Inheritance diagram for libsbmlcs.FbcModelPlugin:

Detailed Description

fbc Extension of Model.

The FbcModelPlugin object is used to extend the standard SBML Model object with features used in the SBML Level 3 Flux Balance Constraints (“fbc”) package. In Version 1 of the “fbc” specification, the extended Model class has two optional subobjects: ListOfObjectives and ListOfFluxBounds. In Version 2 of the specification, the extended Model object is defined differently: it is extended with a new required attribute named 'strict', and the two optional subobjects ListOfObjectives and ListOfGeneProducts. (ListOfFluxBounds is not used in Version 2.)

The 'strict' attribute on the (extended) Model class

The mandatory attribute 'strict', of type boolean, in Version 2 of this package, is used to apply an additional set of restrictions to the model. The 'strict' attribute helps ensure that the Flux Balance Constraints package can be used to encode legacy flux-balance analysis models expressible as Linear Programs (LP's) for software that is unable to analyze arbitrary mathematical expressions that may appear in an SBML model. In addition, a 'strict' model is fully described and mathematically consistent, for example, by ensuring that all fluxes have a valid upper or lower bound.

The following restrictions are in effect if an “fbc” model object has a value of 'true' for the attribute 'strict' on Model:

Each Reaction in a Model must define values for the attributes 'lowerFluxBound' and 'upperFluxBound', with each attribute pointing to a valid Parameter object defined in the current Model.

Each Parameter object referred to by the Reaction attributes 'lowerFluxBound' and 'upperFluxBound' must have its 'constant' attribute set to the value 'true' and its 'value' attribute set to a value of type double. This value may not be 'NaN'.

SpeciesReference objects in Reaction objects must have their 'stoichiometry' attribute set to a double value that is not 'NaN', nor '-INF', nor 'INF'. In addition, the value of their 'constant' attribute must be set to 'true'.

InitialAssignment objects may not target the Parameter objects referenced by the Reaction attributes 'lowerFluxBound' and 'upperFluxBound', nor any SpeciesReference objects.

All defined FluxObjective objects must have their coefficient attribute set to a double value that is not 'NaN', nor '-INF', nor 'INF'.

A Reaction 'lowerFluxBound' attribute may not point to a Parameter object that has a value of 'INF'.

A Reaction 'upperFluxBound' attribute may not point to a Parameter object that has a value of '-INF'.

For all Reaction objects, the value of a 'lowerFluxBound' attribute must be less than or equal to the value of the 'upperFluxBound' attribute.

While it is not compulsory for a 'strict' Flux Balance Constraints model to define an Objective, doing so does does allow the model to be formulated as a Linear Program and optimized. However, this decision is left to the modeler. Note that all other properties of the objects referred to in the list above are to be set as specified in the relevant SBML Level 3 Version 1 Core and Flux Balance Constraints (“fbc”) specifications.

Alternatively, if the value of the strict attribute is 'false', then none of these restrictions apply and the model creator can choose to define “fbc” models that are not necessarily encodable as an LP. For example, if strict is 'false', the InitialAssignment construct may be used to set any valid numerical entity, including Parameter values and stoichiometric coefficients, with any value of type double. In addition, Parameter elements are no longer required to be flagged as constant, thus allowing for a Flux Balance Constraints model's use in alternative, hybrid modeling strategies.

Lists of subobjects on the (extended) Model class

The ListOfObjectives is used to define the objectives of a given “fbc” model. Objectives generally consist of linear combinations of model variables (fluxes) and a direction for the optimality constraint (either maximization or minimization). Each Objective has a ListOfFluxObjectives subobjects.

In Version 2 of “fbc”, the ListOfGeneProducts is used to define the gene products represented by the “fbc” model.

In Version 1 of “fbc”, there is no ListOfGeneProducts, and instead, Model can have an optional ListOfFluxBounds.

