de.bioforscher.singa.simulation.model.graphs

Class AutomatonNode

java.lang.Object

de.bioforscher.singa.mathematics.graphs.model.AbstractNode<AutomatonNode,Vector2D,Integer>

de.bioforscher.singa.simulation.model.graphs.AutomatonNode

All Implemented Interfaces:

Node<AutomatonNode,Vector2D,Integer>

public class AutomatonNode
extends AbstractNode<AutomatonNode,Vector2D,Integer>

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

Author:

cl

Constructor Summary

Constructors

Constructor and Description
AutomatonNode(int identifier) Creates a new plain automaton node.

Method Summary

Modifier and Type	Method and Description
void	addPotentialDelta(Delta potentialDelta) Adds a potential delta to this node.
void	addPotentialDeltas(List<Delta> potentialDeltas) Adds a list of potential deltas to this node.
void	applyDeltas() Applies all final deltas and clears the delta list.
void	clearPotentialDeltas() Clears the list of potential deltas.
Map<ChemicalEntity<?>,javax.measure.Quantity<MolarConcentration>>	getAllConcentrations() Returns all concentrations of all chemical entities.
Map<ChemicalEntity<?>,javax.measure.Quantity<MolarConcentration>>	getAllConcentrationsForSection(CellSection cellSection) Returns all concentrations of all chemical entities in the given cell section.
Set<ChemicalEntity<?>>	getAllReferencedEntities() Returns all chemical entities referenced in this node.
Set<CellSection>	getAllReferencedSections() Returns all referenced sections in this node.
javax.measure.Quantity<MolarConcentration>	getAvailableConcentration(ChemicalEntity entity, CellSection cellSection) Returns the concentration of the given chemical entity in the given compartment.
CellSection	getCellSection() Returns the primary cell section of this node (Membrane nodes may belong to multiple sections).
javax.measure.Quantity<MolarConcentration>	getConcentration(ChemicalEntity entity) Gets the concentration of the given chemical entity.
ConcentrationContainer	getConcentrationContainer() Returns the ConcentrationContainer used by this node.
List<Delta>	getDeltas() Returns all deltas that are going to be applied to this node.
NodeState	getState() Returns the node state.
boolean	isObserved() Returns true if this node is observed.
void	setAvailableConcentration(ChemicalEntity entity, CellSection cellSection, javax.measure.Quantity<MolarConcentration> quantity) Gets the concentration of the given chemical entity in the given compartment.
void	setCellSection(CellSection cellSection) Sets the cell section of this node and references the node in the corresponding section.
void	setConcentration(ChemicalEntity entity, double concentration) Sets the concentration of the entity in mol/l.
void	setConcentration(ChemicalEntity entity, javax.measure.Quantity<MolarConcentration> quantity) Sets the concentration of the entity.
void	setConcentrationContainer(ConcentrationContainer concentrationContainer) Sets the ConcentrationContainer for this node.
void	setConcentrations(double concentration, ChemicalEntity... entities) Sets the concentration of the given chemical entities.
void	setObserved(boolean isObserved) Sets the observed state of this node.
void	setState(NodeState state) Sets the state.
void	shiftDeltas() Shifts the deltas from the potential delta list to the final delta list.
String	toString()

Methods inherited from class de.bioforscher.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

Methods inherited from interface de.bioforscher.singa.mathematics.graphs.model.Node

getCopy

Constructor Detail

AutomatonNode

public AutomatonNode(int identifier)

Creates a new plain automaton node. Initialized as NodeState.AQUEOUS in a "default" compartment with a SimpleConcentrationContainer.

Parameters:

identifier - The identifier of the node.

Method Detail

setConcentrations

public void setConcentrations(double concentration,
                              ChemicalEntity... entities)

Sets the concentration of the given chemical entities.

Parameters:

concentration - The concentration in mol/l

entities - The chemical entities.

setConcentration

public void setConcentration(ChemicalEntity entity,
                             double concentration)

Sets the concentration of the entity in mol/l.

Parameters:

entity - The entity.

concentration - The concentration in mol/l.

setConcentration

public void setConcentration(ChemicalEntity entity,
                             javax.measure.Quantity<MolarConcentration> quantity)

Sets the concentration of the entity.

Parameters:

entity - The chemical entity.

quantity - The quantity.

getAllConcentrations

public Map<ChemicalEntity<?>,javax.measure.Quantity<MolarConcentration>> getAllConcentrations()

Returns all concentrations of all chemical entities.

Returns:

All concentrations of all chemical entities.

getAllConcentrationsForSection

public Map<ChemicalEntity<?>,javax.measure.Quantity<MolarConcentration>> getAllConcentrationsForSection(CellSection cellSection)

Returns all concentrations of all chemical entities in the given cell section.

Parameters:

cellSection - The cell section.

Returns:

All concentrations of all chemical entities.

getConcentration

public javax.measure.Quantity<MolarConcentration> getConcentration(ChemicalEntity entity)

Gets the concentration of the given chemical entity.

Parameters:

entity - The chemical entity.

Returns:

The concentration in mol/l.

setAvailableConcentration

public void setAvailableConcentration(ChemicalEntity entity,
                                      CellSection cellSection,
                                      javax.measure.Quantity<MolarConcentration> quantity)

Gets the concentration of the given chemical entity in the given compartment.

Parameters:

entity - The chemical entity.

cellSection - The cell section.

quantity - The quantity.

getAvailableConcentration

public javax.measure.Quantity<MolarConcentration> getAvailableConcentration(ChemicalEntity entity,
                                                                            CellSection cellSection)

Returns the concentration of the given chemical entity in the given compartment.

Parameters:

entity - The chemical entity.

cellSection - The cell section.

Returns:

The concentration of the given chemical entity.

getDeltas

public List<Delta> getDeltas()

Returns all deltas that are going to be applied to this node.

Returns:

All deltas that are going to be applied to this node.

addPotentialDeltas

public void addPotentialDeltas(List<Delta> potentialDeltas)

Adds a list of potential deltas to this node.

Parameters:

potentialDeltas - The potential deltas.

addPotentialDelta

public void addPotentialDelta(Delta potentialDelta)

Adds a potential delta to this node.

Parameters:

potentialDelta - The potential delta.

clearPotentialDeltas

public void clearPotentialDeltas()

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

shiftDeltas

public void shiftDeltas()

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

applyDeltas

public void applyDeltas()

Applies all final deltas and clears the delta list.

getAllReferencedSections

public Set<CellSection> getAllReferencedSections()

Returns all referenced sections in this node.

Returns:

all referenced sections in this node.

getAllReferencedEntities

public Set<ChemicalEntity<?>> getAllReferencedEntities()

Returns all chemical entities referenced in this node.

Returns:

All chemical entities referenced in this node.

getState

public NodeState getState()

Returns the node state.

Returns:

The node state.

setState

public void setState(NodeState state)

Sets the state.

Parameters:

state - The node state.

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.

getCellSection

public CellSection getCellSection()

Returns the primary cell section of this node (Membrane nodes may belong to multiple sections).

Returns:

The primary cell section of this node.

setCellSection

public void setCellSection(CellSection cellSection)

Sets the cell section of this node and references the node in the corresponding section.

Parameters:

cellSection - The cell section.

getConcentrationContainer

public ConcentrationContainer getConcentrationContainer()

Returns the ConcentrationContainer used by this node.

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.

toString

public String toString()

Overrides:

toString in class AbstractNode<AutomatonNode,Vector2D,Integer>