Package org.biopax.paxtools.query.algorithm

Class CycleBreaker

java.lang.Object

org.biopax.paxtools.query.algorithm.BFS

org.biopax.paxtools.query.algorithm.CycleBreaker

public class CycleBreaker
extends BFS

When an algorithm searches for a paths between multiple source nodes, or from a source to a target node (source and targets may overlap), sometimes there comes paths from and to the same node, i.e cycles. When we want to avoid these cases this class can be used to remove those cycles in the result set.

Author:

Ozgun Babur

Field Summary

Fields inherited from class org.biopax.paxtools.query.algorithm.BFS

BACKWARD, BLACK, colors, direction, dist, DOWNWARD, FORWARD, GRAY, limit, queue, sourceSet, stopSet, UPWARD, WHITE

Constructor Summary

Constructors

Constructor	Description
CycleBreaker(Set<GraphObject> result, Set<Node> ST, int limit)	Constructor with the objects in the result, source and target nodes, and search limit.

Method Summary

Modifier and Type	Method	Description
void	breakCycles()	Run the algorithm.
boolean	isSafe(Node node, Edge edge)	Checks whether an edge is on an unwanted cycle.
protected boolean	processNode2(Node current)	Continue the search from the node.

Methods inherited from class org.biopax.paxtools.query.algorithm.BFS

getColor, getLabel, initMaps, isEquivalentInTheSet, isEquivalentInTheSet, labelEquivRecursive, processNode, run, setColor, setLabel

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

CycleBreaker

public CycleBreaker(Set<GraphObject> result,
 Set<Node> ST,
 int limit)

Constructor with the objects in the result, source and target nodes, and search limit.

Parameters:

result - Result set to search in

ST - Source and target nodes

limit - Search limit

Method Details

breakCycles

public void breakCycles()

Run the algorithm.

isSafe

public boolean isSafe(Node node,
 Edge edge)

Checks whether an edge is on an unwanted cycle.

Parameters:

node - Node that the edge is bound

edge - The edge to check

Returns:

True if no cycle is detected, false otherwise

processNode2

protected boolean processNode2(Node current)

Continue the search from the node. 2 is added because a name clash in the parent class.

Parameters:

current - The node to traverse

Returns:

False if a cycle is detected