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]);
}
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));
}
