Uses of Interface
org.biopax.paxtools.query.model.GraphObject

Packages that use GraphObject

Package	Description
org.biopax.paxtools.query.algorithm	This package contains the SIF rules for BioPAX Level 3.
org.biopax.paxtools.query.model	This package contains the SIF rules for BioPAX Level 3.
org.biopax.paxtools.query.wrapperL3	This package contains TODO annotate!
org.biopax.paxtools.query.wrapperL3undirected	This package contains TODO annotate!

Uses of GraphObject in org.biopax.paxtools.query.algorithm

Fields in org.biopax.paxtools.query.algorithm with type parameters of type GraphObject

Modifier and Type	Field and Description
protected Map<GraphObject,Integer>	BFS.colors Color labels.
protected Map<GraphObject,Integer>	BFS.dist Distance labels.

Methods in org.biopax.paxtools.query.algorithm that return types with arguments of type GraphObject

Modifier and Type	Method and Description
Set<GraphObject>	NeighborhoodQuery.run() Executes the query.
Set<GraphObject>	PathsBetweenQuery.run()
Set<GraphObject>	CommonStreamQuery.run() Method to run the query.
Map<GraphObject,Integer>	BFS.run() Executes the algorithm.
Set<GraphObject>	Prune.run() Executes the algorithm.
Set<GraphObject>	PathsFromToQuery.run() Executes the algorithm.

Methods in org.biopax.paxtools.query.algorithm with parameters of type GraphObject

Modifier and Type	Method and Description
int	BFS.getLabel(GraphObject go) Gets the distance label of the object.
protected void	BFS.setLabel(GraphObject go, int label) Sets the distance label.

Constructor parameters in org.biopax.paxtools.query.algorithm with type arguments of type GraphObject

Constructor and Description
CycleBreaker(Set<GraphObject> result, Set<Node> ST, int limit) Constructor with the objects in the result, source and target nodes, and search limit.
Prune(Set<GraphObject> result, Set<Node> ST) Constructor with the input.

Uses of GraphObject in org.biopax.paxtools.query.model

Subinterfaces of GraphObject in org.biopax.paxtools.query.model

Modifier and Type	Interface and Description
interface	Edge Wrapper interface for edges in a graph to be queried.
interface	Node Node interface to use in graph algorithms.

Classes in org.biopax.paxtools.query.model that implement GraphObject

Modifier and Type	Class and Description
class	AbstractEdge The base class for an edge in the traversed graph.
class	AbstractNode

Fields in org.biopax.paxtools.query.model with type parameters of type GraphObject

Modifier and Type	Field and Description
protected Map<String,GraphObject>	AbstractGraph.objectMap Objects are stored in this map.

Methods in org.biopax.paxtools.query.model that return GraphObject

Modifier and Type	Method and Description
GraphObject	AbstractGraph.getGraphObject(Object obj) Gets the related wrapper for the given object, creates the wrapper if not created before.
GraphObject	Graph.getGraphObject(Object obj) Gets the wrapper of the related object.
GraphObject	AbstractGraph.getGraphObject(String id) Gets the wrapper object with its id (key).

Methods in org.biopax.paxtools.query.model that return types with arguments of type GraphObject

Modifier and Type	Method and Description
Map<String,GraphObject>	AbstractGraph.getObjectMap()

Method parameters in org.biopax.paxtools.query.model with type arguments of type GraphObject

Modifier and Type	Method and Description
Set<Object>	Graph.getWrappedSet(Set<? extends GraphObject> wrappers) Gets the wrapped objects of the given wrapper set.

Uses of GraphObject in org.biopax.paxtools.query.wrapperL3

Classes in org.biopax.paxtools.query.wrapperL3 that implement GraphObject

Modifier and Type	Class and Description
class	ControlWrapper Wrapper for the Control class.
class	ConversionWrapper Wrapper for the Conversion class.
class	EdgeL3 Wrapper for links between L3 objects.
class	EventWrapper This is the parent wrapper class for both Conversion and TemplateReaction objects.
class	PhysicalEntityWrapper Wrapper for PhysicalEntity.
class	TemplateReactionWrapper Wrapper for TemplateReaction class.

Method parameters in org.biopax.paxtools.query.wrapperL3 with type arguments of type GraphObject

Modifier and Type	Method and Description
Set<Object>	GraphL3.getWrappedSet(Set<? extends GraphObject> wrappers) Gets the wrapped objects of the given wrappers.

Uses of GraphObject in org.biopax.paxtools.query.wrapperL3undirected

Classes in org.biopax.paxtools.query.wrapperL3undirected that implement GraphObject

Modifier and Type	Class and Description
class	InteractionWrapper Wrapper for Interaction class, excluding Control objects.

Method parameters in org.biopax.paxtools.query.wrapperL3undirected with type arguments of type GraphObject

Modifier and Type	Method and Description
Set<Object>	GraphL3Undirected.getWrappedSet(Set<? extends GraphObject> wrappers) Gets the wrapped objects of the given wrappers.