libSBML Perl API  libSBML 5.13.0 Perl API
FbcModelPlugin Class Reference
Inheritance diagram for FbcModelPlugin:
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Detailed Description

{fbc}

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, 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".
  • 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 (const FluxBound *bound)
 Adds a copy of the given FluxBound object to the list of FluxBounds. More...
 
int addGeneAssociation (const GeneAssociation *association)
 Adds a copy of the given GeneAssociation annotation object to the list of GeneAssociations. More...
 
int addGeneProduct (const GeneProduct *gp)
 Adds a copy the given "GeneProduct" to this FbcModelPlugin. More...
 
int addObjective (const Objective *o)
 Adds a copy the given "Objective" to this FbcModelPlugin. More...
 
virtual FbcModelPluginclone () const
 Creates and returns a deep copy of this FbcModelPlugin object. More...
 
FluxBoundcreateFluxBound ()
 Creates a new FluxBound object and adds it to the list of FluxBound objects and returns it. More...
 
GeneAssociationcreateGeneAssociation ()
 Creates a new GeneAssociation annotation object and adds it to the list of GeneAssociation objects and returns it. More...
 
GeneProductcreateGeneProduct ()
 Creates a new GeneProduct object, adds it to this FbcModelPlugins ListOfGeneProducts and returns the GeneProduct object created. More...
 
ObjectivecreateObjective ()
 Creates a new Objective object, adds it to this FbcModelPlugins ListOfObjectives and returns the Objective object created. More...
 
 FbcModelPlugin (const std::string &uri, const std::string &prefix, FbcPkgNamespaces *fbcns)
 Creates a new FbcModelPlugin. More...
 
 FbcModelPlugin (const FbcModelPlugin &orig)
 Copy constructor for FbcModelPlugin. More...
 
ObjectivegetActiveObjective ()
 Returns the current active objective. More...
 
const ObjectivegetActiveObjective () const
 Returns the current active objective. More...
 
std::string getActiveObjectiveId () const
 returns the id of the current active objective. More...
 
virtual ListgetAllElements (ElementFilter *filter=NULL)
 doxygenLibsbmlInternal More...
 
virtual SBasegetElementByMetaId (const std::string &metaid)
 Return the first child object found with a given meta identifier. More...
 
virtual SBasegetElementBySId (const std::string &id)
 Return the first child object found with a given identifier. More...
 
const std::string & getElementNamespace () const
 Returns the namespace URI of the package to which this plugin object belongs. More...
 
const FluxBoundgetFluxBound (unsigned int n) const
 Returns the FluxBound object that belongs to the given index. More...
 
FluxBoundgetFluxBound (unsigned int n)
 Returns the FluxBound object that belongs to the given index. More...
 
FluxBoundgetFluxBound (const std::string &sid)
 Returns the FluxBound object based on its identifier. More...
 
const FluxBoundgetFluxBound (const std::string &sid) const
 Returns the FluxBound object based on its identifier. More...
 
ListOfFluxBoundsgetFluxBoundsForReaction (const std::string &reaction) const
 
const GeneAssociationgetGeneAssociation (unsigned int n) const
 Returns the GeneAssociation annotation object that belongs to the given index. More...
 
GeneAssociationgetGeneAssociation (unsigned int n)
 Returns the GeneAssociation annotation object that belongs to the given index. More...
 
GeneAssociationgetGeneAssociation (const std::string &sid)
 Returns the GeneAssociation annotation object based on its identifier. More...
 
const GeneAssociationgetGeneAssociation (const std::string &sid) const
 Returns the GeneAssociation annotation object based on its identifier. More...
 
GeneProductgetGeneProduct (unsigned int n)
 Get a GeneProduct from the ListOfGeneProducts. More...
 
const GeneProductgetGeneProduct (unsigned int n) const
 Get a GeneProduct from the ListOfGeneProducts. More...
 
GeneProductgetGeneProduct (const std::string &sid)
 Get a GeneProduct from the ListOfGeneProducts based on its identifier. More...
 
const GeneProductgetGeneProduct (const std::string &sid) const
 Get a GeneProduct from the ListOfGeneProducts based on its identifier. More...
 
GeneProductgetGeneProductByLabel (const std::string &label)
 Get a GeneProduct from the ListOfGeneProducts based on its label. More...
 
unsigned int getLevel () const
 Returns the SBML Level of the package extension of this plugin object. More...
 
const ListOfFluxBoundsgetListOfFluxBounds () const
 Returns the ListOfFluxBounds in this plugin object. More...
 
ListOfFluxBoundsgetListOfFluxBounds ()
 Returns the ListOfFluxBounds in this plugin object. More...
 
const ListOfGeneAssociationsgetListOfGeneAssociations () const
 Returns the ListOfGeneAssociations annotation object for level 1 in this plugin object. More...
 
ListOfGeneAssociationsgetListOfGeneAssociations ()
 Returns the ListOfGeneAssociations annotation object for level 1 in this plugin object. More...
 
const ListOfGeneProductsgetListOfGeneProducts () const
 Returns the "ListOfGeneProducts" in this FbcModelPlugin object. More...
 
ListOfGeneProductsgetListOfGeneProducts ()
 Returns the "ListOfGeneProducts" in this FbcModelPlugin object. More...
 
const ListOfObjectivesgetListOfObjectives () const
 Returns the "ListOfObjectives" in this FbcModelPlugin object. More...
 
ListOfObjectivesgetListOfObjectives ()
 Returns the "ListOfObjectives" in this FbcModelPlugin object. More...
 
unsigned int getNumFluxBounds () const
 Returns the number of FluxBound object in this plugin object. More...
 
int getNumGeneAssociations () const
 Returns the number of GeneAssociation annotation object in this plugin object. More...
 
unsigned int getNumGeneProducts () const
 Get the number of GeneProduct objects in this FbcModelPlugin. More...
 
unsigned int getNumObjectives () const
 Get the number of Objective objects in this FbcModelPlugin. More...
 
ObjectivegetObjective (unsigned int n)
 Get a Objective from the ListOfObjectives. More...
 
const ObjectivegetObjective (unsigned int n) const
 Get a Objective from the ListOfObjectives. More...
 
ObjectivegetObjective (const std::string &sid)
 Get a Objective from the ListOfObjectives based on its identifier. More...
 
const ObjectivegetObjective (const std::string &sid) const
 Get a Objective from the ListOfObjectives based on its identifier. More...
 
const std::string & getPackageName () const
 Returns the short-form name of the package to which this plugin object belongs. More...
 
unsigned int getPackageVersion () const
 Returns the package version of the package extension of this plugin object. More...
 
SBasegetParentSBMLObject ()
 Returns the parent object to which this plugin object is connected. More...
 
const SBasegetParentSBMLObject () const
 Returns the parent object to which this plugin object is connected. More...
 
const std::string & getPrefix () const
 Returns the XML namespace prefix of the package to which this plugin object belongs. More...
 
SBMLDocumentgetSBMLDocument ()
 Returns the SBMLDocument object containing this object instance. More...
 
const SBMLDocumentgetSBMLDocument () const
 Returns the SBMLDocument object containing this object instance. More...
 
virtual bool getStrict () const
 Returns the value of the "strict" attribute of this FbcModelPlugin. More...
 
std::string getURI () const
 Returns the XML namespace URI for the package to which this object belongs. More...
 
unsigned int getVersion () const
 Returns the Version within the SBML Level of the package extension of this plugin object. More...
 
virtual bool isSetStrict () const
 Predicate returning true if this FbcModelPlugin's "strict" attribute is set. More...
 
virtual bool isValidTypeForList (SBase *item) const
 
FbcModelPluginoperator= (const FbcModelPlugin &rhs)
 Assignment operator for FbcModelPlugin. More...
 
FluxBoundremoveFluxBound (unsigned int n)
 Removes the nth FluxBound object from this plugin object and returns a pointer to it. More...
 
FluxBoundremoveFluxBound (const std::string &sid)
 Removes the FluxBound object with the given sid attribute from this plugin object and returns a pointer to it. More...
 
GeneAssociationremoveGeneAssociation (unsigned int n)
 Removes the nth GeneAssociation annotation object from this plugin object and returns a pointer to it. More...
 
GeneAssociationremoveGeneAssociation (const std::string &sid)
 Removes the GeneAssociation annotation object with the given sid attribute from this plugin object and returns a pointer to it. More...
 
GeneProductremoveGeneProduct (unsigned int n)
 Removes the nth GeneProduct from the ListOfGeneProducts within this FbcModelPlugin. More...
 
GeneProductremoveGeneProduct (const std::string &sid)
 Removes the GeneProduct with the given identifier from the ListOfGeneProducts within this FbcModelPlugin and returns a pointer to it. More...
 
ObjectiveremoveObjective (unsigned int n)
 Removes the nth Objective from the ListOfObjectives within this FbcModelPlugin. More...
 
ObjectiveremoveObjective (const std::string &sid)
 Removes the Objective with the given identifier from the ListOfObjectives within this FbcModelPlugin and returns a pointer to it. More...
 
virtual void renameMetaIdRefs (const std::string &oldid, const std::string &newid)
 
virtual void renameSIdRefs (const std::string &oldid, const std::string &newid)
 
virtual void renameUnitSIdRefs (const std::string &oldid, const std::string &newid)
 
int setActiveObjectiveId (const std::string &objectiveId)
 Sets the id of the active objective. More...
 
int setElementNamespace (const std::string &uri)
 Sets the XML namespace to which this object belongs. More...
 
virtual int setStrict (bool strict)
 Sets the value of the "strict" attribute of this FbcModelPlugin. More...
 
void unsetActiveObjectiveId ()
 Unsets the active objective. More...
 
virtual int unsetStrict ()
 Unsets the value of the "strict" attribute of this FbcModelPlugin. More...
 
virtual ~FbcModelPlugin ()
 Destructor for FbcModelPlugin. More...
 

Constructor & Destructor Documentation

◆ FbcModelPlugin() [1/2]

FbcModelPlugin::FbcModelPlugin ( const std::string &  uri,
const std::string &  prefix,
FbcPkgNamespaces fbcns 
)

Creates a new FbcModelPlugin.

◆ FbcModelPlugin() [2/2]

FbcModelPlugin::FbcModelPlugin ( const FbcModelPlugin orig)

Copy constructor for FbcModelPlugin.

Parameters
orig;the FbcModelPlugin instance to copy.

◆ ~FbcModelPlugin()

FbcModelPlugin::~FbcModelPlugin ( )
virtual

Destructor for FbcModelPlugin.

Member Function Documentation

◆ addFluxBound()

int FbcModelPlugin::addFluxBound ( const FluxBound bound)

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

Parameters
boundthe FluxBound object to be added to the list of FluxBounds.

◆ addGeneAssociation()

int FbcModelPlugin::addGeneAssociation ( const GeneAssociation association)

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

Parameters
associationthe GeneAssociation annotation object to be added to the list of GeneAssociations.

◆ addGeneProduct()

int FbcModelPlugin::addGeneProduct ( const GeneProduct gp)

Adds a copy the given "GeneProduct" to this FbcModelPlugin.

Parameters
gp;the GeneProduct object to add
Returns
integer value indicating success/failure of the function. The possible values returned by this function are:

◆ addObjective()

int FbcModelPlugin::addObjective ( const 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:

◆ clone()

FbcModelPlugin * FbcModelPlugin::clone ( ) const
virtual

Creates and returns a deep copy of this FbcModelPlugin object.

Returns
a (deep) copy of this FbcModelPlugin object.

Reimplemented from SBasePlugin.

◆ createFluxBound()

FluxBound * 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

◆ createGeneAssociation()

GeneAssociation * 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

◆ createGeneProduct()

GeneProduct * FbcModelPlugin::createGeneProduct ( )

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

Returns
a new GeneProduct object instance
See also
addGeneProduct(const GeneProduct* gp)

◆ createObjective()

Objective * FbcModelPlugin::createObjective ( )

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

Returns
a new Objective object instance
See also
addObjective(const Objective* o)

◆ getActiveObjective() [1/2]

Objective * FbcModelPlugin::getActiveObjective ( )

Returns the current active objective.

◆ getActiveObjective() [2/2]

const Objective * FbcModelPlugin::getActiveObjective ( ) const

Returns the current active objective.

◆ getActiveObjectiveId()

std::string FbcModelPlugin::getActiveObjectiveId ( ) const

returns the id of the current active objective.

◆ getAllElements()

List * FbcModelPlugin::getAllElements ( ElementFilter filter = NULL)
virtual

doxygenLibsbmlInternal

doxygenLibsbmlInternal doxygenLibsbmlInternal doxygenLibsbmlInternal doxygenLibsbmlInternal doxygenLibsbmlInternal Returns a List of all child SBase objects, including those nested to an arbitrary depth.

Parameters
filteran ElementFilter that may impose restrictions on the objects to be retrieved.
Returns
a List* of pointers to all child objects.

doxygenLibsbmlInternal doxygenLibsbmlInternal

Reimplemented from SBasePlugin.

◆ getElementByMetaId()

SBase * SBasePlugin::getElementByMetaId ( const std::string &  metaid)
virtualinherited

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
metaidstring, the metaid of the object to find.
Returns
pointer to the first object found with the given metaid.

Reimplemented in GroupsModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.

◆ getElementBySId()

SBase * SBasePlugin::getElementBySId ( const std::string &  id)
virtualinherited

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
idstring representing the identifier of the object to find
Returns
pointer to the first object with the given id.

Reimplemented in GroupsModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.

◆ getElementNamespace()

const std::string & SBasePlugin::getElementNamespace ( ) const
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.

◆ getFluxBound() [1/4]

const FluxBound * FbcModelPlugin::getFluxBound ( unsigned int  n) const

Returns the FluxBound object that belongs to the given index.

If the index is invalid, NULL is returned.

Parameters
nthe index number of the FluxBound to get.
Returns
the nth FluxBound in the ListOfFluxBounds.

◆ getFluxBound() [2/4]

FluxBound * FbcModelPlugin::getFluxBound ( unsigned int  n)

Returns the FluxBound object that belongs to the given index.

If the index is invalid, NULL is returned.

Parameters
nthe index number of the FluxBound to get.
Returns
the nth FluxBound in the ListOfFluxBounds.

◆ getFluxBound() [3/4]

FluxBound * FbcModelPlugin::getFluxBound ( const std::string &  sid)

Returns the FluxBound object based on its identifier.

Parameters
sida 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()

◆ getFluxBound() [4/4]

const FluxBound * FbcModelPlugin::getFluxBound ( const std::string &  sid) const

Returns the FluxBound object based on its identifier.

Parameters
sida 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()

◆ getFluxBoundsForReaction()

ListOfFluxBounds * FbcModelPlugin::getFluxBoundsForReaction ( const std::string &  reaction) const
Parameters
reactionthe id of an reaction to find fluxBounds for
Returns
a listOfFluxBounds for the given reaction id

◆ getGeneAssociation() [1/4]

const GeneAssociation * FbcModelPlugin::getGeneAssociation ( unsigned int  n) const

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

If the index is invalid, NULL is returned.

Parameters
nthe index number of the GeneAssociation annotation to get.
Returns
the nth GeneAssociation annotation in the ListOfGeneAssociations.

◆ getGeneAssociation() [2/4]

GeneAssociation * FbcModelPlugin::getGeneAssociation ( unsigned int  n)

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

If the index is invalid, NULL is returned.

Parameters
nthe index number of the GeneAssociation annotation to get.
Returns
the nth GeneAssociation annotation in the ListOfGeneAssociations.

◆ getGeneAssociation() [3/4]

GeneAssociation * FbcModelPlugin::getGeneAssociation ( const std::string &  sid)

Returns the GeneAssociation annotation object based on its identifier.

Parameters
sida 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()

◆ getGeneAssociation() [4/4]

const GeneAssociation * FbcModelPlugin::getGeneAssociation ( const std::string &  sid) const

Returns the GeneAssociation annotation object based on its identifier.

Parameters
sida 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()

◆ getGeneProduct() [1/4]

GeneProduct * FbcModelPlugin::getGeneProduct ( unsigned int  n)

Get a GeneProduct from the ListOfGeneProducts.

Parameters
nthe index number of the GeneProduct to get.
Returns
the nth GeneProduct in the ListOfGeneProducts within this FbcModelPlugin.
See also
getNumGeneProducts()

◆ getGeneProduct() [2/4]

const GeneProduct * FbcModelPlugin::getGeneProduct ( unsigned int  n) const

Get a GeneProduct from the ListOfGeneProducts.

Parameters
nthe index number of the GeneProduct to get.
Returns
the nth GeneProduct in the ListOfGeneProducts within this FbcModelPlugin.
See also
getNumGeneProducts()

◆ getGeneProduct() [3/4]

GeneProduct * FbcModelPlugin::getGeneProduct ( const std::string &  sid)

Get a GeneProduct from the ListOfGeneProducts based on its identifier.

Parameters
sida 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()

◆ getGeneProduct() [4/4]

const GeneProduct * FbcModelPlugin::getGeneProduct ( const std::string &  sid) const

Get a GeneProduct from the ListOfGeneProducts based on its identifier.

Parameters
sida 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()

◆ getGeneProductByLabel()

GeneProduct * FbcModelPlugin::getGeneProductByLabel ( const std::string &  label)

Get a GeneProduct from the ListOfGeneProducts based on its label.

Parameters
labela 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()

◆ getLevel()

unsigned int SBasePlugin::getLevel ( ) const
inherited

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

Returns
the SBML Level.
See also
getVersion()

◆ getListOfFluxBounds() [1/2]

const ListOfFluxBounds * FbcModelPlugin::getListOfFluxBounds ( ) const

Returns the ListOfFluxBounds in this plugin object.

Returns
ListOfFluxBounds object in this plugin object.

◆ getListOfFluxBounds() [2/2]

ListOfFluxBounds * FbcModelPlugin::getListOfFluxBounds ( )

Returns the ListOfFluxBounds in this plugin object.

Returns
ListOfFluxBounds object in this plugin object.

◆ getListOfGeneAssociations() [1/2]

const ListOfGeneAssociations * FbcModelPlugin::getListOfGeneAssociations ( ) const

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

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

◆ getListOfGeneAssociations() [2/2]

ListOfGeneAssociations * FbcModelPlugin::getListOfGeneAssociations ( )

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

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

◆ getListOfGeneProducts() [1/2]

const ListOfGeneProducts * FbcModelPlugin::getListOfGeneProducts ( ) const

Returns the "ListOfGeneProducts" in this FbcModelPlugin object.

Returns
the "ListOfGeneProducts" attribute of this FbcModelPlugin.

◆ getListOfGeneProducts() [2/2]

ListOfGeneProducts * FbcModelPlugin::getListOfGeneProducts ( )

Returns the "ListOfGeneProducts" in this FbcModelPlugin object.

Returns
the "ListOfGeneProducts" attribute of this FbcModelPlugin.

◆ getListOfObjectives() [1/2]

const ListOfObjectives * FbcModelPlugin::getListOfObjectives ( ) const

Returns the "ListOfObjectives" in this FbcModelPlugin object.

Returns
the "ListOfObjectives" attribute of this FbcModelPlugin.

◆ getListOfObjectives() [2/2]

ListOfObjectives * FbcModelPlugin::getListOfObjectives ( )

Returns the "ListOfObjectives" in this FbcModelPlugin object.

Returns
the "ListOfObjectives" attribute of this FbcModelPlugin.

◆ getNumFluxBounds()

unsigned int FbcModelPlugin::getNumFluxBounds ( ) const

Returns the number of FluxBound object in this plugin object.

Returns
the number of FluxBound object in this plugin object.

◆ getNumGeneAssociations()

int FbcModelPlugin::getNumGeneAssociations ( ) const

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

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

◆ getNumGeneProducts()

unsigned int FbcModelPlugin::getNumGeneProducts ( ) const

Get the number of GeneProduct objects in this FbcModelPlugin.

Returns
the number of GeneProduct objects in this FbcModelPlugin

◆ getNumObjectives()

unsigned int FbcModelPlugin::getNumObjectives ( ) const

Get the number of Objective objects in this FbcModelPlugin.

Returns
the number of Objective objects in this FbcModelPlugin

◆ getObjective() [1/4]

Objective * FbcModelPlugin::getObjective ( unsigned int  n)

Get a Objective from the ListOfObjectives.

Parameters
nthe index number of the Objective to get.
Returns
the nth Objective in the ListOfObjectives within this FbcModelPlugin.
See also
getNumObjectives()

◆ getObjective() [2/4]

const Objective * FbcModelPlugin::getObjective ( unsigned int  n) const

Get a Objective from the ListOfObjectives.

Parameters
nthe index number of the Objective to get.
Returns
the nth Objective in the ListOfObjectives within this FbcModelPlugin.
See also
getNumObjectives()

◆ getObjective() [3/4]

Objective * FbcModelPlugin::getObjective ( const std::string &  sid)

Get a Objective from the ListOfObjectives based on its identifier.

Parameters
sida 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()

◆ getObjective() [4/4]

const Objective * FbcModelPlugin::getObjective ( const std::string &  sid) const

Get a Objective from the ListOfObjectives based on its identifier.

