Refactor the TopologyManager:

 * Moved the Shortest Path computations to new class ShortestPath
   inside file  topology/ShortestPath.java
 * Moved the topology-related state to new class Topology
   inside file  topology/Topology.java
 * Renamed/cleanup the TopologyManager API:
   - prepareShortestPathTopo() -> newDatabaseTopology()
   - dropShortestPathTopo() -> dropTopology()
   - getTopoShortestPath() -> getTopologyShortestPath()
   - getShortestPath() -> getDatabaseShortestPath()
diff --git a/src/main/java/net/onrc/onos/ofcontroller/topology/Topology.java b/src/main/java/net/onrc/onos/ofcontroller/topology/Topology.java
new file mode 100644
index 0000000..a2f2c21
--- /dev/null
+++ b/src/main/java/net/onrc/onos/ofcontroller/topology/Topology.java
@@ -0,0 +1,174 @@
+package net.onrc.onos.ofcontroller.topology;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import net.onrc.onos.graph.GraphDBOperation;
+import net.onrc.onos.ofcontroller.core.INetMapTopologyObjects.ISwitchObject;
+import net.onrc.onos.ofcontroller.core.ISwitchStorage.SwitchState;
+
+import org.openflow.util.HexString;
+
+import com.tinkerpop.blueprints.Direction;
+import com.tinkerpop.blueprints.Vertex;
+
+/**
+ * A class for storing Node and Link information for fast computation
+ * of shortest paths.
+ */
+class Node {
+    /**
+     * A class for storing Link information for fast computation of shortest
+     * paths.
+     */
+    class Link {
+	public Node me;			// The node this link originates from
+	public Node neighbor;		// The neighbor node on the other side
+	public short myPort;		// Local port number for the link
+	public short neighborPort;	// Neighbor port number for the link
+
+	/**
+	 * Link constructor.
+	 *
+	 * @param me the node this link originates from.
+	 * @param the neighbor node on the other side of the link.
+	 * @param myPort local port number for the link.
+	 * @param neighborPort neighrobr port number for the link.
+	 */
+	public Link(Node me, Node neighbor, short myPort, short neighborPort) {
+	    this.me = me;
+	    this.neighbor = neighbor;
+	    this.myPort = myPort;
+	    this.neighborPort = neighborPort;
+	}
+    };
+
+    public long nodeId;			// The node ID
+    public HashMap<Short, Link> links;	// The links originating from this node
+
+    /**
+     * Node constructor.
+     *
+     * @param nodeId the node ID.
+     */
+    public Node(long nodeId) {
+	this.nodeId = nodeId;
+	links = new HashMap<Short, Link>();
+    }
+
+    /**
+     * Add a neighbor.
+     *
+     * A new link to the neighbor will be created. 
+     *
+     * @param neighbor the neighbor to add.
+     * @param myPort the local port number for the link to the neighbor.
+     * @param neighborPort the neighbor port number for the link.
+     */
+    public void addNeighbor(Node neighbor, short myPort, short neighborPort) {
+	Link link = new Link(this, neighbor, myPort, neighborPort);
+	links.put(myPort, link);
+    }
+};
+
+/**
+ * A class for storing topology information.
+ */
+public class Topology {
+    private Map<Long, Node> nodesMap;	// The dpid->Node mapping
+
+    public Topology() {
+	nodesMap = new HashMap<Long, Node>();
+    }
+
+    /**
+     * Get a node for a give Node ID.
+     *
+     * @param nodeId the Node ID to use.
+     * @return the corresponding Node if found, otherwise null.
+     */
+    Node getNode(long nodeId) {
+	return nodesMap.get(nodeId);
+    }
+
+    /**
+     * Read topology state from the database.
+     *
+     * @param dbHandler the Graph Database handler to use.
+     */
+    public void readFromDatabase(GraphDBOperation dbHandler) {
+	//
+	// Fetch the relevant info from the Switch and Port vertices
+	// from the Titan Graph.
+	//
+	Iterable<ISwitchObject> activeSwitches = dbHandler.getActiveSwitches();
+	for (ISwitchObject switchObj : activeSwitches) {
+	    Vertex nodeVertex = switchObj.asVertex();
+	    //
+	    // The Switch info
+	    //
+	    String nodeDpid = nodeVertex.getProperty("dpid").toString();
+	    long nodeId = HexString.toLong(nodeDpid);
+	    Node me = nodesMap.get(nodeId);
+	    if (me == null) {
+		me = new Node(nodeId);
+		nodesMap.put(nodeId, me);
+	    }
+
+	    //
+	    // The local Port info
+	    //
+	    for (Vertex myPortVertex : nodeVertex.getVertices(Direction.OUT, "on")) {
+		// Ignore inactive ports
+		if (! myPortVertex.getProperty("state").toString().equals("ACTIVE"))
+		    continue;
+
+		short myPort = 0;
+		Object obj = myPortVertex.getProperty("number");
+		if (obj instanceof Short) {
+		    myPort = (Short)obj;
+		} else if (obj instanceof Integer) {
+		    Integer int_nodeId = (Integer)obj;
+		    myPort = int_nodeId.shortValue();
+		}
+
+		//
+		// The neighbor Port info
+		//
+		for (Vertex neighborPortVertex : myPortVertex.getVertices(Direction.OUT, "link")) {
+		    // Ignore inactive ports
+		    if (! neighborPortVertex.getProperty("state").toString().equals("ACTIVE"))
+			continue;
+
+		    short neighborPort = 0;
+		    obj = neighborPortVertex.getProperty("number");
+		    if (obj instanceof Short) {
+			neighborPort = (Short)obj;
+		    } else if (obj instanceof Integer) {
+			Integer int_nodeId = (Integer)obj;
+			neighborPort = int_nodeId.shortValue();
+		    }
+		    //
+		    // The neighbor Switch info
+		    //
+		    for (Vertex neighborVertex : neighborPortVertex.getVertices(Direction.IN, "on")) {
+			// Ignore inactive switches
+			String state = neighborVertex.getProperty("state").toString();
+			if (! state.equals(SwitchState.ACTIVE.toString()))
+			    continue;
+
+			String neighborDpid = neighborVertex.getProperty("dpid").toString();
+			long neighborId = HexString.toLong(neighborDpid);
+			Node neighbor = nodesMap.get(neighborId);
+			if (neighbor == null) {
+			    neighbor = new Node(neighborId);
+			    nodesMap.put(neighborId, neighbor);
+			}
+			me.addNeighbor(neighbor, myPort, neighborPort);
+		    }
+		}
+	    }
+	}
+	dbHandler.commit();
+    }
+}