CDataVector< CType > Class Template Reference

#include <CDataVector.h>

Inheritance diagram for CDataVector< CType >:

Classes
class	const_iterator
class	iterator

Public Types
typedef CDataObjectMap::const_type_iterator< CType >	const_name_iterator
typedef CDataObjectMap::type_iterator< CType >	name_iterator
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

Public Member Functions
virtual bool	add (CDataObject *pObject, const bool &adopt=true)
virtual bool	add (const CType &src)
virtual bool	applyData (const CData &data, CUndoData::CChangeSet &changes)
iterator	begin ()
const_iterator	begin () const
name_iterator	beginName ()
const_name_iterator	beginName () const
	CDataVector (const CDataVector< CType > &src, const CDataContainer *pParent)
	CDataVector (const std::string &name="NoName", const CDataContainer *pParent=NO_PARENT, const CFlags< Flag > &flag=CFlags< Flag >::None)
virtual void	cleanup ()
virtual void	clear ()
virtual void	createUndoData (CUndoData &undoData, const CUndoData::Type &, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const
void	deepCopy (const CDataVector< CType > &source)
virtual bool	empty () const
iterator	end ()
const_iterator	end () const
name_iterator	endName ()
const_name_iterator	endName () const
virtual size_t	getIndex (const CDataObject *pObject) const
virtual const CObjectInterface *	getObject (const CCommonName &name) const
virtual CUndoObjectInterface *	insert (const CData &data)
bool	operator!= (const CDataVector< CType > &rhs)
CDataVector< CType > &	operator= (const CDataVector< CType > &rhs)
CDataVector< CType > &	operator= (const std::vector< CType * > &rhs)
CType &	operator[] (const size_t &index)
const CType &	operator[] (const size_t &index) const
virtual bool	remove (CDataObject *pObject)
virtual void	remove (const size_t &index)
virtual void	resize (const size_t &newSize)
virtual size_t	size () const
virtual void	swap (const size_t &indexFrom, const size_t &indexTo)
virtual CData	toData () const
virtual void	updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject)
virtual	~CDataVector ()
Public Member Functions inherited from CDataContainer
virtual bool	appendDeletedDependentData (CUndoData &undoData) const
	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 std::string	getChildObjectUnits (const CDataObject *pObject) const
void	getDescendants (CDataObject::DataObjectSet &descendants, const bool &recursive=false) const
virtual objectMap &	getObjects ()
virtual const objectMap &	getObjects () const
virtual const std::string	getUnits () const override
virtual const CDataObject *	getValueObject () const override
void	objectRenamed (CDataObject *pObject, const std::string &oldName)
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	~CUndoObjectInterface ()

Protected Member Functions
	CDataVector (const CDataVector< CType > &src)
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)

Friends
std::ostream &	operator<< (std::ostream &os, const CDataVector< CType > &d)

Additional Inherited Members
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 *)
Static Public Attributes inherited from CDataContainer
static const CObjectInterface::ContainerList	EmptyList
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

Detailed Description

template<class CType>
class CDataVector< CType >

CCopasiXMLInterface class. The class CCopasiXMLInterface is the interface to various XML document containing COPASI relevant information.

Created for COPASI by Stefan Hoops 2003

Member Typedef Documentation

const_name_iterator

template<class CType >

typedef CDataObjectMap::const_type_iterator< CType > CDataVector< CType >::const_name_iterator

name_iterator

template<class CType >

typedef CDataObjectMap::type_iterator< CType > CDataVector< CType >::name_iterator

Constructor & Destructor Documentation

CDataVector() [1/3]

template<class CType >

CDataVector< CType >::CDataVector ( const CDataVector< CType > &  src )

protected

CDataVector() [2/3]

template<class CType >

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

inline

Default constructor

Parameters

const	const std::string & name (Default: "NoName")
const	CDataContainer * pParent (Default: NULL)
const	size_t & flag (Default: flag | CDataObject::Vector)

References CONSTRUCTOR_TRACE.

CDataVector() [3/3]

template<class CType >

CDataVector< CType >::CDataVector ( const CDataVector< CType > &  src, const CDataContainer *  pParent  )

inline

Copy constructor

Parameters

const	CDataVector < CType > & src
const	CDataContainer * pParent (Default: NULL)

References CDataVector< CType >::begin(), CONSTRUCTOR_TRACE, CCopasiMessage::EXCEPTION, MCopasiBase, and CDataVector< CType >::size().

~CDataVector()

template<class CType >

virtual CDataVector< CType >::~CDataVector ( )

inlinevirtual

Destructor

References CDataVector< CType >::cleanup(), and DESTRUCTOR_TRACE.

Member Function Documentation

add() [1/2]

template<class CType >

virtual bool CDataVector< CType >::add ( CDataObject *  pObject, const bool &  adopt = true  )

inlinevirtual

Add an object to the end of the vector, if adopt is true the vector. becomes the parent of the object.

