CFitTask Class Reference

#include <CFitTask.h>

Inheritance diagram for CFitTask:

Collaboration diagram for CFitTask:

Public Member Functions
	CFitTask (const CCopasiTask::Type &type=CCopasiTask::parameterFitting, const CCopasiContainer *pParent=NULL)
	CFitTask (const CFitTask &src, const CCopasiContainer *pParent=NULL)
void	cleanup ()
virtual CCopasiMethod *	createMethod (const int &type) const
void	fixBuild55 ()
virtual bool	initialize (const OutputFlag &of, COutputHandler *pOutputHandler, std::ostream *pOstream)
virtual bool	process (const bool &useInitialValues)
virtual bool	setCallBack (CProcessReport *pCallBack)
virtual bool	setMethodType (const int &type)
	~CFitTask ()
Public Member Functions inherited from COptTask
void	cleanup ()
	COptTask (const CCopasiTask::Type &type=CCopasiTask::optimization, const CCopasiContainer *pParent=NULL)
	COptTask (const COptTask &src, const CCopasiContainer *pParent=NULL)
	~COptTask ()
Public Member Functions inherited from CCopasiTask
	CCopasiTask (const std::string &name="NoName", const CCopasiContainer *pParent=NULL, const std::string &type="Task")
	CCopasiTask (const Type &taskType, const CCopasiContainer *pParent=NULL, const std::string &type="Task")
	CCopasiTask (const CCopasiTask &src, const CCopasiContainer *pParent=NULL)
void	cleanup ()
CProcessReport *	getCallBack () const
const CDescription &	getDescription () const
virtual const std::string &	getKey () const
CCopasiMethod *	getMethod ()
const CCopasiMethod *	getMethod () const
COutputHandler *	getOutputHandler () const
const OutputFlag &	getOutputMode () const
CCopasiProblem *	getProblem ()
const CCopasiProblem *	getProblem () const
CReport &	getReport ()
const CResult &	getResult () const
CCopasiParameterGroup *	getSliders ()
Type	getType () const
const bool &	isScheduled () const
const bool &	isUpdateModel () const
virtual void	output (const COutputInterface::Activity &activity)
virtual bool	restore ()
virtual void	separate (const COutputInterface::Activity &activity)
void	setScheduled (const bool &scheduled)
void	setType (const Type &type)
void	setUpdateModel (const bool &updateModel)
virtual bool	updateMatrices ()
virtual	~CCopasiTask ()
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 CObjectInterface *	getObject (const CCopasiObjectName &cn) 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 CCopasiObjectName	getCN () const
virtual const DataObjectSet &	getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const
CCopasiContainer *	getObjectAncestor (const std::string &type) const
CCopasiDataModel *	getObjectDataModel ()
const CCopasiDataModel *	getObjectDataModel () const
virtual std::string	getObjectDisplayName (bool regular=true, bool richtext=false) 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
virtual void *	getValuePointer () 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
virtual void	print (std::ostream *ostream) 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 ()

Additional Inherited Members
Public Types inherited from CCopasiTask
enum	eOutputFlagBase {   INITIALIZE = 0x01, STREAM = 0x02, FINISH = 0x04, REPORT = 0x10,   PLOT = 0x20, TIME_SERIES = 0x40 }
enum	OutputFlag {   NO_OUTPUT = 0, OUTPUT_BEFORE = INITIALIZE, OUTPUT_AFTER = FINISH, OUTPUT = REPORT | PLOT | STREAM,   OUTPUT_SE = REPORT | PLOT | INITIALIZE | STREAM | FINISH, OUTPUT_UI = REPORT | PLOT | TIME_SERIES | INITIALIZE | STREAM | FINISH, ONLY_TIME_SERIES = TIME_SERIES | INITIALIZE | STREAM | FINISH }
enum	Type {   steadyState = 0, timeCourse, scan, fluxMode,   optimization, parameterFitting, mca, lyap,   tssAnalysis, sens, moieties, crosssection,   lna, unset }
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 CCopasiTask
static bool	isValidMethod (const unsigned int &method, const unsigned int *validMethods)
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)
Public Attributes inherited from CCopasiTask
std::string	Error
std::string	Warning
Static Public Attributes inherited from COptTask
static const unsigned int	ValidMethods []
Static Public Attributes inherited from CCopasiTask
static const std::string	TypeName []
static const unsigned int	ValidMethods []
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 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 CCopasiTask
CDescription	mDescription
OutputFlag	mDoOutput
std::string	mKey
unsigned C_INT32	mOutputCounter
CProcessReport *	mpCallBack
CState *	mpInitialState
CCopasiMethod *	mpMethod
COutputHandler *	mpOutputHandler
CCopasiProblem *	mpProblem
CCopasiParameterGroup *	mpSliders
CReport	mReport
CResult	mResult
bool	mScheduled
Type	mType
bool	mUpdateModel
Protected Attributes inherited from CCopasiContainer
objectMap	mObjects
Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

Detailed Description

CFitTask class.

This class implements a parameter estimation task which is comprised of a of a problem and a method.

Definition at line 28 of file CFitTask.h.

Constructor & Destructor Documentation

CFitTask::CFitTask	(	const CCopasiTask::Type &	type = CCopasiTask::parameterFitting,
		const CCopasiContainer *	pParent = NULL
	)

default constructor

Parameters

const	CCopasiTask::Type & type (default: parameterFitting)
const	CCopasiContainer * pParent (default: NULL)

CFitTask class.

This class implements a parameter estimation task which is comprised of a of a problem and a method.

Definition at line 30 of file CFitTask.cpp.

References CCopasiContainer::add(), CFitMethod::createMethod(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, and pdelete.

                                                    :
  COptTask(type, pParent)
{
  pdelete(mpProblem);
  mpProblem = new CFitProblem(type, this);
  pdelete(mpMethod);
  mpMethod = CFitMethod::createMethod();
  this->add(mpMethod, true);

  ((COptMethod *) mpMethod)->setProblem((COptProblem *) mpProblem);
}

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

Copy constructor

Parameters

const	CFitTask & src
const	CCopasiContainer * pParent (default: NULL)

Definition at line 43 of file CFitTask.cpp.

References CCopasiContainer::add(), CFitMethod::createMethod(), CCopasiMethod::getSubType(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, and pdelete.

                                                    :
  COptTask(src, pParent)
{
  pdelete(mpProblem);
  mpProblem = new CFitProblem(*(CFitProblem *) src.mpProblem, this);
  pdelete(mpMethod);
  mpMethod = CFitMethod::createMethod(src.mpMethod->getSubType());
  this->add(mpMethod, true);

  ((COptMethod *) mpMethod)->setProblem((COptProblem *) mpProblem);
}

CFitTask::~CFitTask

(

)

Destructor

Definition at line 56 of file CFitTask.cpp.

References cleanup().

{cleanup();}

Member Function Documentation

void CFitTask::cleanup

(

)

cleanup()

Definition at line 59 of file CFitTask.cpp.

Referenced by ~CFitTask().

{}

CCopasiMethod * CFitTask::createMethod ( const int &  type ) const

virtual

Create a method of the specified type to solve the task. It is the duty of the caller to release the CCopasiMethod.

Parameters

const

CCopasiMethod::SubType & type

Returns

CCopasiMethod *

Reimplemented from COptTask.

Definition at line 122 of file CFitTask.cpp.

References CFitMethod::createMethod().

Referenced by setMethodType().

{
  CCopasiMethod::SubType Type = (CCopasiMethod::SubType) type;

  return CFitMethod::createMethod(Type);
}

void CFitTask::fixBuild55

(

)

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

Definition at line 129 of file CFitTask.cpp.

References CFitProblem::fixBuild55(), and CCopasiTask::mpProblem.

Referenced by CCopasiXML::fixBuild55().

{
  CFitProblem * pFitProblem = dynamic_cast< CFitProblem * >(mpProblem);

  if (pFitProblem == NULL) return;

  pFitProblem->fixBuild55();

  return;
}

bool CFitTask::initialize ( const OutputFlag &  of, COutputHandler *  pOutputHandler, std::ostream *  pOstream  )

virtual

Initialize the task. If an ostream is given this ostream is used instead of the target specified in the report. This allows nested tasks to share the same output device.

Parameters

const	OutputFlag & of
COutputHandler	* pOutputHandler
std::ostream	* pOstream (default: NULL)

Returns

bool success

Reimplemented from COptTask.

Definition at line 72 of file CFitTask.cpp.

References COptTask::initialize().

{
  return COptTask::initialize(of, pOutputHandler, pOstream);
}

bool CFitTask::process ( const bool &  useInitialValues )

virtual

Process the task with or without initializing to the initial state.

Parameters

const

bool & useInitialValues

Returns

bool success

Reimplemented from COptTask.

Definition at line 79 of file CFitTask.cpp.

References COutputInterface::AFTER, COutputInterface::BEFORE, CFitProblem::calculateStatistics(), CCopasiMethod::isValidProblem(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, COptMethod::optimise(), CCopasiTask::output(), COptProblem::randomizeStartValues(), COptProblem::rememberStartValues(), and CFitProblem::updateInitialState().

{
  CFitProblem * pProblem = dynamic_cast<CFitProblem *>(mpProblem);
  COptMethod * pMethod = dynamic_cast<COptMethod *>(mpMethod);

  if (!pProblem || !pMethod) return false;

  mpMethod->isValidProblem(mpProblem);

  if (useInitialValues)
    {
      pProblem->updateInitialState();
    }

  pProblem->randomizeStartValues();
  pProblem->rememberStartValues();

  output(COutputInterface::BEFORE);

  bool success = pMethod->optimise();

  pProblem->calculateStatistics();

  output(COutputInterface::AFTER);

  return success;
}

bool CFitTask::setCallBack ( CProcessReport *  pCallBack )

virtual

Set the call back of the task

Parameters

CProcessReport

* pCallBack

Returns

bool succes

Reimplemented from COptTask.

Definition at line 61 of file CFitTask.cpp.

References CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiProblem::setCallBack(), CCopasiMethod::setCallBack(), and CCopasiTask::setCallBack().

{
  bool success = CCopasiTask::setCallBack(pCallBack);

  if (!mpProblem->setCallBack(pCallBack)) success = false;

  if (!mpMethod->setCallBack(pCallBack)) success = false;

  return success;
}

bool CFitTask::setMethodType ( const int &  type )

virtual

Set the method type applied to solve the task

Parameters

const

CCopasiMethod::SubType & type

Returns

bool success

Reimplemented from COptTask.

Definition at line 107 of file CFitTask.cpp.

References CCopasiContainer::add(), createMethod(), CCopasiMethod::getSubType(), CCopasiTask::mpMethod, and pdelete.

{
  CCopasiMethod::SubType Type = (CCopasiMethod::SubType) type;

  if (mpMethod->getSubType() == Type) return true;

  pdelete(mpMethod);

  mpMethod = createMethod(Type);
  this->add(mpMethod, true);

  return true;
}

---

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

• CFitTask.h
• CFitTask.cpp