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COPASI API
4.40.278
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#include <CTrajectoryTask.h>
Public Member Functions | |
| CTrajectoryTask (const CDataContainer *pParent, const CTaskEnum::Task &type=CTaskEnum::Task::timeCourse) | |
| CTrajectoryTask (const CTrajectoryTask &src, const CDataContainer *pParent) | |
| const CTimeSeries & | getTimeSeries () const |
| virtual const CTaskEnum::Method * | getValidMethods () const |
| virtual bool | initialize (const OutputFlag &of, COutputHandler *pOutputHandler, std::ostream *pOstream) |
| void | load (CReadConfig &configBuffer) |
| virtual bool | process (const bool &useInitialValues) |
| bool | processStart (const bool &useInitialValues) |
| bool | processStep (const C_FLOAT64 &nextTime, const bool &final=false) |
| virtual bool | processTrajectory (const bool &useInitialValues) |
| virtual bool | processValues (const bool &useInitialValues) |
| ~CTrajectoryTask () | |
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 CProcessReportLevel & | getCallBack () const |
| const CDescription & | getDescription () const |
| virtual const std::string & | getKey () const |
| CMathContainer * | getMathContainer () const |
| CCopasiMethod * | getMethod () |
| const CCopasiMethod * | getMethod () const |
| COutputHandler * | getOutputHandler () const |
| const OutputFlag & | getOutputMode () const |
| CCopasiProblem * | getProblem () |
| const CCopasiProblem * | getProblem () const |
| CReport & | getReport () |
| const CReport & | getReport () const |
| const CResult & | getResult () const |
| CCopasiParameterGroup * | getSliders () |
| 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) |
| virtual bool | setCallBack (CProcessReportLevel callBack) |
| 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 CObjectInterface * | getObject (const CCommonName &cn) const override |
| virtual objectMap & | getObjects () |
| virtual const objectMap & | getObjects () const |
| virtual const std::string | getUnits () const override |
| virtual const CDataObject * | getValueObject () const override |
| virtual CUndoObjectInterface * | insert (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 CDataObject * | getDataObject () const override |
| CDataContainer * | getObjectAncestor (const std::string &type) const |
| CDataModel * | getObjectDataModel () const |
| virtual std::string | getObjectDisplayName () const override |
| const CObjectInterface * | getObjectFromCN (const CCommonName &cn) const |
| const std::string & | getObjectName () const |
| CDataContainer * | getObjectParent () const |
| const std::string & | getObjectType () const |
| virtual const CObjectInterface::ObjectSet & | getPrerequisites () const override |
| virtual const CValidity & | getValidity () 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 () |
Static Public Attributes | |
| static const CTaskEnum::Method | ValidMethods [] |
Static Public Attributes inherited from CDataContainer | |
| static const CObjectInterface::ContainerList | EmptyList |
Protected Member Functions | |
| virtual void | signalMathContainerChanged () |
| virtual void | signalMethodChanged () |
Protected Member Functions inherited from CCopasiTask | |
| bool | isTaskValid () const |
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) | |
Private Member Functions | |
| void | cleanup () |
| CTrajectoryTask () | |
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 CCopasiTask * | fromData (const CData &data, CUndoObjectInterface *pParent) |
| static bool | isValidMethod (const CTaskEnum::Method &method, const CTaskEnum::Method *validMethods) |
Static Public Member Functions inherited from CDataContainer | |
| static CDataContainer * | fromData (const CData &data, CUndoObjectInterface *pParent) |
Static Public Member Functions inherited from CDataObject | |
| static CDataObject * | fromData (const CData &data, CUndoObjectInterface *pParent) |
| static void | sanitizeObjectName (std::string &name) |
Static Public Member Functions inherited from CObjectInterface | |
| static const CDataObject * | DataObject (const CObjectInterface *pInterface) |
| static CObjectInterface * | GetObjectFromCN (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 |
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private |
Default constructor
| CTrajectoryTask::CTrajectoryTask | ( | const CDataContainer * | pParent, |
| const CTaskEnum::Task & | type = CTaskEnum::Task::timeCourse |
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Specific constructor
| const | CDataContainer * pParent |
| const | CTaskEnum::Task & type (default: timeCourse) |
References CMethodFactory::create(), CTaskEnum::deterministic, CCopasiTask::getType(), CCopasiTask::mpMethod, mUpdateMoieties, and signalMathContainerChanged().
| CTrajectoryTask::CTrajectoryTask | ( | const CTrajectoryTask & | src, |
| const CDataContainer * | pParent | ||
| ) |
Copy constructor
| const | CTrajectoryTask & src |
| const | CDataContainer * pParent (default: NULL) |
References CCopasiTask::mpMethod, mUpdateMoieties, and signalMathContainerChanged().
| CTrajectoryTask::~CTrajectoryTask | ( | ) |
Destructor
References cleanup().
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private |
Referenced by ~CTrajectoryTask().
| const CTimeSeries & CTrajectoryTask::getTimeSeries | ( | ) | const |
gets a reference to the time series
References mTimeSeries.
Referenced by CTrajectoryProblem::printResult().
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Retrieve the list of valid methods
Reimplemented from CCopasiTask.
Reimplemented in CCrossSectionTask, and CAnalyticsTask.
References ValidMethods.
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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.
| const | OutputFlag & of |
| COutputHandler | * pOutputHandler |
| std::ostream | * pOstream (default: NULL) |
Reimplemented from CCopasiTask.
Reimplemented in CCrossSectionTask, and CAnalyticsTask.
References COutputHandler::addInterface(), CTimeSeries::allocate(), CTimeSeries::clear(), CDataObject::getObjectDataModel(), CTrajectoryProblem::getStartInSteadyState(), CTrajectoryProblem::getStepNumber(), CDataModel::getTaskList(), CCopasiTask::initialize(), CSteadyStateTask::initialize(), CCopasiMethod::isValidProblem(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, mpSteadyState, mpTrajectoryMethod, mpTrajectoryProblem, mTimeSeries, mTimeSeriesRequested, mUpdateMoieties, CTrajectoryMethod::setProblem(), signalMathContainerChanged(), CCopasiTask::TIME_SERIES, and CTrajectoryProblem::timeSeriesRequested().
Referenced by CFitProblem::initialize(), CNewtonMethod::initialize(), CAnalyticsTask::initialize(), and CCrossSectionTask::initialize().
| void CTrajectoryTask::load | ( | CReadConfig & | configBuffer | ) |
Loads parameters for this solver with data coming from a CReadConfig object. (CReadConfig object reads an input stream)
| configbuffer | reference to a CReadConfig object. |
References CMethodFactory::create(), CTaskEnum::deterministic, CCopasiTask::getType(), CReadConfig::getVariable(), CReadConfig::LOOP, CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiTask::mScheduled, mUpdateMoieties, and pdelete.
Referenced by CDataModel::loadModel().
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Process the task with or without initializing to the initial state.
| const | bool & useInitialValues |
Reimplemented from CCopasiTask.
Reimplemented in CCrossSectionTask, and CAnalyticsTask.
References CTrajectoryProblem::getUseValues(), mpTrajectoryProblem, processTrajectory(), and processValues().
Referenced by CNewtonMethod::doIntegration().
| bool CTrajectoryTask::processStart | ( | const bool & | useInitialValues | ) |
Starts the process of integration by calling CTrajectoryMethod::start
| const | bool & useInitialValues |
References CMathContainer::applyInitialValues(), CVectorCore< CType >::array(), CCopasiMessage::ERROR, CMathContainer::getCountFixedEventTargets(), CTrajectoryProblem::getStartInSteadyState(), CMathContainer::getState(), CVectorCore< CType >::initialize(), mContainerState, CCopasiTask::mpContainer, mpContainerStateTime, mpSteadyState, mpTrajectoryMethod, mpTrajectoryProblem, mUpdateMoieties, CSteadyStateTask::process(), and CTrajectoryMethod::start().
Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), CAnalyticsTask::process(), CCrossSectionTask::process(), processTrajectory(), and processValues().
| bool CTrajectoryTask::processStep | ( | const C_FLOAT64 & | nextTime, |
| const bool & | final = false |
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Integrates one step
| const | C_FLOAT64 & nextTime |
| const | bool & final (default: false) |
References C_FLOAT64, COutputInterface::DURING, CCopasiMessage::EXCEPTION, CTrajectoryMethod::FAILURE, CTrajectoryProblem::getAutomaticStepSize(), CTrajectoryProblem::getOutputEvent(), CMathContainer::getProcessQueueExecutionTime(), CTrajectoryMethod::getRoots(), CMathContainer::getState(), mContainerState, MCTrajectoryMethod, min, mOutputStartTime, CCopasiTask::mpContainer, mpContainerStateTime, mpLessOrEqual, CCopasiTask::mProcessReport, mpTrajectoryMethod, mpTrajectoryProblem, mUpdateMoieties, CFlags< eStateChange >::None, CTrajectoryMethod::NORMAL, CCopasiTask::output(), CProcessReportLevel::proceed(), CMathContainer::processQueue(), CMathContainer::processRoots(), CTrajectoryMethod::ROOT, CMathContainer::setState(), CTrajectoryMethod::stateChange(), CTrajectoryMethod::step(), CMathContainer::updateRootValues(), and CMathContainer::updateSimulatedValues().
Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), CAnalyticsTask::process(), CCrossSectionTask::process(), processTrajectory(), and processValues().
