#include <CMoiety.h>

Inheritance diagram for CMoiety:

Collaboration diagram for CMoiety:

Public Member Functions
void	add (C_FLOAT64 value, CMetab *metabolite)

void	cleanup ()

	CMoiety (const std::string &name="NoName", const CCopasiContainer *pParent=NULL)

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

const C_FLOAT64 &	dependentNumber ()

const C_FLOAT64 &	getAmount () const

const C_FLOAT64 &	getDependentNumber () const

CCopasiObject *	getDependentNumberReference () const

std::string	getDescription (const CModel *model) const

const std::vector< std::pair < C_FLOAT64, CMetab * > > &	getEquation () const

std::string	getExpression () const

CCopasiObject *	getInitialValueReference () const

virtual const std::string &	getKey () const

C_FLOAT64	getNumber () const

CCopasiObject *	getTotalNumberReference () const

CCopasiObject *	getValueReference () const

void	refreshAmount ()

void	refreshDependentNumber ()

void	refreshInitialValue ()

void	refreshValue ()

virtual bool	setObjectParent (const CCopasiContainer *pParent)

	~CMoiety ()

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 CObjectInterface *	getObject (const CCopasiObjectName &cn) 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 CCopasiObjectName	getCN () const

virtual const DataObjectSet &	getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const

CCopasiContainer *	getObjectAncestor (const std::string &type) const

CCopasiDataModel *	getObjectDataModel ()

const CCopasiDataModel *	getObjectDataModel () const

virtual std::string	getObjectDisplayName (bool regular=true, bool richtext=false) 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

virtual void *	getValuePointer () 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

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

void	removeDirectDependency (const CCopasiObject *pObject)

void	setDirectDependencies (const DataObjectSet &directDependencies)

bool	setObjectName (const std::string &name)

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	initConversionFactor ()

void	initObjects ()

Private Attributes
std::vector< std::pair < C_FLOAT64, CMetab * > >	mEquation

C_FLOAT64	mIAmount

C_FLOAT64	mINumber

std::string	mKey

C_FLOAT64	mNumber

const C_FLOAT64 *	mpConversionFactor

CDependentNumberReference *	mpDNumberReference

CTotalNumberReference *	mpINumberReference

CTotalNumberReference *	mpNumberReference

Static Private Attributes
static const C_FLOAT64	DefaultFactor

Additional Inherited Members
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 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 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 CCopasiContainer
objectMap	mObjects

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

Detailed Description

Definition at line 119 of file CMoiety.h.

Constructor & Destructor Documentation

CMoiety::CMoiety	(	const std::string &	name = `"NoName"`,
		const CCopasiContainer *	pParent = `NULL`
	)

Default constructor

Parameters

const	std::string & name (default: "NoName")
const	CCopasiContainer * pParent (default: NULL)

Definition at line 36 of file CMoiety.cpp.

References CONSTRUCTOR_TRACE, and initObjects().

                                                   :
   CCopasiContainer(name, pParent, "Moiety"),
   mKey(CCopasiRootContainer::getKeyFactory()->add("Moiety", this)), //By G
   mNumber(0),
   mINumber(0),
   mIAmount(0),
   mEquation(),
   mpINumberReference(NULL),
   mpNumberReference(NULL),
   mpDNumberReference(NULL),
   mpConversionFactor(&CMoiety::DefaultFactor)
 {
   initObjects();
   CONSTRUCTOR_TRACE;
 }

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

Copy constructor

Parameters

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

Definition at line 53 of file CMoiety.cpp.

References CONSTRUCTOR_TRACE, and initObjects().

                                                   :
   CCopasiContainer(src, pParent),
   mKey(CCopasiRootContainer::getKeyFactory()->add("Moiety", this)), //By G
   mNumber(src.mNumber),
   mINumber(src.mINumber),
   mIAmount(src.mIAmount),
   mEquation(src.mEquation),
   mpINumberReference(NULL),
   mpNumberReference(NULL),
   mpDNumberReference(NULL),
   mpConversionFactor(src.mpConversionFactor)
 {
   initObjects();
   CONSTRUCTOR_TRACE;
 }

CMoiety::~CMoiety ( )

Destructor

Definition at line 70 of file CMoiety.cpp.

References DESTRUCTOR_TRACE, CCopasiRootContainer::getKeyFactory(), mKey, and CKeyFactory::remove().

 {
   CCopasiRootContainer::getKeyFactory()->remove(mKey);
   DESTRUCTOR_TRACE;
 }

Member Function Documentation

void CMoiety::add	(	C_FLOAT64	value,
		CMetab *	metabolite
	)

Add a metabolite to a moiety

Parameters

C_FLOAT64	value
CMetab	* metabolite

Definition at line 96 of file CMoiety.cpp.

References CCopasiObject::addDirectDependency(), mEquation, mpINumberReference, CModelEntity::mpIValueReference, mpNumberReference, CModelEntity::mpValueReference, and CMetab::setDependentOn().

Referenced by CModel::buildMoieties().

 {
   if (!mEquation.size())
     pMetabolite->setDependentOn(this);
   else
     addDirectDependency(pMetabolite->mpValueReference);
 
   mpINumberReference->addDirectDependency(pMetabolite->mpIValueReference);
   mpNumberReference->addDirectDependency(pMetabolite->mpValueReference);
 
   std::pair<C_FLOAT64, CMetab *> element;
 
   element.first = value;
   element.second = pMetabolite;
 
   mEquation.push_back(element);
 }

void CMoiety::cleanup ( )

Definition at line 114 of file CMoiety.cpp.

References CCopasiObject::clearDirectDependencies(), mEquation, mpINumberReference, and mpNumberReference.

 {
   clearDirectDependencies();
   mEquation.clear();
   mpINumberReference->clearDirectDependencies();
   mpNumberReference->clearDirectDependencies();
 }

const C_FLOAT64 & CMoiety::dependentNumber ( )

Retrieve and refresh the dependent number;

Returns: const C_FLOAT64 & dependentNumber

Definition at line 139 of file CMoiety.cpp.

References mNumber, and refreshDependentNumber().

 {
   refreshDependentNumber();
   return mNumber;
 }

const C_FLOAT64 & CMoiety::getAmount ( ) const

Retrieve the total amount

Returns: const C_FLOAT64 & amount

Definition at line 257 of file CMoiety.cpp.

References mIAmount.

 {
   return mIAmount;
 }

const C_FLOAT64 & CMoiety::getDependentNumber ( ) const

Retrieve the dependent number;

Returns: const C_FLOAT64 & dependentNumber

Definition at line 145 of file CMoiety.cpp.

References mNumber.

Referenced by CMetab::calculate().

146 {return mNumber;}

CMoiety::mNumber

C_FLOAT64 mNumber

Definition: CMoiety.h:136

CCopasiObject * CMoiety::getDependentNumberReference ( ) const

Retrieve the object for the dependent particle number

Returns: CCopasiObject * dependentNumberReference

Definition at line 151 of file CMoiety.cpp.

References mpDNumberReference.

Referenced by CMathObject::compileValue(), and CParticleReference::getPrerequisites().

152 {return mpDNumberReference;}

CMoiety::mpDNumberReference

CDependentNumberReference * mpDNumberReference

Definition: CMoiety.h:169

std::string CMoiety::getDescription ( const CModel * model ) const

get the string representation of the moiety using the CMetabNameInterface

Definition at line 164 of file CMoiety.cpp.

References CMetabNameInterface::getDisplayName(), and mEquation.

 {
   std::ostringstream Description;
   Description.imbue(std::locale::classic());
   Description.precision(16);
 
   std::vector< std::pair< C_FLOAT64, CMetab * > >::const_iterator it = mEquation.begin();
   std::vector< std::pair< C_FLOAT64, CMetab * > >::const_iterator end = mEquation.end();
 
   for (; it != end; ++it)
     {
       if (it != mEquation.begin())
         {
           if (it->first < 0.0)
             Description << " - ";
           else
             Description << " + ";
         }
 
       if (fabs(it->first) > 1.0 + 100.0 * std::numeric_limits< C_FLOAT64 >::epsilon() ||
           fabs(it->first) < 1.0 - 100.0 * std::numeric_limits< C_FLOAT64 >::epsilon())
         Description << fabs(it->first) << "*";
 
       Description << CMetabNameInterface::getDisplayName(model, *it->second, false);
     }
 
   return Description.str();
 }

const std::vector< std::pair< C_FLOAT64, CMetab * > > & CMoiety::getEquation ( ) const

Retrieve the components of the total mass equation

Returns: const std::vector<std::pair< C_FLOAT64, CMetab * > > & equation

Definition at line 267 of file CMoiety.cpp.

References mEquation.

Referenced by CMathObject::compileDependentMass(), CMathObject::compileTotalMass(), and QConservedSpeciesAnimation::getScales().

 {
   return mEquation;
 }

std::string CMoiety::getExpression ( ) const

Retrieve the infix expression, which can be used to calculate the total amount.

Returns: std::string expression

Definition at line 228 of file CMoiety.cpp.

References mEquation.

Referenced by CQMoietiesTaskResult::slotCreateGlobalQuantity().

