Package org.biopax.paxtools.query.wrapperL3undirected

Class EventWrapper

java.lang.Object

org.biopax.paxtools.query.model.AbstractNode

org.biopax.paxtools.query.wrapperL3undirected.EventWrapper

All Implemented Interfaces:

GraphObject, Node

Direct Known Subclasses:

InteractionWrapper

public abstract class EventWrapper
extends AbstractNode

This is the parent wrapper class for both Conversion and TemplateReaction 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	Description
protected	EventWrapper(GraphL3Undirected graph)	Constructor with the owner graph.

Method Summary

Modifier and Type	Method	Description
protected void	addToDownstream(PhysicalEntity pe, Graph graph)	Bind the wrapper of the given PhysicalEntity to the downstream.
protected void	addToUpstream(BioPAXElement ele, Graph graph)	Bind the wrapper of the given element to the upstream.
Collection<Node>	getLowerEquivalent()	Events do not have equivalent objects.
int	getSign()	Events have a positive sign.
Collection<Node>	getUpperEquivalent()	Events do not have equivalent objects.
boolean	isBreadthNode()	Events are not breadth nodes.
abstract boolean	isTranscription()	Say if the event is a transcription.
boolean	isUbique()	Events are not ubiquitous molecules.

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

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

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biopax.paxtools.query.model.GraphObject

getKey

Constructor Details

EventWrapper

protected EventWrapper(GraphL3Undirected graph)

Constructor with the owner graph.

Parameters:

graph - Owner graph

Method Details

isBreadthNode

public boolean isBreadthNode()

Events are not breadth nodes.

Returns:

False

getSign

public int getSign()

Events have a positive sign.

Returns:

POSITIVE (1)

isUbique

public boolean isUbique()

Events are not ubiquitous molecules.

Returns:

False

isTranscription

public abstract boolean isTranscription()

Say if the event is a transcription.

Specified by:

isTranscription in interface Node

Overrides:

isTranscription in class AbstractNode

Returns:

Whether the event is a transcription

addToUpstream

protected void addToUpstream(BioPAXElement ele,
 Graph graph)

Bind the wrapper of the given element to the upstream.

Parameters:

ele - Element to bind

graph - Owner graph.

addToDownstream

protected void addToDownstream(PhysicalEntity pe,
 Graph graph)

Bind the wrapper of the given PhysicalEntity to the downstream.

Parameters:

pe - PhysicalEntity to bind

graph - Owner graph.

getUpperEquivalent

public Collection<Node> getUpperEquivalent()

Events do not have equivalent objects.

Specified by:

getUpperEquivalent in interface Node

Overrides:

getUpperEquivalent in class AbstractNode

Returns:

Empty set

getLowerEquivalent

public Collection<Node> getLowerEquivalent()

Events do not have equivalent objects.

Specified by:

getLowerEquivalent in interface Node

Overrides:

getLowerEquivalent in class AbstractNode

Returns:

Empty set