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References CProcessReportLevel::addItem(), COutputInterface::AFTER, COutputInterface::BEFORE, bl(), ble(), C_FLOAT64, C_INT32, C_INVALID_INDEX, COutputInterface::DURING, CCopasiMessage::ERROR, CCopasiMessage::EXCEPTION, CProcessReportLevel::finishItem(), fl(), fle(), CTrajectoryProblem::getAutomaticStepSize(), CTrajectoryProblem::getDuration(), CCopasiException::getMessage(), CTrajectoryProblem::getOutputStartTime(), CMathContainer::getState(), CTrajectoryProblem::getStepSize(), mContainerState, MCTrajectoryMethod, MCTrajectoryProblem, min, mOutputStartTime, CCopasiTask::mpContainer, mpContainerStateTime, mpLess, mpLessOrEqual, CCopasiTask::mProcessReport, mpTrajectoryMethod, mpTrajectoryProblem, mUpdateMoieties, CCopasiTask::output(), CMathContainer::processQueue(), processStart(), processStep(), CProcessReportLevel::progressItem(), CMathContainer::pushAllTransientValues(), CProcessReportLevel::setName(), CMathContainer::setState(), CTrajectoryMethod::stateChange(), CMathContainer::updateSimulatedValues(), and CMathContainer::updateTransientDataValues().
Referenced by process().
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References CProcessReportLevel::addItem(), COutputInterface::AFTER, COutputInterface::BEFORE, C_FLOAT64, C_INVALID_INDEX, COutputInterface::DURING, CCopasiMessage::ERROR, CCopasiMessage::EXCEPTION, CProcessReportLevel::finishItem(), fl(), fle(), CCopasiException::getMessage(), CTrajectoryProblem::getOutputStartTime(), CMathContainer::getState(), CTrajectoryProblem::getValues(), mContainerState, MCTrajectoryMethod, MCTrajectoryProblem, min, mOutputStartTime, CCopasiTask::mpContainer, mpContainerStateTime, mpLess, mpLessOrEqual, CCopasiTask::mProcessReport, mpTrajectoryMethod, mpTrajectoryProblem, mUpdateMoieties, CCopasiTask::output(), CMathContainer::processQueue(), processStart(), processStep(), CProcessReportLevel::progressItem(), CMathContainer::pushAllTransientValues(), CProcessReportLevel::setName(), CMathContainer::setState(), CTrajectoryMethod::stateChange(), CMathContainer::updateSimulatedValues(), and CMathContainer::updateTransientDataValues().
Referenced by process().
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Signal that the math container has changed
Reimplemented from CCopasiTask.
References CVectorCore< CType >::array(), CMathContainer::getCountFixedEventTargets(), CMathContainer::getState(), CVectorCore< CType >::initialize(), mContainerState, CCopasiTask::mpContainer, mpContainerStateTime, and mUpdateMoieties.
Referenced by CTrajectoryTask(), initialize(), and CCrossSectionTask::removeEvent().
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Signal that the method has changed
Reimplemented from CCopasiTask.
References CCopasiTask::mpMethod, and mUpdateMoieties.
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The current state of the integration.
Referenced by CAnalyticsTask::eventCallBack(), CCrossSectionTask::eventCallBack(), CAnalyticsTask::process(), CCrossSectionTask::process(), processStart(), processStep(), processTrajectory(), processValues(), and signalMathContainerChanged().
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A pointer to the time at which the output starts.
Referenced by CAnalyticsTask::eventCallBack(), CCrossSectionTask::eventCallBack(), CAnalyticsTask::process(), CCrossSectionTask::process(), processStep(), processTrajectory(), and processValues().
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A pointer to the current time of the integration.
Referenced by CAnalyticsTask::eventCallBack(), CCrossSectionTask::eventCallBack(), CAnalyticsTask::finish(), CAnalyticsTask::process(), CCrossSectionTask::process(), processStart(), processStep(), processTrajectory(), processValues(), and signalMathContainerChanged().
A pointer to less comparison
Referenced by processTrajectory(), and processValues().
A pointer to lessOrEqual comparison
Referenced by processStep(), processTrajectory(), and processValues().
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Pointer to CSteadyStateTask. To be used in processStart() to start simulation in steady state
Referenced by initialize(), and processStart().
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A pointer to the trajectory method
Referenced by initialize(), processStart(), processStep(), processTrajectory(), and processValues().
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A pointer to the trajectory Problem
Referenced by initialize(), process(), processStart(), processStep(), processTrajectory(), and processValues().
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the time series (if requested)
Referenced by getTimeSeries(), and initialize().
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whether the time series should be stored in mTimeSeries
Referenced by initialize().
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Indicates whether we need to update moieties.
Referenced by CTrajectoryTask(), CAnalyticsTask::eventCallBack(), CCrossSectionTask::eventCallBack(), initialize(), load(), CAnalyticsTask::process(), CCrossSectionTask::process(), processStart(), processStep(), processTrajectory(), processValues(), signalMathContainerChanged(), and signalMethodChanged().
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Referenced by getValidMethods(), CAnalyticsTask::getValidMethods(), and CCrossSectionTask::getValidMethods().