bio.singa.simulation.model.modules.displacement

Class Vesicle

java.lang.Object

bio.singa.simulation.model.modules.displacement.Vesicle

All Implemented Interfaces:

Featureable, Updatable

public class Vesicle
extends Object
implements Updatable, Featureable

Author:

cl

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Vesicle.AttachmentState
static class	Vesicle.TargetDirection

Field Summary

Fields

Modifier and Type	Field and Description
protected static Set<Class<? extends Feature>>	availableFeatures
protected FeatureContainer	features

Constructor Summary

Constructors

Constructor and Description
Vesicle(String identifier, Vector2D position, javax.measure.Quantity<javax.measure.quantity.Length> radius)
Vesicle(Vector2D position, javax.measure.Quantity<javax.measure.quantity.Length> radius)

Method Summary

Modifier and Type	Method and Description
void	addAssociatedNode(AutomatonNode node, javax.measure.Quantity<javax.measure.quantity.Area> associatedArea)
void	addPotentialDelta(ConcentrationDelta delta)
void	addPotentialSpatialDelta(DisplacementDelta spatialDelta)
void	applyDeltas()
Vector2D	calculateTotalDisplacement()
void	clearAssociatedNodes()
void	clearPotentialConcentrationDeltas()
void	clearPotentialDeltasBut(UpdateModule module)
void	clearPotentialDisplacementDeltas()
Set<CellSubsection>	getAllReferencedSections()
javax.measure.Quantity<javax.measure.quantity.Area>	getArea()
Map<AutomatonNode,javax.measure.Quantity<javax.measure.quantity.Area>>	getAssociatedNodes()
SkeletalFilament	getAttachedFilament()
Vesicle.AttachmentState	getAttachmentState()
Set<Class<? extends Feature>>	getAvailableFeatures()
CellRegion	getCellRegion()
Circle	getCircleRepresentation()
javax.measure.Quantity<MolarConcentration>	getConcentration(CellSubsection cellSection, ChemicalEntity chemicalEntity)
javax.measure.Quantity<MolarConcentration>	getConcentration(ChemicalEntity entity)
ConcentrationContainer	getConcentrationContainer()
Vector2D	getCurrentPosition()
<FeatureType extends Feature> FeatureType	getFeature(Class<FeatureType> featureTypeClass)
Collection<Feature<?>>	getFeatures()
Vector2D	getNextPosition()
List<ConcentrationDelta>	getPotentialSpatialDeltas()
javax.measure.Quantity<javax.measure.quantity.Length>	getRadius()
ListIterator<Vector2D>	getSegmentIterator()
DisplacementDelta	getSpatialDelta(DisplacementBasedModule module)
String	getStringIdentifier()
Vesicle.TargetDirection	getTargetDirection()
javax.measure.Quantity<javax.measure.quantity.Volume>	getVolume()
boolean	hasDeltas()
<FeatureType extends Feature> boolean	hasFeature(Class<FeatureType> featureTypeClass)
boolean	isObserved() Returns true if this node is observed.
void	resetNextPosition()
void	setAttachedFilament(SkeletalFilament attachedFilament)
void	setAttachmentState(Vesicle.AttachmentState attachmentState)
void	setConcentration(ChemicalEntity entity, javax.measure.Quantity<MolarConcentration> concentration)
<FeatureType extends Feature> void	setFeature(Class<FeatureType> featureTypeClass)
<FeatureType extends Feature> void	setFeature(FeatureType feature)
void	setObserved(boolean isObserved) Sets the observed state of this node.
void	setRadius(javax.measure.Quantity<javax.measure.quantity.Length> radius)
void	setSegmentIterator(ListIterator<Vector2D> segmentIterator)
void	setTargetDirection(Vesicle.TargetDirection targetDirection)
void	shiftDeltas()
String	toString()
void	updatePosition()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface bio.singa.features.model.Featureable

canBeFeaturedWith, meetsAllRequirements, scaleScalableFeatures

Field Detail

availableFeatures

protected static final Set<Class<? extends Feature>> availableFeatures

features

protected FeatureContainer features

Constructor Detail

Vesicle

public Vesicle(String identifier,
               Vector2D position,
               javax.measure.Quantity<javax.measure.quantity.Length> radius)

Vesicle

public Vesicle(Vector2D position,
               javax.measure.Quantity<javax.measure.quantity.Length> radius)

Method Detail

getStringIdentifier

public String getStringIdentifier()

Specified by:

getStringIdentifier in interface Updatable

getCurrentPosition

public Vector2D getCurrentPosition()

getRadius

public javax.measure.Quantity<javax.measure.quantity.Length> getRadius()

getArea

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

getVolume

public javax.measure.Quantity<javax.measure.quantity.Volume> getVolume()

getNextPosition

public Vector2D getNextPosition()

getAttachmentState

public Vesicle.AttachmentState getAttachmentState()

setAttachmentState

public void setAttachmentState(Vesicle.AttachmentState attachmentState)

getAttachedFilament

public SkeletalFilament getAttachedFilament()

setAttachedFilament

public void setAttachedFilament(SkeletalFilament attachedFilament)

getTargetDirection

public Vesicle.TargetDirection getTargetDirection()

setTargetDirection

public void setTargetDirection(Vesicle.TargetDirection targetDirection)

getSegmentIterator

public ListIterator<Vector2D> getSegmentIterator()

setSegmentIterator

public void setSegmentIterator(ListIterator<Vector2D> segmentIterator)

addPotentialSpatialDelta

public void addPotentialSpatialDelta(DisplacementDelta spatialDelta)

getSpatialDelta

public DisplacementDelta getSpatialDelta(DisplacementBasedModule module)

setRadius

public void setRadius(javax.measure.Quantity<javax.measure.quantity.Length> radius)

setConcentration

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

getConcentration

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

getAssociatedNodes

public Map<AutomatonNode,javax.measure.Quantity<javax.measure.quantity.Area>> getAssociatedNodes()

addAssociatedNode

public void addAssociatedNode(AutomatonNode node,
                              javax.measure.Quantity<javax.measure.quantity.Area> associatedArea)

clearAssociatedNodes

public void clearAssociatedNodes()

calculateTotalDisplacement

public Vector2D calculateTotalDisplacement()

clearPotentialDisplacementDeltas

public void clearPotentialDisplacementDeltas()

resetNextPosition

public void resetNextPosition()

updatePosition

public void updatePosition()

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.

getConcentrationContainer

public ConcentrationContainer getConcentrationContainer()

Specified by:

getConcentrationContainer in interface Updatable

getConcentration

public javax.measure.Quantity<MolarConcentration> getConcentration(CellSubsection cellSection,
                                                                   ChemicalEntity chemicalEntity)

Specified by:

getConcentration in interface Updatable

getCellRegion

public CellRegion getCellRegion()

Specified by:

getCellRegion in interface Updatable

getAllReferencedSections

public Set<CellSubsection> getAllReferencedSections()

Specified by:

getAllReferencedSections in interface Updatable

getPotentialSpatialDeltas

public List<ConcentrationDelta> getPotentialSpatialDeltas()

Specified by:

getPotentialSpatialDeltas in interface Updatable

addPotentialDelta

public void addPotentialDelta(ConcentrationDelta delta)

Specified by:

addPotentialDelta in interface Updatable

clearPotentialConcentrationDeltas

public void clearPotentialConcentrationDeltas()

Specified by:

clearPotentialConcentrationDeltas in interface Updatable

clearPotentialDeltasBut

public void clearPotentialDeltasBut(UpdateModule module)

Specified by:

clearPotentialDeltasBut in interface Updatable

hasDeltas

public boolean hasDeltas()

Specified by:

hasDeltas in interface Updatable

shiftDeltas

public void shiftDeltas()

Specified by:

shiftDeltas in interface Updatable

applyDeltas

public void applyDeltas()

Specified by:

applyDeltas in interface Updatable

getCircleRepresentation

public Circle getCircleRepresentation()

getFeatures

public Collection<Feature<?>> getFeatures()

Specified by:

getFeatures in interface Featureable

getFeature

public <FeatureType extends Feature> FeatureType getFeature(Class<FeatureType> featureTypeClass)

Specified by:

getFeature in interface Featureable

setFeature

public <FeatureType extends Feature> void setFeature(Class<FeatureType> featureTypeClass)

Specified by:

setFeature in interface Featureable

setFeature

public <FeatureType extends Feature> void setFeature(FeatureType feature)

Specified by:

setFeature in interface Featureable

hasFeature

public <FeatureType extends Feature> boolean hasFeature(Class<FeatureType> featureTypeClass)

Specified by:

hasFeature in interface Featureable

getAvailableFeatures

public Set<Class<? extends Feature>> getAvailableFeatures()

Specified by:

getAvailableFeatures in interface Featureable

toString

public String toString()

Overrides:

toString in class Object