#include <CCopasiRootContainer.h>

Inheritance diagram for CCopasiRootContainer:

Collaboration diagram for CCopasiRootContainer:

Public Member Functions
virtual	~CCopasiRootContainer ()

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

	CCopasiContainer (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=CCopasiObject::Container)

	CCopasiContainer (const CCopasiContainer &src, const CCopasiContainer *pParent=NULL)

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

virtual const CObjectInterface *	getObject (const CCopasiObjectName &cn) const

virtual const objectMap &	getObjects () const

virtual std::string	getUnits () const

virtual const CCopasiObject *	getValueObject () const

virtual bool	remove (CCopasiObject *pObject)

virtual	~CCopasiContainer ()

Public Member Functions inherited from CCopasiObject
void	addDirectDependency (const CCopasiObject *pObject)

	CCopasiObject (const CCopasiObject &src, const CCopasiContainer *pParent=NULL)

void	clearDirectDependencies ()

void	clearRefresh ()

bool	dependsOn (DataObjectSet candidates, const DataObjectSet &context=DataObjectSet()) const

void	getAllDependencies (DataObjectSet &dependencies, const DataObjectSet &context) const

virtual CCopasiObjectName	getCN () const

virtual const DataObjectSet &	getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const

virtual const std::string &	getKey () const

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

CCopasiDataModel *	getObjectDataModel ()

const CCopasiDataModel *	getObjectDataModel () const

virtual std::string	getObjectDisplayName (bool regular=true, bool richtext=false) const

const std::string &	getObjectName () const

CCopasiContainer *	getObjectParent () const

const std::string &	getObjectType () const

virtual const CObjectInterface::ObjectSet &	getPrerequisites () const

virtual Refresh *	getRefresh () const

UpdateMethod *	getUpdateMethod () const

virtual void *	getValuePointer () const

bool	hasCircularDependencies (DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const

bool	hasUpdateMethod () const

bool	isArray () const

bool	isContainer () const

bool	isDataModel () const

bool	isMatrix () const

bool	isNameVector () const

bool	isNonUniqueName () const

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

bool	isReference () const

bool	isRoot () const

bool	isSeparator () const

bool	isStaticString () const

bool	isValueBool () const

bool	isValueDbl () const

bool	isValueInt () const

bool	isValueInt64 () const

bool	isValueString () const

bool	isVector () const

virtual bool	mustBeDeleted (const DataObjectSet &deletedObjects) const

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

void	removeDirectDependency (const CCopasiObject *pObject)

void	setDirectDependencies (const DataObjectSet &directDependencies)

bool	setObjectName (const std::string &name)

virtual bool	setObjectParent (const CCopasiContainer *pParent)

void	setObjectValue (const C_FLOAT64 &value)

void	setObjectValue (const C_INT32 &value)

void	setObjectValue (const bool &value)

template<class CType >
void	setRefresh (CType pType, void(CType::method)(void))

template<class CType >
void	setUpdateMethod (CType pType, void(CType::method)(const C_FLOAT64 &))

template<class CType >
void	setUpdateMethod (CType pType, void(CType::method)(const C_INT32 &))

template<class CType >
void	setUpdateMethod (CType pType, void(CType::method)(const bool &))

virtual	~CCopasiObject ()

Public Member Functions inherited from CObjectInterface
	CObjectInterface ()

virtual	~CObjectInterface ()

Static Public Member Functions
static CCopasiDataModel *	addDatamodel ()

static void	destroy ()

static CConfigurationFile *	getConfiguration ()

static CCopasiVector < CCopasiDataModel > *	getDatamodelList ()

static CFunctionDB *	getFunctionList ()

static CKeyFactory *	getKeyFactory ()

static const char *	getLicenseHTML ()

static const char *	getLicenseTxt ()

static const CCopasiContainer *	getRoot ()

static CFunction *	getUndefinedFunction ()

static const CMIRIAMResource &	getUnknownMiriamResource ()

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

static bool	removeDatamodel (const CCopasiDataModel *pDatamodel)

static bool	removeDatamodel (const unsigned C_INT32 index)

Static Public Member Functions inherited from CCopasiObject
static std::vector< Refresh * >	buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet())

static void	setRenameHandler (CRenameHandler *rh)

Protected Attributes
CKeyFactory	mKeyFactory

CConfigurationFile *	mpConfiguration

CCopasiVector< CCopasiDataModel > *	mpDataModelList

CFunctionDB *	mpFunctionList

CFunction *	mpUndefined

CMIRIAMResource *	mpUnknownResource

bool	mWithGUI

Protected Attributes inherited from CCopasiContainer
objectMap	mObjects

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

	CCopasiRootContainer (const CCopasiRootContainer &src)

void	initializeChildren ()

CCopasiRootContainer &	operator= (const CCopasiRootContainer &src)

Additional Inherited Members
Public Types inherited from CCopasiContainer
typedef std::multimap < std::string, CCopasiObject * >	objectMap

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

typedef std::vector< Refresh * >	DataUpdateSequence

Public Types inherited from CObjectInterface
typedef std::set< const CObjectInterface * >	ObjectSet

typedef std::vector < CObjectInterface * >	UpdateSequence

Static Public Attributes inherited from CCopasiContainer
static const std::vector < CCopasiContainer * >	EmptyList

Protected Types inherited from CCopasiObject
enum	Flag { Container = 0x1, Vector = 0x2, Matrix = 0x4, NameVector = 0x8, Reference = 0x10, ValueBool = 0x20, ValueInt = 0x40, ValueInt64 = 0x80, ValueDbl = 0x100, NonUniqueName = 0x200, StaticString = 0x400, ValueString = 0x800, Separator = 0x1000, ModelEntity = 0x2000, Array = 0x4000, DataModel = 0x8000, Root = 0x10000, Gui = 0x20000 }

Protected Member Functions inherited from CCopasiContainer
template<class CType >
CCopasiObject *	addMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

template<class CType >
CCopasiObject *	addObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

template<class CType >
CCopasiObject *	addVectorReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

void	initObjects ()

Protected Member Functions inherited from CCopasiObject
	CCopasiObject ()

	CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0)

Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

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 CCopasiRootContainer 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.

Definition at line 41 of file CCopasiRootContainer.h.

Constructor & Destructor Documentation

CCopasiRootContainer::CCopasiRootContainer ( 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.

Definition at line 35 of file CCopasiRootContainer.cpp.

Referenced by init().

                                                               :
   CCopasiContainer("Root", NULL, "CN", CCopasiObject::Root),
   mKeyFactory(),
   mpUnknownResource(NULL),
   mpFunctionList(NULL),
   mpConfiguration(NULL),
   mpDataModelList(NULL),
   mWithGUI(withGUI),
   mpUndefined(NULL)
 {}

CCopasiRootContainer::CCopasiRootContainer ( const CCopasiRootContainer & 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 CCopasiRootContainer & src

CCopasiRootContainer::~CCopasiRootContainer ( )

virtual

Definition at line 47 of file CCopasiRootContainer.cpp.

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

 {
   // save and delete the configuration
   if (mpConfiguration != NULL &&
       mWithGUI)
     {
       mpConfiguration->save();
     }
 
   // delete the configuration
   pdelete(mpConfiguration);
 
   // delete the unkown resource
   pdelete(mpUnknownResource);
 
   // delete the model list
   pdelete(mpDataModelList);
 
   // delete the function list
   pdelete(mpFunctionList);
 
   // delete the undefined and the unsupported delay function
   pdelete(mpUndefined);
 
   // delete other static variables
   pdelete(DEFAULT_STYLES);
 }

Member Function Documentation

CCopasiDataModel * CCopasiRootContainer::addDatamodel ( )

static

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

Definition at line 149 of file CCopasiRootContainer.cpp.

References CCopasiVector< T >::add(), mpDataModelList, and mWithGUI.

 {
   CCopasiDataModel* pDataModel = new CCopasiDataModel(pRootContainer->mWithGUI);
   pRootContainer->mpDataModelList->add(pDataModel, true);
   return pDataModel;
 }

void CCopasiRootContainer::destroy ( )

static

Definition at line 92 of file CCopasiRootContainer.cpp.

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

 {
   if (pRootContainer != NULL)
     {
       delete pRootContainer;
       pRootContainer = NULL;
     }
 
   pdelete(CFunctionParameterMap::pUnmappedObject);
 
   COptions::cleanup();
 }

CConfigurationFile * CCopasiRootContainer::getConfiguration ( )

static

Returns the a pointer to the configuration.

Definition at line 131 of file CCopasiRootContainer.cpp.

References mpConfiguration.

 {
   return pRootContainer->mpConfiguration;
 }

CCopasiVector< CCopasiDataModel > * CCopasiRootContainer::getDatamodelList ( )

static

Returns a pointer to the list of data models.

Definition at line 143 of file CCopasiRootContainer.cpp.

References mpDataModelList.

 {
   return pRootContainer->mpDataModelList;
 }

CFunctionDB * CCopasiRootContainer::getFunctionList ( )

static

Returns a pointer to the global function database.

Definition at line 137 of file CCopasiRootContainer.cpp.

References mpFunctionList.

Referenced by CCopasiXML::buildFunctionList(), CEvaluationNodeCall::calls(), CSBMLExporter::checkForPiecewiseFunctions(), CSBMLExporter::collectIds(), CEvaluationNodeCall::compile(), CFunction::completeFunctionList(), CQMessageBox::confirmDelete(), CModel::convert2NonReversible(), CSBMLExporter::createEvent(), CSBMLExporter::createFunctionDefinitions(), CSBMLExporter::createInitialAssignment(), CSBMLExporter::createRule(), CQFunctionDM::data(), COptProblem::elevateChildren(), CSBMLExporter::exportEventAssignments(), CODEExporterC::exportSingleFunction(), CODEExporter::exportSingleFunction(), SBMLImporter::findFunctionCalls(), CODEExporter::findFunctionsCalls(), CEvaluationNodeCall::getCalledTree(), CReactionInterface::getListOfPossibleFunctions(), SEDMLImporter::importFirstSBMLModel(), CCopasiDataModel::importSBML(), CCopasiDataModel::importSBMLFromString(), CQFunctionDM::insertRows(), CQFunctionDM::isFunctionReadOnly(), FunctionWidget1::leave(), CQBrowserPaneDM::load(), CModel::load(), DataModelGUI::loadFunctionDB(), CCopasiDataModel::loadModel(), CODEExporter::modifyTreeForMassAction(), stress_test::normalizeFunctionDB(), CCopasiDataModel::ObjectFromCN(), CQFunctionDM::removeRows(), CCopasiDataModel::removeSBMLIdFromFunctions(), SBMLImporter::removeUnusedFunctions(), CQFunctionDM::rowCount(), DataModelGUI::saveFunctionDB(), CQFunctionDM::setData(), CODEExporterC::setExportNameOfFunction(), CQExpressionWidget::setExpression(), CReaction::setFunction(), CReactionInterface::setFunctionAndDoMapping(), CSBMLExporter::setFunctionSBMLIds(), CReactionInterface::setFunctionWithEmptyMapping(), FunctionWidget1::slotBtnDelete(), FunctionWidget1::slotBtnNew(), CQFunctionsWidget::slotDoubleClicked(), ReactionsWidget1::slotNewFunction(), test000058::test_bug1025_10(), test000058::test_bug1025_5(), test000067::test_bug1060(), test_compare_utilities::test_copasi_function_expansion(), test000075::test_import_time_dependent_function_definition(), test000078::test_l2v4_import_unordered_functions(), test000059::test_unique_id_17(), test000059::test_unique_id_18(), test000059::test_unique_id_19(), test000059::test_unique_id_20(), test000059::test_unique_id_21(), test000059::test_unique_id_21_2(), and CEvaluationNodeCall::toAST().

 {
   return pRootContainer->mpFunctionList;
 }

CKeyFactory * CCopasiRootContainer::getKeyFactory ( )

static

Returns a pointer to the KeyFactory.

Definition at line 163 of file CCopasiRootContainer.cpp.

References mKeyFactory.

 {
   return &pRootContainer->mKeyFactory;
 }

const char * CCopasiRootContainer::getLicenseHTML ( )

static

Definition at line 202 of file CCopasiRootContainer.cpp.

References CopasiLicenseHtml.

Referenced by CopasiUI3Window::license(), and CQSplashWidget::slotViewLicense().

 {
   return CopasiLicenseHtml;
 }

const char * CCopasiRootContainer::getLicenseTxt ( )

static

Definition at line 196 of file CCopasiRootContainer.cpp.

References CopasiLicenseTxt.

Referenced by main().

 {
   return CopasiLicenseTxt;
 }

const CCopasiContainer * CCopasiRootContainer::getRoot ( )

static

Retrieve the root container

Definition at line 125 of file CCopasiRootContainer.cpp.

References pRootContainer.

Referenced by CEvaluationNodeCall::compile(), ObjectBrowserWidget::loadData(), and CCopasiParameter::~CCopasiParameter().

 {
   return pRootContainer;
 }

CFunction * CCopasiRootContainer::getUndefinedFunction ( )

static

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

Returns: CFunction * pUnsupportedDelay

Definition at line 157 of file CCopasiRootContainer.cpp.

References mpUndefined.

Referenced by CReaction::calculateParticleFlux(), CReaction::compile(), CReaction::CReaction(), CSBMLExporter::createReaction(), CCopasiXMLParser::KineticLawElement::end(), CReactionInterface::initFromReaction(), CCopasiXML::saveModel(), CReaction::setFunction(), CCopasiXMLParser::KineticLawElement::start(), and test000062::test_kineticlaw_without_math().

 {
   return pRootContainer->mpUndefined;
 }

const CMIRIAMResource & CCopasiRootContainer::getUnknownMiriamResource ( )

static

Definition at line 169 of file CCopasiRootContainer.cpp.

References mpUnknownResource.

Referenced by CMIRIAMResources::getMIRIAMResource().

 {
   return *pRootContainer->mpUnknownResource;
 }

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

static

This method creates the only root container.

Definition at line 78 of file CCopasiRootContainer.cpp.

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

 {
   COptions::init(argc, argv);
 
   CCopasiMessage::setIsGUI(withGUI);
 
   if (pRootContainer == NULL)
     pRootContainer = new CCopasiRootContainer(withGUI);
 
   if (pRootContainer != NULL)
     pRootContainer->initializeChildren();
 }

void CCopasiRootContainer::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.

Definition at line 105 of file CCopasiRootContainer.cpp.

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

Referenced by init().

 {
   mpUnknownResource = new CMIRIAMResource("Unknown Resource");
   mpUnknownResource->setMIRIAMDisplayName("-- select --");
   mpUnknownResource->setMIRIAMURI("urn:miriam:unknown");
 
   mpFunctionList = new CFunctionDB("FunctionDB", this);
   mpFunctionList->load();
 
   mpDataModelList = new CCopasiVector<CCopasiDataModel>("ModelList", this);
 
   mpConfiguration = new CConfigurationFile;
   mpConfiguration->load();
 
   mpUndefined = new CFunction("undefined", this);
   mpUndefined->setInfix("nan");
   mpUndefined->compile();
 }

CCopasiRootContainer& CCopasiRootContainer::operator= ( const CCopasiRootContainer & src )

private

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

Parameters

const CCopasiRootContainer & src

Returns: CCopasiRootContainer &

bool CCopasiRootContainer::removeDatamodel ( const CCopasiDataModel * pDatamodel )

static

Definition at line 175 of file CCopasiRootContainer.cpp.

References mpDataModelList, pdelete, and CCopasiVector< T >::remove().

Referenced by removeDatamodel().

 {
   if (!pDatamodel)
     {
       return false;
     }
 
   pRootContainer->mpDataModelList->remove((CCopasiDataModel *)pDatamodel);
   pdelete(pDatamodel);
 
   return true;
 }

bool CCopasiRootContainer::removeDatamodel ( const unsigned C_INT32 index )

static

Definition at line 189 of file CCopasiRootContainer.cpp.

References getDatamodelList(), and removeDatamodel().

 {
   const CCopasiDataModel* pDatamodel = (*CCopasiRootContainer::getDatamodelList())[index];
   return CCopasiRootContainer::removeDatamodel(pDatamodel);
 }