COPASI API  4.40.278
CSBMLExporter.cpp File Reference
#include <cmath>
#include "CSBMLExporter.h"
#include "SBMLUtils.h"
#include "SBMLImporter.h"
#include "copasi/utilities/CCopasiException.h"
#include "copasi/utilities/CUnit.h"
#include "sbml/SBMLDocument.h"
#include "sbml/Compartment.h"
#include "sbml/LocalParameter.h"
#include <sbml/packages/layout/extension/LayoutModelPlugin.h>
#include <sbml/packages/layout/extension/LayoutExtension.h>
#include <sbml/conversion/ConversionProperties.h>
#include "copasi/layout/CLDefaultStyles.h"
#include <sbml/packages/render/extension/RenderExtension.h>
#include <sbml/packages/render/extension/RenderListOfLayoutsPlugin.h>
#include <sbml/packages/render/sbml/GlobalRenderInformation.h>
#include "sbml/Model.h"
#include "sbml/Species.h"
#include "sbml/Parameter.h"
#include "sbml/Reaction.h"
#include "sbml/KineticLaw.h"
#include "sbml/SBMLWriter.h"
#include "sbml/SpeciesReference.h"
#include "sbml/math/ASTNode.h"
#include "sbml/annotation/ModelHistory.h"
#include "sbml/annotation/CVTerm.h"
#include "sbml/SBMLErrorLog.h"
#include "sbml/SBMLError.h"
#include "copasi/CopasiDataModel/CDataModel.h"
#include "SBMLIncompatibility.h"
#include "copasi/model/CCompartment.h"
#include "copasi/model/CModel.h"
#include "copasi/model/CEvent.h"
#include "copasi/model/CMetab.h"
#include "copasi/function/CExpression.h"
#include "copasi/function/CEvaluationNode.h"
#include "copasi/model/CAnnotation.h"
#include "copasi/model/CReaction.h"
#include "copasi/utilities/CCopasiParameter.h"
#include "copasi/model/CModelValue.h"
#include "copasi/function/CFunction.h"
#include "copasi/report/CKeyFactory.h"
#include "ConverterASTNode.h"
#include "copasi/utilities/CCopasiTree.h"
#include "copasi/model/CChemEqElement.h"
#include "copasi/utilities/CVersion.h"
#include "sbml/Trigger.h"
#include "sbml/Event.h"
#include "sbml/EventAssignment.h"
#include <sbml/xml/XMLInputStream.h>
#include "copasi/compareExpressions/compare_utilities.h"
#include "copasi/MIRIAM/CRDFUtilities.h"
#include "copasi/MIRIAM/CModelMIRIAMInfo.h"
#include "copasi/MIRIAM/CReference.h"
#include "copasi/MIRIAM/CBiologicalDescription.h"
#include "copasi/MIRIAM/CConstants.h"
#include "copasi/MIRIAM/CCreator.h"
#include "copasi/MIRIAM/CModified.h"
#include "copasi/MIRIAM/CRDFPredicate.h"
#include "copasi/MIRIAM/CRDFParser.h"
#include "copasi/layout/CListOfLayouts.h"
#include "copasi/core/CRootContainer.h"
#include "copasi/commandline/CLocaleString.h"

Macros

#define INIT_DEFAULTS(element)
 
#define USE_LAYOUT   1
 

Functions

Unit * addCUnitComponentToUnitDefinition (UnitDefinition *result, const CUnitComponent &component, const std::string &unitExpression)
 
void addParticleNumberToInitialValueMap (std::map< const std::string, Parameter * > *initialMap, std::map< std::string, const SBase * > &idMap, const CMetab *pMetab, int sbmlLevel, int sbmlVersion)
 
std::string addRateOfIfItDoesNotExist (SBMLDocument *pSBMLDocument, std::map< std::string, const SBase * > &idMap, const char *id)
 
void addSymbolComponentToUnitDefinition (UnitDefinition *result, CUnit::SymbolComponent &component, const std::string &unitExpression)
 
void addToInitialValueMap (std::map< const std::string, Parameter * > *initialMap, std::map< std::string, const SBase * > &idMap, const CDataObject *pObject, const CDataObject *pObjectParent, int sbmlLevel, int sbmlVersion)
 
void adjustNames (ASTNode *node, SBMLDocument *pSBMLDocument, std::map< std::string, const SBase * > &idMap)
 
size_t convertBaseUnit (CBaseUnit::Kind unit)
 
std::string convertExpression (const std::string &expression, const std::map< const std::string, Parameter * > &initialValueMap)
 
size_t convertSymbol (const std::string &unit)
 
std::string createFunctionDefinitonForURI (SBMLDocument *pSBMLDocument, std::map< std::string, const SBase * > &idMap, const char *id, const std::string &sNamespace, const std::string &elementName, const std::string &definition, const std::string &lambda)
 
std::string getAnnotationStringFor (const CDataObject *pObjectParent, const std::string &type)
 
std::string getUserDefinedFuctionForName (SBMLDocument *pSBMLDocument, std::map< std::string, const SBase * > &idMap, const char *id)
 
std::string hasFunctionDefinitionForURI (SBMLDocument *pSBMLDocument, const std::string &sNamespace, const std::string &elementName, const std::string &definition)
 
void removeStickyTagFromElements (SBMLDocument *pSBMLDocument)
 
void renameAstNodes (ASTNode *pFunNode, const std::map< std::string, std::string > &renameList)
 

Macro Definition Documentation

◆ INIT_DEFAULTS

#define INIT_DEFAULTS (   element)
Value:
{\
element.initDefaults();\
}

◆ USE_LAYOUT

#define USE_LAYOUT   1

Function Documentation

◆ addCUnitComponentToUnitDefinition()

Unit* addCUnitComponentToUnitDefinition ( UnitDefinition *  result,
const CUnitComponent component,
const std::string &  unitExpression 
)

◆ addParticleNumberToInitialValueMap()

void addParticleNumberToInitialValueMap ( std::map< const std::string, Parameter * > *  initialMap,
std::map< std::string, const SBase * > &  idMap,
const CMetab pMetab,
int  sbmlLevel,
int  sbmlVersion 
)

◆ addRateOfIfItDoesNotExist()

std::string addRateOfIfItDoesNotExist ( SBMLDocument *  pSBMLDocument,
std::map< std::string, const SBase * > &  idMap,
const char *  id 
)

◆ addSymbolComponentToUnitDefinition()

◆ addToInitialValueMap()

void addToInitialValueMap ( std::map< const std::string, Parameter * > *  initialMap,
std::map< std::string, const SBase * > &  idMap,
const CDataObject pObject,
const CDataObject pObjectParent,
int  sbmlLevel,
int  sbmlVersion 
)

◆ adjustNames()

void adjustNames ( ASTNode *  node,
SBMLDocument *  pSBMLDocument,
std::map< std::string, const SBase * > &  idMap 
)

◆ convertBaseUnit()

◆ convertExpression()

std::string convertExpression ( const std::string &  expression,
const std::map< const std::string, Parameter * > &  initialValueMap 
)

◆ convertSymbol()

size_t convertSymbol ( const std::string &  unit)

◆ createFunctionDefinitonForURI()

std::string createFunctionDefinitonForURI ( SBMLDocument *  pSBMLDocument,
std::map< std::string, const SBase * > &  idMap,
const char *  id,
const std::string &  sNamespace,
const std::string &  elementName,
const std::string &  definition,
const std::string &  lambda 
)

◆ getAnnotationStringFor()

std::string getAnnotationStringFor ( const CDataObject pObjectParent,
const std::string &  type 
)

◆ getUserDefinedFuctionForName()

std::string getUserDefinedFuctionForName ( SBMLDocument *  pSBMLDocument,
std::map< std::string, const SBase * > &  idMap,
const char *  id 
)

◆ hasFunctionDefinitionForURI()

std::string hasFunctionDefinitionForURI ( SBMLDocument *  pSBMLDocument,
const std::string &  sNamespace,
const std::string &  elementName,
const std::string &  definition 
)

◆ removeStickyTagFromElements()

void removeStickyTagFromElements ( SBMLDocument *  pSBMLDocument)

◆ renameAstNodes()

void renameAstNodes ( ASTNode *  pFunNode,
const std::map< std::string, std::string > &  renameList 
)

function going through all children of pFunNode, and renaming elements if they are in the rename list

Referenced by CSBMLExporter::createFunctionDefinition().