CScanTask Class Reference

#include <CScanTask.h>

Inheritance diagram for CScanTask:

Collaboration diagram for CScanTask:

Public Member Functions
void	cleanup ()
virtual CCopasiMethod *	createMethod (const int &type) const
	CScanTask (const CCopasiContainer *pParent=NULL)
	CScanTask (const CScanTask &src, const CCopasiContainer *pParent=NULL)
void	fixBuild81 ()
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 ()
virtual bool	restore ()
	~CScanTask ()
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 void	separate (const COutputInterface::Activity &activity)
virtual bool	setCallBack (CProcessReport *pCallBack)
virtual bool	setMethodType (const int &type)
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 ()

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

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_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 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 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

Definition at line 34 of file CScanTask.h.

Constructor & Destructor Documentation

CScanTask::CScanTask

(

const CCopasiContainer *

pParent = NULL

)

default constructor

CScanTask class.

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

Definition at line 47 of file CScanTask.cpp.

References CCopasiContainer::add(), createMethod(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, and CCopasiMethod::scanMethod.

                                                    :
  CCopasiTask(CCopasiTask::scan, pParent),
  mProgress(0),
  mhProgress(C_INVALID_INDEX),
  mpSubtask(NULL),
  mOutputInSubtask(false),
  mUseInitialValues(true)
{
  mpProblem = new CScanProblem(this);
  mpMethod = createMethod(CCopasiMethod::scanMethod);
  this->add(mpMethod, true);
  static_cast< CScanMethod * >(mpMethod)->setProblem(static_cast< CScanProblem * >(mpProblem));
}

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

Copy constructor

Parameters

const

CScanTask & src

Definition at line 61 of file CScanTask.cpp.

References CCopasiContainer::add(), createMethod(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, and CCopasiMethod::scanMethod.

                                                      :
  CCopasiTask(src, pParent),
  mProgress(0),
  mhProgress(C_INVALID_INDEX),
  mpSubtask(NULL),
  mOutputInSubtask(false),
  mUseInitialValues(true)
{
  mpProblem = new CScanProblem(*(CScanProblem *) src.mpProblem, this);
  mpMethod = createMethod(CCopasiMethod::scanMethod);
  this->add(mpMethod, true);
  static_cast< CScanMethod * >(mpMethod)->setProblem(static_cast< CScanProblem * >(mpProblem));
}

CScanTask::~CScanTask

(

)

Destructor

Definition at line 76 of file CScanTask.cpp.

References cleanup().

{cleanup();}

Member Function Documentation

void CScanTask::cleanup

(

)

cleanup()

Definition at line 87 of file CScanTask.cpp.

Referenced by ~CScanTask().

{}

CCopasiMethod * CScanTask::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 CCopasiTask.

Definition at line 80 of file CScanTask.cpp.

References CScanMethod::createMethod().

Referenced by CScanTask().

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

  return CScanMethod::createMethod(Type);
}

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.

Definition at line 322 of file CScanTask.cpp.

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

Referenced by CCopasiXML::fixBuild81().

{
  CScanProblem * pProblem = dynamic_cast< CScanProblem * >(mpProblem);

  if (pProblem == NULL) return;

  pProblem->fixBuild81();

  return;
}

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.

Definition at line 90 of file CScanTask.cpp.

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

{
  assert(mpProblem && mpMethod);

  mpMethod->isValidProblem(mpProblem);

  bool success = true;

  if ((of & REPORT) &&
      pOutputHandler != NULL)
    {
      if (mReport.open(getObjectDataModel(), pOstream))
        pOutputHandler->addInterface(&mReport);
      else
        CCopasiMessage(CCopasiMessage::COMMANDLINE, MCCopasiTask + 5, getObjectName().c_str());
    }

  success &= initSubtask(of, pOutputHandler, mReport.getStream());
  success &= CCopasiTask::initialize(of, pOutputHandler, mReport.getStream());

  return success;
}

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

protected

Init the subtask

Parameters

const	OutputFlag & of
COutputHandler	* pOutputHandler

Returns

success

Definition at line 235 of file CScanTask.cpp.

References CCopasiTask::crosssection, fatalError, CScanProblem::getContinueFromCurrentState(), CCopasiDataModel::getModel(), CCopasiObject::getObjectDataModel(), CCopasiTask::getProblem(), CCopasiDataModel::getTaskList(), CCopasiParameterGroup::getValue(), CCopasiTask::initialize(), CCopasiTask::lna, CCopasiTask::lyap, CCopasiTask::mca, mOutputInSubtask, CCopasiTask::mpProblem, mpSubtask, mUseInitialValues, CCopasiTask::NO_OUTPUT, CCopasiTask::optimization, CCopasiTask::OUTPUT, CCopasiTask::parameterFitting, CCopasiParameter::Value::pBOOL, CCopasiParameter::Value::pUINT, CCopasiTask::sens, CCopasiTask::setCallBack(), CCopasiProblem::setModel(), CCopasiTask::steadyState, CCopasiTask::timeCourse, CCopasiTask::tssAnalysis, and CCopasiTask::TypeName.

Referenced by initialize().

{
  if (!mpProblem) fatalError();

  CScanProblem * pProblem = dynamic_cast<CScanProblem *>(mpProblem);

  if (!pProblem) fatalError();

  //get the parameters from the problem
  CCopasiTask::Type type = *(CCopasiTask::Type*) pProblem->getValue("Subtask").pUINT;
  CCopasiDataModel* pDataModel = getObjectDataModel();
  assert(pDataModel != NULL);

  switch (type)
    {
      case CCopasiTask::steadyState:
        mpSubtask = dynamic_cast<CCopasiTask*>
                    ((*pDataModel->getTaskList())["Steady-State"]);
        break;

      case CCopasiTask::timeCourse:
        mpSubtask = dynamic_cast<CCopasiTask*>
                    ((*pDataModel->getTaskList())["Time-Course"]);
        break;

      case CCopasiTask::mca:
        mpSubtask = dynamic_cast<CCopasiTask*>
                    ((*pDataModel->getTaskList())["Metabolic Control Analysis"]);
        break;

      case CCopasiTask::lyap:
        mpSubtask = dynamic_cast<CCopasiTask*>
                    ((*pDataModel->getTaskList())["Lyapunov Exponents"]);
        break;

      case CCopasiTask::optimization:
        mpSubtask = dynamic_cast<CCopasiTask*>
                    ((*pDataModel->getTaskList())["Optimization"]);
        break;

      case CCopasiTask::parameterFitting:
        mpSubtask = dynamic_cast<CCopasiTask*>
                    ((*pDataModel->getTaskList())["Parameter Estimation"]);
        break;

      case CCopasiTask::sens:
        mpSubtask = dynamic_cast<CCopasiTask*>
                    ((*pDataModel->getTaskList())["Sensitivities"]);
        break;

      case CCopasiTask::lna:
        mpSubtask = dynamic_cast<CCopasiTask*>
                    ((*pDataModel->getTaskList())["Linear Noise Approximation"]);
        break;

      case CCopasiTask::tssAnalysis :
        mpSubtask = dynamic_cast<CCopasiTask*>
                    ((*pDataModel->getTaskList())[CCopasiTask::TypeName[tssAnalysis]]);
        break;

      case CCopasiTask::crosssection:
        mpSubtask = dynamic_cast<CCopasiTask*>
                    ((*pDataModel->getTaskList())["Cross Section"]);
        break;

      default:
        mpSubtask = NULL;
    }

  mOutputInSubtask = * pProblem->getValue("Output in subtask").pBOOL;
  mUseInitialValues = !pProblem->getContinueFromCurrentState();

  if (!mpSubtask) return false;

  mpSubtask->getProblem()->setModel(pDataModel->getModel()); //TODO
  mpSubtask->setCallBack(NULL);

  if (mOutputInSubtask)
    return mpSubtask->initialize(OUTPUT, pOutputHandler, pOstream);
  else
    return mpSubtask->initialize(NO_OUTPUT, pOutputHandler, pOstream);

  return true;
}

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.

Definition at line 115 of file CScanTask.cpp.

{}

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.

Definition at line 227 of file CScanTask.cpp.

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

{
  if ((!isLast) || mOutputInSubtask)
    separate(COutputInterface::DURING);

  return true;
}

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.

Definition at line 118 of file CScanTask.cpp.

References CProcessReport::addItem(), COutputInterface::AFTER, CModel::applyInitialValues(), COutputInterface::BEFORE, C_INT32, CCrossSectionTask::createEvent(), fatalError, CCopasiProblem::getModel(), CScanMethod::getTotalNumberOfSteps(), CScanMethod::init(), mhProgress, CCopasiTask::mpCallBack, CCopasiTask::mpMethod, CCopasiTask::mpProblem, mProgress, mpSubtask, CCopasiTask::output(), CCrossSectionTask::removeEvent(), CScanMethod::scan(), CCopasiTask::setCallBack(), CProcessReport::setName(), and CScanMethod::setProblem().

{
  if (!mpProblem) fatalError();

  if (!mpMethod) fatalError();

  CScanProblem * pProblem = dynamic_cast<CScanProblem *>(mpProblem);

  if (!pProblem) fatalError();

  CScanMethod * pMethod = dynamic_cast<CScanMethod *>(mpMethod);

  if (!pMethod) fatalError();

  bool success = true;

  CCrossSectionTask* task = dynamic_cast<CCrossSectionTask*>(mpSubtask);

  if (task != NULL)
    task->createEvent();

  if (useInitialValues)
    {
      mpProblem->getModel()->applyInitialValues();
    }

  //TODO: reports

  // initialize the method (parsing the ScanItems)
  pMethod->setProblem(pProblem);

  if (!pMethod->init()) return false;

  // init progress bar
  mProgress = 0;

  if (mpCallBack)
    {
      mpCallBack->setName("performing parameter scan...");

      unsigned C_INT32 totalSteps = (unsigned C_INT32) pMethod->getTotalNumberOfSteps();
      mhProgress = mpCallBack->addItem("Number of Steps",
                                       mProgress,
                                       &totalSteps);

      if (mpSubtask)
        mpSubtask->setCallBack(mpCallBack);
    }

  // init output handler (plotting)
  output(COutputInterface::BEFORE);

  //calling the scanner, output is done in the callback
  if (!pMethod->scan()) success = false;

  if (task != NULL)
    task->removeEvent();

  //finishing progress bar and output
  //if (mpCallBack) mpCallBack->finish();
  //if (mpOutputHandler) mpOutputHandler->finish();
  output(COutputInterface::AFTER);

  if (mpSubtask)
    mpSubtask->setCallBack(NULL);

  return success;
}

bool CScanTask::processCallback

(

)

Do the subtask and the output

Definition at line 201 of file CScanTask.cpp.

References COutputInterface::DURING, CCopasiTask::getProblem(), CCopasiTask::isUpdateModel(), mhProgress, mOutputInSubtask, CCopasiTask::mpCallBack, mProgress, mpSubtask, mUseInitialValues, CCopasiTask::output(), CCopasiTask::process(), CProcessReport::progressItem(), and COptProblem::restoreModel().

Referenced by CScanMethod::calculate().

{
  bool success = mpSubtask->process(mUseInitialValues);

  //do output
  if (success && !mOutputInSubtask)
    output(COutputInterface::DURING);

  if (mpSubtask->isUpdateModel())
    {
      COptProblem* problem = dynamic_cast<COptProblem*>(mpSubtask->getProblem());

      if (problem != NULL)
        {
          problem->restoreModel(true);
        }
    }

  //do progress bar
  ++mProgress;

  if (mpCallBack) return mpCallBack->progressItem(mhProgress);

  return true;
}

bool CScanTask::restore ( )

virtual

Perform necessary cleanup procedures

Reimplemented from CCopasiTask.

Definition at line 187 of file CScanTask.cpp.

References mpSubtask, and CCopasiTask::restore().

{
  bool success = true;

  if (mpSubtask != NULL)
    {
      success &= mpSubtask->restore();
    }

  success = CCopasiTask::restore();

  return success;
}

Member Data Documentation

size_t CScanTask::mhProgress

private

Handle to process item

Definition at line 52 of file CScanTask.h.

Referenced by process(), and processCallback().

bool CScanTask::mOutputInSubtask

private

Definition at line 59 of file CScanTask.h.

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

unsigned C_INT32 CScanTask::mProgress

private

Pointer to the output stream for reporting for progress bar

Definition at line 47 of file CScanTask.h.

Referenced by process(), and processCallback().

CCopasiTask* CScanTask::mpSubtask

private

the subtask

Definition at line 57 of file CScanTask.h.

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

bool CScanTask::mUseInitialValues

private

Definition at line 61 of file CScanTask.h.

Referenced by initSubtask(), and processCallback().

---

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

• CScanTask.h
• CScanTask.cpp