#include <COscillationTask.h>

Inheritance diagram for COscillationTask:

Collaboration diagram for COscillationTask:

Public Member Functions
void	cleanup ()

	COscillationTask (const CCopasiTask::Type &type, const CCopasiContainer *pParent)

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

virtual CCopasiMethod *	createMethod (const int &type) const

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)

	~COscillationTask ()

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 ()

Static Public Attributes
static unsigned C_INT32	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

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

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

Definition at line 34 of file COscillationTask.h.

Constructor & Destructor Documentation

COscillationTask::COscillationTask	(	const CCopasiTask::Type &	type,
		const CCopasiContainer *	pParent
	)

default constructor

Parameters

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

Definition at line 36 of file COscillationTask.cpp.

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

                                                                     :
     CCopasiTask(type, pParent)
 {
   mpProblem = new COscillationProblem(type, this);
   mpMethod = COscillationMethod::createMethod();
   this->add(mpMethod, true);
   ((COscillationMethod *) mpMethod)->setProblem((COscillationProblem *) mpProblem);
 }

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

Copy constructor

Parameters

const COscillationTask & src

Definition at line 46 of file COscillationTask.cpp.

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

                                                                     :
     CCopasiTask(src, pParent)
 {
   mpProblem = new COscillationProblem(*(COscillationProblem *) src.mpProblem, this);
   mpMethod = COscillationMethod::createMethod(src.mpMethod->getSubType());
   this->add(mpMethod, true);
   ((COscillationMethod *) mpMethod)->setProblem((COscillationProblem *) mpProblem);
 }

COscillationTask::~COscillationTask ( )

Destructor

Definition at line 56 of file COscillationTask.cpp.

References cleanup().

57 {cleanup();}

COscillationTask::cleanup

void cleanup()

Definition: COscillationTask.cpp:59

Member Function Documentation

void COscillationTask::cleanup ( )

cleanup()

Definition at line 59 of file COscillationTask.cpp.

Referenced by ~COscillationTask().

59 {}

CCopasiMethod * COscillationTask::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 130 of file COscillationTask.cpp.

References COscillationMethod::createMethod().

Referenced by setMethodType().

 {
   CCopasiMethod::SubType Type = (CCopasiMethod::SubType) type;
 
   return COscillationMethod::createMethod(Type);
 }

bool COscillationTask::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 72 of file COscillationTask.cpp.

References COscillationProblem::initialize(), CCopasiTask::initialize(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, and COscillationMethod::setProblem().

 {
   COscillationProblem * pProblem = dynamic_cast<COscillationProblem *>(mpProblem);
   COscillationMethod * pMethod = dynamic_cast<COscillationMethod *>(mpMethod);
 
   if (!pProblem || !pMethod) return false;
 
   //initialize reporting
   bool success = true;
 
   if (!CCopasiTask::initialize(of, pOutputHandler, pOstream)) success = false;
 
   //if (!mReport.open(pOstream)) success = false;
   //if (!mReport.compile()) success = false;
 
   if (!pProblem->initialize()) success = false;
 
   pMethod->setProblem(pProblem);
   //  if (!pMethod->initialize()) return false;
 
   return success;
 }

bool COscillationTask::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 97 of file COscillationTask.cpp.

References COutputInterface::AFTER, COutputInterface::BEFORE, CCopasiMethod::isValidProblem(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiTask::output(), and COscillationMethod::run().

 {
   COscillationProblem * pProblem = dynamic_cast<COscillationProblem *>(mpProblem);
   COscillationMethod * pMethod = dynamic_cast<COscillationMethod *>(mpMethod);
 
   if (!pProblem || !pMethod) return false;
 
   mpMethod->isValidProblem(mpProblem);
 
   output(COutputInterface::BEFORE);
 
   bool success = pMethod->run();
 
   output(COutputInterface::AFTER);
 
   return success;
 }

bool COscillationTask::setCallBack ( CProcessReport * pCallBack )

virtual

Set the call back of the task

Parameters

CProcessReport * pCallBack

Returns: bool succes

Reimplemented from CCopasiTask.

Definition at line 61 of file COscillationTask.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 COscillationTask::setMethodType ( const int & type )

virtual

Set the method type applied to solve the task

Parameters

const CCopasiMethod::SubType & type

Returns: bool success

Reimplemented from CCopasiTask.

Definition at line 115 of file COscillationTask.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;
 }

Member Data Documentation

const unsigned int COscillationTask::ValidMethods

static

Initial value:

=
{
  CCopasiMethod::oscillationIntegrate,
  CCopasiMethod::unset
}

The methods which can be selected for preforming this task.

Definition at line 42 of file COscillationTask.h.

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

Public Member Functions

Static Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation