Exemplo n.º 1
0
 protected void finalize() throws Throwable {
   super.finalize();
   nodes.clear();
   nodes.getRecordManager().commit();
   nodes.getRecordManager().close();
   nodesReverse.clear();
   nodesReverse.getRecordManager().commit();
   nodesReverse.getRecordManager().close();
 }
Exemplo n.º 2
0
 public Graph(WeightedBVGraph graph, String[] names) {
   org.apache.log4j.Logger logger =
       org.apache.log4j.Logger.getLogger("it.unimi.dsi.webgraph.ImmutableGraph");
   logger.setLevel(org.apache.log4j.Level.FATAL);
   if (names.length != graph.numNodes())
     throw new Error("Problem with the list of names for the nodes in the graph.");
   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);
   this.graph = graph;
   WeightedArcSet list = new WeightedArcSet();
   ArcLabelledNodeIterator it = graph.nodeIterator();
   while (it.hasNext()) {
     if (commit++ % COMMIT_SIZE == 0) {
       commit();
       list.commit();
     }
     Integer aux1 = it.nextInt();
     Integer aux2 = null;
     ArcLabelledNodeIterator.LabelledArcIterator suc = it.successors();
     while ((aux2 = suc.nextInt()) != null && aux2 >= 0 && (aux2 < graph.numNodes()))
       try {
         WeightedArc arc = (WeightedArc) cons[0].newInstance(aux2, aux1, suc.label().getFloat());
         list.add(arc);
         this.nodes.put(aux1, names[aux1]);
         this.nodes.put(aux2, names[aux2]);
         this.nodesReverse.put(names[aux1], aux1);
         this.nodesReverse.put(names[aux2], aux2);
       } catch (Exception ex) {
         throw new Error(ex);
       }
   }
   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();
 }
Exemplo n.º 3
0
 public void commit() {
   try {
     nodes.getRecordManager().commit();
   } catch (IOException e) {
     throw new Error(e);
   }
   try {
     nodesReverse.getRecordManager().commit();
   } catch (IOException e) {
     throw new Error(e);
   }
 };
Exemplo n.º 4
0
 public void writeIdToVertexMap(String filePath) {
   try {
     BufferedWriter bw = new BufferedWriter(new FileWriter(new File(filePath)));
     for (Entry<Integer, String> entry : nodes.entrySet()) {
       bw.write(entry.getKey() + " " + entry.getValue() + "\n");
     }
     bw.close();
   } catch (Exception ex) {
     ex.printStackTrace();
     System.exit(-1);
   }
 }
Exemplo n.º 5
0
 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;
 }
Exemplo n.º 6
0
 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);
 }
Exemplo n.º 7
0
 public void setNode(int nodeNum, String node) {
   nodes.put(nodeNum, node);
 }
Exemplo n.º 8
0
 public int node(String node) {
   return nodesReverse.get(node);
 }
Exemplo n.º 9
0
 public String node(int nodeNum) {
   return nodes.get(nodeNum);
 }
Exemplo n.º 10
0
 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();
 }
Exemplo n.º 11
0
 public Graph(BVGraph graph) {
   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);
   Integer aux1 = null;
   WeightedArcSet list = new WeightedArcSet();
   it.unimi.dsi.webgraph.NodeIterator it = graph.nodeIterator();
   while ((aux1 = it.nextInt()) != null) {
     LazyIntIterator suc = it.successors();
     Integer aux2 = null;
     while ((aux2 = suc.nextInt()) != null && aux2 >= 0 && (aux2 < graph.numNodes()))
       try {
         if (commit++ % COMMIT_SIZE == 0) {
           list.commit();
         }
         list.add((WeightedArc) cons[0].newInstance(aux1, aux2, (float) 1.0));
       } catch (Exception ex) {
         throw new Error(ex);
       }
   }
   this.graph = new WeightedBVGraph(list.toArray(new WeightedArc[0]));
   list = new WeightedArcSet();
   it = graph.nodeIterator();
   while ((aux1 = it.nextInt()) != null) {
     LazyIntIterator suc = it.successors();
     Integer aux2 = null;
     while ((aux2 = suc.nextInt()) != null && aux2 >= 0 && (aux2 < graph.numNodes()))
       try {
         if (commit++ % COMMIT_SIZE == 0) {
           commit();
           list.commit();
         }
         list.add((WeightedArc) cons[0].newInstance(aux2, aux1, (float) 1.0));
         this.nodes.put(aux1, "" + aux1);
         this.nodes.put(aux2, "" + aux2);
         this.nodesReverse.put("" + aux1, aux1);
         this.nodesReverse.put("" + aux2, aux2);
       } catch (Exception ex) {
         throw new Error(ex);
       }
   }
   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();
 }