COPASI API
4.16.103
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#include <iostream>
#include <vector>
#include <sstream>
#include <map>
#include <limits>
#include <cmath>
#include <sbml/SBMLReader.h>
#include <sbml/SBMLDocument.h>
#include <sbml/Compartment.h>
#include <sbml/Species.h>
#include <sbml/SpeciesReference.h>
#include <sbml/Reaction.h>
#include <sbml/LocalParameter.h>
#include <sbml/KineticLaw.h>
#include <sbml/math/FormulaFormatter.h>
#include <sbml/Model.h>
#include <sbml/UnitKind.h>
#include <sbml/Unit.h>
#include <sbml/Parameter.h>
#include <sbml/InitialAssignment.h>
#include <sbml/Rule.h>
#include <sbml/FunctionDefinition.h>
#include <sbml/UnitDefinition.h>
#include "copasi.h"
#include "report/CKeyFactory.h"
#include "model/CModel.h"
#include "model/CCompartment.h"
#include "model/CMetab.h"
#include "model/CReaction.h"
#include "model/CModelValue.h"
#include "model/CEvent.h"
#include "function/CNodeK.h"
#include "function/CFunctionDB.h"
#include "function/CEvaluationTree.h"
#include "function/CExpression.h"
#include "function/CFunctionParameters.h"
#include "report/CCopasiObjectReference.h"
#include "utilities/CCopasiTree.h"
#include "utilities/CNodeIterator.h"
#include "CopasiDataModel/CCopasiDataModel.h"
#include "report/CCopasiRootContainer.h"
#include "MIRIAM/CRDFGraphConverter.h"
#include "compareExpressions/CEvaluationNodeNormalizer.h"
#include "commandline/CLocaleString.h"
#include "commandline/COptions.h"
#include "SBMLImporter.h"
#include "SBMLUtils.h"
#include "ConverterASTNode.h"
#include "utilities/CProcessReport.h"
#include "copasi/commandline/CConfigurationFile.h"
#include "layout/SBMLDocumentLoader.h"
#include "layout/CListOfLayouts.h"
#include "utilities/CCopasiMessage.h"
Go to the source code of this file.
Macros | |
#define | INIT_DEFAULTS(element) |
#define | USE_LAYOUT 1 |
Functions | |
bool | addToKnownFunctionToMap (std::map< std::string, std::string > &map, const FunctionDefinition *sbmlFunction) |
int | AstStrCmp (const void *s1, const void *s2) |
bool | containsKey (const CCopasiVector< CChemEqElement > &list, const std::string &key) |
void | ensureAllArgsAreBeingUsedInFunctionDefinition (const FunctionDefinition *sbmlFunction) |
CFunction * | findFunction (CCopasiVectorN< CFunction > &db, const CFunction *func) |
CFunction * | getFunctionForKey (CCopasiVectorN< CFunction > &functionDb, const std::string &key) |
std::string | getInitialCNForSBase (SBase *sbase, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap) |
std::string | getOriginalSBMLId (Parameter *parameter) |
std::string | isKnownCustomFunctionDefinition (const FunctionDefinition *sbmlFunction, const std::string &sNamespace, const std::string &elementName, const std::string &definition) |
#define INIT_DEFAULTS | ( | element | ) |
Definition at line 49 of file SBMLImporter.cpp.
Referenced by SBMLImporter::createCModelFromSBMLDocument().
#define USE_LAYOUT 1 |
Definition at line 22 of file SBMLImporter.cpp.
bool addToKnownFunctionToMap | ( | std::map< std::string, std::string > & | map, |
const FunctionDefinition * | sbmlFunction | ||
) |
Definition at line 1590 of file SBMLImporter.cpp.
References isKnownCustomFunctionDefinition().
Referenced by SBMLImporter::createCFunctionFromFunctionDefinition().
Definition at line 1654 of file SBMLImporter.cpp.
Referenced by ensureAllArgsAreBeingUsedInFunctionDefinition().
bool containsKey | ( | const CCopasiVector< CChemEqElement > & | list, |
const std::string & | key | ||
) |
Definition at line 5724 of file SBMLImporter.cpp.
References CCopasiVector< T >::begin(), and CCopasiVector< T >::end().
Referenced by SBMLImporter::doMapping().
void ensureAllArgsAreBeingUsedInFunctionDefinition | ( | const FunctionDefinition * | sbmlFunction | ) |
This function checks the function definition for unused arguments (that would not be properly displayed in the CopasiUI). If found, the function body will be replaced with one including all arguments.
Definition at line 1675 of file SBMLImporter.cpp.
References AstStrCmp().
Referenced by SBMLImporter::createCFunctionFromFunctionDefinition().
CFunction* findFunction | ( | CCopasiVectorN< CFunction > & | db, |
const CFunction * | func | ||
) |
Definition at line 2126 of file SBMLImporter.cpp.
References CCopasiVector< T >::size().
Referenced by CModel::convert2NonReversible().
CFunction* getFunctionForKey | ( | CCopasiVectorN< CFunction > & | functionDb, |
const std::string & | key | ||
) |
Definition at line 1926 of file SBMLImporter.cpp.
References CCopasiVector< T >::begin(), and CCopasiVector< T >::end().
std::string getInitialCNForSBase | ( | SBase * | sbase, |
std::map< CCopasiObject *, SBase * > & | copasi2sbmlmap | ||
) |
Definition at line 212 of file SBMLImporter.cpp.
References CCopasiObject::getCN(), CMetab::getInitialConcentrationReference(), and CModelEntity::getInitialValueReference().
Referenced by SBMLImporter::createCModelFromSBMLDocument().
std::string getOriginalSBMLId | ( | Parameter * | parameter | ) |
Definition at line 189 of file SBMLImporter.cpp.
Referenced by SBMLImporter::createCModelFromSBMLDocument().
std::string isKnownCustomFunctionDefinition | ( | const FunctionDefinition * | sbmlFunction, |
const std::string & | sNamespace, | ||
const std::string & | elementName, | ||
const std::string & | definition | ||
) |