#include <CMCATask.h>

Inheritance diagram for CMCATask:

Collaboration diagram for CMCATask:

Public Member Functions
	CMCATask (const CCopasiContainer *pParent=NULL)

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

virtual CCopasiMethod *	createMethod (const int &type) const

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

void	load (CReadConfig &configBuffer)

void	printResult (std::ostream *ostream) const

virtual bool	process (const bool &useInitialValues)

virtual bool	restore ()

virtual bool	updateMatrices ()

virtual	~CMCATask ()

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	~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 ()

Private Member Functions
void	cleanup ()

Friends
std::ostream &	operator<< (std::ostream &os, const CMCATask &A)

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 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 46 of file CMCATask.h.

Constructor & Destructor Documentation

CMCATask::CMCATask ( const CCopasiContainer * pParent = NULL )

A pointer to the found elasticities A pointer to the found flux control coefficients. A pointer to the found concentration control coefficients. Default constructor

Parameters

const CCopasiContainer * pParent (default: NULL)

Definition at line 40 of file CMCATask.cpp.

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

                                                   :
   CCopasiTask(CCopasiTask::mca, pParent)
 {
   mpProblem = new CMCAProblem(this);
 
   mpMethod = createMethod(CCopasiMethod::mcaMethodReder);
   this->add(mpMethod, true);
 }

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

Copy constructor

Parameters

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

Definition at line 49 of file CMCATask.cpp.

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

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

CMCATask::~CMCATask ( )

virtual

Destructor

Definition at line 60 of file CMCATask.cpp.

61 {}

Member Function Documentation

void CMCATask::cleanup ( )

private

cleanup()

Definition at line 71 of file CMCATask.cpp.

72 {}

CCopasiMethod * CMCATask::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 64 of file CMCATask.cpp.

References CMCAMethod::createMethod().

Referenced by CMCATask().

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

bool CMCATask::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 102 of file CMCATask.cpp.

References CModel::compileIfNecessary(), CCopasiProblem::getModel(), CReport::getStream(), CMCAProblem::getSubTask(), CSteadyStateTask::initialize(), CCopasiTask::initialize(), CCopasiMethod::isValidProblem(), CCopasiTask::mpCallBack, CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiTask::mReport, CCopasiTask::NO_OUTPUT, and updateMatrices().

 {
   assert(mpProblem && mpMethod);
 
   CMCAProblem* pProblem =
     dynamic_cast<CMCAProblem *>(mpProblem);
   assert(pProblem);
 
   if (!mpMethod->isValidProblem(mpProblem)) return false;
 
   //we need to resize an initialize the result matrices before initializing the output
   if (!updateMatrices()) return false;
 
   bool success = true;
 
   //initialize reporting
   if (!CCopasiTask::initialize(of, pOutputHandler, pOstream)) success = false;
 
   if (!pProblem->getModel()->compileIfNecessary(mpCallBack)) success = false;
 
   CSteadyStateTask *pSubTask = pProblem->getSubTask();
 
   if (pSubTask)
     success = pSubTask->initialize(CCopasiTask::NO_OUTPUT, NULL, mReport.getStream());
 
   //success = pSubTask->initialize(of, mReport.getStream());
 
   return success;
 }

void CMCATask::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 74 of file CMCATask.cpp.

References CReadConfig::getVariable(), CReadConfig::LOOP, CCopasiTask::mpMethod, CCopasiTask::mpProblem, and CCopasiTask::mScheduled.

 {
   configBuffer.getVariable("MCA", "bool", &mScheduled,
                            CReadConfig::LOOP);
 
   ((CMCAProblem *) mpProblem)->load(configBuffer);
 
   ((CMCAMethod *) mpMethod)->load(configBuffer);
 }

void CMCATask::printResult ( std::ostream * ostream ) const

This functionality is expected from the problem but has to be implemented here for the moment. This is called from the corresponding method of the problem

Definition at line 201 of file CMCATask.cpp.

References CSteadyStateMethod::found, CSteadyStateMethod::foundEquilibrium, CSteadyStateMethod::foundNegative, CCopasiProblem::getModel(), CMCAMethod::getScaledConcentrationCCAnn(), CMCAMethod::getScaledElasticitiesAnn(), CMCAMethod::getScaledFluxCCAnn(), CMCAMethod::getSteadyStateStatus(), CMCAProblem::getSubTask(), CMCAMethod::getUnscaledConcentrationCCAnn(), CMCAMethod::getUnscaledElasticitiesAnn(), CMCAMethod::getUnscaledFluxCCAnn(), CMCAProblem::isSteadyStateRequested(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, CSteadyStateMethod::notFound, and CMCAMethod::setModel().

Referenced by CMCAProblem::printResult().

