COPASI API  4.40.278
CTrajectoryTask Class Reference

#include <CTrajectoryTask.h>

Inheritance diagram for CTrajectoryTask:
[legend]

Public Member Functions

 CTrajectoryTask (const CDataContainer *pParent, const CTaskEnum::Task &type=CTaskEnum::Task::timeCourse)
 
 CTrajectoryTask (const CTrajectoryTask &src, const CDataContainer *pParent)
 
const CTimeSeries & getTimeSeries () const
 
virtual const CTaskEnum::Method * getValidMethods () const
 
virtual bool initialize (const OutputFlag &of, COutputHandler *pOutputHandler, std::ostream *pOstream)
 
void load (CReadConfig &configBuffer)
 
virtual bool process (const bool &useInitialValues)
 
bool processStart (const bool &useInitialValues)
 
bool processStep (const C_FLOAT64 &nextTime, const bool &final=false)
 
virtual bool processTrajectory (const bool &useInitialValues)
 
virtual bool processValues (const bool &useInitialValues)
 
 ~CTrajectoryTask ()
 
- Public Member Functions inherited from CCopasiTask
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 ()
 
- Public Member Functions inherited from CDataContainer
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 ()
 
- Public Member Functions inherited from CDataObject
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 ()
 
- Public Member Functions inherited from CObjectInterface
 CObjectInterface ()
 
 CObjectInterface (const CObjectInterface &src)
 
virtual ~CObjectInterface ()
 
- Public Member Functions inherited from CUndoObjectInterface
 CUndoObjectInterface ()
 
 CUndoObjectInterface (const CUndoObjectInterface &src)
 
bool generateUuid ()
 
const xg::Guid & getUuid () const
 
bool setUuid (const std::string &uuid)
 
bool setUuid (const xg::Guid &uuid)
 
virtual void updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject)
 
virtual ~CUndoObjectInterface ()
 

Static Public Attributes

static const CTaskEnum::Method ValidMethods []
 
- Static Public Attributes inherited from CDataContainer
static const CObjectInterface::ContainerList EmptyList
 

Protected Member Functions

virtual void signalMathContainerChanged ()
 
virtual void signalMethodChanged ()
 
- Protected Member Functions inherited from CCopasiTask
bool isTaskValid () const
 
- Protected Member Functions inherited from CDataContainer
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 ()
 
- Protected Member Functions inherited from CDataObject
 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)
 

Protected Attributes

CVectorCore< C_FLOAT64 > mContainerState
 
C_FLOAT64 mOutputStartTime
 
C_FLOAT64 * mpContainerStateTime
 
bool(* mpLess )(const C_FLOAT64 &, const C_FLOAT64 &)
 
bool(* mpLessOrEqual )(const C_FLOAT64 &, const C_FLOAT64 &)
 
CSteadyStateTask * mpSteadyState
 
CTrajectoryMethod * mpTrajectoryMethod
 
CTrajectoryProblem * mpTrajectoryProblem
 
CTimeSeries mTimeSeries
 
bool mTimeSeriesRequested
 
bool mUpdateMoieties
 
- Protected Attributes inherited from CCopasiTask
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
 
- Protected Attributes inherited from CDataContainer
objectMap mObjects
 
- Protected Attributes inherited from CDataObject
ObjectSet mPrerequisits
 
std::set< CDataContainer * > mReferences
 
- Protected Attributes inherited from CObjectInterface
CValidity mValidity
 

Private Member Functions

void cleanup ()
 
 CTrajectoryTask ()
 

Additional Inherited Members

- Public Types inherited from CCopasiTask
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
}
 
- Public Types inherited from CDataContainer
typedef CDataObjectMap objectMap
 
- Public Types inherited from CDataObject
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
}
 
- Public Types inherited from CObjectInterface
typedef std::vector< const CDataContainer * > ContainerList
 
typedef std::set< const CObjectInterface * > ObjectSet
 
- Static Public Member Functions inherited from CCopasiTask
static CCopasiTask * fromData (const CData &data, CUndoObjectInterface *pParent)
 
static bool isValidMethod (const CTaskEnum::Method &method, const CTaskEnum::Method *validMethods)
 
- Static Public Member Functions inherited from CDataContainer
static CDataContainer * fromData (const CData &data, CUndoObjectInterface *pParent)
 
- Static Public Member Functions inherited from CDataObject
static CDataObject * fromData (const CData &data, CUndoObjectInterface *pParent)
 
static void sanitizeObjectName (std::string &name)
 
- Static Public Member Functions inherited from CObjectInterface
static const CDataObject * DataObject (const CObjectInterface *pInterface)
 
static CObjectInterface * GetObjectFromCN (const ContainerList &listOfContainer, const CCommonName &objName)
 
- Static Public Member Functions inherited from CUndoObjectInterface
template<class CType >
static CType * fromData (const CData &, CUndoObjectInterface *)
 
- Public Attributes inherited from CCopasiTask
std::string Error
 
std::string Warning
 

Constructor & Destructor Documentation

◆ CTrajectoryTask() [1/3]

CTrajectoryTask::CTrajectoryTask ( )
private

Default constructor

◆ CTrajectoryTask() [2/3]

CTrajectoryTask::CTrajectoryTask ( const CDataContainer *  pParent,
const CTaskEnum::Task &  type = CTaskEnum::Task::timeCourse 
)

Specific constructor

Parameters
constCDataContainer * pParent
constCTaskEnum::Task & type (default: timeCourse)

References CMethodFactory::create(), CTaskEnum::deterministic, CCopasiTask::getType(), CCopasiTask::mpMethod, mUpdateMoieties, and signalMathContainerChanged().

◆ CTrajectoryTask() [3/3]

CTrajectoryTask::CTrajectoryTask ( const CTrajectoryTask &  src,
const CDataContainer *  pParent 
)

Copy constructor

Parameters
constCTrajectoryTask & src
constCDataContainer * pParent (default: NULL)

References CCopasiTask::mpMethod, mUpdateMoieties, and signalMathContainerChanged().

◆ ~CTrajectoryTask()

CTrajectoryTask::~CTrajectoryTask ( )

Destructor

References cleanup().

Member Function Documentation

◆ cleanup()

void CTrajectoryTask::cleanup ( )
private

cleanup()

Referenced by ~CTrajectoryTask().

◆ getTimeSeries()

const CTimeSeries & CTrajectoryTask::getTimeSeries ( ) const

gets a reference to the time series

Returns
time series

References mTimeSeries.

Referenced by CTrajectoryProblem::printResult().

◆ getValidMethods()

const CTaskEnum::Method * CTrajectoryTask::getValidMethods ( ) const
virtual

Retrieve the list of valid methods

Returns
const CTaskEnum::Method * pValidMethods

Reimplemented from CCopasiTask.

Reimplemented in CCrossSectionTask, and CAnalyticsTask.

References ValidMethods.

◆ initialize()

bool CTrajectoryTask::initialize ( const OutputFlag &  of,
COutputHandler *  pOutputHandler,
std::ostream *  pOstream 
)
virtual

◆ load()

void CTrajectoryTask::load ( CReadConfig &  configBuffer)

Loads parameters for this solver with data coming from a CReadConfig object. (CReadConfig object reads an input stream)

Parameters
configbufferreference to a CReadConfig object.

References CMethodFactory::create(), CTaskEnum::deterministic, CCopasiTask::getType(), CReadConfig::getVariable(), CReadConfig::LOOP, CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiTask::mScheduled, mUpdateMoieties, and pdelete.

Referenced by CDataModel::loadModel().

◆ process()

bool CTrajectoryTask::process ( const bool &  useInitialValues)
virtual

Process the task with or without initializing to the initial state.

Parameters
constbool & useInitialValues
Returns
bool success

Reimplemented from CCopasiTask.

Reimplemented in CCrossSectionTask, and CAnalyticsTask.

References CTrajectoryProblem::getUseValues(), mpTrajectoryProblem, processTrajectory(), and processValues().

Referenced by CNewtonMethod::doIntegration().

◆ processStart()

◆ processStep()

◆ processTrajectory()

◆ processValues()

◆ signalMathContainerChanged()

void CTrajectoryTask::signalMathContainerChanged ( )
protectedvirtual

◆ signalMethodChanged()

void CTrajectoryTask::signalMethodChanged ( )
protectedvirtual

Signal that the method has changed

Reimplemented from CCopasiTask.

References CCopasiTask::mpMethod, and mUpdateMoieties.

Member Data Documentation

◆ mContainerState

◆ mOutputStartTime

C_FLOAT64 CTrajectoryTask::mOutputStartTime
protected

◆ mpContainerStateTime

◆ mpLess

bool(* CTrajectoryTask::mpLess) (const C_FLOAT64 &, const C_FLOAT64 &)
protected

A pointer to less comparison

Referenced by processTrajectory(), and processValues().

◆ mpLessOrEqual

bool(* CTrajectoryTask::mpLessOrEqual) (const C_FLOAT64 &, const C_FLOAT64 &)
protected

A pointer to lessOrEqual comparison

Referenced by processStep(), processTrajectory(), and processValues().

◆ mpSteadyState

CSteadyStateTask* CTrajectoryTask::mpSteadyState
protected

Pointer to CSteadyStateTask. To be used in processStart() to start simulation in steady state

Referenced by initialize(), and processStart().

◆ mpTrajectoryMethod

CTrajectoryMethod* CTrajectoryTask::mpTrajectoryMethod
protected

A pointer to the trajectory method

Referenced by initialize(), processStart(), processStep(), processTrajectory(), and processValues().

◆ mpTrajectoryProblem

CTrajectoryProblem* CTrajectoryTask::mpTrajectoryProblem
protected

A pointer to the trajectory Problem

Referenced by initialize(), process(), processStart(), processStep(), processTrajectory(), and processValues().

◆ mTimeSeries

CTimeSeries CTrajectoryTask::mTimeSeries
protected

the time series (if requested)

Referenced by getTimeSeries(), and initialize().

◆ mTimeSeriesRequested

bool CTrajectoryTask::mTimeSeriesRequested
protected

whether the time series should be stored in mTimeSeries

Referenced by initialize().

◆ mUpdateMoieties

◆ ValidMethods


The documentation for this class was generated from the following files: