Inheritance diagram for libsbmlcs.FbcSpeciesPlugin:

Detailed Description

{fbc}

fbc Implementation of the 'fbc' package extention to the Species construct.

The Flux Balance Constraints package extends the SBML Level 3 Version 1 Core Species class with the addition of two attributes: 'charge' and 'chemicalFormula'.

Public Member Functions
SBasePlugin	clone ()
	Creates and returns a deep copy of this FbcSpeciesPlugin object. More...

void	connectToParent (SBase sbase)
	Sets the parent SBML object of this plugin object to this object and child elements (if any). 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...

	FbcSpeciesPlugin (string uri, string prefix, FbcPkgNamespaces fbcns)
	Constructor. More...

	FbcSpeciesPlugin (FbcSpeciesPlugin orig)
	Copy constructor. More...

int	getCharge ()
	Returns the value of the 'charge' attribute of this FbcSpeciesPlugin. More...

string	getChemicalFormula ()
	Returns the value of the 'chemicalFormula' attribute of this FbcSpeciesPlugin. 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 `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 ()

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...

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	isSetCharge ()
	Predicate returning `true` or `false` depending on whether this FbcSpeciesPlugin 'charge' attribute has been set. More...

bool	isSetChemicalFormula ()
	Predicate returning `true` or `false` depending on whether this FbcSpeciesPlugin 'chemicalFormula' 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...

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	setCharge (int charge)
	Sets the value of the 'charge' attribute of this FbcSpeciesPlugin. More...

int	setChemicalFormula (string chemicalFormula)
	Sets the value of the 'chemicalFormula' attribute of this FbcSpeciesPlugin. More...

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

bool	stripPackage (string pkgPrefix, bool flag)

int	transformIdentifiers (IdentifierTransformer sidTransformer)

int	unsetCharge ()
	Unsets the value of the 'charge' attribute of this FbcSpeciesPlugin. More...

int	unsetChemicalFormula ()
	Unsets the value of the 'chemicalFormula' attribute of this FbcSpeciesPlugin. More...

Protected Attributes
bool	swigCMemOwn

Constructor & Destructor Documentation

libsbmlcs.FbcSpeciesPlugin.FbcSpeciesPlugin	(	string	uri,
		string	prefix,
		FbcPkgNamespaces	fbcns
	)

Constructor.

libsbmlcs.FbcSpeciesPlugin.FbcSpeciesPlugin ( FbcSpeciesPlugin orig )

Copy constructor.

Creates a copy of this FbcSpeciesPlugin object.

Member Function Documentation

SBasePlugin libsbmlcs.FbcSpeciesPlugin.clone ( )

Creates and returns a deep copy of this FbcSpeciesPlugin object.

Returns: a (deep) copy of this FbcSpeciesPlugin object

void libsbmlcs.FbcSpeciesPlugin.connectToParent ( SBase sbase )

Sets the parent SBML object of this plugin object to this object and child elements (if any).

(Creates a child-parent relationship by this plugin object)

This function is called when this object is created by the parent element. Subclasses must override this this function if they have one or more child elements.Also, SBasePlugin::connectToParent() must be called in the overridden function.

Parameters

sbase the SBase object to use

See also: setSBMLDocument; enablePackageInternal

override void libsbmlcs.FbcSpeciesPlugin.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.FbcSpeciesPlugin.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::enablePakcageInternal() function)

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

See also: setSBMLDocument; connectToParent

int libsbmlcs.FbcSpeciesPlugin.getCharge ( )

Returns the value of the 'charge' attribute of this FbcSpeciesPlugin.

Returns: the value of the 'charge' attribute of this FbcSpeciesPlugin.

string libsbmlcs.FbcSpeciesPlugin.getChemicalFormula ( )

Returns the value of the 'chemicalFormula' attribute of this FbcSpeciesPlugin.

Returns: the value of the 'chemicalFormula' attribute of this FbcSpeciesPlugin.

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.SBasePlugin.getElementByMetaId ( string metaid )

inherited

Returns the first child element it can find with the given metaid, or null if no such object is found.

Parameters

metaid string representing the metaid of objects to find

Returns: pointer to the first element found with the given metaid.

SBase libsbmlcs.SBasePlugin.getElementBySId ( string id )

inherited

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: pointer to the first element found 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

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.

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.FbcSpeciesPlugin.isSetCharge ( )

Predicate returning true or false depending on whether this FbcSpeciesPlugin 'charge' attribute has been set.

Returns: true if this FbcSpeciesPlugin 'charge' attribute has been set, otherwise false is returned.

bool libsbmlcs.FbcSpeciesPlugin.isSetChemicalFormula ( )

Predicate returning true or false depending on whether this FbcSpeciesPlugin 'chemicalFormula' attribute has been set.

Returns: true if this FbcSpeciesPlugin 'chemicalFormula' attribute has been set, otherwise false is returned.

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.

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.FbcSpeciesPlugin.setCharge ( int charge )

Sets the value of the 'charge' attribute of this FbcSpeciesPlugin.

Returns

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

LIBSBML_OPERATION_SUCCESS

int libsbmlcs.FbcSpeciesPlugin.setChemicalFormula ( string chemicalFormula )

Sets the value of the 'chemicalFormula' attribute of this FbcSpeciesPlugin.

The format of chemicalFormula must consist only of atomic names (as in the Periodic Table) or user defined compounds either of which take the form of a single capital letter followed by zero or more lowercase letters. Where there is more than a single atom present, this is indicated with an integer. With regards to order (and enhance inter-operability) it is recommended to use the Hill system order. (However, no error-checking is performed by this routine.)

Returns

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

LIBSBML_OPERATION_SUCCESS

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:

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

inherited

int libsbmlcs.SBasePlugin.transformIdentifiers ( IdentifierTransformer sidTransformer )

inherited

int libsbmlcs.FbcSpeciesPlugin.unsetCharge ( )

Unsets the value of the 'charge' attribute of this FbcSpeciesPlugin.

Returns

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

LIBSBML_OPERATION_SUCCESS

int libsbmlcs.FbcSpeciesPlugin.unsetChemicalFormula ( )

Unsets the value of the 'chemicalFormula' attribute of this FbcSpeciesPlugin.

Returns

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

LIBSBML_OPERATION_SUCCESS

Member Data Documentation

bool libsbmlcs.SBasePlugin.swigCMemOwn

protectedinherited

Detailed Description

Public Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation