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

Packages that use Node

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.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 Node in org.biopax.paxtools.query

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

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 Node in org.biopax.paxtools.query.algorithm

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

Modifier and Type	Field	Description
protected LinkedList<Node>	BFS.queue	BFS queue.
protected Set<Node>	BFS.sourceSet	BFS starts from source nodes.
protected Set<Node>	BFS.stopSet	BFS will not further traverse neighbors of any node in the stopSet.

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

Modifier and Type	Method	Description
protected int	BFS.getColor(Node node)	Gets color tag of the node
protected boolean	BFS.isEquivalentInTheSet(Node node, boolean direction, Set<Node> set)	Checks if an equivalent of the given node is in the set.
protected boolean	BFS.isEquivalentInTheSet(Node node, Set<Node> set)	Checks if an equivalent of the given node is in the set.
boolean	CycleBreaker.isSafe(Node node, Edge edge)	Checks whether an edge is on an unwanted cycle.
protected void	BFS.labelEquivRecursive(Node node, boolean up, int dist, boolean enqueue, boolean head)	Labels equivalent nodes recursively.
protected void	BFS.processNode(Node current)	Processes a node.
protected boolean	CycleBreaker.processNode2(Node current)	Continue the search from the node.
protected void	BFS.setColor(Node node, int color)	Sets color tag

Method parameters in org.biopax.paxtools.query.algorithm with type arguments of type Node

Modifier and Type	Method	Description
protected boolean	BFS.isEquivalentInTheSet(Node node, boolean direction, Set<Node> set)	Checks if an equivalent of the given node is in the set.
protected boolean	BFS.isEquivalentInTheSet(Node node, Set<Node> set)	Checks if an equivalent of the given node is in the set.

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

Modifier	Constructor	Description
	BFS(Set<Node> sourceSet, Set<Node> stopSet, Direction direction, int limit)	Constructor with all parameters.
	CommonStreamQuery(Collection<Set<Node>> sourceStateSet, Direction direction, int limit)	Constructor for Common Stream with Entity States.
	CommonStreamQuery(Set<Node> sourceNodeSet, Direction direction, int limit)	Constructor for Common Stream with Selected Nodes.
	NeighborhoodQuery(Set<Node> sourceNodes, Direction direction, int limit)	Constructor with parameters.
	PathsBetweenQuery(Collection<Set<Node>> sourceSet, int limit)	Constructor with parameters
	PathsFromToQuery(Set<Node> sourceSet, Set<Node> targetSet, LimitType limitType, int stopDistance, boolean strict)	Constructor with parameters.

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

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

Modifier and Type	Class	Description
class	AbstractNode

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

Modifier and Type	Field	Description
protected Set<Node>	AbstractNode.banned	For saying: "If the algorithm traverses this node, it cannot traverse those others".
protected Set<Node>	AbstractNode.lowerEquivalent	If there are equivalent nodes in the graph, and they have a hierarchy, like an homology node and members, then this set is for the child equivalents of this node.
protected Set<Node>	AbstractNode.upperEquivalent	If there are equivalent nodes in the graph, and they have a hierarchy, like an homology node and members, then this set is for the parent equivalents of this node.

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

Modifier and Type	Method	Description
Node	AbstractEdge.getSourceNode()
Node	Edge.getSourceNode()
Node	AbstractEdge.getTargetNode()
Node	Edge.getTargetNode()
abstract Node	AbstractGraph.wrap(Object obj)	Creates the wrapper for the given object.

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

Modifier and Type	Method	Description
Set<Node>	AbstractNode.getBanned()
Collection<Node>	AbstractNode.getLowerEquivalent()
Collection<Node>	Node.getLowerEquivalent()
Collection<Node>	AbstractNode.getUpperEquivalent()
Collection<Node>	Node.getUpperEquivalent()
Map<Object,Node>	Graph.getWrapperMap(Set<?> objects)	Gets a map from objects to their wrappers.
Set<Node>	Graph.getWrapperSet(Set<?> objects)	Gets the set of wrappers for the given wrapped object set.

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

Modifier and Type	Method	Description
void	AbstractNode.setBanned(Set<Node> banned)

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

Modifier	Constructor	Description
	AbstractEdge(Node source, Node target, Graph graph)	Edges should know their source and target nodes, and their graph.

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

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

Modifier and Type	Class	Description
class	ControlWrapper	Wrapper for the Control class.
class	ConversionWrapper	Wrapper for the Conversion class.
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.

Methods in org.biopax.paxtools.query.wrapperL3 that return Node

Modifier and Type	Method	Description
Node	GraphL3.wrap(Object obj)	This method creates a wrapper for every wrappable L3 element.

Methods in org.biopax.paxtools.query.wrapperL3 that return types with arguments of type Node

Modifier and Type	Method	Description
Collection<Node>	ControlWrapper.getLowerEquivalent()	Control cannot have an equivalent.
Collection<Node>	EventWrapper.getLowerEquivalent()	Events do not have equivalent objects.
Collection<Node>	PhysicalEntityWrapper.getLowerEquivalent()
Collection<Node>	ControlWrapper.getUpperEquivalent()	Control cannot have an equivalent.
Collection<Node>	EventWrapper.getUpperEquivalent()	Events do not have equivalent objects.
Collection<Node>	PhysicalEntityWrapper.getUpperEquivalent()
Map<Object,Node>	GraphL3.getWrapperMap(Set<?> objects)	Gets an element-to-wrapper map for the given elements.
Set<Node>	GraphL3.getWrapperSet(Set<?> objects)	Gets wrappers of given elements

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

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

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

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

Modifier and Type	Class	Description
class	ControlWrapper	Wrapper for the Control class.
class	EventWrapper	This is the parent wrapper class for both Conversion and TemplateReaction objects.
class	InteractionWrapper	Wrapper for Interaction class, excluding Control objects.
class	PhysicalEntityWrapper	Wrapper for PhysicalEntity.

Methods in org.biopax.paxtools.query.wrapperL3undirected that return Node

Modifier and Type	Method	Description
Node	GraphL3Undirected.wrap(Object obj)	This method creates a wrapper for every wrappable L3 element.

Methods in org.biopax.paxtools.query.wrapperL3undirected that return types with arguments of type Node

Modifier and Type	Method	Description
Collection<Node>	ControlWrapper.getLowerEquivalent()	Control cannot have an equivalent.
Collection<Node>	EventWrapper.getLowerEquivalent()	Events do not have equivalent objects.
Collection<Node>	PhysicalEntityWrapper.getLowerEquivalent()
Collection<Node>	ControlWrapper.getUpperEquivalent()	Control cannot have an equivalent.
Collection<Node>	EventWrapper.getUpperEquivalent()	Events do not have equivalent objects.
Collection<Node>	PhysicalEntityWrapper.getUpperEquivalent()
Map<Object,Node>	GraphL3Undirected.getWrapperMap(Set<?> objects)	Gets an element-to-wrapper map for the given elements.
Set<Node>	GraphL3Undirected.getWrapperSet(Set<?> objects)	Gets wrappers of given elements

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

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