CODEExporter Class Reference

#include <CODEExporter.h>

Inheritance diagram for CODEExporter:

List of all members.

Public Types
enum	Object {   INITIAL = 0, FIXED, ASSIGNMENT, HEADERS,   FUNCTIONS, ODEs }
Public Member Functions
	CODEExporter ()
virtual	~CODEExporter ()
bool	exportMathModel (const CCopasiDataModel *pDataModel, std::string mmasciiFilename, std::string Filter, bool overwriteFile)
virtual bool	preprocess (const CModel *copasiModel)
virtual bool	exportTitleData (const CModel *copasiModel, std::ofstream &outFile)
virtual bool	exportMetabolites (const CModel *copasiModel)
virtual bool	exportMetabolitesConcentrations (const CModel *copasiModel)
bool	exportCompartments (const CModel *copasiModel)
bool	exportModelValues (const CModel *copasiModel)
void	exportObjectNodesFromModel (const CCopasiDataModel *pDataModel)
CCopasiObject *	findObjectFromRefresh (const CCopasiObject *tmp, const Refresh *ref)
void	exportSimulatedObject (CCopasiObject *obj, const CCopasiDataModel *pDataModel)
bool	exportModelEntityExpression (CCopasiObject *obj, const CCopasiDataModel *pDataModel)
std::string	isModelEntityExpressionODEExporterCompatible (CModelEntity *tmp, const CExpression *pExpression, const CCopasiDataModel *pDataModel)
std::string	exportExpression (const CExpression *pExpression, const CCopasiDataModel *pDataModel)
virtual bool	exportSingleModelEntity (const CModelEntity *tmp, std::string &expression, std::string &comments)
virtual std::string	getDisplayExpressionString (CExpression *tmp)
bool	exportReacParamsAndFuncs (const CModel *copasiModel)
bool	exportODEs (const CModel *copasiModel)
virtual bool	exportClosingData (const CModel *copasiModel, std::ofstream &outFile)
virtual void	setReservedNames ()
virtual std::string	translateTimeVariableName ()
virtual std::string	translateObjectName (const std::string &realName)
virtual std::string	setConcentrationName (const std::string &objName)
virtual std::string	setODEName (const std::string &objName)
virtual bool	exportSingleObject (std::ostringstream &which, std::string &name, std::string &expression, std::string &comments)
virtual bool	exportSingleMetabolite (const CMetab *metab, std::string &expression, std::string &comments)
virtual bool	exportSingleCompartment (const CCompartment *comp, std::string &expression, std::string &comments)
virtual bool	exportSingleModVal (const CModelValue *modval, std::string &expression, std::string &comments)
virtual bool	exportSingleParameter (const CCopasiParameter *param, std::string &expression, std::string &comments)
virtual std::string	getDisplayFunctionString (CFunction *func)
bool	exportSingleFunction (CEvaluationNode *pNode, const CReaction *reac, unsigned C_INT32 &index)
virtual bool	exportKineticFunction (CReaction *reac)
virtual bool	exportSingleODE (const CModelEntity *mentity, std::string &equation, std::string &comments)
virtual bool	exportKineticFunctionGroup (const CModel *copasiModel)
virtual std::string	KineticFunction2ODEmember (const CReaction *reac)
virtual std::string	exportTitleString (const unsigned C_INT32 tmp)
virtual std::string	exportClosingString (const unsigned C_INT32 tmp)
virtual bool	isEmptyString (std::string &str)
void	modifyTreeForMassAction (CFunction *tmpfunc)
void	assembleSubTreeForMassAction (CEvaluationNode *newNode, CEvaluationNode *child1, CEvaluationNode *child2)
Public Attributes
std::map< std::string, std::string >	NameMap
std::string	timeKey
std::map< std::string, std::string >	equations
std::ostringstream	initial
std::ostringstream	fixed
std::ostringstream	assignment
std::ostringstream	functions
std::ostringstream	headers
std::ostringstream	ode

---

Member Enumeration Documentation

enum CODEExporter::Object

Enumerator:

INITIAL
FIXED
ASSIGNMENT
HEADERS
FUNCTIONS
ODEs

---

Constructor & Destructor Documentation

CODEExporter::CODEExporter

(

)

Constructor for the exporter.

CODEExporter::~CODEExporter

(

)

[virtual]

Destructor for the exporter.

---

Member Function Documentation

void CODEExporter::assembleSubTreeForMassAction	(	CEvaluationNode *	newNode,
		CEvaluationNode *	child1,
		CEvaluationNode *	child2
	)

This method assembles an expression sub tree for some internal call of Mass Action. The sub tree has to be included in the tree of corresponding root kinetic function in order to export this function whithout the user defined internall Mass Action calls

bool CODEExporter::exportClosingData	(	const CModel *	copasiModel,
		std::ofstream &	outFile
	)		[virtual]

Reimplemented in CODEExporterXPPAUT.

std::string CODEExporter::exportClosingString

(

const unsigned C_INT32

tmp

)

[virtual]

Reimplemented in CODEExporterC.

bool CODEExporter::exportCompartments

(

const CModel *

copasiModel

)

std::string CODEExporter::exportExpression	(	const CExpression *	pExpression,
		const CCopasiDataModel *	pDataModel
	)

bool CODEExporter::exportKineticFunction

(

CReaction *

reac

)

[virtual]

Reimplemented in CODEExporterC.

bool CODEExporter::exportKineticFunctionGroup

(

const CModel *

copasiModel

)

[virtual]

Reimplemented in CODEExporterC.

bool CODEExporter::exportMathModel	(	const CCopasiDataModel *	pDataModel,
		std::string	mmasciiFilename,
		std::string	Filter,
		bool	overwriteFile
	)

bool CODEExporter::exportMetabolites

(

const CModel *

copasiModel

)

[virtual]

bool CODEExporter::exportMetabolitesConcentrations

(

const CModel *

copasiModel

)

[virtual]

bool CODEExporter::exportModelEntityExpression	(	CCopasiObject *	obj,
		const CCopasiDataModel *	pDataModel
	)

bool CODEExporter::exportModelValues

(

const CModel *

copasiModel

)

void CODEExporter::exportObjectNodesFromModel

(

const CCopasiDataModel *

pDataModel

)

bool CODEExporter::exportODEs

(

const CModel *

copasiModel

)

bool CODEExporter::exportReacParamsAndFuncs

(

const CModel *

copasiModel

)

void CODEExporter::exportSimulatedObject	(	CCopasiObject *	obj,
		const CCopasiDataModel *	pDataModel
	)

bool CODEExporter::exportSingleCompartment	(	const CCompartment *	comp,
		std::string &	expression,
		std::string &	comments
	)		[virtual]

Reimplemented in CODEExporterC, CODEExporterXPPAUT, and CODEExporterBM.

bool CODEExporter::exportSingleFunction	(	CEvaluationNode *	pNode,
		const CReaction *	reac,
		unsigned C_INT32 &	index
	)

bool CODEExporter::exportSingleMetabolite	(	const CMetab *	metab,
		std::string &	expression,
		std::string &	comments
	)		[virtual]

Reimplemented in CODEExporterC, CODEExporterXPPAUT, and CODEExporterBM.

bool CODEExporter::exportSingleModelEntity	(	const CModelEntity *	tmp,
		std::string &	expression,
		std::string &	comments
	)		[virtual]

Reimplemented in CODEExporterC, CODEExporterXPPAUT, and CODEExporterBM.

bool CODEExporter::exportSingleModVal	(	const CModelValue *	modval,
		std::string &	expression,
		std::string &	comments
	)		[virtual]

Reimplemented in CODEExporterC, CODEExporterXPPAUT, and CODEExporterBM.

bool CODEExporter::exportSingleObject	(	std::ostringstream &	which,
		std::string &	name,
		std::string &	expression,
		std::string &	comments
	)		[virtual]

Reimplemented in CODEExporterC, CODEExporterXPPAUT, and CODEExporterBM.

bool CODEExporter::exportSingleODE	(	const CModelEntity *	mentity,
		std::string &	equation,
		std::string &	comments
	)		[virtual]

Reimplemented in CODEExporterC, CODEExporterXPPAUT, and CODEExporterBM.

bool CODEExporter::exportSingleParameter	(	const CCopasiParameter *	param,
		std::string &	expression,
		std::string &	comments
	)		[virtual]

Reimplemented in CODEExporterC, CODEExporterXPPAUT, and CODEExporterBM.

bool CODEExporter::exportTitleData	(	const CModel *	copasiModel,
		std::ofstream &	outFile
	)		[virtual]

Reimplemented in CODEExporterC.

std::string CODEExporter::exportTitleString

(

const unsigned C_INT32

tmp

)

[virtual]

Reimplemented in CODEExporterC, CODEExporterXPPAUT, and CODEExporterBM.

CCopasiObject * CODEExporter::findObjectFromRefresh	(	const CCopasiObject *	tmp,
		const Refresh *	ref
	)

std::string CODEExporter::getDisplayExpressionString

(

CExpression *

tmp

)

[virtual]

Reimplemented in CODEExporterC, CODEExporterXPPAUT, and CODEExporterBM.

std::string CODEExporter::getDisplayFunctionString

(

CFunction *

func

)

[virtual]

Reimplemented in CODEExporterXPPAUT, and CODEExporterBM.

bool CODEExporter::isEmptyString

(

std::string &

str

)

[virtual]

This method tests if a string consists only of whitespace characters

std::string CODEExporter::isModelEntityExpressionODEExporterCompatible	(	CModelEntity *	tmp,
		const CExpression *	pExpression,
		const CCopasiDataModel *	pDataModel
	)

std::string CODEExporter::KineticFunction2ODEmember

(

const CReaction *

reac

)

[virtual]

Reimplemented in CODEExporterC, CODEExporterXPPAUT, and CODEExporterBM.

void CODEExporter::modifyTreeForMassAction

(

CFunction *

tmpfunc

)

This method modifies the export tree of the function for internal calls of Mass Action

bool CODEExporter::preprocess

(

const CModel *

copasiModel

)

[virtual]

Reimplemented in CODEExporterC.

std::string CODEExporter::setConcentrationName

(

const std::string &

objName

)

[virtual]

Reimplemented in CODEExporterBM, and CODEExporterXPPAUT.

std::string CODEExporter::setODEName

(

const std::string &

objName

)

[virtual]

Reimplemented in CODEExporterC, CODEExporterXPPAUT, and CODEExporterBM.

void CODEExporter::setReservedNames

(

)

[virtual]

Reimplemented in CODEExporterC, CODEExporterXPPAUT, and CODEExporterBM.

std::string CODEExporter::translateObjectName

(

const std::string &

realName

)

[virtual]

Reimplemented in CODEExporterC, CODEExporterXPPAUT, and CODEExporterBM.

std::string CODEExporter::translateTimeVariableName

(

)

[virtual]

Reimplemented in CODEExporterC, CODEExporterXPPAUT, and CODEExporterBM.

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Member Data Documentation

std::ostringstream CODEExporter::assignment

std::map< std::string, std::string > CODEExporter::equations

std::ostringstream CODEExporter::fixed

std::ostringstream CODEExporter::functions

std::ostringstream CODEExporter::headers

std::ostringstream CODEExporter::initial

std::map< std::string, std::string > CODEExporter::NameMap

std::ostringstream CODEExporter::ode

std::string CODEExporter::timeKey

---

The documentation for this class was generated from the following files:

• copasi/tss/CODEExporter.h
• copasi/tss/CODEExporter.cpp