Inheritance diagram for libsbmlcs.CompSBMLDocumentPlugin:

Detailed Description

{comp}

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

The CompSBMLDocumentPlugin class inherits from the SBMLDocumentPlugin class, and codifies the extentions to the SBMLDocument class defined in the SBML Level 3 comp package (“comp”). This extention allows multiple Model objects to be defined in a single SBMLDocument, stored in an optional child ListOfModelDefinitions object, as well as define references to Model objects in other files, stored in the optional child ListOfExternalModelDefinitions object. These model definitions, if present, allow Submodel objects to reference other Models to instantiate.

The presence of ModelDefinitions and ExternalModelDefinitions in an SBMLDocument does not change the default Model in the file. If a SBMLDocument is submitted somewhere to be simulated, it is still the <model> child of the <sbml> element that should be simulated.

In addition, as all packages do, the CompSBMLDocumentPlugin defines a required flag named required, which indicates whether “comp” constructs can be used to change the core mathematics of the <model> child of the <sbml> element. Because they can, this attribute must be set true.

Public Member Functions
int	addExternalModelDefinition (ExternalModelDefinition externalModelDefinition)
	Adds a copy of the given ExternalModelDefinition object to the list of ExternalModelDefinitions. More...

int	addModelDefinition (ModelDefinition modelDefinition)
	Adds a copy of the given ModelDefinition object to the list of ModelDefinitions. More...

long	checkConsistency ()
	Check consistency function. More...

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

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

	CompSBMLDocumentPlugin (CompSBMLDocumentPlugin 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...

ExternalModelDefinition	createExternalModelDefinition ()
	Creates a ExternalModelDefinition object, adds it to the end of the ExternalModelDefinition objects list and returns a pointer to the newly created object. More...

ModelDefinition	createModelDefinition ()
	Creates a ModelDefinition object, adds it to the end of the ModelDefinition objects list and returns a pointer to the newly created object. More...

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

ExternalModelDefinition	getExternalModelDefinition (long n)
	Returns the ExternalModelDefinition with the given index. More...

ExternalModelDefinition	getExternalModelDefinition (string sid)
	Returns the model definition object based on its identifier. 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 ()

ListOfExternalModelDefinitions	getListOfExternalModelDefinitions ()
	Returns the ListOf object that holds all ExternalModelDefinitions. More...

ListOfModelDefinitions	getListOfModelDefinitions ()
	Returns the ListOf object that holds all ModelDefinitions. More...

SBase	getModel (string sid)
	Searches the model namespace of the document and returns the Model, ModelDefinition, or ExternalModelDefintion object with the given identifier. More...

ModelDefinition	getModelDefinition (long n)
	Returns the ModelDefinition with the given index. More...

ModelDefinition	getModelDefinition (string sid)
	Returns the model definition object based on its identifier. More...

long	getNumExternalModelDefinitions ()
	Returns the number of ExternalModelDefinitions for this SBMLDocumentPlugin. More...

long	getNumModelDefinitions ()
	Returns the number of ModelDefinitions for this SBMLDocumentPlugin. More...

bool	getOverrideCompFlattening ()

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...

bool	getRequired ()
	Returns the bool value of 'required' attribute of corresponding package in SBMLDocument element. 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	isCompFlatteningImplemented ()

bool	isSetRequired ()
	Predicate returning `true` or `false` depending on whether this SBMLDocumentPlugin's 'required' attribute has been set. 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...

ExternalModelDefinition	removeExternalModelDefinition (long index)
	Removes the ExternalModelDefinition with the given index. More...

ExternalModelDefinition	removeExternalModelDefinition (string id)
	Removes the ExternalModelDefinition with the given `id`. More...

ModelDefinition	removeModelDefinition (long index)
	Removes the ModelDefinition with the given index from the CompSBMLDocumentPlugin. More...

ModelDefinition	removeModelDefinition (string id)
	Removes the ModelDefinition with the given `id` from the CompSBMLDocumentPlugin. 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...

void	setOverrideCompFlattening (bool overrideCompFlattening)

int	setRequired (bool value)
	Sets the bool value of 'required' attribute of corresponding package in SBMLDocument element. More...

bool	stripPackage (string pkgPrefix, bool flag)

int	transformIdentifiers (IdentifierTransformer sidTransformer)

int	unsetRequired ()
	Unsets the value of the 'required' attribute of this SBMLDocumentPlugin. More...

Protected Attributes
bool	swigCMemOwn

Constructor & Destructor Documentation

libsbmlcs.CompSBMLDocumentPlugin.CompSBMLDocumentPlugin	(	string	uri,
		string	prefix,
		CompPkgNamespaces	compns
	)

Constructor.

libsbmlcs.CompSBMLDocumentPlugin.CompSBMLDocumentPlugin ( CompSBMLDocumentPlugin orig )

Copy constructor.

Creates a copy of this CompSBMLDocumentPlugin object.

Member Function Documentation

int libsbmlcs.CompSBMLDocumentPlugin.addExternalModelDefinition ( ExternalModelDefinition externalModelDefinition )

Adds a copy of the given ExternalModelDefinition object to the list of ExternalModelDefinitions.

Parameters

externalModelDefinition the ExternalModelDefinition object to be added to the list of ExternalModelDefinitions. Fails if the added ExternalModelDefinition is null, does not match the level/version/package of the parent object, or cannot be added to the list of external model definitions.

Returns

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

int libsbmlcs.CompSBMLDocumentPlugin.addModelDefinition ( ModelDefinition modelDefinition )

Adds a copy of the given ModelDefinition object to the list of ModelDefinitions.

Parameters

modelDefinition the ModelDefinition object to be added to the list of ModelDefinitions. Fails if the added ModelDefinition 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:

long libsbmlcs.CompSBMLDocumentPlugin.checkConsistency ( )

Check consistency function.

SBasePlugin libsbmlcs.CompSBMLDocumentPlugin.clone ( )

Creates and returns a deep copy of this CompSBMLDocumentPlugin object.

Returns: a (deep) copy of this CompSBMLDocumentPlugin object

void libsbmlcs.CompSBMLDocumentPlugin.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.CompSBMLDocumentPlugin.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

ExternalModelDefinition libsbmlcs.CompSBMLDocumentPlugin.createExternalModelDefinition ( )

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

Returns: a newly created ExternalModelDefinition object

ModelDefinition libsbmlcs.CompSBMLDocumentPlugin.createModelDefinition ( )

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

Returns: a newly created ModelDefinition object

SBase libsbmlcs.CompSBMLDocumentPlugin.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.

override void libsbmlcs.CompSBMLDocumentPlugin.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.CompSBMLDocumentPlugin.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.CompSBMLDocumentPlugin.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 meta identifier of objects to find

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

SBase libsbmlcs.CompSBMLDocumentPlugin.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 identifier of objects to find

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

Note: The comp SBML document plugin has multiple model-wide SId namespaces, so a valid document may well contain multiple elements with the same SId that reside in separate models. It is not recommended to ever call this function—instead, call the function on the child ModelDefinition objects.

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.

ExternalModelDefinition libsbmlcs.CompSBMLDocumentPlugin.getExternalModelDefinition ( long n )

Returns the ExternalModelDefinition with the given index.

Parameters

n	the index number of the ExternalModelDefinition to get.

Returns: the nth ExternalModelDefinition in the ListOfExternalModelDefinitions. If the index is invalid, null is returned.

ExternalModelDefinition libsbmlcs.CompSBMLDocumentPlugin.getExternalModelDefinition ( string sid )

Returns the model definition object based on its identifier.

Parameters

sid	a string representing the identifier of the model definition to get.

Returns: ExternalModelDefinition in the ListOfExternalModelDefinitions with the given sid or null if no such ExternalModelDefinition exists.

See also: getExternalModelDefinition(long n); getListOfExternalModelDefinitions()

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

ListOfExternalModelDefinitions libsbmlcs.CompSBMLDocumentPlugin.getListOfExternalModelDefinitions ( )

Returns the ListOf object that holds all ExternalModelDefinitions.

Returns: the ListOf object that holds all ExternalModelDefinitions.

ListOfModelDefinitions libsbmlcs.CompSBMLDocumentPlugin.getListOfModelDefinitions ( )

Returns the ListOf object that holds all ModelDefinitions.

Returns: the ListOf object that holds all ModelDefinitions.

SBase libsbmlcs.CompSBMLDocumentPlugin.getModel ( string sid )

Searches the model namespace of the document and returns the Model, ModelDefinition, or ExternalModelDefintion object with the given identifier.

Parameters

sid	a string representing the identifier of the model definition to get.

Returns: The SBase corresponding to the given sid or null if no such model exists. If no such model exists, this will return null.

ModelDefinition libsbmlcs.CompSBMLDocumentPlugin.getModelDefinition ( long n )

Returns the ModelDefinition with the given index.

Parameters

n	the index number of the ModelDefinition to get.

Returns: the nth ModelDefinition in the ListOfModelDefinitions. If the index is invalid, null is returned.

ModelDefinition libsbmlcs.CompSBMLDocumentPlugin.getModelDefinition ( string sid )

Returns the model definition object based on its identifier.

Parameters

sid	a string representing the identifier of the model definition to get.

Returns: ModelDefinition in the ListOfModelDefinitions with the given sid or null if no such ModelDefinition exists.

See also: getModelDefinition(long n); getListOfModelDefinitions()

long libsbmlcs.CompSBMLDocumentPlugin.getNumExternalModelDefinitions ( )

Returns the number of ExternalModelDefinitions for this SBMLDocumentPlugin.

Returns: the number of ExternalModelDefinitions for this SBMLDocumentPlugin.

long libsbmlcs.CompSBMLDocumentPlugin.getNumModelDefinitions ( )

Returns the number of ModelDefinitions for this SBMLDocumentPlugin.

Returns: the number of ModelDefinitions.

bool libsbmlcs.CompSBMLDocumentPlugin.getOverrideCompFlattening ( )

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.

bool libsbmlcs.SBMLDocumentPlugin.getRequired ( )

inherited

Returns the bool value of 'required' attribute of corresponding package in SBMLDocument element.

Returns: the bool value of 'required' attribute of corresponding package in SBMLDocument element.

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.CompSBMLDocumentPlugin.isCompFlatteningImplemented ( )

bool libsbmlcs.SBMLDocumentPlugin.isSetRequired ( )

inherited

Predicate returning true or false depending on whether this SBMLDocumentPlugin's 'required' attribute has been set.

Returns: true if the 'required' attribute of this SBMLDocument has been set, false otherwise.

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.

ExternalModelDefinition libsbmlcs.CompSBMLDocumentPlugin.removeExternalModelDefinition ( long index )

Removes the ExternalModelDefinition with the given index.

A pointer to the ExternalModelDefinition that was removed is returned. If no ExternalModelDefinition has been removed, null is returned.

Parameters

index the index of the ExternalModelDefinition object to remove

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

ExternalModelDefinition libsbmlcs.CompSBMLDocumentPlugin.removeExternalModelDefinition ( string id )

Removes the ExternalModelDefinition with the given id.

A pointer to the ExternalModelDefinition that was removed is returned. If no ExternalModelDefinition has been removed, null is returned.

Parameters

id	the id of the ExternalModelDefinition object to remove

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

ModelDefinition libsbmlcs.CompSBMLDocumentPlugin.removeModelDefinition ( long index )

Removes the ModelDefinition with the given index from the CompSBMLDocumentPlugin.

A pointer to the ModelDefinition that was removed is returned. If no ModelDefinition has been removed, null is returned.

Parameters

index the index of the ModelDefinition object to remove

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

ModelDefinition libsbmlcs.CompSBMLDocumentPlugin.removeModelDefinition ( string id )

Removes the ModelDefinition with the given id from the CompSBMLDocumentPlugin.

A pointer to the ModelDefinition that was removed is returned. If no ModelDefinition has been removed, null is returned.

Parameters

id	the id of the ModelDefinition object to remove

Returns: the ModelDefinition 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:

void libsbmlcs.CompSBMLDocumentPlugin.setOverrideCompFlattening ( bool overrideCompFlattening )

int libsbmlcs.CompSBMLDocumentPlugin.setRequired ( bool value )

Sets the bool value of 'required' attribute of corresponding package in SBMLDocument element.

The only legal value is 'true' for the Hierarchical Model Composition package.

Parameters

value the bool value of 'required' attribute of corresponding package in SBMLDocument element.

Returns

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

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

inherited

int libsbmlcs.SBasePlugin.transformIdentifiers ( IdentifierTransformer sidTransformer )

inherited

int libsbmlcs.SBMLDocumentPlugin.unsetRequired ( )

inherited

Unsets the value of the 'required' attribute of this SBMLDocumentPlugin.

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