Package bio.singa.simulation.entities

Class ComplexEntity

java.lang.Object

bio.singa.mathematics.graphs.model.AbstractMapGraph<GraphComplexNode,GraphComplexEdge,bio.singa.mathematics.vectors.Vector2D,Integer>

bio.singa.simulation.entities.ComplexEntity

All Implemented Interfaces:

bio.singa.features.model.Featureable, bio.singa.mathematics.graphs.model.Graph<GraphComplexNode,GraphComplexEdge,Integer>, ChemicalEntity

public class ComplexEntity
extends bio.singa.mathematics.graphs.model.AbstractMapGraph<GraphComplexNode,GraphComplexEdge,bio.singa.mathematics.vectors.Vector2D,Integer>
implements ChemicalEntity

Author:

cl

Field Summary

Fields

Modifier and Type	Field	Description
static Set<Class<? extends bio.singa.features.model.Feature>>	availableFeatures

Fields inherited from class bio.singa.mathematics.graphs.model.AbstractMapGraph

edges

Constructor Summary

Constructors

Constructor	Description
ComplexEntity()

Method Summary

Modifier and Type	Method	Description
Optional<ComplexEntity>	add(ChemicalEntity otherEntity, BindingSite bindingSite)
void	addBindingSite(ChemicalEntity first, BindingSite bindingSite)
int	addEdgeBetween(int identifier, GraphComplexNode source, GraphComplexNode target)
int	addEdgeBetween(GraphComplexNode source, GraphComplexNode target)
int	addEdgeBetween(GraphComplexNode source, GraphComplexNode target, BindingSite bindingSite)
Optional<ComplexEntity>	bind(ComplexEntity otherComplex, BindingSite bindingSite)
void	combine(GraphComplexNode first, GraphComplexNode second, ComplexEntity secondGraph, BindingSite bindingSite)
boolean	containsEntity(ChemicalEntity entity)
long	countParts(ChemicalEntity entity)
boolean	equals(Object o)
static ComplexEntity	from(ChemicalEntity chemicalEntity)
static ComplexEntity	from(ChemicalEntity chemicalEntity, BindingSite bindingSite)
static ComplexEntity	from(ChemicalEntity first, ChemicalEntity second)
static ComplexEntity	from(ChemicalEntity chemicalEntity, Collection<BindingSite> bindingSites)
List<bio.singa.features.identifiers.model.Identifier>	getAllIdentifiers()
Set<Class<? extends bio.singa.features.model.Feature>>	getAvailableFeatures()
ComplexEntity	getCopy()
<FeatureType extends bio.singa.features.model.Feature> FeatureType	getFeature(Class<FeatureType> featureTypeClass)
Collection<bio.singa.features.model.Feature<?>>	getFeatures()
String	getIdentifier()
List<GraphComplexNode>	getNodesWithUnoccupiedBindingSite(BindingSite bindingSite)
Optional<GraphComplexNode>	getNodeWithUnoccupiedBindingSite(BindingSite bindingSite)
<FeatureType extends bio.singa.features.model.Feature> boolean	hasFeature(Class<FeatureType> featureTypeClass)
int	hashCode()
boolean	isMembraneBound()
boolean	isSmall()
int	nextEdgeIdentifier()
Integer	nextNodeIdentifier()
Optional<ComplexEntity>	remove(ChemicalEntity chemicalEntity, BindingSite bindingSite)
<FeatureType extends bio.singa.features.model.Feature> void	setFeature(FeatureType feature)
<FeatureType extends bio.singa.features.model.Feature> void	setFeature(Class<FeatureType> featureTypeClass)
void	setMembraneBound(boolean membraneBound)
void	snapTo(ChemicalEntity chemicalEntity, Set<BindingSite> bindingSites)
String	toString()
Optional<List<ComplexEntity>>	unbind(BindingSite bindingSite)
void	update()

Methods inherited from class bio.singa.mathematics.graphs.model.AbstractMapGraph

addEdgeBetween, addNode, addNodeIf, appendGraph, appendNode, containsEdge, containsEdge, containsNode, containsNode, getAllNodes, getEdge, getEdge, getEdges, getMaximumDegree, getNode, getNode, getNodes, removeEdge, removeEdge, removeNode, removeNode

Methods inherited from class java.lang.Object

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

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

canBeFeaturedWith, meetsAllRequirements

Methods inherited from interface bio.singa.mathematics.graphs.model.Graph

getEdgeBetween, getTouchingNodes

Field Detail

availableFeatures

public static final Set<Class<? extends bio.singa.features.model.Feature>> availableFeatures

Constructor Detail

ComplexEntity

public ComplexEntity()

Method Detail

from

public static ComplexEntity from(ChemicalEntity chemicalEntity)

from

public static ComplexEntity from(ChemicalEntity chemicalEntity,
                                 BindingSite bindingSite)

from

public static ComplexEntity from(ChemicalEntity chemicalEntity,
                                 Collection<BindingSite> bindingSites)

from

public static ComplexEntity from(ChemicalEntity first,
                                 ChemicalEntity second)

addEdgeBetween

public int addEdgeBetween(int identifier,
                          GraphComplexNode source,
                          GraphComplexNode target)

Specified by:

addEdgeBetween in interface bio.singa.mathematics.graphs.model.Graph<GraphComplexNode,GraphComplexEdge,Integer>

Specified by:

addEdgeBetween in class bio.singa.mathematics.graphs.model.AbstractMapGraph<GraphComplexNode,GraphComplexEdge,bio.singa.mathematics.vectors.Vector2D,Integer>

addEdgeBetween

public int addEdgeBetween(GraphComplexNode source,
                          GraphComplexNode target)

Specified by:

addEdgeBetween in interface bio.singa.mathematics.graphs.model.Graph<GraphComplexNode,GraphComplexEdge,Integer>

Specified by:

addEdgeBetween in class bio.singa.mathematics.graphs.model.AbstractMapGraph<GraphComplexNode,GraphComplexEdge,bio.singa.mathematics.vectors.Vector2D,Integer>

addEdgeBetween

public int addEdgeBetween(GraphComplexNode source,
                          GraphComplexNode target,
                          BindingSite bindingSite)

addBindingSite

public void addBindingSite(ChemicalEntity first,
                           BindingSite bindingSite)

containsEntity

public boolean containsEntity(ChemicalEntity entity)

countParts

public long countParts(ChemicalEntity entity)

nextNodeIdentifier

public Integer nextNodeIdentifier()

Specified by:

nextNodeIdentifier in interface bio.singa.mathematics.graphs.model.Graph<GraphComplexNode,GraphComplexEdge,Integer>

nextEdgeIdentifier

public int nextEdgeIdentifier()

Specified by:

nextEdgeIdentifier in interface bio.singa.mathematics.graphs.model.Graph<GraphComplexNode,GraphComplexEdge,Integer>

Overrides:

nextEdgeIdentifier in class bio.singa.mathematics.graphs.model.AbstractMapGraph<GraphComplexNode,GraphComplexEdge,bio.singa.mathematics.vectors.Vector2D,Integer>

isMembraneBound

public boolean isMembraneBound()

Specified by:

isMembraneBound in interface ChemicalEntity

setMembraneBound

public void setMembraneBound(boolean membraneBound)

Specified by:

setMembraneBound in interface ChemicalEntity

isSmall

public boolean isSmall()

Specified by:

isSmall in interface ChemicalEntity

getAllIdentifiers

public List<bio.singa.features.identifiers.model.Identifier> getAllIdentifiers()

Specified by:

getAllIdentifiers in interface ChemicalEntity

getFeatures

public Collection<bio.singa.features.model.Feature<?>> getFeatures()

Specified by:

getFeatures in interface bio.singa.features.model.Featureable

getFeature

public <FeatureType extends bio.singa.features.model.Feature> FeatureType getFeature(Class<FeatureType> featureTypeClass)

Specified by:

getFeature in interface bio.singa.features.model.Featureable

setFeature

public <FeatureType extends bio.singa.features.model.Feature> void setFeature(Class<FeatureType> featureTypeClass)

Specified by:

setFeature in interface bio.singa.features.model.Featureable

setFeature

public <FeatureType extends bio.singa.features.model.Feature> void setFeature(FeatureType feature)

Specified by:

setFeature in interface bio.singa.features.model.Featureable

hasFeature

public <FeatureType extends bio.singa.features.model.Feature> boolean hasFeature(Class<FeatureType> featureTypeClass)

Specified by:

hasFeature in interface bio.singa.features.model.Featureable

getAvailableFeatures

public Set<Class<? extends bio.singa.features.model.Feature>> getAvailableFeatures()

Specified by:

getAvailableFeatures in interface bio.singa.features.model.Featureable

getCopy

public ComplexEntity getCopy()

Specified by:

getCopy in interface bio.singa.mathematics.graphs.model.Graph<GraphComplexNode,GraphComplexEdge,Integer>

bind

public Optional<ComplexEntity> bind(ComplexEntity otherComplex,
                                    BindingSite bindingSite)

add

public Optional<ComplexEntity> add(ChemicalEntity otherEntity,
                                   BindingSite bindingSite)

combine

public void combine(GraphComplexNode first,
                    GraphComplexNode second,
                    ComplexEntity secondGraph,
                    BindingSite bindingSite)

unbind

public Optional<List<ComplexEntity>> unbind(BindingSite bindingSite)

remove

public Optional<ComplexEntity> remove(ChemicalEntity chemicalEntity,
                                      BindingSite bindingSite)

getNodesWithUnoccupiedBindingSite

public List<GraphComplexNode> getNodesWithUnoccupiedBindingSite(BindingSite bindingSite)

getNodeWithUnoccupiedBindingSite

public Optional<GraphComplexNode> getNodeWithUnoccupiedBindingSite(BindingSite bindingSite)

snapTo

public void snapTo(ChemicalEntity chemicalEntity,
                   Set<BindingSite> bindingSites)

update

public void update()

getIdentifier

public String getIdentifier()

Specified by:

getIdentifier in interface ChemicalEntity

toString

public String toString()

Overrides:

toString in class bio.singa.mathematics.graphs.model.AbstractMapGraph<GraphComplexNode,GraphComplexEdge,bio.singa.mathematics.vectors.Vector2D,Integer>

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object