#include <CRootContainer.h>

Inheritance diagram for CRootContainer:

Public Member Functions
virtual	~CRootContainer ()

Public Member Functions inherited from CDataContainer
virtual bool	add (CDataObject *pObject, const bool &adopt=true)

virtual bool	appendDeletedDependentData (CUndoData &undoData) const

virtual bool	applyData (const CData &data, CUndoData::CChangeSet &changes) override

	CDataContainer (const CDataContainer &src, const CDataContainer *pParent)

	CDataContainer (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)

virtual void	createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const override

virtual std::string	getChildObjectUnits (const CDataObject *pObject) const

void	getDescendants (CDataObject::DataObjectSet &descendants, const bool &recursive=false) const

virtual size_t	getIndex (const CDataObject *pObject) const

virtual const CObjectInterface *	getObject (const CCommonName &cn) const override

virtual objectMap &	getObjects ()

virtual const objectMap &	getObjects () const

virtual const std::string	getUnits () const override

virtual const CDataObject *	getValueObject () const override

virtual CUndoObjectInterface *	insert (const CData &data) override

void	objectRenamed (CDataObject *pObject, const std::string &oldName)

virtual bool	remove (CDataObject *pObject)

virtual CData	toData () const override

virtual	~CDataContainer ()

Public Member Functions inherited from CDataObject
void	addIssue (const CIssue &issue)

void	addReference (const CDataContainer *pReference)

virtual void	calculateValue () override

	CDataObject (const CDataObject &src, const CDataContainer *pParent=NULL)

virtual void	destruct () override

virtual CCommonName	getCN () const override

virtual const CDataObject *	getDataObject () const override

virtual const std::string &	getKey () const

CDataContainer *	getObjectAncestor (const std::string &type) const

CDataModel *	getObjectDataModel () const

virtual std::string	getObjectDisplayName () const override

const CObjectInterface *	getObjectFromCN (const CCommonName &cn) const

const std::string &	getObjectName () const

CDataContainer *	getObjectParent () const

const std::string &	getObjectType () const

virtual const CObjectInterface::ObjectSet &	getPrerequisites () const override

virtual const CValidity &	getValidity () const override

virtual void *	getValuePointer () const override

bool	hasFlag (const Flag &flag) const

virtual bool	isPrerequisiteForContext (const CObjectInterface *pObject, const CCore::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const override

bool	prerequisitsContains (const DataObjectSet &objects) const

virtual void	print (std::ostream *ostream) const override

void	removeIssue (const CIssue &issue)

void	removeReference (const CDataContainer *pReference)

bool	setObjectName (const std::string &name)

virtual bool	setObjectParent (const CDataContainer *pParent)

void	validityChanged (const CValidity &changedValidity) override

void	validityRemoved (const CValidity &changedValidity)

virtual	~CDataObject ()

Public Member Functions inherited from CObjectInterface
	CObjectInterface ()

	CObjectInterface (const CObjectInterface &src)

virtual	~CObjectInterface ()

Public Member Functions inherited from CUndoObjectInterface
	CUndoObjectInterface ()

	CUndoObjectInterface (const CUndoObjectInterface &src)

bool	generateUuid ()

const xg::Guid &	getUuid () const

bool	setUuid (const std::string &uuid)

bool	setUuid (const xg::Guid &uuid)

virtual void	updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject)

virtual	~CUndoObjectInterface ()

Static Public Member Functions
static CDataModel *	addDatamodel ()

static void	destroy ()

static void	functionDefinitionChanged (const CFunction *pFunction)

static CConfigurationFile *	getConfiguration ()

static CDataVector< CDataModel > *	getDatamodelList ()

static CFunctionDB *	getFunctionList ()

static CKeyFactory *	getKeyFactory ()

static const char *	getLicenseHTML ()

static const char *	getLicenseTxt ()

static const CDataContainer *	getRoot ()

static CFunction *	getUndefinedFunction ()

static const CUnitDefinition *	getUnitDefFromSymbol (const std::string symbol)

static CUnitDefinitionDB *	getUnitList ()

static const CMIRIAMResource &	getUnknownMiriamResource ()

static void	init (int argc, char *argv[], const bool &withGui=false)

static std::string	quoteUnitDefSymbol (const std::string &symbol)

static bool	removeDatamodel (const CDataModel *pDatamodel)

static bool	removeDatamodel (const unsigned C_INT32 index)

static void	replaceSymbol (const std::string &oldSymbol, const std::string &newSymbol)

Static Public Member Functions inherited from CDataContainer
static CDataContainer *	fromData (const CData &data, CUndoObjectInterface *pParent)

Static Public Member Functions inherited from CDataObject
static CDataObject *	fromData (const CData &data, CUndoObjectInterface *pParent)

static void	sanitizeObjectName (std::string &name)

Static Public Member Functions inherited from CObjectInterface
static const CDataObject *	DataObject (const CObjectInterface *pInterface)

static CObjectInterface *	GetObjectFromCN (const ContainerList &listOfContainer, const CCommonName &objName)

Static Public Member Functions inherited from CUndoObjectInterface
template<class CType >
static CType *	fromData (const CData &, CUndoObjectInterface *)

Protected Attributes
CKeyFactory	mKeyFactory

CConfigurationFile *	mpConfiguration

CDataVector< CDataModel > *	mpDataModelList

CFunctionDB *	mpFunctionList

CFunction *	mpUndefined

CUnitDefinitionDB *	mpUnitDefinitionList

CMIRIAMResource *	mpUnknownResource

bool	mWithGUI

Protected Attributes inherited from CDataContainer
objectMap	mObjects

Protected Attributes inherited from CDataObject
ObjectSet	mPrerequisits

std::set< CDataContainer * >	mReferences

Protected Attributes inherited from CObjectInterface
CValidity	mValidity

Private Member Functions
	CRootContainer (const bool &withGUI=false)

	CRootContainer (const CRootContainer &src)

void	initializeChildren ()

CRootContainer &	operator= (const CRootContainer &src)

Additional Inherited Members
Public Types inherited from CDataContainer
typedef CDataObjectMap	objectMap

Public Types inherited from CDataObject
typedef std::set< const CDataObject * >	DataObjectSet

enum	Flag { Container , Vector , Matrix , NameVector , Reference , ValueBool , ValueInt , ValueInt64 , ValueDbl , NonUniqueName , StaticString , ValueString , Separator , DisplayName , ModelEntity , Array , DataModel , Root , Gui , __SIZE }

Public Types inherited from CObjectInterface
typedef std::vector< const CDataContainer * >	ContainerList

typedef std::set< const CObjectInterface * >	ObjectSet

Static Public Attributes inherited from CDataContainer
static const CObjectInterface::ContainerList	EmptyList

Protected Member Functions inherited from CDataContainer
template<class CType >
CDataMatrixReference< CType > *	addMatrixReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)

template<class CType >
CDataObjectReference< CType > *	addObjectReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)

template<class CType >
CDataVectorReference< CType > *	addVectorReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)

	CDataContainer (const CDataContainer &src)

void	initObjects ()

Protected Member Functions inherited from CDataObject
	CDataObject ()

	CDataObject (const std::string &name, const CDataContainer pParent=static_cast< CDataContainer >((void *) 0), const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)

Detailed Description

This is the new root container class. It will hold some attributes that are used by all datamodels, e.g.the global function database and the configuration, and it will hold a list of datamodels. Currently all methods to create new instances of CRootContainer are declared private. This ensures that there can be only one root container which is initialized by the init method. If this is necessary or not needs to be discussed.

Constructor & Destructor Documentation

◆ CRootContainer() [1/2]

CRootContainer::CRootContainer ( const bool & withGUI = false )

private

The default constructor should be private so that nobody can create new instances of the root container. The only way to create a root container is through the static init method. Maybe this restriction is not necessary. We have to discuss this later.

The default constructor should be private so that nobody can create new instances of the root container. The only way to create a root container is through the static init method.

Referenced by init().

◆ CRootContainer() [2/2]

CRootContainer::CRootContainer ( const CRootContainer & src )

private

The copy constructor is private as well to make sure that there is only one root container that can be initialized through the init call.

Parameters

const CRootContainer & src

◆ ~CRootContainer()

CRootContainer::~CRootContainer ( )

virtual

References DEFAULT_STYLES, mpConfiguration, mpDataModelList, mpFunctionList, mpUndefined, mpUnitDefinitionList, mpUnknownResource, mWithGUI, pdelete, and CConfigurationFile::save().

Member Function Documentation

◆ addDatamodel()

CDataModel * CRootContainer::addDatamodel ( )

static

Creates a new datamodel instance and adds it to the list. The new instance is returned by the method.

References CDataVector< CType >::add(), mpDataModelList, mWithGUI, and pRootContainer.

Referenced by CDataModel::addModel(), CDataModel::loadModelParameterSets(), Copasi2SBMLTranslator::translate(), Copasi2SBMLTranslator::translateFileToSBML(), and Copasi2SBMLTranslator::translateToSBML().

◆ destroy()

void CRootContainer::destroy ( )

static

References COptions::cleanup(), CRDFGraphConverter::deleteConverterData(), pdelete, pRootContainer, and CFunctionParameterMap::pUnmappedObject.

◆ functionDefinitionChanged()

void CRootContainer::functionDefinitionChanged ( const CFunction * pFunction )

static

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

Referenced by CFunction::setInfix().

◆ getConfiguration()

CConfigurationFile * CRootContainer::getConfiguration ( )

static

Returns the a pointer to the configuration.

References mpConfiguration, and pRootContainer.

Referenced by CMIRIAMInfo::addDefaultCreator(), SBMLImporter::checkValidityOfSourceDocument(), CMIRIAMResources::isCitation(), CJitCompiler::JitEnabled(), CInfo::update(), CProvenanceXMLWriter::updateCurrentSessionProvenance(), and CProvenanceXMLWriter::updateOrigionOfProvenance().

◆ getDatamodelList()

CDataVector< CDataModel > * CRootContainer::getDatamodelList ( )

static

Returns a pointer to the list of data models.

References mpDataModelList, and pRootContainer.

Referenced by CDataModel::addModel(), CDataModel::loadModelParameterSets(), CFunctionDB::purgeUnusedUserDefinedFunctions(), removeDatamodel(), and CFunctionDB::removeFunction().

◆ getFunctionList()

CFunctionDB * CRootContainer::getFunctionList ( )

static

Returns a pointer to the global function database.

References mpFunctionList, and pRootContainer.

Referenced by CCopasiXML::buildFunctionList(), CEvaluationNodeCall::calls(), CSBMLExporter::checkForPiecewiseFunctions(), CSBMLExporter::collectIds(), CEvaluationNodeCall::compile(), CFunction::completeFunctionList(), CModel::convert2NonReversible(), SBMLImporter::createCFunctionFromFunctionDefinition(), SBMLImporter::createCModelFromSBMLDocument(), SBMLImporter::createCReactionFromReaction(), CSBMLExporter::createEvent(), CSBMLExporter::createFunctionDefinitions(), CReaction::createFunctionFromExpression(), CSBMLExporter::createInitialAssignment(), CSBMLExporter::createRule(), COptProblem::elevateChildren(), CSBMLExporter::exportEventAssignments(), CODEExporter::exportSingleFunction(), CODEExporterC::exportSingleFunction(), SBMLImporter::findCorrespondingFunction(), SBMLImporter::findFunctionCalls(), CODEExporter::findFunctionsCalls(), CEvaluationNodeCall::getCalledTree(), CReactionInterface::getListOfPossibleFunctions(), CEvaluationTree::getNodeObject(), SBMLImporter::isConstantFlux(), CModel::load(), CDataModel::loadModel(), CODEExporter::modifyTreeForMassAction(), CDataModel::removeSBMLIdFromFunctions(), SBMLImporter::removeUnusedFunctions(), SBMLImporter::restoreFunctionDB(), CODEExporterC::setExportNameOfFunction(), CReaction::setFunction(), CReactionInterface::setFunctionAndDoMapping(), CReaction::setFunctionFromExpressionTree(), CSBMLExporter::setFunctionSBMLIds(), CReactionInterface::setFunctionWithEmptyMapping(), and CEvaluationNodeCall::toAST().

◆ getKeyFactory()

CKeyFactory * CRootContainer::getKeyFactory ( )

static

Returns a pointer to the KeyFactory.

References mKeyFactory, and pRootContainer.

Referenced by CModelAdd::addCompartmentsExpressions(), CModelAdd::addMetabolitesExpressions(), CModelAdd::addModelValuesExpressions(), CModel::applyActiveParameterSet(), CEvent::CEvent(), CEventAssignment::CEventAssignment(), CFunction::CFunction(), CLColorDefinition::CLColorDefinition(), COutputDefinitionVector::cleanup(), CReportDefinition::cleanup(), CReportDefinitionVector::cleanup(), CLEllipse::CLEllipse(), CLGlobalRenderInformation::CLGlobalRenderInformation(), CLGlobalStyle::CLGlobalStyle(), CLGradientStop::CLGradientStop(), CLGroup::CLGroup(), CLImage::CLImage(), CLLinearGradient::CLLinearGradient(), CLLineEnding::CLLineEnding(), CLLocalRenderInformation::CLLocalRenderInformation(), CLLocalStyle::CLLocalStyle(), CLPolygon::CLPolygon(), CLRadialGradient::CLRadialGradient(), CLRectangle::CLRectangle(), CLRenderCurve::CLRenderCurve(), CLText::CLText(), CModelEntity::CModelEntity(), CModelExpansion::SetOfModelElements::contains(), CModelAdd::copyDelayExpression(), CModelAdd::copyEventAssignmentExpression(), CModelAdd::copyExpression(), CModelAdd::copyInitialExpression(), CModelAdd::copyTriggerExpression(), CReaction::CReaction(), CUnitDefinition::CUnitDefinition(), CEvent::deleteAssignment(), CModelExpansion::ElementsMap::exists(), CODEExporterC::exportTitleData(), CFitItem::getCrossValidations(), CMetabNameInterface::getDisplayName(), CFitItem::getExperiments(), CLTextGlyph::getGraphicalObject(), CLMetabReferenceGlyph::getMetabGlyph(), CChemEqElement::getMetabolite(), CLGraphicalObject::getModelObject(), CTimeSeries::getSBMLId(), CLNAProblem::getSubTask(), CMCAProblem::getSubTask(), CLReferenceGlyph::getTargetGlyph(), CLGraphicalObject::hasValidModelReference(), CExperiment::initializeParameter(), CExperimentSet::keyToIndex(), CModelMerging::mergeInExpression(), SBMLDocumentLoader::postprocessTextGlyph(), CFitProblem::printResult(), COPASIHandler::processEnd(), CModel::removeCompartment(), CModel::removeEvent(), CFunctionDB::removeFunction(), CDataModel::removeLayout(), CModel::removeLocalReactionParameter(), CModel::removeMetabolite(), CModel::removeModelValue(), COutputDefinitionVector::removePlotSpec(), CModel::removeReaction(), CReportDefinitionVector::removeReportDefinition(), CSlider::setAssociatedEntityKey(), CChemEqElement::setMetabolite(), CUnitDefinition::setup(), CMMLOutput::writeDifferentialEquations(), CAnnotation::~CAnnotation(), CBiologicalDescription::~CBiologicalDescription(), CCompartment::~CCompartment(), CCopasiParameter::~CCopasiParameter(), CCopasiTask::~CCopasiTask(), CCreator::~CCreator(), CEvent::~CEvent(), CFunction::~CFunction(), CFunctionParameter::~CFunctionParameter(), CLayout::~CLayout(), CLColorDefinition::~CLColorDefinition(), CLEllipse::~CLEllipse(), CLGradientBase::~CLGradientBase(), CLGraphicalObject::~CLGraphicalObject(), CLGroup::~CLGroup(), CLImage::~CLImage(), CListOfLayouts::~CListOfLayouts(), CLPolygon::~CLPolygon(), CLRectangle::~CLRectangle(), CLRenderCurve::~CLRenderCurve(), CLRenderInformationBase::~CLRenderInformationBase(), CLStyle::~CLStyle(), CLText::~CLText(), CMetab::~CMetab(), CModel::~CModel(), CModelParameterSet::~CModelParameterSet(), CModification::~CModification(), CMoiety::~CMoiety(), CReaction::~CReaction(), CReference::~CReference(), CSlider::~CSlider(), and CUnitDefinition::~CUnitDefinition().

◆ getLicenseHTML()

const char * CRootContainer::getLicenseHTML ( )

static

References CopasiLicenseHtml.

◆ getLicenseTxt()

const char * CRootContainer::getLicenseTxt ( )

static

References CopasiLicenseTxt.

◆ getRoot()

const CDataContainer * CRootContainer::getRoot ( )

static

Retrieve the root container

References pRootContainer.

Referenced by CEvaluationNodeCall::compile(), CModelExpansion::ElementsMap::getDuplicateFromCN(), CDataContainer::getObject(), CObjectInterface::GetObjectFromCN(), CUndoData::getParent(), CUnitDefinitionDB::replaceSymbol(), and CCopasiParameter::~CCopasiParameter().

◆ getUndefinedFunction()

CFunction * CRootContainer::getUndefinedFunction ( )

static

Retrieve the pointer for the function used for importing kinetics without a kinetic law

Returns: CFunction * pUnsupportedDelay

References mpUndefined, and pRootContainer.

Referenced by CReaction::compile(), CReaction::CReaction(), CSBMLExporter::createReaction(), CReactionInterface::getFunction(), KineticLawHandler::processStart(), CCopasiXML::saveModel(), CReaction::setFunction(), CReactionInterface::setFunctionAndDoMapping(), and CReactionInterface::setFunctionWithEmptyMapping().

◆ getUnitDefFromSymbol()

const CUnitDefinition * CRootContainer::getUnitDefFromSymbol ( const std::string symbol )

static

Retrieve the unit for the given symbol

References CDataVector< CType >::begin(), C_INVALID_INDEX, CDataVectorN< CType >::getIndex(), CUnitDefinitionDB::getUnitDefFromSymbol(), getUnitList(), mpUnitDefinitionList, and pRootContainer.

◆ getUnitList()

CUnitDefinitionDB * CRootContainer::getUnitList ( )

static

Returns a pointer to the list of units.

References mpUnitDefinitionList, and pRootContainer.

Referenced by CUnit::buildExpression(), SBMLUnitSupport::createUnitExpressionFor(), getUnitDefFromSymbol(), CCopasiXML::mergeUnitDefinitions(), and CCopasiXML::saveUnitDefinitionList().

◆ getUnknownMiriamResource()

const CMIRIAMResource & CRootContainer::getUnknownMiriamResource ( )

static

References mpUnknownResource, and pRootContainer.

Referenced by CMIRIAMResources::getMIRIAMResource().

◆ init()

void CRootContainer::init	(	int	argc,
		char *	argv[],
		const bool &	withGUI = `false`
	)

static

This method creates the only root container.

References CRootContainer(), COptions::init(), initializeChildren(), pRootContainer, and CCopasiMessage::setIsGUI().

Referenced by Copasi2SBMLTranslator::translate(), Copasi2SBMLTranslator::translateFileToSBML(), and Copasi2SBMLTranslator::translateToSBML().

◆ initializeChildren()

void CRootContainer::initializeChildren ( )

private

This method needs to be called after a new root container is constructed. Since many of the children of the root container need to access the key factory through the global Root instance, the global root instance need to be created before the children can be initialized. Calling this Method initializes the children. This method must be protected since it can only be called once by the global init method.

References CEvaluationTree::compile(), CConfigurationFile::load(), CFunctionDB::load(), mpConfiguration, mpDataModelList, mpFunctionList, mpUndefined, mpUnitDefinitionList, mpUnknownResource, CFunction::setInfix(), CMIRIAMResource::setMIRIAMDisplayName(), CMIRIAMResource::setMIRIAMURI(), and CUnitDefinition::updateSIUnitDefinitions().