COPASI API
4.16.103
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#include <cmath>
#include "CSBMLExporter.h"
#include "SBMLUtils.h"
#include "SBMLImporter.h"
#include "utilities/CCopasiException.h"
#include "sbml/SBMLDocument.h"
#include "sbml/Compartment.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 "CopasiDataModel/CCopasiDataModel.h"
#include "SBMLIncompatibility.h"
#include "model/CCompartment.h"
#include "model/CModel.h"
#include "model/CEvent.h"
#include "model/CMetab.h"
#include "function/CExpression.h"
#include "function/CEvaluationNode.h"
#include "model/CAnnotation.h"
#include "model/CReaction.h"
#include "utilities/CCopasiParameter.h"
#include "model/CModelValue.h"
#include "function/CFunction.h"
#include "report/CKeyFactory.h"
#include "ConverterASTNode.h"
#include "utilities/CCopasiTree.h"
#include "model/CChemEqElement.h"
#include "utilities/CVersion.h"
#include "sbml/Trigger.h"
#include "sbml/Event.h"
#include "sbml/EventAssignment.h"
#include <sbml/xml/XMLInputStream.h>
#include "compareExpressions/compare_utilities.h"
#include "MIRIAM/CRDFUtilities.h"
#include "MIRIAM/CModelMIRIAMInfo.h"
#include "MIRIAM/CReference.h"
#include "MIRIAM/CBiologicalDescription.h"
#include "MIRIAM/CConstants.h"
#include "MIRIAM/CCreator.h"
#include "MIRIAM/CModified.h"
#include "MIRIAM/CRDFPredicate.h"
#include "layout/CListOfLayouts.h"
#include "copasi/report/CCopasiRootContainer.h"
#include "commandline/CLocaleString.h"
Go to the source code of this file.
Macros | |
#define | INIT_DEFAULTS(element) |
#define | USE_LAYOUT 1 |
Functions | |
void | addInitialAssignmentsToModel (SBMLDocument *doc, std::map< const std::string, Parameter * > &initialValueMap, const CCopasiDataModel &dataModel) |
std::string | addRateOfIfItDoesNotExist (SBMLDocument *pSBMLDocument, std::map< std::string, const SBase * > &idMap, const char *id) |
void | addToInitialValueMap (std::map< const std::string, Parameter * > *initialMap, const CCopasiObject *pObject, const CCopasiObject *pObjectParent, int sbmlLevel, int sbmlVersion) |
void | adjustNames (ASTNode *node, SBMLDocument *pSBMLDocument, std::map< std::string, const SBase * > &idMap) |
std::string | convertExpression (const std::string &expression, const std::map< const std::string, Parameter * > &initialValueMap) |
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 CCopasiObject *pObjectParent) |
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) |
#define INIT_DEFAULTS | ( | element | ) |
Definition at line 48 of file CSBMLExporter.cpp.
Referenced by CSBMLExporter::createAreaUnit(), CSBMLExporter::createCompartment(), CSBMLExporter::createLengthUnit(), CSBMLExporter::createMetabolite(), CSBMLExporter::createParameter(), CSBMLExporter::createReaction(), CSBMLExporter::createSubstanceUnit(), CSBMLExporter::createTimeUnit(), and CSBMLExporter::createVolumeUnit().
#define USE_LAYOUT 1 |
Definition at line 17 of file CSBMLExporter.cpp.
void addInitialAssignmentsToModel | ( | SBMLDocument * | doc, |
std::map< const std::string, Parameter * > & | initialValueMap, | ||
const CCopasiDataModel & | dataModel | ||
) |
Definition at line 3369 of file CSBMLExporter.cpp.
References CCopasiContainer::getObject(), and CCopasiObject::getObjectParent().
Referenced by CSBMLExporter::createSBMLDocument().
std::string addRateOfIfItDoesNotExist | ( | SBMLDocument * | pSBMLDocument, |
std::map< std::string, const SBase * > & | idMap, | ||
const char * | id | ||
) |
Definition at line 167 of file CSBMLExporter.cpp.
References createFunctionDefinitonForURI(), and hasFunctionDefinitionForURI().
Referenced by getUserDefinedFuctionForName(), and CSBMLExporter::replaceSpeciesReferences().
void addToInitialValueMap | ( | std::map< const std::string, Parameter * > * | initialMap, |
const CCopasiObject * | pObject, | ||
const CCopasiObject * | pObjectParent, | ||
int | sbmlLevel, | ||
int | sbmlVersion | ||
) |
Definition at line 2347 of file CSBMLExporter.cpp.
References C_FLOAT64, getAnnotationStringFor(), CCopasiObject::getCN(), CCopasiObject::getKey(), CCopasiObject::getObjectName(), CCopasiObject::getValuePointer(), and CCopasiObject::isValueDbl().
Referenced by CSBMLExporter::checkForUnsupportedObjectReferences().
void adjustNames | ( | ASTNode * | node, |
SBMLDocument * | pSBMLDocument, | ||
std::map< std::string, const SBase * > & | idMap | ||
) |
Definition at line 7054 of file CSBMLExporter.cpp.
References getUserDefinedFuctionForName().
Referenced by CSBMLExporter::convertToASTNode().
std::string convertExpression | ( | const std::string & | expression, |
const std::map< const std::string, Parameter * > & | initialValueMap | ||
) |
Definition at line 1810 of file CSBMLExporter.cpp.
Referenced by CSBMLExporter::createEvent(), CSBMLExporter::createRule(), and CSBMLExporter::exportEventAssignments().
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 | ||
) |
Definition at line 139 of file CSBMLExporter.cpp.
References CSBMLExporter::createUniqueId().
Referenced by addRateOfIfItDoesNotExist(), and getUserDefinedFuctionForName().
std::string getAnnotationStringFor | ( | const CCopasiObject * | pObjectParent | ) |
Definition at line 2335 of file CSBMLExporter.cpp.
Referenced by addToInitialValueMap().
std::string getUserDefinedFuctionForName | ( | SBMLDocument * | pSBMLDocument, |
std::map< std::string, const SBase * > & | idMap, | ||
const char * | id | ||
) |
Definition at line 190 of file CSBMLExporter.cpp.
References addRateOfIfItDoesNotExist(), createFunctionDefinitonForURI(), and hasFunctionDefinitionForURI().
Referenced by adjustNames().
std::string hasFunctionDefinitionForURI | ( | SBMLDocument * | pSBMLDocument, |
const std::string & | sNamespace, | ||
const std::string & | elementName, | ||
const std::string & | definition | ||
) |
Definition at line 104 of file CSBMLExporter.cpp.
Referenced by addRateOfIfItDoesNotExist(), and getUserDefinedFuctionForName().
void removeStickyTagFromElements | ( | SBMLDocument * | pSBMLDocument | ) |
Definition at line 3222 of file CSBMLExporter.cpp.
Referenced by CSBMLExporter::exportModelToString().