JAL-3111 tidied up preferences dialog documentation

diff --git a/help/help/html/features/preferences.html b/help/help/html/features/preferences.html
index 8c6b699..5fda2df 100755 (executable)
--- a/help/help/html/features/preferences.html
+++ b/help/help/html/features/preferences.html
@@ -201,12 +201,6 @@
     overview that are hidden in the alignment.
   </p>
   <p>
-    <em>Gap Colour</em> - The default colour scheme for a new alignment
-    window. If the chosen option is &quot;User Defined&quot; then the
-    last User Defined Colour loaded or saved via the User Defined
-    Colours panel will be loaded.
-  </p>
-  <p>
     <a name="structure"><strong>&quot;Structure&quot;
         Preferences tab</strong></a><em> added in Jalview 2.8.2</em>
   </p>
@@ -239,6 +233,12 @@
     here, by entering the full path to the Chimera executable program.
     Double-click this field to open a file chooser dialog.
   <p>
+  <p>
+    <em>PDB Fields shown in Search and Structure Summaries</em> - ticks
+    in this table indicate fields shown by default when browsing results
+    of a free text search via the PDB sequence fetcher, or 3D structures
+    offered by the 3D Structure Chooser.<p>
+  <p>
     <a name="connections"><strong>&quot;Connections&quot;
         Preferences tab</strong></a>
   </p>
@@ -264,6 +264,22 @@
       statement</a> for more information.
   </p>
   <p>
+  <a name="backups"><strong>The &quot;Backups&quot; Preferences Tab</strong></a>
+  </p>
+  <p>Since Jalview 2.11.0, overwriting an existing file when saving
+    or exporting data will by default trigger a backup file to be
+    created. Several options are provided to control how backup files
+    are named, and how many old versions will be kept.</p>
+    <p>
+    <em>Schemes</em> - select from three default schemes <em>Single Backup</em>, <em>Keep All Versions</em>, and <em>Rolled Backup Files</em>, or choose <em>Custom</em> to enable a previously defined custom scheme.
+    </p><p>
+    <em>Custom</em> - Check this box to adjust the parameters of the currently selected scheme. Once <em>OK</em> is selected these parameters will be saved as the <em>Custom</em> scheme in your user preferences. To revert changes hit <em>Cancel</em>. 
+    </p>
+    <p><em>Scheme Examples</em> - shows how backup files will appear according to the currently selected scheme and parameters. 
+    </p>
+    <p><em>Deleting Old Backup Files</em> - these settings control how many backups are kept.</p>
+    <p><em>Backup filename strategy</em> - specify the naming convention for numbered backups and how they are ordered.</p> 
+  <p>
     <a name="links"><strong>The &quot;Links&quot; Preferences
         tab</strong></a>
   </p>
@@ -383,6 +399,10 @@
     loaded onto the alignment will automatically sort the alignment.
   </p>
   <p>&nbsp;</p>
+  <em>Web Services Preferences</em> - documentation for this tab is
+  given in the
+  <a href="../webServices/webServicesPrefs.html">Web Services
+    Preferences section</a>.
   <p>&nbsp;</p>
 </body>
 </html>