File i/o help needed

In the code below, I am reading in an xml file and compressing it. Then I am writing the compressed file back out to another file. However, when I place a break point in my code after the writing is suppose to be complete and view the newly created file at that point, it is not complete. It only becomes completely written when the main method is completely finished. Can someone tell me why this is so? Thanks in advance!!
public static void main(String[] args)
     try
              if (args.length == 1)
                    StringBuffer sb = new StringBuffer();
                    FileInputStream fis = new FileInputStream(args[0]);
                    String compressedFileName = args[0].concat(".compressed");
                    XMLOutputCompression2 xmlCompress = new XMLOutputCompression2(new FileOutputStream(compressedFileName));
                    BufferedReader br = new BufferedReader(new FileReader(fis.getFD()));
                    String s;
                    while( (s=br.readLine()) != null)
                          sb.append(s);
                    xmlCompress.write(sb.toString().getBytes());
                    xmlCompress.flush();
                    xmlCompress.close();
                    br.close();
                    fis.close();
                    System.out.println("Finished");
        }catch(Exception e)
            e.printStackTrace();
    }

Hi!
I'm currently having problems while using readLine() for a BufferedReader on a URLConnection.getInputStream() ...
it seem to be frozen sometimes on some URLs, evenif I call BufferedReader.ready() before actually reading the next line..
I think I'll try with read() on a byte-buffer and use available() before
The Cat

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