Beispiel #1
0
 private Interaction[] filterInteractions(Interaction[] interactions) {
   LinkedList<Interaction> l = new LinkedList<Interaction>();
   for (int i = 0; i < interactions.length; i++) {
     Interaction inter = interactions[i];
     if (inter.getEdge() != null) {
       l.add(inter);
     }
   }
   return l.toArray(new Interaction[0]);
 }
Beispiel #2
0
  public ChIAPETNetwork getIntersection(Connection conn, long n1, long n2) throws Exception {
    _aid = 0;
    _iid = 0;

    InteractionData i1 = getAnchors(conn, n1);
    InteractionData i2 = getAnchors(conn, n2);

    TreeMap<Integer, LinkedList<Anchor>> n1anchors = i1.nodetoanchors;
    TreeMap<Integer, LinkedList<Anchor>> n2anchors = i2.nodetoanchors;

    String t1 = "chiapet.Nodes_" + n1;
    String t2 = "chiapet.Nodes_" + n2;

    String sql =
        "SELECT DISTINCT n1.id AS n1id, n2.id AS n2id FROM "
            + t1
            + " AS n1, "
            + t2
            + " AS n2 WHERE n1.chr=n2.chr AND n1.end >= n2.start AND n2.end >= n1.start";

    PreparedStatement ps = conn.prepareStatement(sql);

    NodeIntersection ni = new NodeIntersection();

    ResultSet rs = ps.executeQuery();
    while (rs.next()) {
      int n1id = rs.getInt(1);
      int n2id = rs.getInt(2);
      ni.addIntersection(n1id, n2id);
    }
    rs.close();
    ps.close();

    TreeMap<Integer, Integer> c1 = ni.getN1EdgeMapping();
    TreeMap<Integer, Integer> c2 = ni.getN2EdgeMapping();
    TreeMap<Integer, Node> nodes = ni.getOuterNodes(n1anchors, n2anchors);

    int[] counts = ni.getTotalIntersectingNodes();
    System.out.println("N1 Intersection: " + counts[0] + "N2 Intersection: " + counts[1]);

    String[] iedges = getIntersectionEdgeMap(conn, n1, toArray(c1), n2, toArray(c2));

    LinkedList<Edge> edges = new LinkedList<Edge>();
    int eid = 0;
    for (int i = 0; i < iedges.length; i++) {
      String cur = iedges[i];
      String[] split = cur.split("_");
      Node node1 = nodes.get(Integer.parseInt(split[0]));
      Node node2 = nodes.get(Integer.parseInt(split[1]));

      TreeMap<Integer, Interaction> interactions = new TreeMap<Integer, Interaction>();
      Anchor[] a = node1.getAnchors();
      for (int j = 0; j < a.length; j++) {
        Interaction inter = a[j].getInteraction();
        interactions.put(inter.getId(), inter);
      }
      a = node2.getAnchors();
      for (int j = 0; j < a.length; j++) {
        Interaction inter = a[j].getInteraction();
        interactions.put(inter.getId(), inter);
      }

      LinkedList<Interaction> edgeinteractions = new LinkedList<Interaction>();
      for (Iterator<Interaction> it = interactions.values().iterator(); it.hasNext(); ) {
        Interaction next = it.next();
        Anchor[] ia = next.getAnchors();
        Node a0n = ia[0].getNode();
        Node a1n = ia[1].getNode();
        if (a0n != null && a0n.equals(node1)) {
          if (a1n != null && a1n.equals(node2)) {
            edgeinteractions.add(next);
          }
        } else if (a0n != null && a0n.equals(node2)) {
          if (a1n != null && a1n.equals(node1)) {
            edgeinteractions.add(next);
          }
        }
      }
      if (edgeinteractions.size() > 1) {
        Edge e = new Edge(eid++, node1, node2, edgeinteractions.toArray(new Interaction[0]));
        for (Iterator<Interaction> it = edgeinteractions.iterator(); it.hasNext(); ) {
          it.next().setEdge(e);
        }
        edges.add(e);
        node1.addEdge(e);
        node2.addEdge(e);
      } else {
        throw new Exception("Expecting at least two interactions.");
      }
    }

    i1.anchors.addAll(i2.anchors);
    Anchor[] allanchors = i1.anchors.toArray(new Anchor[0]);
    i1.interactions.addAll(i2.interactions);
    Interaction[] allinteractions = i1.interactions.toArray(new Interaction[0]);

    Node[] nodearray = nodes.values().toArray(new Node[0]);
    Util u = new Util();
    nodearray = u.filterNodes(nodearray);

    ConnectedComponentExtraction cce = new ConnectedComponentExtraction();
    ConnectedComponent[] components = cce.getCCs(nodearray, allinteractions.length + 1, 0, 0);

    return new ChIAPETNetwork(
        filterAnchors(allanchors),
        filterInteractions(allinteractions),
        nodearray,
        edges.toArray(new Edge[0]),
        components,
        new NetworkParameters(-1, -1, -1, -1, -1, -1, -1, -1));
  }