CExperimentObjectMap Class Reference

#include <CExperimentObjectMap.h>

Inheritance diagram for CExperimentObjectMap:

Classes
class	CDataColumn

Public Member Functions
	CExperimentObjectMap (const CCopasiParameterGroup &group, const CDataContainer *pParent)
	CExperimentObjectMap (const CExperimentObjectMap &src, const CDataContainer *pParent)
	CExperimentObjectMap (const std::string &name="Object Map", const CDataContainer *pParent=NO_PARENT)
bool	compile (const CMathContainer *pMathContainer)
virtual bool	elevateChildren ()
void	fixBuild55 ()
const CVector< const CDataObject * > &	getDataObjects () const
C_FLOAT64	getDefaultScale (const size_t &index) const
const size_t &	getLastColumn () const
size_t	getLastNotIgnoredColumn () const
virtual const std::string &	getName (const size_t &index) const
std::string	getNthCnOfType (size_t index, CExperiment::Type role) const
std::string	getObjectCN (const size_t &index) const
CExperiment::Type	getRole (const size_t &index) const
C_FLOAT64	getScale (const size_t &index) const
const CExperimentObjectMap &	operator= (const CCopasiParameterGroup &rhs)
bool	setNumCols (const size_t &numCols)
bool	setObjectCN (const size_t &index, const std::string &objectCN)
bool	setRole (const size_t &index, const CExperiment::Type &role)
bool	setScale (const size_t &index, const C_FLOAT64 &scale)
virtual	~CExperimentObjectMap ()
Public Member Functions inherited from CCopasiParameterGroup
bool	addGroup (const std::string &name)
void	addParameter (CCopasiParameter *pParameter)
bool	addParameter (const CCopasiParameter &parameter)
bool	addParameter (const std::string &name, const CCopasiParameter::Type type, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)
template<class CType >
bool	addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)
virtual bool	applyData (const CData &data, CUndoData::CChangeSet &changes)
CCopasiParameterGroup *	assertGroup (const std::string &name, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)
template<class CType >
CType *	assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)
index_iterator	beginIndex () const
const_name_iterator	beginName () const
	CCopasiParameterGroup (const CCopasiParameterGroup &src, const CDataContainer *pParent=NULL)
	CCopasiParameterGroup (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &objectType="ParameterGroup")
void	clear ()
virtual void	createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const
index_iterator	endIndex () const
const_name_iterator	endName () const
CCopasiParameterGroup &	getElementTemplates ()
const CCopasiParameterGroup &	getElementTemplates () const
CCopasiParameterGroup *	getGroup (const size_t &index)
const CCopasiParameterGroup *	getGroup (const size_t &index) const
CCopasiParameterGroup *	getGroup (const std::string &name)
const CCopasiParameterGroup *	getGroup (const std::string &name) const
virtual size_t	getIndex (const CDataObject *pObject) const
size_t	getIndex (const std::string &name) const
std::string	getKey (const size_t &index) const
std::string	getKey (const std::string &name) const
virtual const CObjectInterface *	getObject (const CCommonName &cn) const
CCopasiParameter *	getParameter (const size_t &index)
const CCopasiParameter *	getParameter (const size_t &index) const
CCopasiParameter *	getParameter (std::string name)
const CCopasiParameter *	getParameter (std::string name) const
CCopasiParameter::Type	getType (const size_t &index) const
CCopasiParameter::Type	getType (const std::string &name) const
std::string	getUniqueParameterName (const CCopasiParameter *pParameter) const
template<class CType >
CType &	getValue (const size_t &index)
template<class CType >
const CType &	getValue (const size_t &index) const
template<class CType >
CType &	getValue (const std::string &name)
template<class CType >
const CType &	getValue (const std::string &name) const
bool	haveTemplate () const
virtual CUndoObjectInterface *	insert (const CData &data)
CCopasiParameterGroup &	operator= (const CCopasiParameterGroup &rhs)
virtual void	print (std::ostream *ostream) const
virtual bool	remove (CDataObject *pObject)
bool	removeParameter (CCopasiParameter *pParameter)
bool	removeParameter (const size_t &index)
bool	removeParameter (const std::string &name)
virtual void	setUserInterfaceFlag (const UserInterfaceFlag &flag)
template<class CType >
bool	setValue (const size_t &index, const CType &value)
template<class CType >
bool	setValue (const std::string &name, const CType &value)
size_t	size (const UserInterfaceFlag &require=UserInterfaceFlag::None, const UserInterfaceFlag &exclude=UserInterfaceFlag::None) const
bool	swap (const size_t &iFrom, const size_t &iTo)
bool	swap (index_iterator &from, index_iterator &to)
virtual CData	toData () const
virtual void	updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject)
virtual	~CCopasiParameterGroup ()
Public Member Functions inherited from CCopasiParameter
	CCopasiParameter (const CCopasiParameter &src, const CDataContainer *pParent)
	CCopasiParameter (const std::string &name, const Type &type, const void *pValue=NULL, const CDataContainer *pParent=NO_PARENT, const std::string &objectType="Parameter")
virtual CCommonName	getCN () const override
template<class CType >
const CType &	getDefault () const
virtual const std::string &	getKey () const override
virtual std::string	getObjectDisplayName () const override
const CCopasiParameter::Type &	getType () const
const UserInterfaceFlag &	getUserInterfaceFlag () const
template<class CType >
std::vector< std::pair< CType, CType > > &	getValidValues ()
template<class CType >
const std::vector< std::pair< CType, CType > > &	getValidValues () const
void *	getValidValuesPointer () const
template<class CType >
CType &	getValue ()
template<class CType >
const CType &	getValue () const
virtual void *	getValuePointer () const override
CDataObject *	getValueReference () const
bool	hasValidValues () const
bool	isBasic () const
bool	isDefault () const
bool	isEditable () const
bool	isUnsupported () const
bool	isValidValue (const bool &value) const
bool	isValidValue (const C_FLOAT64 &value) const
bool	isValidValue (const C_INT32 &value) const
bool	isValidValue (const CCommonName &value) const
template<class CType >
bool	isValidValue (const CType &) const
bool	isValidValue (const std::string &value) const
bool	isValidValue (const std::vector< CCopasiParameter * > &value) const
bool	isValidValue (const unsigned C_INT32 &value) const
CCopasiParameter &	operator= (const CCopasiParameter &rhs)
template<class CType >
bool	setDefault (const CType &defaultValue)
bool	setDefault (const std::vector< CCopasiParameter * > &defaultValue)
virtual bool	setObjectParent (const CDataContainer *pParent) override
template<class CType , class Enum >
bool	setValidValues (const CEnumAnnotation< CType, Enum > &validValues)
template<class CType >
bool	setValidValues (const std::vector< std::pair< CType, CType > > &validValues)
template<class CType >
bool	setValue (const CType &value)
bool	setValue (const std::vector< CCopasiParameter * > &value)
virtual	~CCopasiParameter ()
Public Member Functions inherited from CDataContainer
virtual bool	add (CDataObject *pObject, const bool &adopt=true)
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 const CDataObject *	getDataObject () const override
CDataContainer *	getObjectAncestor (const std::string &type) const
CDataModel *	getObjectDataModel () const
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
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
void	removeIssue (const CIssue &issue)
void	removeReference (const CDataContainer *pReference)
bool	setObjectName (const std::string &name)
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 ()

Private Member Functions
void	initializeParameter ()

Private Attributes
size_t	mLastColumn
CVector< const CDataObject * >	mObjects

Additional Inherited Members
Public Types inherited from CCopasiParameterGroup
typedef CDataObjectMap::const_type_iterator< CCopasiParameter >	const_name_iterator
typedef std::vector< CCopasiParameter * >	elements
typedef elements::iterator	index_iterator
typedef CDataObjectMap::type_iterator< CCopasiParameter >	name_iterator
Public Types inherited from CCopasiParameter
enum class	eUserInterfaceFlag { editable , basic , unsupported , __SIZE }
enum class	Type {   DOUBLE = 0 , UDOUBLE , INT , UINT ,   BOOL , GROUP , STRING , CN ,   KEY , FILE , EXPRESSION , INVALID ,   __SIZE }
typedef CFlags< eUserInterfaceFlag >	UserInterfaceFlag
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 Member Functions inherited from CCopasiParameter
static void	allocateValidValues (const Type &type, void *&pValidValues)
static void	allocateValue (const Type &type, void *&pValue)
static void	assignValue (const Type &type, void *&pValue, const void *pNewValue)
static void	deleteValidValues (const Type &type, void *&pValidValues)
static void	deleteValue (const Type &type, void *&pValue)
static CCopasiParameter *	fromData (const CData &data, CUndoObjectInterface *pParent)
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 CCopasiParameter
static const CEnumAnnotation< std::string, Type >	TypeName
static const CEnumAnnotation< std::string, Type >	XMLType
Static Public Attributes inherited from CDataContainer
static const CObjectInterface::ContainerList	EmptyList
Protected Member Functions inherited from CCopasiParameterGroup
	CCopasiParameterGroup ()
Protected Member Functions inherited from CCopasiParameter
	CCopasiParameter (const CCopasiParameter &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)
Protected Attributes inherited from CCopasiParameter
std::string	mKey
void *	mpDefault
void *	mpValidValues
void *	mpValue
CDataObject *	mpValueReference
UserInterfaceFlag	mUserInterfaceFlag
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

Constructor & Destructor Documentation

CExperimentObjectMap() [1/3]

CExperimentObjectMap::CExperimentObjectMap	(	const std::string &	name = "Object Map",
		const CDataContainer *	pParent = NO_PARENT
	)

Default constructor

Parameters

const	std::string & name (default: Object Map)
const	CDataContainer * pParent (default: NULL)

References initializeParameter().

CExperimentObjectMap() [2/3]

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

Copy constructor

Parameters

const	CExperimentObjectMap & src
const	CDataContainer * pParent (default: NULL)

References initializeParameter().

CExperimentObjectMap() [3/3]

CExperimentObjectMap::CExperimentObjectMap	(	const CCopasiParameterGroup &	group,
		const CDataContainer *	pParent
	)

Specific constructor used for reading copasi files

Parameters

const	CCopasiParameterGroup & group
const	CDataContainer * pParent (default: NULL)

References initializeParameter().

~CExperimentObjectMap()

CExperimentObjectMap::~CExperimentObjectMap ( )

virtual

Destructor

Member Function Documentation

compile()

bool CExperimentObjectMap::compile

(

const CMathContainer *

pMathContainer

)

Compile the map. This function must be called before any operations can be performed.

Parameters

const

CMathContainer * pMathContainer

Returns

bool success

References C_INVALID_INDEX, CObjectInterface::DataObject(), getName(), getObjectCN(), CDataObject::hasFlag(), mLastColumn, mObjects, pMathContainer, CVector< CType >::resize(), CCopasiParameterGroup::size(), and CDataObject::ValueDbl.

Referenced by CExperiment::compile().

elevateChildren()

bool CExperimentObjectMap::elevateChildren ( )

virtual

This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.

Returns

bool success

Reimplemented from CCopasiParameterGroup.

References CCopasiParameterGroup::assertGroup(), CCopasiParameterGroup::assertParameter(), CCopasiParameterGroup::beginIndex(), CCopasiParameterGroup::clear(), CCopasiParameter::CN, CCopasiParameterGroup::endIndex(), CDataObject::getObjectName(), and operator=().

Referenced by CExperimentObjectMap::CDataColumn::initializeParameter(), and initializeParameter().

fixBuild55()

void CExperimentObjectMap::fixBuild55

(

)

Fix files written with Version 4.10.55, which wrote the square root of user defined weights for the parameter fitting task

References CCopasiParameterGroup::beginIndex(), CCopasiParameterGroup::endIndex(), and CExperimentObjectMap::CDataColumn::fixBuild55().

Referenced by CExperiment::fixBuild55().

getDataObjects()

const CVector< const CDataObject * > & CExperimentObjectMap::getDataObjects

(

)

const

Retrieve the vector of mapped objects

Returns

const CVector< const CDataObject * > & mappedObjects

References mObjects.

Referenced by CExperiment::compile(), and CExperiment::printResult().

getDefaultScale()

C_FLOAT64 CExperimentObjectMap::getDefaultScale

(

const size_t &

index

)

const

Retrieve the default scaling factor according to the selected weight method of the indexed column

Parameters

const

size_t & index

Returns

C_FLOAT64 defaultScale

References CExperimentObjectMap::CDataColumn::getDefaultScale(), CCopasiParameterGroup::getGroup(), and StringPrint().

Referenced by CExperimentObjectMap::CDataColumn::getScale(), and CExperimentObjectMap::CDataColumn::setScale().

getLastColumn()

const size_t & CExperimentObjectMap::getLastColumn

(

)

const

Retrieve the last mapped column number

Returns

const size_t & lastColumn

References mLastColumn.

Referenced by CExperiment::compile(), and getNthCnOfType().

getLastNotIgnoredColumn()

size_t CExperimentObjectMap::getLastNotIgnoredColumn

(

)

const

Retrieve the last non ignored column

Returns

size_t lastNotIgnoredColumn

References CCopasiParameterGroup::beginIndex(), C_INT32, CCopasiParameterGroup::endIndex(), CDataObject::getObjectName(), CExperimentObjectMap::CDataColumn::getRole(), and CExperiment::ignore.

Referenced by CExperiment::compile(), and CExperiment::printResult().

getName()

const std::string & CExperimentObjectMap::getName ( const size_t &  index ) const

virtual

Retrieve the name of a parameter or subgroup

Parameters

const

size_t & index

Returns

std::string name

Reimplemented from CCopasiParameterGroup.

References CCopasiParameterGroup::getGroup(), CDataObject::getObjectName(), and StringPrint().

Referenced by compile().

getNthCnOfType()

std::string CExperimentObjectMap::getNthCnOfType	(	size_t	index,
		CExperiment::Type	role
	)		const

Retrieve the nth CN of specified Type

Parameters

index	the index
type	the type to return the column name for @ return name or empty string if not found

References getLastColumn(), getObjectCN(), and getRole().

getObjectCN()

std::string CExperimentObjectMap::getObjectCN

(

const size_t &

index

)

const

Retrieve the object CN of the object mapped to the indexed column

Parameters

const

size_t & index

Returns

std::stringobjctCN

References CCopasiParameterGroup::getGroup(), CExperimentObjectMap::CDataColumn::getObjectCN(), and StringPrint().

Referenced by compile(), CExperiment::elevateChildren(), getNthCnOfType(), and CExperiment::updateFittedPoints().

getRole()

CExperiment::Type CExperimentObjectMap::getRole

(

const size_t &

index

)

const

Retrieve the role of the indexed column

Parameters

const

size_t & index

Returns

CExperiment::Type role

References CCopasiParameterGroup::getGroup(), CExperimentObjectMap::CDataColumn::getRole(), CExperiment::ignore, and StringPrint().

Referenced by CExperiment::compile(), getNthCnOfType(), CExperiment::printResult(), CExperiment::read(), and CExperiment::updateFittedPoints().

getScale()

C_FLOAT64 CExperimentObjectMap::getScale

(

const size_t &

index

)

const

Retrieve the scaling factor of the indexed column

Parameters

const

size_t & index

Returns

C_FLOAT64 scale

References CCopasiParameterGroup::getGroup(), CExperimentObjectMap::CDataColumn::getScale(), and StringPrint().

Referenced by CExperiment::compile().

initializeParameter()

void CExperimentObjectMap::initializeParameter ( )

private

Allocates all group parameters and assures that they are properly initialized.

References elevateChildren().

Referenced by CExperimentObjectMap(), and operator=().

operator=()

const CExperimentObjectMap & CExperimentObjectMap::operator=

(

const CCopasiParameterGroup &

rhs

)

Assignment operator

Parameters

const

CCopasiParameterGroup & rhs

Returns

const CExperimentObjectMap & self

References initializeParameter(), and CCopasiParameterGroup::operator=().

Referenced by elevateChildren().

setNumCols()

bool CExperimentObjectMap::setNumCols

(

const size_t &

numCols

)

Set the number of data columns

Parameters

const

size_t & numCols

Returns

bool success

References CCopasiParameterGroup::assertGroup(), CCopasiParameterGroup::clear(), CCopasiParameter::mpValue, CCopasiParameterGroup::size(), and StringPrint().

Referenced by CExperiment::elevateChildren().

setObjectCN()

bool CExperimentObjectMap::setObjectCN	(	const size_t &	index,
		const std::string &	objectCN
	)

Set the object CN of the object mapped to the indexed column

Parameters

const	size_t & index
const	std::string & objectCN

Returns

bool success

References CCopasiParameterGroup::getGroup(), CExperimentObjectMap::CDataColumn::setObjectCN(), and StringPrint().

Referenced by CExperiment::elevateChildren(), and CExperimentObjectMap::CDataColumn::operator=().

setRole()

bool CExperimentObjectMap::setRole	(	const size_t &	index,
		const CExperiment::Type &	role
	)

Set the role of the indexed column

Parameters

const	size_t & index
const	CExperiment::Type & role

Returns

bool success

References CCopasiParameterGroup::getGroup(), CExperimentObjectMap::CDataColumn::setRole(), and StringPrint().

Referenced by CExperiment::elevateChildren().

setScale()

bool CExperimentObjectMap::setScale	(	const size_t &	index,
		const C_FLOAT64 &	scale
	)

Set the scaling factor for the indexed column

Parameters

const	size_t & index
const	C_FLOAT64 & scale

Returns

bool success

References CCopasiParameterGroup::getGroup(), CExperimentObjectMap::CDataColumn::setScale(), and StringPrint().

Referenced by CExperimentObjectMap::CDataColumn::operator=().

Member Data Documentation

mLastColumn

size_t CExperimentObjectMap::mLastColumn

private

The last mapped column

Referenced by compile(), and getLastColumn().

mObjects

CVector< const CDataObject * > CExperimentObjectMap::mObjects

private

A vector of pointer to the objects corresponding to the data column.

Referenced by compile(), and getDataObjects().

---

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

• CExperimentObjectMap.h
• CExperimentObjectMap.cpp