COPASI API  4.40.278
CTrajectoryMethod Class Reference

#include <CTrajectoryMethod.h>

Inheritance diagram for CTrajectoryMethod:
[legend]

Public Types

enum  Status { FAILURE = -1 , NORMAL = 0 , ROOT = 1 }
 
- Public Types inherited from CCopasiParameterGroup
typedef CDataObjectMap::const_type_iterator< CCopasiParameterconst_name_iterator
 
typedef std::vector< CCopasiParameter * > elements
 
typedef elements::iterator index_iterator
 
typedef CDataObjectMap::type_iterator< CCopasiParametername_iterator
 
- Public Types inherited from CCopasiParameter
enum class  eUserInterfaceFlag { editable , basic , unsupported , __SIZE }
 
enum class  Type {
  DOUBLE = 0 , UDOUBLE , INT , UINT ,
  BOOL , GROUP , STRING , CN ,
  KEY , FILE , EXPRESSION , INVALID ,
  __SIZE
}
 
typedef CFlags< eUserInterfaceFlagUserInterfaceFlag
 
- 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
 

Public Member Functions

 CTrajectoryMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType=CTaskEnum::Task::timeCourse)
 
 CTrajectoryMethod (const CTrajectoryMethod &src, const CDataContainer *pParent)
 
const CVectorCore< C_INT > & getRoots () const
 
const bool & integrateReducedModel () const
 
virtual bool isValidProblem (const CCopasiProblem *pProblem)
 
void setProblem (CTrajectoryProblem *problem)
 
virtual void start ()
 
virtual void stateChange (const CMath::StateChange &change)
 
virtual Status step (const double &deltaT, const bool &final=false)
 
 ~CTrajectoryMethod ()
 
- Public Member Functions inherited from CCopasiMethod
 CCopasiMethod (const CCopasiMethod &src, const CDataContainer *pParent)
 
virtual void clearCallBack ()
 
const CProcessReportLevelgetCallBack () const
 
CMathContainergetMathContainer () const
 
const CTaskEnum::MethodgetSubType () const
 
const CTaskEnum::TaskgetType () const
 
virtual void load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH)
 
CCopasiMethodoperator= (const CCopasiMethod &rhs)
 
virtual void print (std::ostream *ostream) const
 
virtual void printResult (std::ostream *ostream) const
 
virtual bool setCallBack (CProcessReportLevel callBack)
 
void setMathContainer (CMathContainer *pContainer)
 
virtual ~CCopasiMethod ()
 
- Public Member Functions inherited from CCopasiParameterGroup
bool addGroup (const std::string &name)
 
void addParameter (CCopasiParameter *pParameter)
 
bool addParameter (const CCopasiParameter &parameter)
 
bool addParameter (const std::string &name, const CCopasiParameter::Type type, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)
 
template<class CType >
bool addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)
 
virtual bool applyData (const CData &data, CUndoData::CChangeSet &changes)
 
CCopasiParameterGroupassertGroup (const std::string &name, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)
 
template<class CType >
CType * assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)
 
index_iterator beginIndex () const
 
const_name_iterator beginName () const
 
 CCopasiParameterGroup (const CCopasiParameterGroup &src, const CDataContainer *pParent=NULL)
 
 CCopasiParameterGroup (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &objectType="ParameterGroup")
 
void clear ()
 
virtual void createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const
 
virtual bool elevateChildren ()
 
index_iterator endIndex () const
 
const_name_iterator endName () const
 
CCopasiParameterGroupgetElementTemplates ()
 
const CCopasiParameterGroupgetElementTemplates () const
 
CCopasiParameterGroupgetGroup (const size_t &index)
 
const CCopasiParameterGroupgetGroup (const size_t &index) const
 
CCopasiParameterGroupgetGroup (const std::string &name)
 
const CCopasiParameterGroupgetGroup (const std::string &name) const
 
virtual size_t getIndex (const CDataObject *pObject) const
 
size_t getIndex (const std::string &name) const
 
std::string getKey (const size_t &index) const
 
std::string getKey (const std::string &name) const
 
virtual const std::string & getName (const size_t &index) const
 
virtual const CObjectInterfacegetObject (const CCommonName &cn) const
 
CCopasiParametergetParameter (const size_t &index)
 
const CCopasiParametergetParameter (const size_t &index) const
 
CCopasiParametergetParameter (std::string name)
 
const CCopasiParametergetParameter (std::string name) const
 
CCopasiParameter::Type getType (const size_t &index) const
 
CCopasiParameter::Type getType (const std::string &name) const
 
std::string getUniqueParameterName (const CCopasiParameter *pParameter) const
 
template<class CType >
CType & getValue (const size_t &index)
 
template<class CType >
const CType & getValue (const size_t &index) const
 
template<class CType >
CType & getValue (const std::string &name)
 
template<class CType >
const CType & getValue (const std::string &name) const
 
bool haveTemplate () const
 
virtual CUndoObjectInterfaceinsert (const CData &data)
 
CCopasiParameterGroupoperator= (const CCopasiParameterGroup &rhs)
 
virtual bool remove (CDataObject *pObject)
 
bool removeParameter (CCopasiParameter *pParameter)
 
bool removeParameter (const size_t &index)
 
bool removeParameter (const std::string &name)
 
virtual void setUserInterfaceFlag (const UserInterfaceFlag &flag)
 
template<class CType >
bool setValue (const size_t &index, const CType &value)
 
template<class CType >
bool setValue (const std::string &name, const CType &value)
 
size_t size (const UserInterfaceFlag &require=UserInterfaceFlag::None, const UserInterfaceFlag &exclude=UserInterfaceFlag::None) const
 
bool swap (const size_t &iFrom, const size_t &iTo)
 
bool swap (index_iterator &from, index_iterator &to)
 
virtual CData toData () const
 
virtual void updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject)
 
virtual ~CCopasiParameterGroup ()
 
- Public Member Functions inherited from CCopasiParameter
 CCopasiParameter (const CCopasiParameter &src, const CDataContainer *pParent)
 
 CCopasiParameter (const std::string &name, const Type &type, const void *pValue=NULL, const CDataContainer *pParent=NO_PARENT, const std::string &objectType="Parameter")
 
virtual CCommonName getCN () const override
 
template<class CType >
const CType & getDefault () const
 
virtual const std::string & getKey () const override
 
virtual std::string getObjectDisplayName () const override
 
const CCopasiParameter::TypegetType () const
 
const UserInterfaceFlaggetUserInterfaceFlag () const
 
template<class CType >
std::vector< std::pair< CType, CType > > & getValidValues ()
 
template<class CType >
const std::vector< std::pair< CType, CType > > & getValidValues () const
 
void * getValidValuesPointer () const
 
template<class CType >
CType & getValue ()
 
template<class CType >
const CType & getValue () const
 
virtual void * getValuePointer () const override
 
CDataObjectgetValueReference () const
 
bool hasValidValues () const
 
bool isBasic () const
 
bool isDefault () const
 
bool isEditable () const
 
bool isUnsupported () const
 
bool isValidValue (const bool &value) const
 
bool isValidValue (const C_FLOAT64 &value) const
 
bool isValidValue (const C_INT32 &value) const
 
bool isValidValue (const CCommonName &value) const
 
template<class CType >
bool isValidValue (const CType &) const
 
bool isValidValue (const std::string &value) const
 
bool isValidValue (const std::vector< CCopasiParameter * > &value) const
 
bool isValidValue (const unsigned C_INT32 &value) const
 
CCopasiParameteroperator= (const CCopasiParameter &rhs)
 
template<class CType >
bool setDefault (const CType &defaultValue)
 
bool setDefault (const std::vector< CCopasiParameter * > &defaultValue)
 
virtual bool setObjectParent (const CDataContainer *pParent) override
 
template<class CType , class Enum >
bool setValidValues (const CEnumAnnotation< CType, Enum > &validValues)
 
template<class CType >
bool setValidValues (const std::vector< std::pair< CType, CType > > &validValues)
 
template<class CType >
bool setValue (const CType &value)
 
bool setValue (const std::vector< CCopasiParameter * > &value)
 
virtual ~CCopasiParameter ()
 
- 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 objectMapgetObjects ()
 
virtual const objectMapgetObjects () const
 
virtual const std::string getUnits () const override
 
virtual const CDataObjectgetValueObject () const override
 
void objectRenamed (CDataObject *pObject, const std::string &oldName)
 
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 const CDataObjectgetDataObject () const override
 
CDataContainergetObjectAncestor (const std::string &type) const
 
CDataModelgetObjectDataModel () const
 
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
 
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
 
void removeIssue (const CIssue &issue)
 
void removeReference (const CDataContainer *pReference)
 
bool setObjectName (const std::string &name)
 
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 ~CUndoObjectInterface ()
 

Protected Member Functions

void output (const bool &useMoieties)
 
virtual void signalMathContainerChanged ()
 
- Protected Member Functions inherited from CCopasiMethod
 CCopasiMethod (const CCopasiMethod &src)
 
 CCopasiMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType)
 
- Protected Member Functions inherited from CCopasiParameterGroup
 CCopasiParameterGroup ()
 
- Protected Member Functions inherited from CCopasiParameter
 CCopasiParameter (const CCopasiParameter &src)
 
- 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_FLOAT64mContainerState
 
C_FLOAT64mpContainerStateTime
 
CTrajectoryProblemmpProblem
 
const bool * mpReducedModel
 
CTrajectoryTaskmpTask
 
CVectorCore< C_INTmRootsFound
 
- Protected Attributes inherited from CCopasiMethod
CMathContainermpContainer
 
CProcessReportLevel mProcessReport
 
- Protected Attributes inherited from CCopasiParameter
std::string mKey
 
void * mpDefault
 
void * mpValidValues
 
void * mpValue
 
CDataObjectmpValueReference
 
UserInterfaceFlag mUserInterfaceFlag
 
- 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
 

Static Protected Attributes

static const bool ReducedModel
 

Private Member Functions

 CTrajectoryMethod ()
 

Additional Inherited Members

- Static Public Member Functions inherited from CCopasiParameter
static void allocateValidValues (const Type &type, void *&pValidValues)
 
static void allocateValue (const Type &type, void *&pValue)
 
static void assignValue (const Type &type, void *&pValue, const void *pNewValue)
 
static void deleteValidValues (const Type &type, void *&pValidValues)
 
static void deleteValue (const Type &type, void *&pValue)
 
static CCopasiParameterfromData (const CData &data, CUndoObjectInterface *pParent)
 
- 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 *)
 
- Static Public Attributes inherited from CCopasiParameter
static const CEnumAnnotation< std::string, TypeTypeName
 
static const CEnumAnnotation< std::string, TypeXMLType
 
- Static Public Attributes inherited from CDataContainer
static const CObjectInterface::ContainerList EmptyList
 

Member Enumeration Documentation

◆ Status

Enumeration value for the return value

Enumerator
FAILURE 
NORMAL 
ROOT 

Constructor & Destructor Documentation

◆ CTrajectoryMethod() [1/3]

CTrajectoryMethod::CTrajectoryMethod ( )
private

Default constructor.

◆ CTrajectoryMethod() [2/3]

CTrajectoryMethod::CTrajectoryMethod ( const CDataContainer pParent,
const CTaskEnum::Method methodType,
const CTaskEnum::Task taskType = CTaskEnum::Task::timeCourse 
)

Specific constructor

Parameters
constCDataContainer * pParent
constCTaskEnum::Method & methodType
constCTaskEnum::Task & taskType (default: timeCourse)

Default constructor.

References CDataObject::getObjectParent(), and mpTask.

◆ CTrajectoryMethod() [3/3]

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

Copy constructor.

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

Copy constructor.

Parameters
const CTrajectoryMethod &src

References CDataObject::getObjectParent(), and mpTask.

◆ ~CTrajectoryMethod()

CTrajectoryMethod::~CTrajectoryMethod ( )

Destructor.

References DESTRUCTOR_TRACE.

Member Function Documentation

◆ getRoots()

const CVectorCore< C_INT > & CTrajectoryMethod::getRoots ( ) const

Retrieve the roots.

Returns
const CVectorCore< C_INT > & roots

References mRootsFound.

Referenced by CTrajectoryTask::processStep().

◆ integrateReducedModel()

const bool & CTrajectoryMethod::integrateReducedModel ( ) const

Check whether to integrate the reduced model

Returns
const bool & integrateReducedModel

References mpReducedModel.

◆ isValidProblem()

◆ output()

◆ setProblem()

void CTrajectoryMethod::setProblem ( CTrajectoryProblem problem)

Set a pointer to the problem. This method is used by CTrajectory

Parameters
CTrajectoryProblem *problem

References mpProblem.

Referenced by CTrajectoryTask::initialize().

◆ signalMathContainerChanged()

void CTrajectoryMethod::signalMathContainerChanged ( )
protectedvirtual

◆ start()

◆ stateChange()

void CTrajectoryMethod::stateChange ( const CMath::StateChange change)
virtual

◆ step()

CTrajectoryMethod::Status CTrajectoryMethod::step ( const double &  deltaT,
const bool &  final = false 
)
virtual

This instructs the method to calculate a time step of deltaT starting with the current state, i.e., the result of the previous step. The new state (after deltaT) is expected in the current state. The return value is the actual timestep taken.

Parameters
constdouble & deltaT
constbool & final (default: false)
Returns
Status status

This instructs the method to calculate a a time step of deltaT starting with the current state, i.e., the result of the previous step. The new state (after deltaT) is expected in the current state. The return value is the actual timestep taken.

Parameters
const double &deltaT

Reimplemented in CTrajectoryMethodDsaLsodar, CTrajAdaptiveSA, CTauLeapMethod, CStochMethod, CStochDirectMethod, CStochasticRungeKuttaRI5, CRadau5Method, CLsodaMethod, CHybridMethodODE45, and CHybridMethod.

References FAILURE.

Referenced by CTrajectoryTask::processStep().

Member Data Documentation

◆ mContainerState

◆ mpContainerStateTime

C_FLOAT64* CTrajectoryMethod::mpContainerStateTime
protected

A pointer to the time value of the current state.

Referenced by CStochasticRungeKuttaRI5::buildStage1(), CStochasticRungeKuttaRI5::buildStage2(), CStochasticRungeKuttaRI5::buildStage3(), CStochasticRungeKuttaRI5::calculateStateVariables(), CTrajAdaptiveSA::doSingleSSAStep(), CHybridMethod::doSingleStep(), CHybridMethodODE45::doSingleStep(), CStochDirectMethod::doSingleStep(), CStochNextReactionMethod::doSingleStep(), CTrajAdaptiveSA::doSingleTauLeapStep(), CHybridMethodODE45::evalF(), CHybridNextReactionLSODAMethod::LSODA::evalF(), CLsodaMethod::evalF(), CLsodaMethod2::evalF(), CRadau5Method::evalF(), CTrajectoryMethodDsaLsodar::evalF(), CLsodaMethod::evalR(), CRadau5Method::evalR(), CHybridMethodODE45::evalR(), CLsodaMethod2::evalRoot(), CStochasticRungeKuttaRI5::evalRoot(), CHybridNextReactionLSODAMethod::LSODA::getTime(), CStochNextReactionMethod::initMethod(), CHybridMethodODE45::integrateDeterministicPart(), CStochasticRungeKuttaRI5::internalStep(), CRadau5Method::output(), CHybridMethod::partitionSystem(), CLsodaMethod2::peekAhead(), CLsodaMethod2::resetState(), CLsodaMethod::resetState(), CRadau5Method::resetState(), CStochDirectMethod::rootValue(), CLsodaMethod2::saveState(), CLsodaMethod::saveState(), CRadau5Method::saveState(), CHybridMethod::setupPriorityQueue(), signalMathContainerChanged(), CHybridMethodODE45::start(), CLsodaMethod::start(), CLsodaMethod2::start(), CRadau5Method::start(), CStochasticRungeKuttaRI5::start(), CStochDirectMethod::start(), CStochMethod::start(), CTrajAdaptiveSA::start(), start(), CLsodaMethod::stateChange(), CLsodaMethod2::stateChange(), CRadau5Method::stateChange(), CLsodaMethod2::step(), CHybridMethod::step(), CHybridMethodODE45::step(), CLsodaMethod::step(), CRadau5Method::step(), CStochDirectMethod::step(), CStochMethod::step(), CTauLeapMethod::step(), CTrajAdaptiveSA::step(), and CTrajectoryMethodDsaLsodar::step().

◆ mpProblem

◆ mpReducedModel

◆ mpTask

CTrajectoryTask* CTrajectoryMethod::mpTask
protected

The task calling the method

Referenced by CTrajectoryMethod(), and output().

◆ mRootsFound

◆ ReducedModel

const bool CTrajectoryMethod::ReducedModel
staticprotected

Default value whether indicating whether to integrate the reduced model initialized to false.

CTrajectoryMethod class. This class describes the interface to all integration methods. The various method like LSODA or Gillespie have to be derived from this class.

Created for COPASI by Stefan Hoops 2002


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