org.biopax.paxtools.query.wrapperL3undirected

Class PhysicalEntityWrapper

java.lang.Object

org.biopax.paxtools.query.model.AbstractNode

org.biopax.paxtools.query.wrapperL3undirected.PhysicalEntityWrapper

All Implemented Interfaces:

GraphObject, Node

public class PhysicalEntityWrapper
extends AbstractNode

Wrapper for PhysicalEntity.

Author:

Ozgun Babur

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	lowerEquivalentInited Flag to remember if child equivalents initialized.
protected PhysicalEntity	pe Wrapped PhysicalEntity.
protected boolean	ubique Flag to say this is a ubiquitous molecule.
protected boolean	upperEquivalentInited Flag to remember if parent equivalents initialized.

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

Constructor and Description
PhysicalEntityWrapper(PhysicalEntity pe, GraphL3Undirected graph) Constructor with the wrapped PhysicalEntity and the owner graph.

Method Summary

Modifier and Type	Method and Description
String	getKey() RDF ID of the PhysicalEntity is used as key.
Collection<Node>	getLowerEquivalent()
PhysicalEntity	getPhysicalEntity()
int	getSign() PhysicalEntity have positive sign.
Collection<Node>	getUpperEquivalent()
void	initDownstream() Binds to downstream interactions.
protected void	initLowerEquivalent() Finds member nodes if this is a homology node
protected void	initUpperEquivalent() Finds homology parent.
void	initUpstream() Binds to upstream interactions.
boolean	isBreadthNode() PhysicalEntity is a breadth node.
boolean	isUbique() In biological graphs, some nodes are used ubiquitously like ATP, H2O, etc.
void	setUbique(boolean ubique) Set the ubique flag.
String	toString()

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

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

Methods inherited from class java.lang.Object

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

Field Detail

pe

protected PhysicalEntity pe

Wrapped PhysicalEntity.

upperEquivalentInited

protected boolean upperEquivalentInited

Flag to remember if parent equivalents initialized.

lowerEquivalentInited

protected boolean lowerEquivalentInited

Flag to remember if child equivalents initialized.

ubique

protected boolean ubique

Flag to say this is a ubiquitous molecule.

Constructor Detail

PhysicalEntityWrapper

public PhysicalEntityWrapper(PhysicalEntity pe,
                             GraphL3Undirected graph)

Constructor with the wrapped PhysicalEntity and the owner graph.

Parameters:

pe - PhysicalEntity to wrap

graph - Owner graph

Method Detail

isUbique

public boolean isUbique()

Description copied from interface: Node

In biological graphs, some nodes are used ubiquitously like ATP, H2O, etc. While traversing a graph we do not want these molecules to link two reactions. So they should be labeled.

Returns:

Whether this is ubique

setUbique

public void setUbique(boolean ubique)

Set the ubique flag.

Parameters:

ubique - Whether this is a ubiquitous molecule

initUpstream

public void initUpstream()

Binds to upstream interactions.

Overrides:

initUpstream in class AbstractNode

initDownstream

public void initDownstream()

Binds to downstream interactions.

Overrides:

initDownstream in class AbstractNode

getUpperEquivalent

public Collection<Node> getUpperEquivalent()

Specified by:

getUpperEquivalent in interface Node

Overrides:

getUpperEquivalent in class AbstractNode

Returns:

Parent equivalent objects

getLowerEquivalent

public Collection<Node> getLowerEquivalent()

Specified by:

getLowerEquivalent in interface Node

Overrides:

getLowerEquivalent in class AbstractNode

Returns:

Child equivalent objects

initUpperEquivalent

protected void initUpperEquivalent()

Finds homology parent.

initLowerEquivalent

protected void initLowerEquivalent()

Finds member nodes if this is a homology node

isBreadthNode

public boolean isBreadthNode()

PhysicalEntity is a breadth node.

Returns:

True

getSign

public int getSign()

PhysicalEntity have positive sign.

Returns:

POSITIVE (1)

getKey

public String getKey()

RDF ID of the PhysicalEntity is used as key.

Returns:

Key

getPhysicalEntity

public PhysicalEntity getPhysicalEntity()

Returns:

Wrapped PhysicalEntity

toString

public String toString()

Overrides:

toString in class Object

Returns:

display name with ID added