#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/SBMLTransforms.h>
#include "IdList.h"
#include <sbml/conversion/ConversionProperties.h>
#include <sbml/packages/layout/extension/LayoutModelPlugin.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/copasi.h"
#include "copasi/report/CKeyFactory.h"
#include "copasi/model/CModel.h"
#include "copasi/model/CCompartment.h"
#include "copasi/model/CMetab.h"
#include "copasi/model/CReaction.h"
#include "copasi/model/CModelValue.h"
#include "copasi/model/CEvent.h"
#include "copasi/function/CNodeK.h"
#include "copasi/function/CFunctionDB.h"
#include "copasi/function/CEvaluationTree.h"
#include "copasi/function/CExpression.h"
#include "copasi/function/CFunctionParameters.h"
#include "copasi/core/CDataObjectReference.h"
#include "copasi/utilities/CCopasiTree.h"
#include "copasi/utilities/CNodeIterator.h"
#include "copasi/utilities/CUnit.h"
#include "copasi/CopasiDataModel/CDataModel.h"
#include "copasi/core/CRootContainer.h"
#include "copasi/MIRIAM/CRDFGraphConverter.h"
#include "copasi/compareExpressions/CEvaluationNodeNormalizer.h"
#include "copasi/commandline/CLocaleString.h"
#include "copasi/commandline/COptions.h"
#include "SBMLImporter.h"
#include "SBMLUtils.h"
#include "ConverterASTNode.h"
#include "copasi/utilities/CProcessReport.h"
#include "copasi/commandline/CConfigurationFile.h"
#include "copasi/layout/SBMLDocumentLoader.h"
#include "copasi/layout/CListOfLayouts.h"
#include "copasi/utilities/CCopasiMessage.h"
#include <copasi/MIRIAM/CBiologicalDescription.h>
#include <copasi/MIRIAM/CModelMIRIAMInfo.h>

Classes
class	SbmlProgressCallback

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 CDataVector< CChemEqElement > &list, const std::string &key)

void	ensureAllArgsAreBeingUsedInFunctionDefinition (const FunctionDefinition *sbmlFunction)

CFunction *	findFunction (CDataVectorN< CFunction > &db, const CFunction *func)

CFunction *	getFunctionForKey (CDataVectorN< CFunction > &functionDb, const std::string &key)

std::string	getInitialCNForSBase (SBase sbase, std::map< const CDataObject , SBase * > &copasi2sbmlmap, const std::string &type)

std::string	getOriginalSBMLId (Parameter *parameter, std::string &type)

bool	hasCopasiAnnotation (const SBase *sbmlObject, const std::string &sNamespace)

std::string	isKnownCustomFunctionDefinition (const FunctionDefinition *sbmlFunction, const std::string &sNamespace, const std::string &elementName, const std::string &definition)

void	renameShadowingFluxReferences (KineticLaw kLaw, Model pSBMLModel, const std::string &prefix)

Macro Definition Documentation

◆ INIT_DEFAULTS

#define INIT_DEFAULTS ( element )

Value:

  {\
    element.initDefaults();\
  }

◆ USE_LAYOUT

#define USE_LAYOUT 1

Function Documentation

◆ addToKnownFunctionToMap()

bool addToKnownFunctionToMap	(	std::map< std::string, std::string > &	map,
		const FunctionDefinition *	sbmlFunction
	)

References isKnownCustomFunctionDefinition().

Referenced by SBMLImporter::createCFunctionFromFunctionDefinition().

◆ AstStrCmp()

int AstStrCmp	(	const void *	s1,
		const void *	s2
	)

Referenced by ensureAllArgsAreBeingUsedInFunctionDefinition().

◆ containsKey()

bool containsKey	(	const CDataVector< CChemEqElement > &	list,
		const std::string &	key
	)

References CDataVector< CType >::begin(), and CDataVector< CType >::end().

Referenced by SBMLImporter::doMapping().

◆ ensureAllArgsAreBeingUsedInFunctionDefinition()

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.

References AstStrCmp(), and free().

Referenced by SBMLImporter::createCFunctionFromFunctionDefinition().

◆ findFunction()

CFunction* findFunction	(	CDataVectorN< CFunction > &	db,
		const CFunction *	func
	)

References CDataVector< CType >::size().

Referenced by CModel::convert2NonReversible(), SBMLImporter::createCFunctionFromFunctionDefinition(), and CReaction::setFunctionFromExpressionTree().

◆ getFunctionForKey()

CFunction* getFunctionForKey	(	CDataVectorN< CFunction > &	functionDb,
		const std::string &	key
	)

References CDataVector< CType >::begin(), CDataVector< CType >::end(), and CDataObject::getKey().

◆ getInitialCNForSBase()

std::string getInitialCNForSBase	(	SBase *	sbase,
		std::map< const CDataObject , SBase > &	copasi2sbmlmap,
		const std::string &	type
	)

References CDataObject::getCN(), CMetab::getInitialConcentrationReference(), and CModelEntity::getInitialValueReference().

Referenced by SBMLImporter::createCModelFromSBMLDocument().

◆ getOriginalSBMLId()

std::string getOriginalSBMLId	(	Parameter *	parameter,
		std::string &	type
	)

Referenced by SBMLImporter::createCModelFromSBMLDocument().

◆ hasCopasiAnnotation()

bool hasCopasiAnnotation	(	const SBase *	sbmlObject,
		const std::string &	sNamespace
	)

Referenced by SBMLImporter::importEvent().

◆ isKnownCustomFunctionDefinition()

std::string isKnownCustomFunctionDefinition	(	const FunctionDefinition *	sbmlFunction,
		const std::string &	sNamespace,
		const std::string &	elementName,
		const std::string &	definition
	)

Referenced by addToKnownFunctionToMap().

◆ renameShadowingFluxReferences()

void renameShadowingFluxReferences	(	KineticLaw *	kLaw,
		Model *	pSBMLModel,
		const std::string &	prefix
	)

This function replaces any local parameters of the kinetic law that references another reaction with an altered name.

Parameters

kLaw	the kinetic law
pSBMLModel	the model to search for conflicting reactions
prefix	the prefix to use when modifying the id.

Referenced by SBMLImporter::createCReactionFromReaction().

Classes

Macros

Functions