org.biopax.paxtools.query.wrapperL3undirected

Class InteractionWrapper

java.lang.Object

org.biopax.paxtools.query.model.AbstractNode

org.biopax.paxtools.query.wrapperL3undirected.EventWrapper

org.biopax.paxtools.query.wrapperL3undirected.InteractionWrapper

All Implemented Interfaces:

GraphObject, Node

public class InteractionWrapper
extends EventWrapper

Wrapper for Interaction class, excluding Control objects.

Author:

Ozgun Babur

Field Summary

Fields inherited from class org.biopax.paxtools.query.model.AbstractNode

banned, downstream, downstreamInited, graph, lowerEquivalent, pathSign, upperEquivalent, upstream, upstreamInited

Fields inherited from interface org.biopax.paxtools.query.model.Node

NEGATIVE, NEUTRAL, POSITIVE

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	InteractionWrapper(Interaction interaction, GraphL3Undirected graph) Constructor with the Interaction and the owner graph.

Method Summary

Modifier and Type	Method and Description
protected void	addToDownstream(BioPAXElement pe, Graph graph) Binds the given PhysicalEntity to the downstream.
protected void	addToUpstream(BioPAXElement ele, Graph graph) Binds the given element to the upstream.
Interaction	getInteraction() Gets the wrapped TemplateReaction
String	getKey() Uses RDF ID of TemplateReaction as key.
void	initDownstream() Binds to participants and controllers.
void	initUpstream() Binds to participants and controllers.
boolean	isTranscription() Being a transcription is not relevant in the undirected context.

Methods inherited from class org.biopax.paxtools.query.wrapperL3undirected.EventWrapper

addToDownstream, getLowerEquivalent, getSign, getUpperEquivalent, isBreadthNode, isUbique

Methods inherited from class org.biopax.paxtools.query.model.AbstractNode

clear, getBanned, getDownstream, getDownstreamNoInit, getGraph, getPathSign, getUpstream, getUpstreamNoInit, init, initBanned, setBanned, setPathSign

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

InteractionWrapper

protected InteractionWrapper(Interaction interaction,
                             GraphL3Undirected graph)

Constructor with the Interaction and the owner graph.

Parameters:

interaction - Interaction to wrap

graph - Owner graph

Method Detail

initUpstream

public void initUpstream()

Binds to participants and controllers.

Overrides:

initUpstream in class AbstractNode

initDownstream

public void initDownstream()

Binds to participants and controllers.

Overrides:

initDownstream in class AbstractNode

isTranscription

public boolean isTranscription()

Being a transcription is not relevant in the undirected context.

Specified by:

isTranscription in interface Node

Specified by:

isTranscription in class EventWrapper

Returns:

false

addToDownstream

protected void addToDownstream(BioPAXElement pe,
                               Graph graph)

Binds the given PhysicalEntity to the downstream.

Parameters:

pe - PhysicalEntity to bind

graph - Owner graph

addToUpstream

protected void addToUpstream(BioPAXElement ele,
                             Graph graph)

Binds the given element to the upstream.

Overrides:

addToUpstream in class EventWrapper

Parameters:

ele - Element to bind

graph - Owner graph

getKey

public String getKey()

Uses RDF ID of TemplateReaction as key.

Returns:

RDF ID of TemplateReaction

getInteraction

public Interaction getInteraction()

Gets the wrapped TemplateReaction

Returns:

The wrapped TemplateReaction