#include <CExperiment.h>

Inheritance diagram for CExperiment:

Public Types
enum	Type { ignore = 0 , independent , dependent , time }

enum	WeightMethod { MEAN = 0 , MEAN_SQUARE , SD , VALUE_SCALING }

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

Public Member Functions
bool	calculateStatistics ()

bool	calculateWeights ()

	CExperiment (const CCopasiParameterGroup &group, const CDataContainer *pParent)

	CExperiment (const CDataContainer *pParent, const std::string &name="Experiment")

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

bool	compile (const CMathContainer *pMathContainer)

virtual bool	elevateChildren ()

size_t	extendedTimeSeriesSize () const

void	fixBuild55 ()

const std::vector< std::string > &	getColumnNames () const

size_t	getColumnValidValueCount (const CObjectInterface *pObject) const

C_FLOAT64	getDefaultScale (const CObjectInterface *pObject) const

const CMatrix< C_FLOAT64 > &	getDependentData () const

const std::map< const CObjectInterface *, size_t > &	getDependentObjectsMap () const

const C_FLOAT64 &	getErrorMean () const

const C_FLOAT64 &	getErrorMeanSD () const

C_FLOAT64	getErrorMeanSD (const CObjectInterface *pObject, const C_FLOAT64 &errorMean) const

C_FLOAT64	getErrorSum (const CObjectInterface *pObject) const

const CTaskEnum::Task &	getExperimentType () const

const std::string &	getFileName () const

const std::string &	getFileNameOnly () const

const unsigned C_INT32 &	getFirstRow () const

const CDataVector< CFittingPoint > &	getFittingPoints () const

const unsigned C_INT32 &	getHeaderRow () const

const CMatrix< C_FLOAT64 > &	getIndependentData () const

const CObjectInterface::ObjectSet &	getIndependentObjects () const

const unsigned C_INT32 &	getLastRow () const

bool	getNormalizeWeightsPerExperiment () const

const unsigned C_INT32 &	getNumColumns () const

size_t	getNumDataRows () const

const C_FLOAT64 &	getObjectiveValue () const

C_FLOAT64	getObjectiveValue (const CObjectInterface *pObject) const

CExperimentObjectMap &	getObjectMap ()

const CExperimentObjectMap &	getObjectMap () const

const C_FLOAT64 &	getRMS () const

C_FLOAT64	getRMS (const CObjectInterface *pObject) const

const C_FLOAT64 *	getScale (const CObjectInterface *pObject) const

const CMatrix< C_FLOAT64 > &	getScalingMatrix () const

const std::string &	getSeparator () const

const CVector< C_FLOAT64 > &	getTimeData () const

size_t	getTotalValueCount () const

size_t	getValidValueCount () const

const WeightMethod &	getWeightMethod () const

size_t	guessColumnNumber () const

void	initExtendedTimeSeries (size_t s)

const bool &	isRowOriented () const

CExperiment &	operator= (const CExperiment &rhs)

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

bool	read (std::istream &in, size_t &currentLine)

bool	readColumnNames ()

bool	setExperimentType (const CTaskEnum::Task &type)

bool	setFileName (const std::string &fileName)

bool	setFirstRow (const unsigned C_INT32 &firstRow)

bool	setHeaderRow (const unsigned C_INT32 &headerRow)

bool	setIsRowOriented (const bool &isRowOriented)

bool	setLastRow (const unsigned C_INT32 &lastRow)

void	setNormalizeWeightsPerExperiment (bool flag)

bool	setNumColumns (const unsigned C_INT32 &cols)

bool	setSeparator (const std::string &seperator)

bool	setWeightMethod (const WeightMethod &weightMethod)

void	storeExtendedTimeSeriesData (C_FLOAT64 time)

C_FLOAT64	sumOfSquares (const size_t &index, C_FLOAT64 *&residuals) const

C_FLOAT64	sumOfSquaresStore (const size_t &index, C_FLOAT64 *&dependentValues)

void	updateFittedPoints ()

void	updateFittedPointValues (const size_t &index)

void	updateFittedPointValuesFromExtendedTimeSeries (const size_t &index)

bool	updateModelWithIndependentData (const size_t &index)

virtual	~CExperiment ()

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

Static Public Member Functions
static bool	compare (const CExperiment lhs, const CExperiment rhs)

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
static const std::string	TypeName []

static const std::string	WeightMethodName []

static const char *	WeightMethodType []

static const char *	XMLType []

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
	CExperiment (const CExperiment &src)

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)

Private Member Functions
void	initializeParameter ()

void	initializeScalingMatrix ()

Private Attributes
std::vector< std::string >	mColumnName

CVector< C_FLOAT64 >	mColumnObjectiveValue

CVector< C_FLOAT64 >	mColumnRMS

CVector< C_FLOAT64 >	mColumnScale

CVector< size_t >	mColumnValidValueCount

CMatrix< C_FLOAT64 >	mDataDependent

CMatrix< C_FLOAT64 >	mDataIndependent

CVector< C_FLOAT64 >	mDataTime

CVector< C_FLOAT64 >	mDefaultColumnScale

std::map< const CObjectInterface *, size_t >	mDependentObjectsMap

CCore::CUpdateSequence	mDependentUpdateSequence

CVector< C_FLOAT64 * >	mDependentValues

CVector< C_FLOAT64 >	mExtendedTimeSeries

size_t	mExtendedTimeSeriesSize

CDataVector< CFittingPoint >	mFittingPoints

CObjectInterface::ObjectSet	mIndependentObjects

CCore::CUpdateSequence	mIndependentUpdateSequence

CVector< C_FLOAT64 * >	mIndependentValues

C_FLOAT64	mMean

CVector< C_FLOAT64 >	mMeans

C_FLOAT64	mMeanSD

bool	mMissingData

size_t	mNumDataRows

C_FLOAT64	mObjectiveValue

CMathContainer *	mpContainer

C_FLOAT64 *	mpDataDependentCalculated

std::string *	mpFileName

unsigned C_INT32 *	mpFirstRow

unsigned C_INT32 *	mpHeaderRow

unsigned C_INT32 *	mpLastRow

bool *	mpNormalizeWeightsPerExperiment

unsigned C_INT32 *	mpNumColumns

CExperimentObjectMap *	mpObjectMap

bool *	mpRowOriented

std::string *	mpSeparator

CTaskEnum::Task *	mpTaskType

WeightMethod *	mpWeightMethod

C_FLOAT64	mRMS

CVector< C_FLOAT64 >	mRowObjectiveValue

CVector< C_FLOAT64 >	mRowRMS

CMatrix< C_FLOAT64 >	mScale

C_FLOAT64 *	mStorageIt

size_t	mValidValueCount

Friends
bool	operator== (const CExperiment &lhs, const CExperiment &rhs)

