Package | Description |
---|---|
org.biopax.paxtools.query |
Graph-theoretic querying module in Paxtools is used for identifying paths between molecules or identifying other
molecules that is reachable through some specific paths using the BioPAX data model.
|
org.biopax.paxtools.query.model |
This package contains the SIF rules for BioPAX Level 3.
|
org.biopax.paxtools.query.wrapperL3 |
This package contains TODO annotate!
|
org.biopax.paxtools.query.wrapperL3undirected |
This package contains TODO annotate!
|
Modifier and Type | Method and Description |
---|---|
static Set<Node> |
QueryExecuter.getSeedInteractions(Collection<BioPAXElement> elements,
Graph graph)
Extracts the querible interactions from the elements.
|
static Set<Node> |
QueryExecuter.prepareSingleNodeSet(Set<BioPAXElement> elements,
Graph graph)
Gets the related wrappers of the given elements in a set.
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractGraph
Adapter class for a graph that is queried.
|
Modifier and Type | Field and Description |
---|---|
protected Graph |
AbstractNode.graph
Owner graph.
|
Modifier and Type | Method and Description |
---|---|
Graph |
GraphObject.getGraph()
Every graph object should have an owner graph.
|
Graph |
AbstractNode.getGraph() |
Graph |
AbstractEdge.getGraph() |
Constructor and Description |
---|
AbstractEdge(Node source,
Node target,
Graph graph)
Edges should know their source and target nodes, and their graph.
|
AbstractNode(Graph graph)
Constructor with the owner graph.
|
Modifier and Type | Class and Description |
---|---|
class |
GraphL3
Wrapper for L3 Graphs.
|
Modifier and Type | Method and Description |
---|---|
protected void |
TemplateReactionWrapper.addToDownstream(PhysicalEntity pe,
Graph graph)
Binds the given PhysicalEntity to the downstream.
|
protected void |
EventWrapper.addToDownstream(PhysicalEntity pe,
Graph graph)
Bind the wrapper of the given PhysicalEntity to the downstream.
|
protected void |
TemplateReactionWrapper.addToUpstream(BioPAXElement ele,
Graph graph)
Binds the given element to the upstream.
|
protected void |
EventWrapper.addToUpstream(BioPAXElement ele,
Graph graph)
Bind the wrapper of the given element to the upstream.
|
Constructor and Description |
---|
ControlWrapper(Control ctrl,
Graph graph)
Constructor with the Control and the owner graph.
|
EdgeL3(Node source,
Node target,
Graph graph)
Constructor with source and target nodes, and the owner graph.
|
Modifier and Type | Class and Description |
---|---|
class |
GraphL3Undirected
Wrapper for L3 Graphs.
|
Modifier and Type | Method and Description |
---|---|
protected void |
InteractionWrapper.addToDownstream(BioPAXElement pe,
Graph graph)
Binds the given PhysicalEntity to the downstream.
|
protected void |
EventWrapper.addToDownstream(PhysicalEntity pe,
Graph graph)
Bind the wrapper of the given PhysicalEntity to the downstream.
|
protected void |
InteractionWrapper.addToUpstream(BioPAXElement ele,
Graph graph)
Binds the given element to the upstream.
|
protected void |
EventWrapper.addToUpstream(BioPAXElement ele,
Graph graph)
Bind the wrapper of the given element to the upstream.
|
Constructor and Description |
---|
ControlWrapper(Control ctrl,
Graph graph)
Constructor with the Control and the owner graph.
|
EdgeL3(Node source,
Node target,
Graph graph)
Constructor with source and target nodes, and the owner graph.
|
Copyright © 2015 BioPAX. All rights reserved.