DistribExtension.h File Reference

Definition of DistribExtension. More...

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Classes
class	DistribExtension

Macros
#define	DISTRIB_CREATE_NS(variable, sbmlns)   EXTENSION_CREATE_NS(DistribPkgNamespaces, variable, sbmlns);

Typedefs
typedef SBMLExtensionNamespaces< DistribExtension >	DistribPkgNamespaces
	Required typedef definitions. More...

Enumerations
enum	SBMLDistribTypeCode_t {   SBML_DISTRIB_UNCERTPARAMETER = 1500 ,   SBML_DISTRIB_UNCERTAINTY = 1501 ,   SBML_DISTRIB_UNCERTSTATISTICSPAN = 1502 ,   SBML_DISTRIB_DISTRIBBASE = 1503 }
	SBMLDistribTypeCode_t Enumeration of possible types in the libSBML “distrib” package implementation. More...
enum	UncertType_t {   DISTRIB_UNCERTTYPE_DISTRIBUTION ,   DISTRIB_UNCERTTYPE_EXTERNALPARAMETER ,   DISTRIB_UNCERTTYPE_COEFFIENTOFVARIATION ,   DISTRIB_UNCERTTYPE_KURTOSIS ,   DISTRIB_UNCERTTYPE_MEAN ,   DISTRIB_UNCERTTYPE_MEDIAN ,   DISTRIB_UNCERTTYPE_MODE ,   DISTRIB_UNCERTTYPE_SAMPLESIZE ,   DISTRIB_UNCERTTYPE_SKEWNESS ,   DISTRIB_UNCERTTYPE_STANDARDDEVIATION ,   DISTRIB_UNCERTTYPE_STANDARDERROR ,   DISTRIB_UNCERTTYPE_VARIANCE ,   DISTRIB_UNCERTTYPE_CONFIDENCEINTERVAL ,   DISTRIB_UNCERTTYPE_CREDIBLEINTERVAL ,   DISTRIB_UNCERTTYPE_INTERQUARTILERANGE ,   DISTRIB_UNCERTTYPE_RANGE ,   DISTRIB_UNCERTTYPE_INVALID }
	Enumeration of values permitted as the value of the "uncerttype" attribute on Distrib objects. More...

Functions
UncertType_t	UncertType_fromString (const char *code)
	Returns the UncertType_t enumeration corresponding to the given string or DISTRIB_UNCERTTYPE_INVALID if there is no such match. More...
int	UncertType_isValid (UncertType_t ut)
	Predicate returning 1 (true) or 0 (false) depending on whether the given UncertType_t is valid. More...
int	UncertType_isValidString (const char *code)
	Predicate returning 1 (true) or 0 (false) depending on whether the given string is a valid UncertType_t. More...
const char *	UncertType_toString (UncertType_t ut)
	Returns the string version of the provided UncertType_t enumeration. More...

Detailed Description

Definition of DistribExtension.

Author

SBMLTeam

Macro Definition Documentation

DISTRIB_CREATE_NS

#define DISTRIB_CREATE_NS	(		variable,
			sbmlns
	)		EXTENSION_CREATE_NS(DistribPkgNamespaces, variable, sbmlns);

Typedef Documentation

DistribPkgNamespaces

typedef SBMLExtensionNamespaces<DistribExtension> DistribPkgNamespaces

Required typedef definitions.

DistribPkgNamespace is derived from SBMLNamespaces class and used when creating an object of SBase derived classes defined in the distrib package

SBMLExtensionNamespaces<DistribExtension> must be instantiated in DistribExtension.cpp for DLL

Enumeration Type Documentation

SBMLDistribTypeCode_t

enum SBMLDistribTypeCode_t

SBMLDistribTypeCode_t Enumeration of possible types in the libSBML “distrib” 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_DISTRIB_UNCERTPARAMETER	UncertParameter
SBML_DISTRIB_UNCERTAINTY	Uncertainty
SBML_DISTRIB_UNCERTSTATISTICSPAN	UncertSpan
SBML_DISTRIB_DISTRIBBASE	DistribBase

UncertType_t

enum UncertType_t

Enumeration of values permitted as the value of the "uncerttype" attribute on Distrib objects.

See also

Distrib::getUncerttype()

Distrib::setUncerttype()

Enumerator
DISTRIB_UNCERTTYPE_DISTRIBUTION	The distrib uncerttype is "distribution".
DISTRIB_UNCERTTYPE_EXTERNALPARAMETER	The distrib uncerttype is "externalParameter".
DISTRIB_UNCERTTYPE_COEFFIENTOFVARIATION	The distrib uncerttype is "coeffientOfVariation".
DISTRIB_UNCERTTYPE_KURTOSIS	The distrib uncerttype is "kurtosis".
DISTRIB_UNCERTTYPE_MEAN	The distrib uncerttype is "mean".
DISTRIB_UNCERTTYPE_MEDIAN	The distrib uncerttype is "median".
DISTRIB_UNCERTTYPE_MODE	The distrib uncerttype is "mode".
DISTRIB_UNCERTTYPE_SAMPLESIZE	The distrib uncerttype is "sampleSize".
DISTRIB_UNCERTTYPE_SKEWNESS	The distrib uncerttype is "skewness".
DISTRIB_UNCERTTYPE_STANDARDDEVIATION	The distrib uncerttype is "standardDeviation".
DISTRIB_UNCERTTYPE_STANDARDERROR	The distrib uncerttype is "standardError".
DISTRIB_UNCERTTYPE_VARIANCE	The distrib uncerttype is "variance".
DISTRIB_UNCERTTYPE_CONFIDENCEINTERVAL	The distrib uncerttype is "confidenceInterval".
DISTRIB_UNCERTTYPE_CREDIBLEINTERVAL	The distrib uncerttype is "credibleInterval".
DISTRIB_UNCERTTYPE_INTERQUARTILERANGE	The distrib uncerttype is "interquartileRange".
DISTRIB_UNCERTTYPE_RANGE	The distrib uncerttype is "range".
DISTRIB_UNCERTTYPE_INVALID	Invalid UncertType value.

Function Documentation

UncertType_fromString()

UncertType_t UncertType_fromString

(

const char *

code

)

Returns the UncertType_t enumeration corresponding to the given string or DISTRIB_UNCERTTYPE_INVALID if there is no such match.

Parameters

code	the string to convert to a UncertType_t.

Returns

the corresponding UncertType_t or DISTRIB_UNCERTTYPE_INVALID if no match is found.

Note

The matching is case-sensitive: "distribution" will return DISTRIB_UNCERTTYPE_DISTRIBUTION, but "Distribution" will return DISTRIB_UNCERTTYPE_INVALID.

UncertType_isValid()

int UncertType_isValid

(

UncertType_t

ut

)

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

Parameters

ut	the UncertType_t enumeration to query.

Returns

1 (true) if the UncertType_t is DISTRIB_UNCERTTYPE_DISTRIBUTION, DISTRIB_UNCERTTYPE_EXTERNALPARAMETER, DISTRIB_UNCERTTYPE_COEFFIENTOFVARIATION, DISTRIB_UNCERTTYPE_KURTOSIS, DISTRIB_UNCERTTYPE_MEAN, DISTRIB_UNCERTTYPE_MEDIAN, DISTRIB_UNCERTTYPE_MODE, DISTRIB_UNCERTTYPE_SAMPLESIZE, DISTRIB_UNCERTTYPE_SKEWNESS, DISTRIB_UNCERTTYPE_STANDARDDEVIATION, DISTRIB_UNCERTTYPE_STANDARDERROR, DISTRIB_UNCERTTYPE_VARIANCE, DISTRIB_UNCERTTYPE_CONFIDENCEINTERVAL, DISTRIB_UNCERTTYPE_CREDIBLEINTERVAL, DISTRIB_UNCERTTYPE_INTERQUARTILERANGE, or DISTRIB_UNCERTTYPE_RANGE; 0 (false) otherwise (including DISTRIB_UNCERTTYPE_INVALID).

UncertType_isValidString()

int UncertType_isValidString

(

const char *

code

)

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

Parameters

code	the string to query.

Returns

1 (true) if the string is "distribution", "externalParameter", "coeffientOfVariation", "kurtosis", "mean", "median", "mode", "sampleSize", "skewness", "standardDeviation", "standardError", "variance", "confidenceInterval", "credibleInterval", "interquartileRange", "range", or "invalid UncertType value"; 0 (false) otherwise.

Note

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

UncertType_toString()

const char* UncertType_toString

(

UncertType_t

ut

)

Returns the string version of the provided UncertType_t enumeration.

Parameters

ut	the UncertType_t enumeration value to convert.

Returns

A string corresponding to the given type: "distribution", "externalParameter", "coeffientOfVariation", "kurtosis", "mean", "median", "mode", "sampleSize", "skewness", "standardDeviation", "standardError", "variance", "confidenceInterval", "credibleInterval", "interquartileRange", "range", "invalid UncertType value", or NULL if the value is DISTRIB_UNCERTTYPE_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.