#include <CLyapMethod.h>

Inheritance diagram for CLyapMethod:

Collaboration diagram for CLyapMethod:

Public Member Functions
virtual bool	calculate ()=0

	CLyapMethod (const CLyapMethod &src, const CCopasiContainer *pParent=NULL)

virtual bool	isValidProblem (const CCopasiProblem *pProblem)

void	setProblem (CLyapProblem *problem)

virtual void	start (const CState *initialState)

virtual double	step (const double &deltaT)

	~CLyapMethod ()

Public Member Functions inherited from CCopasiMethod
	CCopasiMethod (const CCopasiMethod &src, const CCopasiContainer *pParent=NULL)

const CCopasiMethod::SubType &	getSubType () const

const CCopasiTask::Type &	getType () const

virtual void	load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH)

virtual void	print (std::ostream *ostream) const

virtual void	printResult (std::ostream *ostream) const

virtual bool	setCallBack (CProcessReport *pCallBack)

virtual	~CCopasiMethod ()

Public Member Functions inherited from CCopasiParameterGroup
bool	addGroup (const std::string &name)

bool	addParameter (const CCopasiParameter &parameter)

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 ()

virtual bool	elevateChildren ()

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 ()

Public Member Functions inherited from CCopasiParameter
	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 ()

Public Member Functions inherited from CCopasiContainer
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 ()

Public Member Functions inherited from CCopasiObject
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 ()

Public Member Functions inherited from CObjectInterface
	CObjectInterface ()

virtual	~CObjectInterface ()

Static Public Member Functions
static CLyapMethod *	createMethod (CCopasiMethod::SubType subType=CCopasiMethod::lyapWolf)

static bool	isValidSubType (const CCopasiMethod::SubType &subType)

Static Public Member Functions inherited from CCopasiObject
static std::vector< Refresh * >	buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet())

static void	setRenameHandler (CRenameHandler *rh)

Static Public Attributes
static const CLyapValidSubTypes	ValidSubTypes

Static Public Attributes inherited from CCopasiMethod
static const std::string	SubTypeName []

static const char *	XMLSubType []

Static Public Attributes inherited from CCopasiParameter
static const std::string	TypeName []

static const char *	XMLType []

Static Public Attributes inherited from CCopasiContainer
static const std::vector < CCopasiContainer * >	EmptyList

Protected Member Functions
	CLyapMethod (const CCopasiMethod::SubType &subType, const CCopasiContainer *pParent=NULL)

Protected Member Functions inherited from CCopasiMethod
	CCopasiMethod (const CCopasiTask::Type &taskType, const SubType &subType, const CCopasiContainer *pParent=NULL)

Protected Member Functions inherited from CCopasiParameterGroup
	CCopasiParameterGroup ()

Protected Member Functions inherited from CCopasiContainer
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 ()

Protected Member Functions inherited from CCopasiObject
	CCopasiObject ()

	CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0)

Protected Attributes
CLyapProblem *	mpProblem

Protected Attributes inherited from CCopasiMethod
CProcessReport *	mpCallBack

Protected Attributes inherited from CCopasiParameter
std::string	mKey

CCopasiObject *	mpValueReference

size_t	mSize

Value	mValue

Protected Attributes inherited from CCopasiContainer
objectMap	mObjects

Private Member Functions
	CLyapMethod ()

Additional Inherited Members
Public Types inherited from CCopasiMethod
enum	SubType { unset = 0, RandomSearch, RandomSearchMaster, SimulatedAnnealing, CoranaWalk, DifferentialEvolution, ScatterSearch, GeneticAlgorithm, EvolutionaryProgram, SteepestDescent, HybridGASA, GeneticAlgorithmSR, HookeJeeves, LevenbergMarquardt, NelderMead, SRES, Statistics, ParticleSwarm, Praxis, TruncatedNewton, Newton, deterministic, LSODAR, directMethod, stochastic, tauLeap, adaptiveSA, hybrid, hybridLSODA, hybridODE45, DsaLsodar, tssILDM, tssILDMModified, tssCSP, mcaMethodReder, scanMethod, lyapWolf, sensMethod, EFMAlgorithm, EFMBitPatternTreeAlgorithm, EFMBitPatternAlgorithm, Householder, crossSectionMethod, linearNoiseApproximation }

Public Types inherited from CCopasiParameterGroup
typedef parameterGroup::iterator	index_iterator

typedef CCopasiContainer::objectMap::iterator	name_iterator

typedef std::vector < CCopasiParameter * >	parameterGroup

Public Types inherited from CCopasiParameter
enum	Type { DOUBLE = 0, UDOUBLE, INT, UINT, BOOL, GROUP, STRING, CN, KEY, FILE, EXPRESSION, INVALID }

Public Types inherited from CCopasiContainer
typedef std::multimap < std::string, CCopasiObject * >	objectMap

Public Types inherited from CCopasiObject
typedef std::set< const CCopasiObject * >	DataObjectSet

typedef std::vector< Refresh * >	DataUpdateSequence

Public Types inherited from CObjectInterface
typedef std::set< const CObjectInterface * >	ObjectSet

typedef std::vector < CObjectInterface * >	UpdateSequence

Protected Types inherited from CCopasiObject
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 }

Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

Detailed Description

Definition at line 47 of file CLyapMethod.h.

Constructor & Destructor Documentation

CLyapMethod::CLyapMethod ( )

private

Default constructor.

CLyapMethod::CLyapMethod	(	const CCopasiMethod::SubType &	subType,
		const CCopasiContainer *	pParent = `NULL`
	)

protected

Default constructor.

Parameters

const	CCopasiMethod::SubType & subType
const	CCopasiContainer * pParent (default: NULL)

Default constructor.

Definition at line 79 of file CLyapMethod.cpp.

References CONSTRUCTOR_TRACE.

                                                            :
     CCopasiMethod(CCopasiTask::lyap, subType, pParent),
     //mpCurrentState(NULL),
     mpProblem(NULL)
 {CONSTRUCTOR_TRACE;}

CLyapMethod::CLyapMethod	(	const CLyapMethod &	src,
		const CCopasiContainer *	pParent = `NULL`
	)

Copy constructor.

Parameters

const CLyapMethod &	src
const	CCopasiContainer * pParent (default: NULL)

Copy constructor.

Parameters

const CLyapMethod & src

Definition at line 90 of file CLyapMethod.cpp.

References CONSTRUCTOR_TRACE.

                                                           :
     CCopasiMethod(src, pParent),
     //mpCurrentState(src.mpCurrentState),
     mpProblem(src.mpProblem)
 {CONSTRUCTOR_TRACE;}

CLyapMethod::~CLyapMethod ( )

Destructor.

Definition at line 100 of file CLyapMethod.cpp.

References DESTRUCTOR_TRACE.

101 {DESTRUCTOR_TRACE;}

DESTRUCTOR_TRACE

#define DESTRUCTOR_TRACE

Definition: copasi.h:206

Member Function Documentation

virtual bool CLyapMethod::calculate ( )

pure virtual

Implemented in CLyapWolfMethod.

Referenced by CLyapTask::process().

CLyapMethod * CLyapMethod::createMethod ( CCopasiMethod::SubType subType = CCopasiMethod::lyapWolf )

static

Create a trajectory method for a special problem. Note: the returned object has to be released after use with delete a problem is also passed so that the method has a chance to choose an appropriate simulation method.

Definition at line 58 of file CLyapMethod.cpp.

References fatalError, CCopasiMethod::lyapWolf, and CCopasiMethod::unset.

Referenced by CLyapTask::CLyapTask(), CQLyapWidget::createMethod(), and CLyapTask::createMethod().

 {
   CLyapMethod * pMethod = NULL;
 
   switch (subType)
     {
       case unset:
       case lyapWolf:
         pMethod = new CLyapWolfMethod();
         break;
 
       default:
         fatalError();
     }
 
   return pMethod;
 }

bool CLyapMethod::isValidProblem ( const CCopasiProblem * pProblem )

virtual

Check if the method is suitable for this problem

Returns: bool suitability of the method

Reimplemented from CCopasiMethod.

Reimplemented in CLyapWolfMethod.

Definition at line 140 of file CLyapMethod.cpp.

References C_INT32, CLyapProblem::divergenceRequested(), CCopasiMessage::ERROR, CLyapProblem::getExponentNumber(), CCopasiProblem::getModel(), CState::getNumIndependent(), CModel::getState(), CCopasiMethod::isValidProblem(), and MCLyap.

Referenced by CLyapWolfMethod::isValidProblem().

 {
   if (!CCopasiMethod::isValidProblem(pProblem)) return false;
 
   const CLyapProblem * pLP = dynamic_cast<const CLyapProblem *>(pProblem);
 
   if (!pLP)
     {
       //not a LyapProblem
       CCopasiMessage(CCopasiMessage::ERROR, MCLyap + 1);
       return false;
     }
 
   if ((!pLP->divergenceRequested()) && (pLP->getExponentNumber() < 1))
     {
       CCopasiMessage(CCopasiMessage::ERROR, MCLyap + 2);
       return false;
     }
 
   unsigned C_INT32 tmp = (unsigned C_INT32) pLP->getModel()->getState().getNumIndependent();
 
   if (pLP->getExponentNumber() > tmp)
     {
       //to few exponents
       CCopasiMessage(CCopasiMessage::ERROR, MCLyap + 3, tmp, tmp);
       return false;
     }
 
   return true;
 }

bool CLyapMethod::isValidSubType ( const CCopasiMethod::SubType & subType )

static

Checks whether the given sub type is a valid method

Parameters

const CCopasiMethod::SubType & subType

Returns: bool isValidSubType

Definition at line 48 of file CLyapMethod.cpp.

Referenced by CLyapTask::setMethodType().

 {
   size_t i, imax = CLyapMethod::ValidSubTypes.size();
 
   for (i = 0; i < imax; i++)
     if (CLyapMethod::ValidSubTypes[i] == subType) return true;
 
   return false;
 }

void CLyapMethod::setProblem ( CLyapProblem * problem )

Set a pointer to the current state. This method is used by CLyapTask::process() The results of the simulation are passed via this CState variable

Parameters

CState *	currentState Set a pointer to the problem. This method is used by CLyap
CLyapProblem *	problem

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

Parameters

CLyapProblem * problem

Definition at line 113 of file CLyapMethod.cpp.

References mpProblem.

Referenced by CLyapTask::initialize().

114 {mpProblem = problem;}

CLyapMethod::mpProblem

CLyapProblem * mpProblem

Definition: CLyapMethod.h:74

void CLyapMethod::start ( const CState * initialState )

virtual

This instructs the method to prepare for integration starting with the initialState given.

Parameters

const CState * initialState

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

Parameters

double &	deltaT
const CState *	initialState

Returns: "const double &" actualDeltaT

Definition at line 136 of file CLyapMethod.cpp.

137 {return;}

double CLyapMethod::step ( const double & deltaT )

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

const double & deltaT

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 CLyapWolfMethod.

Definition at line 124 of file CLyapMethod.cpp.

125 {return 0;}

Member Data Documentation

CLyapProblem* CLyapMethod::mpProblem

protected

A pointer to the current state. This is set from outside with the setState() method and never changed anywhere else. It�s used to report the results to the calling LyapTask A pointer to the trajectory problem.

Definition at line 74 of file CLyapMethod.h.

Referenced by CLyapWolfMethod::calculate(), CLyapWolfMethod::evalF(), setProblem(), and CLyapWolfMethod::start().

const CLyapValidSubTypes CLyapMethod::ValidSubTypes

static

A list of valid trajectory method types;

Definition at line 53 of file CLyapMethod.h.

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

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation