#include <CCopasiTask.h>

Inheritance diagram for CCopasiTask:

Classes
class	CDescription
class	CResult
Public Types
enum	Type { steadyState = 0, timeCourse, scan, fluxMode, optimization, parameterFitting, mca, lyap, tssAnalysis, sens, moieties, crosssection, unset }
enum	eOutputFlagBase { INITIALIZE = 0x01, STREAM = 0x02, FINISH = 0x04, REPORT = 0x10, PLOT = 0x20, TIME_SERIES = 0x40 }
enum	OutputFlag { NO_OUTPUT = 0, OUTPUT = REPORT \| PLOT \| TIME_SERIES \| STREAM, OUTPUT_COMPLETE = REPORT \| PLOT \| TIME_SERIES \| INITIALIZE \| STREAM \| FINISH, ONLY_TIME_SERIES = TIME_SERIES \| INITIALIZE \| STREAM \| FINISH }
Public Member Functions
	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)
virtual	~CCopasiTask ()
Type	getType () const
void	setType (const Type &type)
virtual const std::string &	getKey () const
void	setScheduled (const bool &scheduled)
const bool &	isScheduled () const
void	setUpdateModel (const bool &updateModel)
const bool &	isUpdateModel () const
virtual bool	setCallBack (CProcessReport *pCallBack)
CProcessReport *	getCallBack () const
virtual bool	updateMatrices ()
virtual bool	initialize (const OutputFlag &of, COutputHandler pOutputHandler, std::ostream pOstream)
virtual bool	process (const bool &useInitialValues)
virtual bool	restore ()
CCopasiProblem *	getProblem ()
const CCopasiProblem *	getProblem () const
virtual bool	setMethodType (const int &type)
CCopasiMethod *	getMethod ()
const CCopasiMethod *	getMethod () const
CReport &	getReport ()
const CDescription &	getDescription () const
const CResult &	getResult () const
void	cleanup ()
CCopasiParameterGroup *	getSliders ()
virtual void	output (const COutputInterface::Activity &activity)
virtual void	separate (const COutputInterface::Activity &activity)
const OutputFlag &	getOutputMode () const
COutputHandler *	getOutputHandler () const
Static Public Member Functions
static bool	isValidMethod (const unsigned C_INT32 &method, const unsigned C_INT32 *validMethods)
Static Public Attributes
static const std::string	TypeName []
static const char *	XMLType []
static const unsigned C_INT32	ValidMethods []
Protected Attributes
Type	mType
std::string	mKey
CDescription	mDescription
CResult	mResult
bool	mScheduled
bool	mUpdateModel
CState *	mpInitialState
CCopasiProblem *	mpProblem
CCopasiMethod *	mpMethod
CReport	mReport
CProcessReport *	mpCallBack
CCopasiParameterGroup *	mpSliders
OutputFlag	mDoOutput
COutputHandler *	mpOutputHandler
unsigned C_INT32	mOutputCounter

Member Enumeration Documentation

enum CCopasiTask::eOutputFlagBase

Enumerator:

INITIALIZE
STREAM
FINISH
REPORT
PLOT
TIME_SERIES

enum CCopasiTask::OutputFlag

Enumerator:

NO_OUTPUT
OUTPUT
OUTPUT_COMPLETE
ONLY_TIME_SERIES

enum CCopasiTask::Type

Enumeration of the types of tasks known to COPASI.

Enumerator:

steadyState
timeCourse
scan
fluxMode
optimization
parameterFitting
mca
lyap
tssAnalysis
sens
moieties
crosssection
unset

Constructor & Destructor Documentation

CCopasiTask::CCopasiTask	(	const std::string &	name = `"NoName"`,
		const CCopasiContainer *	pParent = `NULL`,
		const std::string &	type = `"Task"`
	)

Default constructor

CCopasiTask::CCopasiTask	(	const Type &	taskType,
		const CCopasiContainer *	pParent = `NULL`,
		const std::string &	type = `"Task"`
	)

Specific constructor

Parameters:

const	Type & taskType
const	CCopasiContainer * pParent (default: NULL)
const	std::string & type (default: "Task")

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

Copy constructor

Parameters:

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

CCopasiTask::~CCopasiTask ( ) [virtual]

Destructor

Member Function Documentation

void CCopasiTask::cleanup ( )

Cleanup function

Reimplemented in CScanTask, COptTask, and CFitTask.

CProcessReport * CCopasiTask::getCallBack ( ) const

const CCopasiTask::CDescription & CCopasiTask::getDescription ( ) const

Retrieve the description

const std::string & CCopasiTask::getKey ( ) const [virtual]

Retrieve the key for the task.

Returns:: std::string key

Reimplemented from CCopasiObject.

CCopasiMethod * CCopasiTask::getMethod ( )

Retrieve the method

const CCopasiMethod * CCopasiTask::getMethod ( ) const

Retrieve the method

COutputHandler * CCopasiTask::getOutputHandler ( ) const

const OutputFlag& CCopasiTask::getOutputMode ( ) const [inline]

CCopasiProblem * CCopasiTask::getProblem ( )

Retrieve the problem

const CCopasiProblem * CCopasiTask::getProblem ( ) const

Retrieve the problem

CReport & CCopasiTask::getReport ( )

Retrieve the report

const CCopasiTask::CResult & CCopasiTask::getResult ( ) const

Retrieve the result

Reimplemented in CSteadyStateTask.

CCopasiParameterGroup * CCopasiTask::getSliders ( )

Retrieve a pointer to the group of sliders.

Returns:: CCopasiParameterGroup * pSliders

CCopasiTask::Type CCopasiTask::getType ( void ) const

Retrieve the type of the task

Returns:: CCopasiTask::Type type

bool CCopasiTask::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 in CSteadyStateTask, CTrajectoryTask, CScanTask, CLyapTask, CTSSATask, CMCATask, CEFMTask, COptTask, CFitTask, CSensTask, CMoietiesTask, and CCrossSectionTask.

const bool & CCopasiTask::isScheduled ( ) const

Check whether the task is scheduled

Returns:: const bool & scheduled

const bool & CCopasiTask::isUpdateModel ( ) const

Check whether the task must update the model

Returns:: const bool & updateModel

bool CCopasiTask::isValidMethod	(	const unsigned C_INT32 &	method,
		const unsigned C_INT32 *	validMethods
	)		`[static]`

Check whether the given method is in the list of valid methods This list must end with CCopasiMethod::unset

Parameters:

const	unsigned C_INT32 & method
const	unsigned C_INT32 * validMethods

Returns:: bool isValid

Reimplemented in CEFMTask.

void CCopasiTask::output ( const COutputInterface::Activity & activity ) [virtual]

Perform an output event for the current activity

Parameters:

const Activity & activity

bool CCopasiTask::process ( const bool & useInitialValues ) [virtual]

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

Parameters:

const bool & useInitialValues

Returns:: bool success

Reimplemented in CSteadyStateTask, CTrajectoryTask, CScanTask, CLyapTask, CTSSATask, CMCATask, CEFMTask, COptTask, CFitTask, CSensTask, CMoietiesTask, and CCrossSectionTask.

bool CCopasiTask::restore ( ) [virtual]

Perform necessary cleanup procedures

Reimplemented in CSteadyStateTask, CTrajectoryTask, CTSSATask, CLyapTask, CMCATask, and CFitTask.

void CCopasiTask::separate ( const COutputInterface::Activity & activity ) [virtual]

Introduce an additional separator into the output

Parameters:

const Activity & activity

bool CCopasiTask::setCallBack ( CProcessReport * pCallBack ) [virtual]

Set the call back of the task

Parameters:

CProcessReport * pCallBack

Returns:: bool success

Reimplemented in CEFMTask, COptTask, CFitTask, and CMoietiesTask.

bool CCopasiTask::setMethodType ( const int & type ) [virtual]

