#include <CExperimentSet.h>

Inheritance diagram for CCrossValidationSet:

Collaboration diagram for CCrossValidationSet:

Public Member Functions
	CCrossValidationSet (const CCopasiContainer *pParent, const std::string &name="Validation Set")

	CCrossValidationSet (const CCrossValidationSet &src, const CCopasiContainer *pParent=NULL)

	CCrossValidationSet (const CCopasiParameterGroup &group, const CCopasiContainer *pParent=NULL)

const unsigned C_INT32 &	getThreshold () const

const C_FLOAT64 &	getWeight () const

void	setThreshold (const unsigned C_INT32 &threshold)

void	setWeight (const C_FLOAT64 &weight)

virtual	~CCrossValidationSet ()

Public Member Functions inherited from CExperimentSet
CExperiment *	addExperiment (const CExperiment &experiment)

bool	calculateStatistics ()

	CExperimentSet (const CCopasiContainer *pParent, const std::string &name="Experiment Set")

	CExperimentSet (const CExperimentSet &src, const CCopasiContainer *pParent=NULL)

	CExperimentSet (const CCopasiParameterGroup &group, const CCopasiContainer *pParent=NULL)

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

virtual bool	elevateChildren ()

void	fixBuild55 ()

size_t	getDataPointCount () const

const CMatrix< C_FLOAT64 > &	getDependentData (const size_t &index) const

const CVector< C_FLOAT64 > &	getDependentErrorMean () const

const CVector< C_FLOAT64 > &	getDependentErrorMeanSD () const

const CVector< C_FLOAT64 > &	getDependentObjectiveValues () const

const CVector< CCopasiObject * > &	getDependentObjects () const

const CVector< C_FLOAT64 > &	getDependentRMS () const

CExperiment *	getExperiment (const size_t &index)

const CExperiment *	getExperiment (const size_t &index) const

CExperiment *	getExperiment (const std::string &name)

const CExperiment *	getExperiment (const std::string &name) const

size_t	getExperimentCount () const

const CCopasiTask::Type &	getExperimentType (const size_t &index) const

std::vector< std::string >	getFileNames () const

const CMatrix< C_FLOAT64 > &	getIndependentData (const size_t &index) const

const size_t &	getValidValueCount () const

bool	hasDataForTaskType (const CCopasiTask::Type &type) const

size_t	keyToIndex (const std::string &key) const

void	removeExperiment (const size_t &index)

void	sort ()

virtual	~CExperimentSet ()

Public Member Functions inherited from CCopasiParameterGroup
bool	addGroup (const std::string &name)

bool	addParameter (const CCopasiParameter &parameter)

bool	addParameter (const std::string &name, const CCopasiParameter::Type type)

template<class CType >
bool	addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value)

void	addParameter (CCopasiParameter *pParameter)

CCopasiParameterGroup *	assertGroup (const std::string &name)

template<class CType >
CCopasiParameter *	assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue)

index_iterator	beginIndex () const

name_iterator	beginName () const

	CCopasiParameterGroup (const CCopasiParameterGroup &src, const CCopasiContainer *pParent=NULL)

	CCopasiParameterGroup (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &objectType="ParameterGroup")

void	clear ()

index_iterator	endIndex () const

name_iterator	endName () const

CCopasiParameterGroup *	getGroup (const std::string &name)

const CCopasiParameterGroup *	getGroup (const std::string &name) const

CCopasiParameterGroup *	getGroup (const size_t &index)

const CCopasiParameterGroup *	getGroup (const size_t &index) const

size_t	getIndex (const std::string &name) const

std::string	getKey (const std::string &name) const

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

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

virtual const CObjectInterface *	getObject (const CCopasiObjectName &cn) const

CCopasiParameter *	getParameter (const std::string &name)

const CCopasiParameter *	getParameter (const std::string &name) const

CCopasiParameter *	getParameter (const size_t &index)

const CCopasiParameter *	getParameter (const size_t &index) const

CCopasiParameter::Type	getType (const std::string &name) const

CCopasiParameter::Type	getType (const size_t &index) const

std::string	getUniqueParameterName (const CCopasiParameter *pParameter) const

const CCopasiParameter::Value &	getValue (const std::string &name) const

const CCopasiParameter::Value &	getValue (const size_t &index) const

CCopasiParameter::Value &	getValue (const std::string &name)

CCopasiParameter::Value &	getValue (const size_t &index)

CCopasiParameterGroup &	operator= (const CCopasiParameterGroup &rhs)

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

bool	removeParameter (const std::string &name)

bool	removeParameter (const size_t &index)

template<class CType >
bool	setValue (const std::string &name, const CType &value)

template<class CType >
bool	setValue (const size_t &index, const CType &value)

size_t	size () const

bool	swap (const size_t &iFrom, const size_t &iTo)

bool	swap (index_iterator &from, index_iterator &to)

virtual	~CCopasiParameterGroup ()

Public Member Functions inherited from CCopasiParameter
	CCopasiParameter (const CCopasiParameter &src, const CCopasiContainer *pParent=NULL)

	CCopasiParameter (const std::string &name, const Type &type, const void pValue=NULL, const CCopasiContainer pParent=NULL, const std::string &objectType="Parameter")

virtual CCopasiObjectName	getCN () const

virtual const std::string &	getKey () const

virtual std::string	getObjectDisplayName (bool regular=true, bool richtext=false) const

const CCopasiParameter::Type &	getType () const

const Value &	getValue () const

Value &	getValue ()

virtual void *	getValuePointer () const

CCopasiObject *	getValueReference () const

bool	isValidValue (const C_FLOAT64 &value) const

bool	isValidValue (const C_INT32 &value) const

bool	isValidValue (const unsigned C_INT32 &value) const

bool	isValidValue (const bool &value) const

bool	isValidValue (const std::string &value) const

bool	isValidValue (const CCopasiObjectName &value) const

bool	isValidValue (const std::vector< CCopasiParameter * > &value) const

CCopasiParameter &	operator= (const CCopasiParameter &rhs)

template<class CType >
bool	setValue (const CType &value)

bool	setValue (const std::vector< CCopasiParameter * > &value)

virtual	~CCopasiParameter ()

Public Member Functions inherited from CCopasiContainer
virtual bool	add (CCopasiObject *pObject, const bool &adopt=true)

	CCopasiContainer (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=CCopasiObject::Container)

	CCopasiContainer (const CCopasiContainer &src, const CCopasiContainer *pParent=NULL)

virtual std::string	getChildObjectUnits (const CCopasiObject *pObject) const

virtual const objectMap &	getObjects () const

virtual std::string	getUnits () const

virtual const CCopasiObject *	getValueObject () const

virtual bool	remove (CCopasiObject *pObject)

virtual	~CCopasiContainer ()

Public Member Functions inherited from CCopasiObject
void	addDirectDependency (const CCopasiObject *pObject)

	CCopasiObject (const CCopasiObject &src, const CCopasiContainer *pParent=NULL)

void	clearDirectDependencies ()

void	clearRefresh ()

bool	dependsOn (DataObjectSet candidates, const DataObjectSet &context=DataObjectSet()) const

void	getAllDependencies (DataObjectSet &dependencies, const DataObjectSet &context) const

virtual const DataObjectSet &	getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const

CCopasiContainer *	getObjectAncestor (const std::string &type) const

CCopasiDataModel *	getObjectDataModel ()

const CCopasiDataModel *	getObjectDataModel () const

const std::string &	getObjectName () const

CCopasiContainer *	getObjectParent () const

const std::string &	getObjectType () const

virtual const CObjectInterface::ObjectSet &	getPrerequisites () const

virtual Refresh *	getRefresh () const

UpdateMethod *	getUpdateMethod () const

bool	hasCircularDependencies (DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const

bool	hasUpdateMethod () const

bool	isArray () const

bool	isContainer () const

bool	isDataModel () const

bool	isMatrix () const

bool	isNameVector () const

bool	isNonUniqueName () const

virtual bool	isPrerequisiteForContext (const CObjectInterface *pObject, const CMath::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const

bool	isReference () const

bool	isRoot () const

bool	isSeparator () const

bool	isStaticString () const

bool	isValueBool () const

bool	isValueDbl () const

bool	isValueInt () const

bool	isValueInt64 () const

bool	isValueString () const

bool	isVector () const

virtual bool	mustBeDeleted (const DataObjectSet &deletedObjects) const

void	removeDirectDependency (const CCopasiObject *pObject)

void	setDirectDependencies (const DataObjectSet &directDependencies)

bool	setObjectName (const std::string &name)

virtual bool	setObjectParent (const CCopasiContainer *pParent)

void	setObjectValue (const C_FLOAT64 &value)

void	setObjectValue (const C_INT32 &value)

void	setObjectValue (const bool &value)

template<class CType >
void	setRefresh (CType pType, void(CType::method)(void))

template<class CType >
void	setUpdateMethod (CType pType, void(CType::method)(const C_FLOAT64 &))

template<class CType >
void	setUpdateMethod (CType pType, void(CType::method)(const C_INT32 &))

template<class CType >
void	setUpdateMethod (CType pType, void(CType::method)(const bool &))

virtual	~CCopasiObject ()

Public Member Functions inherited from CObjectInterface
	CObjectInterface ()

virtual	~CObjectInterface ()

Private Member Functions
void	initializeParameter ()

Private Attributes
unsigned C_INT32 *	mpThreshold

C_FLOAT64 *	mpWeight

Additional Inherited Members
Public Types inherited from CCopasiParameterGroup
typedef parameterGroup::iterator	index_iterator

typedef CCopasiContainer::objectMap::iterator	name_iterator

typedef std::vector < CCopasiParameter * >	parameterGroup

Public Types inherited from CCopasiParameter
enum	Type { DOUBLE = 0, UDOUBLE, INT, UINT, BOOL, GROUP, STRING, CN, KEY, FILE, EXPRESSION, INVALID }

Public Types inherited from CCopasiContainer
typedef std::multimap < std::string, CCopasiObject * >	objectMap

Public Types inherited from CCopasiObject
typedef std::set< const CCopasiObject * >	DataObjectSet

typedef std::vector< Refresh * >	DataUpdateSequence

Public Types inherited from CObjectInterface
typedef std::set< const CObjectInterface * >	ObjectSet

typedef std::vector < CObjectInterface * >	UpdateSequence

Static Public Member Functions inherited from CCopasiObject
static std::vector< Refresh * >	buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet())

static void	setRenameHandler (CRenameHandler *rh)

Static Public Attributes inherited from CCopasiParameter
static const std::string	TypeName []

static const char *	XMLType []

Static Public Attributes inherited from CCopasiContainer
static const std::vector < CCopasiContainer * >	EmptyList

Protected Types inherited from CCopasiObject
enum	Flag { Container = 0x1, Vector = 0x2, Matrix = 0x4, NameVector = 0x8, Reference = 0x10, ValueBool = 0x20, ValueInt = 0x40, ValueInt64 = 0x80, ValueDbl = 0x100, NonUniqueName = 0x200, StaticString = 0x400, ValueString = 0x800, Separator = 0x1000, ModelEntity = 0x2000, Array = 0x4000, DataModel = 0x8000, Root = 0x10000, Gui = 0x20000 }

Protected Member Functions inherited from CCopasiParameterGroup
	CCopasiParameterGroup ()

Protected Member Functions inherited from CCopasiContainer
template<class CType >
CCopasiObject *	addMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

template<class CType >
CCopasiObject *	addObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

template<class CType >
CCopasiObject *	addVectorReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

void	initObjects ()

Protected Member Functions inherited from CCopasiObject
	CCopasiObject ()

	CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0)

Protected Attributes inherited from CCopasiParameter
std::string	mKey

CCopasiObject *	mpValueReference

size_t	mSize

Value	mValue

Protected Attributes inherited from CCopasiContainer
objectMap	mObjects

Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

Detailed Description

Definition at line 276 of file CExperimentSet.h.

Constructor & Destructor Documentation

CCrossValidationSet::CCrossValidationSet	(	const CCopasiContainer *	pParent,
		const std::string &	name = `"Validation Set"`
	)

Default constructor

Parameters

const	std::string & name (default: Cross Validation Set)
const	CCopasiContainer * pParent (default: NULL)

Definition at line 479 of file CExperimentSet.cpp.

References initializeParameter().

                            :
   CExperimentSet(name, pParent),
   mpWeight(NULL),
   mpThreshold(NULL)
 {initializeParameter();}

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

Copy constructor

Parameters

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

Definition at line 486 of file CExperimentSet.cpp.

References initializeParameter().

                                      :
   CExperimentSet(src, pParent),
   mpWeight(NULL),
   mpThreshold(NULL)
 {initializeParameter();}

CCrossValidationSet::CCrossValidationSet	(	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)

Definition at line 493 of file CExperimentSet.cpp.

References initializeParameter().

                                      :
   CExperimentSet(group, pParent),
   mpWeight(NULL),
   mpThreshold(NULL)
 {initializeParameter();}

CCrossValidationSet::~CCrossValidationSet ( )

virtual

Destructor

Definition at line 500 of file CExperimentSet.cpp.

500 {}

Member Function Documentation

const unsigned C_INT32 & CCrossValidationSet::getThreshold ( ) const

Retreive the threshold

Returns: const unsigned C_INT32 & threshold

Definition at line 518 of file CExperimentSet.cpp.

References mpThreshold.

Referenced by CFitProblem::calculateCrossValidation(), CQFittingWidget::saveTask(), and CQExperimentData::slotOK().

519 {return *mpThreshold;}

CCrossValidationSet::mpThreshold

unsigned C_INT32 * mpThreshold

Definition: CExperimentSet.h:352

const C_FLOAT64 & CCrossValidationSet::getWeight ( ) const

Retreive the weight

Returns: const C_FLOAT64 & weight

Definition at line 512 of file CExperimentSet.cpp.

References mpWeight.

Referenced by CFitProblem::calculateCrossValidation(), CQFittingWidget::saveTask(), and CQExperimentData::slotOK().

513 {return *mpWeight;}

CCrossValidationSet::mpWeight

C_FLOAT64 * mpWeight

Definition: CExperimentSet.h:345

void CCrossValidationSet::initializeParameter ( )

private

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

Definition at line 521 of file CExperimentSet.cpp.

References CCopasiParameterGroup::assertParameter(), C_FLOAT64, C_INT32, CExperimentSet::elevateChildren(), CCopasiParameter::getValue(), mpThreshold, mpWeight, CCopasiParameter::Value::pUDOUBLE, CCopasiParameter::Value::pUINT, CCopasiParameter::UDOUBLE, and CCopasiParameter::UINT.

Referenced by CCrossValidationSet().

 {
   mpWeight =
     assertParameter("Weight", CCopasiParameter::UDOUBLE, (C_FLOAT64) 1.0)->getValue().pUDOUBLE;
 
   mpThreshold =
     assertParameter("Threshold", CCopasiParameter::UINT, (unsigned C_INT32) 5)->getValue().pUINT;
 
   elevateChildren();
 }

void CCrossValidationSet::setThreshold ( const unsigned C_INT32 & threshold )

Set the threshold

Parameters

const unsigned C_INT32 & threshold

Definition at line 515 of file CExperimentSet.cpp.

References mpThreshold.

Referenced by CQExperimentData::slotOK().

516 {*mpThreshold = threshold;}

CCrossValidationSet::mpThreshold

unsigned C_INT32 * mpThreshold

Definition: CExperimentSet.h:352

void CCrossValidationSet::setWeight ( const C_FLOAT64 & weight )

Set the weight

Parameters

const C_FLOAT64 & weight

Definition at line 502 of file CExperimentSet.cpp.

References mpWeight.

Referenced by CQFittingWidget::saveTask(), and CQExperimentData::slotOK().

 {
   if (weight < 0.0)
     *mpWeight = 0.0;
   else if (weight > 1.0)
     *mpWeight = 1.0;
   else
     *mpWeight = weight;
 }

Member Data Documentation

unsigned C_INT32* CCrossValidationSet::mpThreshold

private

The threshold indicates the number of failed successive checks for which the objective function has not improved needed to terminate the parameter estimation.

Definition at line 352 of file CExperimentSet.h.

Referenced by getThreshold(), initializeParameter(), and setThreshold().

C_FLOAT64* CCrossValidationSet::mpWeight

private

The weight of each datapoint relative to a data point of the experiment set, i.e. 1 gives each point the same weight

Definition at line 345 of file CExperimentSet.h.

Referenced by getWeight(), initializeParameter(), and setWeight().

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

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation