X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpreferences.html;h=52e88dbb8ef7f97fcab90aa93192c5187318cce5;hb=ce7259404dbb5bbeeb296d32b6a2543b30a7c924;hp=fb2183641dc866450d6945ee5349b577db00f18c;hpb=3c2ee3e1b9c507c7dfa550bc8546a43ff305f85a;p=jalview.git

diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html
index fb21836..52e88db 100755
--- a/help/html/features/preferences.html
+++ b/help/html/features/preferences.html
@@ -41,6 +41,9 @@
         Preferences</a> tab allows you to configure default colourschemes
       for a new alignment window.
     </li>
+    <li>The <a href="#overview"><strong>&quot;Overview&quot;</strong>
+        Preferences</a> tab configures defaults for the overview window.
+    </li>
     <li>The <a href="#structure"><strong>&quot;Structure&quot;</strong>
         Preferences</a> tab allows you to configure options for obtaining
       and displaying structure information.
@@ -62,10 +65,6 @@
         Preferences</a> tab contains settings affecting the export of
       sequence alignments and EPS files.
     </li>
-    <li>The <a href="dassettings.html"><strong>&quot;DAS
-          Settings&quot;</strong> Preferences</a> tab allows you to select which DAS
-      sources to use when fetching DAS Features.
-    </li>
     <li>The <a href="../webServices/webServicesPrefs.html"><strong>&quot;Web
           Service&quot;</strong> Preferences</a> tab allows you to configure the <a
       href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
@@ -89,10 +88,11 @@
   <p>
     <em>Show Annotations</em> - If this is selected the new window will
     display an annotation panel below the sequences. This annotation
-    panel may have several rows describing the whole alignment. The 3
-    standard annotations <em>Conservation</em>, <em>Quality</em> and <em>Consensus</em>
-    for the alignment may be shown or hidden by default using the
-    checkboxes below.
+    panel may have several rows describing the whole alignment. The 4
+    standard annotations <em>Conservation</em>, <em>Quality</em>, 
+    <em>Occupancy</em> and <em>Consensus</em> for the alignment may 
+    be shown or hidden by default using the checkboxes adjacent and
+    below.
   </p>
   <p>
     <em>Show group: Conservation and Consensus</em> controls the display
@@ -180,6 +180,33 @@
       by Annotation...</a> is selected from the alignment window's colours
     menu.
   </p>
+   <p>
+    <a name="overview"><strong>&quot;Overview&quot;
+        Preferences tab</strong>
+  </p>
+  <p>
+    <em>Use legacy gap colouring (gaps are white)</em> - when enabled,
+    Jalview's overview shows gaps as white, and sequences with no
+    colourscheme applied as grey.
+  </p>
+  <p>
+    <em>Show Hidden regions when opening overview</em> - default setting
+    for inclusion of hidden regions.
+  </p>
+  <p>
+    <em>Gap Colour</em> - When legacy gap colouring is not enabled, this
+    configures the default colour for gaps in the overview.
+  </p>
+  <p>
+    <em>Hidden Colour</em> - colour used to highlight regions in the
+    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>
@@ -260,7 +287,11 @@
     The <em>Custom only</em> button limits the entries in the table to
     just those you have configured yourself <em>via</em> the <em>Edit
       Links</em> buttons. Press <em>Show all</em> to clear any filters.
-  <p>
+  </p>
+  <p>The links table is prepoulated with persistent URLs for many common
+    bioinformatics databases (since 2.10.2). These links are downloaded by Jalview from
+    the <em>identifiers.org</em> website, and the names and URLs are not
+    user editable.
     <a href="../webServices/urllinks.html#urllinks">Read more about configuring
       URL links.</a>
   </p>
@@ -332,7 +363,7 @@
     and PDB file association (if available). The Jalview id/start-end
     option is ignored if Modeller output is selected.
   <p>
-    <a name="editing"><strong>Editing Preferences tab</strong></a>
+    <a name="editing"><strong>&quot;Editing&quot; Preferences tab</strong></a>
   </p>
   <p>There are currently three options available which can be
     selected / deselected.</p>