How difficult can it be to add a one-line conditional to the standard
idiom...

 BufferedReader br = new BufferedReader(...);
 String line;

 while ((line = br.readLine()) != null) {
   if (line.trim().length() != 0) {
     // whatever
   }
 }

 br.close();

Note too that you should be using a Reader to handle text files, not
an InputStream.

/gordon