CScanTask Class Reference

#include <CScanTask.h>

Inheritance diagram for CScanTask:

Public Member Functions
void	cleanup ()
	CScanTask (const CDataContainer *pParent, const CTaskEnum::Task &type=CTaskEnum::Task::scan)
	CScanTask (const CScanTask &src, const CDataContainer *pParent)
void	fixBuild81 ()
virtual const CTaskEnum::Method *	getValidMethods () const
virtual bool	initialize (const OutputFlag &of, COutputHandler *pOutputHandler, std::ostream *pOstream)
void	load (CReadConfig &configBuffer)
bool	outputSeparatorCallback (bool isLast=false)
virtual bool	process (const bool &useInitialValues)
bool	processCallback ()
	~CScanTask ()
Public Member Functions inherited from CCopasiTask
virtual bool	applyData (const CData &data, CUndoData::CChangeSet &changes)
	CCopasiTask (const CCopasiTask &src, const CDataContainer *pParent)
	CCopasiTask (const CDataContainer *pParent, const CTaskEnum::Task &taskType, const std::string &type="Task")
void	cleanup ()
virtual void	clearCallBack ()
virtual void	createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const
const CProcessReportLevel &	getCallBack () const
const CDescription &	getDescription () const
virtual const std::string &	getKey () const
CMathContainer *	getMathContainer () const
CCopasiMethod *	getMethod ()
const CCopasiMethod *	getMethod () const
COutputHandler *	getOutputHandler () const
const OutputFlag &	getOutputMode () const
CCopasiProblem *	getProblem ()
const CCopasiProblem *	getProblem () const
CReport &	getReport ()
const CReport &	getReport () const
const CResult &	getResult () const
CCopasiParameterGroup *	getSliders ()
CTaskEnum::Task	getType () const
const bool &	isScheduled () const
const bool &	isUpdateModel () const
virtual void	output (const COutputInterface::Activity &activity)
virtual bool	restore (const bool &updateModel=true)
virtual void	separate (const COutputInterface::Activity &activity)
virtual bool	setCallBack (CProcessReportLevel callBack)
void	setIgnoreProblemData (const bool &ignoreProblemData)
void	setMathContainer (CMathContainer *pContainer)
bool	setMethodType (const CTaskEnum::Method &type)
void	setScheduled (const bool &scheduled)
void	setType (const CTaskEnum::Task &type)
virtual void	setUpdateModel (const bool &updateModel)
virtual CData	toData () const
virtual bool	updateMatrices ()
virtual	~CCopasiTask ()
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 size_t	getIndex (const CDataObject *pObject) const
virtual const CObjectInterface *	getObject (const CCommonName &cn) const override
virtual objectMap &	getObjects ()
virtual const objectMap &	getObjects () const
virtual const std::string	getUnits () const override
virtual const CDataObject *	getValueObject () const override
virtual CUndoObjectInterface *	insert (const CData &data) override
void	objectRenamed (CDataObject *pObject, const std::string &oldName)
virtual bool	remove (CDataObject *pObject)
virtual	~CDataContainer ()
Public Member Functions inherited from CDataObject
void	addIssue (const CIssue &issue)
void	addReference (const CDataContainer *pReference)
virtual void	calculateValue () override
	CDataObject (const CDataObject &src, const CDataContainer *pParent=NULL)
virtual void	destruct () override
virtual CCommonName	getCN () const override
virtual const CDataObject *	getDataObject () const override
CDataContainer *	getObjectAncestor (const std::string &type) const
CDataModel *	getObjectDataModel () const
virtual std::string	getObjectDisplayName () const override
const CObjectInterface *	getObjectFromCN (const CCommonName &cn) const
const std::string &	getObjectName () const
CDataContainer *	getObjectParent () const
const std::string &	getObjectType () const
virtual const CObjectInterface::ObjectSet &	getPrerequisites () const override
virtual const CValidity &	getValidity () const override
virtual void *	getValuePointer () const override
bool	hasFlag (const Flag &flag) const
virtual bool	isPrerequisiteForContext (const CObjectInterface *pObject, const CCore::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const override
bool	prerequisitsContains (const DataObjectSet &objects) const
virtual void	print (std::ostream *ostream) const override
void	removeIssue (const CIssue &issue)
void	removeReference (const CDataContainer *pReference)
bool	setObjectName (const std::string &name)
virtual bool	setObjectParent (const CDataContainer *pParent)
void	validityChanged (const CValidity &changedValidity) override
void	validityRemoved (const CValidity &changedValidity)
virtual	~CDataObject ()
Public Member Functions inherited from CObjectInterface
	CObjectInterface ()
	CObjectInterface (const CObjectInterface &src)
virtual	~CObjectInterface ()
Public Member Functions inherited from CUndoObjectInterface
	CUndoObjectInterface ()
	CUndoObjectInterface (const CUndoObjectInterface &src)
bool	generateUuid ()
const xg::Guid &	getUuid () const
bool	setUuid (const std::string &uuid)
bool	setUuid (const xg::Guid &uuid)
virtual void	updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject)
virtual	~CUndoObjectInterface ()

