#include <CLayout.h>

Inheritance diagram for CLayout:

Collaboration diagram for CLayout:

Public Member Functions
void	addCompartmentGlyph (CLCompartmentGlyph *glyph)

void	addGeneralGlyph (CLGeneralGlyph *glyph)

void	addLocalRenderInformation (CLLocalRenderInformation *pRenderInfo)

void	addMetaboliteGlyph (CLMetabGlyph *glyph)

void	addReactionGlyph (CLReactionGlyph *glyph)

void	addTextGlyph (CLTextGlyph *glyph)

void	calculateAndAssignBounds ()

CLBoundingBox	calculateBoundingBox () const

	CLayout (const std::string &name="Layout", const CCopasiContainer *pParent=NULL)

	CLayout (const CLayout &src, const CCopasiContainer *pParent=NULL)

	CLayout (const Layout &sbml, std::map< std::string, std::string > &layoutmap, const CCopasiContainer *pParent=NULL)

void	exportToDotFile (std::ostream &os) const

void	exportToSBML (Layout layout, const std::map< const CCopasiObject , SBase * > &copasimodelmap, std::map< std::string, const SBase * > &sbmlIDs, const std::map< std::string, std::string > &globalKeyToIdMap) const

const CLDimensions &	getDimensions () const

virtual const std::string &	getKey () const

const CCopasiVector < CLCompartmentGlyph > &	getListOfCompartmentGlyphs () const

CCopasiVector < CLCompartmentGlyph > &	getListOfCompartmentGlyphs ()

const CCopasiVector < CLGeneralGlyph > &	getListOfGeneralGlyphs () const

CCopasiVector< CLGeneralGlyph > &	getListOfGeneralGlyphs ()

const CCopasiVector < CLLocalRenderInformation > &	getListOfLocalRenderInformationObjects () const

CCopasiVector < CLLocalRenderInformation > &	getListOfLocalRenderInformationObjects ()

const CCopasiVector < CLMetabGlyph > &	getListOfMetaboliteGlyphs () const

CCopasiVector< CLMetabGlyph > &	getListOfMetaboliteGlyphs ()

const CCopasiVector < CLReactionGlyph > &	getListOfReactionGlyphs () const

CCopasiVector< CLReactionGlyph > &	getListOfReactionGlyphs ()

const CCopasiVector < CLTextGlyph > &	getListOfTextGlyphs () const

CCopasiVector< CLTextGlyph > &	getListOfTextGlyphs ()

const CLLocalRenderInformation *	getRenderInformation (size_t index) const

CLLocalRenderInformation *	getRenderInformation (size_t index)

virtual void	moveBy (const CLPoint &p)

void	print (std::ostream *ostream) const

virtual void	scale (const double &scaleFactor)

void	setDimensions (const CLDimensions &d)

	~CLayout ()

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 ()

Protected Member Functions
void	writeDotEdge (std::ostream &os, const std::string &id1, const std::string &id2, int t=0) const

void	writeDotNode (std::ostream &os, const std::string &id, const std::string &label, int t=0) const

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
CLDimensions	mDimensions

std::string	mKey

CCopasiVector< CLCompartmentGlyph >	mvCompartments

CCopasiVector< CLGeneralGlyph >	mvGraphicalObjects

CCopasiVector< CLTextGlyph >	mvLabels

CCopasiVector < CLLocalRenderInformation >	mvLocalRenderInformationObjects

CCopasiVector< CLMetabGlyph >	mvMetabs

CCopasiVector< CLReactionGlyph >	mvReactions

Protected Attributes inherited from CLBase
std::string	mTag

Protected Attributes inherited from CCopasiContainer
objectMap	mObjects

Friends
std::ostream &	operator<< (std::ostream &os, const CLayout &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 }

Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

Detailed Description

This class describes a reaction network layout. Its structure is exactly corresponding to the sbml layout extension

Definition at line 34 of file CLayout.h.

Constructor & Destructor Documentation

CLayout::CLayout	(	const std::string &	name = `"Layout"`,
		const CCopasiContainer *	pParent = `NULL`
	)

Definition at line 38 of file CLayout.cpp.

   : CLBase(),
     CCopasiContainer(name, pParent, "Layout"),
     mKey(CCopasiRootContainer::getKeyFactory()->add("Layout", this)),
     mDimensions(),
     mvCompartments("ListOfCompartmentGlyphs", this),
     mvMetabs("ListOfMetaboliteGlyphs", this),
     mvReactions("ListOfReactionGlyphs", this),
     mvLabels("ListOfTextGlyphs", this),
     mvGraphicalObjects("ListOfGraphicalObjects", this)
     , mvLocalRenderInformationObjects("ListOfLocalRenderInformationObjects", this)
 {}

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

Definition at line 52 of file CLayout.cpp.

References CCopasiVector< T >::add(), CCopasiVector< T >::begin(), CCopasiVector< T >::end(), CLTextGlyph::getGraphicalObjectKey(), CLGraphicalObject::getKey(), CCopasiObject::getKey(), CLReactionGlyph::getListOfMetabReferenceGlyphs(), CLGeneralGlyph::getListOfReferenceGlyphs(), CLGeneralGlyph::getListOfSubglyphs(), CLMetabReferenceGlyph::getMetabGlyphKey(), CLReferenceGlyph::getTargetGlyphKey(), mvCompartments, mvGraphicalObjects, mvLabels, mvMetabs, mvReactions, CLTextGlyph::setGraphicalObjectKey(), CLMetabReferenceGlyph::setMetabGlyphKey(), CLReferenceGlyph::setTargetGlyphKey(), and CCopasiVector< T >::size().

   : CLBase(src),
     CCopasiContainer(src, pParent),
     mKey(CCopasiRootContainer::getKeyFactory()->add("Layout", this)),
     mDimensions(src.mDimensions),
     mvCompartments("ListOfCompartmentGlyphs", this),
     mvMetabs("ListOfMetaboliteGlyphs", this),
     mvReactions("ListOfReactionGlyphs", this),
     mvLabels("ListOfTextGlyphs", this),
     mvGraphicalObjects("ListOfGraphicalObjects", this)
     , mvLocalRenderInformationObjects(src.mvLocalRenderInformationObjects, this)
 {
   //TODO references from one glyph to another have to be reconstructed after
   //     copying. This applies to Labels and species reference glyphs
 
   std::map<std::string, std::string> forward;
   std::map<std::string, std::string> reverse;
 
   CCopasiVector<CLCompartmentGlyph>::const_iterator compIt = src.mvCompartments.begin();
 
   for (; compIt != src.mvCompartments.end(); ++compIt)
     {
       CLCompartmentGlyph *comp = new CLCompartmentGlyph(*(*compIt));
       mvCompartments.add(comp, true);
       forward[(*compIt)->getKey()] = comp->getKey();
       reverse[comp->getKey()] = (*compIt)->getKey();
     }
 
   CCopasiVector<CLMetabGlyph>::const_iterator metabIt = src.mvMetabs.begin();
 
   for (; metabIt != src.mvMetabs.end(); ++metabIt)
     {
       CLMetabGlyph *metab = new CLMetabGlyph(*(*metabIt));
       mvMetabs.add(metab, true);
       forward[(*metabIt)->getKey()] = metab->getKey();
       reverse[metab->getKey()] = (*metabIt)->getKey();
     }
 
   CCopasiVector<CLReactionGlyph>::const_iterator reactIt = src.mvReactions.begin();
 
   for (; reactIt != src.mvReactions.end(); ++reactIt)
     {
       CLReactionGlyph *r = new CLReactionGlyph(*(*reactIt));
       mvReactions.add(r, true);
       forward[(*reactIt)->getKey()] = r->getKey();
       reverse[r->getKey()] = (*reactIt)->getKey();
 
       for (size_t i = 0; i < r->getListOfMetabReferenceGlyphs().size(); ++i)
         {
           forward[(*reactIt)->getListOfMetabReferenceGlyphs()[i]->getKey()]
           = r->getListOfMetabReferenceGlyphs()[i]->getKey();
           reverse[r->getListOfMetabReferenceGlyphs()[i]->getKey()]
           = (*reactIt)->getListOfMetabReferenceGlyphs()[i]->getKey();
         }
     }
 
   CCopasiVector<CLTextGlyph>::const_iterator textIt = src.mvLabels.begin();
 
   for (; textIt != src.mvLabels.end(); ++textIt)
     {
       CLTextGlyph *text = new CLTextGlyph(*(*textIt));
       mvLabels.add(text, true);
       forward[(*textIt)->getKey()] = text->getKey();
       reverse[text->getKey()] = (*textIt)->getKey();
     }
 
   CCopasiVector<CLGeneralGlyph>::const_iterator generalIt = src.mvGraphicalObjects.begin();
 
   for (; generalIt != src.mvGraphicalObjects.end(); ++generalIt)
     {
       CLGeneralGlyph *general = new CLGeneralGlyph(*(*generalIt));
       mvGraphicalObjects.add(general, true);
       forward[(*generalIt)->getKey()] = general->getKey();
       reverse[general->getKey()] = (*generalIt)->getKey();
 
       for (size_t i = 0; i < general->getListOfReferenceGlyphs().size(); ++i)
         {
           forward[(*generalIt)->getListOfReferenceGlyphs()[i]->getKey()]
           = general->getListOfReferenceGlyphs()[i]->getKey();
           reverse[general->getListOfReferenceGlyphs()[i]->getKey()]
           = (*generalIt)->getListOfReferenceGlyphs()[i]->getKey();
         }
 
       for (size_t i = 0; i < general->getListOfSubglyphs().size(); ++i)
         {
           forward[(*generalIt)->getListOfSubglyphs()[i]->getKey()]
           = general->getListOfSubglyphs()[i]->getKey();
           reverse[general->getListOfSubglyphs()[i]->getKey()]
           = (*generalIt)->getListOfSubglyphs()[i]->getKey();
         }
     }
 
   {
 
     // by now we have collected all keys, now we need to replace them
     std::map<std::string, std::string>::const_iterator constIt;
     CCopasiVector<CLTextGlyph>::iterator textIt = mvLabels.begin();
 
     for (; textIt != mvLabels.end(); ++textIt)
       {
         CLTextGlyph *text = *textIt;
         const std::string& key = text->getGraphicalObjectKey();
         constIt = forward.find(key);
 
         if (constIt == forward.end())
           continue;
 
         text->setGraphicalObjectKey(constIt->second);
       }
 
     CCopasiVector<CLReactionGlyph>::iterator reactIt = mvReactions.begin();
 
     for (; reactIt != mvReactions.end(); ++reactIt)
       {
         CLReactionGlyph *r = *reactIt;
         CCopasiVector<CLMetabReferenceGlyph>::iterator refIt = r->getListOfMetabReferenceGlyphs().begin();
 
         for (; refIt != r->getListOfMetabReferenceGlyphs().end(); ++refIt)
           {
             CLMetabReferenceGlyph* current = *refIt;
             const std::string& key = current->getMetabGlyphKey();
             constIt = forward.find(key);
 
             if (constIt == forward.end())
               continue;
 
             current->setMetabGlyphKey(constIt->second);
           }
       }
 
     CCopasiVector<CLGeneralGlyph>::iterator generalIt = mvGraphicalObjects.begin();
 
     for (; generalIt != mvGraphicalObjects.end(); ++generalIt)
       {
         CLGeneralGlyph *g = *generalIt;
         CCopasiVector<CLReferenceGlyph>::iterator refIt = g->getListOfReferenceGlyphs().begin();
 
         for (; refIt != g->getListOfReferenceGlyphs().end(); ++refIt)
           {
             CLReferenceGlyph* current = *refIt;
             const std::string& key = current->getTargetGlyphKey();
             constIt = forward.find(key);
 
             if (constIt == forward.end())
               continue;
 
             current->setTargetGlyphKey(constIt->second);
           }
 
         //CCopasiVector<CLGraphicalObject>::iterator refIt = g->getListOfSubglyphs().begin();
         //for(;refIt != g->getListOfReferenceGlyphs().end(); ++refIt)
         //{
         //  CLGraphicalObject* current = *refIt;
         //  const std::string& key = current->getTargetGlyphKey();
         //  constIt = forward.find(key);
         //  if (constIt == forward.end())
         //    continue;
         //  current->setTargetGlyphKey(constIt->second);
         //}
       }
   }
 }

CLayout::CLayout	(	const Layout &	sbml,
		std::map< std::string, std::string > &	layoutmap,
		const CCopasiContainer *	pParent = `NULL`
	)

constructor from libsbml object. Does not read the whole libsbml tree. Additional work is done in SBMLDocumentLoader

Definition at line 216 of file CLayout.cpp.

References mKey.

   : CLBase(sbml),
     CCopasiContainer(sbml.getId(), pParent, "Layout"),
     mKey(CCopasiRootContainer::getKeyFactory()->add("Layout", this)),
     mDimensions(*sbml.getDimensions()),
     mvCompartments("ListOfCompartmentGlyphs", this),
     mvMetabs("ListOfMetaboliteGlyphs", this),
     mvReactions("ListOfReactionGlyphs", this),
     mvLabels("ListOfTextGlyphs", this),
     mvGraphicalObjects("ListOfGraphicalObjects", this)
     , mvLocalRenderInformationObjects("ListOfLocalRenderInformationObjects", this)
 {
   //add the copasi key to the map
   layoutmap[sbml.getId()] = mKey;
 }

CLayout::~CLayout ( )

Definition at line 234 of file CLayout.cpp.

References CCopasiRootContainer::getKeyFactory(), mKey, and CKeyFactory::remove().

 {
   CCopasiRootContainer::getKeyFactory()->remove(mKey);
 }

Member Function Documentation

void CLayout::addCompartmentGlyph ( CLCompartmentGlyph * glyph )

add Glyph to layout. The layout takes ownership of the glyph.

Definition at line 239 of file CLayout.cpp.

References CCopasiVector< T >::add(), and mvCompartments.

Referenced by SBMLDocumentLoader::createLayout(), CCopasiSpringLayout::createLayout(), test000097::createModel(), and CCopasiXMLParser::CompartmentGlyphElement::start().

 {
   if (glyph)
     mvCompartments.add(glyph, true); //true means vector takes ownership
 }

void CLayout::addGeneralGlyph ( CLGeneralGlyph * glyph )

add Glyph to layout. The layout takes ownership of the glyph.

Definition at line 263 of file CLayout.cpp.

References CCopasiVector< T >::add(), and mvGraphicalObjects.

Referenced by SBMLDocumentLoader::createLayout(), CCopasiSpringLayout::createLayout(), and CCopasiXMLParser::AdditionalGOElement::start().

 {
   if (glyph)
     mvGraphicalObjects.add(glyph, true); //true means vector takes ownership
 }

void CLayout::addLocalRenderInformation ( CLLocalRenderInformation * pRenderInfo )

add local render information to layout. The layout takes ownership of the object.

Definition at line 646 of file CLayout.cpp.

References CCopasiVector< T >::add(), and mvLocalRenderInformationObjects.

Referenced by SBMLDocumentLoader::createLayout(), and CCopasiXMLParser::LocalRenderInformationElement::start().

 {
   if (pRenderInfo)
     {
       this->mvLocalRenderInformationObjects.add(pRenderInfo, true); //true means vector takes ownership
     }
 }

void CLayout::addMetaboliteGlyph ( CLMetabGlyph * glyph )

add Glyph to layout. The layout takes ownership of the glyph.

Definition at line 245 of file CLayout.cpp.

References CCopasiVector< T >::add(), and mvMetabs.

Referenced by SBMLDocumentLoader::createLayout(), CCopasiSpringLayout::createLayout(), and CCopasiXMLParser::MetaboliteGlyphElement::start().

 {
   if (glyph)
     mvMetabs.add(glyph, true); //true means vector takes ownership
 }

void CLayout::addReactionGlyph ( CLReactionGlyph * glyph )

add Glyph to layout. The layout takes ownership of the glyph.

Definition at line 251 of file CLayout.cpp.

References CCopasiVector< T >::add(), and mvReactions.

Referenced by SBMLDocumentLoader::createLayout(), CCopasiSpringLayout::createLayout(), and CCopasiXMLParser::ReactionGlyphElement::start().

 {
   if (glyph)
     mvReactions.add(glyph, true); //true means vector takes ownership
 }

void CLayout::addTextGlyph ( CLTextGlyph * glyph )

add Glyph to layout. The layout takes ownership of the glyph.

Definition at line 257 of file CLayout.cpp.

References CCopasiVector< T >::add(), and mvLabels.

Referenced by SBMLDocumentLoader::createLayout(), CCopasiSpringLayout::createLayout(), and CCopasiXMLParser::TextGlyphElement::start().

 {
   if (glyph)
     mvLabels.add(glyph, true); //true means vector takes ownership
 }

void CLayout::calculateAndAssignBounds ( )

Calculates the Bounding Box, moves the layout to the origin and assigns it to the layout.

Definition at line 955 of file CLayout.cpp.

References calculateBoundingBox(), CLBoundingBox::getDimensions(), CLBoundingBox::getPosition(), CLPoint::getX(), CLPoint::getY(), CLPoint::getZ(), moveBy(), and setDimensions().

Referenced by CCopasiSpringLayout::finalizeState().

 {
   CLBoundingBox bb = calculateBoundingBox();
   // move into the origin
   CLPoint differenceToOrigin(
     -bb.getPosition().getX(),
     -bb.getPosition().getY()
     , -bb.getPosition().getZ()
   );
   moveBy(differenceToOrigin);
   setDimensions(bb.getDimensions());
 }

CLBoundingBox CLayout::calculateBoundingBox ( ) const

This methods calculates the bounding box of the layout. It traverses all layout objects and looks for the minimal and maximal x and y values that occur in the layout. These values are returned in the form of a bounding box where the minimal values are stored in the position and the maxima are given as the minimal values plus the corresponding dimension.

Definition at line 684 of file CLayout.cpp.

References CLCurve::calculateBoundingBox(), CLGraphicalObject::getBoundingBox(), CLGlyphWithCurve::getCurve(), CLBoundingBox::getDimensions(), CLDimensions::getHeight(), getListOfCompartmentGlyphs(), getListOfGeneralGlyphs(), getListOfMetaboliteGlyphs(), CLReactionGlyph::getListOfMetabReferenceGlyphs(), getListOfReactionGlyphs(), CLGeneralGlyph::getListOfReferenceGlyphs(), getListOfTextGlyphs(), CLCurve::getNumCurveSegments(), CLBoundingBox::getPosition(), CLDimensions::getWidth(), CLPoint::getX(), CLPoint::getY(), max, and CCopasiVector< T >::size().

Referenced by CQGLLayoutPainter::calculateAndAssignBounds(), calculateAndAssignBounds(), and CCopasiSpringLayout::createLayout().

 {
   double minX = std::numeric_limits<double>::max();
   double minY = minX;
   double maxX = -minX;
   double maxY = -minX;
 
   const CLGraphicalObject* pObject = NULL;
   const CLCurve* pCurve = NULL;
   const CLBoundingBox* pBB;
   const CLPoint* pP = NULL;
   const CLDimensions* pDim;
   size_t i, iMax = this->getListOfCompartmentGlyphs().size();
   double x, y, x2, y2;
 
   for (i = 0; i < iMax; ++i)
     {
       pObject = this->getListOfCompartmentGlyphs()[i];
       pBB = &pObject->getBoundingBox();
       pP = &pBB->getPosition();
       x = pP->getX();
       y = pP->getY();
       pDim = &pBB->getDimensions();
       x2 = x + pDim->getWidth();
       y2 = y + pDim->getHeight();
       minX = (minX < x) ? minX : x;
       minY = (minY < y) ? minY : y;
       maxX = (maxX > x2) ? maxX : x2;
       maxY = (maxY > y2) ? maxY : y2;
     }
 
   iMax = this->getListOfMetaboliteGlyphs().size();
 
   for (i = 0; i < iMax; ++i)
     {
       pObject = this->getListOfMetaboliteGlyphs()[i];
       pBB = &pObject->getBoundingBox();
       pP = &pBB->getPosition();
       x = pP->getX();
       y = pP->getY();
       pDim = &pBB->getDimensions();
       x2 = x + pDim->getWidth();
       y2 = y + pDim->getHeight();
       minX = (minX < x) ? minX : x;
       minY = (minY < y) ? minY : y;
       maxX = (maxX > x2) ? maxX : x2;
       maxY = (maxY > y2) ? maxY : y2;
     }
 
   iMax = this->getListOfTextGlyphs().size();
 
   for (i = 0; i < iMax; ++i)
     {
       pObject = this->getListOfTextGlyphs()[i];
       pBB = &pObject->getBoundingBox();
       pP = &pBB->getPosition();
       x = pP->getX();
       y = pP->getY();
       pDim = &pBB->getDimensions();
       x2 = x + pDim->getWidth();
       y2 = y + pDim->getHeight();
       minX = (minX < x) ? minX : x;
       minY = (minY < y) ? minY : y;
       maxX = (maxX > x2) ? maxX : x2;
       maxY = (maxY > y2) ? maxY : y2;
     }
 
   size_t j, jMax;
   const CLGeneralGlyph* pGG = NULL;
   const CLReferenceGlyph* pRefG = NULL;
   iMax = this->getListOfGeneralGlyphs().size();
 
   for (i = 0; i < iMax; ++i)
     {
       pGG = this->getListOfGeneralGlyphs()[i];
 
       if (pGG->getCurve().getNumCurveSegments() > 0)
         {
           pCurve = &pGG->getCurve();
           CLBoundingBox bb = pCurve->calculateBoundingBox();
           pP = &bb.getPosition();
           x = pP->getX();
           y = pP->getY();
           pDim = &bb.getDimensions();
           x2 = x + pDim->getWidth();
           y2 = y + pDim->getHeight();
           minX = (minX < x) ? minX : x;
           minY = (minY < y) ? minY : y;
           maxX = (maxX > x2) ? maxX : x2;
           maxY = (maxY > y2) ? maxY : y2;
         }
       else
         {
           pBB = &pGG->getBoundingBox();
           pP = &pBB->getPosition();
           x = pP->getX();
           y = pP->getY();
           pDim = &pBB->getDimensions();
           x2 = x + pDim->getWidth();
           y2 = y + pDim->getHeight();
           minX = (minX < x) ? minX : x;
           minY = (minY < y) ? minY : y;
           maxX = (maxX > x2) ? maxX : x2;
           maxY = (maxY > y2) ? maxY : y2;
         }
 
       jMax = pGG->getListOfReferenceGlyphs().size();
 
       for (j = 0; j < jMax; ++j)
         {
           pRefG = pGG->getListOfReferenceGlyphs()[j];
 
           if (pRefG->getCurve().getNumCurveSegments() > 0)
             {
               pCurve = &pRefG->getCurve();
               CLBoundingBox bb = pCurve->calculateBoundingBox();
               pP = &bb.getPosition();
               x = pP->getX();
               y = pP->getY();
               pDim = &bb.getDimensions();
               x2 = x + pDim->getWidth();
               y2 = y + pDim->getHeight();
               minX = (minX < x) ? minX : x;
               minY = (minY < y) ? minY : y;
               maxX = (maxX > x2) ? maxX : x2;
               maxY = (maxY > y2) ? maxY : y2;
             }
           else
             {
               pBB = &pRefG->getBoundingBox();
               pP = &pBB->getPosition();
               x = pP->getX();
               y = pP->getY();
               pDim = &pBB->getDimensions();
               x2 = x + pDim->getWidth();
               y2 = y + pDim->getHeight();
               minX = (minX < x) ? minX : x;
               minY = (minY < y) ? minY : y;
               maxX = (maxX > x2) ? maxX : x2;
               maxY = (maxY > y2) ? maxY : y2;
             }
         }
     }
 
   const CLReactionGlyph* pRG = NULL;
 
   const CLMetabReferenceGlyph* pSRG = NULL;
 
   iMax = this->getListOfReactionGlyphs().size();
 
   for (i = 0; i < iMax; ++i)
     {
       pRG = this->getListOfReactionGlyphs()[i];
 
       if (pRG->getCurve().getNumCurveSegments() > 0)
         {
           pCurve = &pRG->getCurve();
           CLBoundingBox bb = pCurve->calculateBoundingBox();
           pP = &bb.getPosition();
           x = pP->getX();
           y = pP->getY();
           pDim = &bb.getDimensions();
           x2 = x + pDim->getWidth();
           y2 = y + pDim->getHeight();
           minX = (minX < x) ? minX : x;
           minY = (minY < y) ? minY : y;
           maxX = (maxX > x2) ? maxX : x2;
           maxY = (maxY > y2) ? maxY : y2;
         }
       else
         {
           pBB = &pRG->getBoundingBox();
           pP = &pBB->getPosition();
           x = pP->getX();
           y = pP->getY();
           pDim = &pBB->getDimensions();
           x2 = x + pDim->getWidth();
           y2 = y + pDim->getHeight();
           minX = (minX < x) ? minX : x;
           minY = (minY < y) ? minY : y;
           maxX = (maxX > x2) ? maxX : x2;
           maxY = (maxY > y2) ? maxY : y2;
         }
 
       jMax = pRG->getListOfMetabReferenceGlyphs().size();
 
       for (j = 0; j < jMax; ++j)
         {
           pSRG = pRG->getListOfMetabReferenceGlyphs()[j];
 
           if (pSRG->getCurve().getNumCurveSegments() > 0)
             {
               pCurve = &pSRG->getCurve();
               CLBoundingBox bb = pCurve->calculateBoundingBox();
               pP = &bb.getPosition();
               x = pP->getX();
               y = pP->getY();
               pDim = &bb.getDimensions();
               x2 = x + pDim->getWidth();
               y2 = y + pDim->getHeight();
               minX = (minX < x) ? minX : x;
               minY = (minY < y) ? minY : y;
               maxX = (maxX > x2) ? maxX : x2;
               maxY = (maxY > y2) ? maxY : y2;
             }
           else
             {
               pBB = &pSRG->getBoundingBox();
               pP = &pBB->getPosition();
               x = pP->getX();
               y = pP->getY();
               pDim = &pBB->getDimensions();
               x2 = x + pDim->getWidth();
               y2 = y + pDim->getHeight();
               minX = (minX < x) ? minX : x;
               minY = (minY < y) ? minY : y;
               maxX = (maxX > x2) ? maxX : x2;
               maxY = (maxY > y2) ? maxY : y2;
             }
         }
     }
 
   return CLBoundingBox(CLPoint(minX, minY), CLDimensions(maxX - minX, maxY - minY));
 }

void CLayout::exportToDotFile ( std::ostream & os ) const

Definition at line 331 of file CLayout.cpp.

References getKey(), CCopasiObject::getKey(), CLMetabReferenceGlyph::getMetabGlyphKey(), CLMetabReferenceGlyph::getRole(), mvMetabs, mvReactions, CLMetabReferenceGlyph::PRODUCT, CCopasiVector< T >::size(), CLMetabReferenceGlyph::SUBSTRATE, writeDotEdge(), and writeDotNode().

 {
   os << "digraph G {\n";
 
   //species glyphs
   size_t i, imax = mvMetabs.size();
 
   for (i = 0; i < imax; ++i)
     {
       writeDotNode(os, mvMetabs[i]->getKey(), mvMetabs[i]->getModelObjectDisplayName());
     }
 
   //reaction glyphs
   imax = mvReactions.size();
 
   for (i = 0; i < imax; ++i)
     {
       writeDotNode(os, mvReactions[i]->getKey() + "_S", "", 1);
       writeDotNode(os, mvReactions[i]->getKey() + "_P", "", 1);
       writeDotEdge(os, mvReactions[i]->getKey() + "_S", mvReactions[i]->getKey() + "_P", 1);
 
       size_t j, jmax = mvReactions[i]->getListOfMetabReferenceGlyphs().size();
 
       for (j = 0; j < jmax; ++j)
         {
           CLMetabReferenceGlyph* mrg = mvReactions[i]->getListOfMetabReferenceGlyphs()[j];
 
           if (mrg->getRole() == CLMetabReferenceGlyph::SUBSTRATE)
             writeDotEdge(os, mrg->getMetabGlyphKey(), mvReactions[i]->getKey() + "_S");
           else if (mrg->getRole() == CLMetabReferenceGlyph::PRODUCT)
             writeDotEdge(os, mvReactions[i]->getKey() + "_P", mrg->getMetabGlyphKey());
         }
     }
 
   os << "}" << std::endl;
 }

void CLayout::exportToSBML	(	Layout *	layout,
		const std::map< const CCopasiObject , SBase > &	copasimodelmap,
		std::map< std::string, const SBase * > &	sbmlIDs,
		const std::map< std::string, std::string > &	globalKeyToIdMap
	)		const

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

Definition at line 392 of file CLayout.cpp.

References SBMLDocumentLoader::convertLayoutObjectKeys(), CSBMLExporter::createUniqueId(), CLTextGlyph::exportReferenceToSBML(), CLMetabGlyph::exportToSBML(), CLCompartmentGlyph::exportToSBML(), CLTextGlyph::exportToSBML(), CLGeneralGlyph::exportToSBML(), CLReactionGlyph::exportToSBML(), getKey(), CLGraphicalObject::getKey(), CLGeneralGlyph::getListOfReferenceGlyphs(), CLDimensions::getSBMLDimensions(), mDimensions, mvCompartments, mvGraphicalObjects, mvLabels, mvLocalRenderInformationObjects, mvMetabs, mvReactions, and CCopasiVector< T >::size().

Referenced by CListOfLayouts::exportToSBML().

 {
   if (!layout) return;
 
   //Name and ID
   std::string id = CSBMLExporter::createUniqueId(sbmlIDs, "layout", true);
   layout->setId(id);
   sbmlIDs.insert(std::pair<const std::string, const SBase*>(id, layout));
   //we do not check if the layout is already present in the libsbml data
   //structures. This is no big deal since at the moment no software
   //relies on persistent IDs for layout elements.
 
   //Dimensions
   Dimensions tmpDim = mDimensions.getSBMLDimensions();
   layout->setDimensions(&tmpDim);
 
   //some of the following code is not used at the moment:  the COPASI model map
   //does not contain glyphs. Since this may change in the future I leave the code
   //below.
 
   // create a map from COPASI layout object to SBML objects. We do not put
   //the layout objects into the global map (copasimodelmap) but we need to have
   //access to all objects in the current layout since speciesReferenceGlyph and
   //textGlyph need to reference other graphical objects.
   std::map<const CLBase*, const SBase*> layoutmap;
 
   //Compartment glyphs
   size_t i, imax = mvCompartments.size();
 
   for (i = 0; i < imax; ++i)
     {
       CLCompartmentGlyph * tmp = mvCompartments[i];
 
       //check if the compartment glyph exists in the libsbml data
       std::map<const CCopasiObject*, SBase*>::const_iterator it;
       it = copasimodelmap.find(tmp);
 
       CompartmentGlyph * pCG;
 
       if (it == copasimodelmap.end()) //not found
         {
           pCG = layout->createCompartmentGlyph();
         }
       else
         {
           pCG = dynamic_cast<CompartmentGlyph*>(it->second);
         }
 
       layoutmap.insert(std::pair<const CLBase*, const SBase*>(tmp, pCG));
       tmp->exportToSBML(pCG, copasimodelmap, sbmlIDs);
     }
 
   //Species glyphs
   imax = mvMetabs.size();
 
   for (i = 0; i < imax; ++i)
     {
       CLMetabGlyph * tmp = mvMetabs[i];
 
       //check if the glyph exists in the libsbml data
       std::map<const CCopasiObject*, SBase*>::const_iterator it;
       it = copasimodelmap.find(tmp);
 
       SpeciesGlyph * pG;
 
       if (it == copasimodelmap.end()) //not found
         {
           pG = layout->createSpeciesGlyph();
         }
       else
         {
           pG = dynamic_cast<SpeciesGlyph*>(it->second);
         }
 
       layoutmap.insert(std::pair<const CLBase*, const SBase*>(tmp, pG));
       tmp->exportToSBML(pG, copasimodelmap, sbmlIDs);
     }
 
   //Reaction glyphs
   imax = mvReactions.size();
 
   for (i = 0; i < imax; ++i)
     {
       CLReactionGlyph * tmp = mvReactions[i];
 
       //check if the glyph exists in the libsbml data
       std::map<const CCopasiObject*, SBase*>::const_iterator it;
       it = copasimodelmap.find(tmp);
 
       ReactionGlyph * pG;
 
       if (it == copasimodelmap.end()) //not found
         {
           pG = layout->createReactionGlyph();
         }
       else
         {
           pG = dynamic_cast<ReactionGlyph*>(it->second);
         }
 
       layoutmap.insert(std::pair<const CLBase*, const SBase*>(tmp, pG));
       //we need to pass the layoutmap here for 2 reasons:
       //1. the metabreferenceglyphs need to be added
       //2. the metabreferenceglyphs need to resolve the reference to the metabglyph
       tmp->exportToSBML(pG, copasimodelmap, sbmlIDs, layoutmap);
     }
 
   //Text glyphs
   imax = mvLabels.size();
 
   for (i = 0; i < imax; ++i)
     {
       CLTextGlyph * tmp = mvLabels[i];
 
       //check if the glyph exists in the libsbml data
       std::map<const CCopasiObject*, SBase*>::const_iterator it;
       it = copasimodelmap.find(tmp);
 
       TextGlyph * pG;
 
       if (it == copasimodelmap.end()) //not found
         {
           pG = layout->createTextGlyph();
         }
       else
         {
           pG = dynamic_cast<TextGlyph*>(it->second);
         }
 
       layoutmap.insert(std::pair<const CLBase*, const SBase*>(tmp, pG));
       tmp->exportToSBML(pG, copasimodelmap, sbmlIDs);
     }
 
   //generic glyphs
   imax = mvGraphicalObjects.size();
 
   for (i = 0; i < imax; ++i)
     {
       CLGeneralGlyph * tmp = mvGraphicalObjects[i];
 
       //check if the glyph exists in the libsbml data
       std::map<const CCopasiObject*, SBase*>::const_iterator it;
       it = copasimodelmap.find(tmp);
 
       GraphicalObject * pG;
 
       if (it == copasimodelmap.end()) //not found
         {
 #if LIBSBML_VERSION >= 50800
 
           if (tmp->getListOfReferenceGlyphs().size() > 0)
             pG = layout->createGeneralGlyph();
           else
 #endif // LIBSBML_VERSION >= 50800
             pG = layout->createAdditionalGraphicalObject();
         }
       else
         {
           pG = dynamic_cast<GraphicalObject*>(it->second);
         }
 
       layoutmap.insert(std::pair<const CLBase*, const SBase*>(tmp, pG));
       tmp->exportToSBML(pG, copasimodelmap, sbmlIDs, layoutmap);
     }
 
   //now that we have all graphical objects in the layoutmap we can resolve the references
   //in the text glyphs
   imax = mvLabels.size();
 
   for (i = 0; i < imax; ++i)
     {
       const CLTextGlyph * tmp = mvLabels[i];
 
       //find the corresponding SBML object
       std::map<const CLBase*, const SBase*>::const_iterator it = layoutmap.find(tmp);
 
       if (it != layoutmap.end() && it->second && dynamic_cast<const TextGlyph*>(it->second))
         {
           tmp->exportReferenceToSBML(const_cast<TextGlyph*>(dynamic_cast<const TextGlyph*>(it->second)), layoutmap);
         }
     }
 
   // export the local render information
   imax = this->mvLocalRenderInformationObjects.size();
   LocalRenderInformation* pLRI = NULL;
   std::map<std::string, std::string> keyToIdMap;
 
   /*
   std::map<std::string,std::string> colorKeyToIdMap;
   std::map<std::string,std::string> gradientKeyToIdMap;
   std::map<std::string,std::string> lineEndingKeyToIdMap;
   std::map<std::string,std::map<std::string,std::string> > colorKeyToIdMapMap;
   std::map<std::string,std::map<std::string,std::string> > gradientKeyToIdMapMap;
   std::map<std::string,std::map<std::string,std::string> > lineEndingKeyToIdMapMap;
   */
   for (i = 0; i < imax; ++i)
     {
       //colorKeyToIdMap.clear();
       //gradientKeyToIdMap.clear();
       //lineEndingKeyToIdMap.clear();
       //pLRI=this->mvLocalRenderInformationObjects[i]->toSBML(colorKeyToIdMap,gradientKeyToIdMap,lineEndingKeyToIdMap);
       pLRI = this->mvLocalRenderInformationObjects[i]->toSBML(layout->getLevel(), layout->getVersion());
       keyToIdMap.insert(std::pair<std::string, std::string>(this->mvLocalRenderInformationObjects[i]->getKey(), pLRI->getId()));
       //colorKeyToIdMapMap.insert(std::pair<std::string,std::map<std::string,std::string> >(pLRI->getId(),colorKeyToIdMap));
       //gradientKeyToIdMapMap.insert(std::pair<std::string,std::map<std::string,std::string> >(pLRI->getId(),gradientKeyToIdMap));
       //lineEndingKeyToIdMapMap.insert(std::pair<std::string,std::map<std::string,std::string> >(pLRI->getId(),lineEndingKeyToIdMap));
       // fix the references to layout objects in id lists
       std::map<const CLBase*, const SBase*>::const_iterator layoutMapIt = layoutmap.begin(), layoutMapEndit = layoutmap.end();
       std::map<std::string, std::string> layoutObjectKeyToIdMap;
       const CLGraphicalObject* pGObject = NULL;
 
       while (layoutMapIt != layoutMapEndit)
         {
           pGObject = dynamic_cast<const CLGraphicalObject*>(layoutMapIt->first);
 
           if (pGObject != NULL)
             {
               layoutObjectKeyToIdMap.insert(std::pair<std::string, std::string>(pGObject->getKey(), layoutMapIt->second->getId()));
             }
 
           ++layoutMapIt;
         }
 
       size_t j, jMax = pLRI->getNumStyles();
 
       for (j = 0; j < jMax; ++j)
         {
           SBMLDocumentLoader::convertLayoutObjectKeys(*(pLRI->getStyle((unsigned int) j)), layoutObjectKeyToIdMap);
         }
 
       RenderLayoutPlugin* rlolPlugin = (RenderLayoutPlugin*) layout->getPlugin("render");
 
       if (rlolPlugin == NULL)
         {
           const std::string uri = (layout->getLevel() < 3 ? RenderExtension::getXmlnsL2() : RenderExtension::getXmlnsL3V1V1());
           layout->enablePackage(uri, "render", true);
 
           if (layout->getLevel() > 2)
             layout->getSBMLDocument()->setPackageRequired("render", false);
 
           rlolPlugin = (RenderLayoutPlugin*) layout->getPlugin("render");
         }
 
       if (rlolPlugin != NULL)
         rlolPlugin->getListOfLocalRenderInformation()->appendAndOwn(pLRI);
     }
 }

const CLDimensions& CLayout::getDimensions ( ) const

inline

Definition at line 76 of file CLayout.h.

References mDimensions.

Referenced by CQGLLayoutPainter::calculateAndAssignBounds(), CQGLNetworkPainter::createGraph(), CLLayoutRenderer::draw_layout(), CCopasiSpringLayout::randomize(), and CCopasiXML::saveLayoutList().

76 {return mDimensions;};

CLayout::mDimensions

CLDimensions mDimensions

Definition: CLayout.h:40

virtual const std::string& CLayout::getKey ( ) const

inlinevirtual

Retrieves the key of the layout

Reimplemented from CCopasiObject.

Definition at line 71 of file CLayout.h.

References mKey.

Referenced by CQLayoutsWidget::createLayoutWindow(), exportToDotFile(), exportToSBML(), CCopasiXML::saveLayoutList(), CQLayoutsWidget::slotShowLayout(), and CQNewMainWindow::updateLayoutList().

72 {return mKey;};

CLayout::mKey

std::string mKey

Definition: CLayout.h:38

const CCopasiVector<CLCompartmentGlyph>& CLayout::getListOfCompartmentGlyphs ( ) const

inline

Definition at line 81 of file CLayout.h.

References mvCompartments.

Referenced by CLayoutState::applyTo(), calculateBoundingBox(), CLayoutState::CLayoutState(), CQGLNetworkPainter::createGraph(), CQLayoutScene::fillFromLayout(), CLLayoutRenderer::getObjectsAt(), CLLayoutRenderer::getObjectsInBoundingBox(), CCopasiSpringLayout::initFromLayout(), moveBy(), CCopasiSpringLayout::randomize(), CCopasiXML::saveLayoutList(), CQNewMainWindow::slotCalculateDimensions(), CQNewMainWindow::slotRunRandomizeLayout(), CLayoutState::tagLayout(), and CLLayoutRenderer::update_associations().

82 {return mvCompartments;};

CLayout::mvCompartments

CCopasiVector< CLCompartmentGlyph > mvCompartments

Definition: CLayout.h:42

CCopasiVector<CLCompartmentGlyph>& CLayout::getListOfCompartmentGlyphs ( )

inline

Definition at line 84 of file CLayout.h.

References mvCompartments.

85 {return mvCompartments;};

CLayout::mvCompartments

CCopasiVector< CLCompartmentGlyph > mvCompartments

Definition: CLayout.h:42

const CCopasiVector<CLGeneralGlyph>& CLayout::getListOfGeneralGlyphs ( ) const

inline

Definition at line 133 of file CLayout.h.

References mvGraphicalObjects.

Referenced by CLayoutState::applyTo(), calculateBoundingBox(), CLayoutState::CLayoutState(), CCopasiSpringLayout::createVariables(), CQLayoutScene::fillFromLayout(), CCopasiSpringLayout::finalizeState(), CLLayoutRenderer::getObjectsAt(), CLLayoutRenderer::getObjectsInBoundingBox(), CCopasiSpringLayout::getPotential(), moveBy(), CCopasiXML::saveLayoutList(), CLayoutState::tagLayout(), and CLLayoutRenderer::update_associations().

134 {return mvGraphicalObjects;};

CLayout::mvGraphicalObjects

CCopasiVector< CLGeneralGlyph > mvGraphicalObjects

Definition: CLayout.h:46

CCopasiVector<CLGeneralGlyph>& CLayout::getListOfGeneralGlyphs ( )

inline

Definition at line 136 of file CLayout.h.

References mvGraphicalObjects.

137 {return mvGraphicalObjects;};

CLayout::mvGraphicalObjects

CCopasiVector< CLGeneralGlyph > mvGraphicalObjects

Definition: CLayout.h:46

const CCopasiVector<CLLocalRenderInformation>& CLayout::getListOfLocalRenderInformationObjects ( ) const

inline

Returns a const reference to the list of local render information objects.

Definition at line 149 of file CLayout.h.

References mvLocalRenderInformationObjects.

Referenced by CLLayoutRenderer::change_style(), SBMLDocumentLoader::createLayout(), CQLayoutScene::initializeResolver(), CCopasiXML::saveLayoutList(), CQNewMainWindow::slotRenderInfoChanged(), CQLayoutView::slotRenderInformationChanged(), CCopasiXMLParser::LocalRenderInformationElement::start(), updateRenderInformationList(), and CQNewMainWindow::updateRenderInformationList().

150 {return this->mvLocalRenderInformationObjects;};

CLayout::mvLocalRenderInformationObjects

CCopasiVector< CLLocalRenderInformation > mvLocalRenderInformationObjects

Definition: CLayout.h:47

CCopasiVector<CLLocalRenderInformation>& CLayout::getListOfLocalRenderInformationObjects ( )

inline

Returns a reference to the list of local render information objects.

Definition at line 155 of file CLayout.h.

References mvLocalRenderInformationObjects.

156 {return this->mvLocalRenderInformationObjects;};

CLayout::mvLocalRenderInformationObjects

CCopasiVector< CLLocalRenderInformation > mvLocalRenderInformationObjects

Definition: CLayout.h:47

const CCopasiVector<CLMetabGlyph>& CLayout::getListOfMetaboliteGlyphs ( ) const

inline

Definition at line 94 of file CLayout.h.

References mvMetabs.

Referenced by CLayoutState::applyTo(), calculateBoundingBox(), CLayoutState::CLayoutState(), CQGLNetworkPainter::createGraph(), CCopasiSpringLayout::createLayout(), CCopasiSpringLayout::createVariables(), CQLayoutScene::fillFromLayout(), getMetabGlyphForKey(), CLLayoutRenderer::getObjectsAt(), CLLayoutRenderer::getObjectsInBoundingBox(), CCopasiSpringLayout::getPotential(), CCopasiSpringLayout::initFromLayout(), moveBy(), CCopasiSpringLayout::randomize(), CCopasiXML::saveLayoutList(), CQNewMainWindow::selectMetabolite(), CQNewMainWindow::slotCalculateDimensions(), CQNewMainWindow::slotRunRandomizeLayout(), CLayoutState::tagLayout(), and CLLayoutRenderer::update_associations().

95 {return mvMetabs;};

CLayout::mvMetabs

CCopasiVector< CLMetabGlyph > mvMetabs

Definition: CLayout.h:43

CCopasiVector<CLMetabGlyph>& CLayout::getListOfMetaboliteGlyphs ( )

inline

Definition at line 97 of file CLayout.h.

References mvMetabs.

98 {return mvMetabs;};

CLayout::mvMetabs

CCopasiVector< CLMetabGlyph > mvMetabs

Definition: CLayout.h:43

const CCopasiVector<CLReactionGlyph>& CLayout::getListOfReactionGlyphs ( ) const

inline

Definition at line 107 of file CLayout.h.

References mvReactions.

Referenced by CLayoutState::applyTo(), calculateBoundingBox(), CLayoutState::CLayoutState(), CQGLNetworkPainter::createGraph(), CCopasiSpringLayout::createVariables(), CQLayoutScene::fillFromLayout(), CCopasiSpringLayout::finalizeState(), CLLayoutRenderer::getObjectsAt(), CLLayoutRenderer::getObjectsInBoundingBox(), CCopasiSpringLayout::getPotential(), CCopasiSpringLayout::initFromLayout(), moveBy(), CCopasiSpringLayout::randomize(), CCopasiXML::saveLayoutList(), CQNewMainWindow::selectReaction(), CLLayoutRenderer::setDeduceSpeciesReferenceRoles(), CLayoutState::tagLayout(), and CLLayoutRenderer::update_associations().

108 {return mvReactions;};

CLayout::mvReactions

CCopasiVector< CLReactionGlyph > mvReactions

Definition: CLayout.h:44

CCopasiVector<CLReactionGlyph>& CLayout::getListOfReactionGlyphs ( )

inline

Definition at line 110 of file CLayout.h.

References mvReactions.

111 {return mvReactions;};

CLayout::mvReactions

CCopasiVector< CLReactionGlyph > mvReactions

Definition: CLayout.h:44

const CCopasiVector<CLTextGlyph>& CLayout::getListOfTextGlyphs ( ) const

inline

Definition at line 120 of file CLayout.h.

References mvLabels.

Referenced by CLayoutState::applyTo(), calculateBoundingBox(), CLayoutState::CLayoutState(), CQGLNetworkPainter::createGraph(), CQLayoutScene::fillFromLayout(), CLLayoutRenderer::getObjectsAt(), CLLayoutRenderer::getObjectsInBoundingBox(), getTextForItem(), CCopasiSpringLayout::initFromLayout(), moveBy(), placeTextGlyphs(), CCopasiXML::saveLayoutList(), CLayoutState::tagLayout(), and CLLayoutRenderer::update_associations().

121 {return mvLabels;};

CLayout::mvLabels

CCopasiVector< CLTextGlyph > mvLabels

Definition: CLayout.h:45

CCopasiVector<CLTextGlyph>& CLayout::getListOfTextGlyphs ( )

inline

Definition at line 123 of file CLayout.h.

References mvLabels.

124 {return mvLabels;};

CLayout::mvLabels

CCopasiVector< CLTextGlyph > mvLabels

Definition: CLayout.h:45

const CLLocalRenderInformation * CLayout::getRenderInformation ( size_t index ) const

Returns a const pointer to the local render information with the given index or NULL if the index is invalid.

Definition at line 658 of file CLayout.cpp.

References mvLocalRenderInformationObjects, and CCopasiVector< T >::size().

Referenced by CQNewMainWindow::slotRenderInfoChanged(), and CQNewMainWindow::updateRenderInformationList().

 {
   if (index >= this->mvLocalRenderInformationObjects.size()) return NULL;
 
   return this->mvLocalRenderInformationObjects[index];
 }

CLLocalRenderInformation * CLayout::getRenderInformation ( size_t index )

Returns a pointer to the local render information with the given index or NULL if the index is invalid.

Definition at line 669 of file CLayout.cpp.

References mvLocalRenderInformationObjects, and CCopasiVector< T >::size().

 {
   if (index >= this->mvLocalRenderInformationObjects.size()) return NULL;
 
   return this->mvLocalRenderInformationObjects[index];
 }

void CLayout::moveBy ( const CLPoint & p )

virtual

Reimplemented from CLBase.

Definition at line 909 of file CLayout.cpp.

References getListOfCompartmentGlyphs(), getListOfGeneralGlyphs(), getListOfMetaboliteGlyphs(), getListOfReactionGlyphs(), getListOfTextGlyphs(), CLPoint::isEmpty(), CLGraphicalObject::moveBy(), and CCopasiVector< T >::size().

Referenced by CQGLLayoutPainter::calculateAndAssignBounds(), and calculateAndAssignBounds().

 {
   if (p.isEmpty()) return;
 
   CLGraphicalObject* pObject = NULL;
   size_t i, iMax = this->getListOfCompartmentGlyphs().size();
 
   for (i = 0; i < iMax; ++i)
     {
       pObject = this->getListOfCompartmentGlyphs()[i];
       pObject->moveBy(p);
     }
 
   iMax = this->getListOfMetaboliteGlyphs().size();
 
   for (i = 0; i < iMax; ++i)
     {
       pObject = this->getListOfMetaboliteGlyphs()[i];
       pObject->moveBy(p);
     }
 
   iMax = this->getListOfReactionGlyphs().size();
 
   for (i = 0; i < iMax; ++i)
     {
       pObject = this->getListOfReactionGlyphs()[i];
       pObject->moveBy(p);
     }
 
   iMax = this->getListOfTextGlyphs().size();
 
   for (i = 0; i < iMax; ++i)
     {
       pObject = this->getListOfTextGlyphs()[i];
       pObject->moveBy(p);
     }
 
   iMax = this->getListOfGeneralGlyphs().size();
 
   for (i = 0; i < iMax; ++i)
     {
       pObject = this->getListOfGeneralGlyphs()[i];
       pObject->moveBy(p);
     }
 }

void CLayout::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 328 of file CLayout.cpp.

329 {*os << *this;}

virtual void CLayout::scale ( const double & scaleFactor )

inlinevirtual

Definition at line 190 of file CLayout.h.

References mDimensions, and CLDimensions::scale().

190 {this->mDimensions.scale(scaleFactor);}

CLayout::mDimensions

CLDimensions mDimensions

Definition: CLayout.h:40

CLDimensions::scale

void scale(const double &scaleFactor)

Definition: CLBase.h:223

void CLayout::setDimensions ( const CLDimensions & d )

inline

Definition at line 77 of file CLayout.h.

References mDimensions.

Referenced by calculateAndAssignBounds(), CCopasiSpringLayout::createLayout(), test000097::createModel(), and CCopasiXMLParser::LayoutElement::start().

77 {mDimensions = d;};

CLayout::mDimensions

CLDimensions mDimensions

Definition: CLayout.h:40

void CLayout::writeDotEdge	(	std::ostream &	os,
		const std::string &	id1,
		const std::string &	id2,
		int	t = `0`
	)		const

protected

Definition at line 380 of file CLayout.cpp.

Referenced by exportToDotFile().

 {
   std::string tmp;
 
   if (t == 1)
     tmp = " [len=0.2] ";
 
   os << id1 << " -> " << id2 << tmp << "\n"; //[label=\"" << label << "\"] \n";
 }

void CLayout::writeDotNode	(	std::ostream &	os,
		const std::string &	id,
		const std::string &	label,
		int	t = `0`
	)		const

protected

Definition at line 368 of file CLayout.cpp.

Referenced by exportToDotFile().

 {
   std::string tmp;
 
   if (t == 1)
     tmp = " shape=point ";
 
   os << id << " [" << tmp << " label=\"" << label << "\"] \n";
 }

Friends And Related Function Documentation

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

friend

insert operator

Definition at line 269 of file CLayout.cpp.

 {
   size_t i, imax;
 
   os << "Layout  \"" << l.getObjectName() << "\" " << l.mDimensions << "\n\n";
 
   imax = l.mvCompartments.size();
 
   if (imax)
     {
       os << "List of compartment glyphs: \n\n";
 
       for (i = 0; i < imax; ++i)
         os << *l.mvCompartments[i];
     }
 
   imax = l.mvMetabs.size();
 
   if (imax)
     {
       os << "\nList of species glyphs: \n\n";
 
       for (i = 0; i < imax; ++i)
         os << *l.mvMetabs[i];
     }
 
   imax = l.mvReactions.size();
 
   if (imax)
     {
       os << "\nList of reaction glyphs: \n\n";
 
       for (i = 0; i < imax; ++i)
         os << *l.mvReactions[i];
     }
 
   imax = l.mvLabels.size();
 
   if (imax)
     {
       os << "\nList of labels: \n\n";
 
       for (i = 0; i < imax; ++i)
         os << *l.mvLabels[i];
     }
 
   imax = l.mvGraphicalObjects.size();
 
   if (imax)
     {
       os << "\nList of graphical objects: \n\n";
 
       for (i = 0; i < imax; ++i)
         os << *l.mvGraphicalObjects[i];
     }
 
   return os;
 }