#include <CLyapProblem.h>

Inheritance diagram for CLyapProblem:

Collaboration diagram for CLyapProblem:

Public Member Functions
	CLyapProblem (const CCopasiContainer *pParent=NULL)

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

bool	divergenceRequested () const

virtual bool	elevateChildren ()

const unsigned C_INT32 &	getExponentNumber () const

const C_FLOAT64 &	getTransientTime () const

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

void	setDivergenceRequested (bool flag)

void	setExponentNumber (const unsigned C_INT32 &number)

void	setTransientTime (const C_FLOAT64 &endTime)

	~CLyapProblem ()

Public Member Functions inherited from CCopasiProblem
	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 bool	restore (const bool &updateModel)

virtual bool	setCallBack (CProcessReport *pCallBack)

virtual bool	setModel (CModel *pModel)

virtual	~CCopasiProblem ()

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 ()

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 ()

Private Member Functions
void	initializeParameter ()

Private Attributes
bool *	mpDivergenceRequested

unsigned C_INT32 *	mpExponentNumber

C_FLOAT64 *	mpTransientTime

Additional Inherited Members
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

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 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 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 }

Protected Member Functions inherited from CCopasiProblem
	CCopasiProblem (const CCopasiTask::Type &type, 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 inherited from CCopasiProblem
CProcessReport *	mpCallBack

CModel *	mpModel

CReport *	mpReport

Protected Attributes inherited from CCopasiParameter
std::string	mKey

CCopasiObject *	mpValueReference

size_t	mSize

Value	mValue

Protected Attributes inherited from CCopasiContainer
objectMap	mObjects

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

Detailed Description

CLyapProblem class.

Definition at line 25 of file CLyapProblem.h.

Constructor & Destructor Documentation

CLyapProblem::CLyapProblem ( const CCopasiContainer * pParent = NULL )

Default constructor.

Parameters

const CCopasiContainer * pParent (default: NULL)

CLyapProblem class. Default constructor.

Definition at line 35 of file CLyapProblem.cpp.

References CONSTRUCTOR_TRACE, and initializeParameter().

                                                           :
     CCopasiProblem(CCopasiTask::lyap, pParent),
     mpExponentNumber(NULL),
     //mpTimeSeriesRequested(NULL),
     mpDivergenceRequested(NULL),
     mpTransientTime(NULL)
 {
   initializeParameter();
   CONSTRUCTOR_TRACE;
 }

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

Copy constructor.

Parameters

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

Copy constructor.

Parameters

const CLyapProblem & src

Definition at line 50 of file CLyapProblem.cpp.

References CONSTRUCTOR_TRACE, and initializeParameter().

                                                             :
     CCopasiProblem(src, pParent),
     mpExponentNumber(NULL),
     //mpTimeSeriesRequested(NULL),
     mpDivergenceRequested(NULL),
     mpTransientTime(NULL)
 {
   initializeParameter();
   CONSTRUCTOR_TRACE;
 }

CLyapProblem::~CLyapProblem ( )

Destructor.

Definition at line 65 of file CLyapProblem.cpp.

References DESTRUCTOR_TRACE.

66 {DESTRUCTOR_TRACE;}

DESTRUCTOR_TRACE

#define DESTRUCTOR_TRACE

Definition: copasi.h:206

Member Function Documentation

bool CLyapProblem::divergenceRequested ( ) const

Definition at line 115 of file CLyapProblem.cpp.

References mpDivergenceRequested.

Referenced by CLyapMethod::isValidProblem(), CQLyapWidget::loadTask(), CLyapTask::printResult(), CLyapTask::process(), CQLyapWidget::saveTask(), and CLyapWolfMethod::start().

116 {return *mpDivergenceRequested;}

CLyapProblem::mpDivergenceRequested

bool * mpDivergenceRequested

Definition: CLyapProblem.h:42

bool CLyapProblem::elevateChildren ( )

virtual

This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.

Returns: bool success

Reimplemented from CCopasiParameterGroup.

Definition at line 68 of file CLyapProblem.cpp.

Referenced by initializeParameter().

 {
   return true;
 }

const unsigned C_INT32 & CLyapProblem::getExponentNumber ( ) const

Retrieve the number of exponents to calculate.

Returns: "const unsigned C_INT32 &"

Definition at line 90 of file CLyapProblem.cpp.

References mpExponentNumber.

Referenced by CLyapTask::calculationsBeforeOutput(), CLyapTask::initialize(), CLyapMethod::isValidProblem(), CQLyapResultWidget::loadFromBackend(), CQLyapWidget::loadTask(), CLyapTask::printResult(), CLyapTask::process(), CQLyapWidget::saveTask(), and CLyapWolfMethod::start().

91 {return *mpExponentNumber;}

CLyapProblem::mpExponentNumber

unsigned C_INT32 * mpExponentNumber

Definition: CLyapProblem.h:32

const C_FLOAT64 & CLyapProblem::getTransientTime ( ) const

Retrieve the end time.

Returns: "const C_FLOAT64 &" endTime

Definition at line 98 of file CLyapProblem.cpp.

References mpTransientTime.

Referenced by CLyapWolfMethod::calculate(), CLyapWolfMethod::isValidProblem(), CQLyapWidget::loadTask(), and CQLyapWidget::saveTask().

99 {return *mpTransientTime;}

CLyapProblem::mpTransientTime

C_FLOAT64 * mpTransientTime

Definition: CLyapProblem.h:48

void CLyapProblem::initializeParameter ( )

private

Load a trajectory problem

Parameters

CReadConfig &	configBuffer
"CReadConfig::Mode	mode (Default: CReadConfig::NEXT) Allocates all group parameters and assures that they are properly initialized.

Definition at line 73 of file CLyapProblem.cpp.

References CCopasiParameterGroup::assertParameter(), CCopasiParameter::BOOL, C_FLOAT64, C_INT32, CCopasiParameter::DOUBLE, elevateChildren(), CCopasiParameter::getValue(), mpDivergenceRequested, mpExponentNumber, mpTransientTime, CCopasiParameter::Value::pBOOL, CCopasiParameter::Value::pDOUBLE, CCopasiParameter::Value::pUINT, and CCopasiParameter::UINT.

Referenced by CLyapProblem().

 {
   mpExponentNumber =
     assertParameter("ExponentNumber", CCopasiParameter::UINT, (unsigned C_INT32) 3)->getValue().pUINT;
   mpDivergenceRequested =
     assertParameter("DivergenceRequested", CCopasiParameter::BOOL, (bool) true)->getValue().pBOOL;
   mpTransientTime =
     assertParameter("TransientTime", CCopasiParameter::DOUBLE, (C_FLOAT64) 0.0)->getValue().pDOUBLE;
 
   elevateChildren();
 }

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

virtual

This is the output method for any result of a problem. The default implementation provided with CCopasiProblem. Does only print "Not implmented." To overide this default behaviour one needs to reimplement the virtual printResult function.

Parameters

std::ostream * ostream

Reimplemented from CCopasiProblem.

Definition at line 118 of file CLyapProblem.cpp.

References CCopasiObject::getObjectParent(), and CLyapTask::printResult().

 {
   CLyapTask* parent = dynamic_cast<CLyapTask*>(getObjectParent());
 
   if (!parent) return;
 
   parent->printResult(ostream);
 }

void CLyapProblem::setDivergenceRequested ( bool flag )

Definition at line 110 of file CLyapProblem.cpp.

References mpDivergenceRequested.

Referenced by CQLyapWidget::saveTask().

 {
   *mpDivergenceRequested = flag;
 }

void CLyapProblem::setExponentNumber ( const unsigned C_INT32 & number )

Set the number of exponents to calculate

Parameters

const unsigned C_INT32 &

Definition at line 85 of file CLyapProblem.cpp.

References mpExponentNumber.

Referenced by CQLyapWidget::saveTask().

 {
   *mpExponentNumber = number;
 }

void CLyapProblem::setTransientTime ( const C_FLOAT64 & endTime )

Set the end time.

Parameters

const C_FLOAT64 & endTime

Definition at line 93 of file CLyapProblem.cpp.

References mpTransientTime.

Referenced by CQLyapWidget::saveTask().

 {
   *mpTransientTime = startTime;
 }

Member Data Documentation

bool* CLyapProblem::mpDivergenceRequested

private

whether the divergence should also be calculated

Definition at line 42 of file CLyapProblem.h.

Referenced by divergenceRequested(), initializeParameter(), and setDivergenceRequested().

unsigned C_INT32* CLyapProblem::mpExponentNumber

private

Number of exponents to calculate. 0 means all.

Definition at line 32 of file CLyapProblem.h.

Referenced by getExponentNumber(), initializeParameter(), and setExponentNumber().

C_FLOAT64* CLyapProblem::mpTransientTime

private

Indicates at which point of time the calculation of exponents should be started.

Definition at line 48 of file CLyapProblem.h.

Referenced by getTransientTime(), initializeParameter(), and setTransientTime().

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

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation