CDataArray Class Reference

#include <CDataArray.h>

Inheritance diagram for CDataArray:

Public Types
typedef C_FLOAT64	data_type
typedef CArray::index_type	index_type
enum class	Mode {   Objects , Vector , VectorOnTheFly , Strings ,   Numbers , __SIZE }
typedef std::vector< std::string >	name_index_type
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
const CDataObject *	addElementReference (C_INT32 u) const
const CDataObject *	addElementReference (C_INT32 u, C_INT32 v) const
const CDataObject *	addElementReference (const index_type &index) const
const CDataObject *	addElementReference (const name_index_type &nameIndex) const
CArrayInterface *	array ()
const CArrayInterface *	array () const
	CDataArray (const std::string &name, const CDataContainer *pParent, CArrayInterface *array, const bool &adopt)
index_type	cnToIndex (const name_index_type &cnIndex) const
size_t	dimensionality () const
name_index_type	displayNamesToCN (const std::vector< std::string > &DisplayNames) const
const std::vector< CRegisteredCommonName > &	getAnnotationsCN (size_t d) const
const std::vector< std::string > &	getAnnotationsString (size_t d, bool display=true) const
CArrayInterface *	getArray () const
Mode	getDefaultMode () const
const std::string &	getDescription () const
const std::string &	getDimensionDescription (size_t d) const
Mode	getMode (size_t d) const
virtual const CObjectInterface *	getObject (const CCommonName &cn) const
virtual std::string	getObjectDisplayName () const
bool	isEmpty ()
data_type &	operator[] (const name_index_type &nameIndex)
const data_type &	operator[] (const name_index_type &nameIndex) const
virtual void	print (std::ostream *ostream) const
void	printRecursively (std::ostream &ostream, size_t level, CArrayInterface::index_type &index, const std::vector< std::vector< std::string > > &display) const
void	reDimensionalize (size_t d)
void	resize ()
void	resizeOneDimension (size_t d)
void	setAnnotation (size_t d, size_t i, const CDataObject *pObject)
void	setAnnotationString (size_t d, size_t i, const std::string s)
void	setArray (CArrayInterface *a)
template<class CType >
void	setCopasiVector (size_t d, const CDataVector< CType > &v)
void	setDescription (const std::string &s)
void	setDimensionDescription (size_t d, const std::string &s)
void	setMode (Mode m)
void	setMode (size_t d, Mode m)
CArrayInterface::index_type	size () const
virtual	~CDataArray ()
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 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
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
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 ()

Private Member Functions
	CDataArray ()
	CDataArray (const CDataArray &)
std::string	createDisplayName (const std::string &cn) const
CDataArray &	operator= (const CDataArray &)
void	updateDisplayNames () const

Private Attributes
std::vector< std::vector< CRegisteredCommonName > >	mAnnotationsCN
std::vector< std::vector< std::string > >	mAnnotationsString
Mode	mDefaultMode
std::string	mDescription
bool	mDestructArray
std::vector< std::string >	mDimensionDescriptions
std::vector< Mode >	mModes
CArrayInterface *	mpArray

Friends
std::ostream &	operator<< (std::ostream &os, const CDataArray &o)

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 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 CDataContainer
objectMap	mObjects
Protected Attributes inherited from CDataObject
ObjectSet	mPrerequisits
std::set< CDataContainer * >	mReferences
Protected Attributes inherited from CObjectInterface
CValidity	mValidity

Detailed Description

This class contains the annotations to a n-dimensional array. Annotations can be provided for the array as such, for each of the dimensions, and for each of the indices (rows, columns, ...)

Member Typedef Documentation

data_type

typedef C_FLOAT64 CDataArray::data_type

index_type

typedef CArray::index_type CDataArray::index_type

name_index_type

typedef std::vector< std::string > CDataArray::name_index_type

Member Enumeration Documentation

Mode

enum CDataArray::Mode

strong

The annotation to an array can work in different modes. The mode for each dimension can be changed independently.

OBJECTS: The CNs for the rows, cols, ... of the array are given explicitly

VECTOR: A CDataVector is provided from which the CNs are generated at the time the vector is set

VectorOnTheFly: A CDataVector is provided, but the CNs are generated every time the annotations are retrieved (so that they are always up to date).

STRINGS: The annotations for the rows, cols, ... are given explicitly as strings.

NUMBERS: The rows, cols, ... of the array are only annotation with running numbers (starting with 0)-

Enumerator
Objects
Vector
VectorOnTheFly
Strings
Numbers
__SIZE

Constructor & Destructor Documentation

CDataArray() [1/3]

CDataArray::CDataArray ( )

private

CDataArray() [2/3]

CDataArray::CDataArray ( const CDataArray &  )

private

CDataArray() [3/3]

CDataArray::CDataArray	(	const std::string &	name,
		const CDataContainer *	pParent,
		CArrayInterface *	array,
		const bool &	adopt
	)

References mpArray, and resize().

~CDataArray()

CDataArray::~CDataArray ( )

virtual

References mDestructArray, mpArray, and pdelete.

Member Function Documentation

addElementReference() [1/4]

const CDataObject * CDataArray::addElementReference

(

C_INT32

u

)

const

a convenience function for 1-dimensional arrays.

References addElementReference().

addElementReference() [2/4]

const CDataObject * CDataArray::addElementReference	(	C_INT32	u,
		C_INT32	v
	)		const

a convenience function for 2-dimensional arrays.

References addElementReference().

addElementReference() [3/4]

const CDataObject * CDataArray::addElementReference

(

const index_type &

index

)

const

an object that will act as a reference to one element of an array will be created and inserted as a child of the array annotation. Basically most of the work will be done by getObject(). If the element already exists, the existing element will be returned.

References mAnnotationsCN, and StringPrint().

Referenced by COutputAssistant::add2DDataArrayToVector(), addElementReference(), CObjectLists::getListOfConstObjects(), and getObject().

addElementReference() [4/4]

const CDataObject * CDataArray::addElementReference

(

const name_index_type &

nameIndex

)

const

array() [1/2]

CArrayInterface* CDataArray::array ( )

inline

References mpArray.

Referenced by printRecursively().

array() [2/2]

const CArrayInterface* CDataArray::array ( ) const

inline

References mpArray.

cnToIndex()

CDataArray::index_type CDataArray::cnToIndex

(

const name_index_type &

cnIndex

)

const

References C_INVALID_INDEX, dimensionality(), mAnnotationsCN, and strToIndex().

Referenced by operator[]().

createDisplayName()

std::string CDataArray::createDisplayName ( const std::string &  cn ) const

private

References CObjectInterface::DataObject(), CDataObject::getObjectDisplayName(), and CDataObject::getObjectFromCN().

Referenced by displayNamesToCN(), getAnnotationsString(), and updateDisplayNames().

dimensionality()

size_t CDataArray::dimensionality

(

)

const

References mModes.

Referenced by COutputAssistant::add2DDataArrayToVector(), cnToIndex(), displayNamesToCN(), CObjectLists::getListOfConstObjects(), isEmpty(), printRecursively(), setAnnotation(), setAnnotationString(), and setCopasiVector().

displayNamesToCN()

CDataArray::name_index_type CDataArray::displayNamesToCN

(

const std::vector< std::string > &

DisplayNames

)

const

References C_INVALID_INDEX, createDisplayName(), dimensionality(), mAnnotationsCN, strToIndex(), and CCommonName::unescape().

Referenced by getObject().

getAnnotationsCN()

const std::vector< CRegisteredCommonName > & CDataArray::getAnnotationsCN

(

size_t

d

)

const

returns the vector of CNs that correspond to the rows, columns, ... of the array. This method must not be called if the mode for the dimension d is STRINGS or NUMBERS

References mAnnotationsCN.

getAnnotationsString()

const std::vector< std::string > & CDataArray::getAnnotationsString	(	size_t	d,
		bool	display = true
	)		const

This returns strings that annotate the rows, columns, ... of the array. If the mode is OBJECTS, VECTOR, or VectorOnTheFly the display argument determines if the object name or the object display name is used. Note that this method returns a reference. The content that the reference points to may be changes by later calls to the getAnnotationsCN() method with the same value for d. Specifically if you use this method to obtain a reference to the list of display names and then call the method again to get the plain object names, the first reference will after that also point to the plain object names.

References createDisplayName(), mAnnotationsCN, mAnnotationsString, mModes, Numbers, and StringPrint().

getArray()

CArrayInterface * CDataArray::getArray

(

)

const

References mpArray.

Referenced by CFitProblem::calculate().

getDefaultMode()

Mode CDataArray::getDefaultMode ( ) const

inline

References mDefaultMode.

getDescription()

const std::string & CDataArray::getDescription

(

)

const

References mDescription.

getDimensionDescription()

const std::string & CDataArray::getDimensionDescription

(

size_t

d

)

const

References mDimensionDescriptions.

Referenced by printRecursively().

getMode()

Mode CDataArray::getMode ( size_t  d ) const

inline

References mModes.

getObject()

const CObjectInterface * CDataArray::getObject ( const CCommonName &  cn ) const

virtual

Resolve a cn. Since this is an array, the CN can start with an index like "[2][3]". Since this is also a container, this is not necessarily the case.

Reimplemented from CDataContainer.

