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

Packages that use Graph

Package	Description
org.biopax.paxtools.query	Graph-theoretic querying module in Paxtools is used for identifying paths between molecules or identifying other molecules that is reachable through some specific paths using the BioPAX data model.
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 Graph in org.biopax.paxtools.query

Methods in org.biopax.paxtools.query with parameters of type Graph

Modifier and Type	Method	Description
static Set<Node>	QueryExecuter.getSeedInteractions(Collection<BioPAXElement> elements, Graph graph)	Extracts the querible interactions from the elements.
static Set<Node>	QueryExecuter.prepareSingleNodeSet(Set<BioPAXElement> elements, Graph graph)	Gets the related wrappers of the given elements in a set.
static Set<Node>	QueryExecuter.prepareSingleNodeSetFromSets(Set<Set<BioPAXElement>> sets, Graph graph)	Gets the related wrappers of the given elements in the sets.

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

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

Modifier and Type	Class	Description
class	AbstractGraph	Adapter class for a graph that is queried.

Fields in org.biopax.paxtools.query.model declared as Graph

Modifier and Type	Field	Description
protected Graph	AbstractNode.graph	Owner graph.

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

Modifier and Type	Method	Description
Graph	AbstractEdge.getGraph()
Graph	AbstractNode.getGraph()
Graph	GraphObject.getGraph()	Every graph object should have an owner graph.

Constructors in org.biopax.paxtools.query.model with parameters of type Graph

Modifier	Constructor	Description
	AbstractEdge(Node source, Node target, Graph graph)	Edges should know their source and target nodes, and their graph.
protected	AbstractNode(Graph graph)	Constructor with the owner graph.

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

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

Modifier and Type	Class	Description
class	GraphL3	Wrapper for L3 Graphs.

Methods in org.biopax.paxtools.query.wrapperL3 with parameters of type Graph

Modifier and Type	Method	Description
protected void	EventWrapper.addToDownstream(PhysicalEntity pe, Graph graph)	Bind the wrapper of the given PhysicalEntity to the downstream.
protected void	TemplateReactionWrapper.addToDownstream(PhysicalEntity pe, Graph graph)	Binds the given PhysicalEntity to the downstream.
protected void	EventWrapper.addToUpstream(BioPAXElement ele, Graph graph)	Bind the wrapper of the given element to the upstream.
protected void	TemplateReactionWrapper.addToUpstream(BioPAXElement ele, Graph graph)	Binds the given element to the upstream.

Constructors in org.biopax.paxtools.query.wrapperL3 with parameters of type Graph

Modifier	Constructor	Description
protected	ControlWrapper(Control ctrl, Graph graph)	Constructor with the Control and the owner graph.
	EdgeL3(Node source, Node target, Graph graph)	Constructor with source and target nodes, and the owner graph.

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

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

Modifier and Type	Class	Description
class	GraphL3Undirected	Wrapper for L3 Graphs.

Methods in org.biopax.paxtools.query.wrapperL3undirected with parameters of type Graph

Modifier and Type	Method	Description
protected void	EventWrapper.addToDownstream(PhysicalEntity pe, Graph graph)	Bind the wrapper of the given PhysicalEntity to the downstream.
protected void	InteractionWrapper.addToDownstream(BioPAXElement pe, Graph graph)	Binds the given PhysicalEntity to the downstream.
protected void	EventWrapper.addToUpstream(BioPAXElement ele, Graph graph)	Bind the wrapper of the given element to the upstream.
protected void	InteractionWrapper.addToUpstream(BioPAXElement ele, Graph graph)	Binds the given element to the upstream.

Constructors in org.biopax.paxtools.query.wrapperL3undirected with parameters of type Graph

Modifier	Constructor	Description
protected	ControlWrapper(Control ctrl, Graph graph)	Constructor with the Control and the owner graph.
	EdgeL3(Node source, Node target, Graph graph)	Constructor with source and target nodes, and the owner graph.