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.
|
Modifier and Type | Method and Description |
---|---|
static Set<BioPAXElement> |
QueryExecuter.runCommonStream(Set<BioPAXElement> sourceSet,
Model model,
Direction direction,
int limit,
Filter... filters)
Gets the elements in the common upstream or downstream of the seed
|
static Set<BioPAXElement> |
QueryExecuter.runCommonStreamWithPOI(Set<BioPAXElement> sourceSet,
Model model,
Direction direction,
int limit,
Filter... filters)
First finds the common stream, then completes it with the paths between seed and common
stream.
|
static Set<BioPAXElement> |
QueryExecuter.runNeighborhood(Set<BioPAXElement> sourceSet,
Model model,
int limit,
Direction direction,
Filter... filters)
Gets neighborhood of the source set.
|
Modifier and Type | Field and Description |
---|---|
protected Direction |
BFS.direction
Whether the direction is FORWARD, it is REVERSE otherwise.
|
Modifier and Type | Method and Description |
---|---|
static Direction |
Direction.valueOf(String name)
Returns the enum constant of this type with the specified name.
|
static Direction[] |
Direction.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
Constructor and Description |
---|
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.
|
NeighborhoodQuery(Set<Node> sourceNodes,
Direction direction,
int limit)
Constructor with parameters.
|
Copyright © 2015 BioPAX. All rights reserved.