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FbcSpeciesPlugin Class Reference
Inheritance diagram for FbcSpeciesPlugin:
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Detailed Description

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

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

Public Member Functions

virtual FbcSpeciesPluginclone () const
 Creates and returns a deep copy of this FbcSpeciesPlugin object. More...
 
 FbcSpeciesPlugin (const std::string &uri, const std::string &prefix, FbcPkgNamespaces *fbcns)
 Constructor. More...
 
 FbcSpeciesPlugin (const FbcSpeciesPlugin &orig)
 Copy constructor. More...
 
virtual ListgetAllElements (ElementFilter *filter=NULL)
 Returns a List of all child SBase objects, including those nested to an arbitrary depth. More...
 
virtual int getCharge () const
 Returns the value of the "charge" attribute of this FbcSpeciesPlugin. More...
 
virtual const std::string & getChemicalFormula () const
 Returns the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin. More...
 
virtual SBasegetElementByMetaId (const std::string &metaid)
 Returns the first child element it can find with the given metaid, or NULL if no such object is found. More...
 
virtual SBasegetElementBySId (const std::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...
 
const std::string & getElementNamespace () const
 Returns the XML namespace (URI) of the package extension of this plugin object. More...
 
unsigned int getLevel () const
 Returns the SBML level of the package extension of this plugin object. More...
 
const std::string & getPackageName () const
 Returns the package name of this plugin object. More...
 
unsigned int getPackageVersion () const
 Returns the package version of the package extension of this plugin object. More...
 
SBasegetParentSBMLObject ()
 Returns the parent SBase object to which this plugin object connected. More...
 
const SBasegetParentSBMLObject () const
 Returns the parent SBase object to which this plugin object connected. More...
 
const std::string & getPrefix () const
 Returns the prefix of the package extension of this plugin object. More...
 
SBMLDocumentgetSBMLDocument ()
 Returns the parent SBMLDocument of this plugin object. More...
 
const SBMLDocumentgetSBMLDocument () const
 Returns the parent SBMLDocument of this plugin object. More...
 
std::string getURI () const
 Gets the URI to which this element belongs to. More...
 
unsigned int getVersion () const
 Returns the SBML version of the package extension of this plugin object. More...
 
virtual bool isSetCharge () const
 Predicate returning true or false depending on whether this FbcSpeciesPlugin "charge" attribute has been set. More...
 
virtual bool isSetChemicalFormula () const
 Predicate returning true or false depending on whether this FbcSpeciesPlugin "chemicalFormula" attribute has been set. More...
 
FbcSpeciesPluginoperator= (const FbcSpeciesPlugin &orig)
 Assignment operator for FbcSpeciesPlugin . More...
 
virtual int setCharge (int charge)
 Sets the value of the "charge" attribute of this FbcSpeciesPlugin. More...
 
virtual int setChemicalFormula (const std::string &chemicalFormula)
 Sets the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin. More...
 
int setElementNamespace (const std::string &uri)
 Sets the XML namespace to which this element belongs to. More...
 
virtual int unsetCharge ()
 Unsets the value of the "charge" attribute of this FbcSpeciesPlugin. More...
 
virtual int unsetChemicalFormula ()
 Unsets the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin. More...
 
virtual ~FbcSpeciesPlugin ()
 Destroy this object. More...
 

Constructor & Destructor Documentation

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

Constructor.

FbcSpeciesPlugin::FbcSpeciesPlugin ( const FbcSpeciesPlugin orig)

Copy constructor.

Creates a copy of this FbcSpeciesPlugin object.

FbcSpeciesPlugin::~FbcSpeciesPlugin ( )
virtual

Destroy this object.

Member Function Documentation

FbcSpeciesPlugin * FbcSpeciesPlugin::clone ( ) const
virtual

Creates and returns a deep copy of this FbcSpeciesPlugin object.

Returns
a (deep) copy of this FbcSpeciesPlugin object

Implements SBasePlugin.

List * SBasePlugin::getAllElements ( ElementFilter *  filter = NULL)
virtualinherited

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

Returns
a List of pointers to all children objects.

Reimplemented in LayoutModelPlugin, FbcModelPlugin, CompModelPlugin, CompSBasePlugin, CompSBMLDocumentPlugin, and QualModelPlugin.

int FbcSpeciesPlugin::getCharge ( ) const
virtual

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

Returns
the value of the "charge" attribute of this FbcSpeciesPlugin.
const std::string & FbcSpeciesPlugin::getChemicalFormula ( ) const
virtual

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

Returns
the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin.
SBase * SBasePlugin::getElementByMetaId ( const std::string &  metaid)
virtualinherited

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

Parameters
metaidstring representing the metaid of objects to find
Returns
pointer to the first element found with the given metaid.

Reimplemented in FbcModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.

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

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
idstring representing the id of objects to find
Returns
pointer to the first element found with the given id.

Reimplemented in FbcModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.

const std::string & SBasePlugin::getElementNamespace ( ) const
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.
unsigned int SBasePlugin::getLevel ( ) const
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.
const std::string & SBasePlugin::getPackageName ( ) const
inherited

Returns the package name of this plugin object.

Returns
the package name of this plugin object.
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.
SBase * 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.
const SBase * SBasePlugin::getParentSBMLObject ( ) const
inherited

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

Returns
the parent SBase object to which this plugin object connected.
const std::string & SBasePlugin::getPrefix ( ) const
inherited

Returns the prefix of the package extension of this plugin object.

Returns
the prefix of the package extension of this plugin object.
SBMLDocument * SBasePlugin::getSBMLDocument ( )
inherited

Returns the parent SBMLDocument of this plugin object.

Returns
the parent SBMLDocument object of this plugin object.
const SBMLDocument * SBasePlugin::getSBMLDocument ( ) const
inherited

Returns the parent SBMLDocument of this plugin object.

Returns
the parent SBMLDocument object of this plugin object.
std::string SBasePlugin::getURI ( ) const
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()
unsigned int SBasePlugin::getVersion ( ) const
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 FbcSpeciesPlugin::isSetCharge ( ) const
virtual

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

Returns
true if this FbcSpeciesPlugin "charge" attribute has been set, otherwise false is returned.
bool FbcSpeciesPlugin::isSetChemicalFormula ( ) const
virtual

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

Returns
true if this FbcSpeciesPlugin "chemicalFormula" attribute has been set, otherwise false is returned.
FbcSpeciesPlugin & FbcSpeciesPlugin::operator= ( const FbcSpeciesPlugin orig)

Assignment operator for FbcSpeciesPlugin .

int FbcSpeciesPlugin::setCharge ( int  charge)
virtual

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

Returns
integer value indicating success/failure of the function. The only possible value returned by this function is:
int FbcSpeciesPlugin::setChemicalFormula ( const std::string &  chemicalFormula)
virtual

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

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

Returns
integer value indicating success/failure of the function. The only possible value returned by this function is:
int SBasePlugin::setElementNamespace ( const std::string &  uri)
inherited

Sets the XML namespace to which this element belongs to.

For example, all elements that belong to SBML Level 3 Version 1 Core must set the namespace to "http://www.sbml.org/sbml/level3/version1/core"; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must set the namespace to "http://www.sbml.org/sbml/level3/version1/layout/version1/"

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
int FbcSpeciesPlugin::unsetCharge ( )
virtual

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

Returns
integer value indicating success/failure of the function. The only possible value returned by this function is:
int FbcSpeciesPlugin::unsetChemicalFormula ( )
virtual

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

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