Problem in writing to file or in console

Question

Hi friends,
I am here once again with one more problem.
I read from a file and process each line and write back the result on the console. The result is strange.
On console it starts from middle of the file and goes on reading till the end of file . Each time it trims some.
For example I have 1500 lines. It reads, processes and writes 900 (the total is 1500) next time it may be 850 like this...
why is like this ?
public static void main (String[] args)throws Exception
          List one=new ArrayList();
          List A=new ArrayList();
          MyVertex j,startNode,s,targetNode;
     //load Graph
          File n=new File("nodes.txt");
          File e=new File("relation.txt");
          ts=new Test(n,e);
          //System.out.println(ts.toString());
          vs=ts.getVertexSet();
          es=ts.getEdgeSet();
          //read from file          
          BufferedReader br=new BufferedReader(new FileReader("test.txt"));
          startNodeName=br.readLine();
          while((startNodeName!=null))
               System.out.println("START NODE : "+ startNodeName);
                              System.out.println("links for startNodes are :     "+counter1);
                              first(startNodeName);
               targetNodeName=br.readLine();
               System.out.println("TARGET NODE : "+ targetNodeName);
               second(targetNodeName);
               System.out.println();
               shared();
               System.out.println();
               startNodeName=br.readLine();
     public static void first(String s)
     System.out.println(vs.toString());
          Iterator i=vs.iterator();
          while(i.hasNext())
               j=(MyVertex)i.next();
               startNode=j;
               if(startNode.getName().equals(s))
                    one=ts.outwardNodes(startNode);
                    System.out.println(one.toString());
          counter1=one.size()+1;
     public static void second(String s)
          Iterator j=vs.iterator();
          while(j.hasNext())
               k=(MyVertex)j.next();
               targetNode=k;
               if(targetNode.getName().equals(s))
                    B=ts.outwardNodes(targetNode);
                    System.out.println(B.toString());
          counter2=B.size();
          System.out.println("Links for target Nodes are :     "+counter2);
     public static void shared()
          counter3=1;
          Iterator i=one.iterator();
          while(i.hasNext())
               s=(MyVertex)i.next();
               if(B.contains(s))
                    counter3++;
          System.out.println("Number of common links are :     "+counter3);
          relWeight=(double)counter3/counter1;
          System.out.println("Relation weight is :     "+relWeight);
}//end of classThanks once again

Answer 1

I tried to write to a text file it is still strange. It trims some of the last lines.
out f 1500 lines it only reads 1400 lines.
I am using Eclipse, so I meant the console of Eclipse not windows console. In both the cases the problem remains.
Can any one suggest me how to get rid of this problem ?
Thanks a lot for yur time.