References addElementReference(), C_INT32, displayNamesToCN(), CDataObjectMap::equal_range(), CCommonName::escape(), CCommonName::getElementName(), CDataContainer::getObject(), CDataObject::getObject(), CCommonName::getRemainder(), and CDataContainer::mObjects.

getObjectDisplayName()

std::string CDataArray::getObjectDisplayName ( ) const

virtual

generate a display name for the array annotation.

Reimplemented from CDataObject.

References CDataObject::getObjectDisplayName(), CDataObject::getObjectName(), CDataObject::getObjectParent(), and CDataObject::getObjectType().

isEmpty()

bool CDataArray::isEmpty

(

)

Check whether the size of array is greater than 0 for each dimension. Return true, if so. Otherwise, false.

References dimensionality(), and size().

operator=()

CDataArray& CDataArray::operator= ( const CDataArray &  )

private

operator[]() [1/2]

CDataArray::data_type & CDataArray::operator[]

(

const name_index_type &

nameIndex

)

References cnToIndex(), and mpArray.

operator[]() [2/2]

const CDataArray::data_type & CDataArray::operator[]

(

const name_index_type &

nameIndex

)

const

References cnToIndex(), and mpArray.

print()

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

virtual

This is the output method for any object. The default implementation provided with CDataObject uses the ostream operator<< of the object to print the object.To override this default behavior one needs to reimplement the virtual print function.

Parameters

std::ostream

* ostream

Reimplemented from CDataObject.

printRecursively()

void CDataArray::printRecursively	(	std::ostream &	ostream,
		size_t	level,
		CArrayInterface::index_type &	index,
		const std::vector< std::vector< std::string > > &	display
	)		const

References array(), dimensionality(), getDimensionDescription(), size(), and SPC.

reDimensionalize()

void CDataArray::reDimensionalize

(

size_t

d

)

resize the internal vectors according to the dimensionality of the array

References mAnnotationsCN, mAnnotationsString, mDefaultMode, mDimensionDescriptions, and mModes.

Referenced by resize().

resize()

void CDataArray::resize

(

)

adjust the dimensionality and size to that of the array

References CArrayInterface::dimensionality(), mpArray, reDimensionalize(), and resizeOneDimension().

Referenced by CFitProblem::calculateStatistics(), CDataArray(), CFitProblem::initialize(), CSensMethod::initialize(), CCSPMethod::initializeOutput(), CTimeSensMethod::initResult(), CLNAMethod::resizeAllMatrices(), CMCAMethod::resizeAllMatrices(), CCSPMethod::setAnnotationM(), CILDMMethod::setAnnotationM(), CILDMModifiedMethod::setAnnotationM(), CCSPMethod::start(), CSteadyStateTask::updateMatrices(), and CModel::updateMatrixAnnotations().

resizeOneDimension()

void CDataArray::resizeOneDimension

(

size_t

d

)

References mAnnotationsCN, mAnnotationsString, mpArray, and CArrayInterface::size().

Referenced by resize(), setAnnotation(), and setMode().

setAnnotation()

void CDataArray::setAnnotation	(	size_t	d,
		size_t	i,
		const CDataObject *	pObject
	)

References dimensionality(), CDataObject::getCN(), CDataObject::getObjectDisplayName(), mAnnotationsCN, mAnnotationsString, resizeOneDimension(), and size().

Referenced by CSensMethod::initialize(), CTimeSensMethod::initResult(), CSteadyStateTask::updateMatrices(), and CModel::updateMatrixAnnotations().

setAnnotationString()

void CDataArray::setAnnotationString	(	size_t	d,
		size_t	i,
		const std::string	s
	)

References dimensionality(), CCommonName::escape(), mAnnotationsCN, mAnnotationsString, and size().

Referenced by CFitProblem::calculateStatistics(), CFitProblem::initialize(), CCSPMethod::initializeOutput(), CMCAMethod::resizeAllMatrices(), CCSPMethod::setAnnotationM(), CILDMMethod::setAnnotationM(), and CILDMModifiedMethod::setAnnotationM().

setArray()

void CDataArray::setArray

(

CArrayInterface *

a

)

let the ArrayAnnotation point to a different array. If you use this method without updating the annotations afterwards it is your responsibility to make sure the new array fits the existing annotation (in dimensionality and, if not in VectorOnTheFly mode, in size).

References mpArray.

setCopasiVector()

template<class CType >

void CDataArray::setCopasiVector ( size_t  d, const CDataVector< CType > &  v  )

inline

Associates a dimension d of the array with a CDataVector of CDataObjects. If the mode of the dimension d is VECTOR than the CNs of the objects in the vector are generated and stored immediately. If the mode is VectorOnTheFly the CNs are generated when getAnnotationsCN() or getAnnotationsString() is called.

References dimensionality(), CDataObject::getCN(), mAnnotationsCN, mModes, CDataVector< CType >::size(), Vector, and VectorOnTheFly.

Referenced by CCSPMethod::initializeOutput(), CModel::initObjects(), CLNAMethod::resizeAllMatrices(), CMCAMethod::resizeAllMatrices(), CCSPMethod::setAnnotationM(), CILDMMethod::setAnnotationM(), CILDMModifiedMethod::setAnnotationM(), CCSPMethod::start(), and CModel::updateMatrixAnnotations().

setDescription()

void CDataArray::setDescription

(

const std::string &

s

)

References mDescription.

Referenced by CCSPMethod::createAnnotationsM(), CILDMMethod::createAnnotationsM(), CILDMModifiedMethod::createAnnotationsM(), CLNAMethod::initObjects(), CModel::initObjects(), CFitProblem::initObjects(), CSensProblem::initObjects(), CMCAMethod::initObjects(), CSteadyStateTask::initObjects(), and CTimeSensProblem::initObjects().

setDimensionDescription()

void CDataArray::setDimensionDescription	(	size_t	d,
		const std::string &	s
	)

References mDimensionDescriptions.

Referenced by CCSPMethod::createAnnotationsM(), CILDMMethod::createAnnotationsM(), CILDMModifiedMethod::createAnnotationsM(), CSensMethod::initialize(), CLNAMethod::initObjects(), CModel::initObjects(), CFitProblem::initObjects(), CMCAMethod::initObjects(), CSteadyStateTask::initObjects(), and CTimeSensMethod::initResult().

setMode() [1/2]

void CDataArray::setMode

(

Mode

m

)

set the mode for all dimensions, this also sets the default mode that is used when resizing the ArrayAnnotion to a larger dimensionality

References mDefaultMode, mModes, and setMode().

setMode() [2/2]

void CDataArray::setMode	(	size_t	d,
		Mode	m
	)

set the mode for the dimension d

References mModes, and resizeOneDimension().

Referenced by CCSPMethod::createAnnotationsM(), CILDMMethod::createAnnotationsM(), CILDMModifiedMethod::createAnnotationsM(), CLNAMethod::initObjects(), CModel::initObjects(), CFitProblem::initObjects(), CSensProblem::initObjects(), CMCAMethod::initObjects(), CSteadyStateTask::initObjects(), CTimeSensProblem::initObjects(), and setMode().

size()

CArrayInterface::index_type CDataArray::size ( ) const

inline

References mpArray, and CArrayInterface::size().

Referenced by COutputAssistant::add2DDataArrayToVector(), CObjectLists::getListOfConstObjects(), isEmpty(), printRecursively(), setAnnotation(), and setAnnotationString().

updateDisplayNames()

void CDataArray::updateDisplayNames ( ) const

private

References createDisplayName(), mAnnotationsCN, and mAnnotationsString.

Friends And Related Function Documentation

operator<<

std::ostream& operator<< ( std::ostream &  os, const CDataArray &  o  )

friend

Member Data Documentation

mAnnotationsCN

std::vector< std::vector< CRegisteredCommonName > > CDataArray::mAnnotationsCN

private

Referenced by addElementReference(), cnToIndex(), displayNamesToCN(), getAnnotationsCN(), getAnnotationsString(), reDimensionalize(), resizeOneDimension(), setAnnotation(), setAnnotationString(), setCopasiVector(), and updateDisplayNames().

mAnnotationsString

std::vector< std::vector< std::string > > CDataArray::mAnnotationsString

mutableprivate

Referenced by getAnnotationsString(), reDimensionalize(), resizeOneDimension(), setAnnotation(), setAnnotationString(), and updateDisplayNames().

mDefaultMode

Mode CDataArray::mDefaultMode

private

This contains the default mode that is used if during a resize() the dimensionality is increased.

Referenced by getDefaultMode(), reDimensionalize(), and setMode().

mDescription

std::string CDataArray::mDescription

private

Referenced by getDescription(), and setDescription().

mDestructArray

bool CDataArray::mDestructArray

private

Referenced by ~CDataArray().

mDimensionDescriptions

std::vector< std::string > CDataArray::mDimensionDescriptions

private

Referenced by getDimensionDescription(), reDimensionalize(), and setDimensionDescription().

mModes

std::vector<Mode> CDataArray::mModes

private

This contains the mode for the different dimensions

Referenced by dimensionality(), getAnnotationsString(), getMode(), reDimensionalize(), setCopasiVector(), and setMode().

mpArray

CArrayInterface* CDataArray::mpArray

private

Referenced by array(), CDataArray(), getArray(), operator[](), resize(), resizeOneDimension(), setArray(), size(), and ~CDataArray().

---

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

• CDataArray.h
• CDataArray.cpp