 {
   std::ostringstream Infix;
   Infix.imbue(std::locale::classic());
   Infix.precision(16);
 
   std::vector< std::pair< C_FLOAT64, CMetab * > >::const_iterator it = mEquation.begin();
   std::vector< std::pair< C_FLOAT64, CMetab * > >::const_iterator end = mEquation.end();
 
   for (; it != end; ++it)
     {
       if (it != mEquation.begin())
         {
           if (it->first < 0.0)
             Infix << "-";
           else
             Infix << "+";
         }
 
       if (fabs(it->first) > 1.0 + 100.0 * std::numeric_limits< C_FLOAT64 >::epsilon() ||
           fabs(it->first) < 1.0 - 100.0 * std::numeric_limits< C_FLOAT64 >::epsilon())
         Infix << fabs(it->first) << "*";
 
       Infix << "<" << it->second->getInitialValueReference()->getCN() << ">";
     }
 
   return Infix.str();
 }

CCopasiObject * CMoiety::getInitialValueReference ( ) const

Retrieve the object for the total particle number

Returns: CCopasiObject * initialValueReference

Definition at line 206 of file CMoiety.cpp.

References mpINumberReference.

207 {return mpINumberReference;}

CMoiety::mpINumberReference

CTotalNumberReference * mpINumberReference

Definition: CMoiety.h:158

const std::string & CMoiety::getKey ( ) const

virtual

Returns a string with the name of this compartment.

Returns: std::string key

Reimplemented from CCopasiObject.

Definition at line 154 of file CMoiety.cpp.

References mKey.

154 {return mKey;} //By G

CMoiety::mKey

std::string mKey

Definition: CMoiety.h:131

C_FLOAT64 CMoiety::getNumber ( ) const

Definition at line 209 of file CMoiety.cpp.

References mINumber.

 {
   return mINumber;
 }

CCopasiObject * CMoiety::getTotalNumberReference ( ) const

Retrieve the object for the dependent particle number

Returns: CCopasiObject * totalNumberReference

Definition at line 148 of file CMoiety.cpp.

References mpNumberReference.

Referenced by CMathObject::compileDependentMass().

149 {return mpNumberReference;}

CMoiety::mpNumberReference

CTotalNumberReference * mpNumberReference

Definition: CMoiety.h:164

CCopasiObject * CMoiety::getValueReference ( ) const

Retrieve the object for the total particle number

Returns: CCopasiObject * valueReference

Definition at line 223 of file CMoiety.cpp.

References mpNumberReference.

 {
   return mpNumberReference;
 }

void CMoiety::initConversionFactor ( )

private

Initialize the number to amount conversion factor

Definition at line 272 of file CMoiety.cpp.

References DefaultFactor, CModel::getNumber2QuantityFactor(), CCopasiObject::getObjectAncestor(), and mpConversionFactor.

Referenced by setObjectParent().

 {
   const CModel * pModel = dynamic_cast< const CModel * >(getObjectAncestor("Model"));
 
   if (pModel != NULL)
     {
       mpConversionFactor = &pModel->getNumber2QuantityFactor();
     }
   else
     {
       mpConversionFactor = &DefaultFactor;
     }
 }

void CMoiety::initObjects ( )

private

Initialize the contained CCopasiObjects

Definition at line 76 of file CMoiety.cpp.

References CCopasiObject::addDirectDependency(), CCopasiContainer::addObjectReference(), mIAmount, mINumber, mNumber, mpDNumberReference, mpINumberReference, mpNumberReference, refreshAmount(), refreshDependentNumber(), refreshInitialValue(), refreshValue(), CCopasiObject::setRefresh(), and CCopasiObject::ValueDbl.

Referenced by CMoiety().

 {
   setRefresh(this, &CMoiety::refreshDependentNumber);
 
   mpINumberReference = new CTotalNumberReference("InitialValue", this, mINumber);
   mpINumberReference->setRefresh(this, &CMoiety::refreshInitialValue);
 
   mpNumberReference = new CTotalNumberReference("Value", this, mNumber);
   mpNumberReference->setRefresh(this, &CMoiety::refreshValue);
 
   mpDNumberReference = new CDependentNumberReference("DependentValue", this, mNumber);
   mpDNumberReference->addDirectDependency(this);
 
   CCopasiObject * pObject = addObjectReference("Amount", mIAmount, CCopasiObject::ValueDbl);
   pObject->setRefresh(this, &CMoiety::refreshAmount);
   pObject->addDirectDependency(mpNumberReference);
 
   return;
 }

void CMoiety::refreshAmount ( )

Refresh the total amount

Definition at line 262 of file CMoiety.cpp.

References mIAmount, mINumber, and mpConversionFactor.

Referenced by initObjects().

 {
   mIAmount = mINumber * *mpConversionFactor;
 }

void CMoiety::refreshDependentNumber ( )

Refreshes the value of the dependent number

Definition at line 122 of file CMoiety.cpp.

References mEquation, mINumber, and mNumber.

Referenced by dependentNumber(), and initObjects().

 {
   mNumber = mINumber;
 
   std::vector< std::pair< C_FLOAT64, CMetab * > >::iterator it = mEquation.begin() + 1;
   std::vector< std::pair< C_FLOAT64, CMetab * > >::iterator end = mEquation.end();
 
   for (; it != end; ++it)
     mNumber -= it->first * it->second->getValue();
 
   // It is save to update the particle number of the dependent species here.
   // We are mimicking the behavior of the new math container by doing it.
   mEquation.begin()->second->setValue(mNumber);
 
   return;
 }

void CMoiety::refreshInitialValue ( )

Refresh the initial total particle number

Definition at line 193 of file CMoiety.cpp.

References mEquation, and mINumber.

Referenced by initObjects().

 {
   mINumber = 0;
 
   std::vector< std::pair< C_FLOAT64, CMetab * > >::iterator it = mEquation.begin();
   std::vector< std::pair< C_FLOAT64, CMetab * > >::iterator end = mEquation.end();
 
   for (; it != end; ++it)
     mINumber += it->first * it->second->getInitialValue();
 
   return;
 }

void CMoiety::refreshValue ( )

Refresh the total particle number

Definition at line 214 of file CMoiety.cpp.

References mEquation, and mINumber.

Referenced by initObjects().

 {
   std::vector< std::pair< C_FLOAT64, CMetab * > >::iterator it = mEquation.begin();
   std::vector< std::pair< C_FLOAT64, CMetab * > >::iterator end = mEquation.end();
 
   for (; it != end; ++it)
     mINumber += it->first * it->second->getValue();
 }

bool CMoiety::setObjectParent ( const CCopasiContainer * pParent )

virtual

Sets the parent of the moiety;

Parameters

const CCopasiContainer * pParent

Returns: bool success

Reimplemented from CCopasiObject.

Definition at line 156 of file CMoiety.cpp.

References initConversionFactor(), and CCopasiObject::setObjectParent().

 {
   bool success = CCopasiContainer::setObjectParent(pParent);
   initConversionFactor();
 
   return success;
 }

Member Data Documentation

const C_FLOAT64 CMoiety::DefaultFactor

staticprivate

The default conversion factor used if the moiety is not part of a model

Definition at line 126 of file CMoiety.h.

Referenced by initConversionFactor().

std::vector<std::pair< C_FLOAT64, CMetab * > > CMoiety::mEquation

private

Vector of linear dependent CChemEqElement 0..*

Definition at line 153 of file CMoiety.h.

Referenced by add(), cleanup(), getDescription(), getEquation(), getExpression(), refreshDependentNumber(), refreshInitialValue(), and refreshValue().

C_FLOAT64 CMoiety::mIAmount

private

The total Amount of the Moiety.

Definition at line 146 of file CMoiety.h.

Referenced by getAmount(), initObjects(), and refreshAmount().

C_FLOAT64 CMoiety::mINumber

private

Initial Number of Particles of Moiety.

Definition at line 141 of file CMoiety.h.

Referenced by getNumber(), initObjects(), refreshAmount(), refreshDependentNumber(), refreshInitialValue(), and refreshValue().

std::string CMoiety::mKey

private

The key of the moiety

Definition at line 131 of file CMoiety.h.

Referenced by getKey(), and ~CMoiety().

C_FLOAT64 CMoiety::mNumber

private

Number of Particles of Moiety.

Definition at line 136 of file CMoiety.h.

Referenced by dependentNumber(), getDependentNumber(), initObjects(), and refreshDependentNumber().

const C_FLOAT64* CMoiety::mpConversionFactor

private

A pointer to the conversion factor between the particle number and the amount.

Definition at line 174 of file CMoiety.h.

Referenced by initConversionFactor(), and refreshAmount().

CDependentNumberReference* CMoiety::mpDNumberReference

private

A pointer to the object for the dependent particle number

Definition at line 169 of file CMoiety.h.

Referenced by getDependentNumberReference(), and initObjects().

CTotalNumberReference* CMoiety::mpINumberReference

private

A pointer to the object for the initial total particle number

Definition at line 158 of file CMoiety.h.

Referenced by add(), cleanup(), getInitialValueReference(), and initObjects().

CTotalNumberReference* CMoiety::mpNumberReference

private

A pointer to the object for the total particle number This is used during events

Definition at line 164 of file CMoiety.h.

Referenced by add(), cleanup(), getTotalNumberReference(), getValueReference(), and initObjects().

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

Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation