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.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 | 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 | Field and Description |
---|---|
protected LinkedList<Node> |
BFS.queue
BFS queue.
|
protected Set<Node> |
BFS.sourceSet
BFS starts from source nodes.
|
protected Set<Node> |
BFS.stopSet
BFS will not further traverse neighbors of any node in the stopSet.
|
Modifier and Type | Method and Description |
---|---|
protected int |
BFS.getColor(Node node)
Gets color tag of the node
|
protected boolean |
BFS.isEquivalentInTheSet(Node node,
boolean direction,
Set<Node> set)
Checks if an equivalent of the given node is in the set.
|
protected boolean |
BFS.isEquivalentInTheSet(Node node,
Set<Node> set)
Checks if an equivalent of the given node is in the set.
|
boolean |
CycleBreaker.isSafe(Node node,
Edge edge)
Checks whether an edge is on an unwanted cycle.
|
protected void |
BFS.labelEquivRecursive(Node node,
boolean up,
int dist,
boolean enqueue,
boolean head)
Labels equivalent nodes recursively.
|
protected void |
BFS.processNode(Node current)
Processes a node.
|
protected boolean |
CycleBreaker.processNode2(Node current)
Continue the search from the node.
|
protected void |
BFS.setColor(Node node,
int color)
Sets color tag
|
Modifier and Type | Method and Description |
---|---|
protected boolean |
BFS.isEquivalentInTheSet(Node node,
boolean direction,
Set<Node> set)
Checks if an equivalent of the given node is in the set.
|
protected boolean |
BFS.isEquivalentInTheSet(Node node,
Set<Node> set)
Checks if an equivalent of the given node is in the set.
|
Constructor and Description |
---|
BFS(Set<Node> sourceSet,
Set<Node> stopSet,
Direction direction,
int limit)
Constructor with all parameters.
|
BFS(Set<Node> sourceSet,
Set<Node> stopSet,
Direction direction,
int limit)
Constructor with all parameters.
|
CommonStreamQuery(Collection<Set<Node>> sourceStateSet,
Direction direction,
int limit)
Constructor for Common Stream with Entity States.
|
CommonStreamQuery(Set<Node> sourceNodeSet,
Direction direction,
int limit)
Constructor for Common Stream with Selected Nodes.
|
CycleBreaker(Set<GraphObject> result,
Set<Node> ST,
int limit)
Constructor with the objects in the result, source and target nodes, and search limit.
|
NeighborhoodQuery(Set<Node> sourceNodes,
Direction direction,
int limit)
Constructor with parameters.
|
PathsBetweenQuery(Collection<Set<Node>> sourceSet,
int limit)
Constructor with parameters
|
PathsFromToQuery(Set<Node> sourceSet,
Set<Node> targetSet,
LimitType limitType,
int stopDistance,
boolean strict)
Constructor with parameters.
|
PathsFromToQuery(Set<Node> sourceSet,
Set<Node> targetSet,
LimitType limitType,
int stopDistance,
boolean strict)
Constructor with parameters.
|
Prune(Set<GraphObject> result,
Set<Node> ST)
Constructor with the input.
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractNode |
Modifier and Type | Field and Description |
---|---|
protected Set<Node> |
AbstractNode.banned
For saying: "If the algorithm traverses this node, it cannot traverse those others".
|
protected Set<Node> |
AbstractNode.lowerEquivalent
If there are equivalent nodes in the graph, and they have a hierarchy, like an homology node
and members, then this set is for the child equivalents of this node.
|
protected Set<Node> |
AbstractNode.upperEquivalent
If there are equivalent nodes in the graph, and they have a hierarchy, like an homology node
and members, then this set is for the parent equivalents of this node.
|
Modifier and Type | Method and Description |
---|---|
Node |
Edge.getSourceNode() |
Node |
AbstractEdge.getSourceNode() |
Node |
Edge.getTargetNode() |
Node |
AbstractEdge.getTargetNode() |
abstract Node |
AbstractGraph.wrap(Object obj)
Creates the wrapper for the given object.
|
Modifier and Type | Method and Description |
---|---|
Set<Node> |
AbstractNode.getBanned() |
Collection<Node> |
Node.getLowerEquivalent() |
Collection<Node> |
AbstractNode.getLowerEquivalent() |
Collection<Node> |
Node.getUpperEquivalent() |
Collection<Node> |
AbstractNode.getUpperEquivalent() |
Map<Object,Node> |
Graph.getWrapperMap(Set<?> objects)
Gets a map from objects to their wrappers.
|
Set<Node> |
Graph.getWrapperSet(Set<?> objects)
Gets the set of wrappers for the given wrapped object set.
|
Modifier and Type | Method and Description |
---|---|
void |
AbstractNode.setBanned(Set<Node> banned) |
Constructor and Description |
---|
AbstractEdge(Node source,
Node target,
Graph graph)
Edges should know their source and target nodes, and their graph.
|
Modifier and Type | Class and Description |
---|---|
class |
ControlWrapper
Wrapper for the Control class.
|
class |
ConversionWrapper
Wrapper for the Conversion class.
|
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 |
---|---|
Node |
GraphL3.wrap(Object obj)
This method creates a wrapper for every wrappable L3 element.
|
Modifier and Type | Method and Description |
---|---|
Collection<Node> |
PhysicalEntityWrapper.getLowerEquivalent() |
Collection<Node> |
EventWrapper.getLowerEquivalent()
Events do not have equivalent objects.
|
Collection<Node> |
ControlWrapper.getLowerEquivalent()
Control cannot have an equivalent.
|
Collection<Node> |
PhysicalEntityWrapper.getUpperEquivalent() |
Collection<Node> |
EventWrapper.getUpperEquivalent()
Events do not have equivalent objects.
|
Collection<Node> |
ControlWrapper.getUpperEquivalent()
Control cannot have an equivalent.
|
Map<Object,Node> |
GraphL3.getWrapperMap(Set<?> objects)
Gets an element-to-wrapper map for the given elements.
|
Set<Node> |
GraphL3.getWrapperSet(Set<?> objects)
Gets wrappers of given elements
|
Constructor and Description |
---|
EdgeL3(Node source,
Node target,
Graph graph)
Constructor with source and target nodes, and the owner graph.
|
Modifier and Type | Class and Description |
---|---|
class |
InteractionWrapper
Wrapper for Interaction class, excluding Control objects.
|
Modifier and Type | Method and Description |
---|---|
Node |
GraphL3Undirected.wrap(Object obj)
This method creates a wrapper for every wrappable L3 element.
|
Modifier and Type | Method and Description |
---|---|
Collection<Node> |
PhysicalEntityWrapper.getLowerEquivalent() |
Collection<Node> |
EventWrapper.getLowerEquivalent()
Events do not have equivalent objects.
|
Collection<Node> |
ControlWrapper.getLowerEquivalent()
Control cannot have an equivalent.
|
Collection<Node> |
PhysicalEntityWrapper.getUpperEquivalent() |
Collection<Node> |
EventWrapper.getUpperEquivalent()
Events do not have equivalent objects.
|
Collection<Node> |
ControlWrapper.getUpperEquivalent()
Control cannot have an equivalent.
|
Map<Object,Node> |
GraphL3Undirected.getWrapperMap(Set<?> objects)
Gets an element-to-wrapper map for the given elements.
|
Set<Node> |
GraphL3Undirected.getWrapperSet(Set<?> objects)
Gets wrappers of given elements
|
Constructor and Description |
---|
EdgeL3(Node source,
Node target,
Graph graph)
Constructor with source and target nodes, and the owner graph.
|
Copyright © 2015 BioPAX. All rights reserved.