public Graph neighbourhoodGraph(int nnodes[], int hops) { PrimaryHashMap<Integer, String> nodes; PrimaryHashMap<String, Integer> nodesReverse; try { File auxFile = File.createTempFile("graph-maps-" + System.currentTimeMillis(), "aux"); auxFile.deleteOnExit(); RecordManager recMan = RecordManagerFactory.createRecordManager(auxFile.getAbsolutePath()); nodes = recMan.hashMap("nodes"); nodesReverse = recMan.hashMap("nodesReverse"); } catch (IOException ex) { throw new Error(ex); } nodes.clear(); nodesReverse.clear(); WeightedArcSet list1 = new WeightedArcSet(); Int2IntAVLTreeMap map = new Int2IntAVLTreeMap(); IntSet set = new IntLinkedOpenHashSet(); int numIterators = 100; Constructor[] cons = WeightedArc.class.getDeclaredConstructors(); for (int i = 0; i < cons.length; i++) cons[i].setAccessible(true); for (int n : nnodes) map.put(n, 0); NodeIterator its[] = new NodeIterator[numIterators]; int itNum[] = new int[numIterators]; for (int n = 0; n < its.length; n++) { its[n] = nodeIterator(); itNum[n] = 0; } while (map.size() != 0) { Integer node = 0; for (int n = 0; n < its.length; n++) if (itNum[n] <= node) node = itNum[n]; node = map.tailMap(node).firstKey(); if (node == null) map.firstKey(); NodeIterator it = null; Integer aux1 = 0; int iit = 0; for (int n = 0; n < its.length; n++) { if (!its[n].hasNext()) { its[n] = nodeIterator(); itNum[n] = 0; } if (itNum[n] == node) { it = its[n]; aux1 = itNum[n]; iit = 0; break; } if (itNum[n] < node && itNum[n] >= aux1) { it = its[n]; aux1 = itNum[n]; iit = n; } } if (it == null) { its[0] = nodeIterator(); itNum[0] = 0; it = its[0]; } while (it != null && (aux1 = it.nextInt()) != null && aux1 >= 0 && aux1 < node) {} itNum[iit] = aux1 + 1; Integer aux2 = null; ArcLabelledNodeIterator.LabelledArcIterator suc = it.successors(); while ((aux2 = suc.nextInt()) != null && aux2 >= 0 && (aux2 < graph.numNodes())) try { if (commit++ % COMMIT_SIZE == 0) { try { nodes.getRecordManager().commit(); } catch (IOException e) { throw new Error(e); } try { nodesReverse.getRecordManager().commit(); } catch (IOException e) { throw new Error(e); } } if (!nodesReverse.containsKey(this.nodes.get(aux1))) { nodes.put(nodes.size(), this.nodes.get(aux1)); nodesReverse.put(this.nodes.get(aux1), nodesReverse.size()); } if (!nodesReverse.containsKey(this.nodes.get(aux2))) { nodes.put(nodes.size(), this.nodes.get(aux2)); nodesReverse.put(this.nodes.get(aux2), nodesReverse.size()); } int aaux1 = nodesReverse.get(this.nodes.get(aux1)); int aaux2 = nodesReverse.get(this.nodes.get(aux2)); WeightedArc arc1 = (WeightedArc) cons[0].newInstance(aaux1, aaux2, suc.label().getFloat()); list1.add(arc1); if (map.get(node) < hops) { if (!set.contains(aux1) && (map.get(aux1) == null || map.get(aux1) > map.get(node) + 1)) map.put(aux1.intValue(), map.get(node) + 1); if (!set.contains(aux2) && (map.get(aux2) == null || map.get(aux2) > map.get(node) + 1)) map.put(aux2.intValue(), map.get(node) + 1); } } catch (Exception ex) { ex.printStackTrace(); throw new Error(ex); } ArcLabelledNodeIterator.LabelledArcIterator anc = it.ancestors(); while ((aux2 = anc.nextInt()) != null && aux2 >= 0 && (aux2 < graph.numNodes())) try { if (commit++ % COMMIT_SIZE == 0) { try { nodes.getRecordManager().commit(); } catch (IOException e) { throw new Error(e); } try { nodesReverse.getRecordManager().commit(); } catch (IOException e) { throw new Error(e); } } if (!nodesReverse.containsKey(this.nodes.get(aux1))) { nodes.put(nodes.size(), this.nodes.get(aux1)); nodesReverse.put(this.nodes.get(aux1), nodesReverse.size()); } if (!nodesReverse.containsKey(this.nodes.get(aux2))) { nodes.put(nodes.size(), this.nodes.get(aux2)); nodesReverse.put(this.nodes.get(aux2), nodesReverse.size()); } int aaux1 = nodesReverse.get(this.nodes.get(aux1)); int aaux2 = nodesReverse.get(this.nodes.get(aux2)); WeightedArc arc1 = (WeightedArc) cons[0].newInstance(aaux2, aaux1, anc.label().getFloat()); list1.add(arc1); if (map.get(node) < hops) { if (!set.contains(aux1) && (map.get(aux1) == null || map.get(aux1) > map.get(node) + 1)) map.put(aux1.intValue(), map.get(node) + 1); if (!set.contains(aux2) && (map.get(aux2) == null || map.get(aux2) > map.get(node) + 1)) map.put(aux2.intValue(), map.get(node) + 1); } } catch (Exception ex) { ex.printStackTrace(); throw new Error(ex); } map.remove(node); set.add(node); } Graph newGraph = new Graph(list1.toArray(new WeightedArc[0])); newGraph.nodes.clear(); newGraph.nodesReverse.clear(); newGraph.nodes = nodes; newGraph.nodesReverse = nodesReverse; return newGraph; }
public Graph neighbourhoodGraph(String nodes[], int hops) { int nnodes[] = new int[nodes.length]; for (int i = 0; i < nodes.length; i++) nnodes[i] = nodesReverse.get(nodes[i]); return neighbourhoodGraph(nnodes, hops); }
public String node(int nodeNum) { return nodes.get(nodeNum); }
public int node(String node) { return nodesReverse.get(node); }
public Graph(String file) throws IOException { org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger("it.unimi.dsi.webgraph.ImmutableGraph"); logger.setLevel(org.apache.log4j.Level.FATAL); try { File auxFile = File.createTempFile("graph-maps-" + System.currentTimeMillis(), "aux"); auxFile.deleteOnExit(); RecordManager recMan = RecordManagerFactory.createRecordManager(auxFile.getAbsolutePath()); nodes = recMan.hashMap("nodes"); nodesReverse = recMan.hashMap("nodesReverse"); } catch (IOException ex) { throw new Error(ex); } nodes.clear(); nodesReverse.clear(); Constructor[] cons = WeightedArc.class.getDeclaredConstructors(); for (int i = 0; i < cons.length; i++) cons[i].setAccessible(true); String aux = null; Float weight = (float) 1.0; WeightedArcSet list = new WeightedArcSet(); BufferedReader br; try { br = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(file)))); } catch (Exception ex) { br = new BufferedReader(new FileReader(file)); } while ((aux = br.readLine()) != null) try { if (commit++ % COMMIT_SIZE == 0) { commit(); list.commit(); } String parts[] = aux.split("\t"); String l1 = new String(parts[0]); String l2 = new String(parts[1]); if (!nodesReverse.containsKey(l1)) { nodesReverse.put(l1, nodesReverse.size()); nodes.put(nodes.size(), l1); } if (!nodesReverse.containsKey(l2)) { nodesReverse.put(l2, nodesReverse.size()); nodes.put(nodes.size(), l2); } if (parts.length == 3) weight = new Float(parts[2]); list.add( (WeightedArc) cons[0].newInstance(nodesReverse.get(l1), nodesReverse.get(l2), weight)); } catch (Exception ex) { throw new Error(ex); } this.graph = new WeightedBVGraph(list.toArray(new WeightedArc[0])); br.close(); list = new WeightedArcSet(); br = new BufferedReader(new FileReader(file)); while ((aux = br.readLine()) != null) try { if (commit++ % COMMIT_SIZE == 0) { commit(); list.commit(); } String parts[] = aux.split("\t"); String l1 = new String(parts[0]); String l2 = new String(parts[1]); if (parts.length == 3) weight = new Float(parts[2]); list.add( (WeightedArc) cons[0].newInstance(nodesReverse.get(l2), nodesReverse.get(l1), weight)); } catch (Exception ex) { throw new Error(ex); } br.close(); this.reverse = new WeightedBVGraph(list.toArray(new WeightedArc[0])); numArcs = list.size(); iterator = nodeIterator(); try { File auxFile = File.createTempFile("graph" + System.currentTimeMillis(), "aux"); auxFile.deleteOnExit(); String basename = auxFile.getAbsolutePath(); store(basename); } catch (IOException ex) { throw new Error(ex); } commit(); }