package medusa.georgios.ClusteringAlgorithms;
/*
 * ClusteringMain.java
 *
 * Created on December 11, 2006, 5:45 PM
 */


import java.util.ArrayList;
import medusa.georgios.enhanced_mcl.MarkovClustering;


/**
 *
 * @author  Georgios
 */
public class ClusteringMain {

//    public static void runKmeans(ArrayList list, int num_of_clusters)
//    {
//       System.out.println("Running Kmeans");
//       List2Graph g = new List2Graph(list);
//       Kmeans km =  new Kmeans(num_of_clusters, g.A ,g.labels);
//       System.out.println(km.perform_and_get_results());
//    }
//     public static void runAffinity(ArrayList list)
//    {
//       System.out.println("Running Affinity Propagation");
//       Affinity_Propagation clustering = new Affinity_Propagation(list);
//       System.out.println("Number of clusters="+clustering.getNumberOfClusters());
//       System.out.println(clustering.Save_To_File("Affinity_Propagation.txt"));
//    }
//       public static void runMCL(ArrayList list)
//    {
////        System.out.println("Running Markov Clustering");
////        MarkovClustering mcl = new MarkovClustering(list);
////        System.out.println("Number of clusters="+mcl.getNumberOfClusters());
////        System.out.println(mcl.Save_To_File("MCL_results.txt"));
//    }
//
//         public static void runHCL(ArrayList list)
//    {
//          System.out.println("Running Hierarchical Clustering");
//          List2Graph g = new List2Graph(list);
//          int elements=g.labels.size();
//          HCL HCE2 = new  HCL(g.A,g.labels);
//          System.out.println(HCE2.get_NewickFormat_HCL());
//    }
//          public static void runNJ(ArrayList list)
//    {
//          System.out.println("Running Neighbor Joining");
//           Clustering_NJ_UPGMA tree = new Clustering_NJ_UPGMA(list,2);
//           System.out.println(tree.get_NewickFormat_NeighborJoining()+"\n\n");
//    }
//          public static void runUPGMA(ArrayList list)
//    {
//           System.out.println("Running Neighbor Joining");
//           Clustering_NJ_UPGMA tree = new Clustering_NJ_UPGMA(list,1);
//           System.out.println(tree.get_NewickFormat_UPGMA()+"\n\n");
//    }
//
//
//    public static void main(String args[]) {
//       ArrayList connections = new ArrayList();
//       connections.add("cat\that\t0.2");
//       connections.add("hat\tbat\t0.16");
//       connections.add("bat\tcat\t1.0");
//       connections.add("bat\tbit\t0.125");
//       connections.add("bit\tfit\t0.25");
//       connections.add("fit\thit\t0.5");
//       connections.add("hit\tbit\t0.16");
//
//      // runAffinity(connections);
//       //runMCL(connections);
//       //runKmeans(connections,2);
//       //runHCL(connections);
//       //runNJ(connections);
//       //runUPGMA(connections);
//
//      // System.exit(0);
//
//
//          String filename;
//          int elements=6;
//          filename="C:\\Documents and Settings\\Georgios\\Desktop\\test5.txt";
//
//          System.out.println("Run like");
//          System.out.println("java -jar jarfilename NJ filename elements");
//          System.out.println("java -jar jarfilename UPGMA filename elements");
//          System.out.println("java -jar jarfilename HCL filename elements");
//          System.out.println("java -jar jarfilename MCL filename elements");
//          System.out.println("java -jar jarfilename AFFINITY filename ");
//          System.out.println("java -jar jarfilename Kmeans filename elements clusters");
//
//
//      if(args[0].compareToIgnoreCase("kmeans")==0)
//      {
//       System.out.println("Running Kmeans");
//       filename=args[1];
//       List2Graph g = new List2Graph(filename);
//       int num_of_clusters = Integer.parseInt(args[3]);
//       Kmeans km =  new Kmeans(num_of_clusters, g.A ,g.labels);
//       System.out.println(km.perform_and_get_results());
//       System.exit(0);
//      }
//
//
//      if(args[0].compareToIgnoreCase("mcl")==0)
//      {
//       System.out.println("Running Markov Clustering");
//        filename=args[1];
////        MarkovClustering mcl = new MarkovClustering(filename);
////        System.out.println("Number of clusters="+mcl.getNumberOfClusters());
////        mcl.Save_To_File("MCL_results.txt");
////        mcl.show_clusters();
//       System.exit(0);
//      }
//
//      if(args[0].compareToIgnoreCase("affinity")==0)
//      {
//       System.out.println("Running Affinity Propagation");
//       filename=args[1];
//       Affinity_Propagation clustering = new Affinity_Propagation(filename);
//       System.out.println("Number of clusters="+clustering.getNumberOfClusters());
//       clustering.Save_To_File("Affinity_Propagation.txt");
//       System.exit(0);
//      }
//
//      if(args[0].compareToIgnoreCase("kmeans")==0)
//      {
//       System.out.println("Running Kmeans");
//       filename=args[1];
//       List2Graph g = new List2Graph(filename);
//       int num_of_clusters = Integer.parseInt(args[3]);
//       Kmeans km =  new Kmeans(num_of_clusters, g.A ,g.labels);
//       System.out.println(km.perform_and_get_results());
//       System.exit(0);
//      }
//
//
//
//       if(args[0].compareToIgnoreCase("hcl")==0)
//      {
//       System.out.println("Running Hierarchical Clustering");
//       filename=args[1];
//       elements=Integer.parseInt(args[2]);
//          List2Graph g = new List2Graph(filename);
//          HCL HCE2 = new  HCL(g.A,g.labels);
//          System.out.println(HCE2.get_NewickFormat_HCL());
//          System.exit(0);
//      }
//
//       if(args[0].compareToIgnoreCase("upgma")==0)
//      {
//       System.out.println("Running UPGMA");
//       filename=args[1];
//       elements=Integer.parseInt(args[2]); 
//       Clustering_NJ_UPGMA tree = new Clustering_NJ_UPGMA(filename,1);
//       System.out.println(tree.get_NewickFormat_UPGMA()+"\n\n");
//       System.exit(0);
//      }
//      if(args[0].compareToIgnoreCase("nj")==0)
//      {
//       System.out.println("Running Neighbor Joining");
//       filename=args[1];
//       elements=Integer.parseInt(args[2]);
//       Clustering_NJ_UPGMA tree = new Clustering_NJ_UPGMA(filename,2);
//       System.out.println(tree.get_NewickFormat_NeighborJoining()+"\n\n");
//       System.exit(0);
//      }
//
//    }
//
//    // Variables declaration - do not modify//GEN-BEGIN:variables
//    // End of variables declaration//GEN-END:variables
    
}