bio.singa.simulation.model.agents.organelles

Class OrganelleTemplate

java.lang.Object

bio.singa.simulation.model.agents.organelles.OrganelleTemplate

public class OrganelleTemplate
extends Object

Author:

cl

Constructor Summary

Constructors

Constructor and Description
OrganelleTemplate(javax.measure.Quantity<javax.measure.quantity.Length> scale, bio.singa.mathematics.geometry.model.Polygon polygon, Map<Integer,Set<bio.singa.mathematics.vectors.Vector2D>> groups)

Method Summary

Modifier and Type	Method and Description
Map<Integer,Set<bio.singa.mathematics.vectors.Vector2D>>	getGroups()
CellRegion	getInnerRegion()
Map<bio.singa.mathematics.vectors.Vector2D,CellRegion>	getInverseRegionMap()
CellRegion	getMembraneRegion()
bio.singa.mathematics.geometry.model.Polygon	getPolygon()
CellRegion	getRegion(bio.singa.mathematics.vectors.Vector2D vector)
Map<CellRegion,Set<bio.singa.mathematics.vectors.Vector2D>>	getRegionMap()
Collection<CellRegion>	getRegions()
javax.measure.Quantity<javax.measure.quantity.Length>	getScale()
void	initializeGroup(CellRegion region)
void	initializeGroup(int groupIdentifier, CellRegion region)
CellRegion	initializeGroup(int groupIdentifier, String identifier, String goTerm)
boolean	isGrouped()
void	mapToSystemExtend()
void	move(bio.singa.mathematics.vectors.Vector2D targetLocation)
void	reduce()
void	scale(double scalingFactor)
void	setGroups(Map<Integer,Set<bio.singa.mathematics.vectors.Vector2D>> groups)
void	setInnerRegion(CellRegion innerRegion)
void	setMembraneRegion(CellRegion membraneRegion)
void	setPolygon(bio.singa.mathematics.geometry.model.Polygon polygon)
void	setScale(javax.measure.Quantity<javax.measure.quantity.Length> scale)

Methods inherited from class java.lang.Object

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

Constructor Detail

OrganelleTemplate

public OrganelleTemplate(javax.measure.Quantity<javax.measure.quantity.Length> scale,
                         bio.singa.mathematics.geometry.model.Polygon polygon,
                         Map<Integer,Set<bio.singa.mathematics.vectors.Vector2D>> groups)

Method Detail

mapToSystemExtend

public void mapToSystemExtend()

getScale

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

setScale

public void setScale(javax.measure.Quantity<javax.measure.quantity.Length> scale)

getPolygon

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

reduce

public void reduce()

scale

public void scale(double scalingFactor)

move

public void move(bio.singa.mathematics.vectors.Vector2D targetLocation)

setPolygon

public void setPolygon(bio.singa.mathematics.geometry.model.Polygon polygon)

getGroups

public Map<Integer,Set<bio.singa.mathematics.vectors.Vector2D>> getGroups()

setGroups

public void setGroups(Map<Integer,Set<bio.singa.mathematics.vectors.Vector2D>> groups)

getRegions

public Collection<CellRegion> getRegions()

isGrouped

public boolean isGrouped()

initializeGroup

public CellRegion initializeGroup(int groupIdentifier,
                                  String identifier,
                                  String goTerm)

initializeGroup

public void initializeGroup(int groupIdentifier,
                            CellRegion region)

initializeGroup

public void initializeGroup(CellRegion region)

getInnerRegion

public CellRegion getInnerRegion()

setInnerRegion

public void setInnerRegion(CellRegion innerRegion)

getMembraneRegion

public CellRegion getMembraneRegion()

setMembraneRegion

public void setMembraneRegion(CellRegion membraneRegion)

getInverseRegionMap

public Map<bio.singa.mathematics.vectors.Vector2D,CellRegion> getInverseRegionMap()

getRegion

public CellRegion getRegion(bio.singa.mathematics.vectors.Vector2D vector)

getRegionMap

public Map<CellRegion,Set<bio.singa.mathematics.vectors.Vector2D>> getRegionMap()