#include <CODEExporterBM.h>

Inheritance diagram for CODEExporterBM:

Public Member Functions
	CODEExporterBM ()

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

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

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

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

virtual bool	exportSingleObject (std::ostringstream &which, const std::string &name, const std::string &expression, const std::string &comments)

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

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

virtual bool	exportTitleData (const CDataModel *pDataModel, std::ostream &os)

virtual std::string	exportTitleString (const size_t tmp)

virtual std::string	getDisplayExpressionString (CExpression *tmp)

virtual std::string	getDisplayFunctionString (CFunction *func)

virtual std::string	KineticFunction2ODEmember (const CReaction *reac)

std::string	setConcentrationName (const std::string &objName)

std::string	setODEName (const std::string &objName)

virtual void	setReservedNames ()

std::string	testName (const std::string &name)

virtual std::string	translateObjectName (const std::string &realName)

virtual std::string	translateTimeVariableName ()

Public Member Functions inherited from CODEExporter
void	assembleSubTreeForMassAction (CEvaluationNode newNode, CEvaluationNode child1, CEvaluationNode *child2)

	CODEExporter ()

virtual bool	exportClosingData (const CModel *copasiModel, std::ostream &os)

virtual std::string	exportClosingString (const size_t tmp)

bool	exportCompartments (const CModel *copasiModel)

std::string	exportExpression (const CExpression pExpression, const CDataModel pDataModel)

virtual bool	exportKineticFunction (const CReaction *reac)

virtual bool	exportKineticFunctionGroup (const CModel *copasiModel)

virtual bool	exportMetabolites (const CModel *copasiModel)

virtual bool	exportMetabolitesConcentrations (const CModel *copasiModel)

bool	exportModelEntityExpression (const CDataObject obj, const CDataModel pDataModel)

bool	exportModelValues (const CModel *copasiModel)

bool	exportModelValuesExpressions (const CModel *copasiModel)

virtual std::string	exportNumber (double number)

void	exportObjectNodesFromModel (const CDataModel *pDataModel)

bool	exportODEs (const CModel *copasiModel)

bool	exportReacParamsAndFuncs (const CModel *copasiModel)

void	exportSimulatedObject (const CDataObject obj, const CDataModel pDataModel)

bool	exportSingleFunction (CEvaluationNode pNode, const CReaction reac, size_t &index)

bool	exportSingleFunction (CEvaluationNode *pNode, const std::string &key, size_t &index)

bool	exportSingleFunction (const CFunction *func)

virtual bool	exportSingleFunction (const CFunction *func, std::set< std::string > &isExported)

virtual bool	exportTitleData (const CModel *copasiModel, std::ostream &os)

bool	exportToStream (const CDataModel *pDataModel, std::ostream &os)

void	findFunctionsCalls (const CEvaluationNode *pNode)

virtual std::string	getSingleLineComment ()

virtual bool	isEmptyString (std::string &str)

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

void	modifyTreeForMassAction (CFunction *tmpfunc)

virtual bool	preprocess (const CModel *copasiModel)

virtual	~CODEExporter ()

Public Attributes
std::map< std::string, size_t >	Frequancy

std::set< std::string >	NameSet

Public Attributes inherited from CODEExporter
std::ostringstream	assignment

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

std::ostringstream	fixed

std::ostringstream	functions

std::ostringstream	headers

std::ostringstream	initial

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

std::ostringstream	ode

std::string	timeKey

Additional Inherited Members
Public Types inherited from CODEExporter
enum	Object { INITIAL = 0 , FIXED , ASSIGNMENT , HEADERS , FUNCTIONS , ODEs }

Protected Attributes inherited from CODEExporter
std::set< std::string >	mExportedFunctions

Constructor & Destructor Documentation

◆ CODEExporterBM()

CODEExporterBM::CODEExporterBM ( )

Constructor for the exporter.

Member Function Documentation

◆ exportSingleCompartment()

bool CODEExporterBM::exportSingleCompartment	(	const CCompartment *	comp,
		std::string &	expression,
		std::string &	comments
	)

virtual

Reimplemented from CODEExporter.

References CModelEntity::ASSIGNMENT, CODEExporter::assignment, exportSingleObject(), CModelEntity::FIXED, CODEExporter::fixed, CModelEntity::getKey(), CModelEntity::getStatus(), CODEExporter::initial, CODEExporter::NameMap, and CModelEntity::ODE.

◆ exportSingleMetabolite()

bool CODEExporterBM::exportSingleMetabolite	(	const CMetab *	metab,
		std::string &	expression,
		std::string &	comments
	)

virtual

Reimplemented from CODEExporter.

References CModelEntity::ASSIGNMENT, CODEExporter::assignment, exportSingleObject(), CModelEntity::FIXED, CODEExporter::fixed, CModelEntity::getKey(), CModelEntity::getStatus(), CODEExporter::initial, CMetab::isDependent(), CODEExporter::NameMap, CModelEntity::ODE, and CModelEntity::REACTIONS.

◆ exportSingleModelEntity()

bool CODEExporterBM::exportSingleModelEntity	(	const CModelEntity *	tmp,
		std::string &	expression,
		std::string &	comments
	)

virtual

Reimplemented from CODEExporter.

References CModelEntity::ASSIGNMENT, CODEExporter::assignment, exportSingleObject(), CModelEntity::FIXED, CODEExporter::fixed, CModelEntity::getKey(), CModelEntity::getStatus(), CODEExporter::initial, CODEExporter::NameMap, and CModelEntity::ODE.

◆ exportSingleModVal()

bool CODEExporterBM::exportSingleModVal	(	const CModelValue *	modval,
		std::string &	expression,
		std::string &	comments
	)

virtual

Reimplemented from CODEExporter.

References CModelEntity::ASSIGNMENT, CODEExporter::assignment, exportSingleObject(), CModelEntity::FIXED, CODEExporter::fixed, CModelEntity::getKey(), CModelEntity::getStatus(), CODEExporter::initial, CODEExporter::NameMap, and CModelEntity::ODE.

◆ exportSingleObject()

bool CODEExporterBM::exportSingleObject	(	std::ostringstream &	which,
		const std::string &	name,
		const std::string &	expression,
		const std::string &	comments
	)

virtual

Reimplemented from CODEExporter.

Referenced by exportSingleCompartment(), exportSingleMetabolite(), exportSingleModelEntity(), exportSingleModVal(), exportSingleODE(), and exportSingleParameter().

◆ exportSingleODE()

bool CODEExporterBM::exportSingleODE	(	const CModelEntity *	mentity,
		std::string &	equation,
		std::string &	comments
	)

virtual

Reimplemented from CODEExporter.

References exportSingleObject(), CModelEntity::getKey(), CODEExporter::NameMap, and CODEExporter::ode.

◆ exportSingleParameter()

bool CODEExporterBM::exportSingleParameter	(	const CCopasiParameter *	param,
		std::string &	expression,
		std::string &	comments
	)

virtual

Reimplemented from CODEExporter.

References exportSingleObject(), CODEExporter::fixed, CCopasiParameter::getKey(), and CODEExporter::NameMap.

◆ exportTitleData()

bool CODEExporterBM::exportTitleData	(	const CDataModel *	pDataModel,
		std::ostream &	os
	)

virtual

References CTrajectoryProblem::getDuration(), CCopasiTask::getProblem(), and CTrajectoryProblem::getStepSize().

◆ exportTitleString()

std::string CODEExporterBM::exportTitleString ( const size_t tmp )

virtual

Reimplemented from CODEExporter.

References CODEExporter::ASSIGNMENT, CODEExporter::FIXED, CODEExporter::FUNCTIONS, CODEExporter::HEADERS, CODEExporter::INITIAL, and CODEExporter::ODEs.

◆ getDisplayExpressionString()

std::string CODEExporterBM::getDisplayExpressionString ( CExpression * tmp )

virtual

Reimplemented from CODEExporter.

References CEvaluationNode::buildBerkeleyMadonnaString(), and CEvaluationTree::getRoot().

◆ getDisplayFunctionString()

std::string CODEExporterBM::getDisplayFunctionString ( CFunction * func )

virtual

Reimplemented from CODEExporter.

References CEvaluationNode::buildBerkeleyMadonnaString(), and CEvaluationTree::getRoot().

◆ KineticFunction2ODEmember()

std::string CODEExporterBM::KineticFunction2ODEmember ( const CReaction * reac )

virtual

Reimplemented from CODEExporter.

References CReaction::getKey(), and CODEExporter::NameMap.

◆ setConcentrationName()

std::string CODEExporterBM::setConcentrationName ( const std::string & objName )

virtual

Reimplemented from CODEExporter.

◆ setODEName()

std::string CODEExporterBM::setODEName ( const std::string & objName )

virtual

Reimplemented from CODEExporter.

◆ setReservedNames()

void CODEExporterBM::setReservedNames ( )

virtual

Reimplemented from CODEExporter.

◆ testName()

std::string CODEExporterBM::testName ( const std::string & name )

This method tests whether the given Berkeley Madonna name already assigned, put the new name (in cappital letters: all names can be upper or lower case) in the set of assigned names or modify the name

References Frequancy, and NameSet.

Referenced by translateObjectName().

◆ translateObjectName()

std::string CODEExporterBM::translateObjectName ( const std::string & realName )

virtual

This method adapt a Copasi name for Berkeley Madonna syntax: Names can not start with a number. Any other combination of letters and numbers is valid as is the underscore.

Reimplemented from CODEExporter.

References testName().

◆ translateTimeVariableName()

std::string CODEExporterBM::translateTimeVariableName ( )

virtual

Reimplemented from CODEExporter.

Member Data Documentation

◆ Frequancy

std::map< std::string, size_t > CODEExporterBM::Frequancy

Referenced by testName().

◆ NameSet

std::set<std::string> CODEExporterBM::NameSet

Referenced by testName().

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

Public Member Functions

Public Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ CODEExporterBM()

Member Function Documentation

◆ exportSingleCompartment()

◆ exportSingleMetabolite()

◆ exportSingleModelEntity()

◆ exportSingleModVal()

◆ exportSingleObject()

◆ exportSingleODE()

◆ exportSingleParameter()

◆ exportTitleData()

◆ exportTitleString()

◆ getDisplayExpressionString()

◆ getDisplayFunctionString()

◆ KineticFunction2ODEmember()

◆ setConcentrationName()

◆ setODEName()

◆ setReservedNames()

◆ testName()

◆ translateObjectName()

◆ translateTimeVariableName()

Member Data Documentation

◆ Frequancy

◆ NameSet