bio.singa.simulation.model.graphs

Class AutomatonNode

java.lang.Object

bio.singa.mathematics.graphs.model.AbstractNode<AutomatonNode,Vector2D,RectangularCoordinate>

bio.singa.simulation.model.graphs.AutomatonNode

All Implemented Interfaces:

Node<AutomatonNode,Vector2D,RectangularCoordinate>, Updatable

public class AutomatonNode
extends AbstractNode<AutomatonNode,Vector2D,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

Constructor Summary

Constructors

Constructor and Description
AutomatonNode(int column, int row)
AutomatonNode(RectangularCoordinate identifier)

Method Summary

Modifier and Type	Method and Description
void	addLineLikeAgentSegment(LineLikeAgent lineLikeAgent, Vector2D segment)
void	addMembraneSegment(MembraneSegment segment)
void	addPotentialDelta(ConcentrationDelta potentialDelta) Adds a potential delta to this node.
void	addSubsectionRepresentation(CellSubsection subsection, Polygon representation)
void	applyDeltas() Applies all final deltas and clears the delta list.
void	clearPotentialConcentrationDeltas() Clears the list of potential deltas.
void	clearPotentialDeltasBut(UpdateModule module)
Set<CellSubsection>	getAllReferencedSections() Returns all referenced sections in this node.
Map<LineLikeAgent,Set<Vector2D>>	getAssociatedLineLikeAgents()
CellRegion	getCellRegion()
ConcentrationContainer	getConcentrationContainer() Returns the ConcentrationContainer used by this node.
AutomatonNode	getCopy()
javax.measure.Quantity<javax.measure.quantity.Area>	getMembraneArea()
List<MembraneSegment>	getMembraneSegments()
List<ConcentrationDelta>	getPotentialConcentrationDeltas()
Polygon	getSpatialRepresentation()
String	getStringIdentifier()
Map<CellSubsection,Polygon>	getSubsectionRepresentations()
ConcentrationDeltaManager	getUpdateManager()
boolean	hasDeltas()
boolean	isConcentrationFixed()
boolean	isObserved() Returns true if this node is observed.
void	setCellRegion(CellRegion cellRegion)
void	setConcentrationContainer(ConcentrationContainer concentrationContainer) Sets the ConcentrationContainer for this node.
void	setConcentrationFixed(boolean concentrationFixed)
void	setObserved(boolean isObserved) Sets the observed state of this node.
void	setSpatialRepresentation(Polygon spatialRepresentation)
void	setUpdateManager(ConcentrationDeltaManager updateManager)
void	shiftDeltas() Shifts the deltas from the potential delta list to the final delta list.
String	toString()

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

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

Methods inherited from class java.lang.Object

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

Constructor Detail

AutomatonNode

public AutomatonNode(RectangularCoordinate identifier)

AutomatonNode

public AutomatonNode(int column,
                     int row)

Method Detail

getSubsectionRepresentations

public Map<CellSubsection,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.

clearPotentialConcentrationDeltas

public void clearPotentialConcentrationDeltas()

Clears the list of potential deltas. Usually done after shiftDeltas() or after rejecting a time step.

Specified by:

clearPotentialConcentrationDeltas in interface Updatable

clearPotentialDeltasBut

public void clearPotentialDeltasBut(UpdateModule module)

Specified by:

clearPotentialDeltasBut in interface Updatable

shiftDeltas

public void shiftDeltas()

Shifts the deltas from the potential delta list to the final delta list.

Specified by:

shiftDeltas in interface Updatable

applyDeltas

public void applyDeltas()

Applies all final deltas and clears the delta list.

Specified by:

applyDeltas in interface Updatable

hasDeltas

public boolean hasDeltas()

Specified by:

hasDeltas in interface Updatable

getPotentialConcentrationDeltas

public List<ConcentrationDelta> getPotentialConcentrationDeltas()

Specified by:

getPotentialConcentrationDeltas in interface Updatable

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.

Specified by:

isObserved in interface Updatable

Returns:

true if this node is observed.

setObserved

public void setObserved(boolean isObserved)

Sets the observed state of this node.

Specified by:

setObserved in interface Updatable

Parameters:

isObserved - true if this node is observed.

isConcentrationFixed

public boolean isConcentrationFixed()

setConcentrationFixed

public void setConcentrationFixed(boolean concentrationFixed)

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 Polygon getSpatialRepresentation()

setSpatialRepresentation

public void setSpatialRepresentation(Polygon spatialRepresentation)

getUpdateManager

public ConcentrationDeltaManager getUpdateManager()

setUpdateManager

public void setUpdateManager(ConcentrationDeltaManager updateManager)

getAssociatedLineLikeAgents

public Map<LineLikeAgent,Set<Vector2D>> getAssociatedLineLikeAgents()

addLineLikeAgentSegment

public void addLineLikeAgentSegment(LineLikeAgent lineLikeAgent,
                                    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,
                                        Polygon representation)

toString

public String toString()

Overrides:

toString in class AbstractNode<AutomatonNode,Vector2D,RectangularCoordinate>

getCopy

public AutomatonNode getCopy()

Specified by:

getCopy in interface Node<AutomatonNode,Vector2D,RectangularCoordinate>