From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 4 Nov 2014 09:37:50 +0000 (+0000)
Subject: JAL-1152 help updates for Preferences
X-Git-Tag: Release_2_8_2b1^2~36^2~7^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=75b47e184be550e80822f0ac6ec06bcdb747f362;p=jalview.git

JAL-1152 help updates for Preferences
---

diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html
index e57289f..3e45043 100755
--- a/help/html/features/preferences.html
+++ b/help/html/features/preferences.html
@@ -79,15 +79,18 @@ for a new alignment window.</p>
 References and Non-positional annotation in the tooltip displayed when
 the mouse is over a sequence's ID.</p>
 <p><em>Sequence Name Italics</em> - select to apply the italicised
-vbersion of the font to sequence labels.</p>
+version of the font to sequence labels.</p>
 <p><em>Smooth Font</em> - Toggles anti-aliasing on / off for faster
 rendering of the alignment.</p>
 <p><em>Wrap Alignment</em> - Select whether to open new alignment
 windows in wrapped mode or not.</p>
 <p><em>Gap Symbol</em> - The default gap symbol may be set to either
 &quot;-&quot; or &quot;.&quot;</p>
-<p><em>Sort by</em> - When the alignment is loaded in, it will can
-be sorted by Id or pairwise identity.</p>
+<p><em>Sort alignment by</em> - When the alignment is loaded in, it can
+be ordered as read (No sort), or sorted by Id or pairwise identity.</p>
+<p><em>Sort annotations by</em> - Annotations can be unsorted, sorted by the order of the related sequences in 
+the alignment, or by label. Autocalculated annotations (e.g. Consensus) can be shown either last (below sequence 
+annotations) or first (above sequence annotations). <em>Since Jalview 2.8.2.</em></p>
 <p><em>Open file</em> - If this is selected then the default
 alignment file will be opened when Jalview is started. You can change
 the default file by clicking on file name and either typing in the file