Set the method type applied to solve the task

Parameters:

const CCopasiMethod::SubType & type

Returns:: bool success

Reimplemented in CLyapTask, CTrajectoryTask, CTSSATask, CEFMTask, COptTask, CFitTask, and CMoietiesTask.

void CCopasiTask::setScheduled ( const bool & scheduled )

Set whether the task is scheduled

Parameters:

const bool & scheduled

void CCopasiTask::setType ( const Type & type )

Set the type of the task

Parameters:

CCopasiTask::Type & type

void CCopasiTask::setUpdateModel ( const bool & updateModel )

Set whether the task must update the model

Parameters:

const bool & updateModel

virtual bool CCopasiTask::updateMatrices ( ) [inline, virtual]

Resizes result matrices and updates array annotations for a specific task. For now this will be hard coded in the respective derived classes. We may introduce a more generic mechanism for this in the future. This is used when we need to know about the data structures of a task result without actually performing the task, e.g. when selecting objects for output. For now we assume that this functionality is also performed when initialize() is called.

Reimplemented in CSteadyStateTask, CMCATask, and CSensTask.

Member Data Documentation

CDescription CCopasiTask::mDescription [protected]

The description of the task.

OutputFlag CCopasiTask::mDoOutput [protected]

std::string CCopasiTask::mKey [protected]

The key of the task

unsigned C_INT32 CCopasiTask::mOutputCounter [protected]

CProcessReport* CCopasiTask::mpCallBack [protected]

progress bar handler

CState* CCopasiTask::mpInitialState [protected]

The state of the model before execution of the task. If mUpdateModel is false this state is restored.

CCopasiMethod* CCopasiTask::mpMethod [protected]

The method used to solve the problem.

COutputHandler* CCopasiTask::mpOutputHandler [protected]

CCopasiProblem* CCopasiTask::mpProblem [protected]

The problem of the task

CCopasiParameterGroup* CCopasiTask::mpSliders [protected]

Pointer to group of sliders associated with the task.

CReport CCopasiTask::mReport [protected]

The report that belongs to this specific task

CResult CCopasiTask::mResult [protected]

The result of the task.

bool CCopasiTask::mScheduled [protected]

Tells whether the task is scheduled for execution

Type CCopasiTask::mType [protected]

The type of the task

bool CCopasiTask::mUpdateModel [protected]

Tells whether the task shall update the model with the result. The restore method must act accordingly.

const std::string CCopasiTask::TypeName [static]

Initial value:

{
  "Steady-State",
  "Time-Course",
  "Scan",
  "Elementary Flux Modes",
  "Optimization",
  "Parameter Estimation",
  "Metabolic Control Analysis",
  "Lyapunov Exponents",
  "Time Scale Separation Analysis",


 
  "Sensitivities",
  "Moieties",
  "Cross Section",
  ""
}

String literals for the GUI to display type names of tasks known to COPASI.

CCopasiTask class. This class is used to describe a task in COPASI. This class is intended to be used as the parent class for all tasks within COPASI.

Created for COPASI by Stefan Hoops 2003

const unsigned C_INT32 CCopasiTask::ValidMethods [static]

Initial value:

{
  CCopasiMethod::unset
}

The methods which can be selected for performing this task.

Reimplemented in CTrajectoryTask, COptTask, CTSSATask, CEFMTask, and CMoietiesTask.

const char * CCopasiTask::XMLType [static]

Initial value:

{
  "steadyState",
  "timeCourse",
  "scan",
  "fluxMode",
  "optimization",
  "parameterFitting",
  "metabolicControlAnalysis",
  "lyapunovExponents",
  "timeScaleSeparationAnalysis",


 
  "sensitivities",
  "moieties",
  "crosssection",
  NULL
}

XML type names of tasks known to COPASI.

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

copasi/utilities/CCopasiTask.h
copasi/randomGenerator/CRandom.cpp
copasi/utilities/CCopasiTask.cpp

Classes

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Attributes

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation