Merge branch 'develop' into features/mchmmer

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

diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html
index acd7ba6..5bca358 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.
@@ -59,8 +62,10 @@
       sequence alignments and EPS files.
     </li>
     <li>The <a href="#editing"><strong>&quot;Editing&quot;</strong>
-        Preferences</a> tab contains settings affecting the export of
-      sequence alignments and EPS files.
+        Preferences</a> tab contains settings affecting the behaviour of alignments as you edit them.
+    </li>
+    <li>The <a href="#hmmer"><strong>&quot;HMMER&quot;</strong>
+        Preferences</a> tab allows you to configure locally installed HMMER tools.
     </li>
     <li>The <a href="dassettings.html"><strong>&quot;DAS
           Settings&quot;</strong> Preferences</a> tab allows you to select which DAS
@@ -181,6 +186,33 @@
       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>
@@ -337,7 +369,7 @@
     and PDB file association (if available). The Jalview id/start-end
     option is ignored if Modeller output is selected.
   <p>
-    <a name="editing"><strong>e&quot;Editinge&quot; 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>
@@ -357,7 +389,13 @@
     <em>Sort with New Tree</em> - When selected, any trees calculated or
     loaded onto the alignment will automatically sort the alignment.
   </p>
-  <p>&nbsp;</p>
-  <p>&nbsp;</p>
+  <p>
+    <a name="hmmer"><strong>&quot;HMMER&quot; Preferences tab</strong></a>
+  </p>
+  <p>If you have installed HMMER tools (available from <a href="http://hmmerorg">hmmer.org</a>),
+  then you should specify on this screen the location of the installation (the path to the folder 
+  containing binary executable programs). Double-click in the input field to open a file browser.</p>
+  <p>When this path is configured, the <a href="../menus/alwhmmer.html">HMMER menu</a> will be
+  enabled in the Alignment window.</p>
 </body>
 </html>