Package org.biopax.paxtools.query.algorithm

package org.biopax.paxtools.query.algorithm

This package contains the SIF rules for BioPAX Level 3.

Related Packages

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.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!

Class	Description
BFS	Implements breadth-first search.
CommonStreamQuery	Searches common downstream or common upstream of a specified set of entities based on the given direction within the boundaries of a specified length limit.
CycleBreaker	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.
Direction	Direction is used for specifying upstream, downstream or both.
LimitType	Specifies whether the length limit is a normal limit or shortest_plus_k limit.
NeighborhoodQuery	Searches the neighborhood of given source set of nodes
PathsBetweenQuery	Finds the paths between the specified source set of states within the boundaries of a specified length limit.
PathsFromToQuery	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.
Prune	This algorithm is used internally by PathsBetween and PathsFromTo algorithms.