Parameters
sida 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()

◆ getPackageName()

const std::string & SBasePlugin::getPackageName ( ) const
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.

◆ getPackageVersion()

unsigned int SBasePlugin::getPackageVersion ( ) const
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()

◆ getParentSBMLObject() [1/2]

SBase * SBasePlugin::getParentSBMLObject ( )
inherited

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

Returns
the parent object of this object.

◆ getParentSBMLObject() [2/2]

const SBase * SBasePlugin::getParentSBMLObject ( ) const
inherited

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

Returns
the parent object of this object.

◆ getPrefix()

const std::string & SBasePlugin::getPrefix ( ) const
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.

◆ getSBMLDocument() [1/2]

SBMLDocument * 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()

◆ getSBMLDocument() [2/2]

const SBMLDocument * SBasePlugin::getSBMLDocument ( ) const
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()

◆ getStrict()

bool FbcModelPlugin::getStrict ( ) const
virtual

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

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

◆ getURI()

std::string SBasePlugin::getURI ( ) const
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()

◆ getVersion()

unsigned int SBasePlugin::getVersion ( ) const
inherited

Returns the Version within the SBML Level of the package extension of this plugin object.

Returns
the SBML Version.
See also
getLevel()

◆ isSetStrict()

bool FbcModelPlugin::isSetStrict ( ) const
virtual

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

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

◆ isValidTypeForList()

virtual bool SBasePlugin::isValidTypeForList ( SBase item) const
virtualinherited

◆ operator=()

FbcModelPlugin & FbcModelPlugin::operator= ( const FbcModelPlugin rhs)

Assignment operator for FbcModelPlugin.

Parameters
rhs;the object whose values are used as the basis of the assignment

◆ removeFluxBound() [1/2]

FluxBound * FbcModelPlugin::removeFluxBound ( unsigned int  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.

Parameters
nthe 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.

◆ removeFluxBound() [2/2]

FluxBound * FbcModelPlugin::removeFluxBound ( const std::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.

Parameters
sidthe 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.

◆ removeGeneAssociation() [1/2]

GeneAssociation * FbcModelPlugin::removeGeneAssociation ( unsigned int  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.

Parameters
nthe 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.

◆ removeGeneAssociation() [2/2]

GeneAssociation * FbcModelPlugin::removeGeneAssociation ( const std::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.

Parameters
sidthe 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.

◆ removeGeneProduct() [1/2]

GeneProduct * FbcModelPlugin::removeGeneProduct ( unsigned int  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.

Parameters
nthe index of the GeneProduct to remove.
See also
getNumGeneProducts()

◆ removeGeneProduct() [2/2]

GeneProduct * FbcModelPlugin::removeGeneProduct ( const std::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.

Parameters
sidthe identifier of the GeneProduct to remove.
Returns
the GeneProduct removed. As mentioned above, the caller owns the returned item.

◆ removeObjective() [1/2]

Objective * FbcModelPlugin::removeObjective ( unsigned int  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
nthe index of the Objective to remove.
See also
getNumObjectives()

◆ removeObjective() [2/2]

Objective * FbcModelPlugin::removeObjective ( const std::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
sidthe identifier of the Objective to remove.
Returns
the Objective removed. As mentioned above, the caller owns the returned item.

◆ renameMetaIdRefs()

virtual void SBasePlugin::renameMetaIdRefs ( const std::string &  oldid,
const std::string &  newid 
)
virtualinherited

◆ renameSIdRefs()

virtual void SBasePlugin::renameSIdRefs ( const std::string &  oldid,
const std::string &  newid 
)
virtualinherited

Reimplemented in FbcReactionPlugin.

◆ renameUnitSIdRefs()

virtual void SBasePlugin::renameUnitSIdRefs ( const std::string &  oldid,
const std::string &  newid 
)
virtualinherited

◆ setActiveObjectiveId()

int FbcModelPlugin::setActiveObjectiveId ( const std::string &  objectiveId)

Sets the id of the active objective.

◆ setElementNamespace()

int SBasePlugin::setElementNamespace ( const std::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
urithe URI to assign to this object.

◆ setStrict()

int FbcModelPlugin::setStrict ( bool  strict)
virtual

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

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:

◆ unsetActiveObjectiveId()

void FbcModelPlugin::unsetActiveObjectiveId ( )

Unsets the active objective.

◆ unsetStrict()

int FbcModelPlugin::unsetStrict ( )
virtual

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

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