FbcExtension.h File Reference

Definition of FbcExtension, the core module of fbc package. More...

Include dependency graph for FbcExtension.h:

This graph shows which files directly or indirectly include this file:

Classes
class	FbcExtension
	fbc Base extension class for the “fbc” package. More...

Macros
#define	FBC_CREATE_NS(variable, sbmlns)   EXTENSION_CREATE_NS(FbcPkgNamespaces, variable, sbmlns);
#define	FBC_CREATE_NS_WITH_VERSION(variable, sbmlns, version)   EXTENSION_CREATE_NS_WITH_VERSION(FbcPkgNamespaces, variable, sbmlns, version);

Typedefs
typedef SBMLExtensionNamespaces< FbcExtension >	FbcPkgNamespaces

Enumerations
enum	SBMLFbcTypeCode_t {   SBML_FBC_V1ASSOCIATION = 800,   SBML_FBC_FLUXBOUND = 801,   SBML_FBC_FLUXOBJECTIVE = 802,   SBML_FBC_GENEASSOCIATION = 803,   SBML_FBC_OBJECTIVE = 804,   SBML_FBC_ASSOCIATION = 805,   SBML_FBC_GENEPRODUCTASSOCIATION = 806,   SBML_FBC_GENEPRODUCT = 807,   SBML_FBC_GENEPRODUCTREF = 808,   SBML_FBC_AND = 809,   SBML_FBC_OR = 810 }
	SBMLFbcTypeCode_t Enumeration of possible types in the libSBML “fbc” package implementation. More...

Detailed Description

Definition of FbcExtension, the core module of fbc package.

Author

Frank T. Bergmann

Macro Definition Documentation

#define FBC_CREATE_NS	(		variable,
			sbmlns
	)		EXTENSION_CREATE_NS(FbcPkgNamespaces, variable, sbmlns);

#define FBC_CREATE_NS_WITH_VERSION	(		variable,
			sbmlns,
			version
	)		EXTENSION_CREATE_NS_WITH_VERSION(FbcPkgNamespaces, variable, sbmlns, version);

Typedef Documentation

typedef SBMLExtensionNamespaces<FbcExtension> FbcPkgNamespaces

Enumeration Type Documentation

enum SBMLFbcTypeCode_t

SBMLFbcTypeCode_t Enumeration of possible types in the libSBML “fbc” package implementation.

LibSBML attaches an identifying code to every kind of SBML object. These are integer constants known as SBML type codes. The names of all the codes begin with the characters SBML_. The set of possible type codes for core elements is defined in the enumeration SBMLTypeCode_t, and in addition, libSBML plug-ins for SBML Level 3 packages define their own extra enumerations of type codes (e.g., SBMLLayoutTypeCode_t for the Level 3 Layout package). Note that different Level 3 package plug-ins may use overlapping type codes; to identify the package to which a given object belongs, call the SBase::getPackageName() method on the object.

The exception to this is lists: all SBML-style list elements have the type SBML_LIST_OF, regardless of what package they are from.

Here follow some additional general information about libSBML type codes:

• The codes are the possible return values (integers) for the following functions:
  • SBase::getTypeCode()
  • ListOf::getItemTypeCode()
  (Compatibility note: in libSBML 5, the type of return values of these functions changed from an enumeration to an integer for extensibility in the face of different programming languages.)

• Each package extension must define similar sets of values for each SBase subclass (e.g. SBMLLayoutTypeCode_t for the SBML Level 3 Layout extension, SBMLFbcTypeCode_t for the SBML Level 3 Flux Balance Constraints extension, etc.).

• The value of each package-specific type code can be duplicated between those of different packages. (This is necessary because the development of libSBML extensions for different SBML packages may be undertaken by different developers at different times; requiring the developers to coordinate their use of type codes would be nettlesome and probably doomed to failure.)

• To distinguish between the type codes of different packages, both the return value of SBase::getTypeCode() and SBase::getPackageName() must be checked. This is particularly important for functions that take an SBML type code as an argument, such as SBase::getAncestorOfType(), which by default assumes you are handing it a core type, and will return NULL if the value you give it is actually from a package.

The following example code illustrates the combined use of SBase::getPackageName() and SBase::getTypeCode():

void example (const SBase *sb)
{
  cons std::string pkgName = sb->getPackageName();
  if (pkgName == "core")
  {
    switch (sb->getTypeCode())
    {
      case SBML_MODEL:
         ....
         break;
      case SBML_REACTION:
         ....
    }
  }
  else if (pkgName == "layout")
  {
    switch (sb->getTypeCode())
    {
      case SBML_LAYOUT_LAYOUT:
         ....
         break;
      case SBML_LAYOUT_REACTIONGLYPH:
         ....
    }
  }
  ...
}

Enumerator
SBML_FBC_V1ASSOCIATION	Association (only used in Version 1; replaced in Version 2 with FbcAssociation)
SBML_FBC_FLUXBOUND	FluxBound
SBML_FBC_FLUXOBJECTIVE	FluxObjective
SBML_FBC_GENEASSOCIATION	GeneAssociation (only used in Version 1; replaced in Version 2 with GeneProductAssociation)
SBML_FBC_OBJECTIVE	Objective
SBML_FBC_ASSOCIATION	FbcAssociation
SBML_FBC_GENEPRODUCTASSOCIATION	GeneProductAssociation
SBML_FBC_GENEPRODUCT	GeneProduct
SBML_FBC_GENEPRODUCTREF	GeneProductRef
SBML_FBC_AND	FbcAnd
SBML_FBC_OR	FbcOr