COPASI API
4.16.103
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#include <CTrajectoryProblem.h>
Public Member Functions | |
CTrajectoryProblem (const CCopasiContainer *pParent=NULL) | |
CTrajectoryProblem (const CTrajectoryProblem &src, const CCopasiContainer *pParent=NULL) | |
virtual bool | elevateChildren () |
const bool & | getContinueSimultaneousEvents () const |
const C_FLOAT64 & | getDuration () const |
const bool & | getOutputEvent () const |
const C_FLOAT64 & | getOutputStartTime () const |
const unsigned C_INT32 & | getStepNumber () const |
const C_FLOAT64 & | getStepSize () const |
void | load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::NEXT) |
void | setContinueSimultaneousEvents (const bool &continueSimultaneousEvents) |
void | setDuration (const C_FLOAT64 &duration) |
void | setOutputEvent (const bool &outputEvent) |
void | setOutputStartTime (const C_FLOAT64 &endTime) |
void | setStepNumber (const unsigned C_INT32 &stepNumber) |
void | setStepSize (const C_FLOAT64 &stepSize) |
void | setTimeSeriesRequested (bool flag) |
bool | timeSeriesRequested () const |
~CTrajectoryProblem () | |
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CCopasiProblem (const CCopasiProblem &src, const CCopasiContainer *pParent=NULL) | |
CModel * | getModel () const |
const CCopasiTask::Type & | getType () const |
virtual bool | initialize () |
virtual void | print (std::ostream *ostream) const |
virtual void | printResult (std::ostream *ostream) const |
virtual bool | restore (const bool &updateModel) |
virtual bool | setCallBack (CProcessReport *pCallBack) |
virtual bool | setModel (CModel *pModel) |
virtual | ~CCopasiProblem () |
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bool | addGroup (const std::string &name) |
bool | addParameter (const CCopasiParameter ¶meter) |
bool | addParameter (const std::string &name, const CCopasiParameter::Type type) |
template<class CType > | |
bool | addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value) |
void | addParameter (CCopasiParameter *pParameter) |
CCopasiParameterGroup * | assertGroup (const std::string &name) |
template<class CType > | |
CCopasiParameter * | assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue) |
index_iterator | beginIndex () const |
name_iterator | beginName () const |
CCopasiParameterGroup (const CCopasiParameterGroup &src, const CCopasiContainer *pParent=NULL) | |
CCopasiParameterGroup (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &objectType="ParameterGroup") | |
void | clear () |
index_iterator | endIndex () const |
name_iterator | endName () const |
CCopasiParameterGroup * | getGroup (const std::string &name) |
const CCopasiParameterGroup * | getGroup (const std::string &name) const |
CCopasiParameterGroup * | getGroup (const size_t &index) |
const CCopasiParameterGroup * | getGroup (const size_t &index) const |
size_t | getIndex (const std::string &name) const |
std::string | getKey (const std::string &name) const |
std::string | getKey (const size_t &index) const |
virtual const std::string & | getName (const size_t &index) const |
virtual const CObjectInterface * | getObject (const CCopasiObjectName &cn) const |
CCopasiParameter * | getParameter (const std::string &name) |
const CCopasiParameter * | getParameter (const std::string &name) const |
CCopasiParameter * | getParameter (const size_t &index) |
const CCopasiParameter * | getParameter (const size_t &index) const |
CCopasiParameter::Type | getType (const std::string &name) const |
CCopasiParameter::Type | getType (const size_t &index) const |
std::string | getUniqueParameterName (const CCopasiParameter *pParameter) const |
const CCopasiParameter::Value & | getValue (const std::string &name) const |
const CCopasiParameter::Value & | getValue (const size_t &index) const |
CCopasiParameter::Value & | getValue (const std::string &name) |
CCopasiParameter::Value & | getValue (const size_t &index) |
CCopasiParameterGroup & | operator= (const CCopasiParameterGroup &rhs) |
bool | removeParameter (const std::string &name) |
bool | removeParameter (const size_t &index) |
template<class CType > | |
bool | setValue (const std::string &name, const CType &value) |
template<class CType > | |
bool | setValue (const size_t &index, const CType &value) |
size_t | size () const |
bool | swap (const size_t &iFrom, const size_t &iTo) |
bool | swap (index_iterator &from, index_iterator &to) |
virtual | ~CCopasiParameterGroup () |
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CCopasiParameter (const CCopasiParameter &src, const CCopasiContainer *pParent=NULL) | |
CCopasiParameter (const std::string &name, const Type &type, const void *pValue=NULL, const CCopasiContainer *pParent=NULL, const std::string &objectType="Parameter") | |
virtual CCopasiObjectName | getCN () const |
virtual const std::string & | getKey () const |
virtual std::string | getObjectDisplayName (bool regular=true, bool richtext=false) const |
const CCopasiParameter::Type & | getType () const |
const Value & | getValue () const |
Value & | getValue () |
virtual void * | getValuePointer () const |
CCopasiObject * | getValueReference () const |
bool | isValidValue (const C_FLOAT64 &value) const |
bool | isValidValue (const C_INT32 &value) const |
bool | isValidValue (const unsigned C_INT32 &value) const |
bool | isValidValue (const bool &value) const |
bool | isValidValue (const std::string &value) const |
bool | isValidValue (const CCopasiObjectName &value) const |
bool | isValidValue (const std::vector< CCopasiParameter * > &value) const |
CCopasiParameter & | operator= (const CCopasiParameter &rhs) |
template<class CType > | |
bool | setValue (const CType &value) |
bool | setValue (const std::vector< CCopasiParameter * > &value) |
virtual | ~CCopasiParameter () |
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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 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 const DataObjectSet & | getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const |
CCopasiContainer * | getObjectAncestor (const std::string &type) const |
CCopasiDataModel * | getObjectDataModel () |
const CCopasiDataModel * | getObjectDataModel () 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 |
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 |
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 () |
Protected Attributes | |
bool * | mpContinueSimultaneousEvents |
C_FLOAT64 * | mpDuration |
bool * | mpOutputEvent |
C_FLOAT64 * | mpOutputStartTime |
unsigned C_INT32 * | mpStepNumber |
C_FLOAT64 * | mpStepSize |
bool * | mpTimeSeriesRequested |
bool | mStepNumberSetLast |
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CProcessReport * | mpCallBack |
CModel * | mpModel |
CReport * | mpReport |
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std::string | mKey |
CCopasiObject * | mpValueReference |
size_t | mSize |
Value | mValue |
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objectMap | mObjects |
Private Member Functions | |
void | initializeParameter () |
void | initObjects () |
bool | sync () |
Additional Inherited Members | |
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typedef parameterGroup::iterator | index_iterator |
typedef CCopasiContainer::objectMap::iterator | name_iterator |
typedef std::vector < CCopasiParameter * > | parameterGroup |
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enum | Type { DOUBLE = 0, UDOUBLE, INT, UINT, BOOL, GROUP, STRING, CN, KEY, FILE, EXPRESSION, INVALID } |
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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 std::vector< Refresh * > | buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet()) |
static void | setRenameHandler (CRenameHandler *rh) |
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static const std::string | TypeName [] |
static const char * | XMLType [] |
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static const std::vector < CCopasiContainer * > | EmptyList |
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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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CCopasiProblem (const CCopasiTask::Type &type, const CCopasiContainer *pParent=NULL) | |
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CCopasiParameterGroup () | |
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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 |
CTrajectoryProblem class. This class describes the trajectory problem, i.e., it allows to specify for example initial conditions and number of steps.
Created for Copasi by Stefan Hoops 2002
Definition at line 31 of file CTrajectoryProblem.h.
CTrajectoryProblem::CTrajectoryProblem | ( | const CCopasiContainer * | pParent = NULL | ) |
Default constructor.
const | CCopasiContainer * pParent (default: NULL) |
CTrajectoryProblem class. This class describes the trajectory problem, i.e., it allows to specify for example initial conditions and number of steps.
Created for COPASI by Stefan Hoops 2002 Default constructor.
Definition at line 37 of file CTrajectoryProblem.cpp.
References CONSTRUCTOR_TRACE, initializeParameter(), and initObjects().
CTrajectoryProblem::CTrajectoryProblem | ( | const CTrajectoryProblem & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor.
const | CTrajectoryProblem & src CCopasiContainer * pParent (default: NULL) |
Copy constructor.
const CTrajectoryProblem & | src |
Definition at line 57 of file CTrajectoryProblem.cpp.
References CONSTRUCTOR_TRACE, initializeParameter(), and initObjects().
CTrajectoryProblem::~CTrajectoryProblem | ( | ) |
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This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.
Reimplemented from CCopasiParameterGroup.
Definition at line 98 of file CTrajectoryProblem.cpp.
References C_FLOAT64, mpDuration, mpStepNumber, mpStepSize, and setDuration().
const bool & CTrajectoryProblem::getContinueSimultaneousEvents | ( | ) | const |
Retrieve whether to continue on simultaneous events.
Definition at line 210 of file CTrajectoryProblem.cpp.
References mpContinueSimultaneousEvents.
Referenced by CTrajectoryTask::initialize(), CQTrajectoryWidget::loadTask(), and CQTrajectoryWidget::saveTask().
const C_FLOAT64 & CTrajectoryProblem::getDuration | ( | ) | const |
Retrieve the end time.
Definition at line 178 of file CTrajectoryProblem.cpp.
References mpDuration.
Referenced by CODEExporterBM::exportTitleData(), CODEExporterXPPAUT::exportTitleData(), CTauLeapMethod::isValidProblem(), CHybridMethod::isValidProblem(), CHybridMethodODE45::isValidProblem(), CHybridMethodLSODA::isValidProblem(), CStochDirectMethod::isValidProblem(), CTrajAdaptiveSA::isValidProblem(), CStochMethod::isValidProblem(), CTrajectoryMethodDsaLsodar::isValidProblem(), CQTrajectoryWidget::loadTask(), CTrajectoryTask::process(), CCrossSectionTask::process(), and CQTrajectoryWidget::saveTask().
const bool & CTrajectoryProblem::getOutputEvent | ( | ) | const |
Retrieve whether to do additional output for events.
Definition at line 202 of file CTrajectoryProblem.cpp.
References mpOutputEvent.
Referenced by CQTrajectoryWidget::loadTask(), CTrajectoryTask::processStep(), and CQTrajectoryWidget::saveTask().
const C_FLOAT64 & CTrajectoryProblem::getOutputStartTime | ( | ) | const |
Retrieve the end time.
Definition at line 186 of file CTrajectoryProblem.cpp.
References mpOutputStartTime.
Referenced by CSEDMLExporter::createTimeCourseTask(), CODEExporter::exportExpression(), CQCrossSectionTaskWidget::loadTask(), CQTrajectoryWidget::loadTask(), CTrajectoryTask::process(), CCrossSectionTask::process(), CQTrajectoryWidget::saveTask(), and CQCrossSectionTaskWidget::updateValues().
const unsigned C_INT32 & CTrajectoryProblem::getStepNumber | ( | ) | const |
Retrieve the number of time steps the trajectory method should integrate.
Definition at line 138 of file CTrajectoryProblem.cpp.
References mpStepNumber.
Referenced by CSEDMLExporter::createTimeCourseTask(), CTrajectoryTask::initialize(), CQTrajectoryWidget::loadTask(), CQTrajectoryWidget::saveTask(), CQTrajectoryWidget::slotDuration(), and CQTrajectoryWidget::slotIntervalSize().
const C_FLOAT64 & CTrajectoryProblem::getStepSize | ( | ) | const |
Retrieve the size a integration step the trajectory method should do.
Definition at line 158 of file CTrajectoryProblem.cpp.
References mpStepSize.
Referenced by CSEDMLExporter::createTimeCourseTask(), CODEExporterBM::exportTitleData(), CODEExporterXPPAUT::exportTitleData(), CQTrajectoryWidget::loadTask(), CTrajectoryTask::process(), CQTrajectoryWidget::saveTask(), CQTrajectoryWidget::slotDuration(), CQTrajectoryWidget::slotIntervals(), and CQTrajectoryWidget::slotIntervalSize().
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Initialize the method parameter
Definition at line 80 of file CTrajectoryProblem.cpp.
References CCopasiParameterGroup::assertParameter(), CCopasiParameter::BOOL, C_FLOAT64, C_INT32, CCopasiParameter::DOUBLE, CCopasiParameter::getValue(), mpContinueSimultaneousEvents, mpDuration, mpOutputEvent, mpOutputStartTime, mpStepNumber, mpStepSize, mpTimeSeriesRequested, CCopasiParameter::Value::pBOOL, CCopasiParameter::Value::pDOUBLE, CCopasiParameter::Value::pUINT, and CCopasiParameter::UINT.
Referenced by CTrajectoryProblem().
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Definition at line 108 of file CTrajectoryProblem.cpp.
References C_INT32, CCopasiParameterGroup::getParameter(), CCopasiParameter::getValueReference(), setDuration(), setStepNumber(), setStepSize(), and CCopasiObject::setUpdateMethod().
Referenced by CTrajectoryProblem().
void CTrajectoryProblem::load | ( | CReadConfig & | configBuffer, |
CReadConfig::Mode | mode = CReadConfig::NEXT |
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Load a trajectory problem
CReadConfig & | configBuffer |
"CReadConfig::Mode | mode (Default: CReadConfig::NEXT) |
Load a trajectory problem
CReadConfig & | configBuffer |
Definition at line 219 of file CTrajectoryProblem.cpp.
References CCopasiDataModel::getModel(), CCopasiObject::getObjectDataModel(), CReadConfig::getVariable(), CReadConfig::getVersion(), CReadConfig::LOOP, mpDuration, CCopasiProblem::mpModel, mpStepNumber, mStepNumberSetLast, and sync().
void CTrajectoryProblem::setContinueSimultaneousEvents | ( | const bool & | continueSimultaneousEvents | ) |
Set whether to continue on simultaneous events
const | bool & continueSimultaneousEvents |
Definition at line 205 of file CTrajectoryProblem.cpp.
References mpContinueSimultaneousEvents.
Referenced by CQTrajectoryWidget::saveTask(), and SEDMLImporter::updateCopasiTaskForSimulation().
Set the end time.
const C_FLOAT64 & | duration bool success |
Definition at line 166 of file CTrajectoryProblem.cpp.
References mpDuration, and sync().
Referenced by CNewtonMethod::doIntegration(), elevateChildren(), initObjects(), CQTrajectoryWidget::saveTask(), CQTrajectoryWidget::slotDuration(), test000087::test_simulate_reaction_flux_reference_1(), and SEDMLImporter::updateCopasiTaskForSimulation().
void CTrajectoryProblem::setOutputEvent | ( | const bool & | outputEvent | ) |
Set whether to output events in addition to the normal steps
const | bool & outputEvent |
Definition at line 197 of file CTrajectoryProblem.cpp.
References mpOutputEvent.
Referenced by CQTrajectoryWidget::saveTask().
Set the end time.
const C_FLOAT64 & | endTime |
Definition at line 181 of file CTrajectoryProblem.cpp.
References mpOutputStartTime.
Referenced by CQCrossSectionTaskWidget::commitInput(), CQCrossSectionTaskWidget::saveTask(), CQTrajectoryWidget::saveTask(), CQCrossSectionTaskWidget::slotOutputDelay(), and SEDMLImporter::updateCopasiTaskForSimulation().
Set the number of time steps the trajectory method should integrate.
const unsigned C_INT32 & | stepNumber bool success |
Set the number of time steps the trajectory method should integrate.
const unsigned C_INT32 & | stepNumber |
Definition at line 125 of file CTrajectoryProblem.cpp.
References mpStepNumber, mStepNumberSetLast, and sync().
Referenced by CNewtonMethod::doIntegration(), CNewtonMethod::initialize(), initObjects(), CQTrajectoryWidget::saveTask(), CQTrajectoryWidget::slotIntervals(), test000087::test_simulate_reaction_flux_reference_1(), and SEDMLImporter::updateCopasiTaskForSimulation().
Set the size a integration step the trajectory method should do.
const C_FLOAT64 & | stepSize bool success |
Set the size a integration step the trajectory method should do.
const C_FLOAT64 & | stepSize |
Definition at line 145 of file CTrajectoryProblem.cpp.
References mpStepSize, mStepNumberSetLast, and sync().
Referenced by initObjects(), CQTrajectoryWidget::saveTask(), and CQTrajectoryWidget::slotIntervalSize().
void CTrajectoryProblem::setTimeSeriesRequested | ( | bool | flag | ) |
Definition at line 189 of file CTrajectoryProblem.cpp.
References mpTimeSeriesRequested.
Referenced by CQTrajectoryWidget::saveTask(), and test000087::test_simulate_reaction_flux_reference_1().
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This function synchronizes step size and number
This function synchronizes step size and number
Definition at line 241 of file CTrajectoryProblem.cpp.
References C_FLOAT64, C_INT32, MCTrajectoryProblem, min, mpDuration, mpStepNumber, mpStepSize, mStepNumberSetLast, and CCopasiMessage::WARNING.
Referenced by load(), setDuration(), setStepNumber(), and setStepSize().
bool CTrajectoryProblem::timeSeriesRequested | ( | ) | const |
Definition at line 194 of file CTrajectoryProblem.cpp.
References mpTimeSeriesRequested.
Referenced by CTrajectoryTask::initialize(), CQTrajectoryWidget::loadTask(), and CQTrajectoryWidget::saveTask().
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Pointer to parameter value indicating whether to continue when simultaneous events are encountered
Definition at line 206 of file CTrajectoryProblem.h.
Referenced by getContinueSimultaneousEvents(), initializeParameter(), and setContinueSimultaneousEvents().
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Pointer to parameter value for duration.
Definition at line 173 of file CTrajectoryProblem.h.
Referenced by elevateChildren(), getDuration(), CCrossSectionProblem::getTimeLimit(), initializeParameter(), load(), setDuration(), CCrossSectionProblem::setTimeLimit(), and sync().
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Pointer to parameter value indicating whether events should be added to the output
Definition at line 200 of file CTrajectoryProblem.h.
Referenced by getOutputEvent(), initializeParameter(), and setOutputEvent().
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Pointer to parameter value for output start time
Definition at line 194 of file CTrajectoryProblem.h.
Referenced by getOutputStartTime(), initializeParameter(), and setOutputStartTime().
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Pointer to parameter value for step number
Definition at line 183 of file CTrajectoryProblem.h.
Referenced by elevateChildren(), getStepNumber(), initializeParameter(), load(), setStepNumber(), and sync().
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Pointer to parameter value for step size.
Definition at line 178 of file CTrajectoryProblem.h.
Referenced by elevateChildren(), getStepSize(), initializeParameter(), setStepSize(), and sync().
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Pointer to parameter value indicating whether a time series needs to be stored in memory
Definition at line 189 of file CTrajectoryProblem.h.
Referenced by initializeParameter(), setTimeSeriesRequested(), and timeSeriesRequested().
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Indicate whether the step number or step size was set last.
Definition at line 211 of file CTrajectoryProblem.h.
Referenced by load(), setStepNumber(), setStepSize(), and sync().