CMetabOld Class Reference

#include <CMetab.h>

Inheritance diagram for CMetabOld:

Collaboration diagram for CMetabOld:

Public Member Functions
void	cleanup ()
	CMetabOld (const std::string &name="NoName", const CCopasiContainer *pParent=NULL)
	CMetabOld (const CMetabOld &src, const CCopasiContainer *pParent=NULL)
C_INT32	getIndex () const
C_INT32	load (CReadConfig &configbuffer)
	~CMetabOld ()
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
virtual const std::string &	getKey () 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)
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 Attributes
C_INT32	mCompartment
C_FLOAT64	mIConc
CMetab::Status	mStatus

Friends
class	CMetab

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 485 of file CMetab.h.

Constructor & Destructor Documentation

CMetabOld::CMetabOld	(	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 997 of file CMetab.cpp.

References CONSTRUCTOR_TRACE.

                                                      :
  CCopasiContainer(name, pParent, "Old Metabolite"),
  mIConc(1.0),
  mStatus(CModelEntity::REACTIONS),
  mCompartment()
{CONSTRUCTOR_TRACE;}

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

Copy constructor

Parameters

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

Definition at line 1005 of file CMetab.cpp.

References CONSTRUCTOR_TRACE.

                                                      :
  CCopasiContainer(src, pParent),
  mIConc(src.mIConc),
  mStatus(src.mStatus),
  mCompartment(src.mCompartment)
{CONSTRUCTOR_TRACE;}

CMetabOld::~CMetabOld

(

)

Destructor.

Definition at line 1013 of file CMetab.cpp.

References DESTRUCTOR_TRACE.

{DESTRUCTOR_TRACE;}

Member Function Documentation

void CMetabOld::cleanup

(

)

cleanup()

Definition at line 1015 of file CMetab.cpp.

{}

C_INT32 CMetabOld::getIndex

(

)

const

Definition at line 1075 of file CMetab.cpp.

References mCompartment.

{return mCompartment;}

C_INT32 CMetabOld::load

(

CReadConfig &

configbuffer

)

Loads an object with data coming from a CReadConfig object. (CReadConfig object reads an input stream)

Parameters

pconfigbuffer

reference to a CReadConfig object.

Returns

Fail

Definition at line 1017 of file CMetab.cpp.

References C_INT32, CModelEntity::FIXED, CCopasiObject::getObjectName(), CReadConfig::getVariable(), mCompartment, METAB_MOIETY, mIConc, mStatus, CModelEntity::REACTIONS, CReadConfig::SEARCH, CCopasiObject::setObjectName(), and CCopasiMessage::WARNING.

{
  C_INT32 Fail = 0;
  std::string tmp;
  Fail = configbuffer.getVariable("Metabolite", "string",
                                  (void *) & tmp,
                                  CReadConfig::SEARCH);

  if (Fail)
    return Fail;

  setObjectName(tmp);

  Fail = configbuffer.getVariable("Concentration", "C_FLOAT64",
                                  (void *) & mIConc);

  if (Fail)
    return Fail;

  Fail = configbuffer.getVariable("Compartment", "C_INT32",
                                  (void *) & mCompartment);

  if (Fail)
    return Fail;

  C_INT32 Status;

  Fail = configbuffer.getVariable("Type", "C_INT32",
                                  (void *) & Status);

  if (Status == 0)
    mStatus = CModelEntity::FIXED;
  else
    mStatus = CModelEntity::REACTIONS;

  // sanity check
  if ((mStatus < 0) || (mStatus > 7))
    {
      CCopasiMessage(CCopasiMessage::WARNING,
                     "The file specifies a non-existing type "
                     "for '%s'.\nReset to internal species.",
                     getObjectName().c_str());
      mStatus = CModelEntity::REACTIONS;
    }

  // sanity check
  if ((mStatus != METAB_MOIETY) && (mIConc < 0.0))
    {
      CCopasiMessage(CCopasiMessage::WARNING,
                     "The file specifies a negative concentration "
                     "for '%s'.\nReset to default.",
                     getObjectName().c_str());
      mIConc = 1.0;
    }

  return Fail;
}

Friends And Related Function Documentation

friend class CMetab

friend

Definition at line 487 of file CMetab.h.

Member Data Documentation

C_INT32 CMetabOld::mCompartment

private

Index of the compartment the metabolite is located in.

Definition at line 506 of file CMetab.h.

Referenced by getIndex(), and load().

C_FLOAT64 CMetabOld::mIConc

private

Concentration of the metabolite.

Definition at line 495 of file CMetab.h.

Referenced by load(), and CMetab::operator=().

CMetab::Status CMetabOld::mStatus

private

Status of the metabolite. One of (METAB_FIXED, METAB_VARIABLE, METAB_DEPENDENT, METAB_MOIETY).

Definition at line 501 of file CMetab.h.

Referenced by load(), and CMetab::operator=().

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

• CMetab.h
• CMetab.cpp