Protected Member Functions
bool	initSubtask (const OutputFlag &of, COutputHandler *pOutputHandler, std::ostream *pOstream)
Protected Member Functions inherited from CCopasiTask
bool	isTaskValid () const
virtual void	signalMathContainerChanged ()
virtual void	signalMethodChanged ()
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
	CScanTask ()

Private Attributes
size_t	mhProgress
bool	mOutputInSubtask
unsigned C_INT32	mProgress
CCopasiTask *	mpSubTask
bool	mUseInitialValues

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_DURING = STREAM , 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 }
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
Static Public Member Functions inherited from CCopasiTask
static CCopasiTask *	fromData (const CData &data, CUndoObjectInterface *pParent)
static bool	isValidMethod (const CTaskEnum::Method &method, const CTaskEnum::Method *validMethods)
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 *)
Public Attributes inherited from CCopasiTask
std::string	Error
std::string	Warning
Static Public Attributes inherited from CDataContainer
static const CObjectInterface::ContainerList	EmptyList
Protected Attributes inherited from CCopasiTask
CDescription	mDescription
OutputFlag	mDoOutput
bool	mIgnoreProblemData
CVector< C_FLOAT64 >	mInitialState
std::string	mKey
unsigned C_INT32	mOutputCounter
CMathContainer *	mpContainer
CCopasiMethod *	mpMethod
COutputHandler *	mpOutputHandler
CCopasiProblem *	mpProblem
CProcessReportLevel	mProcessReport
CCopasiParameterGroup *	mpSliders
CReport	mReport
CResult	mResult
bool	mScheduled
CTaskEnum::Task	mType
bool	mUpdateModel
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

Constructor & Destructor Documentation

CScanTask() [1/3]

CScanTask::CScanTask ( )

private

Default constructor

CScanTask() [2/3]

CScanTask::CScanTask	(	const CDataContainer *	pParent,
		const CTaskEnum::Task &	type = CTaskEnum::Task::scan
	)

Specific constructor

Parameters

const	CDataContainer * pParent
const	CTaskEnum::Task & type (default: scan)

CScanTask class.

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

References CMethodFactory::create(), CCopasiTask::getType(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, and CTaskEnum::scanMethod.

CScanTask() [3/3]

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

Copy constructor

Parameters

const

CScanTask & src

References CCopasiTask::mpMethod, and CCopasiTask::mpProblem.

~CScanTask()

CScanTask::~CScanTask

(

)

Destructor

References cleanup().

Member Function Documentation

cleanup()

void CScanTask::cleanup

(

)

cleanup()

Referenced by ~CScanTask().

fixBuild81()

void CScanTask::fixBuild81

(

)

Fix files written with Version 4.12.81 and earlier, which wrote the exp(mean) and exp(std. deviation) for normal random distributions in the scan task.

References CScanProblem::fixBuild81(), and CCopasiTask::mpProblem.

Referenced by CCopasiXML::fixBuild81().

getValidMethods()

const CTaskEnum::Method * CScanTask::getValidMethods ( ) const

virtual

Retrieve the list of valid methods

Returns

const CTaskEnum::Method * pValidMethods

Reimplemented from CCopasiTask.

References CTaskEnum::scanMethod, and CTaskEnum::UnsetMethod.

initialize()

bool CScanTask::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 CCopasiTask.

References COutputHandler::addInterface(), CCopasiMessage::COMMANDLINE, CDataObject::getObjectDataModel(), CDataObject::getObjectName(), CReport::getStream(), CCopasiTask::initialize(), initSubtask(), CCopasiTask::isTaskValid(), CCopasiMethod::isValidProblem(), MCCopasiTask, CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiTask::mReport, CReport::open(), and CCopasiTask::REPORT.

initSubtask()

bool CScanTask::initSubtask ( const OutputFlag &  of, COutputHandler *  pOutputHandler, std::ostream *  pOstream  )

protected

Init the subtask

Parameters

const	OutputFlag & of
COutputHandler	* pOutputHandler

Returns

success

References C_INT32, CTaskEnum::crosssection, fatalError, CScanProblem::getContinueFromCurrentState(), CDataObject::getObjectDataModel(), CDataModel::getTaskList(), CCopasiParameterGroup::getValue(), CCopasiTask::initialize(), CTaskEnum::lna, CTaskEnum::lyap, CTaskEnum::mca, mOutputInSubtask, CCopasiTask::mpContainer, CCopasiTask::mpProblem, mpSubTask, mUseInitialValues, CCopasiTask::NO_OUTPUT, CTaskEnum::optimization, CCopasiTask::OUTPUT_DURING, CTaskEnum::parameterFitting, CTaskEnum::sens, CCopasiTask::setCallBack(), CCopasiTask::setMathContainer(), CTaskEnum::steadyState, CTaskEnum::TaskName, CTaskEnum::timeCourse, CTaskEnum::timeSens, and CTaskEnum::tssAnalysis.

Referenced by initialize().

load()

void CScanTask::load

(

CReadConfig &

configBuffer

)

Loads parameters for this solver with data coming from a CReadConfig object. (CReadConfig object reads an input stream)

Parameters

configbuffer

reference to a CReadConfig object.

outputSeparatorCallback()

bool CScanTask::outputSeparatorCallback

(

bool

isLast = false

)

output separators if isLast==true this method has to decide if a separator should be generated dependent on mOutputInSubtask.

References COutputInterface::DURING, mOutputInSubtask, and CCopasiTask::separate().

process()

bool CScanTask::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 CCopasiTask.

References CProcessReportLevel::addItem(), COutputInterface::AFTER, CMathContainer::applyInitialValues(), COutputInterface::BEFORE, C_INT32, CCrossSectionTask::createEvent(), fatalError, CScanMethod::getTotalNumberOfSteps(), CScanMethod::init(), mhProgress, CCopasiTask::mpContainer, CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiTask::mProcessReport, mProgress, mpSubTask, CCopasiTask::output(), CCrossSectionTask::removeEvent(), CScanMethod::scan(), CCopasiTask::setCallBack(), CProcessReportLevel::setName(), and CScanMethod::setProblem().

processCallback()

bool CScanTask::processCallback

(

)

Do the subtask and the output

References COutputInterface::DURING, CCopasiTask::getProblem(), CCopasiTask::isUpdateModel(), mhProgress, mOutputInSubtask, CCopasiTask::mProcessReport, mProgress, mpSubTask, mUseInitialValues, CCopasiTask::output(), CCopasiTask::process(), CProcessReportLevel::progressItem(), and COptProblem::restore().

Referenced by CScanMethod::calculate().

Member Data Documentation

mhProgress

size_t CScanTask::mhProgress

private

Handle to process item

Referenced by process(), and processCallback().

mOutputInSubtask

bool CScanTask::mOutputInSubtask

private

Referenced by initSubtask(), outputSeparatorCallback(), and processCallback().

mProgress

unsigned C_INT32 CScanTask::mProgress

private

Pointer to the output stream for reporting for progress bar

Referenced by process(), and processCallback().

mpSubTask

CCopasiTask* CScanTask::mpSubTask

private

the subtask

Referenced by initSubtask(), process(), and processCallback().

mUseInitialValues

bool CScanTask::mUseInitialValues

private

Referenced by initSubtask(), and processCallback().

---

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

• CScanTask.h
• CScanTask.cpp