de.bioforscher.singa.simulation.model.concentrations

Class SimpleConcentrationContainer

java.lang.Object

de.bioforscher.singa.simulation.model.concentrations.SimpleConcentrationContainer

All Implemented Interfaces:

ConcentrationContainer

public class SimpleConcentrationContainer
extends Object
implements ConcentrationContainer

Author:

cl

Constructor Summary

Constructors

Constructor and Description
SimpleConcentrationContainer(CellSection cellSection)

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.
SimpleConcentrationContainer	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.

Methods inherited from class java.lang.Object

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

Constructor Detail

SimpleConcentrationContainer

public SimpleConcentrationContainer(CellSection cellSection)

Method Detail

getConcentration

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

Description copied from interface: ConcentrationContainer

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

Specified by:

getConcentration in interface ConcentrationContainer

Parameters:

chemicalEntity - The ChemicalEntity.

Returns:

The concentration.

getAllConcentrationsForSection

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

Description copied from interface: ConcentrationContainer

Returns all concentrations for a particular CellSection.

Specified by:

getAllConcentrationsForSection in interface ConcentrationContainer

Parameters:

cellSection - The CellSection

Returns:

All concentrations in this CellSection.

getAvailableConcentration

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

Description copied from interface: ConcentrationContainer

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

Specified by:

getAvailableConcentration in interface ConcentrationContainer

Parameters:

cellSection - The CellSection

chemicalEntity - The ChemicalEntity.

Returns:

The concentration of the ChemicalEntity in the CellSection.

setConcentration

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

Description copied from interface: ConcentrationContainer

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

Specified by:

setConcentration in interface ConcentrationContainer

Parameters:

chemicalEntity - The ChemicalEntity.

concentration - The concentration.

setAvailableConcentration

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

Description copied from interface: ConcentrationContainer

Sets the available concentration based on the given compartment.

Specified by:

setAvailableConcentration in interface ConcentrationContainer

Parameters:

cellSection - The identifier of the compartment.

chemicalEntity - The ChemicalEntity.

concentration - The concentration.

getAllReferencedEntities

public Set<ChemicalEntity<?>> getAllReferencedEntities()

Description copied from interface: ConcentrationContainer

Returns all ChemicalEntities that are referenced in this container.

Specified by:

getAllReferencedEntities in interface ConcentrationContainer

Returns:

All ChemicalEntities that are referenced in this container.

getAllReferencedSections

public Set<CellSection> getAllReferencedSections()

Description copied from interface: ConcentrationContainer

Returns all Compartments that are referenced in this container.

Specified by:

getAllReferencedSections in interface ConcentrationContainer

Returns:

All Compartments that are referenced in this container.

getAllConcentrations

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

Description copied from interface: ConcentrationContainer

Returns the representative concentrations of all referenced chemical entities.

Specified by:

getAllConcentrations in interface ConcentrationContainer

Returns:

The representative concentrations of all referenced chemical entities.

getCopy

public SimpleConcentrationContainer getCopy()

Description copied from interface: ConcentrationContainer

Returns a copy of this concentration container.

Specified by:

getCopy in interface ConcentrationContainer

Returns:

A copy of this concentration container.