public class PhysicalEntityWrapper extends AbstractNode
Modifier and Type | Field and Description |
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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.
|
banned, downstream, downstreamInited, graph, lowerEquivalent, pathSign, upperEquivalent, upstream, upstreamInited
Constructor and Description |
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PhysicalEntityWrapper(PhysicalEntity pe,
GraphL3Undirected graph)
Constructor with the wrapped PhysicalEntity and the owner graph.
|
Modifier and Type | Method and Description |
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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.
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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.
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void |
setUbique(boolean ubique)
Set the ubique flag.
|
String |
toString() |
clear, getBanned, getDownstream, getDownstreamNoInit, getGraph, getPathSign, getUpstream, getUpstreamNoInit, init, initBanned, isTranscription, setBanned, setPathSign
protected PhysicalEntity pe
protected boolean upperEquivalentInited
protected boolean lowerEquivalentInited
protected boolean ubique
public PhysicalEntityWrapper(PhysicalEntity pe, GraphL3Undirected graph)
pe
- PhysicalEntity to wrapgraph
- Owner graphpublic boolean isUbique()
Node
public void setUbique(boolean ubique)
ubique
- Whether this is a ubiquitous moleculepublic void initUpstream()
initUpstream
in class AbstractNode
public void initDownstream()
initDownstream
in class AbstractNode
public Collection<Node> getUpperEquivalent()
getUpperEquivalent
in interface Node
getUpperEquivalent
in class AbstractNode
public Collection<Node> getLowerEquivalent()
getLowerEquivalent
in interface Node
getLowerEquivalent
in class AbstractNode
protected void initUpperEquivalent()
protected void initLowerEquivalent()
public boolean isBreadthNode()
public int getSign()
public PhysicalEntity getPhysicalEntity()
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