 {
   assert(mpProblem && mpMethod);
 
   CMCAProblem* pProblem =
     dynamic_cast<CMCAProblem *>(mpProblem);
   assert(pProblem);
 
   CMCAMethod* pMethod = dynamic_cast<CMCAMethod *>(mpMethod);
   assert(pMethod);
   pMethod->setModel(mpProblem->getModel());
 
   std::ostream & os = *ostream;
 
   bool showCCs = false; //show CCs?
   bool showSS = false; //show Steady State result?
 
   if (pProblem->isSteadyStateRequested())
     {
       if (pMethod->getSteadyStateStatus() == CSteadyStateMethod::found)
         {
           os << "A steady state was found. All coefficients are shown." << std::endl;
           showCCs = true;
           showSS = true;
         }
 
       if (pMethod->getSteadyStateStatus() == CSteadyStateMethod::foundEquilibrium)
         {
           os << "Found equilibrium steady state. Only elasticities available." << std::endl;
           showSS = true;
         }
 
       if (pMethod->getSteadyStateStatus() == CSteadyStateMethod::foundNegative)
         {
           os << "Invalid steady state found (negative concentrations)." << std::endl;
           showSS = true;
         }
 
       if (pMethod->getSteadyStateStatus() == CSteadyStateMethod::notFound)
         {
           os << "No steady state found. Only elasticities available." << std::endl;
         }
     }
   else
     {
       os << "Since no steady state calculation was requested only elasticities are shown." << std::endl;
     }
 
   os << std::endl;
   os << *pMethod->getUnscaledElasticitiesAnn() << std::endl;
   os << *pMethod->getScaledElasticitiesAnn() << std::endl;
 
   if (showCCs)
     {
       os << *pMethod->getUnscaledConcentrationCCAnn() << std::endl;
       os << *pMethod->getScaledConcentrationCCAnn() << std::endl;
 
       os << *pMethod->getUnscaledFluxCCAnn() << std::endl;
       os << *pMethod->getScaledFluxCCAnn() << std::endl;
     }
 
   if (showSS)
     {
       if (!pProblem->getSubTask())
         {
           os << "Problem with steady state calculation. Please report as bug!" << std::endl;
           return;
         }
 
       os << "Results of the steady state subtask (the state for which the MCA was performed):" << std::endl;
       os << *pProblem->getSubTask();
     }
 }

bool CMCATask::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 134 of file CMCATask.cpp.

References COutputInterface::AFTER, CModel::applyInitialValues(), COutputInterface::BEFORE, COutputInterface::DURING, CCopasiProblem::getModel(), CCopasiTask::mpCallBack, CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiTask::output(), CMCAMethod::process(), CSteadyStateTask::process(), CCopasiTask::setCallBack(), and CMCAMethod::setSteadyStateTask().

 {
   bool success = true;
 
   assert(mpMethod);
 
   CMCAMethod* pMethod = dynamic_cast<CMCAMethod *>(mpMethod);
   assert(pMethod);
   //  pMethod->setModel(mpProblem->getModel());
 
   CSteadyStateTask *pSubTask =
     dynamic_cast<CMCAProblem *>(mpProblem)->getSubTask();
 
   if (pSubTask)
     {
       pSubTask->setCallBack(mpCallBack);
       success &= pSubTask->process(useInitialValues);
 
       if (!success && useInitialValues)
         {
           mpProblem->getModel()->applyInitialValues();
         }
 
       pMethod->setSteadyStateTask(pSubTask);
     }
   else
     {
       pMethod->setSteadyStateTask(NULL);
 
       if (useInitialValues)
         {
           mpProblem->getModel()->applyInitialValues();
         }
     }
 
   CCopasiTask::output(COutputInterface::BEFORE);
 
   pMethod->process();
 
   CCopasiTask::output(COutputInterface::DURING);
   CCopasiTask::output(COutputInterface::AFTER);
 
   return success;
 }

bool CMCATask::restore ( )

virtual

Perform neccessary cleaup procedures

Reimplemented from CCopasiTask.

Definition at line 179 of file CMCATask.cpp.

References CCopasiTask::mpProblem, CSteadyStateTask::restore(), and CCopasiTask::restore().

 {
   bool success = CCopasiTask::restore();
 
   CSteadyStateTask *pSubTask =
     dynamic_cast<CMCAProblem *>(mpProblem)->getSubTask();
 
   if (pSubTask)
     success &= pSubTask->restore();
 
   return success;
 }

bool CMCATask::updateMatrices ( )

virtual

Resizes result matrices and updates array annotations for a specific task. 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 from CCopasiTask.

Definition at line 84 of file CMCATask.cpp.

References CCopasiProblem::getModel(), CCopasiMethod::isValidProblem(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, CMCAMethod::resizeAllMatrices(), and CMCAMethod::setModel().

Referenced by initialize().

 {
   assert(mpProblem != NULL && mpMethod != NULL);
 
   assert(dynamic_cast<CMCAProblem *>(mpProblem) != NULL);
 
   if (!mpMethod->isValidProblem(mpProblem)) return false;
 
   CMCAMethod * pMethod = dynamic_cast<CMCAMethod*>(mpMethod);
 
   if (!pMethod) return false;
 
   pMethod->setModel(mpProblem->getModel());
   pMethod->resizeAllMatrices();
 
   return true;
 }

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	os,
		const CMCATask &	A
	)

friend

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

Public Member Functions

Private Member Functions

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation