X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpreferences.html;h=b29b66bf1dc60d890736470108b7337c49969816;hb=c59bb1bde1a05723c7d2392d1e8420463795017b;hp=7a6a4758a68d1013cae3f2c89403dc721dc7597d;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html
index 7a6a475..b29b66b 100755
--- a/help/html/features/preferences.html
+++ b/help/html/features/preferences.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -41,13 +41,21 @@
         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.
     </li>
     <li>The <a href="#connections"><strong>&quot;Connections&quot;</strong>
-        Preferences</a> tab allows you to change the links made from Jalview
-      to your default web browser.
+        Preferences</a> tab allows you to configure Jalview's internet
+      settings and specify your default web browser.
+    </li>
+    <li>The <a href="#links"><strong>&quot;Links&quot;</strong>
+        Preferences</a> tab shows the currently configured <em>URL
+        Links</em> shown in the <strong>Link</strong> submenu in the Sequence
+      ID popup menu.
     </li>
     <li>The <a href="#output"><strong>&quot;Output&quot;</strong>
         Preferences</a> tab contains settings affecting the export of
@@ -84,10 +92,11 @@
   <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
@@ -175,6 +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>
@@ -212,13 +248,6 @@
         Preferences tab</strong></a>
   </p>
   <p>
-    <em>URL Link From Sequence ID</em><br> These definitions are
-    used to generate URLs from a sequence's ID or database cross
-    references. Read more about <a
-      href="../webServices/urllinks.html#urllinks">configuring
-      URL links here</a>.
-  </p>
-  <p>
     <em>Default Browser (Unix)</em><br> Its difficult in Java to
     detect the default web browser for Unix users. If Jalview can't find
     your default web browser, enter the name or full path to your web
@@ -240,6 +269,37 @@
       statement</a> for more information.
   </p>
   <p>
+    <a name="links"><strong>The &quot;Links&quot; Preferences
+        tab</strong></a>
+  </p>
+  <p>
+    This panel shows a table, and two sections - <em>Edit</em> and <em>Filter</em>.
+    The table shows the available URL link definitions (consisting of a
+    database, Name, and URL template string), a checkbox <em>In
+      Menu</em> which indicates if the link is enabled, and <em>Double
+      Click</em> which marks the link that will be opened if a sequence's ID
+    is double clicked. The table can be sorted by clicking on the column headers.
+  </p>
+  <p><em>Edit Links</em><br /> This section contains three buttons,
+    <em>New</em>, <em>Edit</em> and <em>Delete</em>, which allow you to
+    create, modify and remove user-defined URL links from the Sequence
+    ID's links submenu.
+  </p>
+  <p>
+    <em>Filter</em><br /> The <em>Filter text</em> box allows you to
+    quickly show rows in the table containing a particular text string.
+    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>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>
+  <p>
     <a name="output"><strong>Output Preferences tab</strong></a>
   </p>
   <p>
@@ -307,7 +367,7 @@
     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>e&quot;Editinge&quot; Preferences tab</strong></a>
   </p>
   <p>There are currently three options available which can be
     selected / deselected.</p>
