package medusa.georgios.ClusteringAlgorithms;
// The neighbour-joining algorithm.  Make a rooted tree by arbitrarily
// adding a root node with edges to the last two leaves

public class NJ {
  int N;			// The initial number of leaves
  int K;			// The number of clusters created so far
  NJCluster[] cluster;		// The nodes (clusters) of the resulting tree
  float[] r;			// The average distance to other leaves
  public StringBuffer NHX = new StringBuffer("");
  
  public NJ(float[][] ds) {
    N = ds.length;
    cluster = new NJCluster[2*N-1];
    for (int i=0; i= dimdjk
		  || dijdkm == dimdjk && dijdkm >= dikdjm
		  || dikdjm == dimdjk && dikdjm >= dijdkm)) {
	      System.out.println("(i, j, k, m) = ("+i+","+j+","+k+","+m+")");
	      return false;
	    }
	  }
    return true;
  }
  
  
  
   public boolean is_internal(NJCluster cluster)
    {
        if( cluster.left == null &&  cluster.right == null)
            return false;
        else
            return true;              
    }
  
   public String NewickFormat(NJCluster cluster) {
       if(this.is_internal(cluster)){
            NHX.append("(");
            this.NewickFormat(cluster.left);}
        
         if(this.is_internal(cluster)){NHX.append(",");}
        else
        {NHX.append(Clustering_NJ_UPGMA.labels.get(cluster.lab-1));}
        if(this.is_internal(cluster)){
            this.NewickFormat(cluster.right);
        NHX.append(")");
        } 
       return NHX.toString()+";";

  }
  
}