#include <CCopasiSpringLayout.h>

Inheritance diagram for CCopasiSpringLayout:

Classes
struct	CoordinateRelation

class	Parameters

struct	UpdateAction
	this describes one update action that has to be performed during setState() More...

Public Member Functions
	CCopasiSpringLayout (CLayout layout, Parameters ppp=NULL)

bool	createVariables ()

void	finalizeState ()

CLCompartmentGlyph *	findCompartmentForReactionNode (CLReactionGlyph &r)

virtual const std::vector< double > &	getInitialValues () const

virtual double	getPotential ()

virtual const std::vector< UpdateAction > &	getUpdateActions () const

void	randomize ()

virtual bool	setState (const std::vector< double > &vars)

void	updateFixedRelations ()

Public Member Functions inherited from CAbstractLayoutInterface
	CAbstractLayoutInterface ()

virtual const std::vector< double > &	getMassVector () const

std::vector< double >::size_type	getNumVariables () const

const std::vector< VariableDescription > &	getVariablesDescription () const

virtual	~CAbstractLayoutInterface ()

Static Public Member Functions
static CLayout *	createLayout (CDataContainer parent, const std::set< const CCompartment > &compartments, const std::set< const CReaction * > &reactions, const std::set< const CMetab * > &metabs, const std::set< const CMetab * > &sideMetabs, Parameters *mParams=NULL)

Protected Member Functions
void	addCompartmentVariables (CLCompartmentGlyph *cg)
	create variables for size and position of a compartment glyph More...

void	addPositionVariables (CLGraphicalObject *pGO)
	create variables for the position of a species glyph More...

void	addReactionVariables (CLReactionGlyph *rg)
	create variables for the position of a reaction glyph More...

CLPoint	borderProjection (CLGraphicalObject *go, const CLPoint &p, double d)

bool	initFromLayout (CLayout layout, Parameters ppp)
	performs all initializations that are later needed to calculate the potential More...

double	potEdge (const CLMetabReferenceGlyph &e, const CLReactionGlyph &r) const

double	potGeneralEdge (const CLReferenceGlyph &e, const CLGeneralGlyph &r) const

double	potReactionCompartment (const CLReactionGlyph &r, const CLCompartmentGlyph &c) const

double	potReactionReaction (const CLReactionGlyph &a, const CLReactionGlyph &b) const

double	potSecondOrderEdge (const CLMetabReferenceGlyph &e1, const CLMetabReferenceGlyph &e2, double &dist) const

double	potSpeciesCompartment (const CLMetabGlyph &s, const CLCompartmentGlyph &c) const

double	potSpeciesReaction (const CLMetabGlyph &a, const CLReactionGlyph &b) const

double	potSpeciesSpecies (const CLMetabGlyph &a, const CLMetabGlyph &b) const

Static Protected Member Functions
static double	bound_distance (const double &x1, const double &y1, const double &x2, const double &y2, const double &max)

static double	distance (const double &x1, const double &y1, const double &x2, const double &y2)

Protected Attributes
std::map< CLBase , CLCompartmentGlyph >	mCompartmentMap
	this map contains information about the compartment glyph a given glyph is located in More...

std::vector< CoordinateRelation >	mFixedRelations
	a list of fixed positon relations between objects. Should be constructed in initFromLayout() More...

std::vector< double >	mInitialState

CLayout *	mpLayout

Parameters *	mpPar

std::vector< UpdateAction >	mUpdateActions
	this is the list of all update actions that have to be performed during setState(); More...

Protected Attributes inherited from CAbstractLayoutInterface
std::vector< double >	mMassVector

std::vector< VariableDescription >	mVarDescription

Detailed Description

This class defines how a layout optimization algorithm will see a COPASI layout, using a spring approach. No copy of the layout will be generated, meaning that setState() will change the layout.

Constructor & Destructor Documentation

◆ CCopasiSpringLayout()

CCopasiSpringLayout::CCopasiSpringLayout	(	CLayout *	layout,
		Parameters *	ppp = `NULL`
	)

generate a spring layout view of a COPASI layout.

References initFromLayout().

Member Function Documentation

◆ addCompartmentVariables()

void CCopasiSpringLayout::addCompartmentVariables ( CLCompartmentGlyph * cg )

protected

create variables for size and position of a compartment glyph

References CCopasiSpringLayout::UpdateAction::COMPARTMENT_4V, CLGraphicalObject::getHeight(), CLGraphicalObject::getWidth(), CLGraphicalObject::getX(), CLGraphicalObject::getY(), CAbstractLayoutInterface::VariableDescription::isAngle, mInitialState, CAbstractLayoutInterface::mMassVector, mUpdateActions, and CAbstractLayoutInterface::mVarDescription.

◆ addPositionVariables()

void CCopasiSpringLayout::addPositionVariables ( CLGraphicalObject * pGO )

protected

create variables for the position of a species glyph

References CLGraphicalObject::getX(), CLGraphicalObject::getY(), CAbstractLayoutInterface::VariableDescription::isAngle, mInitialState, CAbstractLayoutInterface::mMassVector, mUpdateActions, CAbstractLayoutInterface::mVarDescription, and CCopasiSpringLayout::UpdateAction::POSITION_2V.

Referenced by createVariables().

◆ addReactionVariables()

void CCopasiSpringLayout::addReactionVariables ( CLReactionGlyph * rg )

protected

create variables for the position of a reaction glyph

References C_FLOAT64, CLGlyphWithCurve::getCurve(), CLCurve::getCurveSegments(), CLGraphicalObject::getHeight(), CLCurve::getNumCurveSegments(), CLGraphicalObject::getWidth(), CLGraphicalObject::getX(), CLGraphicalObject::getY(), CAbstractLayoutInterface::VariableDescription::isAngle, mInitialState, CAbstractLayoutInterface::mMassVector, mUpdateActions, CAbstractLayoutInterface::mVarDescription, and CCopasiSpringLayout::UpdateAction::REACTION_2V.

Referenced by createVariables().

◆ borderProjection()

CLPoint CCopasiSpringLayout::borderProjection	(	CLGraphicalObject *	go,
		const CLPoint &	p,
		double	d
	)

protected

calculate a point just outside the bounding box of a given graphical object on the line between the center of the object and the point p. d specifies the distance from the border of the object.

References CLGraphicalObject::getBoundingBox(), CLBoundingBox::getCenter(), CLGraphicalObject::getHeight(), CLGraphicalObject::getWidth(), CLPoint::getX(), and CLPoint::getY().

Referenced by finalizeState().

◆ bound_distance()

static double CCopasiSpringLayout::bound_distance	(	const double &	x1,
		const double &	y1,
		const double &	x2,
		const double &	y2,
		const double &	max
	)

inlinestaticprotected

References max.

Referenced by potReactionReaction(), potSpeciesReaction(), and potSpeciesSpecies().

◆ createLayout()

CLayout * CCopasiSpringLayout::createLayout	(	CDataContainer *	parent,
		const std::set< const CCompartment * > &	compartments,
		const std::set< const CReaction * > &	reactions,
		const std::set< const CMetab * > &	metabs,
		const std::set< const CMetab * > &	sideMetabs,
		Parameters *	mParams = `NULL`
	)

static

This method creates a random layout using the elements in the compartments, reactions, species and side species containers.

References CDataContainer::add(), CLayout::addCompartmentGlyph(), CLayout::addGeneralGlyph(), CLayout::addMetaboliteGlyph(), CLReactionGlyph::addMetabReferenceGlyph(), CLayout::addReactionGlyph(), CLGeneralGlyph::addReferenceGlyph(), CLayout::addTextGlyph(), CModelEntity::ASSIGNMENT, CDataVector< CType >::begin(), CLayout::calculateBoundingBox(), CDataVector< CType >::end(), CMetab::getCompartment(), CLBoundingBox::getDimensions(), CLDimensions::getHeight(), CLGraphicalObject::getKey(), CModelEntity::getKey(), CLayout::getListOfMetaboliteGlyphs(), CLGraphicalObject::getModelObject(), CModelEntity::getStatus(), CLDimensions::getWidth(), CLMetabReferenceGlyph::MODIFIER, CModelEntity::ODE, CLMetabReferenceGlyph::PRODUCT, randomize(), CLayout::setDimensions(), CLGraphicalObject::setDimensions(), CLMetabReferenceGlyph::setFunctionalRole(), CLTextGlyph::setGraphicalObjectKey(), CLMetabReferenceGlyph::setMetabGlyphKey(), CLGraphicalObject::setModelObjectKey(), CLGraphicalObject::setObjectRole(), CLGraphicalObject::setPosition(), CLReferenceGlyph::setRole(), CLMetabReferenceGlyph::setRole(), CLReferenceGlyph::setTargetGlyphKey(), CLMetabReferenceGlyph::SIDEPRODUCT, CLMetabReferenceGlyph::SIDESUBSTRATE, CDataVector< CType >::size(), and CLMetabReferenceGlyph::SUBSTRATE.

◆ createVariables()

bool CCopasiSpringLayout::createVariables ( )

generates the list of variables from the layout. This method will generate variables for the coordinates of all the nodes in the layout. TODO: make it possible to only auto-layout a subset of the graph

References addPositionVariables(), addReactionVariables(), CLayout::getListOfGeneralGlyphs(), CLayout::getListOfMetaboliteGlyphs(), CLayout::getListOfReactionGlyphs(), mInitialState, CAbstractLayoutInterface::mMassVector, mpLayout, and CAbstractLayoutInterface::mVarDescription.

◆ distance()

static double CCopasiSpringLayout::distance	(	const double &	x1,
		const double &	y1,
		const double &	x2,
		const double &	y2
	)

inlinestaticprotected

Referenced by potEdge(), potGeneralEdge(), and potSecondOrderEdge().

◆ finalizeState()

void CCopasiSpringLayout::finalizeState ( )

complete the update of the layout. This updates the things that are not needed for the calculation of the potential. After calling this method the layout should be ready for drawing or storing

References CLCurve::addCurveSegment(), borderProjection(), CLayout::calculateAndAssignBounds(), CLCurve::clear(), CLPoint::dot(), CLGraphicalObject::getBoundingBox(), CLBoundingBox::getCenter(), CLGlyphWithCurve::getCurve(), CLCurve::getCurveSegments(), CLGraphicalObject::getDimensions(), CLMetabReferenceGlyph::getFunctionalRole(), CLDimensions::getHeight(), CLayout::getListOfGeneralGlyphs(), CLReactionGlyph::getListOfMetabReferenceGlyphs(), CLayout::getListOfReactionGlyphs(), CLGeneralGlyph::getListOfReferenceGlyphs(), CLMetabReferenceGlyph::getMetabGlyph(), CLCurve::getNumCurveSegments(), CLGraphicalObject::getPosition(), CLReferenceGlyph::getTargetGlyph(), CLDimensions::getWidth(), CLPoint::getX(), CLPoint::getY(), mpLayout, CLMetabReferenceGlyph::PRODUCT, CLPoint::scale(), CLGraphicalObject::setPosition(), CLMetabReferenceGlyph::SIDEPRODUCT, CLMetabReferenceGlyph::SIDESUBSTRATE, CDataVector< CType >::size(), CLMetabReferenceGlyph::SUBSTRATE, and updateFixedRelations().

Referenced by randomize().

◆ findCompartmentForReactionNode()

CLCompartmentGlyph * CCopasiSpringLayout::findCompartmentForReactionNode ( CLReactionGlyph & r )

if all participants of a reaction are in a single compartment return the compartment glyph, otherwise return NULL

References CLReactionGlyph::getListOfMetabReferenceGlyphs(), and mCompartmentMap.

Referenced by initFromLayout().

◆ getInitialValues()

const std::vector< double > & CCopasiSpringLayout::getInitialValues ( ) const

virtual

Implements CAbstractLayoutInterface.

References mInitialState.

◆ getPotential()

◆ getUpdateActions()

const std::vector< CCopasiSpringLayout::UpdateAction > & CCopasiSpringLayout::getUpdateActions ( ) const

virtual

References mUpdateActions.

◆ initFromLayout()

bool CCopasiSpringLayout::initFromLayout	(	CLayout *	layout,
		Parameters *	ppp
	)

protected

performs all initializations that are later needed to calculate the potential

References CCopasiSpringLayout::CoordinateRelation::diff, findCompartmentForReactionNode(), CMetab::getCompartment(), CModelEntity::getKey(), CLayout::getListOfCompartmentGlyphs(), CLayout::getListOfMetaboliteGlyphs(), CLayout::getListOfReactionGlyphs(), CLayout::getListOfTextGlyphs(), CLGraphicalObject::getPosition(), mCompartmentMap, mFixedRelations, mpLayout, mpPar, CDataVector< CType >::size(), CCopasiSpringLayout::CoordinateRelation::source, and CCopasiSpringLayout::CoordinateRelation::target.

Referenced by CCopasiSpringLayout().

◆ potEdge()

double CCopasiSpringLayout::potEdge	(	const CLMetabReferenceGlyph &	e,
		const CLReactionGlyph &	r
	)		const

protected

References distance(), CLGraphicalObject::getHeight(), CLMetabReferenceGlyph::getMetabGlyph(), CLMetabReferenceGlyph::getRole(), CLGraphicalObject::getWidth(), CLGraphicalObject::getX(), CLGraphicalObject::getY(), CLMetabReferenceGlyph::MODIFIER, mpPar, CLMetabReferenceGlyph::SIDEPRODUCT, CLMetabReferenceGlyph::SIDESUBSTRATE, and CCopasiSpringLayout::Parameters::values.

Referenced by getPotential().

◆ potGeneralEdge()

double CCopasiSpringLayout::potGeneralEdge	(	const CLReferenceGlyph &	e,
		const CLGeneralGlyph &	r
	)		const

protected

References distance(), CLGraphicalObject::getHeight(), CLReferenceGlyph::getTargetGlyph(), CLGraphicalObject::getWidth(), CLGraphicalObject::getX(), and CLGraphicalObject::getY().

Referenced by getPotential().

◆ potReactionCompartment()

double CCopasiSpringLayout::potReactionCompartment	(	const CLReactionGlyph &	r,
		const CLCompartmentGlyph &	c
	)		const

protected

s.charge

References CLGraphicalObject::getHeight(), CLGraphicalObject::getWidth(), CLGraphicalObject::getX(), and CLGraphicalObject::getY().

Referenced by getPotential().

◆ potReactionReaction()

double CCopasiSpringLayout::potReactionReaction	(	const CLReactionGlyph &	a,
		const CLReactionGlyph &	b
	)		const

protected

References bound_distance(), CLGraphicalObject::getHeight(), CLGraphicalObject::getWidth(), CLGraphicalObject::getX(), and CLGraphicalObject::getY().

Referenced by getPotential().

◆ potSecondOrderEdge()

double CCopasiSpringLayout::potSecondOrderEdge	(	const CLMetabReferenceGlyph &	e1,
		const CLMetabReferenceGlyph &	e2,
		double &	dist
	)		const

protected

References distance(), CLGraphicalObject::getHeight(), CLMetabReferenceGlyph::getMetabGlyph(), CLGraphicalObject::getWidth(), CLGraphicalObject::getX(), and CLGraphicalObject::getY().

Referenced by getPotential().

◆ potSpeciesCompartment()

double CCopasiSpringLayout::potSpeciesCompartment	(	const CLMetabGlyph &	s,
		const CLCompartmentGlyph &	c
	)		const

protected

s.charge

References CLGraphicalObject::getHeight(), CLGraphicalObject::getWidth(), CLGraphicalObject::getX(), and CLGraphicalObject::getY().

Referenced by getPotential().

◆ potSpeciesReaction()

double CCopasiSpringLayout::potSpeciesReaction	(	const CLMetabGlyph &	a,
		const CLReactionGlyph &	b
	)		const

protected

References bound_distance(), CLGraphicalObject::getHeight(), CLGraphicalObject::getWidth(), CLGraphicalObject::getX(), and CLGraphicalObject::getY().

Referenced by getPotential().

◆ potSpeciesSpecies()

double CCopasiSpringLayout::potSpeciesSpecies	(	const CLMetabGlyph &	a,
		const CLMetabGlyph &	b
	)		const

protected

References bound_distance(), CLGraphicalObject::getHeight(), CLGraphicalObject::getWidth(), CLGraphicalObject::getX(), and CLGraphicalObject::getY().

Referenced by getPotential().

◆ randomize()

void CCopasiSpringLayout::randomize ( )

Randomizes the layout

This function produces a random layout. It first shufles around metab glyphs and reaction centers, and finally corrects all ars

References CRandom::createGenerator(), finalizeState(), CLGraphicalObject::getBoundingBox(), CLBoundingBox::getCenter(), CMetab::getCompartment(), CLayout::getDimensions(), CModelEntity::getKey(), CLayout::getListOfCompartmentGlyphs(), CLayout::getListOfMetaboliteGlyphs(), CLReactionGlyph::getListOfMetabReferenceGlyphs(), CLayout::getListOfReactionGlyphs(), CLGraphicalObject::getModelObject(), CRandom::getRandomCC(), CRandom::getSystemSeed(), mpLayout, CRandom::mt19937, placeTextGlyphs(), randomlyPlaceGlyphInCompartmentGlyph(), randomlyPlaceGlyphInDimensions(), CLGraphicalObject::setPosition(), and CDataVector< CType >::size().

Referenced by createLayout().

◆ setState()

bool CCopasiSpringLayout::setState ( const std::vector< double > & vars )

virtual

updates the COPASI layout from the state vector. Only the updates that are needed for the calculation of the potential (or for a rough on the fly drawing) are done.

Implements CAbstractLayoutInterface.

References CCopasiSpringLayout::UpdateAction::COMPARTMENT_4V, mUpdateActions, CAbstractLayoutInterface::mVarDescription, CCopasiSpringLayout::UpdateAction::POSITION_2V, and CCopasiSpringLayout::UpdateAction::REACTION_2V.

◆ updateFixedRelations()

void CCopasiSpringLayout::updateFixedRelations ( )

References mFixedRelations.

Referenced by finalizeState().

Member Data Documentation

◆ mCompartmentMap

std::map<CLBase*, CLCompartmentGlyph*> CCopasiSpringLayout::mCompartmentMap

protected

this map contains information about the compartment glyph a given glyph is located in

Referenced by findCompartmentForReactionNode(), getPotential(), and initFromLayout().

◆ mFixedRelations

std::vector<CoordinateRelation> CCopasiSpringLayout::mFixedRelations

protected

a list of fixed positon relations between objects. Should be constructed in initFromLayout()

Referenced by initFromLayout(), and updateFixedRelations().

◆ mInitialState

std::vector<double> CCopasiSpringLayout::mInitialState

protected

Referenced by addCompartmentVariables(), addPositionVariables(), addReactionVariables(), createVariables(), and getInitialValues().

◆ mpLayout

CLayout* CCopasiSpringLayout::mpLayout

protected

Referenced by createVariables(), finalizeState(), getPotential(), initFromLayout(), and randomize().

◆ mpPar

Parameters* CCopasiSpringLayout::mpPar

protected

Referenced by getPotential(), initFromLayout(), and potEdge().

◆ mUpdateActions

std::vector<UpdateAction> CCopasiSpringLayout::mUpdateActions

protected

this is the list of all update actions that have to be performed during setState();

Referenced by addCompartmentVariables(), addPositionVariables(), addReactionVariables(), getUpdateActions(), and setState().

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

Classes

Public Member Functions

Static Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ CCopasiSpringLayout()

Member Function Documentation

◆ addCompartmentVariables()

◆ addPositionVariables()

◆ addReactionVariables()

◆ borderProjection()

◆ bound_distance()

◆ createLayout()

◆ createVariables()

◆ distance()

◆ finalizeState()

◆ findCompartmentForReactionNode()

◆ getInitialValues()

◆ getPotential()

◆ getUpdateActions()

◆ initFromLayout()

◆ potEdge()

◆ potGeneralEdge()

◆ potReactionCompartment()

◆ potReactionReaction()

◆ potSecondOrderEdge()

◆ potSpeciesCompartment()

◆ potSpeciesReaction()

◆ potSpeciesSpecies()

◆ randomize()

◆ setState()

◆ updateFixedRelations()

Member Data Documentation

◆ mCompartmentMap

◆ mFixedRelations

◆ mInitialState

◆ mpLayout

◆ mpPar

◆ mUpdateActions