I am having issues performing a copy of a Java ArrayList containing Node objects. These Nodes have a HashSet<Edge> of Edge objects that point to other Nodes in the ArrayList to form a directed graph. I need to make a copy of this ArrayList while maintaining the directed graph struture so that I can traverse the copied list just the same as I can with the original list. 
The problem is that my deep copy of the list is not "deep" enough. When I copy the array in the method (below) the copies of the Node objects still point to the Nodes in the original array and not in the new array. 
How could I change the cloneList function so that it performs a deep, deep copy of the array so that it maintains the directed graph structure in the output array?
public static ArrayList<Node> cloneList(ArrayList<Node> inList)
{
    ArrayList<Node> clonedList = new ArrayList<Node>(inList.size());
    for(Node aNode : inList)
    {
        clonedList.add(new Node(aNode));
    }
    return clonedList;
}
Node
import java.util.ArrayList;
import java.util.HashSet;
public class Node
{
    public String name;
    public HashSet<Edge> inEdges;
    public HashSet<Edge> outEdges;
    public ArrayList<String> deps;
    public Node(String name, ArrayList<String> deps) {
        this.name = name;
        inEdges = new HashSet<Edge>();
        outEdges = new HashSet<Edge>();
        this.deps = deps;
    }
    public Node addEdge(Node node){
        Edge e = new Edge(this, node);
        outEdges.add(e);
        node.inEdges.add(e);
        return this;
    }
    @Override
    public String toString() {
        return name;
    }
    //Used to copy a given node
    public Node(Node inNode)
    {
        this.name = inNode.name;
        this.inEdges = (HashSet<Edge>)inNode.inEdges.clone();
        this.outEdges = (HashSet<Edge>)inNode.outEdges.clone();
        this.deps = inNode.deps;
    }
}
Edge
public class Edge
{
    public Node from;
    public Node to;
    public Edge(Node from, Node to) {
        this.from = from;
        this.to = to;
    }
    @Override
    public boolean equals(Object obj) {
        Edge e = (Edge)obj;
        return e.from == from && e.to == to;
    }
}
 
     
    