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 Description

ConcentrationContainer()
Creates a new concentration container.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`boolean`	`containsEntity(CellSubsection subsection, ChemicalEntity entity)`
`boolean`	`containsEntity(CellTopology topology, ChemicalEntity entity)`
`Optional<ChemicalEntity>`	`containsHiddenEntity(CellTopology topology, ChemicalEntity query)`
`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.
`double`	`get(CellSubsection subsection, ChemicalEntity entity)`	Returns the concentration of the entity in the corresponding subsection.
`double`	`get(CellTopology topology, ChemicalEntity entity)`	Returns the concentration of the entity in the corresponding topology.
`ConcentrationPool[]`	`getConcentrations()`
`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<bio.singa.features.quantities.MolarConcentration> concentration)`
`void`	`initialize(CellTopology topology, ChemicalEntity entity, javax.measure.Quantity<bio.singa.features.quantities.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(CellTopology topology, ChemicalEntity entity, double 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.
  - getConcentrations
```
public ConcentrationPool[] getConcentrations()
```
  - 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.
  - containsHiddenEntity
```
public Optional<ChemicalEntity> containsHiddenEntity(CellTopology topology,
                                                     ChemicalEntity query)
```
  - containsEntity
```
public boolean containsEntity(CellTopology topology,
                              ChemicalEntity entity)
```
  - containsEntity
```
public boolean containsEntity(CellSubsection subsection,
                              ChemicalEntity entity)
```
  - 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 double 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 double 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,
                double 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<bio.singa.features.quantities.MolarConcentration> concentration)
```
  - set
```
public void set(CellTopology topology,
                ChemicalEntity entity,
                double 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<bio.singa.features.quantities.MolarConcentration> concentration)
```
  - 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.

Class ConcentrationContainer

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ConcentrationContainer

Method Detail

initializeSubsection

putSubsectionPool

removeSubsection

removeSubsection

getConcentrations

getReferencedSubsections

getPoolsOfConcentration

getReferencedEntities

containsHiddenEntity

containsEntity

containsEntity

getPool

getPool

get

get

set

initialize

set

initialize

getSubsection

getInnerSubsection

getOuterSubsection

getMembraneSubsection

emptyCopy

fullCopy