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
	)

References C_INVALID_INDEX, convertBaseUnit(), CUnitComponent::getExponent(), CUnitComponent::getKind(), CUnitComponent::getMultiplier(), CUnitComponent::getScale(), and CCopasiMessage::WARNING.

Referenced by addSymbolComponentToUnitDefinition(), and CSBMLExporter::createUnitDefinitionFor().

addParticleNumberToInitialValueMap()

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

References CSBMLExporter::createUniqueId(), getAnnotationStringFor(), CDataObject::getCN(), CMetab::getCompartment(), CModelEntity::getInitialValue(), CModelEntity::getInitialValueReference(), CModelEntity::getKey(), CDataModel::getModel(), CDataObject::getObjectDataModel(), CDataObject::getObjectName(), and CModel::getQuantity2NumberFactor().

Referenced by CSBMLExporter::checkForUnsupportedObjectReferences().

addRateOfIfItDoesNotExist()

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

References createFunctionDefinitonForURI(), and hasFunctionDefinitionForURI().

Referenced by getUserDefinedFuctionForName(), and CSBMLExporter::replaceSpeciesReferences().

addSymbolComponentToUnitDefinition()

void addSymbolComponentToUnitDefinition	(	UnitDefinition *	result,
		CUnit::SymbolComponent &	component,
		const std::string &	unitExpression
	)

References addCUnitComponentToUnitDefinition(), C_INVALID_INDEX, convertSymbol(), CUnit::SymbolComponent::exponent, CUnit::getComponents(), CUnitComponent::getExponent(), CUnitComponent::getMultiplier(), CUnitComponent::getScale(), CUnit::SymbolComponent::multiplier, CUnit::SymbolComponent::scale, CBaseUnit::scaleFromPrefix(), CUnitComponent::setExponent(), CUnitComponent::setMultiplier(), CUnitComponent::setScale(), and CUnit::SymbolComponent::symbol.

Referenced by CSBMLExporter::createUnitDefinitionFor().

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
	)

References C_FLOAT64, CSBMLExporter::createUniqueId(), getAnnotationStringFor(), CDataObject::getCN(), CDataObject::getKey(), CDataObject::getObjectName(), CDataObject::getValuePointer(), CDataObject::hasFlag(), and CDataObject::ValueDbl.

Referenced by CSBMLExporter::checkForUnsupportedObjectReferences().

adjustNames()

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

References getUserDefinedFuctionForName().

Referenced by CSBMLExporter::convertToASTNode().

convertBaseUnit()

size_t convertBaseUnit

(

CBaseUnit::Kind

unit

)

References CBaseUnit::ampere, CBaseUnit::avogadro, C_INVALID_INDEX, CBaseUnit::candela, CBaseUnit::dimensionless, CBaseUnit::gram, CBaseUnit::item, CBaseUnit::kelvin, CBaseUnit::meter, CBaseUnit::second, and CBaseUnit::undefined.

Referenced by addCUnitComponentToUnitDefinition().

convertExpression()

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

Referenced by CSBMLExporter::createEvent(), CSBMLExporter::createRule(), and CSBMLExporter::exportEventAssignments().

convertSymbol()

size_t convertSymbol

(

const std::string &

unit

)

References C_INVALID_INDEX.

Referenced by addSymbolComponentToUnitDefinition().

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
	)

References CSBMLExporter::createUniqueId().

Referenced by addRateOfIfItDoesNotExist(), and getUserDefinedFuctionForName().

getAnnotationStringFor()

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

Referenced by addParticleNumberToInitialValueMap(), and addToInitialValueMap().

getUserDefinedFuctionForName()

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

References addRateOfIfItDoesNotExist(), createFunctionDefinitonForURI(), and hasFunctionDefinitionForURI().

Referenced by adjustNames().

hasFunctionDefinitionForURI()

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

Referenced by addRateOfIfItDoesNotExist(), and getUserDefinedFuctionForName().

removeStickyTagFromElements()

void removeStickyTagFromElements

(

SBMLDocument *

pSBMLDocument

)

Referenced by CSBMLExporter::exportModelToString().

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().