// PathVisio, // a tool for data visualization and analysis using Biological Pathways // Copyright 2006-2011 BiGCaT Bioinformatics // // Licensed under the Apache License, Version 2.0 (the "License"); // you may not use this file except in compliance with the License. // You may obtain a copy of the License at // // http://www.apache.org/licenses/LICENSE-2.0 // // Unless required by applicable law or agreed to in writing, software // distributed under the License is distributed on an "AS IS" BASIS, // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. // See the License for the specific language governing permissions and // limitations under the License. // package org.pathvisio.core.gpmldiff; import java.util.HashSet; import java.util.Set; import org.pathvisio.core.model.PathwayElement; /** A search node, important part of the Dijkstra algorithm */ public class SearchNode { float cost; SearchNode parent; // pwy elts in use by parent search path, both old and new Set parentSet = new HashSet(); /** return the Parent of this SearchNode, which corresponds to the state of the Search engine when this node was opened */ public SearchNode getParent () { return parent; } PathwayElement oldElt; // corresponding elt in old doc public PathwayElement getOldElt() { return oldElt; } PathwayElement newElt; // corresponding elt in new doc public PathwayElement getNewElt() { return newElt; } /** Determine if a certain pwy elt is already in the ancestry of this Search Node. (old or new doesn't matter, as these sets never overlap) */ public boolean ancestryHasElt(PathwayElement elt) { return parentSet.contains (elt); } /** Create a new SearchNode. note: parent may be null for the first SearchNode. This will mark oldElt and newElt so they can be added only once. */ public SearchNode(SearchNode aParent, PathwayElement anOldElt, PathwayElement aNewElt, float aCost) { cost = aCost; parent = aParent; oldElt = anOldElt; newElt = aNewElt; assert (oldElt != null); assert (newElt != null); if (parent != null) { parentSet = parent.parentSet; } assert (!parentSet.contains(oldElt)); assert (!parentSet.contains(newElt)); parentSet.add (oldElt); parentSet.add (newElt); } }