how to test PageRank algorithm for jung?

Question

I'm trying to test Pagerank algorithm for jung but it seems that I have a problem in doing it. I have created a weighted and indirect graph with this portion of code:

private static String getId(int nodeId) 
    {
        return "Node " + nodeId;
    }

    private static String getId(int nodeId, int neighborId) 
    {
        return "Edge " + nodeId + " -> " + neighborId;
    }


public static Graph<String, Integer> createGraphForPageRank(String graphId, double[][] adjacencyMatrix) 
        {
         Graph<String,Integer> g = new UndirectedSparseGraph <String,Integer>();

            for (int nodeId = 0; nodeId < adjacencyMatrix.length; nodeId++)
                g.addVertex(getId(nodeId));



            for (int nodeId = 0; nodeId < adjacencyMatrix.length; nodeId++)
                for (int neighborId = 0; neighborId < adjacencyMatrix[nodeId].length; neighborId++)
                    if (adjacencyMatrix[nodeId][neighborId]>0)

                     g.addEdge(neighborId,getId(nodeId),getId(neighborId));



            return(g);

       }

then, in the main class, I used this code to test pagerank on my graph:

double[][] adjacencyMatrixForPageRank =FileHelper.calculateSimilaritySentences("E:\\my workspace\\TweetsAnalyser2\\outputFiles\\splittedStemmeredFile-1.txt","");
    Graph<String,Integer> g2=FileHelper.createGraphForPageRank("MyGraphForPageRank",adjacencyMatrixForPageRank);
    PageRank<String,Integer> pagerank= new PageRank<String,Integer>(g2,alpha1);
    pagerank.initialize(); 
    pagerank.setTolerance(0.000001);
    pagerank.setMaxIterations(200);
    pagerank.evaluate();

but eclipse generates this error: Exception in thread "main" java.lang.IllegalArgumentException: edge 4 already exists in this graph with endpoints and cannot be added with endpoints at edu.uci.ics.jung.graph.AbstractGraph.getValidatedEndpoints(AbstractGraph.java:93) at edu.uci.ics.jung.graph.UndirectedSparseGraph.addEdge(UndirectedSparseGraph.java:64) at edu.uci.ics.jung.graph.AbstractGraph.addEdge(AbstractGraph.java:60) at edu.uci.ics.jung.graph.AbstractGraph.addEdge(AbstractGraph.java:55) at com.tweets.helpers.FileHelper.createGraphForPageRank(FileHelper.java:1496) at com.tweets.test.Main.main(Main.java:105)

I know that there is a problem with the graph creation, but I don't know how to solve it!!!! Can someone please help me.

Answer 1

The problem seems to be you defined an undirected graph , and you add the same node twice to it. One in the form of (x,y) , and one in the form of (y,x) - for the same values of x and y .

Solve it by iterating in your inner loop only from the nodeID , and not from 0:

for (int nodeId = 0; nodeId < adjacencyMatrix.length; nodeId++)
   for (int neighborId = nodeId; neighborId < adjacencyMatrix[nodeId].length; neighborId++)
                         ^^^

In addition:

g.addEdge(neighborId,getId(nodeId),getId(neighborId));

your edge ID is not unique, which I think it should be, but I am not familiar enough with the API to be sure.

Answer 2

There are a couple of problems that led to your error.

(1) As @amit observed, since your graph is undirected, you don't need to add an edge from x to y and another one from y to x. However, if you have the following code:

g.addEdge(edgeId, x, y);
...
g.addEdge(edgeId, y, x);

The second call to addEdge() will be silently ignored, which is fine.

(2) You can't reuse edge IDs for different sets of incident nodes; that's what that error message is telling you. Edge objects (and node objects) are analogous to map keys: they have to be unique.

Your code suggests that you don't actually care about the edge objects per se, which means that you can just create a Graph<String, Object> and do this when you add an edge:

g.addEdge(new Object(), x, y);

This will get easier in JUNG in its next version, which I hope will be out in a few months. :)