Package org.biopax.paxtools.query.wrapperL3

Class ConversionWrapper

java.lang.Object

org.biopax.paxtools.query.model.AbstractNode

org.biopax.paxtools.query.wrapperL3.EventWrapper

org.biopax.paxtools.query.wrapperL3.ConversionWrapper

All Implemented Interfaces:

GraphObject, Node

public class ConversionWrapper
extends EventWrapper

Wrapper for the Conversion class.

Author:

Ozgun Babur

Field Summary

Fields

Modifier and Type	Field	Description
protected Conversion	conv	Wrapped Conversion.
protected boolean	direction	The direction that the Conversion is wrapped.
static final boolean	LEFT_TO_RIGHT	Direction LEFT_TO_RIGHT.
static final boolean	RIGHT_TO_LEFT	Direction RIGHT_TO_LEFT.
protected boolean	transcription	Flag to say this Conversion is a transcription.

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	ConversionWrapper(Conversion conv, GraphL3 graph)	Constructor with the Conversion to wrap and the owner graph.

Method Summary

Modifier and Type	Method	Description
Conversion	getConversion()
boolean	getDirection()
String	getKey()	RDF ID of the Conversion and the direction is used for the key.
ConversionWrapper	getReverse()
void	init()	Extracts the direction, creates the reverse if necessary.
void	initDownstream()	Binds products.
void	initUpstream()	Binds inputs and controllers.
boolean	isTranscription()	Say if the event is a transcription.
String	toString()

Methods inherited from class org.biopax.paxtools.query.wrapperL3.EventWrapper

addToDownstream, addToUpstream, getLowerEquivalent, getSign, getUpperEquivalent, isBreadthNode, isUbique

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

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

Methods inherited from class java.lang.Object

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

Field Details

conv

protected Conversion conv

Wrapped Conversion.

direction

protected boolean direction

The direction that the Conversion is wrapped. A separate wrapper is used for each direction if the Conversion is reversible.

transcription

protected boolean transcription

Flag to say this Conversion is a transcription.

LEFT_TO_RIGHT

public static final boolean LEFT_TO_RIGHT

Direction LEFT_TO_RIGHT.

See Also:

• Constant Field Values

RIGHT_TO_LEFT

public static final boolean RIGHT_TO_LEFT

Direction RIGHT_TO_LEFT.

See Also:

• Constant Field Values

Constructor Details

ConversionWrapper

protected ConversionWrapper(Conversion conv,
 GraphL3 graph)

Constructor with the Conversion to wrap and the owner graph.

Parameters:

conv - Conversion to wrap

graph - Owner graph

Method Details

getDirection

public boolean getDirection()

Returns:

Direction of the conversion

getReverse

public ConversionWrapper getReverse()

Returns:

The reverse Conversion wrapper if exists

init

public void init()

Extracts the direction, creates the reverse if necessary.

Specified by:

init in interface Node

Overrides:

init in class AbstractNode

initUpstream

public void initUpstream()

Binds inputs and controllers.

Overrides:

initUpstream in class AbstractNode

initDownstream

public void initDownstream()

Binds products.

Overrides:

initDownstream in class AbstractNode

isTranscription

public boolean isTranscription()

Description copied from class: EventWrapper

Say if the event is a transcription.

Specified by:

isTranscription in interface Node

Specified by:

isTranscription in class EventWrapper

Returns:

Whether this is a transcription

getKey

public String getKey()

RDF ID of the Conversion and the direction is used for the key.

Returns:

Key

getConversion

public Conversion getConversion()

Returns:

Wrapped Conversion

toString

public String toString()

Overrides:

toString in class Object

Returns:

Display name with the ID