code: public void read(Reader in) throws IOException
  	{
  		logger.debug("reading feature index...");
  
  		LineNumberReader lnr = new LineNumberReader(in);
  		map.clear();
  
  		String line;
  		String[] s;
  		Integer id;
  		while ((line = lnr.readLine()) != null)
  		{
  			//line = line.trim();
  			//logger.debug("\"" +line + "\"");
  			if (!line.startsWith("#"))
  			{
  				s = line.split("\t");
  
  				if (s.length == 2)
  				{
  					// feature index
  					map.put(s[1], new Integer(s[0]));
  
  					// SET COUNT
  					count++;
  				}
  				else
  				{
  
  				}
  			}
  		}
  		lnr.close();
  
  
  	}
docs: Reads the feature index from the specified input stream.
  <p>
  This method processes input in features of lines. A natural
  line of input is terminated either by a set of line
  terminator  characters (\n or \r or  \r\n) or by the end
  of the file. A natural line  may be either a blank line,
  a comment line, or hold some part  of a id-feature pair.
  Lines are read from the input stream until  end of file
  is reached.
  <p>
  A natural line that contains only white space characters
  is  considered blank and is ignored. A comment line has
  an ASCII  '#' as its first non-white  space character;
  comment lines are also ignored and do not encode id-feature
  information.
  <p>
  The id contains all of the characters in the line starting
  with the first non-white space character and up to, but
  not  including, the first '\t'. All remaining characters
  on the line become part of  the associated feature string;
  if there are no remaining  characters, the feature is the
  empty string "".
  
  @param in						a <code>Reader</code> object to
  provide the underlying stream.
  @throws IOException	if reading this feature index
  from the specified  input stream
  throws an <code>IOException</code>.