COPASI API  4.16.103
Public Member Functions | Friends | List of all members
CLMetabGlyph Class Reference

#include <CLGlyphs.h>

Inheritance diagram for CLMetabGlyph:
Inheritance graph
Collaboration diagram for CLMetabGlyph:
Collaboration graph

Public Member Functions

 CLMetabGlyph (const std::string &name="MetabGlyph", const CCopasiContainer *pParent=NULL)
 CLMetabGlyph (const CLMetabGlyph &src, const CCopasiContainer *pParent=NULL)
 CLMetabGlyph (const SpeciesGlyph &sbml, const std::map< std::string, std::string > &modelmap, std::map< std::string, std::string > &layoutmap, const CCopasiContainer *pParent=NULL)
virtual CLGraphicalObjectclone () const
virtual void exportToSBML (SpeciesGlyph *g, const std::map< const CCopasiObject *, SBase * > &copasimodelmap, std::map< std::string, const SBase * > &sbmlIDs) const
CLMetabGlyphoperator= (const CLMetabGlyph &rhs)
void print (std::ostream *ostream) const
- Public Member Functions inherited from CLGraphicalObject
 CLGraphicalObject (const std::string &name="GraphicalObject", const CCopasiContainer *pParent=NULL)
 CLGraphicalObject (const CLGraphicalObject &src, const CCopasiContainer *pParent=NULL)
 CLGraphicalObject (const GraphicalObject &sbml, std::map< std::string, std::string > &layoutmap, const CCopasiContainer *pParent=NULL)
virtual void exportToSBML (GraphicalObject *sbmlobject, const std::map< const CCopasiObject *, SBase * > &copasimodelmap, std::map< std::string, const SBase * > &sbmlIDs) const
const CLBoundingBoxgetBoundingBox () const
CLBoundingBoxgetBoundingBox ()
const CLDimensionsgetDimensions () const
const C_FLOAT64getHeight () const
virtual const std::string & getKey () const
CCopasiObjectgetModelObject () const
std::string getModelObjectDisplayName (bool regular=true, bool richtext=false) const
const std::string & getModelObjectKey () const
std::string getModelObjectName () const
const std::string & getObjectRole () const
const CLPointgetPosition () const
const C_FLOAT64getWidth () const
const C_FLOAT64getX () const
const C_FLOAT64getY () const
bool hasValidModelReference () const
virtual void moveBy (const CLPoint &p)
CLGraphicalObjectoperator= (const CLGraphicalObject &rhs)
void print (std::ostream *ostream) const
void setBoundingBox (const CLBoundingBox &bb)
void setDimensions (const CLDimensions &d)
void setHeight (const C_FLOAT64 &h)
void setModelObjectKey (const std::string &k)
void setObjectRole (const std::string &role)
void setPosition (const CLPoint &p)
void setWidth (const C_FLOAT64 &w)
void setX (const C_FLOAT64 &x)
void setY (const C_FLOAT64 &y)
 ~CLGraphicalObject ()
- Public Member Functions inherited from CLBase
 CLBase ()
 CLBase (const CLBase &b)
 CLBase (const SBase &)
const std::string & getTag () const
bool hasTag () const
void setTag (const std::string &tag)
virtual ~CLBase ()
- 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
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
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
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 ()


std::ostream & operator<< (std::ostream &os, const CLMetabGlyph &g)

Additional Inherited Members

- Public Types inherited from CCopasiContainer
typedef std::multimap
< std::string, CCopasiObject * > 
- Public Types inherited from CCopasiObject
typedef std::set< const
CCopasiObject * > 
typedef std::vector< Refresh * > DataUpdateSequence
- Public Types inherited from CObjectInterface
typedef std::set< const
CObjectInterface * > 
typedef std::vector
< CObjectInterface * > 
- 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 * > 
- 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 CLGraphicalObject
CLBoundingBox mBBox
std::string mKey
std::string mModelObjectKey
std::string mObjectRole
- Protected Attributes inherited from CLBase
std::string mTag
- Protected Attributes inherited from CCopasiContainer
objectMap mObjects
- Static Protected Attributes inherited from CCopasiObject
static CRenameHandlersmpRenameHandler = NULL

Detailed Description

Graphical representation of a metabolite

Definition at line 30 of file CLGlyphs.h.

Constructor & Destructor Documentation

CLMetabGlyph::CLMetabGlyph ( const std::string &  name = "MetabGlyph",
const CCopasiContainer pParent = NULL 

Definition at line 36 of file CLGlyphs.cpp.

Referenced by clone().

38  : CLGraphicalObject(name, pParent)
39 {}
CLGraphicalObject(const std::string &name="GraphicalObject", const CCopasiContainer *pParent=NULL)
CLMetabGlyph::CLMetabGlyph ( const CLMetabGlyph src,
const CCopasiContainer pParent = NULL 

Definition at line 41 of file CLGlyphs.cpp.

43  : CLGraphicalObject(src, pParent)
44 {}
CLGraphicalObject(const std::string &name="GraphicalObject", const CCopasiContainer *pParent=NULL)
CLMetabGlyph::CLMetabGlyph ( const SpeciesGlyph &  sbml,
const std::map< std::string, std::string > &  modelmap,
std::map< std::string, std::string > &  layoutmap,
const CCopasiContainer pParent = NULL 

constructor from libsbml object

Definition at line 46 of file CLGlyphs.cpp.

References CLGraphicalObject::setModelObjectKey().

50  : CLGraphicalObject(sbml, layoutmap, pParent)
51 {
52  //get the copasi key corresponding to the sbml id for the species
53  if (sbml.getSpeciesId() != "")
54  {
55  std::map<std::string, std::string>::const_iterator it = modelmap.find(sbml.getSpeciesId());
57  if (it != modelmap.end())
58  setModelObjectKey(it->second);
59  }
60 }
void setModelObjectKey(const std::string &k)
CLGraphicalObject(const std::string &name="GraphicalObject", const CCopasiContainer *pParent=NULL)

Member Function Documentation

virtual CLGraphicalObject* CLMetabGlyph::clone ( ) const

Reimplemented from CLGraphicalObject.

Definition at line 54 of file CLGlyphs.h.

References CLMetabGlyph().

54 {return new CLMetabGlyph(*this, NULL);};
CLMetabGlyph(const std::string &name="MetabGlyph", const CCopasiContainer *pParent=NULL)
Definition: CLGlyphs.cpp:36
void CLMetabGlyph::exportToSBML ( SpeciesGlyph *  g,
const std::map< const CCopasiObject *, SBase * > &  copasimodelmap,
std::map< std::string, const SBase * > &  sbmlIDs 
) const

This method writes the information of the copasi layout object into the corresponding sbml object

Definition at line 73 of file CLGlyphs.cpp.

References CLGraphicalObject::exportToSBML(), and CLGraphicalObject::getModelObject().

Referenced by CLayout::exportToSBML(), and CLGeneralGlyph::exportToSBML().

76 {
77  if (!g) return;
79  //call the coresponding method of the base class
80  CLGraphicalObject::exportToSBML(g, copasimodelmap, sbmlIDs);
82  //reference to model objects
85  if (tmp)
86  {
87  std::map<const CCopasiObject*, SBase*>::const_iterator it = copasimodelmap.find(tmp);
89  if (it != copasimodelmap.end())
90  {
91  if (it->second)
92  g->setSpeciesId(it->second->getId());
93  }
94  }
95 }
virtual void exportToSBML(GraphicalObject *sbmlobject, const std::map< const CCopasiObject *, SBase * > &copasimodelmap, std::map< std::string, const SBase * > &sbmlIDs) const
CCopasiObject * getModelObject() const
CLMetabGlyph & CLMetabGlyph::operator= ( const CLMetabGlyph rhs)

assignment operator

Definition at line 62 of file CLGlyphs.cpp.

References CLGraphicalObject::operator=().

63 {
64  if (this == &rhs) return * this; //do nothing if lhs and rhs are the same
68  //nothing to be done here
70  return *this;
71 }
CLGraphicalObject & operator=(const CLGraphicalObject &rhs)
void CLMetabGlyph::print ( std::ostream *  ostream) const

This is the output method for any object. The default implementation provided with CCopasiObject uses the ostream operator<< of the object to print the object.To override this default behavior one needs to reimplement the virtual print function.

std::ostream* ostream

Reimplemented from CCopasiObject.

Definition at line 103 of file CLGlyphs.cpp.

104 {*ostream << *this;}

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  os,
const CLMetabGlyph g 

insert operator

Definition at line 97 of file CLGlyphs.cpp.

98 {
99  os << "MetabGlyph: " << dynamic_cast<const CLGraphicalObject&>(g);
100  return os;
101 }

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