CSteadyStateProblem Class Reference

#include <CSteadyStateProblem.h>

Inheritance diagram for CSteadyStateProblem:

Collaboration diagram for CSteadyStateProblem:

Public Member Functions
	CSteadyStateProblem (const CCopasiContainer *pParent=NULL)
	CSteadyStateProblem (const CSteadyStateProblem &src, const CCopasiContainer *pParent=NULL)
virtual bool	initialize ()
bool	isJacobianRequested () const
bool	isStabilityAnalysisRequested () const
void	load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::NEXT)
void	setJacobianRequested (bool &jacobianRequested)
void	setStabilityAnalysisRequested (bool &stabilityAnalysisRequested)
virtual	~CSteadyStateProblem ()
Public Member Functions inherited from CCopasiProblem
	CCopasiProblem (const CCopasiProblem &src, const CCopasiContainer *pParent=NULL)
CModel *	getModel () const
const CCopasiTask::Type &	getType () const
virtual void	print (std::ostream *ostream) const
virtual void	printResult (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 ()
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 ()

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

CSteadyStateProblem class. This class describes the steady state problem, i.e., it allows to specify for example initial conditions.

Created for Copasi by Stefan Hoops 2002

Definition at line 29 of file CSteadyStateProblem.h.

Constructor & Destructor Documentation

CSteadyStateProblem::CSteadyStateProblem

(

const CCopasiContainer *

pParent = NULL

)

The initial state, i.e., the starting conditions of the trajectroy. was a initial state set? Default constructor.

Parameters

const

CCopasiContainer * pParent (default: NULL)

CSteadyStateProblem class. This class describes the steady state problem, i.e., it allows to specify for example initial conditions.

Created for Copasi by Stefan Hoops 2002 Default constructor.

Definition at line 43 of file CSteadyStateProblem.cpp.

References CCopasiParameterGroup::addParameter(), CCopasiParameter::BOOL, and CONSTRUCTOR_TRACE.

                                                                        :
    CCopasiProblem(CCopasiTask::steadyState, pParent)
    //mInitialState(),
    //mHasInitialState(false)
{
  addParameter("JacobianRequested", CCopasiParameter::BOOL, true);
  addParameter("StabilityAnalysisRequested", CCopasiParameter::BOOL, true);
  CONSTRUCTOR_TRACE;
}

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

Copy constructor.

Parameters

const CSteadyStateProblem &

src CCopasiContainer * pParent (default: NULL)

Copy constructor.

Parameters

const CSteadyStateProblem &

src

Definition at line 57 of file CSteadyStateProblem.cpp.

References CONSTRUCTOR_TRACE.

                                     :
    CCopasiProblem(src, pParent)
    //mInitialState(src.mInitialState),
    //mHasInitialState(src.mHasInitialState)
{CONSTRUCTOR_TRACE;}

CSteadyStateProblem::~CSteadyStateProblem ( )

virtual

Destructor.

Definition at line 67 of file CSteadyStateProblem.cpp.

References DESTRUCTOR_TRACE.

{DESTRUCTOR_TRACE;}

Member Function Documentation

bool CSteadyStateProblem::initialize ( )

virtual

Do all neccessary initialization so that calls to caluclate will be successful. This is called once from CCopasiTask::process()

Returns

bool succes

Reimplemented from CCopasiProblem.

Definition at line 70 of file CSteadyStateProblem.cpp.

References CCopasiProblem::mpModel.

Referenced by CSteadyStateTask::initialize().

{
  if (!mpModel) return false;

  return true;
}

bool CSteadyStateProblem::isJacobianRequested

(

)

const

Retrieve whether the jacobian is requested.

Returns

bool jacobianRequested

Definition at line 88 of file CSteadyStateProblem.cpp.

References CCopasiParameter::getValue(), and CCopasiParameter::Value::pBOOL.

Referenced by StateSubwidget::loadAll(), SteadyStateWidget::loadTask(), and CSteadyStateTask::process().

{return * getValue("JacobianRequested").pBOOL;}

bool CSteadyStateProblem::isStabilityAnalysisRequested

(

)

const

Retrieve whether the stabilty analysis is requested.

Returns

bool stabilityAnalysisRequested

Definition at line 102 of file CSteadyStateProblem.cpp.

References CCopasiParameter::getValue(), and CCopasiParameter::Value::pBOOL.

Referenced by StateSubwidget::loadAll(), SteadyStateWidget::loadTask(), and CSteadyStateTask::process().

{return * getValue("StabilityAnalysisRequested").pBOOL;}

void CSteadyStateProblem::load	(	CReadConfig &	configBuffer,
		CReadConfig::Mode	mode = CReadConfig::NEXT
	)

Load a trajectory problem

Parameters

CReadConfig &	configBuffer
"CReadConfig::Mode	mode (Default: CReadConfig::NEXT)

Load a steadystate problem

Parameters

CReadConfig &

configBuffer

Definition at line 109 of file CSteadyStateProblem.cpp.

References CCopasiDataModel::getModel(), CCopasiObject::getObjectDataModel(), CCopasiParameter::getValue(), CReadConfig::getVariable(), CReadConfig::getVersion(), CReadConfig::LOOP, CCopasiProblem::mpModel, and CCopasiParameterGroup::setValue().

{
  if (configBuffer.getVersion() < "4.0")
    {
      CCopasiDataModel* pDataModel = getObjectDataModel();
      assert(pDataModel != NULL);
      mpModel = pDataModel->getModel();
      //mInitialState = mpModel->getInitialState();
      //mHasInitialState = false;
      configBuffer.getVariable("RepStabilityAnalysis", "bool" ,
                               getValue("StabilityAnalysisRequested").pBOOL,
                               CReadConfig::LOOP);
      setValue("JacobianRequested",
               * getValue("StabilityAnalysisRequested").pBOOL);
    }
}

void CSteadyStateProblem::setJacobianRequested

(

bool &

jacobianRequested

)

Set whether the jacobian is requested.

Parameters

bool	& jacobianRequested

Set whether the jacobian is requested.

Parameters

bool	* jacobianRequested

Definition at line 81 of file CSteadyStateProblem.cpp.

References CCopasiParameterGroup::setValue().

Referenced by SteadyStateWidget::saveTask().

{setValue("JacobianRequested", jacobianRequested);}

void CSteadyStateProblem::setStabilityAnalysisRequested

(

bool &

stabilityAnalysisRequested

)

Set whether stabilty analysis is requested.

Parameters

bool	& stabilityAnalysisRequested

Set whether stabilty analysis is requested.

Parameters

bool	* stabilityAnalysisRequested

Definition at line 95 of file CSteadyStateProblem.cpp.

References CCopasiParameterGroup::setValue().

Referenced by CLNATask::process(), and SteadyStateWidget::saveTask().

{setValue("StabilityAnalysisRequested", stabilityAnalysisRequested);}

---

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

• CSteadyStateProblem.h
• CSteadyStateProblem.cpp