JAL-3633 Help documentation updated

[jalview.git] / help / help / html / features / preferences.html

diff --git a/help/help/html/features/preferences.html b/help/help/html/features/preferences.html
index 8c6b699..58b06db 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>
@@ -249,11 +249,33 @@
     browser application.
   </p>
   <p>
-    <em>Proxy Server</em><br> If you normally use a proxy server
-    for using the internet, you must tick the box &quot;Use a Proxy
-    Server&quot; and enter the address and port details as necessary.
+    <em>Proxy Server</em><br>
+    There are three settings to choose from:<br>
+    <ul>
+           <li><em>No proxy servers</em> will configure Jalview to use a
+                   direct internet connection.</li>
+           <li><em>System proxy servers</em> will configure Jalview to use
+                   the proxy server passed to it by your system at startup.</li>
+           <li><em>Use these proxy servers:</em> allows you to set a custom
+                   proxy server.</li>
+    </ul>
+    If you normally use a proxy server for using the internet, you must
+    choose one of <em>System proxy servers</em>, or if these have not been
+    passed correctly you should set your own proxy servers to use by selecting
+    <em>Use these proxy servers</em>.
+    You will then need to enter the host and port details as necessary.
     Web Services will not work if you are using a proxy server and do
-    not enter the settings here.
+    not choose the system proxy or enter your own settings here.<br>
+    There are separate host and port settings for HTTP and HTTPS proxies.
+    Often these are the same but you should enter the host and port into both
+    rows.<br>
+    You can also check the <em>Authentication required</em> box if your proxy
+    requires username and password authentication.  You can enter both the
+    <em>Username</em> and <em>Password</em> but only the <em>Username</em> will
+    be stored in Jalview's preferences file, the password will only be stored
+    until the end of the current Jalview session.<br>
+    This means that if the proxy settings are still valid, Jalview will ask for
+    the password when it starts the next session.
   </p>
   <p>
     <em>Usage statistics, Questionnaire and Version checks</em><br>
@@ -264,6 +286,22 @@
       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 +421,10 @@
     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>