Merge branch 'bug/JAL-2691_nomultimermapping' into documentation/JAL-2675_release2102b1

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

diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html
index 6e8d3e4..b29b66b 100755 (executable)
--- 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.
@@ -181,6 +184,33 @@
       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>
@@ -261,7 +291,11 @@
     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>