COPASI API  4.40.278
CEFMTask Class Reference

#include <CEFMTask.h>

Inheritance diagram for CEFMTask:
[legend]

Public Member Functions

 CEFMTask (const CDataContainer *pParent, const CTaskEnum::Task &type=CTaskEnum::Task::fluxMode)
 
 CEFMTask (const CEFMTask &src, const CDataContainer *pParent)
 
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_FLOAT64getSpeciesChanges (const CFluxMode &fluxMode, const CMetab &metab) const
 
virtual const CTaskEnum::MethodgetValidMethods () const
 
virtual bool initialize (const OutputFlag &of, COutputHandler *pOutputHandler, std::ostream *pOstream)
 
virtual bool process (const bool &useInitialValues)
 
virtual bool setCallBack (CProcessReportLevel callBack)
 
virtual ~CEFMTask ()
 
- Public Member Functions inherited from CCopasiTask
virtual bool applyData (const CData &data, CUndoData::CChangeSet &changes)
 
 CCopasiTask (const CCopasiTask &src, const CDataContainer *pParent)
 
 CCopasiTask (const CDataContainer *pParent, const CTaskEnum::Task &taskType, const std::string &type="Task")
 
void cleanup ()
 
virtual void clearCallBack ()
 
virtual void createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const
 
const CProcessReportLevelgetCallBack () const
 
const CDescriptiongetDescription () const
 
virtual const std::string & getKey () const
 
CMathContainergetMathContainer () const
 
CCopasiMethodgetMethod ()
 
const CCopasiMethodgetMethod () const
 
COutputHandlergetOutputHandler () const
 
const OutputFlaggetOutputMode () const
 
CCopasiProblemgetProblem ()
 
const CCopasiProblemgetProblem () const
 
CReportgetReport ()
 
const CReportgetReport () const
 
const CResultgetResult () const
 
CCopasiParameterGroupgetSliders ()
 
CTaskEnum::Task getType () const
 
const bool & isScheduled () const
 
const bool & isUpdateModel () const
 
virtual void output (const COutputInterface::Activity &activity)
 
virtual bool restore (const bool &updateModel=true)
 
virtual void separate (const COutputInterface::Activity &activity)
 
void setIgnoreProblemData (const bool &ignoreProblemData)
 
void setMathContainer (CMathContainer *pContainer)
 
bool setMethodType (const CTaskEnum::Method &type)
 
void setScheduled (const bool &scheduled)
 
void setType (const CTaskEnum::Task &type)
 
virtual void setUpdateModel (const bool &updateModel)
 
virtual CData toData () const
 
virtual bool updateMatrices ()
 
virtual ~CCopasiTask ()
 
- Public Member Functions inherited from CDataContainer
virtual bool add (CDataObject *pObject, const bool &adopt=true)
 
virtual bool appendDeletedDependentData (CUndoData &undoData) const
 
 CDataContainer (const CDataContainer &src, const CDataContainer *pParent)
 
 CDataContainer (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)
 
virtual std::string getChildObjectUnits (const CDataObject *pObject) const
 
void getDescendants (CDataObject::DataObjectSet &descendants, const bool &recursive=false) const
 
virtual size_t getIndex (const CDataObject *pObject) const
 
virtual const CObjectInterfacegetObject (const CCommonName &cn) const override
 
virtual objectMapgetObjects ()
 
virtual const objectMapgetObjects () const
 
virtual const std::string getUnits () const override
 
virtual const CDataObjectgetValueObject () const override
 
virtual CUndoObjectInterfaceinsert (const CData &data) override
 
void objectRenamed (CDataObject *pObject, const std::string &oldName)
 
virtual bool remove (CDataObject *pObject)
 
virtual ~CDataContainer ()
 
- Public Member Functions inherited from CDataObject
void addIssue (const CIssue &issue)
 
void addReference (const CDataContainer *pReference)
 
virtual void calculateValue () override
 
 CDataObject (const CDataObject &src, const CDataContainer *pParent=NULL)
 
virtual void destruct () override
 
virtual CCommonName getCN () const override
 
virtual const CDataObjectgetDataObject () const override
 
CDataContainergetObjectAncestor (const std::string &type) const
 
CDataModelgetObjectDataModel () const
 
virtual std::string getObjectDisplayName () const override
 
const CObjectInterfacegetObjectFromCN (const CCommonName &cn) const
 
const std::string & getObjectName () const
 
CDataContainergetObjectParent () const
 
const std::string & getObjectType () const
 
virtual const CObjectInterface::ObjectSetgetPrerequisites () const override
 
virtual const CValiditygetValidity () const override
 
virtual void * getValuePointer () const override
 
bool hasFlag (const Flag &flag) const
 
virtual bool isPrerequisiteForContext (const CObjectInterface *pObject, const CCore::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const override
 
bool prerequisitsContains (const DataObjectSet &objects) const
 
virtual void print (std::ostream *ostream) const override
 
void removeIssue (const CIssue &issue)
 
void removeReference (const CDataContainer *pReference)
 
bool setObjectName (const std::string &name)
 
virtual bool setObjectParent (const CDataContainer *pParent)
 
void validityChanged (const CValidity &changedValidity) override
 
void validityRemoved (const CValidity &changedValidity)
 
virtual ~CDataObject ()
 
- Public Member Functions inherited from CObjectInterface
 CObjectInterface ()
 
 CObjectInterface (const CObjectInterface &src)
 
virtual ~CObjectInterface ()
 
- Public Member Functions inherited from CUndoObjectInterface
 CUndoObjectInterface ()
 
 CUndoObjectInterface (const CUndoObjectInterface &src)
 
bool generateUuid ()
 
const xg::Guid & getUuid () const
 
bool setUuid (const std::string &uuid)
 
bool setUuid (const xg::Guid &uuid)
 
virtual void updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject)
 
virtual ~CUndoObjectInterface ()
 

Private Member Functions

 CEFMTask ()
 
std::map< const CMetab *, C_FLOAT64getNetReactionData (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_DURING = STREAM , 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
}
 
- Public Types inherited from CDataContainer
typedef CDataObjectMap objectMap
 
- Public Types inherited from CDataObject
typedef std::set< const CDataObject * > DataObjectSet
 
enum  Flag {
  Container , Vector , Matrix , NameVector ,
  Reference , ValueBool , ValueInt , ValueInt64 ,
  ValueDbl , NonUniqueName , StaticString , ValueString ,
  Separator , DisplayName , ModelEntity , Array ,
  DataModel , Root , Gui , __SIZE
}
 
- Public Types inherited from CObjectInterface
typedef std::vector< const CDataContainer * > ContainerList
 
typedef std::set< const CObjectInterface * > ObjectSet
 
- Static Public Member Functions inherited from CCopasiTask
static CCopasiTaskfromData (const CData &data, CUndoObjectInterface *pParent)
 
static bool isValidMethod (const CTaskEnum::Method &method, const CTaskEnum::Method *validMethods)
 
- Static Public Member Functions inherited from CDataContainer
static CDataContainerfromData (const CData &data, CUndoObjectInterface *pParent)
 
- Static Public Member Functions inherited from CDataObject
static CDataObjectfromData (const CData &data, CUndoObjectInterface *pParent)
 
static void sanitizeObjectName (std::string &name)
 
- Static Public Member Functions inherited from CObjectInterface
static const CDataObjectDataObject (const CObjectInterface *pInterface)
 
static CObjectInterfaceGetObjectFromCN (const ContainerList &listOfContainer, const CCommonName &objName)
 
- Static Public Member Functions inherited from CUndoObjectInterface
template<class CType >
static CType * fromData (const CData &, CUndoObjectInterface *)
 
- Public Attributes inherited from CCopasiTask
std::string Error
 
std::string Warning
 
- Static Public Attributes inherited from CDataContainer
static const CObjectInterface::ContainerList EmptyList
 
- Protected Member Functions inherited from CCopasiTask
bool isTaskValid () const
 
virtual void signalMathContainerChanged ()
 
virtual void signalMethodChanged ()
 
- Protected Member Functions inherited from CDataContainer
template<class CType >
CDataMatrixReference< CType > * addMatrixReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)
 
template<class CType >
CDataObjectReference< CType > * addObjectReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)
 
template<class CType >
CDataVectorReference< CType > * addVectorReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)
 
 CDataContainer (const CDataContainer &src)
 
void initObjects ()
 
- Protected Member Functions inherited from CDataObject
 CDataObject ()
 
 CDataObject (const std::string &name, const CDataContainer *pParent=static_cast< CDataContainer * >((void *) 0), const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)
 
- Protected Attributes inherited from CCopasiTask
CDescription mDescription
 
OutputFlag mDoOutput
 
bool mIgnoreProblemData
 
CVector< C_FLOAT64mInitialState
 
std::string mKey
 
unsigned C_INT32 mOutputCounter
 
CMathContainermpContainer
 
CCopasiMethodmpMethod
 
COutputHandlermpOutputHandler
 
CCopasiProblemmpProblem
 
CProcessReportLevel mProcessReport
 
CCopasiParameterGroupmpSliders
 
CReport mReport
 
CResult mResult
 
bool mScheduled
 
CTaskEnum::Task mType
 
bool mUpdateModel
 
- Protected Attributes inherited from CDataContainer
objectMap mObjects
 
- Protected Attributes inherited from CDataObject
ObjectSet mPrerequisits
 
std::set< CDataContainer * > mReferences
 
- Protected Attributes inherited from CObjectInterface
CValidity mValidity
 

Constructor & Destructor Documentation

◆ CEFMTask() [1/3]

CEFMTask::CEFMTask ( )
private

Default constructor

◆ CEFMTask() [2/3]

CEFMTask::CEFMTask ( const CDataContainer pParent,
const CTaskEnum::Task type = CTaskEnum::Task::fluxMode 
)

Specific constructor

Parameters
constCDataContainer * pParent

CEFMTask class.

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

References CMethodFactory::create(), CTaskEnum::EFMAlgorithm, CCopasiTask::getType(), and CCopasiTask::mpMethod.

◆ CEFMTask() [3/3]

CEFMTask::CEFMTask ( const CEFMTask src,
const CDataContainer pParent 
)

Copy constructor

Parameters
constCOptTask & src

◆ ~CEFMTask()

CEFMTask::~CEFMTask ( )
virtual

Destructor

Member Function Documentation

◆ getFluxModeDescription()

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

Retrieve the description of the flux mode

Parameters
constCFluxMode & fluxMode
Returns
std::string fluxModeDescription

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

Referenced by CEFMProblem::printResult().

◆ getFluxModes()

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

Retrieve the Flux Modes

Returns
const std::vector< CFluxMode > &

References CCopasiTask::mpProblem.

Referenced by CEFMProblem::printResult().

◆ getInternalSpecies()

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

Retrieve the internal species for the given flux mode.

Parameters
constCFluxMode & fluxMode
Returns
std::string species

References CMetabNameInterface::getDisplayName(), CMathContainer::getModel(), getNetReactionData(), and CCopasiTask::mpContainer.

Referenced by CEFMProblem::printResult().

◆ getNetReaction()

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

Retrieve the net reaction for the given flux mode.

Parameters
constCFluxMode & fluxMode
Returns
std::string netReaction

References CMetabNameInterface::getDisplayName(), CMathContainer::getModel(), getNetReactionData(), CFluxMode::isReversible(), and CCopasiTask::mpContainer.

Referenced by CEFMProblem::printResult().

◆ getNetReactionData()

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

Retrieve the net reaction data for the given flux mode.

Parameters
constCFluxMode & fluxMode
Returns
std::map< const CMetab *, C_FLOAT64 >g netReactionData

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

Referenced by getInternalSpecies(), and getNetReaction().

◆ getReactionEquation()

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
conststd::map< size_t, C_FLOAT64 >::const_iterator & itReaction
Returns
std::string reactionEquation

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

Referenced by CEFMProblem::printResult().

◆ getSpeciesChanges()

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
constCFluxMode & fluxMode
constCMetab & pMetab
Returns
std::pair< C_FLOAT64, C_FLOAT64 > changes

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

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

◆ getValidMethods()

const CTaskEnum::Method * CEFMTask::getValidMethods ( ) const
virtual

Retrieve the list of valid methods

Returns
const CTaskEnum::Method * pValidMethods

Reimplemented from CCopasiTask.

References CTaskEnum::EFMAlgorithm, CTaskEnum::EFMBitPatternAlgorithm, CTaskEnum::EFMBitPatternTreeAlgorithm, and CTaskEnum::UnsetMethod.

◆ initialize()

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
constOutputFlag & of
COutputHandler* pOutputHandler
std::ostream* pOstream (default: NULL)
Returns
bool success

Reimplemented from CCopasiTask.

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

◆ process()

bool CEFMTask::process ( const bool &  useInitialValues)
virtual

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

Parameters
constbool & useInitialValues
Returns
bool success

Reimplemented from CCopasiTask.

References COutputInterface::AFTER, COutputInterface::BEFORE, CCopasiTask::mpMethod, and CCopasiTask::output().

◆ setCallBack()

bool CEFMTask::setCallBack ( CProcessReportLevel  callBack)
virtual

Set the call back of the task

Parameters
CProcessReport* pCallBack
Returns
bool success

Reimplemented from CCopasiTask.

References CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiTask::mProcessReport, CCopasiMethod::setCallBack(), CCopasiProblem::setCallBack(), and CCopasiTask::setCallBack().


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