Package | Description |
---|---|
org.biopax.paxtools.query.algorithm |
This package contains the SIF rules for BioPAX Level 3.
|
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 | Field and Description |
---|---|
protected Map<GraphObject,Integer> |
BFS.colors
Color labels.
|
protected Map<GraphObject,Integer> |
BFS.dist
Distance labels.
|
Modifier and Type | Method and Description |
---|---|
Set<GraphObject> |
Prune.run()
Executes the algorithm.
|
Set<GraphObject> |
PathsFromToQuery.run()
Executes the algorithm.
|
Set<GraphObject> |
PathsBetweenQuery.run() |
Set<GraphObject> |
NeighborhoodQuery.run()
Executes the query.
|
Set<GraphObject> |
CommonStreamQuery.run()
Method to run the query.
|
Map<GraphObject,Integer> |
BFS.run()
Executes the algorithm.
|
Modifier and Type | Method and Description |
---|---|
int |
BFS.getLabel(GraphObject go)
Gets the distance label of the object.
|
protected void |
BFS.setLabel(GraphObject go,
int label)
Sets the distance label.
|
Constructor and Description |
---|
CycleBreaker(Set<GraphObject> result,
Set<Node> ST,
int limit)
Constructor with the objects in the result, source and target nodes, and search limit.
|
Prune(Set<GraphObject> result,
Set<Node> ST)
Constructor with the input.
|
Modifier and Type | Interface and Description |
---|---|
interface |
Edge
Wrapper interface for edges in a graph to be queried.
|
interface |
Node
Node interface to use in graph algorithms.
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractEdge
The base class for an edge in the traversed graph.
|
class |
AbstractNode |
Modifier and Type | Field and Description |
---|---|
protected Map<String,GraphObject> |
AbstractGraph.objectMap
Objects are stored in this map.
|
Modifier and Type | Method and Description |
---|---|
GraphObject |
Graph.getGraphObject(Object obj)
Gets the wrapper of the related object.
|
GraphObject |
AbstractGraph.getGraphObject(Object obj)
Gets the related wrapper for the given object, creates the wrapper if not created before.
|
GraphObject |
AbstractGraph.getGraphObject(String id)
Gets the wrapper object with its id (key).
|
Modifier and Type | Method and Description |
---|---|
Map<String,GraphObject> |
AbstractGraph.getObjectMap() |
Modifier and Type | Method and Description |
---|---|
Set<Object> |
Graph.getWrappedSet(Set<? extends GraphObject> wrappers)
Gets the wrapped objects of the given wrapper set.
|
Modifier and Type | Class and Description |
---|---|
class |
ControlWrapper
Wrapper for the Control class.
|
class |
ConversionWrapper
Wrapper for the Conversion class.
|
class |
EdgeL3
Wrapper for links between L3 objects.
|
class |
EventWrapper
This is the parent wrapper class for both Conversion and TemplateReaction objects.
|
class |
PhysicalEntityWrapper
Wrapper for PhysicalEntity.
|
class |
TemplateReactionWrapper
Wrapper for TemplateReaction class.
|
Modifier and Type | Method and Description |
---|---|
Set<Object> |
GraphL3.getWrappedSet(Set<? extends GraphObject> wrappers)
Gets the wrapped objects of the given wrappers.
|
Modifier and Type | Class and Description |
---|---|
class |
InteractionWrapper
Wrapper for Interaction class, excluding Control objects.
|
Modifier and Type | Method and Description |
---|---|
Set<Object> |
GraphL3Undirected.getWrappedSet(Set<? extends GraphObject> wrappers)
Gets the wrapped objects of the given wrappers.
|
Copyright © 2015 BioPAX. All rights reserved.