bio.singa.simulation.model.sections

Class ConcentrationContainer

java.lang.Object

bio.singa.simulation.model.sections.ConcentrationContainer

public class ConcentrationContainer
extends Object

The concentration container manages the concentrations of one updatable. MolarConcentrations of ChemicalEntitys can be set and got by the CellSubsection or CellTopology. If no relevant concentration was registered an empty concentration will be returned.

Author:

cl

Constructor Summary

Constructors

Constructor and Description
ConcentrationContainer() Creates a new concentration container.

Method Summary

Modifier and Type	Method and Description
ConcentrationContainer	emptyCopy() Returns a empty copy of this container, keeping subsections and cell topologies associated.
ConcentrationContainer	fullCopy() Returns a full copy of this container, keeping concentrations.
javax.measure.Quantity<MolarConcentration>	get(CellSubsection subsection, ChemicalEntity entity) Returns the concentration of the entity in the corresponding subsection.
javax.measure.Quantity<MolarConcentration>	get(CellTopology topology, ChemicalEntity entity) Returns the concentration of the entity in the corresponding topology.
CellSubsection	getInnerSubsection() Returns the inner subsection.
CellSubsection	getMembraneSubsection() Returns the membrane subsection.
CellSubsection	getOuterSubsection() Returns the outer subsection.
Map.Entry<CellTopology,ConcentrationPool>	getPool(CellSubsection subsection) Returns the topology and concentration pool for the subsection.
Map.Entry<CellSubsection,ConcentrationPool>	getPool(CellTopology topology) Returns the subsection and concentration pool for the topology.
Collection<ConcentrationPool>	getPoolsOfConcentration() Returns all concentration pools in this container.
Set<ChemicalEntity>	getReferencedEntities() Returns all entities referenced in any concentration pool.
Set<CellSubsection>	getReferencedSubSections() Returns all subsections, referenced in this container.
CellSubsection	getSubsection(CellTopology topology) Returns the subsection corresponding to the topology.
void	initialize(CellSubsection subsection, ChemicalEntity entity, javax.measure.Quantity<MolarConcentration> concentration)
void	initialize(CellTopology topology, ChemicalEntity entity, javax.measure.Quantity<MolarConcentration> concentration)
void	initializeSubsection(CellSubsection subsection, CellTopology topology) Initializes a new concentration pool for the corresponding subsection and topology.
void	putSubsectionPool(CellSubsection subsection, CellTopology topology, ConcentrationPool concentrationPool) Adds a concentration pool, referenced to the subsection and topology.
void	removeSubsection(CellSubsection subsection) Removes a subsection, the corresponding topology and concentration pool from the container.
void	removeSubsection(CellTopology topology) Removes a subsection, the given topology and concentration pool from the container.
void	set(CellSubsection subsection, ChemicalEntity entity, double concentration) Sets the concentration of the given entity in the given subsection.
void	set(CellSubsection subsection, ChemicalEntity entity, javax.measure.Quantity<MolarConcentration> concentration) Sets the concentration of the given entity in the given subsection.
void	set(CellTopology topology, ChemicalEntity entity, double concentration) Sets the concentration of the given entity in the subsection corresponding to the topological descriptor.
void	set(CellTopology topology, ChemicalEntity entity, javax.measure.Quantity<MolarConcentration> concentration) Sets the concentration of the given entity in the given topology.

Methods inherited from class java.lang.Object

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

Constructor Detail

ConcentrationContainer

public ConcentrationContainer()

Creates a new concentration container.

Method Detail

initializeSubsection

public void initializeSubsection(CellSubsection subsection,
                                 CellTopology topology)

Initializes a new concentration pool for the corresponding subsection and topology.

Parameters:

subsection - The subsection.

topology - The topology.

putSubsectionPool

public void putSubsectionPool(CellSubsection subsection,
                              CellTopology topology,
                              ConcentrationPool concentrationPool)

Adds a concentration pool, referenced to the subsection and topology.

Parameters:

subsection - The subsection.

topology - The topology.

concentrationPool - The concentration pool.

removeSubsection

public void removeSubsection(CellSubsection subsection)

Removes a subsection, the corresponding topology and concentration pool from the container.

Parameters:

subsection - The subsection to remove.

removeSubsection

public void removeSubsection(CellTopology topology)

Removes a subsection, the given topology and concentration pool from the container.

Parameters:

topology - The topology to remove.

getReferencedSubSections

public Set<CellSubsection> getReferencedSubSections()

Returns all subsections, referenced in this container.

Returns:

All subsections, referenced in this container.

getPoolsOfConcentration

public Collection<ConcentrationPool> getPoolsOfConcentration()

Returns all concentration pools in this container.

Returns:

All concentration pools in this container.

getReferencedEntities

public Set<ChemicalEntity> getReferencedEntities()

Returns all entities referenced in any concentration pool.

Returns:

All entities referenced in any concentration pool.

getPool

public Map.Entry<CellTopology,ConcentrationPool> getPool(CellSubsection subsection)

Returns the topology and concentration pool for the subsection.

Parameters:

subsection - The subsection.

Returns:

The topology and concentration pool for the subsection.

getPool

public Map.Entry<CellSubsection,ConcentrationPool> getPool(CellTopology topology)

Returns the subsection and concentration pool for the topology.

Parameters:

topology - Th topology.

Returns:

The subsection and concentration pool for the topology.

get

public javax.measure.Quantity<MolarConcentration> get(CellSubsection subsection,
                                                      ChemicalEntity entity)

Returns the concentration of the entity in the corresponding subsection.

Parameters:

subsection - The subsection.

entity - The entity.

Returns:

The concentration of the entity in the corresponding subsection.

get

public javax.measure.Quantity<MolarConcentration> get(CellTopology topology,
                                                      ChemicalEntity entity)

Returns the concentration of the entity in the corresponding topology.

Parameters:

topology - The topology.

entity - The entity.

Returns:

The concentration of the entity in the corresponding topology.

set

public void set(CellSubsection subsection,
                ChemicalEntity entity,
                javax.measure.Quantity<MolarConcentration> concentration)

Sets the concentration of the given entity in the given subsection.

Parameters:

subsection - The subsection.

entity - The entity.

concentration - The concentration.

initialize

public void initialize(CellSubsection subsection,
                       ChemicalEntity entity,
                       javax.measure.Quantity<MolarConcentration> concentration)

set

public void set(CellTopology topology,
                ChemicalEntity entity,
                javax.measure.Quantity<MolarConcentration> concentration)

Sets the concentration of the given entity in the given topology.

Parameters:

topology - The topology.

entity - The entity.

concentration - The concentration.

initialize

public void initialize(CellTopology topology,
                       ChemicalEntity entity,
                       javax.measure.Quantity<MolarConcentration> concentration)

set

public void set(CellSubsection subsection,
                ChemicalEntity entity,
                double concentration)

Sets the concentration of the given entity in the given subsection. The concentration is assumed to be UnitProvider.MOLE_PER_LITRE but is transformed to the preferred concentration.

Parameters:

subsection - The subsection.

entity - The entity.

concentration - The concentration in mol/l

set

public void set(CellTopology topology,
                ChemicalEntity entity,
                double concentration)

Sets the concentration of the given entity in the subsection corresponding to the topological descriptor. The concentration is assumed to be UnitProvider.MOLE_PER_LITRE but is transformed to the preferred concentration.

Parameters:

topology - The topological descriptor.

entity - The entity.

concentration - The concentration in mol/l

getSubsection

public CellSubsection getSubsection(CellTopology topology)

Returns the subsection corresponding to the topology.

Parameters:

topology - The topology.

Returns:

The subsection.

getInnerSubsection

public CellSubsection getInnerSubsection()

Returns the inner subsection.

Returns:

The inner subsection.

getOuterSubsection

public CellSubsection getOuterSubsection()

Returns the outer subsection.

Returns:

The outer subsection.

getMembraneSubsection

public CellSubsection getMembraneSubsection()

Returns the membrane subsection.

Returns:

The membrane subsection.

emptyCopy

public ConcentrationContainer emptyCopy()

Returns a empty copy of this container, keeping subsections and cell topologies associated.

Returns:

A empty copy of this container.

fullCopy

public ConcentrationContainer fullCopy()

Returns a full copy of this container, keeping concentrations.

Returns:

A full copy of this container.