COPASI API
4.40.278
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#include <CScanTask.h>
Public Member Functions | |
void | cleanup () |
CScanTask (const CDataContainer *pParent, const CTaskEnum::Task &type=CTaskEnum::Task::scan) | |
CScanTask (const CScanTask &src, const CDataContainer *pParent) | |
void | fixBuild81 () |
virtual const CTaskEnum::Method * | getValidMethods () const |
virtual bool | initialize (const OutputFlag &of, COutputHandler *pOutputHandler, std::ostream *pOstream) |
void | load (CReadConfig &configBuffer) |
bool | outputSeparatorCallback (bool isLast=false) |
virtual bool | process (const bool &useInitialValues) |
bool | processCallback () |
~CScanTask () | |
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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 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 () |
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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 () |
Protected Member Functions | |
bool | initSubtask (const OutputFlag &of, COutputHandler *pOutputHandler, std::ostream *pOstream) |
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bool | isTaskValid () const |
virtual void | signalMathContainerChanged () |
virtual void | signalMethodChanged () |
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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 | |
CScanTask () | |
Private Attributes | |
size_t | mhProgress |
bool | mOutputInSubtask |
unsigned C_INT32 | mProgress |
CCopasiTask * | mpSubTask |
bool | mUseInitialValues |
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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static const CObjectInterface::ContainerList | EmptyList |
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CDescription | mDescription |
OutputFlag | mDoOutput |
bool | mIgnoreProblemData |
CVector< C_FLOAT64 > | mInitialState |
std::string | mKey |
unsigned C_INT32 | mOutputCounter |
CMathContainer * | mpContainer |
CCopasiMethod * | mpMethod |
COutputHandler * | mpOutputHandler |
CCopasiProblem * | mpProblem |
CProcessReportLevel | mProcessReport |
CCopasiParameterGroup * | mpSliders |
CReport | mReport |
CResult | mResult |
bool | mScheduled |
CTaskEnum::Task | mType |
bool | mUpdateModel |
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objectMap | mObjects |
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ObjectSet | mPrerequisits |
std::set< CDataContainer * > | mReferences |
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CValidity | mValidity |
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private |
Default constructor
CScanTask::CScanTask | ( | const CDataContainer * | pParent, |
const CTaskEnum::Task & | type = CTaskEnum::Task::scan |
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Specific constructor
const | CDataContainer * pParent |
const | CTaskEnum::Task & type (default: scan) |
CScanTask class.
This class implements a scan task which is comprised of a of a problem and a method.
References CMethodFactory::create(), CCopasiTask::getType(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, and CTaskEnum::scanMethod.
CScanTask::CScanTask | ( | const CScanTask & | src, |
const CDataContainer * | pParent | ||
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Copy constructor
const | CScanTask & src |
References CCopasiTask::mpMethod, and CCopasiTask::mpProblem.
CScanTask::~CScanTask | ( | ) |
Destructor
References cleanup().
void CScanTask::cleanup | ( | ) |
Referenced by ~CScanTask().
void CScanTask::fixBuild81 | ( | ) |
Fix files written with Version 4.12.81 and earlier, which wrote the exp(mean) and exp(std. deviation) for normal random distributions in the scan task.
References CScanProblem::fixBuild81(), and CCopasiTask::mpProblem.
Referenced by CCopasiXML::fixBuild81().
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Retrieve the list of valid methods
Reimplemented from CCopasiTask.
References CTaskEnum::scanMethod, and CTaskEnum::UnsetMethod.
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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(), CCopasiMessage::COMMANDLINE, CDataObject::getObjectDataModel(), CDataObject::getObjectName(), CReport::getStream(), CCopasiTask::initialize(), initSubtask(), CCopasiTask::isTaskValid(), CCopasiMethod::isValidProblem(), MCCopasiTask, CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiTask::mReport, CReport::open(), and CCopasiTask::REPORT.
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Init the subtask
const | OutputFlag & of |
COutputHandler | * pOutputHandler |
References C_INT32, CTaskEnum::crosssection, fatalError, CScanProblem::getContinueFromCurrentState(), CDataObject::getObjectDataModel(), CDataModel::getTaskList(), CCopasiParameterGroup::getValue(), CCopasiTask::initialize(), CTaskEnum::lna, CTaskEnum::lyap, CTaskEnum::mca, mOutputInSubtask, CCopasiTask::mpContainer, CCopasiTask::mpProblem, mpSubTask, mUseInitialValues, CCopasiTask::NO_OUTPUT, CTaskEnum::optimization, CCopasiTask::OUTPUT_DURING, CTaskEnum::parameterFitting, CTaskEnum::sens, CCopasiTask::setCallBack(), CCopasiTask::setMathContainer(), CTaskEnum::steadyState, CTaskEnum::TaskName, CTaskEnum::timeCourse, CTaskEnum::timeSens, and CTaskEnum::tssAnalysis.
Referenced by initialize().
void CScanTask::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. |
bool CScanTask::outputSeparatorCallback | ( | bool | isLast = false | ) |
output separators if isLast==true this method has to decide if a separator should be generated dependent on mOutputInSubtask.
References COutputInterface::DURING, mOutputInSubtask, and CCopasiTask::separate().
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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, CMathContainer::applyInitialValues(), COutputInterface::BEFORE, C_INT32, CCrossSectionTask::createEvent(), fatalError, CScanMethod::getTotalNumberOfSteps(), CScanMethod::init(), mhProgress, CCopasiTask::mpContainer, CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiTask::mProcessReport, mProgress, mpSubTask, CCopasiTask::output(), CCrossSectionTask::removeEvent(), CScanMethod::scan(), CCopasiTask::setCallBack(), CProcessReportLevel::setName(), and CScanMethod::setProblem().
bool CScanTask::processCallback | ( | ) |
Do the subtask and the output
References COutputInterface::DURING, CCopasiTask::getProblem(), CCopasiTask::isUpdateModel(), mhProgress, mOutputInSubtask, CCopasiTask::mProcessReport, mProgress, mpSubTask, mUseInitialValues, CCopasiTask::output(), CCopasiTask::process(), CProcessReportLevel::progressItem(), and COptProblem::restore().
Referenced by CScanMethod::calculate().
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Handle to process item
Referenced by process(), and processCallback().
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Referenced by initSubtask(), outputSeparatorCallback(), and processCallback().
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Pointer to the output stream for reporting for progress bar
Referenced by process(), and processCallback().
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the subtask
Referenced by initSubtask(), process(), and processCallback().
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Referenced by initSubtask(), and processCallback().