COPASI API
4.16.103
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#include <CTrajectoryTask.h>
Public Member Functions | |
virtual CCopasiMethod * | createMethod (const int &type) const |
CTrajectoryTask (const CCopasiContainer *pParent=NULL) | |
CTrajectoryTask (const CTrajectoryTask &src, const CCopasiContainer *pParent=NULL) | |
CState * | getState () |
const CTimeSeries & | getTimeSeries () const |
virtual bool | initialize (const OutputFlag &of, COutputHandler *pOutputHandler, std::ostream *pOstream) |
void | load (CReadConfig &configBuffer) |
virtual bool | process (const bool &useInitialValues) |
void | processStart (const bool &useInitialValues) |
bool | processStep (const C_FLOAT64 &nextTime) |
virtual bool | restore () |
virtual bool | setMethodType (const int &type) |
~CTrajectoryTask () | |
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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 () |
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 |
const bool & | isScheduled () const |
const bool & | isUpdateModel () const |
virtual void | output (const COutputInterface::Activity &activity) |
virtual void | separate (const COutputInterface::Activity &activity) |
virtual bool | setCallBack (CProcessReport *pCallBack) |
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 Attributes | |
static const unsigned int | ValidMethods [] |
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static const std::string | TypeName [] |
static const unsigned int | ValidMethods [] |
static const char * | XMLType [] |
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static const std::vector < CCopasiContainer * > | EmptyList |
Private Member Functions | |
void | cleanup () |
Private Attributes | |
C_FLOAT64 | mOutputStartTime |
CState * | mpCurrentState |
const C_FLOAT64 * | mpCurrentTime |
bool(* | mpLess )(const C_FLOAT64 &, const C_FLOAT64 &) |
bool(* | mpLessOrEqual )(const C_FLOAT64 &, const C_FLOAT64 &) |
CTrajectoryMethod * | mpTrajectoryMethod |
CTrajectoryProblem * | mpTrajectoryProblem |
CTimeSeries | mTimeSeries |
bool | mTimeSeriesRequested |
bool | mUpdateMoieties |
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_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 |
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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) |
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std::string | Error |
std::string | Warning |
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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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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 |
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static CRenameHandler * | smpRenameHandler = NULL |
Definition at line 37 of file CTrajectoryTask.h.
CTrajectoryTask::CTrajectoryTask | ( | const CCopasiContainer * | pParent = NULL | ) |
Default constructor
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 73 of file CTrajectoryTask.cpp.
References CCopasiContainer::add(), createMethod(), CCopasiMethod::deterministic, CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, mUpdateMoieties, and CCopasiParameter::Value::pBOOL.
CTrajectoryTask::CTrajectoryTask | ( | const CTrajectoryTask & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor
const | CTrajectoryTask & src |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 98 of file CTrajectoryTask.cpp.
References CCopasiContainer::add(), createMethod(), CCopasiParameterGroup::elevateChildren(), CCopasiMethod::getSubType(), CCopasiParameter::getValue(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, mUpdateMoieties, and CCopasiParameter::Value::pBOOL.
CTrajectoryTask::~CTrajectoryTask | ( | ) |
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Definition at line 135 of file CTrajectoryTask.cpp.
References mpCurrentState, and pdelete.
Referenced by ~CTrajectoryTask().
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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 from CCopasiTask.
Definition at line 537 of file CTrajectoryTask.cpp.
References CTrajectoryMethod::createMethod().
Referenced by CTrajectoryTask(), and setMethodType().
CState * CTrajectoryTask::getState | ( | ) |
Retrieves a pointer to current state of the integration.
Definition at line 544 of file CTrajectoryTask.cpp.
References mpCurrentState.
Referenced by CNewtonMethod::doIntegration().
const CTimeSeries & CTrajectoryTask::getTimeSeries | ( | ) | const |
gets a reference to the time series
Definition at line 547 of file CTrajectoryTask.cpp.
References mTimeSeries.
Referenced by CQGLNetworkPainter::createDataSets(), QTimeCourseAnimation::getScales(), getTimeSeriesFromTask(), and QTimeCourseAnimation::initialize().
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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.
Definition at line 161 of file CTrajectoryTask.cpp.
References COutputHandler::addInterface(), CTimeSeries::allocate(), CTimeSeries::clear(), CTrajectoryProblem::getContinueSimultaneousEvents(), CModel::getMathModel(), CCopasiProblem::getModel(), CCopasiParameterGroup::getParameter(), CMathModel::getProcessQueue(), CModel::getState(), CTrajectoryProblem::getStepNumber(), CState::getTime(), CCopasiParameter::getValue(), CCopasiTask::initialize(), CCopasiMethod::isValidProblem(), mpCurrentState, mpCurrentTime, CCopasiTask::mpMethod, CCopasiTask::mpProblem, mpTrajectoryMethod, mpTrajectoryProblem, mTimeSeries, mTimeSeriesRequested, mUpdateMoieties, CCopasiParameter::Value::pBOOL, pdelete, CProcessQueue::setContinueSimultaneousEvents(), CTrajectoryMethod::setProblem(), CCopasiTask::TIME_SERIES, and CTrajectoryProblem::timeSeriesRequested().
Referenced by CFitProblem::initialize(), CNewtonMethod::initialize(), and test000087::test_simulate_reaction_flux_reference_1().
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. |
Definition at line 140 of file CTrajectoryTask.cpp.
References CCopasiContainer::add(), CTrajectoryMethod::createMethod(), CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), CReadConfig::getVariable(), CReadConfig::LOOP, CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiTask::mScheduled, mUpdateMoieties, CCopasiParameter::Value::pBOOL, and pdelete.
Referenced by CCopasiDataModel::loadModel().
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Process the task with or without initializing to the initial state.
const | bool & useInitialValues |
Reimplemented from CCopasiTask.
Definition at line 212 of file CTrajectoryTask.cpp.
References CProcessReport::addItem(), COutputInterface::AFTER, COutputInterface::BEFORE, bl(), ble(), C_FLOAT64, C_INT32, COutputInterface::DURING, CCopasiMessage::ERROR, CCopasiMessage::EXCEPTION, CProcessReport::finishItem(), fl(), fle(), CTrajectoryProblem::getDuration(), CCopasiException::getMessage(), CCopasiProblem::getModel(), CTrajectoryProblem::getOutputStartTime(), CTrajectoryProblem::getStepSize(), MCTrajectoryMethod, MCTrajectoryProblem, min, mOutputStartTime, CCopasiTask::mpCallBack, mpCurrentState, mpCurrentTime, mpLess, mpLessOrEqual, mpTrajectoryProblem, mUpdateMoieties, CCopasiTask::output(), processStart(), processStep(), CProcessReport::progressItem(), CProcessReport::setName(), CModel::setState(), and CModel::updateSimulatedValues().
Referenced by CNewtonMethod::doIntegration(), and test000087::test_simulate_reaction_flux_reference_1().
void CTrajectoryTask::processStart | ( | const bool & | useInitialValues | ) |
Starts the process of integration by calling CTrajectoryMethod::start
const | bool & useInitialValues |
Definition at line 351 of file CTrajectoryTask.cpp.
References CModel::applyInitialValues(), CCopasiProblem::getModel(), CModel::getState(), mpCurrentState, mpTrajectoryMethod, mpTrajectoryProblem, CTrajectoryMethod::setCurrentState(), and CTrajectoryMethod::start().
Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), and process().
bool CTrajectoryTask::processStep | ( | const C_FLOAT64 & | nextTime | ) |
Integrates one step
const | C_FLOAT64 & nextTime |
Definition at line 364 of file CTrajectoryTask.cpp.
References C_FLOAT64, COutputInterface::DURING, CCopasiMessage::EXCEPTION, CTrajectoryMethod::FAILURE, CCopasiProblem::getModel(), CTrajectoryProblem::getOutputEvent(), CModel::getProcessQueueExecutionTime(), CTrajectoryMethod::getRoots(), CModel::getState(), MCTrajectoryMethod, min, mOutputStartTime, CCopasiTask::mpCallBack, mpCurrentState, mpCurrentTime, mpLessOrEqual, mpTrajectoryMethod, mpTrajectoryProblem, mUpdateMoieties, CTrajectoryMethod::NORMAL, CCopasiTask::output(), CProcessReport::proceed(), CModel::processQueue(), CModel::processRoots(), CTrajectoryMethod::ROOT, CModel::setState(), CTrajectoryMethod::stateChanged(), CTrajectoryMethod::step(), and CModel::updateSimulatedValues().
Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), and process().
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Perform necessary cleanup procedures
Reimplemented from CCopasiTask.
Definition at line 497 of file CTrajectoryTask.cpp.
References CCopasiProblem::getModel(), CModel::getState(), mpCurrentState, CCopasiTask::mpProblem, CCopasiTask::mUpdateModel, mUpdateMoieties, CCopasiTask::restore(), CModel::setInitialState(), CModel::setState(), CModel::updateInitialValues(), and CModel::updateSimulatedValues().
Referenced by CFitProblem::restore(), and test000087::test_simulate_reaction_flux_reference_1().
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Set the method type applied to solve the task
const | CCopasiMethod::SubType & type |
Reimplemented from CCopasiTask.
Definition at line 514 of file CTrajectoryTask.cpp.
References CCopasiContainer::add(), createMethod(), CCopasiParameterGroup::getParameter(), CCopasiMethod::getSubType(), CCopasiParameter::getValue(), CCopasiTask::isValidMethod(), CCopasiTask::mpMethod, mUpdateMoieties, CCopasiParameter::Value::pBOOL, pdelete, and ValidMethods.
Referenced by CNewtonMethod::initialize(), test000087::test_simulate_reaction_flux_reference_1(), and SEDMLImporter::updateCopasiTaskForSimulation().
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A pointer to the time at which the output starts.
Definition at line 86 of file CTrajectoryTask.h.
Referenced by process(), and processStep().
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A pointer to the current state of the integration.
Definition at line 76 of file CTrajectoryTask.h.
Referenced by cleanup(), getState(), initialize(), process(), processStart(), processStep(), and restore().
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A pointer to the current time of the integration.
Definition at line 81 of file CTrajectoryTask.h.
Referenced by initialize(), process(), and processStep().
A pointer to less comparison
Definition at line 96 of file CTrajectoryTask.h.
Referenced by process().
A pointer to lessOrEqual comparison
Definition at line 91 of file CTrajectoryTask.h.
Referenced by process(), and processStep().
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A pointer to the trajectory method
Definition at line 66 of file CTrajectoryTask.h.
Referenced by initialize(), processStart(), and processStep().
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A pointer to the trajectory Problem
Definition at line 61 of file CTrajectoryTask.h.
Referenced by initialize(), process(), processStart(), and processStep().
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the time series (if requested)
Definition at line 56 of file CTrajectoryTask.h.
Referenced by getTimeSeries(), and initialize().
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whether the time series should be stored in mTimeSeries
Definition at line 51 of file CTrajectoryTask.h.
Referenced by initialize().
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Indicates whether we need to update moieties.
Definition at line 71 of file CTrajectoryTask.h.
Referenced by CTrajectoryTask(), initialize(), load(), process(), processStep(), restore(), and setMethodType().
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The methods which can be selected for performing this task.
Definition at line 44 of file CTrajectoryTask.h.
Referenced by CQTrajectoryWidget::init(), and setMethodType().