#include <CODEExporterBM.h>

Inheritance diagram for CODEExporterBM:

Collaboration 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 CCopasiDataModel *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 CCopasiDataModel pDataModel)

virtual bool	exportKineticFunction (CReaction *reac)

virtual bool	exportKineticFunctionGroup (const CModel *copasiModel)

virtual bool	exportMetabolites (const CModel *copasiModel)

virtual bool	exportMetabolitesConcentrations (const CModel *copasiModel)

bool	exportModelEntityExpression (CCopasiObject obj, const CCopasiDataModel pDataModel)

bool	exportModelValues (const CModel *copasiModel)

bool	exportModelValuesExpressions (const CModel *copasiModel)

virtual std::string	exportNumber (double number)

void	exportObjectNodesFromModel (const CCopasiDataModel *pDataModel)

bool	exportODEs (const CModel *copasiModel)

bool	exportReacParamsAndFuncs (const CModel *copasiModel)

void	exportSimulatedObject (CCopasiObject obj, const CCopasiDataModel pDataModel)

bool	exportSingleFunction (const CFunction *func)

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

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

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

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

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

void	findFunctionsCalls (const CEvaluationNode *pNode)

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

virtual std::string	getSingleLineComment ()

virtual bool	isEmptyString (std::string &str)

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

Detailed Description

Definition at line 20 of file CODEExporterBM.h.

Constructor & Destructor Documentation

CODEExporterBM::CODEExporterBM ( )

Constructor for the exporter.

Definition at line 54 of file CODEExporterBM.cpp.

55 {}

Member Function Documentation

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

virtual

Reimplemented from CODEExporter.

Definition at line 279 of file CODEExporterBM.cpp.

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

 {
   switch (comp->getStatus())
     {
       case CModelEntity::FIXED:
       {
         if (!exportSingleObject(fixed, NameMap[comp->getKey()], expression, comments))
           return false;
 
         break;
       }
 
       case CModelEntity::ODE:
       {
         initial << "init ";
 
         if (!exportSingleObject(initial, NameMap[comp->getKey()], expression, comments))
           return false;
 
         break;
       }
 
       case CModelEntity::ASSIGNMENT:
       {
         if (!exportSingleObject(assignment, NameMap[comp->getKey()], expression, comments))
           return false;
 
         break;
       }
 
       default:
         return false;
         break;
     }
 
   return true;
 }

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

virtual

Reimplemented from CODEExporter.

Definition at line 218 of file CODEExporterBM.cpp.

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.

 {
   std::string name;
 
   std::ostringstream smKey;
   smKey << "sm_" << metab->getKey();
   name = NameMap[smKey.str()];
 
   switch (metab->getStatus())
     {
       case CModelEntity::FIXED:
 
         if (!exportSingleObject(fixed, name, expression, comments))
           return false;
 
         break;
 
       case CModelEntity::REACTIONS:
       {
         if (metab->isDependent())
           {
             if (!exportSingleObject(assignment, name, expression, comments))
               return false;
           }
         else
           {
             initial << "init ";
 
             if (!exportSingleObject(initial, name, expression, comments))
               return false;
           }
 
         break;
       }
 
       case CModelEntity::ODE:
       {
         initial << "init ";
 
         if (!exportSingleObject(initial, name, expression, comments))
           return false;
 
         break;
       }
 
       case CModelEntity::ASSIGNMENT:
       {
         if (!exportSingleObject(assignment, name, expression, comments))
           return false;
 
         break;
       }
 
       default:
         return false;
         break;
     }
 
   return true;
 }

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

virtual

Reimplemented from CODEExporter.

Definition at line 355 of file CODEExporterBM.cpp.

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

 {
 
   std::string name;
 
   const CMetab* metab;
   metab = dynamic_cast< const CMetab * >(tmp);
 
   if (metab)
     {
       std::ostringstream smKey;
       smKey << "sm_" << metab->getKey();
       name = NameMap[smKey.str()];
     }
   else
     name = NameMap[tmp->getKey()];
 
   switch (tmp->getStatus())
     {
       case CModelEntity::FIXED:
       {
         if (!exportSingleObject(fixed, name, expression, comments))
           return false;
 
         break;
       }
 
       case CModelEntity::ODE:
       {
         if (!exportSingleObject(initial, name, expression, comments))
           return false;
 
         break;
       }
 
       case CModelEntity::ASSIGNMENT:
       {
         if (!exportSingleObject(assignment, name, expression, comments))
           return false;
 
         break;
       }
 
       default:
         return false;
         break;
     }
 
   return true;
 }

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

virtual

Reimplemented from CODEExporter.

Definition at line 317 of file CODEExporterBM.cpp.

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

 {
   switch (modval->getStatus())
     {
       case CModelEntity::FIXED:
       {
         if (!exportSingleObject(fixed, NameMap[modval->getKey()], expression, comments))
           return false;
 
         break;
       }
 
       case CModelEntity::ODE:
       {
         initial << "init ";
 
         if (!exportSingleObject(initial, NameMap[modval->getKey()], expression, comments))
           return false;
 
         break;
       }
 
       case CModelEntity::ASSIGNMENT:
       {
         if (!exportSingleObject(assignment, NameMap[modval->getKey()], expression, comments))
           return false;
 
         break;
       }
 
       default:
         return false;
         break;
     }
 
   return true;
 }

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

virtual

Reimplemented from CODEExporter.

Definition at line 207 of file CODEExporterBM.cpp.

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

 {
   which << name << " = " << expression
         << '\t' << '\t' << "; " << comments << std::endl;
 
   return true;
 }

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

virtual

Reimplemented from CODEExporter.

Definition at line 413 of file CODEExporterBM.cpp.

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

 {
   std::ostringstream odeKey;
 
   odeKey << "ode_" << mentity->getKey();
 
   if (!exportSingleObject(ode, NameMap[odeKey.str()], equation, comments)) return false;
 
   return true;
 }

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

virtual

Reimplemented from CODEExporter.

Definition at line 406 of file CODEExporterBM.cpp.

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

 {
   if (!exportSingleObject(fixed, NameMap[param->getKey()], expression, comments)) return false;
 
   return true;
 }

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

virtual

Definition at line 56 of file CODEExporterBM.cpp.

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

 {
   os << "METHOD stiff" << std::endl;
   os << std::endl;
   os << "STARTTIME = 0" << std::endl;
 
   const CTrajectoryTask * pTrajectory =
     dynamic_cast<const CTrajectoryTask *>((*const_cast<CCopasiDataModel*>(pDataModel)->getTaskList())["Time-Course"]);
   const CTrajectoryProblem * pTrajectoryProblem =
     dynamic_cast<const CTrajectoryProblem *>(pTrajectory->getProblem());
 
   os << "STOPTIME = " << pTrajectoryProblem->getDuration() << std::endl;
   os << "DT = " << pTrajectoryProblem->getStepSize() << std::endl;
   os << std::endl;
 
   return true;
 }

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

virtual

Reimplemented from CODEExporter.

Definition at line 445 of file CODEExporterBM.cpp.

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

 {
   switch (tmp)
     {
       case INITIAL:
         return "{Initial values:}";
 
       case FIXED:
         return "{Fixed Model Entities: }";
 
       case ASSIGNMENT:
         return "{Assignment Model Entities: }";
 
       case FUNCTIONS:
         return "{Kinetics: }";
 
       case HEADERS:
         return " ";
 
       case ODEs:
         return "{Equations:}";
 
       default:
         return " ";
     }
 }

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

virtual

Reimplemented from CODEExporter.

Definition at line 431 of file CODEExporterBM.cpp.

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

 {
   std::string str1;
   str1 = tmp->getRoot()->buildBerkeleyMadonnaString();
   return str1;
 }

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

virtual

Reimplemented from CODEExporter.

Definition at line 424 of file CODEExporterBM.cpp.

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

 {
   std::string str1;
   str1 = func->getRoot()->buildBerkeleyMadonnaString();
   return str1;
 }

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

virtual

Reimplemented from CODEExporter.

Definition at line 438 of file CODEExporterBM.cpp.

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

 {
   std::ostringstream localKey;
   localKey << reac->getKey() << "_root_func";
   return NameMap[localKey.str()];
 }

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

virtual

Reimplemented from CODEExporter.

Definition at line 197 of file CODEExporterBM.cpp.

 {
   return objName + "_c";
 }

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

virtual

Reimplemented from CODEExporter.

Definition at line 202 of file CODEExporterBM.cpp.

 {
   return "d/dt(" + objName + ")";
 }

void CODEExporterBM::setReservedNames ( )

virtual

Reimplemented from CODEExporter.

Definition at line 194 of file CODEExporterBM.cpp.

195 {return;} // TODO

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

Definition at line 158 of file CODEExporterBM.cpp.

References Frequancy, and NameSet.

Referenced by translateObjectName().

 {
   std::locale C("C");
   char ch;
 
   std::ostringstream newname, tmp;
 
   size_t name_size = name.size();
   size_t i;
 
   for (i = 0; i < name_size; i++)
     {
       ch = name[i];
 
       if (std::isalpha(ch, C) && std::islower(ch, C))
         tmp << (char) toupper(ch);
       else
         tmp << ch;
     }
 
   if (NameSet.find(tmp.str()) == NameSet.end())
     {
       NameSet.insert(tmp.str());
       Frequancy[tmp.str()] = 0;
 
       return name;
     }
   else
     {
       Frequancy[tmp.str()]++;
       newname << name << "_" << Frequancy[tmp.str()];
 
       return testName(newname.str());
     }
 }

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.

Definition at line 82 of file CODEExporterBM.cpp.

References testName().

 {
   std::locale C("C");
   char ch;
 
   std::ostringstream tmpName;
 
   size_t realName_size = realName.size();
   size_t i;
 
   ch = realName[0];
 
   if (!std::isalpha(ch, C))
     {
       tmpName << "_";
 
       if (std::isdigit(ch, C)) tmpName << ch;
     }
   else tmpName << ch;
 
   for (i = 1; i < realName_size; i++)
     {
       ch = realName[i];
 
       if (std::isalpha(ch, C))
         {
           if (std::isspace(realName[i - 1], C) && std::islower(ch, C))
             tmpName << (char) toupper(ch);
           else
             tmpName << ch;
         }
 
       if (std::isdigit(ch, C)) tmpName << ch;
 
       if (std::ispunct(ch, C))
         switch (ch)
           {
             case '_':
               tmpName << ch;
               break;
 
             case '-':
               tmpName << "_";
               break;
 
             case '{':
               tmpName << "_";
               break;
 
             case '}':
               tmpName << "_";
               break;
 
             case '(':
               tmpName << "_";
               break;
 
             case ')':
               tmpName << "_";
               break;
 
             default:
               break;
           }
     }
 
   return testName(tmpName.str());
 }

std::string CODEExporterBM::translateTimeVariableName ( )

virtual

Reimplemented from CODEExporter.

Definition at line 74 of file CODEExporterBM.cpp.

75 {return "TIME";}

Member Data Documentation

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

Definition at line 72 of file CODEExporterBM.h.

Referenced by testName().

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

Definition at line 73 of file CODEExporterBM.h.

Referenced by testName().

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

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation