added wording to tutorial to make it easier to figure out what to do …

…with the aligner plugin

docs/tutorial/tutorial.html

@@ -1818,9 +1818,15 @@ <h2><a name="plugins">14. Plugins</a></h2>
 
 <p>
 
-To see these plugins at work, find the option "plugins=" at the top of
-volvox.conf, and modify it to activate the Aligner and
-RestrictionAnnotator plugins:
+To see these plugins at work, first make sure that the database files
+are up to date with this position in the tutorial.  If you are in any
+doubt, remove the current contents of the volvox database directory
+and replace them with the files <a
+href="data_files/volvox_all.gff">volvox_all.gff</a> and <a
+href="data_files/volvox_all.fa">volvox_all.fa</a>.  <p>
+
+Now find the option "plugins=" at the top of volvox.conf, and modify
+it to activate the Aligner and RestrictionAnnotator plugins:
 
 <blockquote class="example"><pre>
 plugins = Aligner RestrictionAnnotator
@@ -1853,12 +1859,11 @@ <h2><a name="plugins">14. Plugins</a></h2>
 
 The Aligner plugin has some additional configuration that you can
 perform.  We'll look at this now as an example of how to configure
-plugins.
+plugins. Open up volvox.conf and add the following configuration
+section:
 
 <p>
 
-Open up volvox.conf and add the following configuration section:
-
 <blockquote class="example"><pre>
 ########################
 # Plugin configuration
@@ -3436,6 +3441,6 @@ <h2><a name="conclusion">22. Conclusion</a></h2>
 <address>Lincoln D. Stein, lstein@cshl.org<br>
 <a href="/">Cold Spring Harbor Laboratory</a></address>
 <!-- hhmts start -->
-Last modified: Thu Jun 24 11:44:10 EDT 2004
+Last modified: Mon Sep  6 16:50:31 EDT 2004
 <!-- hhmts end -->
 </body> </html>

lib/Bio/Graphics/Browser.pm

@@ -1,5 +1,5 @@
 package Bio::Graphics::Browser;
-# $Id: Browser.pm,v 1.160 2004-09-05 04:36:03 allenday Exp $
+# $Id: Browser.pm,v 1.161 2004-09-06 20:51:02 lstein Exp $
 # This package provides methods that support the Generic Genome Browser.
 # Its main utility for plugin writers is to access the configuration file information
 
@@ -1078,7 +1078,6 @@ sub image_and_map {
     }
 
     else {
-
       my @settings = ($conf->default_style,$conf->i18n_style($label,$lang,$length));
       push @settings,(-hilite => $hilite_callback) if $hilite_callback;
       my $track = $panel->add_track(-glyph => 'generic',@settings);