Parameters

CType	* src
const	bool & adopt (Default: false)

Returns

bool success

Reimplemented from CDataContainer.

Reimplemented in CDataVectorN< CType >, CDataVectorN< CEventAssignment >, CDataVectorN< CCopasiTask >, CDataVectorN< CLayout >, CDataVectorN< CUnitDefinition >, CDataVectorN< CPlotSpecification >, CDataVectorN< CModelParameterSet >, CDataVectorN< CEvent >, CDataVectorN< CFunction >, CDataVectorN< CModelValue >, and CDataVectorN< CReportDefinition >.

References CDataContainer::add().

add() [2/2]

template<class CType >

virtual bool CDataVector< CType >::add ( const CType &  src )

inlinevirtual

Add a copy of the object to the end of the vector.

Parameters

const

CType & src

Returns

bool success.

Reimplemented in CDataVectorN< CType >, and CDataVectorN< CEvent >.

References CDataContainer::add(), CCopasiMessage::EXCEPTION, and MCopasiBase.

Referenced by CLGroup::addChildElement(), CLRenderInformationBase::addColorDefinition(), CLayout::addCompartmentGlyph(), CRootContainer::addDatamodel(), CChemEq::addElement(), CLayout::addGeneralGlyph(), CListOfLayouts::addGlobalRenderInformation(), CLRenderInformationBase::addGradientDefinition(), CLGradientBase::addGradientStop(), CLRenderInformationBase::addLineEnding(), CLayout::addLocalRenderInformation(), CLayout::addMetaboliteGlyph(), CLReactionGlyph::addMetabReferenceGlyph(), CLayout::addReactionGlyph(), CLGeneralGlyph::addReferenceGlyph(), CLGlobalRenderInformation::addStyle(), CLLocalRenderInformation::addStyle(), CLGeneralGlyph::addSubglyph(), CLayout::addTextGlyph(), CModel::buildMoieties(), CLayout::CLayout(), CLGlobalRenderInformation::CLGlobalRenderInformation(), CLGroup::CLGroup(), CLLocalRenderInformation::CLLocalRenderInformation(), CLRenderInformationBase::CLRenderInformationBase(), CMIRIAMInfo::createBiologicalDescription(), CLRenderInformationBase::createColorDefinition(), CMIRIAMInfo::createCreator(), CLGroup::createCurve(), CMathContainer::createDiscontinuityDataEvent(), CLGroup::createEllipse(), CLGradientBase::createGradientStop(), CLGroup::createGroup(), CLGroup::createImage(), CPlotSpecification::createItem(), CLRenderInformationBase::createLinearGradientDefinition(), CLRenderInformationBase::createLineEnding(), CModel::createMetabolite(), CMIRIAMInfo::createModification(), CLGroup::createPolygon(), CLRenderInformationBase::createRadialGradientDefinition(), CLGroup::createRectangle(), CMIRIAMInfo::createReference(), CLGlobalRenderInformation::createStyle(), CLLocalRenderInformation::createStyle(), CLGroup::createText(), CModel::initializeMetabolites(), CCSPMethod::initializeOutput(), CModel::load(), CMIRIAMInfo::loadBiologicalDescriptions(), CMIRIAMInfo::loadCreators(), loadDefaultStyles(), CMIRIAMInfo::loadModifications(), CMIRIAMInfo::loadReferences(), CDataVector< CType >::operator=(), MetaboliteHandler::processStart(), SliderHandler::processStart(), CCSPMethod::setAnnotationM(), and CExperiment::updateFittedPoints().

applyData()

template<class CType >

virtual bool CDataVector< CType >::applyData ( const CData &  data, CUndoData::CChangeSet &  changes  )

inlinevirtual

Apply the provided data to the object

Parameters

const

CData & data

Returns

bool success

Reimplemented from CDataContainer.

Reimplemented in CDataVectorN< CType >, CDataVectorN< CEventAssignment >, CDataVectorN< CCopasiTask >, CDataVectorN< CLayout >, CDataVectorN< CUnitDefinition >, CDataVectorN< CPlotSpecification >, CDataVectorN< CModelParameterSet >, CDataVectorN< CEvent >, CDataVectorN< CFunction >, CDataVectorN< CModelValue >, and CDataVectorN< CReportDefinition >.

References CDataVector< CType >::end(), CData::getProperty(), CDataVector< CType >::insert(), CData::OBJECT_INDEX, CDataVector< CType >::operator[](), CDataVector< CType >::size(), CDataValue::toDataVector(), and CData::VECTOR_CONTENT.

begin() [1/2]

template<class CType >

iterator CDataVector< CType >::begin ( )

inline

Referenced by CMathContainer::allocate(), CModel::appendAllDependents(), CDataModel::appendDependentTasks(), CUnitDefinitionDB::appendDependentUnits(), CModel::appendDirectDependents(), SBMLImporter::applyStoichiometricExpressions(), CLayoutState::applyTo(), CSBMLExporter::assignSBMLIdsToReactions(), CFunctionParameters::begin(), CModel::buildDependencyGraphs(), CBitPatternMethod::buildKernelMatrix(), CBitPatternTreeMethod::buildKernelMatrix(), CSSAMethod::buildKineticMatrix(), CModel::buildMoieties(), CModel::buildRedStoi(), CModel::buildStateTemplate(), CModel::buildStoi(), CModel::buildUserOrder(), CDataVector< CType >::CDataVector(), CModel::changeUnitExpressionSymbols(), CSBMLExporter::checkForInitialAssignments(), CSBMLExporter::checkForODESpeciesInNonfixedCompartment(), SBMLUnitSupport::checkForSpatialSizeUnits(), CFixLocalReactionParameters::checkModel(), CLayout::CLayout(), CLayoutState::CLayoutState(), CDataModel::commonAfterLoad(), CMathContainer::compile(), CModel::compile(), CReaction::compile(), CEvent::compile(), CMathEvent::compile(), CMathContainer::compileEvents(), CModel::compileEvents(), CMathObject::compilePropensity(), containsKey(), SBMLImporter::createCModelFromSBMLDocument(), CSBMLExporter::createCompartments(), SBMLImporter::createCReactionFromReaction(), COutputAssistant::createDefaultOutput(), CSBMLExporter::createEvents(), CModelParameterSet::createFromModel(), CReaction::createFunctionFromExpression(), CCopasiSpringLayout::createLayout(), CSBMLExporter::createMetabolites(), CSBMLExporter::createParameters(), CSBMLExporter::createReactions(), CDataVector< CType >::createUndoData(), CMathContainer::createValueChangeProhibited(), CDataVector< CType >::deepCopy(), CSBMLExporter::exportEventAssignments(), CDataModel::exportMathModel(), CDataModel::exportMathModelToString(), CSBMLExporter::findAvogadro(), CDataModel::findObjectByDisplayName(), CCopasiXML::fixBuild113(), CRootContainer::functionDefinitionChanged(), CUnitDefinitionDB::getAllValidUnits(), CChemEq::getCompartments(), CObjectLists::getEventTargets(), getFunctionForKey(), CObjectLists::getListOfConstObjects(), CEFMTask::getNetReactionData(), CEvent::getOriginFor(), getQuantityParameterOrValue(), CEFMTask::getSpeciesChanges(), CScanProblem::getSubTask(), CSensProblem::getSubTask(), CModel::getTreesWithDiscontinuities(), CRootContainer::getUnitDefFromSymbol(), CModel::getUnitSymbolUsage(), CFunctionDB::getUsedFunctions(), CModel::getUsedUnits(), CModel::handleUnusedMetabolites(), CSBMLExporter::hasVolumeAssignment(), SBMLImporter::importMIRIAM(), CMathReaction::initialize(), CMathContainer::initializeEvents(), CMathContainer::initializeMathObjects(), CModel::initializeMetabolites(), CSBMLExporter::isEventSBMLCompatible(), CSBMLExporter::isModelSBMLCompatible(), CLNAMethod::isValidProblem(), CMCAMethod::isValidProblem(), CTSSAMethod::isValidProblem(), CCopasiXML::mergeUnitDefinitions(), CDataModel::openCombineArchive(), CDataVector< CType >::operator!=(), CDataVector< CType >::operator=(), CEFMProblem::printResult(), CMoietiesProblem::printResult(), COPASIHandler::processEnd(), CFunctionDB::removeFunction(), CModel::replaceInExpressions(), CRootContainer::replaceSymbol(), CUnitDefinitionDB::replaceSymbol(), CCopasiXML::saveModel(), CLLayoutRenderer::setDeduceSpeciesReferenceRoles(), SBMLImporter::setInitialValues(), CChemEq::setMultiplicity(), COptProblem::setSubtaskType(), CLayoutState::tagLayout(), CDataVector< CType >::toData(), CExperiment::updateFittedPointValues(), CExperiment::updateFittedPointValuesFromExtendedTimeSeries(), CModel::updateMatrixAnnotations(), and CModel::updateMoietyValues().

begin() [2/2]

template<class CType >

const_iterator CDataVector< CType >::begin ( ) const

inline

beginName() [1/2]

template<class CType >

name_iterator CDataVector< CType >::beginName ( )

inline

References CDataObjectMap::begin(), and CDataContainer::mObjects.

Referenced by CFunctionParameters::begin_name(), CDataVectorN< CType >::createUndoData(), and CDataVectorN< CType >::toData().

beginName() [2/2]

template<class CType >

const_name_iterator CDataVector< CType >::beginName ( ) const

inline

References CDataObjectMap::begin(), and CDataContainer::mObjects.

cleanup()

template<class CType >

virtual void CDataVector< CType >::cleanup ( )

inlinevirtual

Cleanup

Reimplemented in CReportDefinitionVector, and COutputDefinitionVector.

References CDataVector< CType >::clear(), and CDataContainer::remove().

Referenced by CModel::buildMoieties(), CFunctionDB::cleanup(), CFunctionParameters::cleanup(), CChemEq::cleanup(), CCompartment::cleanup(), CPlotSpecification::cleanup(), CKinFunction::createParameters(), CDataVector< CType >::deepCopy(), CSSAMethod::initialize(), CModel::load(), CDataVectorS< CType >::load(), CDataVectorNS< CType >::load(), CMIRIAMInfo::loadBiologicalDescriptions(), CMIRIAMInfo::loadCreators(), CMIRIAMInfo::loadModifications(), CMIRIAMInfo::loadReferences(), CDataVector< CType >::operator=(), and CDataVector< CType >::~CDataVector().

clear()

template<class CType >

virtual void CDataVector< CType >::clear ( )

inlinevirtual

References CValidity::clear(), CObjectInterface::mValidity, CDataContainer::remove(), and CDataVector< CType >::size().

Referenced by CDataVector< CType >::cleanup(), CModel::clearMoieties(), CMathContainer::compile(), CModel::initializeMetabolites(), CLGeneralGlyph::operator=(), COPASIHandler::processStart(), ModelHandler::processStart(), and CExperiment::updateFittedPoints().

createUndoData()

template<class CType >

virtual void CDataVector< CType >::createUndoData ( CUndoData &  undoData, const CUndoData::Type &  , const CData &  oldData = CData(), const CCore::Framework &  framework = CCore::Framework::ParticleNumbers  ) const

inlinevirtual

Create the undo data which represents the changes recording the differences between the provided oldData and the current data.

Parameters

CUndoData	& undoData
const	CUndoData::Type & type
const	CData & oldData (default: empty data)
const	CCore::Framework & framework (default: CCore::Framework::ParticleNumbers)

Returns

CUndoData undoData

Reimplemented from CDataContainer.

Reimplemented in CDataVectorN< CType >, CDataVectorN< CEventAssignment >, CDataVectorN< CCopasiTask >, CDataVectorN< CLayout >, CDataVectorN< CUnitDefinition >, CDataVectorN< CPlotSpecification >, CDataVectorN< CModelParameterSet >, CDataVectorN< CEvent >, CDataVectorN< CFunction >, CDataVectorN< CModelValue >, and CDataVectorN< CReportDefinition >.

References CUndoData::addPostProcessData(), CUndoData::addPreProcessData(), CUndoData::appendData(), CDataVector< CType >::begin(), CUndoData::CHANGE, CUndoData::empty(), CDataVector< CType >::end(), CUndoData::getNewData(), CUndoData::getOldData(), CUndoData::INSERT, CUndoData::REMOVE, and CData::VECTOR_CONTENT.

deepCopy()

template<class CType >

void CDataVector< CType >::deepCopy ( const CDataVector< CType > &  source )

inline

This creates a deep copy of the source, i.e., all objects are copied and the parent of these copies is the current vector.

Parameters

const

CDataVector< CType > & source

References CDataVector< CType >::begin(), CDataVector< CType >::cleanup(), CCopasiMessage::EXCEPTION, MCopasiBase, CDataVector< CType >::resize(), and CDataVector< CType >::size().

Referenced by CFunctionParameters::operator=().

empty()

template<class CType >

virtual bool CDataVector< CType >::empty ( ) const

inlinevirtual

Returns

a boolean indicating whether vector is empty

Referenced by CMIRIAMInfo::addDefaultCreator(), SEDMLImporter::assignReportDefinitions(), CSBMLExporter::assignSBMLIdsToReactions(), CSBMLExporter::checkForEvents(), CSBMLExporter::checkForInitialAssignments(), CEvent::compile(), CSBMLExporter::createKineticLaw(), CSBMLExporter::createReaction(), CSBMLExporter::hasVolumeAssignment(), and SBMLImporter::setInitialValues().

end() [1/2]

template<class CType >

iterator CDataVector< CType >::end ( )

inline

Referenced by CMathContainer::allocate(), CModel::appendAllDependents(), CDataModel::appendDependentTasks(), CUnitDefinitionDB::appendDependentUnits(), CModel::appendDirectDependents(), CDataVector< CType >::applyData(), CDataVectorN< CType >::applyData(), SBMLImporter::applyStoichiometricExpressions(), CLayoutState::applyTo(), CSBMLExporter::assignSBMLIdsToReactions(), CModel::buildDependencyGraphs(), CBitPatternMethod::buildKernelMatrix(), CBitPatternTreeMethod::buildKernelMatrix(), CSSAMethod::buildKineticMatrix(), CModel::buildStateTemplate(), CModel::buildStoi(), CModel::buildUserOrder(), CModel::changeUnitExpressionSymbols(), CSBMLExporter::checkForInitialAssignments(), CSBMLExporter::checkForODESpeciesInNonfixedCompartment(), SBMLUnitSupport::checkForSpatialSizeUnits(), CFixLocalReactionParameters::checkModel(), CLayout::CLayout(), CLayoutState::CLayoutState(), CDataModel::commonAfterLoad(), CMathContainer::compile(), CModel::compile(), CReaction::compile(), CEvent::compile(), CMathEvent::compile(), CMathContainer::compileEvents(), CModel::compileEvents(), CMathObject::compilePropensity(), containsKey(), SBMLImporter::createCModelFromSBMLDocument(), CSBMLExporter::createCompartments(), SBMLImporter::createCReactionFromReaction(), COutputAssistant::createDefaultOutput(), CSBMLExporter::createEvents(), CModelParameterSet::createFromModel(), CReaction::createFunctionFromExpression(), CCopasiSpringLayout::createLayout(), CSBMLExporter::createMetabolites(), CSBMLExporter::createParameters(), CSBMLExporter::createReactions(), CDataVector< CType >::createUndoData(), CDataVectorN< CType >::createUndoData(), CMathContainer::createValueChangeProhibited(), CFunctionParameters::end(), CSBMLExporter::exportEventAssignments(), CDataModel::exportMathModel(), CDataModel::exportMathModelToString(), CSBMLExporter::findAvogadro(), CDataModel::findObjectByDisplayName(), CCopasiXML::fixBuild113(), CRootContainer::functionDefinitionChanged(), CUnitDefinitionDB::getAllValidUnits(), CChemEq::getCompartments(), CObjectLists::getEventTargets(), getFunctionForKey(), CObjectLists::getListOfConstObjects(), CEFMTask::getNetReactionData(), CEvent::getOriginFor(), getQuantityParameterOrValue(), CEFMTask::getSpeciesChanges(), CScanProblem::getSubTask(), CSensProblem::getSubTask(), CModel::getTreesWithDiscontinuities(), CModel::getUnitSymbolUsage(), CFunctionDB::getUsedFunctions(), CModel::getUsedUnits(), CSBMLExporter::hasVolumeAssignment(), SBMLImporter::importMIRIAM(), CMathReaction::initialize(), CMathContainer::initializeEvents(), CMathContainer::initializeMathObjects(), CModel::initializeMetabolites(), CSBMLExporter::isEventSBMLCompatible(), CSBMLExporter::isModelSBMLCompatible(), CLNAMethod::isValidProblem(), CMCAMethod::isValidProblem(), CTSSAMethod::isValidProblem(), CCopasiXML::mergeUnitDefinitions(), CDataModel::openCombineArchive(), CDataVector< CType >::operator!=(), CDataVector< CType >::operator=(), CEFMProblem::printResult(), CMoietiesProblem::printResult(), COPASIHandler::processEnd(), CFunctionDB::removeFunction(), CModel::replaceInExpressions(), CRootContainer::replaceSymbol(), CUnitDefinitionDB::replaceSymbol(), CCopasiXML::saveModel(), SBMLImporter::setInitialValues(), CChemEq::setMultiplicity(), COptProblem::setSubtaskType(), CLayoutState::tagLayout(), CDataVector< CType >::toData(), CExperiment::updateFittedPointValues(), CExperiment::updateFittedPointValuesFromExtendedTimeSeries(), and CModel::updateMoietyValues().

end() [2/2]

template<class CType >

const_iterator CDataVector< CType >::end ( ) const

inline

endName() [1/2]

template<class CType >

name_iterator CDataVector< CType >::endName ( )

inline

References CDataObjectMap::end(), and CDataContainer::mObjects.

Referenced by CDataVectorN< CType >::createUndoData(), CFunctionParameters::end_name(), and CDataVectorN< CType >::toData().

endName() [2/2]

template<class CType >

const_name_iterator CDataVector< CType >::endName ( ) const

inline

References CDataObjectMap::end(), and CDataContainer::mObjects.

getIndex()

template<class CType >

virtual size_t CDataVector< CType >::getIndex ( const CDataObject *  pObject ) const

inlinevirtual

Retrieve the index of the pointed to object in the vector. If the object is not found C_INVALID_INDEX is returned.

Parameters

const

CDataObject * pObject

Returns

size_t index

Reimplemented from CDataContainer.

References CDataContainer::getIndex(), and CDataVector< CType >::size().

Referenced by CReactionInterface::createUndoData(), CDataVectorN< CType >::createUndoData(), getReactionIndex(), CDataVector< CType >::insert(), CDataVector< CType >::remove(), COutputDefinitionVector::removePlotSpec(), CReportDefinitionVector::removeReportDefinition(), and CDataVector< CType >::updateIndex().

getObject()

template<class CType >

virtual const CObjectInterface* CDataVector< CType >::getObject ( const CCommonName &  name ) const

inlinevirtual

Retrieve a the CDataObject with the given name.

Parameters

const

CCommonName &name

Returns

const CObjectInterface * object

Reimplemented from CDataContainer.

Reimplemented in CDataVectorN< CType >, CDataVectorN< CEventAssignment >, CDataVectorN< CCopasiTask >, CDataVectorN< CLayout >, CDataVectorN< CUnitDefinition >, CDataVectorN< CPlotSpecification >, CDataVectorN< CModelParameterSet >, CDataVectorN< CEvent >, CDataVectorN< CFunction >, CDataVectorN< CModelValue >, and CDataVectorN< CReportDefinition >.

References CCommonName::getElementIndex(), CDataContainer::getObject(), CDataObject::getObject(), CCommonName::getRemainder(), and CDataVector< CType >::size().

Referenced by COutputAssistant::createDefaultOutput(), CObjectLists::getListOfConstObjects(), and CDataVectorN< CType >::getObject().

insert()

template<class CType >

virtual CUndoObjectInterface* CDataVector< CType >::insert ( const CData &  data )

inlinevirtual

Create and insert an undo object based on the given data. This method needs to be re-implemented in container which support INSERT and REMOVE

Parameters

const

CData & data

Returns

CUndoObjectInterface * pUndoObject

Reimplemented from CDataContainer.

References CDataContainer::add(), C_INVALID_INDEX, CDataVector< CType >::getIndex(), CData::getProperty(), CData::isSetProperty(), min, CData::OBJECT_INDEX, CData::OBJECT_POINTER, CData::OBJECT_REFERENCE_INDEX, CData::OBJECT_TYPE, CDataValue::toSizeT(), CDataValue::toString(), CDataValue::toVoidPointer(), and CDataVector< CType >::updateIndex().

Referenced by CDataVector< CType >::applyData(), CDataVectorN< CType >::applyData(), CLGeneralGlyph::exportToSBML(), CLayout::exportToSBML(), CLReactionGlyph::exportToSBML(), CFunctionDB::removeFunction(), and CLLayoutRenderer::setDeduceSpeciesReferenceRoles().

operator!=()

template<class CType >

bool CDataVector< CType >::operator!= ( const CDataVector< CType > &  rhs )

inline

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

operator=() [1/2]

template<class CType >

CDataVector< CType >& CDataVector< CType >::operator= ( const CDataVector< CType > &  rhs )

inline

Assignment operator.

Parameters

const

CDataVector< CType > & rhs

Returns

CDataVector< CType > & lhs

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

Referenced by CDataVectorN< CType >::operator=().

operator=() [2/2]

template<class CType >

CDataVector< CType >& CDataVector< CType >::operator= ( const std::vector< CType * > &  rhs )

inline

Assignment operator. The effect of this operator is that both vectors will share the same objects. However, the parentship of the objects is not affected This means that the assigned vector must be used with some care.

Parameters

const

std::vector< CType * > & rhs

Returns

CDataVector< CType > & lhs

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

operator[]() [1/2]

template<class CType >

CType& CDataVector< CType >::operator[] ( const size_t &  index )

inline

Retrieve the indexed object.

Parameters

const

size_t & index

Returns

value_type & object

References CCopasiMessage::EXCEPTION, MCDataVector, and CDataVector< CType >::size().

operator[]() [2/2]

template<class CType >

const CType& CDataVector< CType >::operator[] ( const size_t &  index ) const

inline

Retrieve the indexed object.

Parameters

const

size_t & index

Returns

const value_type & object

References CCopasiMessage::EXCEPTION, MCDataVector, and CDataVector< CType >::size().

Referenced by CDataVector< CType >::applyData(), and CDataVectorN< CType >::operator[]().

remove() [1/2]

template<class CType >

virtual bool CDataVector< CType >::remove ( CDataObject *  pObject )

inlinevirtual

Removes the pointer to the object, from the vector

Parameters

CDataObject

* pObject

Returns

bool success

Reimplemented from CDataContainer.

Reimplemented in CUnitDefinitionDB.

References C_INVALID_INDEX, CDataVector< CType >::getIndex(), and CDataContainer::remove().

remove() [2/2]

template<class CType >

virtual void CDataVector< CType >::remove ( const size_t &  index )

inlinevirtual

Removes the index-th element from the vector

Parameters

const

size_t & index

Reimplemented in CUnitDefinitionDB.

References CDataContainer::remove(), and CDataVector< CType >::size().

Referenced by CUnitDefinitionDB::remove(), CDataVectorN< CType >::remove(), CMIRIAMInfo::removeBiologicalDescription(), CLRenderInformationBase::removeColorDefinition(), CMIRIAMInfo::removeCreator(), CRootContainer::removeDatamodel(), CLRenderInformationBase::removeGradientDefinition(), CLRenderInformationBase::removeLineEnding(), CModel::removeMetabolite(), CMIRIAMInfo::removeModification(), COutputDefinitionVector::removePlotSpec(), CMIRIAMInfo::removeReference(), and CReportDefinitionVector::removeReportDefinition().

resize()

template<class CType >

virtual void CDataVector< CType >::resize ( const size_t &  newSize )

inlinevirtual

Resizes the vector but does not create new member objects

Parameters

const

size_t & newSize

References CDataContainer::remove(), and CDataVector< CType >::size().

Referenced by CDataVector< CType >::deepCopy(), CDataVectorS< CType >::load(), CDataVectorNS< CType >::load(), and CCSPMethod::start().

size()

template<class CType >

virtual size_t CDataVector< CType >::size ( ) const

inlinevirtual

Retrieves the size of the vector

Returns

size_t size

Referenced by CModelAdd::addCompartments(), CModelAdd::addCompartmentsExpressions(), CChemEq::addElement(), CModelAdd::addEvents(), CModelAdd::addMetabolites(), CModelAdd::addMetabolitesExpressions(), CDataModel::addModel(), CModelAdd::addModelValues(), CModelAdd::addModelValuesExpressions(), CModelAdd::addReactions(), CLGradientBase::addSBMLAttributes(), CLRenderInformationBase::addSBMLAttributes(), CMathContainer::allocate(), CMathEvent::allocate(), CDataVector< CType >::applyData(), CSSAMethod::buildKineticMatrix(), CModel::buildStateTemplate(), CModel::buildStoi(), CModel::buildUserOrder(), CLayout::calculateBoundingBox(), CDataVector< CType >::CDataVector(), CSBMLExporter::checkForPiecewiseFunctions(), CHybridMethod::checkModel(), CHybridMethodODE45::checkModel(), CModelAnalyzer::checkReaction(), CDataVector< CType >::clear(), CLGeneralGlyph::CLGeneralGlyph(), CLGroup::CLGroup(), CSBMLExporter::collectIds(), CChemEqInterface::completeCompartments(), CReactionInterface::connectNonMetabolites(), CModel::convert2NonReversible(), SBMLDocumentLoader::convertRenderInformationReferencesIds(), SBMLImporter::createCFunctionFromFunctionDefinition(), SBMLImporter::createCModelFromSBMLDocument(), SBMLImporter::createCReactionFromReaction(), CSEDMLExporter::createDataGenerators(), COutputAssistant::createDefaultOutput(), CPlotSpecification::createDefaultPlot(), CCopasiSpringLayout::createLayout(), CModel::createMetabolite(), CKinFunction::createParameters(), COutputDefinitionVector::createPlotSpec(), CLayoutInitializer::createReactionGlyph(), CXMLParserData::createRenderInformation(), CReportDefinitionVector::createReportDefinition(), CSBMLExporter::createSBMLDocument(), CSBMLExporter::createTimesTree(), CDataVector< CType >::deepCopy(), SBMLImporter::doMapping(), CModelExpansion::duplicateReaction(), CFitProblem::elevateChildren(), CObjectLists::existsFixedMetab(), CODEExporter::exportCompartments(), CODEExporter::exportKineticFunction(), CODEExporterC::exportKineticFunctionGroup(), CODEExporter::exportMetabolites(), CODEExporter::exportMetabolitesConcentrations(), CODEExporter::exportModelValues(), CODEExporter::exportModelValuesExpressions(), CSEDMLExporter::exportNthPlot(), CODEExporter::exportODEs(), CODEExporter::exportReacParamsAndFuncs(), CODEExporterC::exportTitleData(), CLayout::exportToDotFile(), CLGeneralGlyph::exportToSBML(), CLayout::exportToSBML(), CListOfLayouts::exportToSBML(), CLReactionGlyph::exportToSBML(), CCopasiSpringLayout::finalizeState(), SBMLImporter::findCorrespondingFunction(), findFunction(), CFunctionDB::findLoadFunction(), CModel::findMoiety(), CFunctionParameters::findParameterByName(), CLRenderFlattener::flatten(), CLRenderInformationBase::getColorDefinition(), CChemEqInterface::getCompartment(), CMetabNameInterface::getDisplayName(), CLGroup::getElement(), ResultData::getFitTask(), CLRenderInformationBase::getGradientDefinition(), CLGradientBase::getGradientStop(), CDataVector< CType >::getIndex(), CDataVectorN< CType >::getIndex(), CChemEq::getLargestCompartment(), CLRenderInformationBase::getLineEnding(), CChemEq::getMolecularity(), CFunctionParameters::getNumberOfParametersByUsage(), CLRenderInformationBase::getNumColorDefinitions(), getNumDefaultStyles(), CLGroup::getNumElements(), CLRenderInformationBase::getNumGradientDefinitions(), CLGradientBase::getNumGradientStops(), CLRenderInformationBase::getNumLineEndings(), CModel::getNumMetabs(), CModel::getNumModelValues(), CLGlobalRenderInformation::getNumStyles(), CLLocalRenderInformation::getNumStyles(), CDataVector< CType >::getObject(), SEDMLUtils::getObjectForSbmlId(), CLLayoutRenderer::getObjectsAt(), CLLayoutRenderer::getObjectsInBoundingBox(), ResultData::getOptTask(), CFunctionParameters::getParameterByUsage(), CCopasiSpringLayout::getPotential(), CListOfLayouts::getRenderInformation(), CLayout::getRenderInformation(), CLGlobalRenderInformation::getStyle(), CLLocalRenderInformation::getStyle(), CModel::getTotSteps(), CModel::hasReversibleReaction(), CChemEqInterface::init(), CCopasiSpringLayout::initFromLayout(), CMathReaction::initialize(), CCSPMethod::initializeOutput(), CLsodaMethod::initializeParameter(), CReactionInterface::isLocked(), SBMLImporter::isMassActionExpression(), CLNAMethod::isValidProblem(), CTSSAMethod::isValidProblem(), CFunctionParameters::isVector(), CODEExporterC::KineticFunction2ODEmember(), CMMLOutput::listReactionsForMetab(), CModel::load(), CDataVectorS< CType >::load(), CDataVectorNS< CType >::load(), CDataModel::loadModelParameterSets(), CModelMerging::mergeMetabolites(), CLayout::moveBy(), CLGeneralGlyph::moveBy(), CLReactionGlyph::moveBy(), CReaction::object2variable(), CDataVector< CType >::operator!=(), CLGeneralGlyph::operator=(), CLReactionGlyph::operator=(), CDataVector< CType >::operator[](), CODEExporter::preprocess(), CODEExporterC::preprocess(), CCSPMethod::printResult(), CILDMMethod::printResult(), CCopasiSpringLayout::randomize(), CModelAdd::reactionInvolvesCompartment(), CDataVector< CType >::remove(), CLRenderInformationBase::removeColorDefinition(), CLRenderInformationBase::removeGradientDefinition(), CLRenderInformationBase::removeLineEnding(), CDataModel::removeSBMLIdFromFunctions(), SBMLImporter::removeUnusedFunctions(), CModelExpansion::replaceInReaction(), CDataVector< CType >::resize(), CCopasiXML::saveFunctionList(), CCopasiXML::saveGUI(), CCopasiXML::saveLayoutList(), CCopasiXML::saveListOfGlobalRenderInformation(), CCopasiXML::saveListOfLocalRenderInformation(), CCopasiXML::saveModel(), CCopasiXML::saveModelParameterSets(), CCopasiXML::savePlotList(), CCopasiXML::saveReportList(), CCopasiXML::saveTaskList(), CCopasiXML::saveUnitDefinitionList(), CCSPMethod::setAnnotationM(), CDataArray::setCopasiVector(), SBMLImporter::setCorrectUsage(), CLLayoutRenderer::setDeduceSpeciesReferenceRoles(), CReaction::setScalingFactor(), CModelMerging::simpleCall(), CFunctionParameters::size(), CModel::suitableForStochasticSimulation(), CFunctionDB::suitableFunctions(), CDataVector< CType >::swap(), CLGlobalRenderInformation::toSBML(), CLGroup::toSBML(), CLLocalRenderInformation::toSBML(), CLLayoutRenderer::update_associations(), CSBMLExporter::updateMIRIAMAnnotation(), CMMLOutput::writeDifferentialEquations(), and CMMLOutput::writeRHS().

swap()

template<class CType >

virtual void CDataVector< CType >::swap ( const size_t &  indexFrom, const size_t &  indexTo  )

inlinevirtual

Swap two objects in the vector.

Parameters

const	size_t & indexFrom
const	size_t & indexTo

References CCopasiMessage::EXCEPTION, MCDataVector, and CDataVector< CType >::size().

Referenced by CFunctionParameters::swap().

toData()

template<class CType >

virtual CData CDataVector< CType >::toData ( ) const

inlinevirtual

Retrieve the data describing the object

Returns

CData data

Reimplemented from CDataContainer.

Reimplemented in CDataVectorN< CType >, CDataVectorN< CEventAssignment >, CDataVectorN< CCopasiTask >, CDataVectorN< CLayout >, CDataVectorN< CUnitDefinition >, CDataVectorN< CPlotSpecification >, CDataVectorN< CModelParameterSet >, CDataVectorN< CEvent >, CDataVectorN< CFunction >, CDataVectorN< CModelValue >, and CDataVectorN< CReportDefinition >.

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

updateIndex()

template<class CType >

virtual void CDataVector< CType >::updateIndex ( const size_t &  index, const CUndoObjectInterface *  pUndoObject  )

inlinevirtual

Update the index of a contained object This method needs to be re-implemented in container which care about the order of contained objects

Parameters

const	size_t & index
const	CUndoObjectInterface * pUndoObject

Reimplemented from CUndoObjectInterface.

References C_INVALID_INDEX, CDataVector< CType >::getIndex(), and min.

Referenced by CDataVector< CType >::insert().

Friends And Related Function Documentation

operator<<

template<class CType >

std::ostream& operator<< ( std::ostream &  os, const CDataVector< CType > &  d  )

friend

ostream operator

Parameters

std::ostream	& os
const	CDataVector<CType> & d

Returns

std::ostream & os

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The documentation for this class was generated from the following file:

• CDataVector.h