COPASI API  4.16.103
Public Member Functions | Private Member Functions | Private Attributes | Friends | List of all members
CChemEqElement Class Reference

#include <CChemEqElement.h>

Inheritance diagram for CChemEqElement:
Inheritance graph
[legend]
Collaboration diagram for CChemEqElement:
Collaboration graph
[legend]

Public Member Functions

void addToMultiplicity (const C_FLOAT64 multiplicity=1.0)
 
 CChemEqElement (const std::string &name="Chem Eq Element", const CCopasiContainer *pParent=NULL)
 
 CChemEqElement (const CChemEqElement &src, const CCopasiContainer *pParent=NULL)
 
void cleanup ()
 
const CMetabgetMetabolite () const
 
const std::string & getMetaboliteKey () const
 
const C_FLOAT64getMultiplicity () const
 
void setMetabolite (const std::string &key)
 
void setMultiplicity (const C_FLOAT64 multiplicity)
 
 ~CChemEqElement ()
 
- 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 CObjectInterfacegetObject (const CCopasiObjectName &cn) const
 
virtual const objectMapgetObjects () const
 
virtual std::string getUnits () const
 
virtual const CCopasiObjectgetValueObject () 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 DataObjectSetgetDirectDependencies (const DataObjectSet &context=DataObjectSet()) const
 
virtual const std::string & getKey () const
 
CCopasiContainergetObjectAncestor (const std::string &type) const
 
CCopasiDataModelgetObjectDataModel ()
 
const CCopasiDataModelgetObjectDataModel () const
 
virtual std::string getObjectDisplayName (bool regular=true, bool richtext=false) const
 
const std::string & getObjectName () const
 
CCopasiContainergetObjectParent () const
 
const std::string & getObjectType () const
 
virtual const
CObjectInterface::ObjectSet
getPrerequisites () const
 
virtual RefreshgetRefresh () const
 
UpdateMethodgetUpdateMethod () const
 
virtual voidgetValuePointer () 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 Member Functions

void initObjects ()
 

Private Attributes

std::string mMetaboliteKey
 
C_FLOAT64 mMultiplicity
 

Friends

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

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 >
CCopasiObjectaddMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
 
template<class CType >
CCopasiObjectaddObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
 
template<class CType >
CCopasiObjectaddVectorReference (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 CRenameHandlersmpRenameHandler = NULL
 

Detailed Description

Definition at line 41 of file CChemEqElement.h.

Constructor & Destructor Documentation

CChemEqElement::CChemEqElement ( const std::string &  name = "Chem Eq Element",
const CCopasiContainer pParent = NULL 
)

Default constructor

Parameters
conststd::string & name (default: "NoName")
constCCopasiContainer * pParent (default: NULL)

Definition at line 40 of file CChemEqElement.cpp.

References CONSTRUCTOR_TRACE, and initObjects().

41  :
42  CCopasiContainer(name, pParent, "Chemical Equation Element"),
44  mMultiplicity(0)
45  //mpMetabolite(NULL)
46 {
47  initObjects();
49 }
std::string mMetaboliteKey
C_FLOAT64 mMultiplicity
char name[1]
Definition: stdsoap2.h:1342
#define CONSTRUCTOR_TRACE
Definition: copasi.h:202
CChemEqElement::CChemEqElement ( const CChemEqElement src,
const CCopasiContainer pParent = NULL 
)

Copy constructor

Parameters
const CChemEqElement &src
constCCopasiContainer * pParent (default: NULL)

Definition at line 51 of file CChemEqElement.cpp.

References CONSTRUCTOR_TRACE, and initObjects().

52  :
53  CCopasiContainer(src, pParent),
56  //mpMetabolite(src.mpMetabolite)
57 {
58  initObjects();
60 }
std::string mMetaboliteKey
C_FLOAT64 mMultiplicity
#define CONSTRUCTOR_TRACE
Definition: copasi.h:202
CChemEqElement::~CChemEqElement ( )

Destructor

Definition at line 62 of file CChemEqElement.cpp.

References DESTRUCTOR_TRACE.

#define DESTRUCTOR_TRACE
Definition: copasi.h:206

Member Function Documentation

void CChemEqElement::addToMultiplicity ( const C_FLOAT64  multiplicity = 1.0)

Add to the multiplicity of the element.

Parameters
const C_FLOAT64multiplicity (default = 1.0)

Definition at line 92 of file CChemEqElement.cpp.

References mMultiplicity.

93 {mMultiplicity += multiplicity;}
C_FLOAT64 mMultiplicity
void CChemEqElement::cleanup ( )

cleanup

Definition at line 70 of file CChemEqElement.cpp.

70 {}
const CMetab * CChemEqElement::getMetabolite ( ) const
const std::string & CChemEqElement::getMetaboliteKey ( ) const

Retrieve the key of the species

Returns
const std::string & speciesKey

Definition at line 83 of file CChemEqElement.cpp.

References mMetaboliteKey.

Referenced by CChemEq::addElement(), CModelAdd::addReactions(), SBMLImporter::applyStoichiometricExpressions(), CODEExporter::exportKineticFunction(), and SBMLImporter::isMassActionExpression().

84 {return mMetaboliteKey;}
std::string mMetaboliteKey
const C_FLOAT64 & CChemEqElement::getMultiplicity ( ) const
void CChemEqElement::initObjects ( )
private

Definition at line 64 of file CChemEqElement.cpp.

References CCopasiContainer::addObjectReference(), mMetaboliteKey, mMultiplicity, and CCopasiObject::ValueDbl.

Referenced by CChemEqElement().

65 {
67  addObjectReference("Metab Key", mMetaboliteKey);
68 }
std::string mMetaboliteKey
C_FLOAT64 mMultiplicity
CCopasiObject * addObjectReference(const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
void CChemEqElement::setMetabolite ( const std::string &  key)

Set the metabolite of the element.

Parameters
CMetab* metabolite

Definition at line 72 of file CChemEqElement.cpp.

References CKeyFactory::get(), CCopasiRootContainer::getKeyFactory(), CCopasiObject::getObjectName(), mMetaboliteKey, and CCopasiObject::setObjectName().

Referenced by CChemEq::addMetabolite(), CModelMerging::mergeMetabolites(), and CModelExpansion::replaceInReaction().

73 {
74  mMetaboliteKey = key;
76 
77  if (tmp)
78  this->setObjectName("ChEqEl_" + tmp->getObjectName());
79  else
80  this->setObjectName("ChemEqElement");
81 }
const std::string & getObjectName() const
CCopasiObject * get(const std::string &key)
Definition: CMetab.h:178
std::string mMetaboliteKey
static CKeyFactory * getKeyFactory()
bool setObjectName(const std::string &name)
void CChemEqElement::setMultiplicity ( const C_FLOAT64  multiplicity)

Set the multiplicity of the element.

Parameters
const C_FLOAT64multiplicity

Definition at line 89 of file CChemEqElement.cpp.

References mMultiplicity.

Referenced by CChemEq::addElement(), CChemEq::addMetabolite(), and CChemEq::setMultiplicity().

90 {mMultiplicity = multiplicity;}
C_FLOAT64 mMultiplicity

Friends And Related Function Documentation

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

Definition at line 100 of file CChemEqElement.cpp.

101 {
102  os << "CChemEqElement: " << d.mMultiplicity
103  << " * " << d.mMetaboliteKey << std::endl;
104 
105  return os;
106 }
std::string mMetaboliteKey
C_FLOAT64 mMultiplicity

Member Data Documentation

std::string CChemEqElement::mMetaboliteKey
private

The name of the metabolite the element

Definition at line 49 of file CChemEqElement.h.

Referenced by getMetabolite(), getMetaboliteKey(), initObjects(), operator<<(), and setMetabolite().

C_FLOAT64 CChemEqElement::mMultiplicity
private

The multiplicity of the metabolite

Definition at line 54 of file CChemEqElement.h.

Referenced by addToMultiplicity(), getMultiplicity(), initObjects(), operator<<(), and setMultiplicity().


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