org.biopax.paxtools.query.algorithm

Class PathsFromToQuery

java.lang.Object

org.biopax.paxtools.query.algorithm.PathsFromToQuery

public class PathsFromToQuery
extends Object

Finds the paths from a specified source set of states or entities to a specified target set of states or entities within the boundaries of a specified length limit. Takes source set, target set, type of distance limit, distance limit and strict value. Based on these parameters, the interactions within source set and within target set may be omitted and/or "shortest+k" may be used as length limit.

Author:

Ozgun Babur, Merve Cakir

Constructor Summary

Constructors

Constructor and Description
PathsFromToQuery(Set<Node> sourceSet, Set<Node> targetSet, LimitType limitType, int stopDistance, boolean strict) Constructor with parameters.

Method Summary

Modifier and Type	Method and Description
Set<GraphObject>	run() Executes the algorithm.

Methods inherited from class java.lang.Object

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

Constructor Detail

PathsFromToQuery

public PathsFromToQuery(Set<Node> sourceSet,
                        Set<Node> targetSet,
                        LimitType limitType,
                        int stopDistance,
                        boolean strict)

Constructor with parameters.

Parameters:

sourceSet - source set

targetSet - target set

limitType - normal limit or shortest + k type limit

stopDistance - search limit

strict - whether we want to extend and result path towards other source and targets

Method Detail

run

public Set<GraphObject> run()

Executes the algorithm.

Returns:

paths from sources to targets