QualExtension.h File Reference

Definition of QualExtension, the core module of qual package. More...

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Classes
class	QualExtension
	qual Base extension class for the package. More...

Macros
#define	QUAL_CREATE_NS(variable, sbmlns)   EXTENSION_CREATE_NS(QualPkgNamespaces,variable,sbmlns);

Typedefs
typedef SBMLExtensionNamespaces< QualExtension >	QualPkgNamespaces

Enumerations
enum	SBMLQualTypeCode_t {   SBML_QUAL_QUALITATIVE_SPECIES = 1100,   SBML_QUAL_TRANSITION = 1101,   SBML_QUAL_INPUT = 1102,   SBML_QUAL_OUTPUT = 1103,   SBML_QUAL_FUNCTION_TERM = 1104,   SBML_QUAL_DEFAULT_TERM = 1105 }
	SBMLFbcTypeCode_t Enumeration of possible types in the libSBML “qual” package implementation. More...

Detailed Description

Definition of QualExtension, the core module of qual package.

Author

Akiya Jouraku

Macro Definition Documentation

#define QUAL_CREATE_NS	(		variable,
			sbmlns
	)		EXTENSION_CREATE_NS(QualPkgNamespaces,variable,sbmlns);

Typedef Documentation

typedef SBMLExtensionNamespaces<QualExtension> QualPkgNamespaces

Enumeration Type Documentation

enum SBMLQualTypeCode_t

SBMLFbcTypeCode_t Enumeration of possible types in the libSBML “qual” 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_QUAL_QUALITATIVE_SPECIES	QualitativeSpecies
SBML_QUAL_TRANSITION	Transition
SBML_QUAL_INPUT	Input
SBML_QUAL_OUTPUT	Output
SBML_QUAL_FUNCTION_TERM	FunctionTerm
SBML_QUAL_DEFAULT_TERM	DefaultTerm