#include <COptItem.h>

Inheritance diagram for COptItem:

Collaboration diagram for COptItem:

Public Member Functions
virtual C_INT32	checkConstraint () const

C_INT32	checkConstraint (const C_FLOAT64 &value) const

bool	checkLowerBound (const C_FLOAT64 &value) const

bool	checkUpperBound (const C_FLOAT64 &value) const

virtual bool	compile (const std::vector< CCopasiContainer * > listOfContainer=CCopasiContainer::EmptyList)

	COptItem (const CCopasiContainer *pParent, const std::string &name="OptimizationItem")

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

	COptItem (const CCopasiParameterGroup &group, const CCopasiContainer *pParent=NULL)

virtual C_FLOAT64	getConstraintViolation () const

const C_FLOAT64 &	getLastStartValue () const

const std::string	getLowerBound () const

const C_FLOAT64 *	getLowerBoundValue () const

const CCopasiObject *	getObject () const

const CCopasiObjectName	getObjectCN () const

std::string	getObjectDisplayName () const

virtual const C_FLOAT64 *	getObjectValue () const

C_FLOAT64	getRandomValue (CRandom *pRandom=NULL)

const C_FLOAT64 &	getStartValue () const

virtual UpdateMethod *	getUpdateMethod () const

const std::string	getUpperBound () const

const C_FLOAT64 *	getUpperBoundValue () const

virtual bool	isValid () const

void	rememberStartValue ()

bool	setLowerBound (const CCopasiObjectName &lowerBound)

bool	setObjectCN (const CCopasiObjectName &objectCN)

bool	setStartValue (const C_FLOAT64 &value)

bool	setUpperBound (const CCopasiObjectName &upperBound)

virtual	~COptItem ()

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)

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

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 bool	isValid (CCopasiParameterGroup &group)

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)

Protected Member Functions
	COptItem ()

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
C_FLOAT64	mLastStartValue

C_FLOAT64	mLowerBound

const C_FLOAT64 *	mpLowerBound

const CCopasiObject *	mpLowerObject

UpdateMethod *	mpMethod

const CCopasiObject *	mpObject

const C_FLOAT64 *	mpObjectValue

std::string *	mpParmLowerBound

std::string *	mpParmObjectCN

C_FLOAT64 *	mpParmStartValue

std::string *	mpParmUpperBound

const C_FLOAT64 *	mpUpperBound

const CCopasiObject *	mpUpperObject

C_FLOAT64	mUpperBound

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
static CRandom *	mpRandom = NULL

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

Private Member Functions
bool	compileLowerBound (const std::vector< CCopasiContainer * > &listOfContainer)

bool	compileUpperBound (const std::vector< CCopasiContainer * > &listOfContainer)

void	initializeParameter ()

Friends
std::ostream &	operator<< (std::ostream &os, const COptItem &o)

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 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 }

Detailed Description

Definition at line 29 of file COptItem.h.

Constructor & Destructor Documentation

COptItem::COptItem ( )

protected

Default constructor

COptItem::COptItem	(	const CCopasiContainer *	pParent,
		const std::string &	name = `"OptimizationItem"`
	)

Specific constructor

Parameters

const	CCopasiContainer * pParent
const	std::string & name (default: OptimizationItem)

Definition at line 39 of file COptItem.cpp.

References initializeParameter().

                                           :
   CCopasiParameterGroup(name, pParent),
   mpParmObjectCN(NULL),
   mpParmLowerBound(NULL),
   mpParmUpperBound(NULL),
   mpParmStartValue(NULL),
   mpObject(NULL),
   mpMethod(NULL),
   mpObjectValue(NULL),
   mpLowerObject(NULL),
   mpLowerBound(NULL),
   mLowerBound(0.0),
   mpUpperObject(NULL),
   mpUpperBound(NULL),
   mUpperBound(0.0),
   mLastStartValue(std::numeric_limits< C_FLOAT64 >::quiet_NaN())
 {initializeParameter();}

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

Copy constructor

Parameters

const	COptItem & src
const	CCopasiContainer * pParent (default: src data model)

Definition at line 58 of file COptItem.cpp.

References initializeParameter().

                                                     :
   CCopasiParameterGroup(src, (pParent != NULL) ? pParent : src.getObjectDataModel()),
   mpParmObjectCN(NULL),
   mpParmLowerBound(NULL),
   mpParmUpperBound(NULL),
   mpParmStartValue(NULL),
   mpObject(NULL),
   mpMethod(NULL),
   mpObjectValue(NULL),
   mpLowerObject(NULL),
   mpLowerBound(NULL),
   mLowerBound(0.0),
   mpUpperObject(NULL),
   mpUpperBound(NULL),
   mUpperBound(0.0),
   mLastStartValue(src.mLastStartValue)
 {initializeParameter();}

COptItem::COptItem	(	const CCopasiParameterGroup &	group,
		const CCopasiContainer *	pParent = `NULL`
	)

Specific constructor used for reading COPASI files

Parameters

const	CCopasiParameterGroup & group
const	CCopasiContainer * pParent (default: group data model)

Definition at line 77 of file COptItem.cpp.

References initializeParameter().

                                                     :
   CCopasiParameterGroup(group, (pParent != NULL) ? pParent : group.getObjectDataModel()),
   mpParmObjectCN(NULL),
   mpParmLowerBound(NULL),
   mpParmUpperBound(NULL),
   mpParmStartValue(NULL),
   mpObject(NULL),
   mpMethod(NULL),
   mpObjectValue(NULL),
   mpLowerObject(NULL),
   mpLowerBound(NULL),
   mLowerBound(0.0),
   mpUpperObject(NULL),
   mpUpperBound(NULL),
   mUpperBound(0.0),
   mLastStartValue(std::numeric_limits< C_FLOAT64 >::quiet_NaN())
 {initializeParameter();}

COptItem::~COptItem ( )

virtual

Destructor

Definition at line 96 of file COptItem.cpp.

97 {}

Member Function Documentation

C_INT32 COptItem::checkConstraint ( ) const

virtual

This functions check whether the current value is within the limits of the optimization item.

Returns: C_INT32 result (-1: to small, 0: within boundaries, 1 to large)

Reimplemented in CFitConstraint, and CFitItem.

Definition at line 401 of file COptItem.cpp.

References mpLowerBound, mpObjectValue, and mpUpperBound.

 {
   if (*mpLowerBound > *mpObjectValue) return - 1;
 
   if (*mpObjectValue > *mpUpperBound) return 1;
 
   return 0;
 }

C_INT32 COptItem::checkConstraint ( const C_FLOAT64 & value ) const

This functions check whether the value is within the limits of the optimization item.

Parameters

const C_FLOAT64 & value

Returns: C_INT32 result (-1: to small, 0: within boundaries, 1 to large)

Definition at line 426 of file COptItem.cpp.

References mpLowerBound, and mpUpperBound.

 {
   if (*mpLowerBound > value) return - 1;
 
   if (value > *mpUpperBound) return 1;
 
   return 0;
 }

bool COptItem::checkLowerBound ( const C_FLOAT64 & value ) const

Checks whether the value fulfills the lower bound constraint.

Parameters

const C_FLOAT64 & value

Returns: bool fulfills

Definition at line 435 of file COptItem.cpp.

References mpLowerBound.

Referenced by COptMethodEP::creation(), COptMethodSRES::creation(), and CRandomSearch::optimise().

436 {return *mpLowerBound <= value;}

COptItem::mpLowerBound

const C_FLOAT64 * mpLowerBound

Definition: COptItem.h:308

bool COptItem::checkUpperBound ( const C_FLOAT64 & value ) const

Checks whether the value fulfills the upper bound constraint.

Parameters

const C_FLOAT64 & value

Returns: bool fulfills

Definition at line 438 of file COptItem.cpp.

References mpUpperBound.

Referenced by COptMethodEP::creation(), COptMethodSRES::creation(), and CRandomSearch::optimise().

439 {return value <= *mpUpperBound;}

COptItem::mpUpperBound

const C_FLOAT64 * mpUpperBound

Definition: COptItem.h:323

bool COptItem::compile ( const std::vector< CCopasiContainer * > listOfContainer = CCopasiContainer::EmptyList )

virtual

Compile the optimization item. This function must be called before any of the check functions are called.

Parameters

const std::vector< CCopasiContainer * > listOfContainer

Returns: bool success

Reimplemented in CFitItem.

Definition at line 336 of file COptItem.cpp.

References CCopasiObject::addDirectDependency(), C_FLOAT64, CCopasiObject::clearDirectDependencies(), compileLowerBound(), compileUpperBound(), DoNothing, CCopasiMessage::ERROR, getObjectCN(), CCopasiObject::getObjectDataModel(), CCopasiObject::getObjectDisplayName(), CCopasiObject::getUpdateMethod(), CCopasiObject::getValuePointer(), CCopasiObject::isValueDbl(), MCOptimization, mpLowerBound, mpLowerObject, mpMethod, mpObject, mpObjectValue, mpParmLowerBound, mpParmStartValue, mpParmUpperBound, mpUpperBound, mpUpperObject, and NaN.

Referenced by CFitItem::compile(), getObjectDisplayName(), and getRandomValue().

 {
   bool success = true;
   clearDirectDependencies();
 
   std::string Bound;
 
   mpMethod = &DoNothing;
   mpObjectValue = &NaN;
 
   if ((mpObject =
          getObjectDataModel()->ObjectFromName(listOfContainer,
              getObjectCN())) != NULL &&
       mpObject->isValueDbl())
     mpObjectValue = (C_FLOAT64 *) mpObject->getValuePointer();
 
   if (mpObjectValue == &NaN)
     {
       CCopasiMessage(CCopasiMessage::ERROR, MCOptimization + 1, getObjectCN().c_str());
       success = false;
     }
   else
     {
       addDirectDependency(mpObject);
       mpMethod = mpObject->getUpdateMethod();
     }
 
   if (compileLowerBound(listOfContainer))
     {
       if (mpLowerObject != NULL)
         {
           addDirectDependency(mpLowerObject);
         }
     }
   else
     {
       CCopasiMessage(CCopasiMessage::ERROR, MCOptimization + 2, mpParmLowerBound->c_str());
       success = false;
     }
 
   if (compileUpperBound(listOfContainer))
     {
       if (mpUpperObject != NULL)
         {
           addDirectDependency(mpUpperObject);
         }
     }
   else
     {
       CCopasiMessage(CCopasiMessage::ERROR, MCOptimization + 2, mpParmUpperBound->c_str());
       success = false;
     }
 
   if (!mpUpperObject && !mpLowerObject && *mpUpperBound < *mpLowerBound)
     {
       CCopasiMessage(CCopasiMessage::ERROR, MCOptimization + 4, *mpLowerBound, *mpUpperBound, mpObject->getObjectDisplayName().c_str());
       success = false;
     }
 
   if (isnan(*mpParmStartValue))
     *mpParmStartValue = *mpObjectValue;
 
   return success;
 }

bool COptItem::compileLowerBound ( const std::vector< CCopasiContainer * > & listOfContainer )

private

Compile the lower bound to hold the value given by the bound

Parameters

const std::vector< CCopasiContainer * > & listOfContainer

Returns: bool success

Definition at line 444 of file COptItem.cpp.

References C_FLOAT64, CCopasiObject::getObjectDataModel(), CCopasiObject::getValuePointer(), isNumber(), CCopasiObject::isValueDbl(), max, mLowerBound, mpLowerBound, mpLowerObject, mpParmLowerBound, and strToDouble().

Referenced by compile(), and setLowerBound().

 {
   const CCopasiDataModel * pDataModel = getObjectDataModel();
 
   assert(pDataModel != NULL);
 
   mpLowerObject = NULL;
   mpLowerBound = NULL;
 
   if (*mpParmLowerBound == "-inf")
     {
       mLowerBound = - std::numeric_limits< C_FLOAT64 >::max();
       mpLowerBound = &mLowerBound;
     }
   else if (isNumber(*mpParmLowerBound))
     {
       mLowerBound = strToDouble(mpParmLowerBound->c_str(), NULL);
       mpLowerBound = &mLowerBound;
     }
   else if ((mpLowerObject =
               getObjectDataModel()->ObjectFromName(listOfContainer,
                   *mpParmLowerBound)) != NULL &&
            mpLowerObject->isValueDbl())
     {
       mpLowerBound = (C_FLOAT64 *) mpLowerObject->getValuePointer();
     }
 
   return mpLowerBound != NULL;
 }

bool COptItem::compileUpperBound ( const std::vector< CCopasiContainer * > & listOfContainer )

private

Compile the upper bound to hold the value given by the bound

Parameters

const std::vector< CCopasiContainer * > & listOfContainer

Returns: bool success

Definition at line 474 of file COptItem.cpp.

References CCopasiObject::addDirectDependency(), C_FLOAT64, CCopasiObject::getObjectDataModel(), CCopasiObject::getValuePointer(), isNumber(), CCopasiObject::isValueDbl(), max, mpParmUpperBound, mpUpperBound, mpUpperObject, mUpperBound, and strToDouble().

Referenced by compile(), and setUpperBound().

 {
   const CCopasiDataModel * pDataModel = getObjectDataModel();
 
   assert(pDataModel != NULL);
 
   mpUpperObject = NULL;
   mpUpperBound = NULL;
 
   if (*mpParmUpperBound == "inf")
     {
       mUpperBound = std::numeric_limits< C_FLOAT64 >::max();
       mpUpperBound = &mUpperBound;
     }
   else if (isNumber(*mpParmUpperBound))
     {
       mUpperBound = strToDouble(mpParmUpperBound->c_str(), NULL);
       mpUpperBound = &mUpperBound;
     }
   else if ((mpUpperObject =
               getObjectDataModel()->ObjectFromName(listOfContainer,
                   *mpParmUpperBound)) != NULL &&
            mpUpperObject->isValueDbl())
     {
       mpUpperBound = (C_FLOAT64 *) mpUpperObject->getValuePointer();
       addDirectDependency(mpUpperObject);
     }
 
   return mpUpperBound != NULL;
 }

C_FLOAT64 COptItem::getConstraintViolation ( ) const

virtual

Retrieve the magnitude of the constraint violation This is always a positive number

Returns: C_FLOAT64 constraintViolation;

Reimplemented in CFitConstraint, and CFitItem.

Definition at line 410 of file COptItem.cpp.

References checkConstraint(), mpLowerBound, mpObjectValue, and mpUpperBound.

 {
   switch (checkConstraint())
     {
       case - 1:
         return *mpLowerBound - *mpObjectValue;
         break;
 
       case 1:
         return *mpObjectValue - *mpUpperBound;
         break;
     }
 
   return 0.0;
 }

const C_FLOAT64 & COptItem::getLastStartValue ( ) const

Retrieve the start value use in the last optimization.

Returns: const C_FLOAT64 & startValue

Definition at line 220 of file COptItem.cpp.

References mLastStartValue.

Referenced by CQFittingResult::enterProtected().

 {
   return mLastStartValue;
 }

const std::string COptItem::getLowerBound ( ) const

Retrieve the lower bound.

Returns: const std::string lowerBound

Definition at line 164 of file COptItem.cpp.

References mpParmLowerBound.

Referenced by CQFittingResult::enterProtected(), isValid(), CQFittingItemWidget::loadSelection(), operator<<(), CQFittingItemWidget::setTableText(), and CFitItem::updateBounds().

165 {return *mpParmLowerBound;}

COptItem::mpParmLowerBound

std::string * mpParmLowerBound

Definition: COptItem.h:273

const C_FLOAT64* COptItem::getLowerBoundValue ( ) const

inline

Retrieve the value of the lower bound.

Returns: const C_FLOAT64 * lowerBoundValue

Definition at line 191 of file COptItem.h.

References mpLowerBound.

192 {return mpLowerBound;}

COptItem::mpLowerBound

const C_FLOAT64 * mpLowerBound

Definition: COptItem.h:308

const CCopasiObject * COptItem::getObject ( ) const

Retrieve the item object. This may only be called after compile

Returns: const CCopasiObject *

Definition at line 128 of file COptItem.cpp.

References mpObject.

Referenced by CFitProblem::initialize().

129 {return mpObject;}

COptItem::mpObject

const CCopasiObject * mpObject

Definition: COptItem.h:288

const CCopasiObjectName COptItem::getObjectCN ( ) const

Retrieve the object of the optimization item.

Returns: const CCopasiObjectName objectCN

Definition at line 131 of file COptItem.cpp.

References mpParmObjectCN.

Referenced by compile(), getStartValue(), isValid(), CQFittingItemWidget::load(), CQFittingItemWidget::loadSelection(), and CQFittingItemWidget::setTableText().

132 {return *mpParmObjectCN;}

COptItem::mpParmObjectCN

std::string * mpParmObjectCN

Definition: COptItem.h:268

std::string COptItem::getObjectDisplayName ( ) const

Retrieve the display name of the optimization item.

Returns: std::string displayName

Definition at line 134 of file COptItem.cpp.

References compile(), CCopasiObject::getObjectDisplayName(), and mpObject.

Referenced by CFitProblem::initialize().

 {
   if (!mpObject && !const_cast<COptItem *>(this)->compile())
     return "Invalid Optimization Item";
 
   return mpObject->getObjectDisplayName();
 }

const C_FLOAT64 * COptItem::getObjectValue ( ) const

virtual

Retrieve the value of the optimization object.

Returns: const C_FLOAT64 * objectValue

Reimplemented in CFitItem.

Definition at line 441 of file COptItem.cpp.

References mpObjectValue.

442 {return mpObjectValue;}

COptItem::mpObjectValue

const C_FLOAT64 * mpObjectValue

Definition: COptItem.h:298

C_FLOAT64 COptItem::getRandomValue ( CRandom * pRandom = NULL )

Retrieve a random value in the interval (lower bound, upper bound). Optionally one may provide a random number generator to be used to create the random value.

Parameters

CRandom * pRandom (default: NULL)

Returns: C_FLOAT64 randomValue

Definition at line 230 of file COptItem.cpp.

References C_FLOAT64, compile(), CRandom::createGenerator(), CRandom::getRandomCC(), CRandom::getRandomNormal(), max, min, mpLowerBound, mpRandom, mpUpperBound, and NaN.

Referenced by CRandomSearch::optimise().

 {
   C_FLOAT64 RandomValue;
 
   if (mpLowerBound == NULL ||
       mpUpperBound == NULL) compile();
 
   if (mpLowerBound == NULL ||
       mpUpperBound == NULL)
     {
       RandomValue = NaN;
       return RandomValue;
     }
 
   if (pRandom == NULL)
     {
       if (mpRandom == NULL)
         mpRandom = CRandom::createGenerator();
 
       pRandom = mpRandom;
     }
 
   C_FLOAT64 mn = *mpLowerBound;
   C_FLOAT64 mx = *mpUpperBound;
 
   C_FLOAT64 la;
 
   try
     {
       // First determine the location of the interval
       // Secondly determine whether to distribute the parameter linearly or not
       // depending on the location and act upon it.
       if (0.0 <= mn) // the interval [mn, mx) is in [0, inf)
         {
           la = log10(mx) - log10(std::max(mn, std::numeric_limits< C_FLOAT64 >::min()));
 
           if (la < 1.8 || !(mn > 0.0)) // linear
             RandomValue = mn + pRandom->getRandomCC() * (mx - mn);
           else
             RandomValue = pow(10.0, log10(std::max(mn, std::numeric_limits< C_FLOAT64 >::min())) + la * pRandom->getRandomCC());
         }
       else if (mx > 0) // 0 is in the interval (mn, mx)
         {
           la = log10(mx) + log10(-mn);
 
           if (la < 3.6) // linear
             RandomValue = mn + pRandom->getRandomCC() * (mx - mn);
           else
             {
               C_FLOAT64 mean = (mx + mn) * 0.5;
               C_FLOAT64 sigma = std::min(std::numeric_limits< C_FLOAT64 >::max(), mx - mn) / 3.0;
 
               do
                 {
                   RandomValue = pRandom->getRandomNormal(mean, sigma);
                 }
               while ((RandomValue < mn) || (RandomValue > mx));
             }
         }
       else // the interval (mn, mx] is in (-inf, 0]
         {
           // Switch lower and upper bound and change sign, i.e.,
           // we can treat it similarly as location 1:
           mx = - *mpLowerBound;
           mn = - *mpUpperBound;
 
           la = log10(mx) - log10(std::max(mn, std::numeric_limits< C_FLOAT64 >::min()));
 
           if (la < 1.8 || !(mn > 0.0)) // linear
             RandomValue = - (mn + pRandom->getRandomCC() * (mx - mn));
           else
             RandomValue = - pow(10.0, log10(std::max(mn, std::numeric_limits< C_FLOAT64 >::min())) + la * pRandom->getRandomCC());
         }
     }
 
   catch (...)
     {
       RandomValue = (mx + mn) * 0.5;
     }
 
   return RandomValue;
 }

const C_FLOAT64 & COptItem::getStartValue ( ) const

Retrieve the start value of the optimization object.

Returns: const C_FLOAT64 & startValue

Definition at line 199 of file COptItem.cpp.

References C_FLOAT64, CCopasiDataModel::getDataObject(), getObjectCN(), CCopasiObject::getObjectDataModel(), CCopasiObject::getValuePointer(), mpObjectValue, mpParmStartValue, and NaN.

 {
   if (!isnan(*mpParmStartValue))
     return *mpParmStartValue;
 
   if (mpObjectValue == NULL)
     {
       const CCopasiDataModel* pDataModel = getObjectDataModel();
       assert(pDataModel != NULL);
       const CCopasiObject * pObject = pDataModel->getDataObject(getObjectCN());
 
       if (pObject != NULL &&
           pObject->getValuePointer() != NULL)
         return *(C_FLOAT64 *) pObject->getValuePointer();
 
       return NaN;
     }
 
   return *mpObjectValue;
 }

UpdateMethod * COptItem::getUpdateMethod ( ) const

virtual

Retrieve the update method

Returns: UpdateMethod * pUpdateMethod

Reimplemented in CFitItem.

Definition at line 313 of file COptItem.cpp.

References mpMethod.

314 {return mpMethod;}

COptItem::mpMethod

UpdateMethod * mpMethod

Definition: COptItem.h:293

const std::string COptItem::getUpperBound ( ) const

Retrieve the upper bound.

Returns: const std::string upperBound

Definition at line 189 of file COptItem.cpp.

References mpParmUpperBound.

Referenced by CQFittingResult::enterProtected(), isValid(), CQFittingItemWidget::loadSelection(), operator<<(), CQFittingItemWidget::setTableText(), and CFitItem::updateBounds().

190 {return *mpParmUpperBound;}

COptItem::mpParmUpperBound

std::string * mpParmUpperBound

Definition: COptItem.h:278

const C_FLOAT64* COptItem::getUpperBoundValue ( ) const

inline

Retrieve the value of the upper bound.

Returns: const C_FLOAT64 * upperBoundValue

Definition at line 198 of file COptItem.h.

References mpUpperBound.

199 {return mpUpperBound;}

COptItem::mpUpperBound

const C_FLOAT64 * mpUpperBound

Definition: COptItem.h:323

void COptItem::initializeParameter ( )

private

Allocates all group parameters and assures that they are properly initialized.

Definition at line 99 of file COptItem.cpp.

References CCopasiParameterGroup::assertParameter(), CCopasiParameter::CN, CCopasiParameter::DOUBLE, CCopasiParameter::getValue(), mpParmLowerBound, mpParmObjectCN, mpParmStartValue, mpParmUpperBound, NaN, CCopasiParameter::Value::pCN, and CCopasiParameter::Value::pDOUBLE.

Referenced by COptItem().

 {
   mpParmObjectCN =
     assertParameter("ObjectCN", CCopasiParameter::CN, CCopasiObjectName(""))->getValue().pCN;
   mpParmLowerBound =
     assertParameter("LowerBound", CCopasiParameter::CN, CCopasiObjectName("1e-06"))->getValue().pCN;
   mpParmUpperBound =
     assertParameter("UpperBound", CCopasiParameter::CN, CCopasiObjectName("1e+06"))->getValue().pCN;
   mpParmStartValue =
     assertParameter("StartValue", CCopasiParameter::DOUBLE, NaN)->getValue().pDOUBLE;
 }

bool COptItem::isValid ( ) const

virtual

Check the validity of the optimization item.

Reimplemented in CFitItem.

Definition at line 316 of file COptItem.cpp.

References getLowerBound(), getObjectCN(), getUpperBound(), setLowerBound(), setObjectCN(), and setUpperBound().

Referenced by CFitItem::isValid(), and isValid().

 {
   COptItem *pTmp = const_cast<COptItem *>(this);
 
   if (!pTmp->setObjectCN(getObjectCN())) return false;
 
   if (!pTmp->setLowerBound(getLowerBound())) return false;
 
   if (!pTmp->setUpperBound(getUpperBound())) return false;
 
   return true;
 }

bool COptItem::isValid ( CCopasiParameterGroup & group )

static

Check whether the group describes a valid optimization item.

Returns: bool isValid

Definition at line 329 of file COptItem.cpp.

References isValid().

 {
   COptItem tmp(group);
 
   return tmp.isValid();
 }

void COptItem::rememberStartValue ( )

Remember the current start value

Definition at line 225 of file COptItem.cpp.

References getStartValue(), and mLastStartValue.

 {
   mLastStartValue = getStartValue();
 }

bool COptItem::setLowerBound ( const CCopasiObjectName & lowerBound )

Set the lower bound.

Parameters

const CCopasiObjectName & lowerBound

Returns: bool success

Definition at line 142 of file COptItem.cpp.

References C_FLOAT64, compileLowerBound(), CCopasiContainer::EmptyList, getStartValue(), isNumber(), mpParmLowerBound, and strToDouble().

Referenced by isValid(), and CQFittingItemWidget::saveSelection().

 {
   if (lowerBound[0] == '-' &&
       lowerBound[lowerBound.length() - 1] == '%' &&
       isNumber(lowerBound.substr(1, lowerBound.length() - 2)))
     {
       std::stringstream LowerBound;
       C_FLOAT64 StartValue = getStartValue();
 
       LowerBound << StartValue + fabs(StartValue) * strToDouble(lowerBound.c_str(), NULL) / 100.0;
       *mpParmLowerBound = LowerBound.str();
 
       return true;
     }
   else
     {
       *mpParmLowerBound = lowerBound;
     }
 
   return compileLowerBound(CCopasiContainer::EmptyList);
 }

bool COptItem::setObjectCN ( const CCopasiObjectName & objectCN )

Set the object of the optimization item.

Parameters

const CCopasiObjectName & objectCN

Returns: bool success

Definition at line 111 of file COptItem.cpp.

References CCopasiMessage::ERROR, CCopasiDataModel::getDataObject(), CCopasiObject::getObjectDataModel(), CCopasiObject::isValueDbl(), MCOptimization, and mpParmObjectCN.

Referenced by COptProblem::addOptItem(), isValid(), and CQFittingItemWidget::slotParamEdit().

 {
   const CCopasiDataModel * pDataModel = getObjectDataModel();
   assert(pDataModel != NULL);
 
   const CCopasiObject * pObject = pDataModel->getDataObject(objectCN);
 
   if (pObject == NULL || !pObject->isValueDbl())
     {
       CCopasiMessage(CCopasiMessage::ERROR, MCOptimization + 1, objectCN.c_str());
       return false;
     }
 
   *mpParmObjectCN = objectCN;
   return true;
 }

bool COptItem::setStartValue ( const C_FLOAT64 & value )

Set the value start value.

Parameters

const C_FLOAT64 & startValue

Returns: bool success

Definition at line 192 of file COptItem.cpp.

References mpParmStartValue.

Referenced by CFitItem::elevateChildren(), and CQFittingItemWidget::saveSelection().

 {
   *mpParmStartValue = value;
 
   return true;
 }

bool COptItem::setUpperBound ( const CCopasiObjectName & upperBound )

Set the upper bound.

Parameters

const CCopasiObjectName & upperBound

Returns: bool success

Definition at line 167 of file COptItem.cpp.

References C_FLOAT64, compileUpperBound(), CCopasiContainer::EmptyList, getStartValue(), isNumber(), mpParmUpperBound, and strToDouble().

Referenced by isValid(), and CQFittingItemWidget::saveSelection().

 {
   if (upperBound[0] == '+' &&
       upperBound[upperBound.length() - 1] == '%' &&
       isNumber(upperBound.substr(1, upperBound.length() - 2)))
     {
       std::stringstream UpperBound;
       C_FLOAT64 StartValue = getStartValue();
 
       UpperBound << StartValue + fabs(StartValue) * strToDouble(upperBound.c_str(), NULL) / 100.0;
       *mpParmUpperBound = UpperBound.str();
 
       return true;
     }
   else
     {
       *mpParmUpperBound = upperBound;
     }
 
   return compileUpperBound(CCopasiContainer::EmptyList);
 }

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	os,
		const COptItem &	o
	)

friend

Output stream operator

Parameters

ostream	& os
const	COptItem & A

Returns: ostream & os

Definition at line 505 of file COptItem.cpp.

 {
   if (o.mpObject == NULL && !const_cast<COptItem *>(&o)->compile())
     return os << "Invalid Optimization Item";
 
   if (o.mpLowerObject)
     os << o.mpLowerObject->getObjectDisplayName();
   else
     os << o.getLowerBound();
 
   os << " <= ";
   os << o.mpObject->getObjectDisplayName();
   os << " <= ";
 
   if (o.mpUpperObject)
     os << o.mpUpperObject->getObjectDisplayName();
   else
     os << o.getUpperBound();
 
   os << "; Start Value = " << o.getStartValue();
 
   return os;
 }