Package bio.singa.simulation.model.agents.pointlike

Class Vesicle

java.lang.Object

bio.singa.simulation.model.agents.pointlike.Vesicle

All Implemented Interfaces:

bio.singa.features.model.Featureable, Updatable

public class Vesicle
extends Object
implements Updatable, bio.singa.features.model.Featureable

Author:

cl

Field Summary

Fields

Modifier and Type	Field	Description
protected static Set<Class<? extends bio.singa.features.model.Feature>>	availableFeatures
static bio.singa.features.quantities.PixelDiffusivity	DEFAULT_VESICLE_DIFFUSIVITY
protected bio.singa.features.model.FeatureContainer	features
static bio.singa.features.model.Evidence	HOLT2004
static bio.singa.features.model.Evidence	ROTHMAN2016
static AtomicInteger	vesicleCounter

Constructor Summary

Constructors

Constructor	Description
Vesicle(bio.singa.mathematics.vectors.Vector2D position, javax.measure.Quantity<javax.measure.quantity.Length> radius)
Vesicle(CellRegion region, bio.singa.mathematics.vectors.Vector2D position, javax.measure.Quantity<javax.measure.quantity.Length> radius)

Method Summary

Modifier and Type	Method	Description
void	addAssociatedNode(AutomatonNode node, double relativeArea)
void	addPotentialDelta(ConcentrationDelta delta)
void	addPotentialSpatialDelta(DisplacementDelta spatialDelta)
bio.singa.mathematics.vectors.Vector2D	calculateTotalDisplacement()
void	clearAssociatedNodes()
void	clearAttachmentInformation()
void	clearPotentialDisplacementDeltas()
Set<CellSubsection>	getAllReferencedSections()
javax.measure.Quantity<javax.measure.quantity.Area>	getArea()
Map<AutomatonNode,Double>	getAssociatedNodes()
LineLikeAgent	getAttachedFilament()
Set<Class<? extends bio.singa.features.model.Feature>>	getAvailableFeatures()
CellRegion	getCellRegion()
bio.singa.mathematics.geometry.faces.Circle	getCircleRepresentation()
ConcentrationContainer	getConcentrationContainer()
ConcentrationDeltaManager	getConcentrationManager()
<FeatureType extends bio.singa.features.model.Feature> FeatureType	getFeature(Class<FeatureType> featureTypeClass)
Collection<bio.singa.features.model.Feature<?>>	getFeatures()
bio.singa.mathematics.vectors.Vector2D	getNextPosition()
bio.singa.mathematics.vectors.Vector2D	getPosition()
javax.measure.Quantity<javax.measure.quantity.Length>	getRadius()
CellRegion	getRegion()
ListIterator<bio.singa.mathematics.vectors.Vector2D>	getSegmentIterator()
Optional<DisplacementDelta>	getSpatialDelta(DisplacementBasedModule module)
String	getState()
String	getStringIdentifier()
String	getTargetDirection()
javax.measure.Quantity<javax.measure.quantity.Volume>	getVolume()
<FeatureType extends bio.singa.features.model.Feature> boolean	hasFeature(Class<FeatureType> featureTypeClass)
boolean	isObserved()	Returns true if this node is observed.
void	resetNextPosition()
void	setAttachedFilament(LineLikeAgent attachedFilament)
<FeatureType extends bio.singa.features.model.Feature> void	setFeature(FeatureType feature)
<FeatureType extends bio.singa.features.model.Feature> void	setFeature(Class<FeatureType> featureTypeClass)
void	setIdentifier(String identifier)
void	setObserved(boolean isObserved)	Sets the observed state of this node.
void	setRadius(javax.measure.Quantity<javax.measure.quantity.Length> radius)
void	setRegion(CellRegion region)
void	setSegmentIterator(ListIterator<bio.singa.mathematics.vectors.Vector2D> segmentIterator)
void	setState(String state)
void	setTargetDirection(String targetDirection)
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

Field Detail

ROTHMAN2016

public static final bio.singa.features.model.Evidence ROTHMAN2016

HOLT2004

public static final bio.singa.features.model.Evidence HOLT2004

availableFeatures

protected static final Set<Class<? extends bio.singa.features.model.Feature>> availableFeatures

vesicleCounter

public static AtomicInteger vesicleCounter

DEFAULT_VESICLE_DIFFUSIVITY

public static bio.singa.features.quantities.PixelDiffusivity DEFAULT_VESICLE_DIFFUSIVITY

features

protected bio.singa.features.model.FeatureContainer features

Constructor Detail

Vesicle

public Vesicle(CellRegion region,
               bio.singa.mathematics.vectors.Vector2D position,
               javax.measure.Quantity<javax.measure.quantity.Length> radius)

Vesicle

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

Method Detail

setIdentifier

public void setIdentifier(String identifier)

getStringIdentifier

public String getStringIdentifier()

Specified by:

getStringIdentifier in interface Updatable

getPosition

public bio.singa.mathematics.vectors.Vector2D getPosition()

Specified by:

getPosition in interface Updatable

getRadius

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

setRadius

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

getArea

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

getVolume

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

getNextPosition

public bio.singa.mathematics.vectors.Vector2D getNextPosition()

getState

public String getState()

setState

public void setState(String state)

getAttachedFilament

public LineLikeAgent getAttachedFilament()

setAttachedFilament

public void setAttachedFilament(LineLikeAgent attachedFilament)

getTargetDirection

public String getTargetDirection()

setTargetDirection

public void setTargetDirection(String targetDirection)

getSegmentIterator

public ListIterator<bio.singa.mathematics.vectors.Vector2D> getSegmentIterator()

setSegmentIterator

public void setSegmentIterator(ListIterator<bio.singa.mathematics.vectors.Vector2D> segmentIterator)

getRegion

public CellRegion getRegion()

setRegion

public void setRegion(CellRegion region)

clearAttachmentInformation

public void clearAttachmentInformation()

addPotentialSpatialDelta

public void addPotentialSpatialDelta(DisplacementDelta spatialDelta)

getSpatialDelta

public Optional<DisplacementDelta> getSpatialDelta(DisplacementBasedModule module)

getAssociatedNodes

public Map<AutomatonNode,Double> getAssociatedNodes()

addAssociatedNode

public void addAssociatedNode(AutomatonNode node,
                              double relativeArea)

clearAssociatedNodes

public void clearAssociatedNodes()

calculateTotalDisplacement

public bio.singa.mathematics.vectors.Vector2D calculateTotalDisplacement()

clearPotentialDisplacementDeltas

public void clearPotentialDisplacementDeltas()

resetNextPosition

public void resetNextPosition()

updatePosition

public void updatePosition()

getConcentrationManager

public ConcentrationDeltaManager getConcentrationManager()

Specified by:

getConcentrationManager in interface Updatable

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.

getConcentrationContainer

public ConcentrationContainer getConcentrationContainer()

Specified by:

getConcentrationContainer in interface Updatable

getCellRegion

public CellRegion getCellRegion()

Specified by:

getCellRegion in interface Updatable

getAllReferencedSections

public Set<CellSubsection> getAllReferencedSections()

Specified by:

getAllReferencedSections in interface Updatable

addPotentialDelta

public void addPotentialDelta(ConcentrationDelta delta)

Specified by:

addPotentialDelta in interface Updatable

getCircleRepresentation

public bio.singa.mathematics.geometry.faces.Circle getCircleRepresentation()

getFeatures

public Collection<bio.singa.features.model.Feature<?>> getFeatures()

Specified by:

getFeatures in interface bio.singa.features.model.Featureable

getFeature

public <FeatureType extends bio.singa.features.model.Feature> FeatureType getFeature(Class<FeatureType> featureTypeClass)

Specified by:

getFeature in interface bio.singa.features.model.Featureable

setFeature

public <FeatureType extends bio.singa.features.model.Feature> void setFeature(Class<FeatureType> featureTypeClass)

Specified by:

setFeature in interface bio.singa.features.model.Featureable

setFeature

public <FeatureType extends bio.singa.features.model.Feature> void setFeature(FeatureType feature)

Specified by:

setFeature in interface bio.singa.features.model.Featureable

hasFeature

public <FeatureType extends bio.singa.features.model.Feature> boolean hasFeature(Class<FeatureType> featureTypeClass)

Specified by:

hasFeature in interface bio.singa.features.model.Featureable

getAvailableFeatures

public Set<Class<? extends bio.singa.features.model.Feature>> getAvailableFeatures()

Specified by:

getAvailableFeatures in interface bio.singa.features.model.Featureable

toString

public String toString()

Overrides:

toString in class Object