#include <CLReactionGlyph.h>

Inheritance diagram for CLMetabReferenceGlyph:

Collaboration diagram for CLMetabReferenceGlyph:

Public Types
enum	Role { UNDEFINED, SUBSTRATE, PRODUCT, SIDESUBSTRATE, SIDEPRODUCT, MODIFIER, ACTIVATOR, INHIBITOR }

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 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 CLGraphicalObject *	clone () 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

CLMetabGlyph *	getMetabGlyph () const

const std::string &	getMetabGlyphKey () const

Role	getRole () const

const std::string &	getRoleDisplayName () const

CLMetabReferenceGlyph &	operator= (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 CLCurve &	getCurve () const

CLCurve &	getCurve ()

virtual void	moveBy (const CLPoint &p)

CLGlyphWithCurve &	operator= (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 CLBoundingBox &	getBoundingBox () const

CLBoundingBox &	getBoundingBox ()

const CLDimensions &	getDimensions () const

const C_FLOAT64 &	getHeight () const

virtual const std::string &	getKey () const

CCopasiObject *	getModelObject () 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 CLPoint &	getPosition () const

const C_FLOAT64 &	getWidth () const

const C_FLOAT64 &	getX () const

const C_FLOAT64 &	getY () const

bool	hasValidModelReference () const

CLGraphicalObject &	operator= (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 CObjectInterface *	getObject (const CCopasiObjectName &cn) const

virtual const objectMap &	getObjects () const

virtual std::string	getUnits () const

virtual const CCopasiObject *	getValueObject () 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

virtual void *	getValuePointer () 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 * >	EmptyList

Private Attributes
std::string	mMetabGlyphKey

Role	mRole

Friends
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 >
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)

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 CRenameHandler *	smpRenameHandler = 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 CLMetabReferenceGlyph::Role

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

Enumerator
UNDEFINED
SUBSTRATE
PRODUCT
SIDESUBSTRATE
SIDEPRODUCT
MODIFIER
ACTIVATOR
INHIBITOR

Definition at line 150 of file CLReactionGlyph.h.

   {
     UNDEFINED,
     SUBSTRATE,
     PRODUCT,
     SIDESUBSTRATE,
     SIDEPRODUCT,
     MODIFIER,
     ACTIVATOR,
     INHIBITOR
   };

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().

   : CLGlyphWithCurve(name, pParent),
     mMetabGlyphKey(),
     mRole(UNDEFINED)
 {}

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

Definition at line 263 of file CLReactionGlyph.cpp.

   : CLGlyphWithCurve(src, pParent),
     mMetabGlyphKey(src.mMetabGlyphKey),
     mRole(src.mRole)
 {}

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().

   : CLGlyphWithCurve(sbml, modelmap, layoutmap, pParent),
     mMetabGlyphKey(), //initialized in the body below
     mRole((Role)sbml.getRole())
 {
   //get the copasi key corresponding to the sbml id for the species reference
   if (sbml.getSpeciesReferenceId() != "")
     {
       std::map<std::string, std::string>::const_iterator it = modelmap.find(sbml.getSpeciesReferenceId());
 
       if (it != modelmap.end())
         setModelObjectKey(it->second);
     }
 
   //get the copasi key corresponding to the sbml id for the species glyph
   if (sbml.getSpeciesGlyphId() != "")
     {
       std::map<std::string, std::string>::const_iterator it = layoutmap.find(sbml.getSpeciesGlyphId());
 
       if (it != layoutmap.end())
         mMetabGlyphKey = it->second;
     }
 
   //curve
   if (sbml.getCurve())
     {
       CLCurve copy(*sbml.getCurve());
       mCurve = copy;
     }
 }

Member Function Documentation

virtual CLGraphicalObject* CLMetabReferenceGlyph::clone ( ) const

inlinevirtual

Reimplemented from CLGraphicalObject.

Definition at line 212 of file CLReactionGlyph.h.

References CLMetabReferenceGlyph().

212 {return new CLMetabReferenceGlyph(*this, NULL);};

CLMetabReferenceGlyph::CLMetabReferenceGlyph

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

Definition: CLReactionGlyph.cpp:256

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

virtual

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().

 {
   if (!g) return;
 
   //call the coresponding method of the base class
   CLGraphicalObject::exportToSBML(g, copasimodelmap, sbmlIDs);
 
   //reference to species glyph
   CLMetabGlyph* tmp = getMetabGlyph();
 
   if (tmp)
     {
       std::map<const CLBase*, const SBase*>::const_iterator it = layoutmap.find(tmp);
 
       if (it != layoutmap.end())
         {
           if (it->second)
             {
               //we need to cast here since layout objects in libsbml don´t inherit the getId() method
               //from SBase
               const GraphicalObject* pGO = dynamic_cast<const GraphicalObject*>(it->second);
 
               if (pGO)
                 g->setSpeciesGlyphId(pGO->getId());
             }
         }
     }
 
   //curve
   mCurve.exportToSBML(g->getCurve(), copasimodelmap);
 
   //Role
   g->setRole((SpeciesReferenceRole_t)mRole);
   //this depends on the copasi role enum being synchronous to the sbml one
 }

CLMetabGlyph * CLMetabReferenceGlyph::getMetabGlyph ( ) const

Definition at line 317 of file CLReactionGlyph.cpp.

References CKeyFactory::get(), CCopasiRootContainer::getKeyFactory(), and mMetabGlyphKey.

Referenced by exportToSBML(), CCopasiSpringLayout::finalizeState(), operator<<(), CCopasiSpringLayout::potEdge(), and CCopasiSpringLayout::potSecondOrderEdge().

 {
   CCopasiObject* tmp = CCopasiRootContainer::getKeyFactory()->get(mMetabGlyphKey);
   return dynamic_cast<CLMetabGlyph*>(tmp);
 }

const std::string& CLMetabReferenceGlyph::getMetabGlyphKey ( ) const

inline

Definition at line 202 of file CLReactionGlyph.h.

References mMetabGlyphKey.

Referenced by CLayout::CLayout(), CLayout::exportToDotFile(), CCopasiXML::saveLayoutList(), and CLLayoutRenderer::update_associations().

202 {return mMetabGlyphKey;};

CLMetabReferenceGlyph::mMetabGlyphKey

std::string mMetabGlyphKey

Definition: CLReactionGlyph.h:178

Role CLMetabReferenceGlyph::getRole ( ) const

inline

Definition at line 206 of file CLReactionGlyph.h.

References mRole.

Referenced by CLayout::exportToDotFile(), CCopasiSpringLayout::finalizeState(), operator<<(), CCopasiSpringLayout::potEdge(), CLRenderResolver::resolveStyle(), and CCopasiXML::saveLayoutList().

206 {return mRole;};

CLMetabReferenceGlyph::mRole

Role mRole

Definition: CLReactionGlyph.h:180

const std::string& CLMetabReferenceGlyph::getRoleDisplayName ( ) const

inline

Definition at line 209 of file CLReactionGlyph.h.

References mRole, and RoleName.

210 {return RoleName[mRole];};

CLMetabReferenceGlyph::RoleName

static const std::string RoleName[]

Definition: CLReactionGlyph.h:166

CLMetabReferenceGlyph::mRole

Role mRole

Definition: CLReactionGlyph.h:180

CLMetabReferenceGlyph & CLMetabReferenceGlyph::operator= ( const CLMetabReferenceGlyph & rhs )

assignment operator.

Definition at line 304 of file CLReactionGlyph.cpp.

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

 {
   if (this == &rhs) return * this; //do nothing if lhs and rhs are the same
 
   CLGlyphWithCurve::operator=(rhs);
 
   //handle the specific glyph stuff:
   mMetabGlyphKey = rhs.mMetabGlyphKey;
   mRole = rhs.mRole;
 
   return *this;
 }

void CLMetabReferenceGlyph::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 CLGlyphWithCurve.

Definition at line 379 of file CLReactionGlyph.cpp.

380 {*ostream << *this;}

void CLMetabReferenceGlyph::setMetabGlyphKey ( const std::string & k )

inline

Definition at line 204 of file CLReactionGlyph.h.

References mMetabGlyphKey.

Referenced by CLayout::CLayout(), CCopasiSpringLayout::createLayout(), CLayoutInitializer::createReactionGlyph(), and CCopasiXMLParser::MetaboliteReferenceGlyphElement::start().

204 {mMetabGlyphKey = k;};

CLMetabReferenceGlyph::mMetabGlyphKey

std::string mMetabGlyphKey

Definition: CLReactionGlyph.h:178

void CLMetabReferenceGlyph::setRole ( Role r )

inline

Definition at line 207 of file CLReactionGlyph.h.

References mRole.

Referenced by CCopasiSpringLayout::createLayout(), CLayoutInitializer::createReactionGlyph(), and CCopasiXMLParser::MetaboliteReferenceGlyphElement::start().

207 {mRole = r;};

CLMetabReferenceGlyph::mRole

Role mRole

Definition: CLReactionGlyph.h:180

Friends And Related Function Documentation

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

friend

insert operator

Definition at line 362 of file CLReactionGlyph.cpp.

 {
   os << "    MetabReferenceGlyph: " << dynamic_cast<const CLGraphicalObject&>(g);
 
   os << "      Role: " << CLMetabReferenceGlyph::RoleName[g.getRole()] << "\n";
 
   const CLMetabGlyph* tmp = g.getMetabGlyph();
 
   if (tmp)
     os << "      refers to a MetabGlyph that refers to "
        << tmp->getModelObjectDisplayName() << std::endl;
 
   os << g.mCurve;
 
   return os;
 }

Member Data Documentation

std::string CLMetabReferenceGlyph::mMetabGlyphKey

private

Key of a CLMetabGlyph.

Definition at line 178 of file CLReactionGlyph.h.

Referenced by CLMetabReferenceGlyph(), getMetabGlyph(), getMetabGlyphKey(), operator=(), and setMetabGlyphKey().

Role CLMetabReferenceGlyph::mRole

private

Definition at line 180 of file CLReactionGlyph.h.

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

const std::string CLMetabReferenceGlyph::RoleName

static

Initial value:

=
{
  "undefined role",
  "substrate",
  "product",
  "side substrate",
  "side product",
  "modifier",
  "activator",
  "inhibitor"
  ""
}

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

static

Initial value:

=
{
  "undefinedRole",
  "substrate",
  "product",
  "sideSubstrate",
  "sideProduct",
  "modifier",
  "activator",
  "inhibitor",
  ""
}

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:

Public Types

Public Member Functions

Static Public Attributes

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation