COPASI API  4.40.278
CTSSATask Class Reference

#include <CTSSATask.h>

Inheritance diagram for CTSSATask:
[legend]

Public Member Functions

 CTSSATask (const CDataContainer *pParent, const CTaskEnum::Task &type=CTaskEnum::Task::tssAnalysis)
 
 CTSSATask (const CTSSATask &src, const CDataContainer *pParent)
 
const CTimeSeriesgetTimeSeries () const
 
virtual const CTaskEnum::MethodgetValidMethods () const
 
virtual bool initialize (const OutputFlag &of, COutputHandler *pOutputHandler, std::ostream *pOstream)
 
virtual bool process (const bool &useInitialValues)
 
bool processStart (const bool &useInitialValues)
 
bool processStep (const C_FLOAT64 &nextTime)
 
virtual bool updateMatrices ()
 
virtual ~CTSSATask ()
 
- 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 CProcessReportLevelgetCallBack () const
 
const CDescriptiongetDescription () const
 
virtual const std::string & getKey () const
 
CMathContainergetMathContainer () const
 
CCopasiMethodgetMethod ()
 
const CCopasiMethodgetMethod () const
 
COutputHandlergetOutputHandler () const
 
const OutputFlaggetOutputMode () const
 
CCopasiProblemgetProblem ()
 
const CCopasiProblemgetProblem () const
 
CReportgetReport ()
 
const CReportgetReport () const
 
const CResultgetResult () const
 
CCopasiParameterGroupgetSliders ()
 
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 ~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 CObjectInterfacegetObject (const CCommonName &cn) const override
 
virtual objectMapgetObjects ()
 
virtual const objectMapgetObjects () const
 
virtual const std::string getUnits () const override
 
virtual const CDataObjectgetValueObject () const override
 
virtual CUndoObjectInterfaceinsert (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 CDataObjectgetDataObject () const override
 
CDataContainergetObjectAncestor (const std::string &type) const
 
CDataModelgetObjectDataModel () const
 
virtual std::string getObjectDisplayName () const override
 
const CObjectInterfacegetObjectFromCN (const CCommonName &cn) const
 
const std::string & getObjectName () const
 
CDataContainergetObjectParent () const
 
const std::string & getObjectType () const
 
virtual const CObjectInterface::ObjectSetgetPrerequisites () const override
 
virtual const CValiditygetValidity () 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
 

Private Member Functions

 CTSSATask ()
 

Private Attributes

CVectorCore< C_FLOAT64mContainerState
 
C_FLOAT64mpContainerStateTime
 
CTSSAMethodmpTSSAMethod
 
CTSSAProblemmpTSSAProblem
 
CTimeSeries mTimeSeries
 
bool mTimeSeriesRequested
 
bool mUpdateMoieties
 

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 CCopasiTaskfromData (const CData &data, CUndoObjectInterface *pParent)
 
static bool isValidMethod (const CTaskEnum::Method &method, const CTaskEnum::Method *validMethods)
 
- Static Public Member Functions inherited from CDataContainer
static CDataContainerfromData (const CData &data, CUndoObjectInterface *pParent)
 
- Static Public Member Functions inherited from CDataObject
static CDataObjectfromData (const CData &data, CUndoObjectInterface *pParent)
 
static void sanitizeObjectName (std::string &name)
 
- Static Public Member Functions inherited from CObjectInterface
static const CDataObjectDataObject (const CObjectInterface *pInterface)
 
static CObjectInterfaceGetObjectFromCN (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
 
- Protected Member Functions inherited from CCopasiTask
bool isTaskValid () const
 
virtual void signalMathContainerChanged ()
 
virtual void signalMethodChanged ()
 
- 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 inherited from CCopasiTask
CDescription mDescription
 
OutputFlag mDoOutput
 
bool mIgnoreProblemData
 
CVector< C_FLOAT64mInitialState
 
std::string mKey
 
unsigned C_INT32 mOutputCounter
 
CMathContainermpContainer
 
CCopasiMethodmpMethod
 
COutputHandlermpOutputHandler
 
CCopasiProblemmpProblem
 
CProcessReportLevel mProcessReport
 
CCopasiParameterGroupmpSliders
 
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
 

Constructor & Destructor Documentation

◆ CTSSATask() [1/3]

CTSSATask::CTSSATask ( )
private

Default constructor

◆ CTSSATask() [2/3]

CTSSATask::CTSSATask ( const CDataContainer pParent,
const CTaskEnum::Task type = CTaskEnum::Task::tssAnalysis 
)

◆ CTSSATask() [3/3]

CTSSATask::CTSSATask ( const CTSSATask src,
const CDataContainer pParent 
)

Copy constructor

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

References CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), CCopasiTask::mpMethod, and mUpdateMoieties.

◆ ~CTSSATask()

CTSSATask::~CTSSATask ( )
virtual

Destructor

Member Function Documentation

◆ getTimeSeries()

const CTimeSeries & CTSSATask::getTimeSeries ( ) const

gets a reference to the time series

Returns
time series

References mTimeSeries.

◆ getValidMethods()

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

Retrieve the list of valid methods

Returns
const CTaskEnum::Method * pValidMethods

Reimplemented from CCopasiTask.

References ValidMethods.

◆ initialize()

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

◆ process()

◆ processStart()

bool CTSSATask::processStart ( const bool &  useInitialValues)

Starts the process of integration by calling CTSSAMethod::start

Parameters
constbool & useInitialValues
Returns
bool success

References CMathContainer::applyInitialValues(), CMathContainer::getState(), CVectorCore< CType >::initialize(), mContainerState, CCopasiTask::mpContainer, mpTSSAMethod, mUpdateMoieties, and CTSSAMethod::start().

Referenced by process().

◆ processStep()

bool CTSSATask::processStep ( const C_FLOAT64 nextTime)

Integrates one step

Parameters
constC_FLOAT64 & nextTime
Returns
bool success;

References C_FLOAT64, CCopasiMessage::EXCEPTION, MCTSSAMethod, CCopasiTask::mpContainer, mpContainerStateTime, mpTSSAMethod, mUpdateMoieties, CTSSAMethod::step(), and CMathContainer::updateSimulatedValues().

Referenced by process().

◆ updateMatrices()

bool CTSSATask::updateMatrices ( )
virtual

Resizes result matrices and updates array annotations for a specific task. 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 from CCopasiTask.

References CTSSAMethod::initializeOutput(), CCopasiMethod::isValidProblem(), CCopasiTask::mpContainer, CCopasiTask::mpMethod, CCopasiTask::mpProblem, and CCopasiMethod::setMathContainer().

Member Data Documentation

◆ mContainerState

CVectorCore< C_FLOAT64 > CTSSATask::mContainerState
private

The current state of the integration.

Referenced by initialize(), and processStart().

◆ mpContainerStateTime

C_FLOAT64* CTSSATask::mpContainerStateTime
private

A pointer to the current time of the integration.

Referenced by initialize(), process(), and processStep().

◆ mpTSSAMethod

CTSSAMethod* CTSSATask::mpTSSAMethod
private

A pointer to the method

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

◆ mpTSSAProblem

CTSSAProblem* CTSSATask::mpTSSAProblem
private

A pointer to the Problem

Referenced by initialize(), and process().

◆ mTimeSeries

CTimeSeries CTSSATask::mTimeSeries
private

the time series (if requested)

Referenced by getTimeSeries(), and initialize().

◆ mTimeSeriesRequested

bool CTSSATask::mTimeSeriesRequested
private

whether the time series should be stored in mTimeSeries

Referenced by initialize().

◆ mUpdateMoieties

bool CTSSATask::mUpdateMoieties
private

Indicates whether we need to update moieties.

Referenced by CTSSATask(), initialize(), process(), processStart(), and processStep().

◆ ValidMethods


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