COPASI API
4.16.103
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#include <CCopasiTask.h>
Classes | |
class | CDescription |
class | CResult |
Public Types | |
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 } |
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typedef std::multimap < std::string, CCopasiObject * > | objectMap |
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typedef std::set< const CCopasiObject * > | DataObjectSet |
typedef std::vector< Refresh * > | DataUpdateSequence |
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typedef std::set< const CObjectInterface * > | ObjectSet |
typedef std::vector < CObjectInterface * > | UpdateSequence |
Public Member Functions | |
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 () |
virtual CCopasiMethod * | createMethod (const int &type) const |
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 |
virtual bool | initialize (const OutputFlag &of, COutputHandler *pOutputHandler, std::ostream *pOstream) |
const bool & | isScheduled () const |
const bool & | isUpdateModel () const |
virtual void | output (const COutputInterface::Activity &activity) |
virtual bool | process (const bool &useInitialValues) |
virtual bool | restore () |
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 bool | updateMatrices () |
virtual | ~CCopasiTask () |
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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 () |
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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 () |
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CObjectInterface () | |
virtual | ~CObjectInterface () |
Static Public Member Functions | |
static bool | isValidMethod (const unsigned int &method, const unsigned int *validMethods) |
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static std::vector< Refresh * > | buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet()) |
static void | setRenameHandler (CRenameHandler *rh) |
Public Attributes | |
std::string | Error |
std::string | Warning |
Static Public Attributes | |
static const std::string | TypeName [] |
static const unsigned int | ValidMethods [] |
static const char * | XMLType [] |
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static const std::vector < CCopasiContainer * > | EmptyList |
Protected Attributes | |
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 |
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objectMap | mObjects |
Private Member Functions | |
void | initObjects () |
Additional Inherited Members | |
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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 } |
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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 () |
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CCopasiObject () | |
CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0) | |
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static CRenameHandler * | smpRenameHandler = NULL |
Definition at line 39 of file CCopasiTask.h.
Enumerator | |
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INITIALIZE | |
STREAM | |
FINISH | |
REPORT | |
PLOT | |
TIME_SERIES |
Definition at line 89 of file CCopasiTask.h.
Enumerator | |
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NO_OUTPUT | |
OUTPUT_BEFORE | |
OUTPUT_AFTER | |
OUTPUT | |
OUTPUT_SE | |
OUTPUT_UI | |
ONLY_TIME_SERIES |
Definition at line 99 of file CCopasiTask.h.
enum CCopasiTask::Type |
Enumeration of the types of tasks known to COPASI.
Enumerator | |
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steadyState | |
timeCourse | |
scan | |
fluxMode | |
optimization | |
parameterFitting | |
mca | |
lyap | |
tssAnalysis | |
sens | |
moieties | |
crosssection | |
lna | |
unset |
Definition at line 45 of file CCopasiTask.h.
CCopasiTask::CCopasiTask | ( | const std::string & | name = "NoName" , |
const CCopasiContainer * | pParent = NULL , |
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const std::string & | type = "Task" |
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Default constructor
Definition at line 100 of file CCopasiTask.cpp.
References initObjects().
CCopasiTask::CCopasiTask | ( | const Type & | taskType, |
const CCopasiContainer * | pParent = NULL , |
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const std::string & | type = "Task" |
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Specific constructor
const | Type & taskType |
const | CCopasiContainer * pParent (default: NULL) |
const | std::string & type (default: "Task") |
Definition at line 120 of file CCopasiTask.cpp.
References initObjects().
CCopasiTask::CCopasiTask | ( | const CCopasiTask & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor
const | CCopasiTask & src |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 141 of file CCopasiTask.cpp.
References initObjects().
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Destructor
Definition at line 161 of file CCopasiTask.cpp.
References CCopasiRootContainer::getKeyFactory(), mKey, mpInitialState, mpMethod, mpProblem, mpSliders, pdelete, and CKeyFactory::remove().
void CCopasiTask::cleanup | ( | ) |
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Create a method of the specified type to solve the task. It is the duty of the caller to release the CCopasiMethod.
const | CCopasiMethod::SubType & type |
Reimplemented in CCrossSectionTask, CLyapTask, CTrajectoryTask, CTSSATask, CSteadyStateTask, CEFMTask, COptTask, COscillationTask, CMoietiesTask, CFitTask, CScanTask, CMCATask, CLNATask, and CSensTask.
Definition at line 307 of file CCopasiTask.cpp.
Referenced by CQTaskMethodWidget::setActiveMethod().
CProcessReport * CCopasiTask::getCallBack | ( | ) | const |
const CCopasiTask::CDescription & CCopasiTask::getDescription | ( | ) | const |
Retrieve the description
Definition at line 318 of file CCopasiTask.cpp.
References mDescription.
Referenced by operator<<().
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Retrieve the key for the task.
Reimplemented from CCopasiObject.
Definition at line 180 of file CCopasiTask.cpp.
References mKey.
Referenced by CCopasiXML::saveTaskList(), CMCAProblem::setSteadyStateRequested(), and CLNAProblem::setSteadyStateRequested().
CCopasiMethod * CCopasiTask::getMethod | ( | ) |
Retrieve the method
Definition at line 312 of file CCopasiTask.cpp.
References mpMethod.
Referenced by CQEFMWidget::createMethod(), CSEDMLExporter::createTimeCourseTask(), CQTSSAResultSubWidget::displayResult(), CCopasiXMLParser::TaskElement::end(), CQTSSAResultWidget::enterProtected(), TaskWidget::enterProtected(), CQTSSAResultSubWidget::init(), CNewtonMethod::initialize(), StateSubwidget::loadAll(), CLNAResultWidget::loadFromBackend(), CMCAResultWidget::loadFromBackend(), CQLNAWidget::loadParameterTable(), CQMCAWidget::loadParameterTable(), SteadyStateWidget::loadTask(), operator<<(), CQSimpleSelectionTree::populateTree(), CTSSAProblem::printResult(), TaskWidget::revertBtnClicked(), CQTSSAWidget::runTask(), CQTaskMethodWidget::saveMethod(), CQLNAWidget::saveParameterTable(), CQMCAWidget::saveParameterTable(), SensitivitiesWidget::saveTask(), SteadyStateWidget::saveTask(), CCopasiXML::saveTaskList(), CQTaskMethodWidget::setTask(), CCopasiXMLParser::MethodElement::start(), and test000087::test_simulate_reaction_flux_reference_1().
const CCopasiMethod * CCopasiTask::getMethod | ( | ) | const |
COutputHandler * CCopasiTask::getOutputHandler | ( | ) | const |
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CCopasiProblem * CCopasiTask::getProblem | ( | ) |
Retrieve the problem
Definition at line 296 of file CCopasiTask.cpp.
References mpProblem.
Referenced by CCopasiDataModel::addTask(), CFitProblem::calculate(), COptProblem::calculate(), CFitProblem::calculateCrossValidation(), CQNewMainWindow::checkForElementaryModesSlot(), COutputAssistant::createDefaultOutput(), COutputAssistant::createPlot(), CSEDMLExporter::createScanTask(), CSEDMLExporter::createSteadyStateTask(), CSEDMLExporter::createTimeCourseTask(), CQTSSAResultSubWidget::displayResult(), CNewtonMethod::doIntegration(), CQNewMainWindow::elementaryModeTriggeredSlot(), CCopasiXMLParser::TaskElement::end(), CQOptimizationResult::enterProtected(), CQFittingResult::enterProtected(), CQSensResultWidget::enterProtected(), CODEExporter::exportExpression(), CODEExporterBM::exportTitleData(), CODEExporterXPPAUT::exportTitleData(), CEFMTask::getInternalSpecies(), CEFMTask::getNetReaction(), QFluxModeAnimation::getScales(), CCopasiDataModel::importSBML(), CCopasiDataModel::importSBMLFromString(), SEDMLImporter::importTasks(), CQTSSAResultSubWidget::init(), CSSAMethod::initialize(), CEFMMethod::initialize(), CFitProblem::initialize(), QFluxModeAnimation::initialize(), CSensMethod::initialize(), CEFMAlgorithm::initialize(), CBitPatternMethod::initialize(), CBitPatternTreeMethod::initialize(), CNewtonMethod::initialize(), CScanTask::initSubtask(), StateSubwidget::loadAll(), CQLyapResultWidget::loadFromBackend(), CQSteadyStateResult::loadResult(), CQCrossSectionTaskWidget::loadTask(), CQLyapWidget::loadTask(), ScanWidget::loadTask(), CQLNAWidget::loadTask(), CQMCAWidget::loadTask(), SensitivitiesWidget::loadTask(), SteadyStateWidget::loadTask(), CQFittingWidget::loadTask(), CQTSSAWidget::loadTask(), CQOptimizationWidget::loadTask(), CQTrajectoryWidget::loadTask(), CQSensResultWidget::newResult(), operator<<(), CQSimpleSelectionTree::populateTree(), Arguments::prepareModel(), CCSPMethod::printResult(), CLNATask::process(), CScanTask::processCallback(), CFitProblem::restore(), CQTSSAResultSubWidget::saveDataToFile(), CQCrossSectionTaskWidget::saveTask(), CQLyapWidget::saveTask(), CQMCAWidget::saveTask(), CQLNAWidget::saveTask(), ScanWidget::saveTask(), SensitivitiesWidget::saveTask(), SteadyStateWidget::saveTask(), CQFittingWidget::saveTask(), CQTSSAWidget::saveTask(), CQOptimizationWidget::saveTask(), CQTrajectoryWidget::saveTask(), CCopasiXML::saveTaskList(), CQEFMReactionDM::setTask(), CQEFMSpeciesDM::setTask(), CCopasiXMLParser::TaskElement::start(), test000087::test_simulate_reaction_flux_reference_1(), and SEDMLImporter::updateCopasiTaskForSimulation().
const CCopasiProblem * CCopasiTask::getProblem | ( | ) | const |
CReport & CCopasiTask::getReport | ( | ) |
Retrieve the report
Definition at line 316 of file CCopasiTask.cpp.
References mReport.
Referenced by CCopasiDataModel::addDefaultReports(), TaskWidget::commonBeforeRunTask(), CSEDMLExporter::createDataGenerators(), COptProblem::initialize(), Arguments::prepareModel(), TaskWidget::reportBtnClicked(), CCopasiXML::saveTaskList(), CCopasiXMLParser::ReportInstanceElement::start(), and test000087::test_simulate_reaction_flux_reference_1().
const CCopasiTask::CResult & CCopasiTask::getResult | ( | ) | const |
Retrieve the result
Definition at line 321 of file CCopasiTask.cpp.
References mResult.
Referenced by CQSensResultWidget::saveToFile(), CQMoietiesTaskResult::slotSave(), CMCAResultSubwidget::slotSave(), CLNAResultSubwidget::slotSave(), and CQEFMResultWidget::slotSave().
CCopasiParameterGroup * CCopasiTask::getSliders | ( | ) |
Retrieve a pointer to the group of sliders.
Definition at line 326 of file CCopasiTask.cpp.
References mpSliders.
CCopasiTask::Type CCopasiTask::getType | ( | void | ) | const |
Retrieve the type of the task
Definition at line 176 of file CCopasiTask.cpp.
References mType.
Referenced by COptProblem::calculate(), COutputAssistant::createPlot(), CCopasiXMLParser::ParameterGroupElement::end(), CCopasiXMLParser::TaskElement::end(), Worker::getIndexForTask(), COutputAssistant::getListOfDefaultOutputDescriptions(), COptProblem::getSubtaskType(), Worker::getWidgetForTask(), and CCopasiXML::saveTaskList().
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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 in CCrossSectionTask, CSteadyStateTask, CTrajectoryTask, CTSSATask, CMCATask, CLyapTask, CScanTask, CEFMTask, COptTask, CLNATask, COscillationTask, CSensTask, CFitTask, and CMoietiesTask.
Definition at line 207 of file CCopasiTask.cpp.
References COutputHandler::addInterface(), CCopasiMessage::COMMANDLINE, COutputHandler::compile(), CModel::compileIfNecessary(), CCopasiMessage::ERROR, CModel::getInitialState(), CCopasiProblem::getModel(), CCopasiObject::getObjectDataModel(), CCopasiObject::getObjectName(), CReport::getTarget(), MCCopasiTask, mDoOutput, mOutputCounter, mpCallBack, mpInitialState, mpMethod, mpOutputHandler, mpProblem, mReport, NO_OUTPUT, CReport::open(), pdelete, REPORT, and CCopasiMessage::WARNING.
Referenced by COptProblem::calculate(), TaskWidget::commonRunTask(), CMoietiesTask::initialize(), CSensTask::initialize(), COscillationTask::initialize(), CLNATask::initialize(), COptTask::initialize(), CEFMTask::initialize(), CSensMethod::initialize(), CScanTask::initialize(), CLyapTask::initialize(), CMCATask::initialize(), CTrajectoryTask::initialize(), CTSSATask::initialize(), CSteadyStateTask::initialize(), CCrossSectionTask::initialize(), COptProblem::initializeSubtaskBeforeOutput(), and CScanTask::initSubtask().
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Definition at line 390 of file CCopasiTask.cpp.
References CCopasiContainer::addObjectReference(), mOutputCounter, CCopasiTimer::PROCESS, CCopasiObject::ValueInt, and CCopasiTimer::WALL.
Referenced by CCopasiTask().
const bool & CCopasiTask::isScheduled | ( | ) | const |
Check whether the task is scheduled
Definition at line 184 of file CCopasiTask.cpp.
References mScheduled.
Referenced by Arguments::getFirstScheduledTask(), TaskWidget::loadCommon(), TaskWidget::saveCommon(), and CCopasiXML::saveTaskList().
const bool & CCopasiTask::isUpdateModel | ( | ) | const |
Check whether the task must update the model
Definition at line 188 of file CCopasiTask.cpp.
References mUpdateModel.
Referenced by CFitProblem::initialize(), CSensMethod::initialize(), TaskWidget::loadCommon(), CScanTask::processCallback(), TaskWidget::saveCommon(), CCopasiXML::saveTaskList(), and CQSteadyStateResult::slotUpdateModel().
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Check whether the given method is in the list of valid methods This list must end with CCopasiMethod::unset
const | unsigned int & method |
const | unsigned int * validMethods |
Definition at line 89 of file CCopasiTask.cpp.
References C_INT32, and CCopasiMethod::unset.
Referenced by CTrajectoryTask::setMethodType(), CTSSATask::setMethodType(), and CCrossSectionTask::setMethodType().
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Perform an output event for the current activity
const | Activity & activity |
Definition at line 331 of file CCopasiTask.cpp.
References COutputInterface::AFTER, COutputInterface::BEFORE, COutputInterface::DURING, mDoOutput, mOutputCounter, mpOutputHandler, NO_OUTPUT, COutputHandler::output(), OUTPUT_AFTER, and OUTPUT_BEFORE.
Referenced by CExperimentSet::calculateStatistics(), COptMethodPS::create(), COptMethodPraxis::evaluateFunction(), CCrossSectionTask::eventCallBack(), CCrossSectionTask::finish(), CLyapTask::methodCallback(), COptMethodPS::move(), COptMethodDE::optimise(), COptMethodSRES::optimise(), COptMethodSS::optimise(), COptMethodPS::optimise(), COptMethodGA::optimise(), COptMethodHookeJeeves::optimise(), COptMethodGASR::optimise(), COptMethodLevenbergMarquardt::optimise(), COptMethodNelderMead::optimise(), COptMethodCoranaWalk::optimise(), COptMethodSA::optimise(), COptMethodPraxis::optimise(), COptMethodTruncatedNewton::optimise(), COptMethodStatistics::optimise(), COptMethodSteepestDescent::optimise(), COptMethodEP::optimise(), CRandomSearch::optimise(), CMoietiesTask::process(), CFitTask::process(), COscillationTask::process(), CLNATask::process(), COptTask::process(), CScanTask::process(), CLyapTask::process(), CMCATask::process(), CTrajectoryTask::process(), CTSSATask::process(), CSteadyStateTask::process(), CCrossSectionTask::process(), CScanTask::processCallback(), CTrajectoryTask::processStep(), and COptMethodTruncatedNewton::sFun().
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Process the task with or without initializing to the initial state.
const | bool & useInitialValues |
Reimplemented in CCrossSectionTask, CSteadyStateTask, CTrajectoryTask, CTSSATask, CMCATask, CLyapTask, CScanTask, CEFMTask, COptTask, CLNATask, COscillationTask, CSensTask, CFitTask, and CMoietiesTask.
Definition at line 274 of file CCopasiTask.cpp.
Referenced by COptProblem::calculate(), CSensMethod::do_target_calculation(), CScanTask::processCallback(), and CQTaskThread::run().
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Perform necessary cleanup procedures
Reimplemented in CCrossSectionTask, CSteadyStateTask, CTrajectoryTask, CTSSATask, CMCATask, CLyapTask, CScanTask, CLNATask, CSensTask, and CMoietiesTask.
Definition at line 277 of file CCopasiTask.cpp.
References CCopasiProblem::getModel(), mpInitialState, mpProblem, mUpdateModel, CCopasiProblem::restore(), setCallBack(), CModel::setInitialState(), and CModel::updateInitialValues().
Referenced by TaskWidget::finishTask(), CLNATask::restore(), CSensMethod::restore(), CScanTask::restore(), CLyapTask::restore(), CMCATask::restore(), COptProblem::restore(), CTrajectoryTask::restore(), CTSSATask::restore(), CSteadyStateTask::restore(), and CCrossSectionTask::restore().
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Introduce an additional separator into the output
const | Activity & activity |
Definition at line 362 of file CCopasiTask.cpp.
References COutputInterface::AFTER, COutputInterface::BEFORE, COutputInterface::DURING, mDoOutput, mpOutputHandler, OUTPUT_AFTER, OUTPUT_BEFORE, and COutputHandler::separate().
Referenced by CScanTask::outputSeparatorCallback().
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Set the call back of the task
CProcessReport | * pCallBack |
Reimplemented in CEFMTask, COptTask, COscillationTask, CFitTask, and CMoietiesTask.
Definition at line 190 of file CCopasiTask.cpp.
References mpCallBack.
Referenced by TaskWidget::commonAfterRunTask(), TaskWidget::commonBeforeRunTask(), CNewtonMethod::doIntegration(), CSensMethod::initialize(), CScanTask::initSubtask(), CSensMethod::process(), CLNATask::process(), CScanTask::process(), CMCATask::process(), restore(), CMoietiesTask::setCallBack(), CFitTask::setCallBack(), COscillationTask::setCallBack(), CEFMTask::setCallBack(), and COptTask::setCallBack().
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Set the method type applied to solve the task
const | CCopasiMethod::SubType & type |
Reimplemented in CCrossSectionTask, CLyapTask, CTrajectoryTask, CTSSATask, CEFMTask, COptTask, COscillationTask, CMoietiesTask, and CFitTask.
Definition at line 301 of file CCopasiTask.cpp.
Referenced by CQEFMWidget::createMethod(), CQTaskMethodWidget::saveMethod(), and CCopasiXMLParser::MethodElement::start().
void CCopasiTask::setScheduled | ( | const bool & | scheduled | ) |
Set whether the task is scheduled
const | bool & scheduled |
Definition at line 182 of file CCopasiTask.cpp.
References mScheduled.
Referenced by SEDMLImporter::importTasks(), TaskWidget::saveCommon(), CCopasiXMLParser::TaskElement::start(), test000087::test_simulate_reaction_flux_reference_1(), and SEDMLImporter::updateCopasiTaskForSimulation().
Set the type of the task
CCopasiTask::Type | & type |
Definition at line 178 of file CCopasiTask.cpp.
References mType.
void CCopasiTask::setUpdateModel | ( | const bool & | updateModel | ) |
Set whether the task must update the model
const | bool & updateModel |
Definition at line 186 of file CCopasiTask.cpp.
References mUpdateModel.
Referenced by CFitProblem::initialize(), CSensMethod::initialize(), CFitProblem::restore(), CSensMethod::restore(), TaskWidget::saveCommon(), CQSteadyStateResult::slotUpdateModel(), and CCopasiXMLParser::TaskElement::start().
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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 in CSteadyStateTask, CTSSATask, CMCATask, CLNATask, and CSensTask.
Definition at line 347 of file CCopasiTask.h.
Referenced by CQSimpleSelectionTree::populateTree().
std::string CCopasiTask::Error |
Definition at line 372 of file CCopasiTask.h.
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The description of the task.
Definition at line 207 of file CCopasiTask.h.
Referenced by getDescription().
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Definition at line 463 of file CCopasiTask.h.
Referenced by getOutputMode(), initialize(), output(), and separate().
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The key of the task
Definition at line 202 of file CCopasiTask.h.
Referenced by getKey(), and ~CCopasiTask().
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Definition at line 465 of file CCopasiTask.h.
Referenced by initialize(), initObjects(), and output().
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progress bar handler
Definition at line 249 of file CCopasiTask.h.
Referenced by CCrossSectionTask::eventCallBack(), CCrossSectionTask::finish(), getCallBack(), CLNATask::initialize(), CMCATask::initialize(), initialize(), CLyapTask::methodCallback(), CSensTask::process(), CLNATask::process(), CScanTask::process(), CLyapTask::process(), CMCATask::process(), CTrajectoryTask::process(), CTSSATask::process(), CSteadyStateTask::process(), CCrossSectionTask::process(), CScanTask::processCallback(), CTrajectoryTask::processStep(), CCrossSectionTask::processStep(), setCallBack(), and CSensTask::updateMatrices().
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The state of the model before execution of the task. If mUpdateModel is false this state is restored.
Definition at line 229 of file CCopasiTask.h.
Referenced by initialize(), restore(), and ~CCopasiTask().
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The method used to solve the problem.
Definition at line 239 of file CCopasiTask.h.
Referenced by CCrossSectionTask::CCrossSectionTask(), CEFMTask::CEFMTask(), CFitTask::CFitTask(), CLNATask::CLNATask(), CLyapTask::CLyapTask(), CMCATask::CMCATask(), CMoietiesTask::CMoietiesTask(), COptTask::COptTask(), COscillationTask::COscillationTask(), CScanTask::CScanTask(), CSensTask::CSensTask(), CSteadyStateTask::CSteadyStateTask(), CTrajectoryTask::CTrajectoryTask(), CTSSATask::CTSSATask(), CEFMTask::getFluxModeDescription(), getMethod(), CEFMTask::getReactionEquation(), CMoietiesTask::initialize(), COscillationTask::initialize(), CLNATask::initialize(), CEFMTask::initialize(), COptTask::initialize(), CScanTask::initialize(), CLyapTask::initialize(), CMCATask::initialize(), CTSSATask::initialize(), CTrajectoryTask::initialize(), CSteadyStateTask::initialize(), CCrossSectionTask::initialize(), initialize(), CLNATask::load(), CMCATask::load(), CTrajectoryTask::load(), CSteadyStateTask::load(), CLNATask::printResult(), CMCATask::printResult(), CMoietiesTask::process(), CFitTask::process(), CSensTask::process(), COscillationTask::process(), CLNATask::process(), COptTask::process(), CEFMTask::process(), CScanTask::process(), CMCATask::process(), CSteadyStateTask::process(), CSensTask::restore(), CMoietiesTask::setCallBack(), CFitTask::setCallBack(), COscillationTask::setCallBack(), COptTask::setCallBack(), CEFMTask::setCallBack(), CFitTask::setMethodType(), CMoietiesTask::setMethodType(), COscillationTask::setMethodType(), COptTask::setMethodType(), CEFMTask::setMethodType(), CTSSATask::setMethodType(), CTrajectoryTask::setMethodType(), CLyapTask::setMethodType(), CCrossSectionTask::setMethodType(), CSensTask::updateMatrices(), CLNATask::updateMatrices(), CMCATask::updateMatrices(), CTSSATask::updateMatrices(), and ~CCopasiTask().
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Definition at line 464 of file CCopasiTask.h.
Referenced by getOutputHandler(), initialize(), output(), CMoietiesTask::process(), and separate().
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The problem of the task
Definition at line 234 of file CCopasiTask.h.
Referenced by CCrossSectionTask::CCrossSectionTask(), CEFMTask::CEFMTask(), CFitTask::CFitTask(), CLNATask::CLNATask(), CLyapTask::CLyapTask(), CMCATask::CMCATask(), CMoietiesTask::CMoietiesTask(), COptTask::COptTask(), COscillationTask::COscillationTask(), CScanTask::CScanTask(), CSensTask::CSensTask(), CSteadyStateTask::CSteadyStateTask(), CTrajectoryTask::CTrajectoryTask(), CTSSATask::CTSSATask(), CCrossSectionTask::eventCallBack(), CFitTask::fixBuild55(), CScanTask::fixBuild81(), CEFMTask::getFluxModeDescription(), CEFMTask::getFluxModes(), CEFMTask::getNetReactionData(), getProblem(), CEFMTask::getReactionEquation(), CEFMTask::getSpeciesChanges(), CMoietiesTask::initialize(), COscillationTask::initialize(), CLNATask::initialize(), CEFMTask::initialize(), COptTask::initialize(), CScanTask::initialize(), CLyapTask::initialize(), CMCATask::initialize(), CTSSATask::initialize(), CTrajectoryTask::initialize(), CSteadyStateTask::initialize(), CCrossSectionTask::initialize(), initialize(), CScanTask::initSubtask(), CLNATask::load(), CMCATask::load(), CTrajectoryTask::load(), CSteadyStateTask::load(), operator<<(), CLNATask::printResult(), CMCATask::printResult(), CFitTask::process(), CSensTask::process(), COscillationTask::process(), CLNATask::process(), COptTask::process(), CScanTask::process(), CMCATask::process(), CSteadyStateTask::process(), CMoietiesTask::restore(), CLNATask::restore(), CLyapTask::restore(), CMCATask::restore(), CTrajectoryTask::restore(), CTSSATask::restore(), CSteadyStateTask::restore(), CCrossSectionTask::restore(), restore(), CMoietiesTask::setCallBack(), CFitTask::setCallBack(), COscillationTask::setCallBack(), COptTask::setCallBack(), CEFMTask::setCallBack(), CSteadyStateTask::setInitialState(), CSensTask::updateMatrices(), CLNATask::updateMatrices(), CMCATask::updateMatrices(), CTSSATask::updateMatrices(), CSteadyStateTask::updateMatrices(), and ~CCopasiTask().
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Pointer to group of sliders associated with the task.
Definition at line 254 of file CCopasiTask.h.
Referenced by getSliders(), and ~CCopasiTask().
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The report that belongs to this specific task
Definition at line 244 of file CCopasiTask.h.
Referenced by getReport(), CLNATask::initialize(), CScanTask::initialize(), CMCATask::initialize(), initialize(), and CSensTask::process().
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Tells whether the task is scheduled for execution
Definition at line 217 of file CCopasiTask.h.
Referenced by isScheduled(), CLNATask::load(), CMCATask::load(), CTrajectoryTask::load(), CSteadyStateTask::load(), and setScheduled().
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The type of the task
Definition at line 197 of file CCopasiTask.h.
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Tells whether the task shall update the model with the result. The restore method must act accordingly.
Definition at line 223 of file CCopasiTask.h.
Referenced by isUpdateModel(), CSensTask::restore(), CLyapTask::restore(), CTrajectoryTask::restore(), CTSSATask::restore(), CSteadyStateTask::restore(), CCrossSectionTask::restore(), restore(), and setUpdateModel().
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String literals for the GUI to display type names of tasks known to COPASI.
CCopasiTask class. This class is used to describe a task in COPASI. This class is intended to be used as the parent class for all tasks within COPASI.
Created for COPASI by Stefan Hoops 2003
Definition at line 67 of file CCopasiTask.h.
Referenced by CCopasiDataModel::addDefaultReports(), CCopasiDataModel::addDefaultTasks(), CCopasiDataModel::addReport(), CQReportDefinition::CQReportDefinition(), CQOptimizationWidget::init(), CScanTask::initSubtask(), CQOptimizationWidget::loadTask(), and CQOptimizationWidget::saveTask().
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The methods which can be selected for performing this task.
Definition at line 77 of file CCopasiTask.h.
std::string CCopasiTask::Warning |
Definition at line 373 of file CCopasiTask.h.
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XML type names of tasks known to COPASI.
Definition at line 72 of file CCopasiTask.h.
Referenced by CCopasiXML::saveReportList(), CCopasiXML::saveTaskList(), CCopasiXMLParser::TaskElement::start(), and CCopasiXMLParser::ReportElement::start().