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

#include <CLReactionGlyph.h>

Inheritance diagram for CLMetabReferenceGlyph:
Inheritance graph
Collaboration diagram for CLMetabReferenceGlyph:
Collaboration graph

Public Types

enum  Role {
- 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 * > 

Public Member Functions

 CLMetabReferenceGlyph (const std::string &name="MetabReferenceGlyph", const CCopasiContainer *pParent=NULL)
 CLMetabReferenceGlyph (const CLMetabReferenceGlyph &src, const CCopasiContainer *pParent=NULL)
 CLMetabReferenceGlyph (const SpeciesReferenceGlyph &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 (SpeciesReferenceGlyph *g, const std::map< const CCopasiObject *, SBase * > &copasimodelmap, std::map< std::string, const SBase * > &sbmlIDs, const std::map< const CLBase *, const SBase * > &layoutmap) const
CLMetabGlyphgetMetabGlyph () const
const std::string & getMetabGlyphKey () const
Role getRole () const
const std::string & getRoleDisplayName () const
CLMetabReferenceGlyphoperator= (const CLMetabReferenceGlyph &rhs)
void print (std::ostream *ostream) const
void setMetabGlyphKey (const std::string &k)
void setRole (Role r)
- Public Member Functions inherited from CLGlyphWithCurve
 CLGlyphWithCurve (const std::string &name="ReferenceGlyph", const CCopasiContainer *pParent=NULL)
 CLGlyphWithCurve (const CLGlyphWithCurve &src, const CCopasiContainer *pParent=NULL)
 CLGlyphWithCurve (const GraphicalObject &sbml, const std::map< std::string, std::string > &modelmap, std::map< std::string, std::string > &layoutmap, const CCopasiContainer *pParent=NULL)
const CLCurvegetCurve () const
CLCurvegetCurve ()
virtual void moveBy (const CLPoint &p)
CLGlyphWithCurveoperator= (const CLGlyphWithCurve &rhs)
void setCurve (const CLCurve &c)
- 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
CLGraphicalObjectoperator= (const CLGraphicalObject &rhs)
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 ()

Static Public Attributes

static const std::string RoleName []
static const std::string XMLRole []
- Static Public Attributes inherited from CCopasiContainer
static const std::vector
< CCopasiContainer * > 

Private Attributes

std::string mMetabGlyphKey
Role mRole


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

Additional Inherited Members

- 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)
- 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 CLGlyphWithCurve
CLCurve mCurve
- 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 CChemEqElement. This correspondents to the sbml SpeciesReferenceGlyph. The copasi equivalent is the CChemEqElement, however it has no key, so it cannot be referred to.

Definition at line 141 of file CLReactionGlyph.h.

Member Enumeration Documentation

Enum type for the role of the metab reference This enum must be synchronized with the corresponding enum in libsbml (sbml/layout/SpeciesReferenceRole.h)


Definition at line 150 of file CLReactionGlyph.h.

Constructor & Destructor Documentation

CLMetabReferenceGlyph::CLMetabReferenceGlyph ( const std::string &  name = "MetabReferenceGlyph",
const CCopasiContainer pParent = NULL 

Definition at line 256 of file CLReactionGlyph.cpp.

Referenced by clone().

258  : CLGlyphWithCurve(name, pParent),
259  mMetabGlyphKey(),
261 {}
CLGlyphWithCurve(const std::string &name="ReferenceGlyph", const CCopasiContainer *pParent=NULL)
CLMetabReferenceGlyph::CLMetabReferenceGlyph ( const CLMetabReferenceGlyph src,
const CCopasiContainer pParent = NULL 

Definition at line 263 of file CLReactionGlyph.cpp.

265  : CLGlyphWithCurve(src, pParent),
267  mRole(src.mRole)
268 {}
CLGlyphWithCurve(const std::string &name="ReferenceGlyph", const CCopasiContainer *pParent=NULL)
CLMetabReferenceGlyph::CLMetabReferenceGlyph ( const SpeciesReferenceGlyph &  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 270 of file CLReactionGlyph.cpp.

References CLGlyphWithCurve::mCurve, mMetabGlyphKey, and CLGraphicalObject::setModelObjectKey().

274  : CLGlyphWithCurve(sbml, modelmap, layoutmap, pParent),
275  mMetabGlyphKey(), //initialized in the body below
276  mRole((Role)sbml.getRole())
277 {
278  //get the copasi key corresponding to the sbml id for the species reference
279  if (sbml.getSpeciesReferenceId() != "")
280  {
281  std::map<std::string, std::string>::const_iterator it = modelmap.find(sbml.getSpeciesReferenceId());
283  if (it != modelmap.end())
284  setModelObjectKey(it->second);
285  }
287  //get the copasi key corresponding to the sbml id for the species glyph
288  if (sbml.getSpeciesGlyphId() != "")
289  {
290  std::map<std::string, std::string>::const_iterator it = layoutmap.find(sbml.getSpeciesGlyphId());
292  if (it != layoutmap.end())
293  mMetabGlyphKey = it->second;
294  }
296  //curve
297  if (sbml.getCurve())
298  {
299  CLCurve copy(*sbml.getCurve());
300  mCurve = copy;
301  }
302 }
void setModelObjectKey(const std::string &k)
CLGlyphWithCurve(const std::string &name="ReferenceGlyph", const CCopasiContainer *pParent=NULL)

Member Function Documentation

virtual CLGraphicalObject* CLMetabReferenceGlyph::clone ( ) const

Reimplemented from CLGraphicalObject.

Definition at line 212 of file CLReactionGlyph.h.

References CLMetabReferenceGlyph().

212 {return new CLMetabReferenceGlyph(*this, NULL);};
CLMetabReferenceGlyph(const std::string &name="MetabReferenceGlyph", const CCopasiContainer *pParent=NULL)
void CLMetabReferenceGlyph::exportToSBML ( SpeciesReferenceGlyph *  g,
const std::map< const CCopasiObject *, SBase * > &  copasimodelmap,
std::map< std::string, const SBase * > &  sbmlIDs,
const std::map< const CLBase *, const SBase * > &  layoutmap 
) const

This method writes the information of the COPASI layout object into the corresponding SBML object layoutmap contains a map from COPASI layout objects to libsbml layout objects. this is needed for resolving the reference to the metab glyph.

Definition at line 323 of file CLReactionGlyph.cpp.

References CLGraphicalObject::exportToSBML(), CLCurve::exportToSBML(), getMetabGlyph(), CLGlyphWithCurve::mCurve, and mRole.

Referenced by CLReactionGlyph::exportToSBML().

327 {
328  if (!g) return;
330  //call the coresponding method of the base class
331  CLGraphicalObject::exportToSBML(g, copasimodelmap, sbmlIDs);
333  //reference to species glyph
334  CLMetabGlyph* tmp = getMetabGlyph();
336  if (tmp)
337  {
338  std::map<const CLBase*, const SBase*>::const_iterator it = layoutmap.find(tmp);
340  if (it != layoutmap.end())
341  {
342  if (it->second)
343  {
344  //we need to cast here since layout objects in libsbml donĀ“t inherit the getId() method
345  //from SBase
346  const GraphicalObject* pGO = dynamic_cast<const GraphicalObject*>(it->second);
348  if (pGO)
349  g->setSpeciesGlyphId(pGO->getId());
350  }
351  }
352  }
354  //curve
355  mCurve.exportToSBML(g->getCurve(), copasimodelmap);
357  //Role
358  g->setRole((SpeciesReferenceRole_t)mRole);
359  //this depends on the copasi role enum being synchronous to the sbml one
360 }
void exportToSBML(Curve *c, const std::map< const CCopasiObject *, SBase * > &copasimodelmap) const
Definition: CLCurve.cpp:148
virtual void exportToSBML(GraphicalObject *sbmlobject, const std::map< const CCopasiObject *, SBase * > &copasimodelmap, std::map< std::string, const SBase * > &sbmlIDs) const
CLMetabGlyph * getMetabGlyph() const
CLMetabGlyph * CLMetabReferenceGlyph::getMetabGlyph ( ) const
const std::string& CLMetabReferenceGlyph::getMetabGlyphKey ( ) const
Role CLMetabReferenceGlyph::getRole ( ) const
const std::string& CLMetabReferenceGlyph::getRoleDisplayName ( ) const

Definition at line 209 of file CLReactionGlyph.h.

References mRole, and RoleName.

210  {return RoleName[mRole];};
static const std::string RoleName[]
CLMetabReferenceGlyph & CLMetabReferenceGlyph::operator= ( const CLMetabReferenceGlyph rhs)

assignment operator.

Definition at line 304 of file CLReactionGlyph.cpp.

References mMetabGlyphKey, mRole, and CLGlyphWithCurve::operator=().

305 {
306  if (this == &rhs) return * this; //do nothing if lhs and rhs are the same
310  //handle the specific glyph stuff:
312  mRole = rhs.mRole;
314  return *this;
315 }
CLGlyphWithCurve & operator=(const CLGlyphWithCurve &rhs)
void CLMetabReferenceGlyph::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 CLGlyphWithCurve.

Definition at line 379 of file CLReactionGlyph.cpp.

380 {*ostream << *this;}
void CLMetabReferenceGlyph::setMetabGlyphKey ( const std::string &  k)
void CLMetabReferenceGlyph::setRole ( Role  r)

Friends And Related Function Documentation

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

insert operator

Definition at line 362 of file CLReactionGlyph.cpp.

363 {
364  os << " MetabReferenceGlyph: " << dynamic_cast<const CLGraphicalObject&>(g);
366  os << " Role: " << CLMetabReferenceGlyph::RoleName[g.getRole()] << "\n";
368  const CLMetabGlyph* tmp = g.getMetabGlyph();
370  if (tmp)
371  os << " refers to a MetabGlyph that refers to "
372  << tmp->getModelObjectDisplayName() << std::endl;
374  os << g.mCurve;
376  return os;
377 }
std::string getModelObjectDisplayName(bool regular=true, bool richtext=false) const
static const std::string RoleName[]
CLMetabGlyph * getMetabGlyph() const

Member Data Documentation

std::string CLMetabReferenceGlyph::mMetabGlyphKey
Role CLMetabReferenceGlyph::mRole

Definition at line 180 of file CLReactionGlyph.h.

Referenced by exportToSBML(), getRole(), getRoleDisplayName(), operator=(), and setRole().

const std::string CLMetabReferenceGlyph::RoleName
Initial value:
"undefined role",
"side substrate",
"side product",

String literals for the GUI to display the role of a metab reference

Definition at line 166 of file CLReactionGlyph.h.

Referenced by getRoleDisplayName().

const std::string CLMetabReferenceGlyph::XMLRole
Initial value:

XML type names of the roles. This is used in the XML importer and exporter

Definition at line 172 of file CLReactionGlyph.h.

Referenced by CCopasiXML::saveLayoutList(), and CCopasiXMLParser::MetaboliteReferenceGlyphElement::start().

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