#include <CCompartment.h>

Inheritance diagram for CCompartment:

Collaboration diagram for CCompartment:

Public Member Functions
bool	addMetabolite (CMetab *metabolite)

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

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

void	cleanup ()

bool	createMetabolite (const CMetab &metabolite)

virtual std::string	getChildObjectUnits (const CCopasiObject *pObject) const

virtual std::set< const CCopasiObject * >	getDeletedObjects () const

unsigned C_INT32	getDimensionality () const

CCopasiVectorNS< CMetab > &	getMetabolites ()

const CCopasiVectorNS< CMetab > &	getMetabolites () const

C_INT32	load (CReadConfig &configbuffer)

bool	setDimensionality (unsigned C_INT32 dim)

virtual	~CCompartment ()

Public Member Functions inherited from CModelEntity
virtual void	calculate ()

	CModelEntity (const std::string &name="NoName", const CCopasiContainer *pParent=NULL, const std::string &type="ModelEntity", const unsigned C_INT32 &flag=CCopasiObject::Container\|CCopasiObject::ValueDbl)

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

virtual bool	compile ()

std::string	getExpression () const

const CExpression *	getExpressionPtr () const

CExpression *	getExpressionPtr ()

std::string	getInitialExpression () const

const CExpression *	getInitialExpressionPtr () const

CExpression *	getInitialExpressionPtr ()

const C_FLOAT64 &	getInitialValue () const

CCopasiObject *	getInitialValueReference () const

virtual const std::string &	getKey () const

const C_FLOAT64 &	getRate () const

CCopasiObject *	getRateReference () const

const std::string &	getSBMLId () const

const CModelEntity::Status &	getStatus () const

const C_FLOAT64 &	getValue () const

virtual const CCopasiObject *	getValueObject () const

virtual void *	getValuePointer () const

CCopasiObject *	getValueReference () const

bool	isFixed () const

const bool &	isUsed () const

virtual bool	mustBeDeleted (const DataObjectSet &deletedObjects) const

virtual void	refreshInitialValue ()

bool	setExpression (const std::string &expression)

bool	setExpressionPtr (CExpression *pExpression)

bool	setInitialExpression (const std::string &expression)

bool	setInitialExpressionPtr (CExpression *pExpression)

virtual void	setInitialValue (const C_FLOAT64 &initialValue)

void	setInitialValuePtr (C_FLOAT64 *pInitialValue)

virtual bool	setObjectParent (const CCopasiContainer *pParent)

void	setRate (const C_FLOAT64 &rate)

void	setSBMLId (const std::string &id)

virtual void	setStatus (const CModelEntity::Status &status)

void	setUsed (const bool &used)

virtual void	setValue (const C_FLOAT64 &value)

void	setValuePtr (C_FLOAT64 *pValue)

	~CModelEntity ()

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 const CObjectInterface *	getObject (const CCopasiObjectName &cn) const

virtual const objectMap &	getObjects () const

virtual std::string	getUnits () 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

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 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 ()

Public Member Functions inherited from CAnnotation
bool	addUnsupportedAnnotation (const std::string &name, const std::string &xml)

	CAnnotation ()

	CAnnotation (const CAnnotation &src)

const std::string &	getMiriamAnnotation () const

const std::string &	getNotes () const

UnsupportedAnnotation &	getUnsupportedAnnotations ()

const UnsupportedAnnotation &	getUnsupportedAnnotations () const

bool	operator== (const CAnnotation &rhs) const

bool	removeUnsupportedAnnotation (const std::string &name)

bool	replaceUnsupportedAnnotation (const std::string &name, const std::string &xml)

void	setMiriamAnnotation (const std::string &miriamAnnotation, const std::string &newId, const std::string &oldId)

void	setNotes (const std::string &notes)

virtual	~CAnnotation ()

Protected Attributes
unsigned C_INT32	mDimensionality

Protected Attributes inherited from CModelEntity
CExpression *	mpExpression

CExpression *	mpInitialExpression

C_FLOAT64 *	mpIValue

CCopasiObjectReference < C_FLOAT64 > *	mpIValueReference

CModel *	mpModel

CCopasiObjectReference < C_FLOAT64 > *	mpRateReference

C_FLOAT64 *	mpValue

CCopasiObjectReference < C_FLOAT64 > *	mpValueReference

C_FLOAT64	mRate

std::string	mSBMLId

Protected Attributes inherited from CCopasiContainer
objectMap	mObjects

Protected Attributes inherited from CAnnotation
std::string	mKey

Private Member Functions
void	initObjects ()

Private Attributes
CCopasiVectorNS< CMetab >	mMetabolites

Friends
std::ostream &	operator<< (std::ostream &os, const CCompartment &d)

Additional Inherited Members
Public Types inherited from CModelEntity
enum	Status { FIXED = 0, ASSIGNMENT, REACTIONS, ODE, TIME }

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

Public Types inherited from CAnnotation
typedef std::map< std::string, std::string >	UnsupportedAnnotation

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 Member Functions inherited from CAnnotation
static CAnnotation *	castObject (CCopasiObject *pObject)

static const CAnnotation *	castObject (const CCopasiObject *pObject)

Static Public Attributes inherited from CModelEntity
static const std::string	StatusName []

static const char *	XMLStatus []

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)

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

Detailed Description

Definition at line 37 of file CCompartment.h.

Constructor & Destructor Documentation

CCompartment::CCompartment	(	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 CCompartment.cpp.

References CKeyFactory::add(), CONSTRUCTOR_TRACE, CModelEntity::FIXED, CCopasiRootContainer::getKeyFactory(), initObjects(), CAnnotation::mKey, CModelEntity::mpIValue, and CModelEntity::setStatus().

                                                             :
   CModelEntity(name, pParent, "Compartment"),
   mMetabolites("Metabolites", this),
   mDimensionality(3)
 {
   initObjects();
 
   mKey = CCopasiRootContainer::getKeyFactory()->add("Compartment", this);
 
   setStatus(FIXED);
 
   *mpIValue = 1.0;
 
   CONSTRUCTOR_TRACE;
 }

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

Copy constructor.

Parameters

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

Definition at line 53 of file CCompartment.cpp.

References CKeyFactory::add(), CONSTRUCTOR_TRACE, CCopasiRootContainer::getKeyFactory(), initObjects(), and CAnnotation::mKey.

                                                             :
   CModelEntity(src, pParent),
   mMetabolites(src.mMetabolites, this),
   mDimensionality(src.mDimensionality)
 {
   mKey = CCopasiRootContainer::getKeyFactory()->add("Compartment", this);
   CONSTRUCTOR_TRACE;
   initObjects();
 }

CCompartment::~CCompartment ( )

virtual

Destructor. The destructor does nothing.

Definition at line 64 of file CCompartment.cpp.

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

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

Member Function Documentation

bool CCompartment::addMetabolite ( CMetab * metabolite )

Adds a metabolite to the compartment. Only the concentration is taken from the metabolite, the number of particles is calculated according to the volume of the compartment

Parameters

CMetab * metabolite;

Returns: bool success

Definition at line 175 of file CCompartment.cpp.

References CCopasiVectorN< CType >::add(), CCopasiObject::getCN(), CCopasiObject::getObjectParent(), CRenameHandler::handle(), mMetabolites, and CCopasiObject::smpRenameHandler.

Referenced by createMetabolite(), CModelExpansion::replaceInMetab(), and CCopasiXMLParser::MetaboliteElement::start().

 {
   if (!pMetabolite) return false;
 
   std::string oldCN = pMetabolite->getCN();
 
   bool success = mMetabolites.add(pMetabolite, true);
 
   //if a metabolite is added to a compartment successfully the CN of
   //the metabolite is changed. This needs to be handled similarly to a
   //rename.
   if (success && smpRenameHandler && getObjectParent())
     {
       std::string newCN = pMetabolite->getCN();
       smpRenameHandler->handle(oldCN, newCN);
     }
 
   return success;
 }

void CCompartment::cleanup ( )

Cleanup

Definition at line 123 of file CCompartment.cpp.

References CCopasiVector< T >::cleanup(), and mMetabolites.

123 {mMetabolites.cleanup();}

CCompartment::mMetabolites

CCopasiVectorNS< CMetab > mMetabolites

Definition: CCompartment.h:45

CCopasiVector::cleanup

virtual void cleanup()

Definition: CCopasiVector.h:200

bool CCompartment::createMetabolite ( const CMetab & metabolite )

Adds a metabolite to the compartment. Only the concentration is taken from the metabolite, the number of particles is calculated according to the volume of the compartment

Parameters

const CMetab & metabolite;

Returns: bool success

Definition at line 165 of file CCompartment.cpp.

References addMetabolite().

 {
   CMetab * pMetab = new CMetab(metabolite);
 
   if (addMetabolite(pMetab)) return true;
 
   delete pMetab;
   return false;
 }

std::string CCompartment::getChildObjectUnits ( const CCopasiObject * pObject ) const

virtual

Retrieve the units of the child object.

Returns: std::string units

Reimplemented from CCopasiContainer.

Definition at line 71 of file CCompartment.cpp.

References CModel::getAreaUnitsDisplayString(), CModel::getLengthUnitsDisplayString(), CModel::getTimeUnitsDisplayString(), CModel::getVolumeUnitsDisplayString(), mDimensionality, CModelEntity::mpIValueReference, CModelEntity::mpModel, CModelEntity::mpRateReference, and CModelEntity::mpValueReference.

Referenced by CMetab::getChildObjectUnits(), and CModelParameter::getUnit().

 {
   if (mpModel == NULL) return "";
 
   if (pObject == mpValueReference ||
       pObject == mpIValueReference)
     {
       switch (mDimensionality)
         {
           case 1:
             return mpModel->getLengthUnitsDisplayString();
             break;
 
           case 2:
             return mpModel->getAreaUnitsDisplayString();
             break;
 
           case 3:
             return mpModel->getVolumeUnitsDisplayString();
             break;
 
           default:
             return "";
             break;
         }
     }
   else if (pObject == mpRateReference)
     {
       std::string Unit = getChildObjectUnits(mpValueReference);
       std::string TimeUnit = mpModel->getTimeUnitsDisplayString();
 
       if (Unit == "")
         {
           if (TimeUnit == "")
             {
               return "";
             }
 
           return "1/" + TimeUnit;
         }
 
       if (TimeUnit == "")
         {
           return Unit;
         }
 
       return Unit + "/" + TimeUnit;
     }
 
   return "";
 }

std::set< const CCopasiObject * > CCompartment::getDeletedObjects ( ) const

virtual

Retrieve the list of deleted numeric child objects;

Returns: std::set< const CCopasiObject * > deletedObjects

Reimplemented from CModelEntity.

Definition at line 125 of file CCompartment.cpp.

References CModelEntity::getDeletedObjects().

Referenced by CModel::appendDependentModelObjects(), CModel::removeCompartment(), CQCompartmentDM::removeRows(), and CQCompartment::slotBtnDelete().

 {
   std::set< const CCopasiObject * > Deleted = CModelEntity::getDeletedObjects();
 
   // We must not add the metabolites as CModel::appendDependentMetabolites does that.
 
   return Deleted;
 }

unsigned C_INT32 CCompartment::getDimensionality ( ) const

Get the dimensionality of the compartment

Definition at line 204 of file CCompartment.cpp.

References mDimensionality.

Referenced by CModelAdd::addCompartments(), CSBMLExporter::createCompartment(), SBMLImporter::createCReactionFromReaction(), CSBMLExporter::createInitialAssignment(), CSBMLExporter::createKineticLaw(), CSBMLExporter::createRule(), CModelExpansion::duplicateCompartment(), CSBMLExporter::exportEventAssignments(), SBMLImporter::importEvent(), SBMLImporter::importInitialAssignments(), SBMLImporter::importRuleForModelEntity(), CQCompartment::load(), CSBMLExporter::replaceSpeciesReferences(), CQCompartment::save(), and CCopasiXML::saveModel().

 {
   return mDimensionality;
 }

CCopasiVectorNS< CMetab > & CCompartment::getMetabolites ( )

Retrieve the vector of contained metabolites

Returns: CCopasiVectorNS < CMetab > & metabolites

Definition at line 157 of file CCompartment.cpp.

References mMetabolites.

Referenced by CQCompartment::copy(), SBMLImporter::createCMetabFromSpecies(), CQSelectionWizardPage::fillTree(), CMetabNameInterface::getMetabolite(), CQCompartment::loadMetaboliteTable(), moveObject(), CModelExpansion::replaceInMetab(), CQExpandModelData::slotCompartmentActivated(), and CQCompartment::slotMetaboliteTableCurrentChanged().

158 {return mMetabolites;}

CCompartment::mMetabolites

CCopasiVectorNS< CMetab > mMetabolites

Definition: CCompartment.h:45

const CCopasiVectorNS< CMetab > & CCompartment::getMetabolites ( ) const

Retrieve the vector of contained metabolites

Returns: const CCopasiVectorNS < CMetab > & metabolites

Definition at line 160 of file CCompartment.cpp.

References mMetabolites.

161 {return mMetabolites;}

CCompartment::mMetabolites

CCopasiVectorNS< CMetab > mMetabolites

Definition: CCompartment.h:45

void CCompartment::initObjects ( )

private

Initialize the contained CCopasiObjects

Definition at line 209 of file CCompartment.cpp.

References CModelEntity::mpIValueReference, CModelEntity::mpValueReference, and CCopasiObject::setObjectName().

Referenced by CCompartment().

 {
   mpIValueReference->setObjectName("InitialVolume");
   mpValueReference->setObjectName("Volume");
 }

C_INT32 CCompartment::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: mFail

See Also: mFail

Definition at line 134 of file CCompartment.cpp.

References C_FLOAT64, C_INT32, CReadConfig::getVariable(), CReadConfig::SEARCH, CModelEntity::setInitialValue(), and CCopasiObject::setObjectName().

 {
   C_INT32 Fail = 0;
   std::string tmp;
 
   if ((Fail = configbuffer.getVariable("Compartment", "string",
                                        (void *) & tmp,
                                        CReadConfig::SEARCH)))
     return Fail;
 
   setObjectName(tmp);
 
   C_FLOAT64 tmpdbl;
 
   if ((Fail = configbuffer.getVariable("Volume", "C_FLOAT64",
                                        (void *) & tmpdbl)))
     return Fail;
 
   setInitialValue(tmpdbl);
 
   return Fail;
 }

bool CCompartment::setDimensionality ( unsigned C_INT32 dim )

Set the dimensionality of the compartment. May be 0, 1, 2, or 3. If the value is not valid it will be ignored and the return value will be false

Definition at line 195 of file CCompartment.cpp.

References mDimensionality.

Referenced by CModelAdd::addCompartments(), SBMLImporter::createCCompartmentFromCompartment(), CModelExpansion::duplicateCompartment(), and CQCompartment::save().

 {
   if (dim > 3)
     return false;
 
   mDimensionality = dim;
   return true;
 }

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	os,
		const CCompartment &	d
	)

friend

Friend declaration for ostream operator <<

Parameters

std::ostream	& os
const	CCompartment & d

Returns: std::ostream & os

Definition at line 215 of file CCompartment.cpp.

 {
   os << "++++CCompartment: " << d.getObjectName() << " mValue " << *d.mpValue;
   os << "    CCompartment.mMetabolites " << std::endl << d.mMetabolites;
   os << "----CCompartment " << std::endl;
 
   return os;
 }

Member Data Documentation

unsigned C_INT32 CCompartment::mDimensionality

protected

The dimensionality of the compartment. Can be 0, 1, 2, or 3

Definition at line 155 of file CCompartment.h.

Referenced by getChildObjectUnits(), getDimensionality(), and setDimensionality().

CCopasiVectorNS< CMetab > CCompartment::mMetabolites

private

Metabolites located in the compartment. 0..* <{CMetab}>

Definition at line 45 of file CCompartment.h.

Referenced by addMetabolite(), cleanup(), getMetabolites(), and operator<<().

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

Public Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation