COPASI API
4.16.103
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#include <CLReactionGlyph.h>
Public Types | |
enum | Role { UNDEFINED, SUBSTRATE, PRODUCT, SIDESUBSTRATE, SIDEPRODUCT, MODIFIER, ACTIVATOR, INHIBITOR } |
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typedef std::multimap < std::string, CCopasiObject * > | objectMap |
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typedef std::set< const CCopasiObject * > | DataObjectSet |
typedef std::vector< Refresh * > | DataUpdateSequence |
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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) |
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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) |
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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 () | |
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CLBase () | |
CLBase (const CLBase &b) | |
CLBase (const SBase &) | |
const std::string & | getTag () const |
bool | hasTag () const |
void | setTag (const std::string &tag) |
virtual | ~CLBase () |
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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 () |
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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 () |
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CObjectInterface () | |
virtual | ~CObjectInterface () |
Static Public Attributes | |
static const std::string | RoleName [] |
static const std::string | XMLRole [] |
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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 | |
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static std::vector< Refresh * > | buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet()) |
static void | setRenameHandler (CRenameHandler *rh) |
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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 } |
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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 () |
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CCopasiObject () | |
CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0) | |
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CLCurve | mCurve |
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CLBoundingBox | mBBox |
std::string | mKey |
std::string | mModelObjectKey |
std::string | mObjectRole |
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std::string | mTag |
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objectMap | mObjects |
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static CRenameHandler * | smpRenameHandler = NULL |
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.
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 | |
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UNDEFINED | |
SUBSTRATE | |
PRODUCT | |
SIDESUBSTRATE | |
SIDEPRODUCT | |
MODIFIER | |
ACTIVATOR | |
INHIBITOR |
Definition at line 150 of file CLReactionGlyph.h.
CLMetabReferenceGlyph::CLMetabReferenceGlyph | ( | const std::string & | name = "MetabReferenceGlyph" , |
const CCopasiContainer * | pParent = NULL |
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Definition at line 256 of file CLReactionGlyph.cpp.
Referenced by clone().
CLMetabReferenceGlyph::CLMetabReferenceGlyph | ( | const CLMetabReferenceGlyph & | src, |
const CCopasiContainer * | pParent = NULL |
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Definition at line 263 of file CLReactionGlyph.cpp.
CLMetabReferenceGlyph::CLMetabReferenceGlyph | ( | const SpeciesReferenceGlyph & | sbml, |
const std::map< std::string, std::string > & | modelmap, | ||
std::map< std::string, std::string > & | layoutmap, | ||
const CCopasiContainer * | pParent = NULL |
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constructor from libsbml object
Definition at line 270 of file CLReactionGlyph.cpp.
References CLGlyphWithCurve::mCurve, mMetabGlyphKey, and CLGraphicalObject::setModelObjectKey().
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Reimplemented from CLGraphicalObject.
Definition at line 212 of file CLReactionGlyph.h.
References CLMetabReferenceGlyph().
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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().
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().
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Definition at line 202 of file CLReactionGlyph.h.
References mMetabGlyphKey.
Referenced by CLayout::CLayout(), CLayout::exportToDotFile(), CCopasiXML::saveLayoutList(), and CLLayoutRenderer::update_associations().
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Definition at line 206 of file CLReactionGlyph.h.
References mRole.
Referenced by CLayout::exportToDotFile(), CCopasiSpringLayout::finalizeState(), operator<<(), CCopasiSpringLayout::potEdge(), CLRenderResolver::resolveStyle(), and CCopasiXML::saveLayoutList().
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CLMetabReferenceGlyph & CLMetabReferenceGlyph::operator= | ( | const CLMetabReferenceGlyph & | rhs | ) |
assignment operator.
Definition at line 304 of file CLReactionGlyph.cpp.
References mMetabGlyphKey, mRole, and CLGlyphWithCurve::operator=().
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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.
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Definition at line 204 of file CLReactionGlyph.h.
References mMetabGlyphKey.
Referenced by CLayout::CLayout(), CCopasiSpringLayout::createLayout(), CLayoutInitializer::createReactionGlyph(), and CCopasiXMLParser::MetaboliteReferenceGlyphElement::start().
Definition at line 207 of file CLReactionGlyph.h.
References mRole.
Referenced by CCopasiSpringLayout::createLayout(), CLayoutInitializer::createReactionGlyph(), and CCopasiXMLParser::MetaboliteReferenceGlyphElement::start().
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insert operator
Definition at line 362 of file CLReactionGlyph.cpp.
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private |
Key of a CLMetabGlyph.
Definition at line 178 of file CLReactionGlyph.h.
Referenced by CLMetabReferenceGlyph(), getMetabGlyph(), getMetabGlyphKey(), operator=(), and setMetabGlyphKey().
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Definition at line 180 of file CLReactionGlyph.h.
Referenced by exportToSBML(), getRole(), getRoleDisplayName(), operator=(), and setRole().
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String literals for the GUI to display the role of a metab reference
Definition at line 166 of file CLReactionGlyph.h.
Referenced by getRoleDisplayName().
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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().