FbcExtension.h File Reference

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

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Classes
class	FbcExtension

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	FbcVariableType_t {   FBC_VARIABLE_TYPE_LINEAR ,   FBC_VARIABLE_TYPE_QUADRATIC ,   FBC_VARIABLE_TYPE_INVALID }
	Enumeration of values permitted as the value of the "fbcvariabletype" attribute on Fbc objects. More...
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 ,   SBML_FBC_USERDEFINEDCONSTRAINTCOMPONENT = 811 ,   SBML_FBC_USERDEFINEDCONSTRAINT = 812 ,   SBML_FBC_KEYVALUEPAIR = 813 }
	SBMLFbcTypeCode_t Enumeration of possible types in the libSBML “fbc” package implementation. More...

Functions
FbcVariableType_t	FbcVariableType_fromString (const char *code)
	Returns the FbcVariableType_t enumeration corresponding to the given string or FBC_VARIABLE_TYPE_INVALID if there is no such match. More...
int	FbcVariableType_isValid (FbcVariableType_t fvt)
	Predicate returning 1 (true) or 0 (false) depending on whether the given FbcVariableType_t is valid. More...
int	FbcVariableType_isValidString (const char *code)
	Predicate returning 1 (true) or 0 (false) depending on whether the given string is a valid FbcVariableType_t. More...
const char *	FbcVariableType_toString (FbcVariableType_t fvt)
	Returns the string version of the provided FbcVariableType_t enumeration. More...

Detailed Description

Definition of FbcExtension, the core module of fbc package.

Author

Frank T. Bergmann

Macro Definition Documentation

FBC_CREATE_NS

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

FBC_CREATE_NS_WITH_VERSION

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

Typedef Documentation

FbcPkgNamespaces

typedef SBMLExtensionNamespaces<FbcExtension> FbcPkgNamespaces

Enumeration Type Documentation

FbcVariableType_t

enum FbcVariableType_t

Enumeration of values permitted as the value of the "fbcvariabletype" attribute on Fbc objects.

See also

Fbc::getFbcvariabletype()

Fbc::setFbcvariabletype()

Enumerator
FBC_VARIABLE_TYPE_LINEAR	The fbc fbcvariabletype is "linear".
FBC_VARIABLE_TYPE_QUADRATIC	The fbc fbcvariabletype is "quadratic".
FBC_VARIABLE_TYPE_INVALID	Invalid FbcVariableType value.

SBMLFbcTypeCode_t

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
SBML_FBC_USERDEFINEDCONSTRAINTCOMPONENT	UserDefinedConstraintComponent
SBML_FBC_USERDEFINEDCONSTRAINT	UserDefinedConstraint
SBML_FBC_KEYVALUEPAIR	KeyValuePair

Function Documentation

FbcVariableType_fromString()

FbcVariableType_t FbcVariableType_fromString

(

const char *

code

)

Returns the FbcVariableType_t enumeration corresponding to the given string or FBC_VARIABLE_TYPE_INVALID if there is no such match.

Parameters

code	the string to convert to a FbcVariableType_t.

Returns

the corresponding FbcVariableType_t or FBC_VARIABLE_TYPE_INVALID if no match is found.

Note

The matching is case-sensitive: "linear" will return FBC_VARIABLE_TYPE_LINEAR, but "Linear" will return FBC_VARIABLE_TYPE_INVALID.

FbcVariableType_isValid()

int FbcVariableType_isValid

(

FbcVariableType_t

fvt

)

Predicate returning 1 (true) or 0 (false) depending on whether the given FbcVariableType_t is valid.

Parameters

fvt	the FbcVariableType_t enumeration to query.

Returns

1 (true) if the FbcVariableType_t is FBC_VARIABLE_TYPE_LINEAR, or FBC_VARIABLE_TYPE_QUADRATIC; 0 (false) otherwise (including FBC_VARIABLE_TYPE_INVALID).

FbcVariableType_isValidString()

int FbcVariableType_isValidString

(

const char *

code

)

Predicate returning 1 (true) or 0 (false) depending on whether the given string is a valid FbcVariableType_t.

Parameters

code	the string to query.

Returns

1 (true) if the string is "linear", "quadratic", or "invalid FbcVariableType value"; 0 (false) otherwise.

Note

The matching is case-sensitive: "linear" will return 1 (true), but "Linear" will return 0 (false).

FbcVariableType_toString()

const char* FbcVariableType_toString

(

FbcVariableType_t

fvt

)

Returns the string version of the provided FbcVariableType_t enumeration.

Parameters

fvt	the FbcVariableType_t enumeration value to convert.

Returns

A string corresponding to the given type: "linear", "quadratic", "invalid FbcVariableType value", or NULL if the value is FBC_VARIABLE_TYPE_INVALID or another invalid enumeration value.

Note

The string returned by this function is a pointer to a string literal defined in the libSBML library, and may not be modified or deleted.