Java tutorial
/** * Licensed to the Apache Software Foundation (ASF) under one or more contributor license agreements. See the NOTICE * file distributed with this work for additional information regarding copyright ownership. The ASF licenses this file * to you 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. * * @author dmyersturnbull */ package org.structnetalign.merge; import java.util.ArrayList; import java.util.Collection; import java.util.Collections; import java.util.Comparator; import java.util.Iterator; import java.util.List; import java.util.NavigableMap; import java.util.NavigableSet; import java.util.Set; import java.util.TreeMap; import java.util.TreeSet; import java.util.concurrent.Callable; import org.apache.commons.collections.CollectionUtils; import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; import org.structnetalign.CleverGraph; import org.structnetalign.HomologyEdge; import org.structnetalign.util.NetworkUtils; /** * A job that takes as input a graph (or subgraph) and returns a list of degenerate vertex sets. * @author dmyersturnbull */ public class BronKerboschMergeJob implements Callable<List<NavigableSet<Integer>>> { private static final Logger logger = LogManager.getLogger("org.structnetalign"); private CleverGraph graph; private int index; private static String hashVertexInteractions(Collection<Integer> vertexInteractionNeighbors) { return NetworkUtils.hash(vertexInteractionNeighbors); } public BronKerboschMergeJob(CleverGraph graph, int index) { super(); this.graph = graph; this.index = index; } @Override public List<NavigableSet<Integer>> call() throws Exception { logger.info("Searching for cliques on job " + index + " containing " + graph.getVertexCount() + " vertices and " + graph.getHomologyCount() + " homology edges"); // find the cliques BronKerboschCliqueFinder<Integer, HomologyEdge> finder = new BronKerboschCliqueFinder<>(); // these cliques are ordered from largest to smallest Collection<Set<Integer>> cliques = finder.transform(graph.getHomology()); // just report the cliques we're using logger.info("Job " + index + ": " + "Found " + cliques.size() + " maximal cliques"); int i = 1; for (Set<Integer> clique : cliques) { logger.debug("Job " + index + ": " + "Clique " + i + ": " + clique); i++; } // partition the cliques by sets of interactions // we call these (maximal) degenerate sets List<NavigableSet<Integer>> simpleDegenerateSets = new ArrayList<NavigableSet<Integer>>(); for (Set<Integer> clique : cliques) { NavigableMap<String, NavigableSet<Integer>> degenerateSetMap = new TreeMap<>(); for (int v : clique) { Collection<Integer> neighbors = graph.getInteractionNeighbors(v); String hash = hashVertexInteractions(neighbors); NavigableSet<Integer> degenerateSet = degenerateSetMap.get(hash); if (degenerateSet == null) { degenerateSet = new TreeSet<>(); degenerateSetMap.put(hash, degenerateSet); } degenerateSet.add(v); logger.trace("Job " + index + ": " + "Found " + hash + " --> " + degenerateSetMap.get(hash)); } for (NavigableSet<Integer> set : degenerateSetMap.values()) { simpleDegenerateSets.add(set); } } /* * Now sort the degenerate sets from largest to smallest. * Take into account the edge case where the sizes are the same. */ Comparator<NavigableSet<Integer>> comparator = new Comparator<NavigableSet<Integer>>() { @Override public int compare(NavigableSet<Integer> clique1, NavigableSet<Integer> clique2) { if (CollectionUtils.isEqualCollection(clique1, clique2)) return 0; if (clique1.size() < clique2.size()) { return 1; } else if (clique1.size() > clique2.size()) { return -1; } else { Iterator<Integer> iter1 = clique1.iterator(); Iterator<Integer> iter2 = clique2.iterator(); while (iter1.hasNext()) { // we know they're the same size int v1 = iter1.next(); int v2 = iter2.next(); if (v1 < v2) { return 1; } else if (v1 > v2) { return -1; } } } // they're the same throughout, so they're equal return 0; } }; List<NavigableSet<Integer>> sortedDegenerateSets = new ArrayList<>(simpleDegenerateSets.size()); sortedDegenerateSets.addAll(simpleDegenerateSets); Collections.sort(sortedDegenerateSets, comparator); /* * Now we want to return only the maximal maximal degenerate sets. */ TreeSet<String> verticesAlreadyUsed = new TreeSet<String>(); List<NavigableSet<Integer>> finalDegenerateSets = new ArrayList<>(sortedDegenerateSets.size()); int nTrivial = 0; int nWeak = 0; // a degenerate set is weak if it contains a vertex that is added first forcliques: for (NavigableSet<Integer> set : sortedDegenerateSets) { // discard trivial degenerate sets if (set.size() < 2) { nTrivial++; continue; } // verify that we haven't already used any vertex in this degenerate set for (int v : set) { String hash = NetworkUtils.hash(v); // use MD5 for safety if (verticesAlreadyUsed.contains(hash)) { // discard this degenerate set and do NOT say we've used any of these vertices nWeak++; continue forcliques; } } // we haven't used any vertex in this degenerate set // now add all of these vertices // do NOT add before, or we'll add vertices we haven't used yet for (int v : set) { String hash = NetworkUtils.hash(v); verticesAlreadyUsed.add(hash); } finalDegenerateSets.add(set); // keep this degenerate set } logger.info("Job " + index + ": " + "Found " + finalDegenerateSets.size() + " strong nontrivial maximal degenerate sets found (" + nTrivial + " trivial and " + nWeak + " weak)"); return finalDegenerateSets; } }