumn ( )

inherited

Returns the column number on which this object first appears in the XML representation of the SBML document.

Returns: the column number of the underlying SBML object.

Note: The column number for each construct in an SBML model is set upon reading the model. The accuracy of the column number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real column number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)

See also: getLine()

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 objects to find

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

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 objects to find

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

string libsbmlcs.SBasePlugin.getElementNamespace ( )

inherited

Returns the XML namespace (URI) of the package extension of this plugin object.

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

long libsbmlcs.SBasePlugin.getLevel ( )

inherited

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

Returns: the SBML level of the package extension of this plugin object.

long libsbmlcs.SBasePlugin.getLine ( )

inherited

Returns the line number on which this object first appears in the XML representation of the SBML document.

Returns: the line number of the underlying SBML object.

Note: The line number for each construct in an SBML model is set upon reading the model. The accuracy of the line number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real line number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)

See also: getColumn()

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 package name of this plugin object.

Returns: the package name of this plugin object.

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.

SBase libsbmlcs.SBasePlugin.getParentSBMLObject ( )

inherited

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

Returns: the parent SBase object to which this plugin object connected.

string libsbmlcs.SBasePlugin.getPrefix ( )

inherited

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

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

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 parent SBMLDocument of this plugin object.

Returns: the parent SBMLDocument object of this plugin object.

SBMLNamespaces libsbmlcs.SBasePlugin.getSBMLNamespaces ( )

inherited

string libsbmlcs.SBasePlugin.getURI ( )

inherited

Gets the URI to which this element belongs to.

For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1/'

Unlike getElementNamespace, this function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. if not found it will return the result of getElementNamespace

Returns: the URI this elements

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

long libsbmlcs.SBasePlugin.getVersion ( )

inherited

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

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

bool libsbmlcs.SBasePlugin.hasIdentifierBeginningWith ( string prefix )

inherited

Check to see if the given prefix is used by any of the IDs defined by extension elements.

A package that defines its own 'id' attribute for a core element would check that attribute here.

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.

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

Helper to log a common type of error.

void libsbmlcs.SBasePlugin.logUnknownElement	(	string	element,
		long	sbmlLevel,
		long	sbmlVersion,
		long	pkgVersion
	)

inherited

Helper to log a common type of error for elements.

void libsbmlcs.SBasePlugin.multiplyAssignmentsToSIdByFunction	(	string	id,
		ASTNode	function
	)

inherited

If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function).

int libsbmlcs.SBasePlugin.prependStringToAllIdentifiers ( string prefix )

inherited

Add the given string to all identifiers in the object.

If the string is added to anything other than an id or a metaid, this code is responsible for tracking down and renaming all *idRefs in the package extention that identifier comes from.

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.

void libsbmlcs.SBasePlugin.replaceSIDWithFunction	(	string	id,
		ASTNode	function
	)

inherited

If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function.

Note: This function does nothing itself–subclasses with ASTNode subelements must override this function.

int libsbmlcs.SBasePlugin.setElementNamespace ( string uri )

inherited

Sets the XML namespace to which this element belongs to.

For example, all elements that belong to SBML Level 3 Version 1 Core must set the namespace to 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must set the namespace to 'http://www.sbml.org/sbml/level3/version1/layout/version1/'

Returns

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

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 operation. The possible return values are:

bool libsbmlcs.SBasePlugin.stripPackage	(	string	pkgPrefix,
		bool	flag
	)

inherited

int libsbmlcs.SBasePlugin.transformIdentifiers ( IdentifierTransformer sidTransformer )

inherited

int libsbmlcs.CompSBasePlugin.unsetReplacedBy ( )

Unsets the child ReplacedBy of this SBase.

Returns

integer value indicating success/failure of the operation. The possible return values 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