#include <CEFMTask.h>

Inheritance diagram for CEFMTask:

Collaboration diagram for CEFMTask:

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

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

virtual CCopasiMethod *	createMethod (const int &type) const

std::string	getFluxModeDescription (const CFluxMode &fluxMode) const

const std::vector< CFluxMode > &	getFluxModes () const

std::string	getInternalSpecies (const CFluxMode &fluxMode) const

std::string	getNetReaction (const CFluxMode &fluxMode) const

std::string	getReactionEquation (const std::map< size_t, C_FLOAT64 >::const_iterator &itReaction) const

std::pair< C_FLOAT64, C_FLOAT64 >	getSpeciesChanges (const CFluxMode &fluxMode, const CMetab &metab) 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)

virtual	~CEFMTask ()

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 Member Functions
static bool	isValidMethod (const unsigned C_INT32 &method, const unsigned C_INT32 *validMethods)

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)

Static Public Attributes
static const unsigned int	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

Private Member Functions
std::map< const CMetab *, C_FLOAT64 >	getNetReactionData (const CFluxMode &fluxMode) const

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

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 41 of file CEFMTask.h.

Constructor & Destructor Documentation

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

default constructor

Parameters

const CCopasiContainer * pParent (default: NULL)

Definition at line 55 of file CEFMTask.cpp.

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

                                                   :
   CCopasiTask(CCopasiTask::fluxMode, pParent)
 {
   mpProblem = new CEFMProblem(this);
   mpMethod = CEFMMethod::createMethod();
 
   this->add(mpMethod, true);
 }

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

Copy constructor

Parameters

const COptTask & src

Definition at line 64 of file CEFMTask.cpp.

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

                                                     :
   CCopasiTask(src, pParent)
 {
   mpProblem = new CCopasiProblem(*static_cast< CEFMProblem * >(src.mpProblem), this);
   mpMethod = CEFMMethod::createMethod(src.mpMethod->getSubType());
 
   this->add(mpMethod, true);
 }

CEFMTask::~CEFMTask ( )

virtual

Destructor

Definition at line 74 of file CEFMTask.cpp.

75 {}

Member Function Documentation

CCopasiMethod * CEFMTask::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 125 of file CEFMTask.cpp.

References CEFMMethod::createMethod().

Referenced by setMethodType().

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

std::string CEFMTask::getFluxModeDescription ( const CFluxMode & fluxMode ) const

Retrieve the description of the flux mode

Parameters

const CFluxMode & fluxMode

Returns: std::string fluxModeDescription

Definition at line 132 of file CEFMTask.cpp.

References CFluxMode::begin(), C_INT32, CFluxMode::end(), getReactionIndex(), CCopasiMethod::getSubType(), CSSAMethod::isReactionReversed(), CCopasiTask::mpMethod, and CCopasiTask::mpProblem.

Referenced by CQNewMainWindow::checkForElementaryModesSlot(), CQFluxModeDM::data(), and CEFMProblem::printResult().

 {
   std::stringstream tmp;
   tmp.flags(std::ios::fixed);
   tmp.precision(0);
 
   const std::vector< const CReaction * > & ReorderedReactions =
     static_cast<CEFMProblem *>(mpProblem)->getReorderedReactions();
 
   unsigned C_INT32 j;
   CFluxMode::const_iterator itMode = fluxMode.begin();
   CFluxMode::const_iterator endMode = fluxMode.end();
 
 #ifdef COPASI_SSA
 
   if (mpMethod->getSubType() == CCopasiMethod::stoichiometricStabilityAnalysis)
     {
       CSSAMethod * method = dynamic_cast<CSSAMethod *>(mpMethod);
 
       for (j = 0; j < jmax; j++)
         {
           if (j) tmp << "\n";
 
           std::string addstrng = "";
 
           if (ReorderedReactions[FluxModes[index].getReactionIndex(j)]->isReversible())
             {
               addstrng = " (Forward)";
 
               if (method->isReactionReversed(FluxModes[index].getReactionIndex(j)))
                 addstrng = " (Backward)";
             }
 
           tmp << FluxModes[index].getMultiplier(j) << " * "
               << ReorderedReactions[FluxModes[index].getReactionIndex(j)]->getObjectName()
               << addstrng;
         }
     }
   else
 #endif
     for (j = 0; itMode != endMode; ++itMode, j++)
       {
         if (j) tmp << "\n";
 
         tmp << itMode->second << " * "
             << ReorderedReactions[itMode->first]->getObjectName();
       }
 
   return tmp.str();
 }

const std::vector< CFluxMode > & CEFMTask::getFluxModes ( ) const

Retrieve the Flux Modes

Returns: const std::vector< CFluxMode > &

Definition at line 183 of file CEFMTask.cpp.

References CCopasiTask::mpProblem.

Referenced by CQEFMResultWidget::loadResult(), CEFMProblem::printResult(), CQEFMReactionDM::setTask(), CQEFMNetReactionDM::setTask(), CQFluxModeDM::setTask(), and CQEFMSpeciesDM::setTask().

 {
   return static_cast<const CEFMProblem *>(mpProblem)->getFluxModes();
 }

std::string CEFMTask::getInternalSpecies ( const CFluxMode & fluxMode ) const

Retrieve the internal species for the given flux mode.

Parameters

const CFluxMode & fluxMode

Returns: std::string species

Definition at line 334 of file CEFMTask.cpp.

References CMetabNameInterface::getDisplayName(), CCopasiProblem::getModel(), getNetReactionData(), and CCopasiTask::getProblem().

Referenced by CQEFMNetReactionDM::data(), and CEFMProblem::printResult().

 {
   const CModel* pModel = getProblem()->getModel();
 
   if (pModel == NULL)
     return "";
 
   std::map< const CMetab *, C_FLOAT64 > Data = getNetReactionData(fluxMode);
 
   std::stringstream Modifiers;
   Modifiers.flags(std::ios::fixed);
   Modifiers.precision(0);
   std::string ModifiersSeparator = "";
 
   std::map< const CMetab *, C_FLOAT64 >::const_iterator it = Data.begin();
   std::map< const CMetab *, C_FLOAT64 >::const_iterator end = Data.end();
 
   for (; it != end; ++it)
     {
       if (fabs(it->second) < 100.0 * std::numeric_limits< C_FLOAT64 >::epsilon())
         {
           Modifiers << ModifiersSeparator;
           Modifiers << CMetabNameInterface::getDisplayName(pModel, *it->first, true);
           ModifiersSeparator = ", ";
         }
     }
 
   return Modifiers.str();
 }

std::string CEFMTask::getNetReaction ( const CFluxMode & fluxMode ) const

Retrieve the net reaction for the given flux mode.

Parameters

const CFluxMode & fluxMode

Returns: std::string netReaction

Definition at line 274 of file CEFMTask.cpp.

References CMetabNameInterface::getDisplayName(), CCopasiProblem::getModel(), getNetReactionData(), CCopasiTask::getProblem(), and CFluxMode::isReversible().

Referenced by CQEFMNetReactionDM::data(), and CEFMProblem::printResult().

 {
   const CModel* pModel = getProblem()->getModel();
 
   if (pModel == NULL)
     return "";
 
   std::map< const CMetab *, C_FLOAT64 > Data = getNetReactionData(fluxMode);
 
   std::stringstream Substrates;
   Substrates.flags(std::ios::fixed);
   Substrates.precision(0);
   std::string SubstratesSeparator = "";
 
   std::stringstream Products;
   Products.flags(std::ios::fixed);
   Products.precision(0);
   std::string ProductsSeparator = "";
 
   std::map< const CMetab *, C_FLOAT64 >::const_iterator it = Data.begin();
   std::map< const CMetab *, C_FLOAT64 >::const_iterator end = Data.end();
 
   for (; it != end; ++it)
     {
       if (it->second > 100.0 * std::numeric_limits< C_FLOAT64 >::epsilon())
         {
           Products << ProductsSeparator;
 
           if (it->second > 1.0 + 100.0 * std::numeric_limits< C_FLOAT64 >::epsilon())
             {
               Products << it->second << " * ";
             }
 
           Products << CMetabNameInterface::getDisplayName(pModel, *it->first, true);
           ProductsSeparator = " + ";
         }
       else if (it->second < -100.0 * std::numeric_limits< C_FLOAT64 >::epsilon())
         {
           Substrates << SubstratesSeparator;
 
           if (it->second < -1.0 - 100.0 * std::numeric_limits< C_FLOAT64 >::epsilon())
             {
               Substrates << -it->second << " * ";
             }
 
           Substrates << CMetabNameInterface::getDisplayName(pModel, *it->first, true);
           SubstratesSeparator = " + ";
         }
     }
 
   if (fluxMode.isReversible())
     {
       return Substrates.str() + " = " + Products.str();
     }
   else
     {
       return Substrates.str() + " -> " + Products.str();
     }
 }

std::map< const CMetab *, C_FLOAT64 > CEFMTask::getNetReactionData ( const CFluxMode & fluxMode ) const

private

Retrieve the net reaction data for the given flux mode.

Parameters

const CFluxMode & fluxMode

Returns: std::map< const CMetab *, C_FLOAT64 >g netReactionData

Definition at line 364 of file CEFMTask.cpp.

References CFluxMode::begin(), CCopasiVector< T >::begin(), CFluxMode::end(), CCopasiVector< T >::end(), CReaction::getChemEq(), CChemEq::getProducts(), getSpeciesChanges(), CChemEq::getSubstrates(), and CCopasiTask::mpProblem.

Referenced by getInternalSpecies(), and getNetReaction().

 {
   std::map< const CMetab *, C_FLOAT64 > NetReaction;
   std::pair< C_FLOAT64, C_FLOAT64 > Changes;
 
   CFluxMode::const_iterator itReaction = fluxMode.begin();
   CFluxMode::const_iterator endReaction = fluxMode.end();
 
   const std::vector< const CReaction * > & ReorderedReactions =
     static_cast<CEFMProblem *>(mpProblem)->getReorderedReactions();
 
   const CMetab * pSpecies;
 
   for (; itReaction != endReaction; ++itReaction)
     {
       const CReaction * pReaction = ReorderedReactions[itReaction->first];
 
       CCopasiVector < CChemEqElement >::const_iterator it = pReaction->getChemEq().getSubstrates().begin();
       CCopasiVector < CChemEqElement >::const_iterator end = pReaction->getChemEq().getSubstrates().end();
 
       for (; it != end; ++it)
         {
           pSpecies = (*it)->getMetabolite();
 
           if (NetReaction.count(pSpecies) == 0)
             {
               Changes = getSpeciesChanges(fluxMode, *pSpecies);
               NetReaction[pSpecies] = Changes.second - Changes.first;
             }
         }
 
       it = pReaction->getChemEq().getProducts().begin();
       end = pReaction->getChemEq().getProducts().end();
 
       for (; it != end; ++it)
         {
           pSpecies = (*it)->getMetabolite();
 
           if (NetReaction.count(pSpecies) == 0)
             {
               Changes = getSpeciesChanges(fluxMode, *pSpecies);
               NetReaction[pSpecies] = Changes.second - Changes.first;
             }
         }
     }
 
   return NetReaction;
 }

std::string CEFMTask::getReactionEquation ( const std::map< size_t, C_FLOAT64 >::const_iterator & itReaction ) const

Retrieve the reaction equation of the part of the flux mode pointed at by itReaction

Parameters

const std::map< size_t, C_FLOAT64 >::const_iterator & itReaction

Returns: std::string reactionEquation

Definition at line 188 of file CEFMTask.cpp.

References CChemEqInterface::getChemEqString(), CCopasiProblem::getModel(), CEFMProblem::getReorderedReactions(), CCopasiMethod::getSubType(), CSSAMethod::isReactionReversed(), CReaction::isReversible(), CCopasiTask::mpMethod, and CCopasiTask::mpProblem.

Referenced by CQFluxModeDM::data(), and CEFMProblem::printResult().

 {
   CEFMProblem * pProblem = static_cast<CEFMProblem *>(mpProblem);
 
   const CReaction * pReaction =
     pProblem->getReorderedReactions()[itReaction->first];
 
 #ifdef COPASI_SSA
 
   if (mpMethod->getSubType() == CCopasiMethod::stoichiometricStabilityAnalysis)
     {
       CSSAMethod * method = static_cast<CSSAMethod *>(mpMethod);
 
       std::string retstring = getReactionEquationForward(index1, index2);
 
       if (pReaction->isReversible())
         {
           if (method->isReactionReversed(pMethod->getFluxModes()[index1].getReactionIndex(index2)))
             retstring = getReactionEquationBackward(index1, index2);
         }
 
       return retstring;
     }
   else
 #endif //COPASI_SSA
     return CChemEqInterface::getChemEqString(mpProblem->getModel(), *pReaction, false);
 }

std::pair< C_FLOAT64, C_FLOAT64 > CEFMTask::getSpeciesChanges	(	const CFluxMode &	fluxMode,
		const CMetab &	metab
	)		const

Retrieve the species changes for the given flux mode and species

Parameters

const	CFluxMode & fluxMode
const	CMetab & pMetab

Returns: std::pair< C_FLOAT64, C_FLOAT64 > changes

Definition at line 216 of file CEFMTask.cpp.

References CFluxMode::begin(), CCopasiVector< T >::begin(), C_FLOAT64, CFluxMode::end(), CCopasiVector< T >::end(), CReaction::getChemEq(), CModelEntity::getKey(), CChemEq::getProducts(), CChemEq::getSubstrates(), and CCopasiTask::mpProblem.

Referenced by CQEFMSpeciesDM::data(), getNetReactionData(), and CEFMProblem::printResult().

 {
   C_FLOAT64 In = 0.0;
   C_FLOAT64 Out = 0.0;
   C_FLOAT64 *pIn, *pOut;
 
   CFluxMode::const_iterator itReaction = fluxMode.begin();
   CFluxMode::const_iterator endReaction = fluxMode.end();
 
   std::string Key = metab.getKey();
 
   const std::vector< const CReaction * > & ReorderedReactions =
     static_cast<CEFMProblem *>(mpProblem)->getReorderedReactions();
 
   for (; itReaction != endReaction; ++itReaction)
     {
       const CReaction * pReaction = ReorderedReactions[itReaction->first];
 
       if (itReaction->second < 0.0)
         {
           pIn = &Out;
           pOut = &In;
         }
       else
         {
           pIn = &In;
           pOut = &Out;
         }
 
       CCopasiVector < CChemEqElement >::const_iterator it = pReaction->getChemEq().getSubstrates().begin();
       CCopasiVector < CChemEqElement >::const_iterator end = pReaction->getChemEq().getSubstrates().end();
 
       for (; it != end; ++it)
         {
           if ((*it)->getMetaboliteKey() == Key)
             {
               *pIn += fabs(itReaction->second) * (*it)->getMultiplicity();
               break;
             }
         }
 
       it = pReaction->getChemEq().getProducts().begin();
       end = pReaction->getChemEq().getProducts().end();
 
       for (; it != end; ++it)
         {
           if ((*it)->getMetaboliteKey() == Key)
             {
               *pOut += fabs(itReaction->second) * (*it)->getMultiplicity();
               break;
             }
         }
     }
 
   return std::make_pair(In, Out);
 }

bool CEFMTask::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 88 of file CEFMTask.cpp.

References CCopasiTask::initialize(), CCopasiMethod::isValidProblem(), CCopasiTask::mpMethod, and CCopasiTask::mpProblem.

 {
   CEFMMethod * pMethod = dynamic_cast<CEFMMethod *>(mpMethod);
 
   if (pMethod == NULL) return false;
 
   if (!mpMethod->isValidProblem(mpProblem))
     {
       return false;
     }
 
   return CCopasiTask::initialize(of, pOutputHandler, pOstream);
 }

static bool CEFMTask::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

bool CEFMTask::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 104 of file CEFMTask.cpp.

References CCopasiTask::mpMethod.

 {
   return static_cast<CEFMMethod *>(mpMethod)->calculate();
 }

bool CEFMTask::setCallBack ( CProcessReport * pCallBack )

virtual

Set the call back of the task

Parameters

CProcessReport * pCallBack

Returns: bool success

Reimplemented from CCopasiTask.

Definition at line 77 of file CEFMTask.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 CEFMTask::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 109 of file CEFMTask.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 CEFMTask::ValidMethods

static

Initial value:

=
{
  CCopasiMethod::EFMAlgorithm,
 
 
  0
}

The methods which can be selected for performing this task.

CEFMTask class.

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

Definition at line 47 of file CEFMTask.h.

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

Public Member Functions

Static Public Member Functions

Static Public Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation