Package bio.singa.simulation.model.graphs

Class AutomatonNode

java.lang.Object

bio.singa.mathematics.graphs.model.AbstractNode<AutomatonNode,bio.singa.mathematics.vectors.Vector2D,bio.singa.mathematics.topology.grids.rectangular.RectangularCoordinate>

bio.singa.simulation.model.graphs.AutomatonNode

All Implemented Interfaces:

bio.singa.mathematics.graphs.model.Node<AutomatonNode,bio.singa.mathematics.vectors.Vector2D,bio.singa.mathematics.topology.grids.rectangular.RectangularCoordinate>, Updatable

public class AutomatonNode
extends bio.singa.mathematics.graphs.model.AbstractNode<AutomatonNode,bio.singa.mathematics.vectors.Vector2D,bio.singa.mathematics.topology.grids.rectangular.RectangularCoordinate>
implements Updatable

A node of the AutomatonGraph. Contains the concentrations of ChemicalEntitys in a ConcentrationContainer and other attributes. Each node holds references to its neighbour nodes.

Author:

cl

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	AutomatonNode.AreaMapping

Constructor Summary

Constructors

Constructor	Description
AutomatonNode(int column, int row)
AutomatonNode(bio.singa.mathematics.topology.grids.rectangular.RectangularCoordinate identifier)

Method Summary

Modifier and Type	Method	Description
void	addAreaMapping(CellSubsection subsection, AutomatonNode.AreaMapping mapping)
void	addLineLikeAgentSegment(LineLikeAgent lineLikeAgent, bio.singa.mathematics.vectors.Vector2D segment)
void	addMembraneSegment(MembraneSegment segment)
void	addPotentialDelta(ConcentrationDelta potentialDelta)	Adds a potential delta to this node.
void	addSubsectionRepresentation(CellSubsection subsection, bio.singa.mathematics.geometry.model.Polygon representation)
void	clearCaches()
Set<CellSubsection>	getAllReferencedSections()	Returns all referenced sections in this node.
Map<LineLikeAgent,Set<bio.singa.mathematics.vectors.Vector2D>>	getAssociatedLineLikeAgents()
CellRegion	getCellRegion()
ConcentrationContainer	getConcentrationContainer()	Returns the ConcentrationContainer used by this node.
ConcentrationDeltaManager	getConcentrationManager()
AutomatonNode	getCopy()
javax.measure.Quantity<javax.measure.quantity.Area>	getMembraneArea()
List<MembraneSegment>	getMembraneSegments()
List<bio.singa.mathematics.vectors.Vector2D>	getMembraneVectors()
bio.singa.mathematics.geometry.model.Polygon	getSpatialRepresentation()
String	getStringIdentifier()
Map<CellSubsection,List<AutomatonNode.AreaMapping>>	getSubsectionAdjacency()
Map<CellSubsection,bio.singa.mathematics.geometry.model.Polygon>	getSubsectionRepresentations()
boolean	isObserved()	Returns true if this node is observed.
void	setCellRegion(CellRegion cellRegion)
void	setConcentrationContainer(ConcentrationContainer concentrationContainer)	Sets the ConcentrationContainer for this node.
void	setConcentrationManager(ConcentrationDeltaManager concentrationManager)
void	setObserved(boolean isObserved)	Sets the observed state of this node.
void	setSpatialRepresentation(bio.singa.mathematics.geometry.model.Polygon spatialRepresentation)
String	toString()

Methods inherited from class bio.singa.mathematics.graphs.model.AbstractNode

addNeighbour, equals, getDegree, getIdentifier, getNeighbours, getPosition, getSpatialPosition, hashCode, hasNeighbour, removeNeighbour, setIdentifier, setNeighbours, setPosition, setSpatialPosition

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface bio.singa.simulation.model.simulation.Updatable

getPosition

Constructor Detail

AutomatonNode

public AutomatonNode(bio.singa.mathematics.topology.grids.rectangular.RectangularCoordinate identifier)

AutomatonNode

public AutomatonNode(int column,
                     int row)

Method Detail

addAreaMapping

public void addAreaMapping(CellSubsection subsection,
                           AutomatonNode.AreaMapping mapping)

getSubsectionAdjacency

public Map<CellSubsection,List<AutomatonNode.AreaMapping>> getSubsectionAdjacency()

getMembraneVectors

public List<bio.singa.mathematics.vectors.Vector2D> getMembraneVectors()

getSubsectionRepresentations

public Map<CellSubsection,bio.singa.mathematics.geometry.model.Polygon> getSubsectionRepresentations()

addPotentialDelta

public void addPotentialDelta(ConcentrationDelta potentialDelta)

Adds a potential delta to this node.

Specified by:

addPotentialDelta in interface Updatable

Parameters:

potentialDelta - The potential delta.

getConcentrationManager

public ConcentrationDeltaManager getConcentrationManager()

Specified by:

getConcentrationManager in interface Updatable

setConcentrationManager

public void setConcentrationManager(ConcentrationDeltaManager concentrationManager)

getAllReferencedSections

public Set<CellSubsection> getAllReferencedSections()

Returns all referenced sections in this node.

Specified by:

getAllReferencedSections in interface Updatable

Returns:

all referenced sections in this node.

isObserved

public boolean isObserved()

Returns true if this node is observed.

Returns:

true if this node is observed.

setObserved

public void setObserved(boolean isObserved)

Sets the observed state of this node.

Parameters:

isObserved - true if this node is observed.

getCellRegion

public CellRegion getCellRegion()

Specified by:

getCellRegion in interface Updatable

setCellRegion

public void setCellRegion(CellRegion cellRegion)

getStringIdentifier

public String getStringIdentifier()

Specified by:

getStringIdentifier in interface Updatable

getConcentrationContainer

public ConcentrationContainer getConcentrationContainer()

Returns the ConcentrationContainer used by this node.

Specified by:

getConcentrationContainer in interface Updatable

Returns:

The ConcentrationContainer used by this node.

setConcentrationContainer

public void setConcentrationContainer(ConcentrationContainer concentrationContainer)

Sets the ConcentrationContainer for this node.

Parameters:

concentrationContainer - The ConcentrationContainer for this node.

getSpatialRepresentation

public bio.singa.mathematics.geometry.model.Polygon getSpatialRepresentation()

setSpatialRepresentation

public void setSpatialRepresentation(bio.singa.mathematics.geometry.model.Polygon spatialRepresentation)

getAssociatedLineLikeAgents

public Map<LineLikeAgent,Set<bio.singa.mathematics.vectors.Vector2D>> getAssociatedLineLikeAgents()

addLineLikeAgentSegment

public void addLineLikeAgentSegment(LineLikeAgent lineLikeAgent,
                                    bio.singa.mathematics.vectors.Vector2D segment)

getMembraneSegments

public List<MembraneSegment> getMembraneSegments()

addMembraneSegment

public void addMembraneSegment(MembraneSegment segment)

getMembraneArea

public javax.measure.Quantity<javax.measure.quantity.Area> getMembraneArea()

addSubsectionRepresentation

public void addSubsectionRepresentation(CellSubsection subsection,
                                        bio.singa.mathematics.geometry.model.Polygon representation)

clearCaches

public void clearCaches()

toString

public String toString()

Overrides:

toString in class bio.singa.mathematics.graphs.model.AbstractNode<AutomatonNode,bio.singa.mathematics.vectors.Vector2D,bio.singa.mathematics.topology.grids.rectangular.RectangularCoordinate>

getCopy

public AutomatonNode getCopy()

Specified by:

getCopy in interface bio.singa.mathematics.graphs.model.Node<AutomatonNode,bio.singa.mathematics.vectors.Vector2D,bio.singa.mathematics.topology.grids.rectangular.RectangularCoordinate>