Additional Inherited Members
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

Member Enumeration Documentation

◆ Type

enum CExperiment::Type

Enumeration of the types of columns known to COPASI.

Enumerator
ignore
independent
dependent
time

◆ WeightMethod

enum CExperiment::WeightMethod

Enumeration of methods to calculate the weight.

Enumerator
MEAN
MEAN_SQUARE
SD
VALUE_SCALING

Constructor & Destructor Documentation

◆ CExperiment() [1/4]

CExperiment::CExperiment ( const CExperiment & src )

protected

◆ CExperiment() [2/4]

CExperiment::CExperiment	(	const CDataContainer *	pParent,
		const std::string &	name = `"Experiment"`
	)

Default constructor

Parameters

const	CDataContainer * pParent
const	std::string & name (default: Experiment)

References CVectorCore< CType >::array(), initializeParameter(), mExtendedTimeSeries, and mStorageIt.

◆ CExperiment() [3/4]

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

Copy constructor

Parameters

const	CExperiment & src
const	CDataContainer * pParent (default: src data model)

References CVectorCore< CType >::array(), initializeParameter(), mExtendedTimeSeries, and mStorageIt.

◆ CExperiment() [4/4]

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

Specific constructor used for reading COPASI files

Parameters

const	CCopasiParameterGroup & group
const	CDataContainer * pParent (default: group data model)

References CVectorCore< CType >::array(), initializeParameter(), mExtendedTimeSeries, and mStorageIt.

◆ ~CExperiment()

CExperiment::~CExperiment ( )

virtual

Destructor

Member Function Documentation

◆ calculateStatistics()

bool CExperiment::calculateStatistics ( )

Calculate statistics by comparing the stored calculated values with the measurements.

Returns: bool success

References CMatrix< CType >::array(), C_FLOAT64, CDataModel::getModel(), CDataObject::getObjectDataModel(), CModel::getTime(), max, mColumnObjectiveValue, mColumnRMS, mColumnValidValueCount, mDataDependent, mMean, mMeanSD, mObjectiveValue, mpDataDependentCalculated, mpTaskType, mRMS, mRowObjectiveValue, mRowRMS, mScale, mValidValueCount, CMatrix< CType >::numCols(), CMatrix< CType >::numRows(), CVector< CType >::resize(), and CTaskEnum::timeCourse.

◆ calculateWeights()

bool CExperiment::calculateWeights ( )

Calculate/set the weights used in the sum of squares.

Returns: bool success

References CVectorCore< CType >::array(), C_FLOAT64, max, mColumnValidValueCount, mDataDependent, mDefaultColumnScale, MEAN, MEAN_SQUARE, mMeans, mMissingData, mNumDataRows, mpNormalizeWeightsPerExperiment, mpWeightMethod, SD, CVectorCore< CType >::size(), and VALUE_SCALING.

Referenced by read().

◆ compare()

bool CExperiment::compare	(	const CExperiment *	lhs,
		const CExperiment *	rhs
	)

static

Comparison used to evaluate the order of the experiment based on the filename and starting line number.

Parameters

const	CExperiment * lhs;
const	CExperiment * rhs;

Returns: bool isLess

References mpFileName, and mpFirstRow.

Referenced by CExperimentSet::sort().

◆ compile()

bool CExperiment::compile ( const CMathContainer * pMathContainer )

Compile the experiment. This function must be called before any evaluations can be performed.

Parameters

const CMathContainer * pMathContainer

Returns: bool success

References C_FLOAT64, C_INVALID_INDEX, CExperimentObjectMap::compile(), CCore::Default, dependent, CCopasiMessage::ERROR, CMathObject::getDataObject(), CExperimentObjectMap::getDataObjects(), CMathContainer::getInitialDependencies(), CMathContainer::getInitialStateObjects(), CExperimentObjectMap::getLastColumn(), CExperimentObjectMap::getLastNotIgnoredColumn(), CMathContainer::getMathObject(), CDataObject::getObjectDisplayName(), CExperimentObjectMap::getRole(), CExperimentObjectMap::getScale(), CMathContainer::getSimulationUpToDateObjects(), CMathContainer::getStateObjects(), CMathContainer::getTransientDependencies(), CMathDependencyGraph::getUpdateSequence(), CMathObject::getValuePointer(), CDataObject::hasFlag(), ignore, independent, initializeScalingMatrix(), MCFitting, mColumnObjectiveValue, mColumnRMS, mColumnScale, mColumnValidValueCount, mDataDependent, mDataIndependent, mDependentObjectsMap, mDependentUpdateSequence, mDependentValues, mIndependentObjects, mIndependentUpdateSequence, mIndependentValues, mMean, mMeanSD, mObjectiveValue, mpContainer, mpNumColumns, mpObjectMap, mpTaskType, mRMS, mRowObjectiveValue, mRowRMS, CMatrix< CType >::numCols(), CMatrix< CType >::numRows(), pMathContainer, CVector< CType >::resize(), time, CTaskEnum::timeCourse, CCore::UpdateMoieties, and CDataObject::ValueDbl.

Referenced by CModel::createEventsForTimeseries().

◆ elevateChildren()

bool CExperiment::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 C_INT32, CCopasiParameterGroup::clear(), CCopasiParameterGroup::getGroup(), CExperimentObjectMap::getObjectCN(), CCopasiParameterGroup::getValue(), mpObjectMap, mpWeightMethod, CCopasiParameterGroup::removeParameter(), SD, CExperimentObjectMap::setNumCols(), CExperimentObjectMap::setObjectCN(), CExperimentObjectMap::setRole(), CCopasiParameterGroup::size(), StringPrint(), and updateFittedPoints().

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

◆ extendedTimeSeriesSize()

size_t CExperiment::extendedTimeSeriesSize ( ) const

References mExtendedTimeSeriesSize.

Referenced by updateFittedPointValuesFromExtendedTimeSeries().

◆ fixBuild55()

void CExperiment::fixBuild55 ( )

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

References CExperimentObjectMap::fixBuild55(), and mpObjectMap.

◆ getColumnNames()

const std::vector< std::string > & CExperiment::getColumnNames ( ) const

Retrieve the column names

Returns: const std::vector< std::string > & columnNames;

References mColumnName.

◆ getColumnValidValueCount()

size_t CExperiment::getColumnValidValueCount ( const CObjectInterface * pObject ) const

Retrieve the data point count for the object.

Parameters

const CObjectInterface * pObject

Returns: size_t count

References mColumnValidValueCount, and mDependentObjectsMap.

◆ getDefaultScale()

C_FLOAT64 CExperiment::getDefaultScale ( const CObjectInterface * pObject ) const

Retrieve the default scaling factor for the object.

Parameters

const CObjectInterface * pObject

Returns: C_FLOAT64 defaultScale

References mDefaultColumnScale, and mDependentObjectsMap.

Referenced by CExperimentObjectMap::CDataColumn::getDefaultScale().

◆ getDependentData()

const CMatrix< C_FLOAT64 > & CExperiment::getDependentData ( ) const

Retrieve the dependent data of the experiment.

Returns: const CMatrix< C_FLOAT64 > & dependentData

References mDataDependent.

Referenced by CFitProblem::calculate(), CModel::createEventsForTimeseries(), CExperimentSet::getDependentData(), and initExtendedTimeSeries().

◆ getDependentObjectsMap()

const std::map< const CObjectInterface *, size_t > & CExperiment::getDependentObjectsMap ( ) const

Retrieve the mapping of dependent data objects to the index of the column, only counting columns with dependent data

Returns: const std::map< const CDataObject *, size_t > & dependentObjects

References mDependentObjectsMap.

Referenced by CFitProblem::calculate(), CFitProblem::calculateStatistics(), and CModel::createEventsForTimeseries().

◆ getErrorMean()

const C_FLOAT64 & CExperiment::getErrorMean ( ) const

Retrieve the mean of the error

Parameters

const C_FLOAT64 & errorMean

References mMean.

◆ getErrorMeanSD() [1/2]

const C_FLOAT64 & CExperiment::getErrorMeanSD ( ) const

Retrieve the std. deviation of the error

Parameters

const C_FLOAT64 & errorMeanSD

References mMeanSD.

◆ getErrorMeanSD() [2/2]

C_FLOAT64 CExperiment::getErrorMeanSD	(	const CObjectInterface *	pObject,
		const C_FLOAT64 &	errorMean
	)		const

Retrieve the error mean std. deviations for the object. More specifically this is the sum of the squared deviations of the residuals from the provided errorMean. The sum is over all data points for the object.

Parameters

const	CObjectInterface * pObject
C_FLOAT64	errorMean

Returns: C_FLOAT64 errorMeanSD

References CMatrix< CType >::array(), C_FLOAT64, max, mDataDependent, mDependentObjectsMap, mpDataDependentCalculated, mScale, CMatrix< CType >::numCols(), and CMatrix< CType >::numRows().

◆ getErrorSum()

C_FLOAT64 CExperiment::getErrorSum ( const CObjectInterface * pObject ) const

Retrieve the sum of errors (scaled residuals) for the object.

Parameters

const CObjectInterface * pObject

Returns: C_FLOAT64 errorSum

References CMatrix< CType >::array(), C_FLOAT64, mColumnScale, mDataDependent, mDependentObjectsMap, mpDataDependentCalculated, CMatrix< CType >::numCols(), and CMatrix< CType >::numRows().

◆ getExperimentType()

const CTaskEnum::Task & CExperiment::getExperimentType ( ) const

Retrieve the experiment type

Returns: const CTaskEnum::Task & experimentType

References mpTaskType.

Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), COutputAssistant::createDefaultOutput(), CModel::createEventsForTimeseries(), and CExperimentSet::getExperimentType().

◆ getFileName()

const std::string & CExperiment::getFileName ( ) const

Retrieve the file name in case it is a relative filename an absolute path to the file will be created.

Returns: const std::string & fileName

References CDirEntry::fileName(), CDataObject::getObjectDataModel(), CDirEntry::isRelativePath(), CDirEntry::makePathAbsolute(), and mpFileName.

Referenced by CDataModel::copyExperimentalDataTo(), CModel::createEventsForTimeseries(), CDataModel::exportCombineArchive(), CDataModel::exportShinyArchive(), guessColumnNumber(), printResult(), readColumnNames(), and CExperimentFileInfo::sync().

◆ getFileNameOnly()

const std::string & CExperiment::getFileNameOnly ( ) const

Returns: returns the fileName only (no changing of paths in case the file is a relative one)

References mpFileName.

Referenced by CDataModel::exportCombineArchive(), CDataModel::exportShinyArchive(), and CDataModel::openCombineArchive().

◆ getFirstRow()

const unsigned C_INT32 & CExperiment::getFirstRow ( ) const

Retrieve the first row

Returns: const unsigned C_INT32 & firstRow

References mpFirstRow.

◆ getFittingPoints()

const CDataVector< CFittingPoint > & CExperiment::getFittingPoints ( ) const

Retrieve the list of fitting points

Returns: const CDataVector< CFittingPoint > & fittingPoints

References mFittingPoints.

Referenced by COutputAssistant::createDefaultOutput().

◆ getHeaderRow()

const unsigned C_INT32 & CExperiment::getHeaderRow ( ) const

Retrieve the header row

Returns: const unsigned C_INT32 & headerRow

References mpHeaderRow.

◆ getIndependentData()

const CMatrix< C_FLOAT64 > & CExperiment::getIndependentData ( ) const

Retrieve the independent data of the experiment.

Returns: const CMatrix< C_FLOAT64 > & independentData

References mDataIndependent.

Referenced by CExperimentSet::getIndependentData().

◆ getIndependentObjects()

const CObjectInterface::ObjectSet & CExperiment::getIndependentObjects ( ) const

Retrieve the list of independent objects

Returns: const CObjectInterface::ObjectSet & independentObjects

References mIndependentObjects.

Referenced by CFitProblem::initialize().

◆ getLastRow()

const unsigned C_INT32 & CExperiment::getLastRow ( ) const

Retrieve the last row

Returns: const unsigned C_INT32 & lastRow

References mpLastRow.

◆ getNormalizeWeightsPerExperiment()

bool CExperiment::getNormalizeWeightsPerExperiment ( ) const

References mpNormalizeWeightsPerExperiment.

◆ getNumColumns()

const unsigned C_INT32 & CExperiment::getNumColumns ( ) const

Retrieve the number of columns

Returns: const unsigned C_INT32 & numColumns

References mpNumColumns.

◆ getNumDataRows()

size_t CExperiment::getNumDataRows ( ) const

Retrieve the number of data rows

Returns: const size_t numDataRows

References mNumDataRows.

Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), CFitProblem::calculateStatistics(), CModel::createEventsForTimeseries(), and getTotalValueCount().

◆ getObjectiveValue() [1/2]

const C_FLOAT64 & CExperiment::getObjectiveValue ( ) const

Retrieve the value of the objective function

Parameters

const C_FLOAT64 & errorMean

References mObjectiveValue.

◆ getObjectiveValue() [2/2]

C_FLOAT64 CExperiment::getObjectiveValue ( const CObjectInterface * pObject ) const

Retrieve the objective value for the object.

Parameters

const CObjectInterface * pObject

Returns: C_FLOAT64 objectiveValue

References mColumnObjectiveValue, and mDependentObjectsMap.

◆ getObjectMap() [1/2]

CExperimentObjectMap & CExperiment::getObjectMap ( )

Retrieve the object map

Returns: CExperimentObjectMap & mpObjectMap

References mpObjectMap.

◆ getObjectMap() [2/2]

const CExperimentObjectMap & CExperiment::getObjectMap ( ) const

Retrieve the object map

Returns: CExperimentObjectMap & mpObjectMap

References mpObjectMap.

◆ getRMS() [1/2]

const C_FLOAT64 & CExperiment::getRMS ( ) const

Retrieve the RMS

Parameters

const C_FLOAT64 & RMS

References mRMS.

◆ getRMS() [2/2]

C_FLOAT64 CExperiment::getRMS ( const CObjectInterface * pObject ) const

Retrieve the RMS for the object.

Parameters

const CObjectInterface * pObject

Returns: C_FLOAT64 RMS

References mColumnRMS, and mDependentObjectsMap.

◆ getScale()

const C_FLOAT64 * CExperiment::getScale ( const CObjectInterface * pObject ) const

Retrieve the scaling factor for the object.

Parameters

const CObjectInterface * pObject

Returns: C_FLOAT64 scale or NULL if object can't be found

References mDependentObjectsMap, and mScale.

◆ getScalingMatrix()

const CMatrix< C_FLOAT64 > & CExperiment::getScalingMatrix ( ) const

Returns: the scaling matrix

References mScale.

Referenced by CFitProblem::calculate().

◆ getSeparator()

const std::string & CExperiment::getSeparator ( ) const

Retrieve the separator

Returns: const std::string & separator

References mpSeparator.

◆ getTimeData()

const CVector< C_FLOAT64 > & CExperiment::getTimeData ( ) const

Retrieve the time data of the experiment.

Returns: const CVector< C_FLOAT64 > & timeData

References mDataTime.

Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), and CModel::createEventsForTimeseries().

◆ getTotalValueCount()

size_t CExperiment::getTotalValueCount ( ) const

get number of independent data points expected given the number of rows and columns

References getNumDataRows(), mDataDependent, and CMatrix< CType >::numCols().

◆ getValidValueCount()

size_t CExperiment::getValidValueCount ( ) const

get number of independent data points for the whole experiment only valid data points (that contain actual data) are counted.

References mValidValueCount.

◆ getWeightMethod()

const CExperiment::WeightMethod & CExperiment::getWeightMethod ( ) const

Retrieve the method used for calculating the default weights.

Returns: const WeightMethod & weightMethod

References mpWeightMethod.

◆ guessColumnNumber()

size_t CExperiment::guessColumnNumber ( ) const

Try to guess the number of columns

Returns: size_t numColumns

References CLocaleString::fromUtf8(), getFileName(), CTableRow::guessColumnNumber(), mpFirstRow, mpLastRow, mpSeparator, and skipLine().

◆ initExtendedTimeSeries()

void CExperiment::initExtendedTimeSeries ( size_t s )

Initialize the storage of an extended time series for plotting. This clears the storage, resizes it to the given size and sets the iterator to the start of the storage. The size given is the number of time points, not the number of data

References CVectorCore< CType >::array(), getDependentData(), mExtendedTimeSeries, mExtendedTimeSeriesSize, mStorageIt, and CVector< CType >::resize().

Referenced by CFitProblem::calculate(), and CFitProblem::calculateCrossValidation().

◆ initializeParameter()

void CExperiment::initializeParameter ( )

private

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

Referenced by CExperiment().

◆ initializeScalingMatrix()

void CExperiment::initializeScalingMatrix ( )

private

Initialize the scaling matrix

References CMatrix< CType >::array(), CVectorCore< CType >::array(), C_FLOAT64, max, mColumnScale, mDataDependent, mpWeightMethod, mScale, CMatrix< CType >::numCols(), CMatrix< CType >::numRows(), CMatrix< CType >::resize(), CMatrix< CType >::size(), CVectorCore< CType >::size(), and VALUE_SCALING.

Referenced by compile().

◆ isRowOriented()

const bool & CExperiment::isRowOriented ( ) const

Check whter the data is row oriented.

Returns: const bool & isRowOriented

References mpRowOriented.

Referenced by setIsRowOriented().

◆ operator=()

CExperiment & CExperiment::operator= ( const CExperiment & rhs )

Assignment operator

Parameters

const CExperiment & rhs

Returns: CExperiment & lhs

References CCopasiParameterGroup::clear(), elevateChildren(), mpFileName, mpFirstRow, mpHeaderRow, mpLastRow, mpNormalizeWeightsPerExperiment, mpNumColumns, mpRowOriented, mpSeparator, mpTaskType, mpWeightMethod, and CCopasiParameterGroup::setValue().

◆ printResult()

void CExperiment::printResult ( std::ostream * ostream ) const

virtual

This is the output method for the statistics for the experiment. This method is called from CFitProblem::printResult.

Parameters

std::ostream * ostream

References C_FLOAT64, dependent, CExperimentObjectMap::getDataObjects(), getFileName(), CExperimentObjectMap::getLastNotIgnoredColumn(), CDataObject::getObjectName(), CExperimentObjectMap::getRole(), mColumnObjectiveValue, mColumnRMS, mColumnScale, mDataDependent, mDataTime, mMean, mNumDataRows, mObjectiveValue, mpDataDependentCalculated, mpObjectMap, mpTaskType, mRMS, mRowObjectiveValue, mRowRMS, mScale, CMatrix< CType >::numCols(), CVectorCore< CType >::size(), and CTaskEnum::timeCourse.

Referenced by CFitProblem::printResult().

◆ read()

bool CExperiment::read	(	std::istream &	in,
		size_t &	currentLine
	)

Reads the experiment data form a the given stream

Parameters

std::istream	& in
size_t	& currentLine

Returns: bool success

References CMatrix< CType >::applyPivot(), CVectorCore< CType >::applyPivot(), CVectorCore< CType >::array(), C_INVALID_INDEX, calculateWeights(), dependent, CCopasiMessage::ERROR, CTableRow::getCells(), CDataObject::getObjectName(), CExperimentObjectMap::getRole(), ignore, independent, InvalidIndex, MCFitting, mColumnName, mColumnScale, mColumnValidValueCount, mDataDependent, mDataIndependent, mDataTime, mDefaultColumnScale, mMeans, mNumDataRows, mpDataDependentCalculated, mpFileName, mpFirstRow, mpHeaderRow, mpLastRow, mpNumColumns, mpObjectMap, mpSeparator, mpTaskType, CMatrix< CType >::resize(), CVector< CType >::resize(), CVectorCore< CType >::size(), CCopasiParameterGroup::size(), skipLine(), sortWithPivot(), time, and CTaskEnum::timeCourse.

Referenced by CModel::createEventsForTimeseries().

◆ readColumnNames()

bool CExperiment::readColumnNames ( )

Reads the header row for the experiment data

Returns: bool success

References CLocaleString::fromUtf8(), CTableRow::getCells(), getFileName(), CCopasiParameterGroup::getName(), InvalidIndex, mColumnName, mpHeaderRow, mpNumColumns, mpSeparator, and skipLine().

◆ setExperimentType()

bool CExperiment::setExperimentType ( const CTaskEnum::Task & type )

set the experiment type

Parameters

const CTaskEnum::Task & experimentType

Returns: bool success

References mpTaskType, CTaskEnum::steadyState, and CTaskEnum::timeCourse.

◆ setFileName()

bool CExperiment::setFileName ( const std::string & fileName )

Set the file name

Parameters

const std::string & fileName

Returns: bool success

References mpFileName.

Referenced by CDataModel::copyExperimentalDataTo(), CDataModel::exportCombineArchive(), and CDataModel::exportShinyArchive().

◆ setFirstRow()

bool CExperiment::setFirstRow ( const unsigned C_INT32 & firstRow )

Set the first row containing data

Parameters

const unsigned C_INT32 & firstRow

Returns: bool success

References mpFirstRow, mpHeaderRow, and mpLastRow.

◆ setHeaderRow()

bool CExperiment::setHeaderRow ( const unsigned C_INT32 & headerRow )

Set the header row containing data

Parameters

const unsigned C_INT32 & headerRow

Returns: bool success

References mpFirstRow, mpHeaderRow, and mpLastRow.

◆ setIsRowOriented()

bool CExperiment::setIsRowOriented ( const bool & isRowOriented )

Set whether the data is row oriented. This only impacts reading the data from a stream

Parameters

const bool & isRowOriented

Returns: bool success

References isRowOriented(), and mpRowOriented.

◆ setLastRow()

bool CExperiment::setLastRow ( const unsigned C_INT32 & lastRow )

Set the last row containing data

Parameters

const unsigned C_INT32 & lastRow

Returns: bool success

References mpFirstRow, mpHeaderRow, and mpLastRow.

◆ setNormalizeWeightsPerExperiment()

void CExperiment::setNormalizeWeightsPerExperiment ( bool flag )

References mpNormalizeWeightsPerExperiment.

◆ setNumColumns()

bool CExperiment::setNumColumns ( const unsigned C_INT32 & cols )

Set the number of columns in a stream

Parameters

const unsigned C_INT32 & cols

Returns: bool success

References mpNumColumns.

◆ setSeparator()

bool CExperiment::setSeparator ( const std::string & seperator )

Set the seperator used when reading a stream

Parameters

const std::string & separator

Returns: bool success

References mpSeparator.

◆ setWeightMethod()

bool CExperiment::setWeightMethod ( const WeightMethod & weightMethod )

Set the weight calculation method and resets manual adjusted weights

Parameters

const WeightMethod & weightMethod

Returns: bool success

References mpObjectMap, mpWeightMethod, and CExperimentObjectMap::CDataColumn::setScale().

◆ storeExtendedTimeSeriesData()

void CExperiment::storeExtendedTimeSeriesData ( C_FLOAT64 time )

Add one dataset to the extended time series. The time and the simulated dependent values are stored and the iterator is increased

References CMathContainer::applyUpdateSequence(), CVectorCore< CType >::array(), C_FLOAT64, mDataDependent, mDependentUpdateSequence, mDependentValues, mpContainer, mStorageIt, CMatrix< CType >::numCols(), and time.

Referenced by CFitProblem::calculate(), and CFitProblem::calculateCrossValidation().

◆ sumOfSquares()

C_FLOAT64 CExperiment::sumOfSquares	(	const size_t &	index,
		C_FLOAT64 *&	residuals
	)		const

Calculate the sum of squares for the indexed row of the experiment. If residuals is not NULL residuals will contain the differences between the calculated and the experiment values.

Parameters

const	size_t & index
C_FLOAT64	*& residuals (may be NULL)

Returns: C_FLOAT64 sumOfSquares

References CMathContainer::applyUpdateSequence(), CVectorCore< CType >::array(), C_FLOAT64, max, mDataDependent, mDependentUpdateSequence, mDependentValues, mMissingData, mpContainer, mScale, and CMatrix< CType >::numCols().

Referenced by CFitProblem::calculate(), and CFitProblem::calculateCrossValidation().

◆ sumOfSquaresStore()

C_FLOAT64 CExperiment::sumOfSquaresStore	(	const size_t &	index,
		C_FLOAT64 *&	dependentValues
	)

Calculate the sum of squares for the indexed row of the experiment. On return dependentValues contains the calculated values. If residuals is not NULL residuals will contain the differences between the calculated and the experiment values.

Parameters

const	size_t & index
C_FLOAT64	*& dependentValues (must not be NULL)

Returns: C_FLOAT64 sumOfSquares

References CMathContainer::applyUpdateSequence(), CVectorCore< CType >::array(), C_FLOAT64, max, mDataDependent, mDependentUpdateSequence, mDependentValues, mMissingData, mpContainer, mpDataDependentCalculated, mScale, and CMatrix< CType >::numCols().

Referenced by CFitProblem::calculate(), and CFitProblem::calculateCrossValidation().

◆ updateFittedPoints()

void CExperiment::updateFittedPoints ( )

This method needs to be called whenever the Object Map is changed

References CDataVector< CType >::add(), CDataVector< CType >::clear(), dependent, CExperimentObjectMap::getObjectCN(), CExperimentObjectMap::getRole(), mFittingPoints, mpObjectMap, and CCopasiParameterGroup::size().

Referenced by elevateChildren().

◆ updateFittedPointValues()

void CExperiment::updateFittedPointValues ( const size_t & index )

This method is used for output to fill the fitted points with the values of the index data record. If index exceeds the number of data records all values are set to NaN.

References CDataVector< CType >::begin(), C_FLOAT64, CDataVector< CType >::end(), mDataDependent, mDataTime, mFittingPoints, mNumDataRows, mpDataDependentCalculated, mpTaskType, mScale, CMatrix< CType >::numCols(), and CTaskEnum::timeCourse.

◆ updateFittedPointValuesFromExtendedTimeSeries()

void CExperiment::updateFittedPointValuesFromExtendedTimeSeries ( const size_t & index )

Fill the fitted points with values from the extended time series

References CDataVector< CType >::begin(), CDataVector< CType >::end(), extendedTimeSeriesSize(), mDataDependent, mExtendedTimeSeries, mFittingPoints, and CMatrix< CType >::numCols().

◆ updateModelWithIndependentData()

bool CExperiment::updateModelWithIndependentData ( const size_t & index )

Update the model with the independent data of the experiment

Parameters

const size_t & index

Returns: bool success

References CMathContainer::applyUpdateSequence(), CVectorCore< CType >::array(), C_FLOAT64, mDataIndependent, mIndependentUpdateSequence, mIndependentValues, mpContainer, and CVectorCore< CType >::size().

Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), CFitProblem::createParameterSets(), and CFitProblem::restore().

Friends And Related Function Documentation

◆ operator==

bool operator==	(	const CExperiment &	lhs,
		const CExperiment &	rhs
	)

friend

Comparison operator

Parameters

const	CExperiment & lhs
const	CExperiment & rhs

Returns: bool equal

Member Data Documentation

◆ mColumnName

std::vector< std::string > CExperiment::mColumnName

private

The column names if available after reading a file

Referenced by getColumnNames(), read(), and readColumnNames().

◆ mColumnObjectiveValue

CVector< C_FLOAT64 > CExperiment::mColumnObjectiveValue

private

Referenced by calculateStatistics(), compile(), getObjectiveValue(), and printResult().

◆ mColumnRMS

CVector< C_FLOAT64 > CExperiment::mColumnRMS

private

Referenced by calculateStatistics(), compile(), getRMS(), and printResult().

◆ mColumnScale

CVector< C_FLOAT64 > CExperiment::mColumnScale

private

Referenced by compile(), getErrorSum(), initializeScalingMatrix(), printResult(), and read().

◆ mColumnValidValueCount

CVector< size_t > CExperiment::mColumnValidValueCount

private

Referenced by calculateStatistics(), calculateWeights(), compile(), getColumnValidValueCount(), and read().

◆ mDataDependent

CMatrix< C_FLOAT64 > CExperiment::mDataDependent

private

The relevant dependent experimental data after reading a file

Referenced by calculateStatistics(), calculateWeights(), compile(), getDependentData(), getErrorMeanSD(), getErrorSum(), getTotalValueCount(), initializeScalingMatrix(), printResult(), read(), storeExtendedTimeSeriesData(), sumOfSquares(), sumOfSquaresStore(), updateFittedPointValues(), and updateFittedPointValuesFromExtendedTimeSeries().

◆ mDataIndependent

CMatrix< C_FLOAT64 > CExperiment::mDataIndependent

private

The relevant independent experimental data after reading a file

Referenced by compile(), getIndependentData(), read(), and updateModelWithIndependentData().

◆ mDataTime

CVector< C_FLOAT64 > CExperiment::mDataTime

private

The vector of time points

Referenced by getTimeData(), printResult(), read(), and updateFittedPointValues().

◆ mDefaultColumnScale

CVector< C_FLOAT64 > CExperiment::mDefaultColumnScale

private

Referenced by calculateWeights(), getDefaultScale(), and read().

◆ mDependentObjectsMap

std::map< const CObjectInterface *, size_t > CExperiment::mDependentObjectsMap

private

A map of all dependent data objects to dependent data columns

Referenced by compile(), getColumnValidValueCount(), getDefaultScale(), getDependentObjectsMap(), getErrorMeanSD(), getErrorSum(), getObjectiveValue(), getRMS(), and getScale().

◆ mDependentUpdateSequence

CCore::CUpdateSequence CExperiment::mDependentUpdateSequence

private

Referenced by compile(), storeExtendedTimeSeriesData(), sumOfSquares(), and sumOfSquaresStore().

◆ mDependentValues

CVector< C_FLOAT64 * > CExperiment::mDependentValues

private

Pointer to the actual independent values in the model in the order in which they occur as colums in the file, which is also the order in which the numbers are stored in the various internal data structures

Referenced by compile(), storeExtendedTimeSeriesData(), sumOfSquares(), and sumOfSquaresStore().

◆ mExtendedTimeSeries

CVector< C_FLOAT64 > CExperiment::mExtendedTimeSeries

private

Referenced by CExperiment(), initExtendedTimeSeries(), and updateFittedPointValuesFromExtendedTimeSeries().

◆ mExtendedTimeSeriesSize

size_t CExperiment::mExtendedTimeSeriesSize

private

Referenced by extendedTimeSeriesSize(), and initExtendedTimeSeries().

◆ mFittingPoints

CDataVector< CFittingPoint > CExperiment::mFittingPoints

private

Referenced by getFittingPoints(), updateFittedPoints(), updateFittedPointValues(), and updateFittedPointValuesFromExtendedTimeSeries().

◆ mIndependentObjects

CObjectInterface::ObjectSet CExperiment::mIndependentObjects

private

Referenced by compile(), and getIndependentObjects().

◆ mIndependentUpdateSequence

CCore::CUpdateSequence CExperiment::mIndependentUpdateSequence

private

Referenced by compile(), and updateModelWithIndependentData().

◆ mIndependentValues

CVector< C_FLOAT64 * > CExperiment::mIndependentValues

private

Referenced by compile(), and updateModelWithIndependentData().

◆ mMean

C_FLOAT64 CExperiment::mMean

private

Referenced by calculateStatistics(), compile(), getErrorMean(), and printResult().

◆ mMeans

CVector< C_FLOAT64 > CExperiment::mMeans

private

Referenced by calculateWeights(), and read().

◆ mMeanSD

C_FLOAT64 CExperiment::mMeanSD

private

Referenced by calculateStatistics(), compile(), and getErrorMeanSD().

◆ mMissingData

bool CExperiment::mMissingData

private

Indicates whether we have missing data

Referenced by calculateWeights(), sumOfSquares(), and sumOfSquaresStore().

◆ mNumDataRows

size_t CExperiment::mNumDataRows

private

Referenced by calculateWeights(), getNumDataRows(), printResult(), read(), and updateFittedPointValues().

◆ mObjectiveValue

C_FLOAT64 CExperiment::mObjectiveValue

private

Referenced by calculateStatistics(), compile(), getObjectiveValue(), and printResult().

◆ mpContainer

CMathContainer* CExperiment::mpContainer

private

Referenced by compile(), storeExtendedTimeSeriesData(), sumOfSquares(), sumOfSquaresStore(), and updateModelWithIndependentData().

◆ mpDataDependentCalculated

C_FLOAT64* CExperiment::mpDataDependentCalculated

private

The relevant dependent experimental data after reading a file

Referenced by calculateStatistics(), getErrorMeanSD(), getErrorSum(), printResult(), read(), sumOfSquaresStore(), and updateFittedPointValues().

◆ mpFileName

std::string* CExperiment::mpFileName

private

This is realized as a CCopasiParameter type STRING

Referenced by compare(), getFileName(), getFileNameOnly(), initializeParameter(), operator=(), read(), and setFileName().

◆ mpFirstRow

unsigned C_INT32* CExperiment::mpFirstRow

private

This is realized as a CCopasiParameter type UINT

Referenced by compare(), getFirstRow(), guessColumnNumber(), initializeParameter(), operator=(), read(), setFirstRow(), setHeaderRow(), and setLastRow().

◆ mpHeaderRow

unsigned C_INT32* CExperiment::mpHeaderRow

private

This is realized as a CCopasiParameter type UINT

Referenced by getHeaderRow(), initializeParameter(), operator=(), read(), readColumnNames(), setFirstRow(), setHeaderRow(), and setLastRow().

◆ mpLastRow

unsigned C_INT32* CExperiment::mpLastRow

private

This is realized as a CCopasiParameter type UINT

Referenced by getLastRow(), guessColumnNumber(), initializeParameter(), operator=(), read(), setFirstRow(), setHeaderRow(), and setLastRow().

◆ mpNormalizeWeightsPerExperiment

bool* CExperiment::mpNormalizeWeightsPerExperiment

private

Indicates whether the weights of this experiment should be normalized to 1

Referenced by calculateWeights(), getNormalizeWeightsPerExperiment(), initializeParameter(), operator=(), and setNormalizeWeightsPerExperiment().

◆ mpNumColumns

unsigned C_INT32* CExperiment::mpNumColumns

private

This is realized as a CCopasiParameter type UINT

Referenced by compile(), getNumColumns(), initializeParameter(), operator=(), read(), readColumnNames(), and setNumColumns().

◆ mpObjectMap

CExperimentObjectMap* CExperiment::mpObjectMap

private

This is realized as a CCopasiParameter type GROUP

Referenced by compile(), elevateChildren(), fixBuild55(), getObjectMap(), printResult(), read(), setWeightMethod(), and updateFittedPoints().

◆ mpRowOriented

bool* CExperiment::mpRowOriented

private

This is realized as a CCopasiParameter type BOOL

Referenced by initializeParameter(), isRowOriented(), operator=(), and setIsRowOriented().

◆ mpSeparator

std::string* CExperiment::mpSeparator

private

This is realized as a CCopasiParameter type STRING

Referenced by getSeparator(), guessColumnNumber(), initializeParameter(), operator=(), read(), readColumnNames(), and setSeparator().

◆ mpTaskType

CTaskEnum::Task* CExperiment::mpTaskType

private

This is realized as a CCopasiParameter type UINT

Referenced by calculateStatistics(), compile(), getExperimentType(), initializeParameter(), operator=(), printResult(), read(), setExperimentType(), and updateFittedPointValues().

◆ mpWeightMethod

WeightMethod* CExperiment::mpWeightMethod

private

This is realized as a CCopasiParameter type UINT

Referenced by calculateWeights(), elevateChildren(), getWeightMethod(), initializeParameter(), initializeScalingMatrix(), operator=(), and setWeightMethod().

◆ mRMS

C_FLOAT64 CExperiment::mRMS

private

Referenced by calculateStatistics(), compile(), getRMS(), and printResult().

◆ mRowObjectiveValue

CVector< C_FLOAT64 > CExperiment::mRowObjectiveValue

private

Referenced by calculateStatistics(), compile(), and printResult().

◆ mRowRMS

CVector< C_FLOAT64 > CExperiment::mRowRMS

private

Referenced by calculateStatistics(), compile(), and printResult().

◆ mScale

CMatrix< C_FLOAT64 > CExperiment::mScale

private

The individual scale for each residual

Referenced by calculateStatistics(), getErrorMeanSD(), getScale(), getScalingMatrix(), initializeScalingMatrix(), printResult(), sumOfSquares(), sumOfSquaresStore(), and updateFittedPointValues().

◆ mStorageIt

C_FLOAT64* CExperiment::mStorageIt

private

Referenced by CExperiment(), initExtendedTimeSeries(), and storeExtendedTimeSeriesData().

◆ mValidValueCount

size_t CExperiment::mValidValueCount

private

Referenced by calculateStatistics(), and getValidValueCount().

◆ TypeName

const std::string CExperiment::TypeName

static

Initial value:

=
{
  "ignored",
  "independent",
  "dependent",
  "Time",
  ""
}

String literals for the GUI to display type names of columns known to COPASI.

◆ WeightMethodName

const std::string CExperiment::WeightMethodName

static

Initial value:

=
{
  "Mean",
  "Mean Square",
  "Standard Deviation",
  "Value Scaling",
  ""
}

String literals for the GUI to display weight method known to COPASI.

◆ WeightMethodType

const char * CExperiment::WeightMethodType

static

Initial value:

=
{
  "Mean",
  "MeanSquare",
  "StandardDeviation",
  "ValueScaling",
  NULL
}

XML type names of weight methods known to COPASI.

◆ XMLType

const char * CExperiment::XMLType

static

Initial value:

=
{
  "ignored",
  "independent",
  "dependent",
  "time",
  NULL
}

XML type names of tasks known to COPASI.

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

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Member Enumeration Documentation

◆ Type

◆ WeightMethod

Constructor & Destructor Documentation

◆ CExperiment() [1/4]

◆ CExperiment() [2/4]

◆ CExperiment() [3/4]

◆ CExperiment() [4/4]

◆ ~CExperiment()

Member Function Documentation

◆ calculateStatistics()

◆ calculateWeights()

◆ compare()

◆ compile()

◆ elevateChildren()

◆ extendedTimeSeriesSize()

◆ fixBuild55()

◆ getColumnNames()

◆ getColumnValidValueCount()

◆ getDefaultScale()

◆ getDependentData()

◆ getDependentObjectsMap()

◆ getErrorMean()

◆ getErrorMeanSD() [1/2]

◆ getErrorMeanSD() [2/2]

◆ getErrorSum()

◆ getExperimentType()

◆ getFileName()

◆ getFileNameOnly()

◆ getFirstRow()

◆ getFittingPoints()

◆ getHeaderRow()

◆ getIndependentData()

◆ getIndependentObjects()

◆ getLastRow()

◆ getNormalizeWeightsPerExperiment()

◆ getNumColumns()

◆ getNumDataRows()

◆ getObjectiveValue() [1/2]

◆ getObjectiveValue() [2/2]

◆ getObjectMap() [1/2]

◆ getObjectMap() [2/2]

◆ getRMS() [1/2]

◆ getRMS() [2/2]

◆ getScale()

◆ getScalingMatrix()

◆ getSeparator()

◆ getTimeData()

◆ getTotalValueCount()

◆ getValidValueCount()

◆ getWeightMethod()

◆ guessColumnNumber()

◆ initExtendedTimeSeries()

◆ initializeParameter()

◆ initializeScalingMatrix()

◆ isRowOriented()

◆ operator=()

◆ printResult()

◆ read()

◆ readColumnNames()

◆ setExperimentType()

◆ setFileName()

◆ setFirstRow()

◆ setHeaderRow()

◆ setIsRowOriented()

◆ setLastRow()

◆ setNormalizeWeightsPerExperiment()

◆ setNumColumns()

◆ setSeparator()

◆ setWeightMethod()

◆ storeExtendedTimeSeriesData()