bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants

Class DynamicChemicalEntity

java.lang.Object

bio.singa.chemistry.entities.AbstractChemicalEntity

bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicChemicalEntity

All Implemented Interfaces:

Annotatable, ChemicalEntity, bio.singa.features.identifiers.model.Identifiable<bio.singa.features.identifiers.SimpleStringIdentifier>, bio.singa.features.model.Featureable

public class DynamicChemicalEntity
extends AbstractChemicalEntity

Author:

cl

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	DynamicChemicalEntity.Builder

Field Summary

Fields inherited from class bio.singa.chemistry.entities.AbstractChemicalEntity

annotations, availableFeatures, features, identifier

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	DynamicChemicalEntity(bio.singa.features.identifiers.SimpleStringIdentifier identifier) Creates a new Chemical Entity with the given identifier.
	DynamicChemicalEntity(String identifier)

Method Summary

Modifier and Type	Method and Description
void	addCompositionCondition(EntityCompositionCondition compositionCondition)
void	addPossibleTopology(CellTopology possibleTopology)
static DynamicChemicalEntity.Builder	create(String identifier)
List<EntityCompositionCondition>	getComposition()
List<ChemicalEntity>	getMatchingEntities(Updatable updatable, CellTopology topology)
List<CellTopology>	getPossibleTopologies()
void	setComposition(List<EntityCompositionCondition> composition)
void	setPossibleTopologies(List<CellTopology> possibleTopologies)

Methods inherited from class bio.singa.chemistry.entities.AbstractChemicalEntity

addAdditionalIdentifier, addAdditionalIdentifiers, addName, equals, getAllIdentifiers, getAnnotations, getAvailableFeatures, getFeature, getFeatures, getIdentifier, getNames, hasFeature, hashCode, setFeature, setFeature, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface bio.singa.chemistry.annotations.Annotatable

addAnnotation, getAnnotationsOfType, getContentOfAnnotation, getContentOfAnnotation, getContentOfAnnotations, getContentOfAnnotations

Methods inherited from interface bio.singa.features.model.Featureable

canBeFeaturedWith, meetsAllRequirements

Constructor Detail

DynamicChemicalEntity

protected DynamicChemicalEntity(bio.singa.features.identifiers.SimpleStringIdentifier identifier)

Creates a new Chemical Entity with the given identifier.

Parameters:

identifier - The pdbIdentifier.

DynamicChemicalEntity

public DynamicChemicalEntity(String identifier)

Method Detail

create

public static DynamicChemicalEntity.Builder create(String identifier)

getComposition

public List<EntityCompositionCondition> getComposition()

setComposition

public void setComposition(List<EntityCompositionCondition> composition)

addCompositionCondition

public void addCompositionCondition(EntityCompositionCondition compositionCondition)

getPossibleTopologies

public List<CellTopology> getPossibleTopologies()

setPossibleTopologies

public void setPossibleTopologies(List<CellTopology> possibleTopologies)

addPossibleTopology

public void addPossibleTopology(CellTopology possibleTopology)

getMatchingEntities

public List<ChemicalEntity> getMatchingEntities(Updatable updatable,
                                                CellTopology topology)