See also: Objective; FluxObjective; FluxBound

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 annotation object to the list of GeneAssociations. More...

int	addGeneProduct (GeneProduct gp)
	Adds a copy the given GeneProduct to this FbcModelPlugin. More...

int	addObjective (Objective o)
	Adds a copy the given Objective to this FbcModelPlugin. More...

int	appendFrom (Model model)

new SBasePlugin	clone ()
	Creates and returns a deep copy of this FbcModelPlugin object. 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 annotation object and adds it to the list of GeneAssociation objects and returns it. More...

GeneProduct	createGeneProduct ()
	Creates a new GeneProduct object, adds it to this FbcModelPlugin's ListOfGeneProducts and returns the GeneProduct object created. More...

Objective	createObjective ()
	Creates a new Objective object, adds it to this FbcModelPlugin's ListOfObjectives and returns the Objective object created. More...

override void	Dispose ()

	FbcModelPlugin (string uri, string prefix, FbcPkgNamespaces fbcns)
	Creates a new FbcModelPlugin object using the given parameters. More...

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

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

string	getActiveObjectiveId ()
	Returns the id of the current active objective. More...

long	getColumn ()

new SBase	getElementByMetaId (string metaid)
	Return the first child object found with a given meta identifier. More...

new SBase	getElementBySId (string id)
	Return the first child object found with a given identifier. More...

string	getElementNamespace ()
	Returns the namespace URI of the package to which this plugin object belongs. 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)
	Creates a new ListOfFluxBounds object that contains only the FluxBound objects associated with the given Reaction. More...

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

GeneAssociation	getGeneAssociation (string sid)
	Returns the GeneAssociation annotation object based on its identifier. More...

GeneProduct	getGeneProduct (long n)
	Get a GeneProduct from the ListOfGeneProducts. More...

GeneProduct	getGeneProduct (string sid)
	Get a GeneProduct from the ListOfGeneProducts based on its identifier. More...

GeneProduct	getGeneProductByLabel (string label)
	Get a GeneProduct from the ListOfGeneProducts based on its label. More...

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

long	getLine ()

SBaseList	getListOfAllElements (ElementFilter filter)

SBaseList	getListOfAllElements ()

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

ListOfGeneAssociations	getListOfGeneAssociations ()
	Returns the ListOfGeneAssociations annotation object for level 1 in this plugin object. More...

ListOfGeneProducts	getListOfGeneProducts ()
	Returns the ListOfGeneProducts in this FbcModelPlugin object. More...

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

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

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

long	getNumGeneProducts ()
	Get the number of GeneProduct objects in this FbcModelPlugin. More...

long	getNumObjectives ()
	Get the number of Objective objects in this FbcModelPlugin. More...

Objective	getObjective (long n)
	Get an Objective from the ListOfObjectives. More...

Objective	getObjective (string sid)
	Get an Objective from the ListOfObjectives based on its identifier. 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...

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

SBMLExtension	getSBMLExtension ()

new bool	getStrict ()
	Returns the value of the 'strict' attribute of this FbcModelPlugin. More...

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...

new bool	isSetStrict ()
	Predicate returning `true` if this FbcModelPlugin's 'strict' attribute is set. More...

new bool	isValidTypeForList (SBase item)

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 annotation object from this plugin object and returns a pointer to it. More...

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

GeneProduct	removeGeneProduct (long n)
	Removes the nth GeneProduct from the ListOfGeneProducts within this FbcModelPlugin. More...

GeneProduct	removeGeneProduct (string sid)
	Removes the GeneProduct with the given identifier from the ListOfGeneProducts within this FbcModelPlugin and returns a pointer to it. More...

Objective	removeObjective (long n)
	Removes the nth Objective from the ListOfObjectives within this FbcModelPlugin. More...

Objective	removeObjective (string sid)
	Removes the Objective with the given identifier from the ListOfObjectives within this FbcModelPlugin and returns a pointer to it. 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	setActiveObjectiveId (string objectiveId)
	Sets the id of the active objective. More...

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

new int	setStrict (bool strict)
	Sets the value of the 'strict' attribute of this FbcModelPlugin. More...

int	unsetActiveObjectiveId ()
	Unsets the 'activeObjective' attribute of the ListOfObjectives. More...

new int	unsetStrict ()
	Unsets the value of the 'strict' attribute of this FbcModelPlugin. More...

Protected Attributes
bool	swigCMemOwn

Constructor & Destructor Documentation

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

Creates a new FbcModelPlugin 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.
fbcns	the namespaces object for the package.

libsbmlcs.FbcModelPlugin.FbcModelPlugin ( FbcModelPlugin orig )

Copy constructor for FbcModelPlugin.

Parameters

orig	the FbcModelPlugin instance to copy.

Member Function Documentation

int libsbmlcs.FbcModelPlugin.addFluxBound ( FluxBound bound )

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

Note: FluxBound objects are only defined for version 1 of the 'Flux Balance Constraints' specification, and are replaced in version 2 by the 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin.

Parameters

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

Returns

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

int libsbmlcs.FbcModelPlugin.addGeneAssociation ( GeneAssociation association )

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

Parameters

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

Note: GeneAssociation objects are not defined in any version of the 'Flux Balance Constraints' specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.

Returns

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

int libsbmlcs.FbcModelPlugin.addGeneProduct ( GeneProduct gp )

Adds a copy the given GeneProduct to this FbcModelPlugin.

Note: GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.

Parameters

gp	the GeneProduct object to add.

Returns

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

int libsbmlcs.FbcModelPlugin.addObjective ( Objective o )

Adds a copy the given Objective to this FbcModelPlugin.

Parameters

o	the Objective object to add.

Returns

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

int libsbmlcs.FbcModelPlugin.appendFrom ( Model model )

new SBasePlugin libsbmlcs.FbcModelPlugin.clone ( )

Creates and returns a deep copy of this FbcModelPlugin object.

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

FluxBound libsbmlcs.FbcModelPlugin.createFluxBound ( )

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

Note: FluxBound objects are only defined for version 1 of the 'Flux Balance Constraints' specification, and are replaced in version 2 by the 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin.

Returns: a newly created FluxBound object.

GeneAssociation libsbmlcs.FbcModelPlugin.createGeneAssociation ( )

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

Returns: a newly created GeneAssociation annotation object.

GeneProduct libsbmlcs.FbcModelPlugin.createGeneProduct ( )

Creates a new GeneProduct object, adds it to this FbcModelPlugin's ListOfGeneProducts and returns the GeneProduct object created.

Note: GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.

Returns: a new GeneProduct object instance.

See also: addGeneProduct(GeneProduct gp)

Objective libsbmlcs.FbcModelPlugin.createObjective ( )

Creates a new Objective object, adds it to this FbcModelPlugin's ListOfObjectives and returns the Objective object created.

Returns: a new Objective object instance.

See also: addObjective(Objective o)

override void libsbmlcs.FbcModelPlugin.Dispose ( )

virtual

Reimplemented from libsbmlcs.SBasePlugin.

Objective libsbmlcs.FbcModelPlugin.getActiveObjective ( )

Returns the current active objective.

Returns: the Objective pointed to by the 'activeObjective' attribute, or null if no such Objective can be found.

string libsbmlcs.FbcModelPlugin.getActiveObjectiveId ( )

Returns the id of the current active objective.

Returns: the value of the 'activeObjective' attribute of the ListOfObjectives.

long libsbmlcs.SBasePlugin.getColumn ( )

inherited

new SBase libsbmlcs.SBasePlugin.getElementByMetaId ( string metaid )

inherited

Return the first child object found with a given meta identifier.

This method searches all the subobjects under this one, compares their meta identifiers to metaid, and returns the first one that machines.

Parameters

metaid string, the metaid of the object to find.

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

new SBase libsbmlcs.SBasePlugin.getElementBySId ( string id )

inherited

Return the first child object found with a given identifier.

This method searches all the subobjects under this one, compares their identifiers to id, and returns the first one that machines.

Normally, SId type identifier values are unique across a model in SBML. However, in some circumstances they may not be, such as if a model is invalid because of multiple objects having the same identifier.

Parameters

id	string representing the identifier of the object to find.

Returns: pointer to the first object 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.

FluxBound libsbmlcs.FbcModelPlugin.getFluxBound ( long n )

Returns the FluxBound object that belongs to the given index.

If the index is invalid, null is returned.

Note: FluxBound objects are only defined for version 1 of the 'Flux Balance Constraints' specification, and are replaced in version 2 by the 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin.

Parameters

n	the index number of the FluxBound to get.

Returns: the nth FluxBound in the ListOfFluxBounds. If the index n is invalid, null is returned.

FluxBound libsbmlcs.FbcModelPlugin.getFluxBound ( string sid )

Returns the FluxBound object based on its identifier.

Note: FluxBound objects are only defined for version 1 of the 'Flux Balance Constraints' specification, and are replaced in version 2 by the 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin.

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(unsigned int n); getListOfFluxBounds()

ListOfFluxBounds libsbmlcs.FbcModelPlugin.getFluxBoundsForReaction ( string reaction )

Creates a new ListOfFluxBounds object that contains only the FluxBound objects associated with the given Reaction.

If no such Reaction can be found, or if there are no FluxBound objects associated with it, returns null.

Note: FluxBound objects are only defined for version 1 of the 'Flux Balance Constraints' specification, and are replaced in version 2 by the 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin.

Parameters

reaction the id of an reaction to find FluxBound objects for.

Returns: a ListOfFluxBounds for the given reaction id.

GeneAssociation libsbmlcs.FbcModelPlugin.getGeneAssociation ( long n )

Returns the GeneAssociation annotation object that belongs to the given index.

If the index is invalid, null is returned.

Note: GeneAssociation objects are not defined in any version of the 'Flux Balance Constraints' specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.

Parameters

n	the index number of the GeneAssociation annotation to get.

Returns: the nth GeneAssociation annotation in the ListOfGeneAssociations. If the index n is invalid, null is returned.

GeneAssociation libsbmlcs.FbcModelPlugin.getGeneAssociation ( string sid )

Returns the GeneAssociation annotation object based on its identifier.

Note: GeneAssociation objects are not defined in any version of the 'Flux Balance Constraints' specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.

Parameters

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

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

See also: getGeneAssociation(unsigned int n); getListOfGeneAssociations()

GeneProduct libsbmlcs.FbcModelPlugin.getGeneProduct ( long n )

Get a GeneProduct from the ListOfGeneProducts.

Note: GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.

Parameters

n	the index number of the GeneProduct to get.

Returns: the nth GeneProduct in the ListOfGeneProducts within this FbcModelPlugin. If the index n is invalid, null is returned.

See also: getNumGeneProducts()

GeneProduct libsbmlcs.FbcModelPlugin.getGeneProduct ( string sid )

Get a GeneProduct from the ListOfGeneProducts based on its identifier.

Note: GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.

Parameters

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

Returns: the GeneProduct in the ListOfGeneProducts with the given id or null if no such GeneProduct exists.

See also: getGeneProduct(unsigned int n); getNumGeneProducts()

GeneProduct libsbmlcs.FbcModelPlugin.getGeneProductByLabel ( string label )

Get a GeneProduct from the ListOfGeneProducts based on its label.

Note: GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.

Parameters

label a string representing the label of the GeneProduct to get.

Returns: the GeneProduct in the ListOfGeneProducts with the given label or null if no such GeneProduct exists.

See also: getGeneProduct(unsigned int n); getNumGeneProducts()

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

ListOfFluxBounds libsbmlcs.FbcModelPlugin.getListOfFluxBounds ( )

Returns the ListOfFluxBounds in this plugin object.

Note: FluxBound objects are only defined for version 1 of the 'Flux Balance Constraints' specification, and are replaced in version 2 by the 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin.

Returns: ListOfFluxBounds object in this plugin object.

ListOfGeneAssociations libsbmlcs.FbcModelPlugin.getListOfGeneAssociations ( )

Returns the ListOfGeneAssociations annotation object for level 1 in this plugin object.

Note: GeneAssociation objects are not defined in any version of the 'Flux Balance Constraints' specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.

Returns: ListOfGeneAssociations annotation object for level 1 in this plugin object.

ListOfGeneProducts libsbmlcs.FbcModelPlugin.getListOfGeneProducts ( )

Returns the ListOfGeneProducts in this FbcModelPlugin object.

Note: GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.

Returns: the ListOfGeneProducts child of this FbcModelPlugin.

ListOfObjectives libsbmlcs.FbcModelPlugin.getListOfObjectives ( )

Returns the ListOfObjectives in this FbcModelPlugin object.

Returns: the ListOfObjectives child of this FbcModelPlugin.

long libsbmlcs.FbcModelPlugin.getNumFluxBounds ( )

Returns the number of FluxBound object in this plugin object.

Note: FluxBound objects are only defined for version 1 of the 'Flux Balance Constraints' specification, and are replaced in version 2 by the 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin.

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

int libsbmlcs.FbcModelPlugin.getNumGeneAssociations ( )

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

Note: GeneAssociation objects are not defined in any version of the 'Flux Balance Constraints' specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.

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

long libsbmlcs.FbcModelPlugin.getNumGeneProducts ( )

Get the number of GeneProduct objects in this FbcModelPlugin.

Note: GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.

Returns: the number of GeneProduct objects in this FbcModelPlugin.

long libsbmlcs.FbcModelPlugin.getNumObjectives ( )

Get the number of Objective objects in this FbcModelPlugin.

Returns: the number of Objective objects in this FbcModelPlugin.

Objective libsbmlcs.FbcModelPlugin.getObjective ( long n )

Get an Objective from the ListOfObjectives.

Parameters

n	the index number of the Objective to get.

Returns: the nth Objective in the ListOfObjectives within this FbcModelPlugin. If the index n is invalid, null is returned.

See also: getNumObjectives()

Objective libsbmlcs.FbcModelPlugin.getObjective ( string sid )

Get an Objective from the ListOfObjectives based on its identifier.

Parameters

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

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

See also: getObjective(unsigned int n); getNumObjectives()

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.

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

new bool libsbmlcs.FbcModelPlugin.getStrict ( )

Returns the value of the 'strict' attribute of this FbcModelPlugin.

Note: The 'strict' attribute of the FbcModelPlugin is only defined for version 2 of the 'Flux Balance Constraints' specification, and has no equivalent in version 1 of the specification.

Returns: the value of the 'strict' attribute of this FbcModelPlugin as a boolean.

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()

new bool libsbmlcs.FbcModelPlugin.isSetStrict ( )

Predicate returning true if this FbcModelPlugin's 'strict' attribute is set.

Note: The 'strict' attribute of the FbcModelPlugin is only defined for version 2 of the 'Flux Balance Constraints' specification, and has no equivalent in version 1 of the specification.

Returns: true if this FbcModelPlugin's 'strict' attribute has been set, otherwise false is returned.

new bool libsbmlcs.SBasePlugin.isValidTypeForList ( SBase item )

inherited

FluxBound libsbmlcs.FbcModelPlugin.removeFluxBound ( long n )

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

The caller owns the returned object and is responsible for deleting it.

Note: FluxBound objects are only defined for version 1 of the 'Flux Balance Constraints' specification, and are replaced in version 2 by the 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin.

Parameters

n	the index of the FluxBound object to remove.

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

FluxBound libsbmlcs.FbcModelPlugin.removeFluxBound ( string sid )

Removes the FluxBound object with the given sid attribute from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Note: FluxBound objects are only defined for version 1 of the 'Flux Balance Constraints' specification, and are replaced in version 2 by the 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin.

Parameters

sid	the id attribute of the FluxBound object to remove.

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

GeneAssociation libsbmlcs.FbcModelPlugin.removeGeneAssociation ( long n )

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

The caller owns the returned object and is responsible for deleting it.

Note: GeneAssociation objects are not defined in any version of the 'Flux Balance Constraints' specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.

Parameters

n	the index of the GeneAssociation annotation object to remove.

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

GeneAssociation libsbmlcs.FbcModelPlugin.removeGeneAssociation ( string sid )

Removes the GeneAssociation annotation object with the given sid attribute from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Note: GeneAssociation objects are not defined in any version of the 'Flux Balance Constraints' specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.

Parameters

sid	the id attribute of the GeneAssociation annotation object to remove.

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

GeneProduct libsbmlcs.FbcModelPlugin.removeGeneProduct ( long n )

Removes the nth GeneProduct from the ListOfGeneProducts within this FbcModelPlugin.

and returns a pointer to it.

The caller owns the returned item and is responsible for deleting it.

Note: GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.

Parameters

n	the index of the GeneProduct to remove.

See also: getNumGeneProducts()

GeneProduct libsbmlcs.FbcModelPlugin.removeGeneProduct ( string sid )

Removes the GeneProduct with the given identifier from the ListOfGeneProducts within this FbcModelPlugin and returns a pointer to it.

The caller owns the returned item and is responsible for deleting it. If none of the items in this list have the identifier sid, then null is returned.

Note: GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.

Parameters

sid	the identifier of the GeneProduct to remove.

Returns: the GeneProduct removed. As mentioned above, the caller owns the returned item.

Objective libsbmlcs.FbcModelPlugin.removeObjective ( long n )

Removes the nth Objective from the ListOfObjectives within this FbcModelPlugin.

and returns a pointer to it.

The caller owns the returned item and is responsible for deleting it.

Parameters

n	the index of the Objective to remove.

See also: getNumObjectives()

Objective libsbmlcs.FbcModelPlugin.removeObjective ( string sid )

Removes the Objective with the given identifier from the ListOfObjectives within this FbcModelPlugin and returns a pointer to it.

The caller owns the returned item and is responsible for deleting it. If none of the items in this list have the identifier sid, then null is returned.

Parameters

sid	the identifier of the Objective to remove.

Returns: the Objective removed. As mentioned above, the caller owns the returned item.

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.FbcModelPlugin.setActiveObjectiveId ( string objectiveId )

Sets the id of the active objective.

Returns

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

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()

new int libsbmlcs.FbcModelPlugin.setStrict ( bool strict )

Sets the value of the 'strict' attribute of this FbcModelPlugin.

Note: The 'strict' attribute of the FbcModelPlugin is only defined for version 2 of the 'Flux Balance Constraints' specification, and has no equivalent in version 1 of the specification.

Parameters

strict bool value of the 'strict' attribute to be set.

Returns

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

LIBSBML_OPERATION_SUCCESS

int libsbmlcs.FbcModelPlugin.unsetActiveObjectiveId ( )

Unsets the 'activeObjective' attribute of the ListOfObjectives.

Returns

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

LIBSBML_OPERATION_SUCCESS

success status

new int libsbmlcs.FbcModelPlugin.unsetStrict ( )

Unsets the value of the 'strict' attribute of this FbcModelPlugin.

Note: The 'strict' attribute of the FbcModelPlugin is only defined for version 2 of the 'Flux Balance Constraints' specification, and has no equivalent in version 1 of the specification.

Returns

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

LIBSBML_OPERATION_SUCCESS

Member Data Documentation

bool libsbmlcs.SBasePlugin.swigCMemOwn

protectedinherited

Detailed Description

The 'strict' attribute on the (extended) Model class

Lists of subobjects on the (extended) Model class

Public Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation