From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 16 Mar 2020 17:42:45 +0000 (+0000)
Subject: JAL-3407 JAL-3549 explicitly mention the ‘no features’ dialog, and how an existing... 
X-Git-Tag: Develop-2_11_2_0-d20201215~77
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a68a0c7648ce58397a503f999cc2eef6215ca3e8;p=jalview.git

JAL-3407 JAL-3549 explicitly mention the ‘no features’ dialog, and how an existing selection affects the sort alignment by feature score/density
---

diff --git a/help/help/html/features/featuresettings.html b/help/help/html/features/featuresettings.html
index 555e2ba..ad6627b 100755
--- a/help/help/html/features/featuresettings.html
+++ b/help/help/html/features/featuresettings.html
@@ -123,11 +123,18 @@
   </p>
   <p>
     <strong><a name="sortbyfeature">Ordering alignment by
-        features</a></strong></p><p>The 'Seq Sort by Score' and 'Seq Sort by
-    Density' buttons will sort the alignment based on the average score
-    or total number of currently active features and groups on each
-    sequence. To order the alignment using a specific feature type, use
-    the <em>sort by ..</em> entries in the pop-up menu for that type.<br>
+        features</a></strong>
+  </p>
+  <p>
+    The 'Seq Sort by Score' and 'Seq Sort by Density' buttons will sort
+    the alignment based on the average score or total number of
+    currently active features and groups on each sequence. A dialog box
+    is shown if there are no features to use for sorting sequences. To
+    order the alignment using a specific feature type, use the
+    <em>sort by ..</em> entries in the pop-up menu for that type.<br> <br>When
+    a selected region exists, only features lying within the columns
+    containing the selected region will be considered, but all sequences
+    (including those not selected) will be reordered.
     <em>Feature sorting and graduated feature colouring were
       introduced in Jalview 2.5</em>
   </p>