COPASI API
4.40.278
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#include <CTimeSensTask.h>
Public Member Functions | |
CTimeSensTask (const CDataContainer *pParent, const CTaskEnum::Task &type=CTaskEnum::Task::timeSens) | |
CTimeSensTask (const CTimeSensTask &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) |
virtual void | output (const COutputInterface::Activity &activity) |
virtual bool | process (const bool &useInitialValues) |
bool | processStart (const bool &useInitialValues) |
bool | processStep (const C_FLOAT64 &nextTime, const bool &final=false) |
virtual bool | updateMatrices () |
~CTimeSensTask () | |
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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 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 | ~CCopasiTask () |
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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 () |
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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 () |
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CObjectInterface () | |
CObjectInterface (const CObjectInterface &src) | |
virtual | ~CObjectInterface () |
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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 [] |
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static const CObjectInterface::ContainerList | EmptyList |
Protected Member Functions | |
virtual void | signalMathContainerChanged () |
virtual void | signalMethodChanged () |
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bool | isTaskValid () const |
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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 () |
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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 () |
CTimeSensTask () | |
Static Private Member Functions | |
static bool | bl (const C_FLOAT64 &d1, const C_FLOAT64 &d2) |
static bool | ble (const C_FLOAT64 &d1, const C_FLOAT64 &d2) |
static bool | fl (const C_FLOAT64 &d1, const C_FLOAT64 &d2) |
static bool | fle (const C_FLOAT64 &d1, const C_FLOAT64 &d2) |
Additional Inherited Members | |
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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 } |
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typedef CDataObjectMap | objectMap |
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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 } |
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typedef std::vector< const CDataContainer * > | ContainerList |
typedef std::set< const CObjectInterface * > | ObjectSet |
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static CCopasiTask * | fromData (const CData &data, CUndoObjectInterface *pParent) |
static bool | isValidMethod (const CTaskEnum::Method &method, const CTaskEnum::Method *validMethods) |
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static CDataContainer * | fromData (const CData &data, CUndoObjectInterface *pParent) |
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static CDataObject * | fromData (const CData &data, CUndoObjectInterface *pParent) |
static void | sanitizeObjectName (std::string &name) |
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static const CDataObject * | DataObject (const CObjectInterface *pInterface) |
static CObjectInterface * | GetObjectFromCN (const ContainerList &listOfContainer, const CCommonName &objName) |
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template<class CType > | |
static CType * | fromData (const CData &, CUndoObjectInterface *) |
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std::string | Error |
std::string | Warning |
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private |
Default constructor
CTimeSensTask::CTimeSensTask | ( | const CDataContainer * | pParent, |
const CTaskEnum::Task & | type = CTaskEnum::Task::timeSens |
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Specific constructor
const | CDataContainer * pParent |
const | CTaskEnum::Task & type (default: timeCourse) |
References CMethodFactory::create(), CCopasiTask::getType(), CCopasiTask::mpMethod, mUpdateMoieties, signalMathContainerChanged(), and CTaskEnum::timeSensLsoda.
CTimeSensTask::CTimeSensTask | ( | const CTimeSensTask & | src, |
const CDataContainer * | pParent | ||
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Copy constructor
const | CTimeSensTask & src |
const | CDataContainer * pParent (default: NULL) |
References CCopasiTask::mpMethod, mUpdateMoieties, and signalMathContainerChanged().
CTimeSensTask::~CTimeSensTask | ( | ) |
Destructor
References cleanup().
Referenced by process().
Referenced by process().
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Referenced by ~CTimeSensTask().
Referenced by process().
Referenced by process().
const CTimeSeries & CTimeSensTask::getTimeSeries | ( | ) | const |
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Retrieve the list of valid methods
Reimplemented from CCopasiTask.
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.
References COutputHandler::addInterface(), CTimeSeries::allocate(), CTimeSeries::clear(), CDataObject::getObjectDataModel(), CTrajectoryProblem::getStartInSteadyState(), CTrajectoryProblem::getStepNumber(), CDataModel::getTaskList(), CCopasiTask::initialize(), CSteadyStateTask::initialize(), CTimeSensMethod::integrateReducedModel(), CCopasiMethod::isValidProblem(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, mpSteadyState, mpTimeSensMethod, mpTimeSensProblem, mTimeSeries, mTimeSeriesRequested, mUpdateMoieties, CTimeSensMethod::setProblem(), signalMathContainerChanged(), CCopasiTask::TIME_SERIES, CTrajectoryProblem::timeSeriesRequested(), and updateMatrices().
Referenced by CFitProblem::initialize().
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Perform an output event for the current activity
const | Activity & activity |
Reimplemented from CCopasiTask.
References CTimeSensMethod::copySensitivitiesToResultMatrix(), mpTimeSensMethod, and CCopasiTask::output().
Referenced by CTimeSensMethod::output(), process(), and processStep().
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Process the task with or without initializing to the initial state.
const | bool & useInitialValues |
Reimplemented from CCopasiTask.
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, mProceed, CCopasiTask::mProcessReport, mpTimeSensMethod, mpTimeSensProblem, mUpdateMoieties, output(), CMathContainer::processQueue(), processStart(), processStep(), CProcessReportLevel::progressItem(), CMathContainer::pushAllTransientValues(), CProcessReportLevel::setName(), CMathContainer::setState(), CTimeSensMethod::stateChange(), CMathContainer::updateSimulatedValues(), and CMathContainer::updateTransientDataValues().
bool CTimeSensTask::processStart | ( | const bool & | useInitialValues | ) |
Starts the process of integration by calling CTimeSensMethod::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, mpTimeSensMethod, mpTimeSensProblem, mUpdateMoieties, CSteadyStateTask::process(), and CTimeSensMethod::start().
Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), and process().
bool CTimeSensTask::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, CTimeSensMethod::FAILURE, CTrajectoryProblem::getAutomaticStepSize(), CTrajectoryProblem::getOutputEvent(), CMathContainer::getProcessQueueExecutionTime(), CTimeSensMethod::getRoots(), CMathContainer::getState(), mContainerState, MCTrajectoryMethod, min, mOutputStartTime, CCopasiTask::mpContainer, mpContainerStateTime, mpLessOrEqual, mProceed, CCopasiTask::mProcessReport, mpTimeSensMethod, mpTimeSensProblem, mUpdateMoieties, CFlags< eStateChange >::None, CTimeSensMethod::NORMAL, output(), CProcessReportLevel::proceed(), CMathContainer::processQueue(), CMathContainer::processRoots(), CTimeSensMethod::ROOT, CMathContainer::setState(), CTimeSensMethod::stateChange(), CTimeSensMethod::step(), CMathContainer::updateRootValues(), and CMathContainer::updateSimulatedValues().
Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), and 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 CTimeSensTask(), and initialize().
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Signal that the method has changed
Reimplemented from CCopasiTask.
References CCopasiTask::mpMethod, and mUpdateMoieties.
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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 from CCopasiTask.
References CTimeSensMethod::initResult(), and CCopasiTask::mpMethod.
Referenced by initialize().
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The current state of the integration.
Referenced by process(), processStart(), processStep(), and signalMathContainerChanged().
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A pointer to the time at which the output starts.
Referenced by process(), and processStep().
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A pointer to the current time of the integration.
Referenced by process(), processStart(), processStep(), and signalMathContainerChanged().
A pointer to less comparison
Referenced by process().
A pointer to lessOrEqual comparison
Referenced by process(), and processStep().
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A Boolean flag indication whether to proceed with the integration
Referenced by process(), and processStep().
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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 time sensitivities method
Referenced by initialize(), output(), process(), processStart(), and processStep().
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A pointer to the time sensitivities Problem
Referenced by initialize(), process(), processStart(), and processStep().
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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 CTimeSensTask(), initialize(), process(), processStart(), processStep(), signalMathContainerChanged(), and signalMethodChanged().
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Referenced by getValidMethods().