Inheritance diagram for libsbmlcs.FbcModelPlugin:

Detailed Description

{fbc}

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

Public Member Functions
int	addFluxBound (FluxBound bound)
	Adds a copy of the given FluxBound object to the list of FluxBounds. More...

int	addGeneAssociation (GeneAssociation association)
	Adds a copy of the given GeneAssociation object to the list of GeneAssociations. More...

int	addObjective (Objective bound)
	Adds a copy of the given Objective object to the list of Objectives. More...

int	appendFrom (Model model)

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

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

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

FluxBound	createFluxBound ()
	Creates a new FluxBound object and adds it to the list of FluxBound objects and returns it. More...

GeneAssociation	createGeneAssociation ()
	Creates a new GeneAssociation object and adds it to the list of GeneAssociation objects and returns it. More...

SBase	createObject (XMLInputStream stream)
	Subclasses must override this method to create, store, and then return an SBML object corresponding to the next XMLToken in the XMLInputStream if they have their specific elements. More...

Objective	createObjective ()
	Creates a new Objective object and adds it to the list of Objective objects and returns it. 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...

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

	FbcModelPlugin (FbcModelPlugin orig)
	Copy constructor. More...

Objective	getActiveObjective ()
	Returns the current active objective. More...

string	getActiveObjectiveId ()
	returns the id of the current active objective. 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...

FluxBound	getFluxBound (long n)
	Returns the FluxBound object that belongs to the given index. More...

FluxBound	getFluxBound (string sid)
	Returns the FluxBound object based on its identifier. More...

ListOfFluxBounds	getFluxBoundsForReaction (string reaction)

GeneAssociation	getGeneAssociation (long n)
	Returns the GeneAssociation object that belongs to the given index. More...

GeneAssociation	getGeneAssociation (string sid)
	Returns the GeneAssociation 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 ()

ListOfFluxBounds	getListOfFluxBounds ()
	Returns the ListOfFluxBounds in this plugin object. More...

ListOfGeneAssociations	getListOfGeneAssociations ()
	Returns the ListOfObjectives in this plugin object. More...

ListOfObjectives	getListOfObjectives ()
	Returns the ListOfObjectives in this plugin object. More...

long	getNumFluxBounds ()
	Returns the number of FluxBound object in this plugin object. More...

int	getNumGeneAssociations ()
	Returns the number of GeneAssociation object in this plugin object. More...

long	getNumObjectives ()
	Returns the number of Objective object in this plugin object. More...

Objective	getObjective (long n)
	Returns the Objective object that belongs to the given index. More...

Objective	getObjective (string sid)
	Returns the Objective object based on its identifier. 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...

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	hasRequiredElements ()
	Checks if this plugin object has all the required elements. 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...

bool	readOtherXML (SBase parentObject, XMLInputStream stream)
	Parses Gene Annotation Extension. More...

FluxBound	removeFluxBound (long n)
	Removes the nth FluxBound object from this plugin object and returns a pointer to it. More...

FluxBound	removeFluxBound (string sid)
	Removes the FluxBound object with the given `sid` attribute from this plugin object and returns a pointer to it. More...

GeneAssociation	removeGeneAssociation (long n)
	Removes the nth GeneAssociation object from this plugin object and returns a pointer to it. More...

GeneAssociation	removeGeneAssociation (string sid)
	Removes the GeneAssociation object with the given `sid` attribute from this plugin object and returns a pointer to it. More...

Objective	removeObjective (long n)
	Removes the nth Objective object from this plugin object and returns a pointer to it. More...

Objective	removeObjective (string sid)
	Removes the Objective object with the given `sid` attribute from this plugin object and returns a pointer to it. 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	setActiveObjectiveId (string objectiveId)
	Sets the id of the active objective. 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)

void	unsetActiveObjectiveId ()
	Unsets the active objective. More...

void	writeAttributes (XMLOutputStream stream)
	This function is a bit tricky. More...

Protected Attributes
bool	swigCMemOwn

Constructor & Destructor Documentation

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

Constructor.

libsbmlcs.FbcModelPlugin.FbcModelPlugin ( FbcModelPlugin orig )

Copy constructor.

Creates a copy of this FbcModelPlugin object.

Member Function Documentation

int libsbmlcs.FbcModelPlugin.addFluxBound ( FluxBound bound )

Adds a copy of the given FluxBound object to the list of FluxBounds.

Parameters

bound the FluxBound object to be added to the list of FluxBounds.

Returns

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

LIBSBML_OPERATION_SUCCESS

int libsbmlcs.FbcModelPlugin.addGeneAssociation ( GeneAssociation association )

Adds a copy of the given GeneAssociation object to the list of GeneAssociations.

Parameters

association the GeneAssociation object to be added to the list of GeneAssociations.

Returns

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

LIBSBML_OPERATION_SUCCESS

int libsbmlcs.FbcModelPlugin.addObjective ( Objective bound )

Adds a copy of the given Objective object to the list of Objectives.

Parameters

bound the Objective object to be added to the list of Objectives.

Returns

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

LIBSBML_OPERATION_SUCCESS

int libsbmlcs.FbcModelPlugin.appendFrom ( Model model )

SBasePlugin libsbmlcs.FbcModelPlugin.clone ( )

Creates and returns a deep copy of this FbcModelPlugin object.

Returns: a (deep) copy of this FbcModelPlugin object

void libsbmlcs.FbcModelPlugin.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.FbcModelPlugin.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

FluxBound libsbmlcs.FbcModelPlugin.createFluxBound ( )

Creates a new FluxBound object and adds it to the list of FluxBound objects and returns it.

Returns: a newly created FluxBound object

GeneAssociation libsbmlcs.FbcModelPlugin.createGeneAssociation ( )

Creates a new GeneAssociation object and adds it to the list of GeneAssociation objects and returns it.

Returns: a newly created GeneAssociation object

SBase libsbmlcs.FbcModelPlugin.createObject ( XMLInputStream stream )

Subclasses must override this method to create, store, and then return an SBML object corresponding to the next XMLToken in the XMLInputStream if they have their specific elements.

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

Objective libsbmlcs.FbcModelPlugin.createObjective ( )

Creates a new Objective object and adds it to the list of Objective objects and returns it.

Returns: a newly created Objective object

override void libsbmlcs.FbcModelPlugin.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.FbcModelPlugin.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

Objective libsbmlcs.FbcModelPlugin.getActiveObjective ( )

Returns the current active objective.

string libsbmlcs.FbcModelPlugin.getActiveObjectiveId ( )

returns the id of the current active objective.

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.FbcModelPlugin.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.FbcModelPlugin.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.

FluxBound libsbmlcs.FbcModelPlugin.getFluxBound ( long n )

Returns the FluxBound object that belongs to the given index.

If the index is invalid, null is returned.

Parameters

n	the index number of the FluxBound to get.

Returns: the nth FluxBound in the ListOfFluxBounds.

FluxBound libsbmlcs.FbcModelPlugin.getFluxBound ( string sid )

Returns the FluxBound object based on its identifier.

Parameters

sid	a string representing the identifier of the FluxBound to get.

Returns: FluxBound in the ListOfFluxBounds with the given sid or null if no such FluxBound exists.

See also: getFluxBound(long n); getListOfFluxBounds()

ListOfFluxBounds libsbmlcs.FbcModelPlugin.getFluxBoundsForReaction ( string reaction )

GeneAssociation libsbmlcs.FbcModelPlugin.getGeneAssociation ( long n )

Returns the GeneAssociation object that belongs to the given index.

If the index is invalid, null is returned.

Parameters

n	the index number of the GeneAssociation to get.

Returns: the nth GeneAssociation in the ListOfGeneAssociations.

GeneAssociation libsbmlcs.FbcModelPlugin.getGeneAssociation ( string sid )

Returns the GeneAssociation object based on its identifier.

Parameters

sid	a string representing the identifier of the GeneAssociation to get.

Returns: GeneAssociation in the ListOfGeneAssociations with the given sid or null if no such GeneAssociation exists.

See also: getGeneAssociation(long n); getListOfGeneAssociations()

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

ListOfFluxBounds libsbmlcs.FbcModelPlugin.getListOfFluxBounds ( )

Returns the ListOfFluxBounds in this plugin object.

Returns: ListOfFluxBounds object in this plugin object.

ListOfGeneAssociations libsbmlcs.FbcModelPlugin.getListOfGeneAssociations ( )

Returns the ListOfObjectives in this plugin object.

Returns: ListOfObjectives object in this plugin object.

ListOfObjectives libsbmlcs.FbcModelPlugin.getListOfObjectives ( )

Returns the ListOfObjectives in this plugin object.

Returns: ListOfObjectives object in this plugin object.

long libsbmlcs.FbcModelPlugin.getNumFluxBounds ( )

Returns the number of FluxBound object in this plugin object.

Returns: the number of FluxBound object in this plugin object.

int libsbmlcs.FbcModelPlugin.getNumGeneAssociations ( )

Returns the number of GeneAssociation object in this plugin object.

Returns: the number of GeneAssociation object in this plugin object.

long libsbmlcs.FbcModelPlugin.getNumObjectives ( )

Returns the number of Objective object in this plugin object.

Returns: the number of Objective object in this plugin object.

Objective libsbmlcs.FbcModelPlugin.getObjective ( long n )

Returns the Objective object that belongs to the given index.

If the index is invalid, null is returned.

Parameters

n	the index number of the Objective to get.

Returns: the nth Objective in the ListOfObjectives.

Objective libsbmlcs.FbcModelPlugin.getObjective ( string sid )

Returns the Objective object based on its identifier.

Parameters

sid	a string representing the identifier of the Objective to get.

Returns: Objective in the ListOfObjectives with the given id or null if no such Objective exists.

See also: getObjective(long n); getListOfObjectives()

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.FbcModelPlugin.hasRequiredElements ( )

Checks if this plugin object has all the required elements.

Subclasses should override this function if they have their specific elements.

Returns: true if this plugin object has all the required elements, otherwise false will be 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.

bool libsbmlcs.FbcModelPlugin.readOtherXML	(	SBase	parentObject,
		XMLInputStream	stream
	)

Parses Gene Annotation Extension.

FluxBound libsbmlcs.FbcModelPlugin.removeFluxBound ( long n )

Removes the nth FluxBound object from this plugin object and returns a pointer to it.