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

#include <CLGlyphs.h>

Inheritance diagram for CLMetabGlyph:
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Collaboration diagram for CLMetabGlyph:
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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
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
 
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 ()
 

Friends

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

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 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());
56 
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
inlinevirtual

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
virtual

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;
78 
79  //call the coresponding method of the base class
80  CLGraphicalObject::exportToSBML(g, copasimodelmap, sbmlIDs);
81 
82  //reference to model objects
84 
85  if (tmp)
86  {
87  std::map<const CCopasiObject*, SBase*>::const_iterator it = copasimodelmap.find(tmp);
88 
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
65 
67 
68  //nothing to be done here
69 
70  return *this;
71 }
CLGraphicalObject & operator=(const CLGraphicalObject &rhs)
void CLMetabGlyph::print ( std::ostream *  ostream) const
virtual

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.

Parameters
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 
)
friend

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: