COPASI API  4.40.278
Public Member Functions | Public Attributes | List of all members
CODEExporterC Class Reference

#include <CODEExporterC.h>

Inheritance diagram for CODEExporterC:
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Public Member Functions

 CODEExporterC ()
 
virtual std::string exportClosingString (const size_t tmp)
 
virtual bool exportKineticFunction (const CReaction *reac)
 
virtual bool exportKineticFunctionGroup (const CModel *copasiModel)
 
virtual std::string exportNumber (double number)
 
virtual bool exportSingleCompartment (const CCompartment *comp, std::string &expression, std::string &comments)
 
virtual bool exportSingleFunction (const CFunction *func, std::set< std::string > &isExported)
 
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 CModel *copasiModel, std::ostream &os)
 
virtual std::string exportTitleString (const size_t tmp)
 
virtual std::string getDisplayExpressionString (CExpression *tmp)
 
virtual std::string getSingleLineComment ()
 
virtual std::string KineticFunction2ODEmember (const CReaction *reac)
 
virtual bool preprocess (const CModel *copasiModel)
 
std::string setConcentrationName (const CModelEntity::Status &status, size_t n[], size_t dependent)
 
std::string setExportName (const CModelEntity::Status &status, size_t n[], size_t dependent)
 
void setExportNameOfFunction (const CEvaluationNode *pNode, std::set< std::string > &tmpset)
 
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)
 
bool exportCompartments (const CModel *copasiModel)
 
std::string exportExpression (const CExpression *pExpression, const CDataModel *pDataModel)
 
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)
 
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)
 
bool exportToStream (const CDataModel *pDataModel, std::ostream &os)
 
void findFunctionsCalls (const CEvaluationNode *pNode)
 
virtual std::string getDisplayFunctionString (CFunction *func)
 
virtual bool isEmptyString (std::string &str)
 
std::string isModelEntityExpressionODEExporterCompatible (const CModelEntity *tmp, const CExpression *pExpression, const CDataModel *pDataModel)
 
void modifyTreeForMassAction (CFunction *tmpfunc)
 
virtual std::string setConcentrationName (const std::string &objName)
 
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

◆ CODEExporterC()

CODEExporterC::CODEExporterC ( )

Constructor for the exporter.

Member Function Documentation

◆ exportClosingString()

std::string CODEExporterC::exportClosingString ( const size_t  tmp)
virtual

Reimplemented from CODEExporter.

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

◆ exportKineticFunction()

bool CODEExporterC::exportKineticFunction ( const CReaction *  reac)
virtual

Reimplemented from CODEExporter.

◆ exportKineticFunctionGroup()

bool CODEExporterC::exportKineticFunctionGroup ( const CModel *  copasiModel)
virtual

Reimplemented from CODEExporter.

References CODEExporter::exportSingleFunction(), CODEExporter::findFunctionsCalls(), CReaction::getFunction(), CModel::getReactions(), CEvaluationTree::getRoot(), CEvaluationTree::getType(), CEvaluationTree::MassAction, and CDataVector< CType >::size().

◆ exportNumber()

std::string CODEExporterC::exportNumber ( double  number)
virtual

Reimplemented from CODEExporter.

◆ exportSingleCompartment()

bool CODEExporterC::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.

◆ exportSingleFunction()

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

Reimplemented from CODEExporter.

References CEvaluationNode::buildCCodeString(), CEvaluationNode::CALL, CFunctionDB::findFunction(), CODEExporter::functions, CRootContainer::getFunctionList(), CFunction::getKey(), CDataObject::getObjectName(), CEvaluationTree::getRoot(), CEvaluationTree::getType(), CFunction::getVariables(), CODEExporter::headers, CDataContainer::insert(), CEvaluationTree::MassAction, CFunctionParameter::MODIFIER, CODEExporter::modifyTreeForMassAction(), CODEExporter::NameMap, NO_PARENT, CFunctionParameter::PARAMETER, CFunctionParameter::PRODUCT, CFunctionParameters::size(), CFunctionParameter::SUBSTRATE, CFunctionParameter::TIME, translateObjectName(), CEvaluationNode::VARIABLE, CFunctionParameter::VARIABLE, and CFunctionParameter::VOLUME.

◆ exportSingleMetabolite()

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

Reimplemented from CODEExporter.

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

◆ exportSingleModVal()

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

Reimplemented from CODEExporter.

References CKeyFactory::get(), CModel::getCompartments(), CReaction::getFunctionParameters(), CRootContainer::getKeyFactory(), CModel::getMetabolitesX(), CModel::getModelValues(), CModel::getNumIndependentReactionMetabs(), CModel::getNumODEMetabs(), CDataObject::getObjectName(), CModel::getReactions(), CReaction::isLocalParameter(), CODEExporter::NameMap, printNameForKey(), CDataVector< CType >::size(), CFunctionParameters::size(), and startsWith().

◆ exportTitleString()

std::string CODEExporterC::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 CODEExporterC::getDisplayExpressionString ( CExpression *  tmp)
virtual

Reimplemented from CODEExporter.

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

◆ getSingleLineComment()

std::string CODEExporterC::getSingleLineComment ( )
virtual

Reimplemented from CODEExporter.

◆ KineticFunction2ODEmember()

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

Reimplemented from CODEExporter.

References CCopasiMessage::EXCEPTION, CReaction::getChemEq(), CReaction::getFunction(), CReaction::getFunctionParameters(), CDataObject::getKey(), CFunction::getKey(), CModelEntity::getKey(), CCopasiParameter::getKey(), CChemEqElement::getMetabolite(), CChemEqElement::getMultiplicity(), CReaction::getParameterObjects(), CChemEq::getProducts(), CChemEq::getSubstrates(), CEvaluationTree::getType(), CReaction::isLocalParameter(), CFunction::isReversible(), CEvaluationTree::MassAction, CODEExporter::NameMap, CDataVector< CType >::size(), CFunctionParameters::size(), CFunctionParameter::TIME, and TriTrue.

◆ preprocess()

bool CODEExporterC::preprocess ( const CModel *  copasiModel)
virtual

Reimplemented from CODEExporter.

References CModel::getCompartments(), CDataObject::getKey(), CFunction::getKey(), CModelEntity::getKey(), CModel::getMetabolitesX(), CModel::getModelValues(), CDataObject::getObjectName(), CModel::getReactions(), CEvaluationTree::getRoot(), CModelEntity::getStatus(), CEvaluationTree::getType(), CMetab::isDependent(), CEvaluationTree::MassAction, CODEExporter::NameMap, CModelEntity::ODE, CModelEntity::REACTIONS, setConcentrationName(), setExportName(), setExportNameOfFunction(), setODEName(), setReservedNames(), CDataVector< CType >::size(), CODEExporter::timeKey, translateObjectName(), and translateTimeVariableName().

◆ setConcentrationName()

std::string CODEExporterC::setConcentrationName ( const CModelEntity::Status &  status,
size_t  n[],
size_t  dependent 
)

References CModelEntity::ASSIGNMENT, CModelEntity::FIXED, CModelEntity::ODE, and CModelEntity::REACTIONS.

Referenced by preprocess().

◆ setExportName()

std::string CODEExporterC::setExportName ( const CModelEntity::Status &  status,
size_t  n[],
size_t  dependent 
)

References CModelEntity::ASSIGNMENT, CModelEntity::FIXED, CModelEntity::ODE, and CModelEntity::REACTIONS.

Referenced by preprocess().

◆ setExportNameOfFunction()

void CODEExporterC::setExportNameOfFunction ( const CEvaluationNode *  pNode,
std::set< std::string > &  tmpset 
)

References CEvaluationNode::CALL, CFunctionDB::findFunction(), CRootContainer::getFunctionList(), CFunction::getKey(), CDataObject::getObjectName(), CEvaluationTree::getRoot(), CEvaluationTree::getType(), CEvaluationTree::MassAction, CODEExporter::NameMap, and translateObjectName().

Referenced by preprocess().

◆ setODEName()

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

Reimplemented from CODEExporter.

Referenced by preprocess().

◆ setReservedNames()

void CODEExporterC::setReservedNames ( )
virtual

Reimplemented from CODEExporter.

Referenced by preprocess().

◆ testName()

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

This method tests whether the given C 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 CODEExporterC::translateObjectName ( const std::string &  realName)
virtual

This method adapt a Copasi name for C 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().

Referenced by exportSingleFunction(), preprocess(), and setExportNameOfFunction().

◆ translateTimeVariableName()

std::string CODEExporterC::translateTimeVariableName ( )
virtual

Reimplemented from CODEExporter.

Referenced by preprocess().

Member Data Documentation

◆ Frequancy

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

Referenced by exportSingleModelEntity(), and testName().

◆ NameSet

std::set<std::string> CODEExporterC::NameSet

Referenced by testName().

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