#include <CExperiment.h>

Inheritance diagram for CExperiment:

Public Types
enum	Type { ignore = 0, independent, dependent, time }
enum	WeightMethod { MEAN = 0, MEAN_SQUARE, SD }
Public Member Functions
	CExperiment (const CCopasiContainer *pParent, const std::string &name="Experiment")
	CExperiment (const CExperiment &src, const CCopasiContainer *pParent=NULL)
	CExperiment (const CCopasiParameterGroup &group, const CCopasiContainer *pParent=NULL)
virtual	~CExperiment ()
CExperiment &	operator= (const CExperiment &rhs)
virtual bool	elevateChildren ()
bool	compile (const std::vector< CCopasiContainer * > listOfContainer=CCopasiContainer::EmptyList)
bool	read (std::istream &in, unsigned C_INT32 &currentLine)
bool	calculateWeights ()
const std::map< CCopasiObject *, unsigned C_INT32 > &	getDependentObjects () const
C_FLOAT64	sumOfSquares (const unsigned C_INT32 &index, C_FLOAT64 *&residuals) const
C_FLOAT64	sumOfSquaresStore (const unsigned C_INT32 &index, C_FLOAT64 *&dependentValues)
bool	calculateStatistics ()
bool	readColumnNames ()
unsigned C_INT32	guessColumnNumber () const
const std::vector< std::string > &	getColumnNames () const
bool	updateModelWithIndependentData (const unsigned C_INT32 &index)
bool	restoreModelIndependentData ()
bool	setExperimentType (const CCopasiTask::Type &type)
const CCopasiTask::Type &	getExperimentType () const
const CVector< C_FLOAT64 > &	getTimeData () const
const CMatrix< C_FLOAT64 > &	getIndependentData () const
const CMatrix< C_FLOAT64 > &	getDependentData () const
const std::string &	getFileName () const
bool	setFileName (const std::string &fileName)
CExperimentObjectMap &	getObjectMap ()
const CCopasiVector < CFittingPoint > &	getFittingPoints () const
void	updateFittedPoints ()
void	updateFittedPointValues (const unsigned C_INT32 &index)
const unsigned C_INT32 &	getNumColumns () const
bool	setNumColumns (const unsigned C_INT32 &cols)
const unsigned C_INT32 &	getFirstRow () const
bool	setFirstRow (const unsigned C_INT32 &firstRow)
const unsigned C_INT32 &	getLastRow () const
bool	setLastRow (const unsigned C_INT32 &lastRow)
const unsigned C_INT32 &	getHeaderRow () const
bool	setHeaderRow (const unsigned C_INT32 &headerRow)
unsigned C_INT32	getNumDataRows () const
const std::string &	getSeparator () const
bool	setSeparator (const std::string &seperator)
const WeightMethod &	getWeightMethod () const
bool	setWeightMethod (const WeightMethod &weightMethod)
const bool &	isRowOriented () const
bool	setIsRowOriented (const bool &isRowOriented)
virtual void	printResult (std::ostream *ostream) const
const C_FLOAT64 &	getObjectiveValue () const
const C_FLOAT64 &	getRMS () const
const C_FLOAT64 &	getErrorMean () const
const C_FLOAT64 &	getErrorMeanSD () const
C_FLOAT64	getObjectiveValue (CCopasiObject *const &pObject) const
C_FLOAT64	getDefaultWeight (const CCopasiObject *const &pObject) const
C_FLOAT64	getRMS (CCopasiObject *const &pObject) const
C_FLOAT64	getErrorMean (CCopasiObject *const &pObject) const
C_FLOAT64	getErrorMeanSD (CCopasiObject *const &pObject, const C_FLOAT64 &errorMean) const
unsigned C_INT32	getCount (CCopasiObject *const &pObject) const
Static Public Member Functions
static bool	compare (const CExperiment lhs, const CExperiment rhs)
Static Public Attributes
static const std::string	TypeName []
static const char *	XMLType []
static const std::string	WeightMethodName []
static const char *	WeightMethodType []
Friends
bool	operator== (const CExperiment &lhs, const CExperiment &rhs)

Member Enumeration Documentation

enum CExperiment::Type

Enumeration of the types of columns known to COPASI.

Enumerator:

ignore
independent
dependent
time

Reimplemented from CCopasiParameter.

enum CExperiment::WeightMethod

Enumaration of methods to calculate the weight.

Enumerator:

MEAN
MEAN_SQUARE
SD

Constructor & Destructor Documentation

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

Default constructor

Parameters:

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

CExperiment::CExperiment	(	const CExperiment &	src,
		const CCopasiContainer *	pParent = `NULL`
	)

Copy constructor

Parameters:

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

CExperiment::CExperiment	(	const CCopasiParameterGroup &	group,
		const CCopasiContainer *	pParent = `NULL`
	)

Specific constructor used for reading COPASI files

Parameters:

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

CExperiment::~CExperiment ( ) [virtual]

Destructor

Member Function Documentation

bool CExperiment::calculateStatistics ( )

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

Returns:: bool success

bool CExperiment::calculateWeights ( )

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

Returns:: bool success

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

bool CExperiment::compile ( const std::vector< CCopasiContainer * > listOfContainer = CCopasiContainer::EmptyList )

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

Parameters:

const std::vector< CCopasiContainer * > listOfContainer

Returns:: bool success

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.

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

Retrieve the column names

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

unsigned C_INT32 CExperiment::getCount ( CCopasiObject *const & pObject ) const

Retrieve the data point caount for the object.

Parameters:

CCopasiObject *const& pObject

Returns:: unsigned C_INT32 count

C_FLOAT64 CExperiment::getDefaultWeight ( const CCopasiObject *const & pObject ) const

Retrieve the default weight for the object.

Parameters:

CCopasiObject *const& pObject

Returns:: C_FLOAT64 weight

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

Retrieve the dependent data of the experiment.

Returns:: const CMatrix< C_FLOAT64 > & dependentData

const std::map< CCopasiObject *, unsigned C_INT32 > & CExperiment::getDependentObjects ( ) const

Retrieve the list of dependent data objects

Returns:: const std::map< CCopasiObject *, unsigned C_INT32 > & dependentObjects

const C_FLOAT64 & CExperiment::getErrorMean ( ) const

Retrieve the mean of the error

Parameters:

const C_FLOAT64 & errorMean

C_FLOAT64 CExperiment::getErrorMean ( CCopasiObject *const & pObject ) const

Retrieve the error mean for the object.

Parameters:

CCopasiObject *const& pObject

Returns:: C_FLOAT64 errorMean

const C_FLOAT64 & CExperiment::getErrorMeanSD ( ) const

Retrieve the std. deviation of the error

Parameters:

const C_FLOAT64 & errorMeanSD

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

Retrieve the error mean std. deviations for the object.

Parameters:

CCopasiObject	*const& pObject
C_FLOAT64	errorMean

Returns:: C_FLOAT64 errorMeanSD

const CCopasiTask::Type & CExperiment::getExperimentType ( ) const

Retrieve the experiment type

Returns:: const CCopasiTask::Type & experimentType

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

Retrieve the file name

Returns:: const std::string & fileName

const unsigned C_INT32 & CExperiment::getFirstRow ( ) const

Retrieve the first row

Returns:: const unsigned C_INT32 & firstRow

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

Retrieve the list of fitting points

Returns:: const CCopasiVector< CFittingPoint > & fittingPoints

const unsigned C_INT32 & CExperiment::getHeaderRow ( ) const

Retrieve the header row

Returns:: const unsigned C_INT32 & headerRow

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

Retrieve the independent data of the experiment.

Returns:: const CMatrix< C_FLOAT64 > & independentData

const unsigned C_INT32 & CExperiment::getLastRow ( ) const

Retrieve the last row

Returns:: const unsigned C_INT32 & lastRow

const unsigned C_INT32 & CExperiment::getNumColumns ( ) const

Retrieve the number of columns

Returns:: const unsigned C_INT32 & numColumns

unsigned C_INT32 CExperiment::getNumDataRows ( ) const

Retrieve the number of data rows

Returns:: const unsigned C_INT32 numDataRows

const C_FLOAT64 & CExperiment::getObjectiveValue ( ) const

Retrieve the value of the objective function

Parameters:

const C_FLOAT64 & errorMean

C_FLOAT64 CExperiment::getObjectiveValue ( CCopasiObject *const & pObject ) const

Retrieve the objective value for the object.

Parameters:

CCopasiObject *const& pObject

Returns:: C_FLOAT64 objectiveValue

CExperimentObjectMap & CExperiment::getObjectMap ( )

Retrieve the object map

Returns:: CExperimentObjectMap & mpObjectMap

const C_FLOAT64 & CExperiment::getRMS ( ) const

Retrieve the RMS

Parameters:

const C_FLOAT64 & RMS

C_FLOAT64 CExperiment::getRMS ( CCopasiObject *const & pObject ) const

Retrieve the RMS for the object.

Parameters:

CCopasiObject *const& pObject

Returns:: C_FLOAT64 RMS

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

Retrieve the separator

Returns:: const std::string & separator

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

Retrieve the time data of the experiment.

Returns:: const CVector< C_FLOAT64 > & timeData

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

Retrieve the method used for calculating the default weights.

Returns:: const WeightMethod & weightMethod

unsigned C_INT32 CExperiment::guessColumnNumber ( ) const

Try to guess the number of columns

Returns:: unsigned C_INT32 numColumns

const bool & CExperiment::isRowOriented ( ) const

Check whter the data is row oriented.

Returns:: const bool & isRowOriented

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

Assignement operator

Parameters:

const CExperiment & rhs

Returns:: CExperiment & lhs

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

bool CExperiment::read	(	std::istream &	in,
		unsigned C_INT32 &	currentLine
	)

Reads the experiment data form a the given stream

Parameters:

std::istream	& in
unsigned	C_INT32 & currentLine

Returns:: bool success

bool CExperiment::readColumnNames ( )

Reads the header row for the experiment data

Returns:: bool success

bool CExperiment::restoreModelIndependentData ( )

Restore the model with the independent data from before the experiment

Returns:: bool success

bool CExperiment::setExperimentType ( const CCopasiTask::Type & type )

set the experiment type

Parameters:

const CCopasiTask::Type & experimentType

Returns:: bool success

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

Set the file name

Parameters:

const std::string & fileName

Returns:: bool success

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

Set the first row containing data

Parameters:

const unsigned C_INT32 & firstRow

Returns:: bool success

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

Set the header row containing data

Parameters:

const unsigned C_INT32 & headerRow

Returns:: bool success

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

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

Set the last row containing data

Parameters:

const unsigned C_INT32 & lastRow

Returns:: bool success

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

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

Set the seperator used when reading a stream

Parameters:

const std::string & separator

Returns:: bool success

bool CExperiment::setWeightMethod ( const WeightMethod & weightMethod )

Set the weight calculation method and resets manual adjusted weights

Parameters:

const WeightMethod & weightMethod

Returns:: bool success

C_FLOAT64 CExperiment::sumOfSquares	(	const unsigned C_INT32 &	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	unsigned C_INT32 & index
C_FLOAT64	*& residuals (may be NULL)

Returns:: C_FLOAT64 sumOfSquares

C_FLOAT64 CExperiment::sumOfSquaresStore	(	const unsigned C_INT32 &	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	unsigned C_INT32 & index
C_FLOAT64	*& dependentValues (must not be NULL)

Returns:: C_FLOAT64 sumOfSquares

void CExperiment::updateFittedPoints ( )

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

void CExperiment::updateFittedPointValues ( const unsigned C_INT32 & index )

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

bool CExperiment::updateModelWithIndependentData ( const unsigned C_INT32 & index )

Update the model with the independent data of the experiment

Parameters:

const unsigned C_INT32 & index

Returns:: bool success

Friends And Related Function Documentation

bool operator==	(	const CExperiment &	lhs,
		const CExperiment &	rhs
	)		`[friend]`

Comparison operator

Parameters:

const	CExperiment & lhs
const	CExperiment & rhs

Returns:: bool equal

Member Data Documentation

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.

Reimplemented from CCopasiParameter.

const std::string CExperiment::WeightMethodName [static]

Initial value:

{
  "Mean",
  "Mean Square",
  "Standard Deviation",
  ""
}

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

const char * CExperiment::WeightMethodType [static]

Initial value:

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

XML type names of weight methods known to COPASI.

const char * CExperiment::XMLType [static]

Initial value:

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

XML type names of tasks known to COPASI.

Reimplemented from CCopasiParameter.

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

copasi/parameterFitting/CExperiment.h
copasi/parameterFitting/CExperiment.cpp

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Friends

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation