#include <CODEExporterXPPAUT.h>

Inheritance diagram for CODEExporterXPPAUT:

Collaboration diagram for CODEExporterXPPAUT:

Public Member Functions
	CODEExporterXPPAUT ()

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

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

void	exportSingleLine (const std::string &line, std::ostringstream &which)

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 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, unsigned C_INT32 >	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 22 of file CODEExporterXPPAUT.h.

Constructor & Destructor Documentation

CODEExporterXPPAUT::CODEExporterXPPAUT ( )

Constructor for the exporter.

Definition at line 54 of file CODEExporterXPPAUT.cpp.

55 {}

Member Function Documentation

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

virtual

Reimplemented from CODEExporter.

Definition at line 624 of file CODEExporterXPPAUT.cpp.

 {
   os << "done" << std::endl;
   return true;
 }

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

virtual

Reimplemented from CODEExporter.

Definition at line 398 of file CODEExporterXPPAUT.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:
       {
         fixed << "#" << comments << std::endl;
         fixed << "param ";
 
         if (!exportSingleObject(fixed, NameMap[comp->getKey()], expression, comments))
           return false;
 
         break;
       }
 
       case CModelEntity::ODE:
       {
         initial << "#" << comments << std::endl;
         initial << "init ";
 
         if (!exportSingleObject(initial, NameMap[comp->getKey()], expression, comments))
           return false;
 
         break;
       }
 
       case CModelEntity::ASSIGNMENT:
       {
 #if 0
         assignment << "#" << comments << std::endl;
 
         if (!exportSingleObject(assignment, NameMap[comp->getKey()], expression, comments))
           return false;
 
 #endif
         break;
       }
 
       default:
         return false;
         break;
     }
 
   return true;
 }

void CODEExporterXPPAUT::exportSingleLine	(	const std::string &	line,
		std::ostringstream &	which
	)

Definition at line 261 of file CODEExporterXPPAUT.cpp.

References MCODEExporter, CCopasiMessage::size(), and CCopasiMessage::WARNING.

Referenced by exportSingleObject().

 {
 
   std::locale C("C");
 
   size_t limit = 256, total = 1000;
 
   //size_t limit = 10, total = 15;
   if (line.size() > total)
     CCopasiMessage(CCopasiMessage::WARNING, MCODEExporter + 1);
 
   if (line.size() > limit)
     {
 
       size_t i, pos0, pos, end = line.size();
 
       pos0 = 0;
       pos = limit - 1;
 
       while (pos < end)
         {
 
           std::string part;
           char ch;
           ch = line[pos];
 
           while (std::isalnum(ch, C) || ch == '_' || ch == ')')
             {
               pos--;
               ch = line[pos];
             }
 
           for (i = pos0; i < pos; i++)
             {
               part += line[i];
             }
 
           part += " \\";
 
           which << part.c_str() << std::endl;
 
           pos0 = pos;
           pos += limit;
         }
 
       if (pos > end)
         {
           std::string part;
 
           for (i = pos0; i < end; i++)
             {
               part += line[i];
             }
 
           which << part.c_str() << std::endl;
         }
     }
   else
     which << line << std::endl;
 
   return;
 }

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

virtual

Reimplemented from CODEExporter.

Definition at line 337 of file CODEExporterXPPAUT.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:
       {
         fixed << "#" << comments << std::endl;
         fixed << "param ";
 
         if (!exportSingleObject(fixed, name, expression, comments))
           return false;
 
         break;
       }
 
       case CModelEntity::ODE:
       case CModelEntity::REACTIONS:
       {
         if (!metab->isDependent())
           {
             initial << "#" << comments << std::endl;
             initial << "init ";
 
             if (!exportSingleObject(initial, name, expression, comments))
               return false;
           }
         else
           {
             assignment << "#" << comments << std::endl;
 
             if (!exportSingleObject(assignment, name, expression, comments))
               return false;
           }
 
         break;
       }
 
       case CModelEntity::ASSIGNMENT:
       {
         assignment << "#" << comments << std::endl;
 
         if (!exportSingleObject(assignment, name, expression, comments))
           return false;
 
         break;
       }
 
       default:
         return false;
         break;
     }
 
   return true;
 }

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

virtual

Reimplemented from CODEExporter.

Definition at line 492 of file CODEExporterXPPAUT.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:
       {
         fixed << "#" << comments << std::endl;
         fixed << "param ";
 
         if (!exportSingleObject(fixed, name, expression, comments))
           return false;
 
         break;
       }
 
       case CModelEntity::ODE:
       {
         initial << "#" << comments << std::endl;
         initial << "init ";
 
         if (!exportSingleObject(initial, name, expression, comments))
           return false;
 
         break;
       }
 
       case CModelEntity::ASSIGNMENT:
       {
         assignment << "#" << comments << std::endl;
 
         if (!exportSingleObject(assignment, name, expression, comments))
           return false;
 
         break;
       }
 
       default:
         return false;
         break;
     }
 
   return true;
 }

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

virtual

Reimplemented from CODEExporter.

Definition at line 445 of file CODEExporterXPPAUT.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:
       {
         fixed << "#" << comments << std::endl;
         fixed << "param ";
 
         if (!exportSingleObject(fixed, NameMap[modval->getKey()], expression, comments))
           return false;
 
         break;
       }
 
       case CModelEntity::ODE:
       {
         initial << "#" << comments << std::endl;
         initial << "init ";
 
         if (!exportSingleObject(initial, NameMap[modval->getKey()], expression, comments))
           return false;
 
         break;
       }
 
       case CModelEntity::ASSIGNMENT:
       {
 #if 0
         assignment << "#" << comments << std::endl;
 
         if (!exportSingleObject(assignment, NameMap[modval->getKey()], expression, comments))
           return false;
 
 #endif
         break;
       }
 
       default:
         return false;
         break;
     }
 
   return true;
 }

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

virtual

Reimplemented from CODEExporter.

Definition at line 324 of file CODEExporterXPPAUT.cpp.

References exportSingleLine().

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

 {
   std::ostringstream line;
 
   line << name << "=" << expression;
   exportSingleLine(line.str(), which);
 
   return true;
 }

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

virtual

Reimplemented from CODEExporter.

Definition at line 584 of file CODEExporterXPPAUT.cpp.

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

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

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

virtual

Reimplemented from CODEExporter.

Definition at line 550 of file CODEExporterXPPAUT.cpp.

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

 {
   fixed << "#" << comments << std::endl;
 
   fixed << "param ";
 
   if (!exportSingleObject(fixed, NameMap[param->getKey()], expression, comments)) return false;
 
   return true;
 }

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

virtual

Definition at line 57 of file CODEExporterXPPAUT.cpp.

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

 {
   os << "@ t0=0,";  //TODO
   const CTrajectoryTask * pTrajectory =
     dynamic_cast<const CTrajectoryTask *>((*const_cast<CCopasiDataModel*>(pDataModel)->getTaskList())["Time-Course"]);
   const CTrajectoryProblem * pTrajectoryProblem =
     dynamic_cast<const CTrajectoryProblem *>(pTrajectory->getProblem());
 
   os << "total=" << pTrajectoryProblem->getDuration() << ",";
   os << "dt=" << pTrajectoryProblem->getStepSize()
      << ",METH=stiff" << std::endl; //gear is the only method with automatic step size
 
   return true;
 }

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

virtual

Reimplemented from CODEExporter.

Definition at line 597 of file CODEExporterXPPAUT.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 CODEExporterXPPAUT::getDisplayExpressionString ( CExpression * tmp )

virtual

Reimplemented from CODEExporter.

Definition at line 568 of file CODEExporterXPPAUT.cpp.

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

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

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

virtual

Reimplemented from CODEExporter.

Definition at line 561 of file CODEExporterXPPAUT.cpp.

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

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

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

virtual

Reimplemented from CODEExporter.

Definition at line 575 of file CODEExporterXPPAUT.cpp.

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

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

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

virtual

Reimplemented from CODEExporter.

Definition at line 251 of file CODEExporterXPPAUT.cpp.

 {
   return objName + "_c";
 }

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

virtual

Reimplemented from CODEExporter.

Definition at line 246 of file CODEExporterXPPAUT.cpp.

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

void CODEExporterXPPAUT::setReservedNames ( )

virtual

Reimplemented from CODEExporter.

Definition at line 224 of file CODEExporterXPPAUT.cpp.

References Frequancy, and NameSet.

 {
   size_t i;
 
   const std::string reserved[45] =
   {
     "SIN", "COS", "TAN", "ATAN", "ATAN2", "SINH", "EXP", "DELAY", "LN", "LOG10",
     "LOG", "T", "PI", "IF", "THEN", "ELSE", "ASIN", "ACOS", "HEAV", "SIGN",
     "CEIL", "FLR", "RAN", "ABS", "MAX", "MIN", "NORMAL", "BESSELJ", "BESSELY", "ERF",
     "ERFS", "ARG1", "ARG2", "ARG2", "ARG4", "ARG5", "ARG6", "ARG7", "ARG8", "ARG9",
     "SHIFT", "NOT", "INT", "SUM", "OF"
   };
 
   for (i = 0; i < 45; i++)
     {
       NameSet.insert(reserved[i]);
       Frequancy[reserved[i]] = 0;
     }
 
   return;
 }

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

This method tests whether the given XPPAUT 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 162 of file CODEExporterXPPAUT.cpp.

References CCopasiMessage::ERROR, fatalError, 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
     {
 
       std::string ecount;
       std::ostringstream tmpecount;
       std::ostringstream tmpname;
       size_t ecount_size, tmpname_size;
 
       Frequancy[tmp.str()]++;
       tmpecount << Frequancy[tmp.str()];
 
       ecount = tmpecount.str();
 
       ecount_size = ecount.size();
 
       if (ecount_size > 6)
         {
           CCopasiMessage(CCopasiMessage::ERROR, "too many repeated names to modify to XPP syntax"); //TODO
           fatalError();
         }
 
       tmpname_size = name_size + ecount_size;
 
       if (tmpname_size > 7)
         {
           for (i = 0; i < (7 - ecount_size); i++)
             tmpname << name[i];
         }
       else
         tmpname << name << ecount;
 
       return testName(tmpname.str());
     }
 }

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

virtual

This method adapt a Copasi name for XPPAUT syntax: all XPPAUT names can have up to 9 letters each. 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 80 of file CODEExporterXPPAUT.cpp.

References testName().

 {
   std::locale C("C");
   char ch;
 
   std::string newName;
   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;
 
             default:
               break;
           }
     }
 
   newName = tmpName.str();
 
   size_t newName_size = newName.size();
 
   if (newName_size > 7)
     {
       std::ostringstream cutName;
 
       for (i = 0; i < 7; i++)
         cutName << newName[i];
 
       newName = cutName.str();
     }
 
   return testName(newName);
 }

std::string CODEExporterXPPAUT::translateTimeVariableName ( )

virtual

Reimplemented from CODEExporter.

Definition at line 72 of file CODEExporterXPPAUT.cpp.

73 {return "t";}

Member Data Documentation

std::map< std::string, unsigned C_INT32 > CODEExporterXPPAUT::Frequancy

Definition at line 78 of file CODEExporterXPPAUT.h.

Referenced by setReservedNames(), and testName().

std::set<std::string> CODEExporterXPPAUT::NameSet

Definition at line 79 of file CODEExporterXPPAUT.h.

Referenced by setReservedNames(), and 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