From 442b6bc246ee877d5e977baf80fd96299e0e05c4 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 5 Aug 2008 15:32:38 +0000
Subject: [PATCH] updated statement of limitations for interactive annotation
 editing with Jalview GUI

---
 help/html/features/annotation.html |   19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html
index 98599e2..812ed50 100755
--- a/help/html/features/annotation.html
+++ b/help/html/features/annotation.html
@@ -7,7 +7,9 @@
   Jalview can display symbols and graphs under the columns of an
   alignment, and allow you to mark particular columns of an alignment and add symbols and text 
   in the annotation area shown below the alignment (which may be hidden if <strong>View&#8594;Show 
-  Annotation</strong> is not ticked). </p>
+  Annotation</strong> is not ticked). Any displayed annotation row can be hidden (using the pop-up 
+  menu obtained by right-clicking the label), or re-ordered by dragging the label to a new 
+  position with the left mouse button.</p>
 <p>Web services can also add annotation to an alignment (see the
   <a href="../webServices/jnet.html">JNet web service</a>), and as of Jalview 2.08 quantitative and symbolic
   annotations can be added to an alignment via an <a href="annotationsFormat.html">Annotations 
@@ -77,14 +79,11 @@ User defined annotation is stored and retrieved using <a
 href="../features/jalarchive.html">Jalview Archives</a>.
 </p>
 <p><em>Current Limitations</em></p>
-
-<p>In the current version of Jalview, reordering of the annotation
-rows is not possible. If you save 
-your annotation as a Jalview file, however, it will be reloaded with user 
-annotations at the top (nearest the alignment), above any of the
-automatically generated Conservation, Quality or consensus
-annotations. Finally, the Jalview GUI will not, as yet, allow you to output
-Jalview annotation files for the current alignment, change the line
-colour, display style, or create groups of quantitative annotation rows.</p>
+<p>As of version 2.4, the Jalview user interface does not support the 
+creation and editing quantitative annotation (histograms and line graphs), or 
+to create annotation associated with a specific sequence. It is also incapable of
+annotation grouping or changing the style of existing annotation (to change between line or bar charts, or to make multiple line graphs). These annotation capabilities are only possible by the import of an 
+<a href="annotationsFormat.html">Annotation file</a>.<br>
+</p>
 </body>
 </html>
-- 
1.7.10.2