X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Ffeaturesettings.html;h=ad6627b6264531d271394e3beb736fc355eab15f;hb=9531c62e5d56d3489e5688c4922a48267564427a;hp=408cdc2e3014a0b077603cf8457d0645087245b9;hpb=f52bfc916cbcc0f3c77707735d6a0fd63c2789c4;p=jalview.git

diff --git a/help/help/html/features/featuresettings.html b/help/help/html/features/featuresettings.html
index 408cdc2..ad6627b 100755
--- a/help/help/html/features/featuresettings.html
+++ b/help/help/html/features/featuresettings.html
@@ -29,7 +29,7 @@
 	<p>
 		Select <strong>View&#8594;Feature Settings...</strong> in an alignment
 		window to open the feature settings dialog box, which allows
-		precise control the visibility and appearance of sequence features for
+		precise control of the visibility and appearance of sequence features for
 		an alignment view.
 	</p>
 	<div align="center">
@@ -39,7 +39,7 @@
 	<p>The top section of the dialog box lists all the sequence feature
 		groups, along with a tickbox for each that controls whether its
 		features are displayed. When many groups are present, their names may
-		be truncated, but the full name be shown in a tooltip when the mouse
+		be truncated, but the full name is shown in a tooltip when the mouse
 		hovers over their checkbox.</p>
 		<p><em>Feature colour schemes and filters</em>
 	<p>
@@ -99,14 +99,14 @@
         columns by feature</strong></a>
   </p>
   <p>
-    Double-clicking a <strong>feature type</strong> in the <strong>Feature
-      Settings</strong> dialog allows you to select columns in the alignment that
-    contain (or do not contain) features of that type that are currently visible (e.g. not filtered out or excluded due to an applied colour scheme threshold). If a region of the
-    alignment is currently selected, then only features in the current
-    selection will be searched. The following keys affect the way in which
-    selections are made:
-  
-  <ul>
+		Double-clicking a <strong>feature type</strong> in the <strong>Feature
+			Settings</strong> dialog allows you to select columns in the
+		alignment that contain (or do not contain) features of that type that
+		are currently visible (e.g. not filtered out or otherwise excluded due
+		to an applied colour scheme threshold). If a region of the alignment
+		is currently selected, then only features in the current selection
+		will be searched. The following keys affect the way in which
+		selections are made:<ul>
     <li>Hold down <strong>Alt</strong> to select columns not
       containing features of a particular type.
     </li>
@@ -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>