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();


	}
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 ) { if ( ! line . startsWith ( "#" ) ) { s = line . split ( "\t" ) ; if ( s . length == 2 ) { map . put ( s [ 1 ] , new Integer ( s [ 0 ] ) ) ; count ++ ; } else { } } } lnr . close ( ) ; }
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>.