de.bioforscher.singa.simulation.model.concentrations

Interface ConcentrationContainer

All Known Implementing Classes:

MembraneContainer, MultiConcentrationContainer, SimpleConcentrationContainer

public interface ConcentrationContainer

Concentration containers are used to manage the concentration inside of a node. Modules may require the node to restrict the availability of a concentration to certain compartments. On the border between two compartments the availability of a chemical entity can be different depending on the compartment of the neighbouring node.

Author:

cl

Method Summary

Modifier and Type	Method and Description
Map<ChemicalEntity<?>,javax.measure.Quantity<MolarConcentration>>	getAllConcentrations() Returns the representative concentrations of all referenced chemical entities.
Map<ChemicalEntity<?>,javax.measure.Quantity<MolarConcentration>>	getAllConcentrationsForSection(CellSection cellSection) Returns all concentrations for a particular CellSection.
Set<ChemicalEntity<?>>	getAllReferencedEntities() Returns all ChemicalEntities that are referenced in this container.
Set<CellSection>	getAllReferencedSections() Returns all Compartments that are referenced in this container.
javax.measure.Quantity<MolarConcentration>	getAvailableConcentration(CellSection cellSection, ChemicalEntity chemicalEntity) Returns the concentration of the specified ChemicalEntity available in the CellSection.
javax.measure.Quantity<MolarConcentration>	getConcentration(ChemicalEntity chemicalEntity) Returns the representative concentration of a chemical entity.
ConcentrationContainer	getCopy() Returns a copy of this concentration container.
void	setAvailableConcentration(CellSection cellSection, ChemicalEntity chemicalEntity, javax.measure.Quantity<MolarConcentration> concentration) Sets the available concentration based on the given compartment.
void	setConcentration(ChemicalEntity chemicalEntity, javax.measure.Quantity<MolarConcentration> concentration) Sets the representative concentration of a chemical entity.

Method Detail

getConcentration

javax.measure.Quantity<MolarConcentration> getConcentration(ChemicalEntity chemicalEntity)

Returns the representative concentration of a chemical entity. If the concentration is available differently for multiple compartments the average concentration is returned.

Parameters:

chemicalEntity - The ChemicalEntity.

Returns:

The concentration.

getAllConcentrationsForSection

Map<ChemicalEntity<?>,javax.measure.Quantity<MolarConcentration>> getAllConcentrationsForSection(CellSection cellSection)

Returns all concentrations for a particular CellSection.

Parameters:

cellSection - The CellSection

Returns:

All concentrations in this CellSection.

getAvailableConcentration

javax.measure.Quantity<MolarConcentration> getAvailableConcentration(CellSection cellSection,
                                                                     ChemicalEntity chemicalEntity)

Returns the concentration of the specified ChemicalEntity available in the CellSection.

Parameters:

cellSection - The CellSection

chemicalEntity - The ChemicalEntity.

Returns:

The concentration of the ChemicalEntity in the CellSection.

setConcentration

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

Sets the representative concentration of a chemical entity. This resets the available concentrations for all registered compartments.

Parameters:

chemicalEntity - The ChemicalEntity.

concentration - The concentration.

setAvailableConcentration

void setAvailableConcentration(CellSection cellSection,
                               ChemicalEntity chemicalEntity,
                               javax.measure.Quantity<MolarConcentration> concentration)

Sets the available concentration based on the given compartment.

Parameters:

cellSection - The identifier of the compartment.

chemicalEntity - The ChemicalEntity.

concentration - The concentration.

getAllReferencedEntities

Set<ChemicalEntity<?>> getAllReferencedEntities()

Returns all ChemicalEntities that are referenced in this container.

Returns:

All ChemicalEntities that are referenced in this container.

getAllReferencedSections

Set<CellSection> getAllReferencedSections()

Returns all Compartments that are referenced in this container.

Returns:

All Compartments that are referenced in this container.

getAllConcentrations

Map<ChemicalEntity<?>,javax.measure.Quantity<MolarConcentration>> getAllConcentrations()

Returns the representative concentrations of all referenced chemical entities.

Returns:

The representative concentrations of all referenced chemical entities.

getCopy

ConcentrationContainer getCopy()

Returns a copy of this concentration container.

Returns:

A copy of this concentration container.