org.biopax.paxtools.query.wrapperL3

Class ControlWrapper

java.lang.Object

org.biopax.paxtools.query.model.AbstractNode

org.biopax.paxtools.query.wrapperL3.ControlWrapper

All Implemented Interfaces:

GraphObject, Node

public class ControlWrapper
extends AbstractNode

Wrapper for the Control class.

Author:

Ozgun Babur

Field Summary

Fields

Modifier and Type	Field and Description
protected Control	ctrl Wrapped control.
protected int	sign Sign of the control.
protected boolean	transcription Flag to indicate if this control is related to 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 and Description
protected	ControlWrapper(Control ctrl, Graph graph) Constructor with the Control and the owner graph.

Method Summary

Modifier and Type	Method and Description
Control	getControl() Gets the wrapped Control.
String	getKey() RDF ID of the Control is its key.
Collection<Node>	getLowerEquivalent() Control cannot have an equivalent.
int	getSign() Some nodes can have a sign (typically non-breadth nodes).
Collection<Node>	getUpperEquivalent() Control cannot have an equivalent.
void	init() Extracts the sign and the type of the Control.
void	initDownstream() Binds the controlled objects.
void	initUpstream() Binds the controller and other Controls that controls this control.
boolean	isBreadthNode() Control is not a breadth node.
boolean	isTranscription() Nodes are not transcription by default.
boolean	isUbique() Controls are not ubiquitous molecules.
void	setTranscription(boolean transcription) Make or not make this control related to a transcription.

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, toString, wait, wait, wait

Field Detail

ctrl

protected Control ctrl

Wrapped control.

sign

protected int sign

Sign of the control.

transcription

protected boolean transcription

Flag to indicate if this control is related to a transcription.

Constructor Detail

ControlWrapper

protected ControlWrapper(Control ctrl,
                         Graph graph)

Constructor with the Control and the owner graph.

Parameters:

ctrl - Control to be wrapped

graph - Owner graph

Method Detail

isBreadthNode

public boolean isBreadthNode()

Control is not a breadth node.

Returns:

False

getSign

public int getSign()

Description copied from interface: Node

Some nodes can have a sign (typically non-breadth nodes).

Returns:

Sign of the Control

isUbique

public boolean isUbique()

Controls are not ubiquitous molecules.

Returns:

False

getKey

public String getKey()

RDF ID of the Control is its key.

Returns:

Key

init

public void init()

Extracts the sign and the type of the Control.

Specified by:

init in interface Node

Overrides:

init in class AbstractNode

initUpstream

public void initUpstream()

Binds the controller and other Controls that controls this control.

Overrides:

initUpstream in class AbstractNode

initDownstream

public void initDownstream()

Binds the controlled objects.

Overrides:

initDownstream in class AbstractNode

getControl

public Control getControl()

Gets the wrapped Control.

Returns:

The Control

getUpperEquivalent

public Collection<Node> getUpperEquivalent()

Control cannot have an equivalent.

Specified by:

getUpperEquivalent in interface Node

Overrides:

getUpperEquivalent in class AbstractNode

Returns:

Empty set

getLowerEquivalent

public Collection<Node> getLowerEquivalent()

Control cannot have an equivalent.

Specified by:

getLowerEquivalent in interface Node

Overrides:

getLowerEquivalent in class AbstractNode

Returns:

Empty set

isTranscription

public boolean isTranscription()

Description copied from class: AbstractNode

Nodes are not transcription by default.

Specified by:

isTranscription in interface Node

Overrides:

isTranscription in class AbstractNode

Returns:

whether this Control is related to a transcription event

setTranscription

public void setTranscription(boolean transcription)

Make or not make this control related to a transcription.

Parameters:

transcription - whether this Control is related to a transcription