X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpreferences.html;h=5bca358d59763652f54ad119748fc85aa82e60ee;hb=f37c3fd4fe12799de498de5f397252e9f457fee9;hp=95a43f72d34cd980533ca1fd33396484b34da4cb;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html
index 95a43f7..5bca358 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 2.9.0b1)
- * 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.
  * 
@@ -41,21 +41,31 @@
         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
       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
@@ -63,8 +73,8 @@
     </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> servers that Jalview uses, and change the layout of the
+      href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
+      servers that Jalview uses, and change the layout of the
       alignment's Web Services menu.
     </li>
   </ul>
@@ -78,17 +88,17 @@
   </p>
   <p>
     <em>Open Overview Window</em> - When this is selected, the <a
-      href="overview.html"
-    >alignment overview</a> panel is opened by default for a new alignment
-    window.
+      href="overview.html">alignment overview</a> panel is opened
+    by default for a new alignment window.
   </p>
   <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
@@ -155,9 +165,9 @@
     <em>Open file</em> - If this is selected then the default alignment
     file will be opened when Jalview is started. You can change the
     default file by clicking on file name and either typing in the file
-    path or selecting it from the file chooser window.<br />
-    <em>Note: The default example alignment is updated periodically
-      to demonstrate new features in Jalview.</em>
+    path or selecting it from the file chooser window.<br /> <em>Note:
+      The default example alignment is updated periodically to
+      demonstrate new features in Jalview.</em>
   </p>
   <p>
     <a name="colours"><strong>&quot;Colours&quot;
@@ -172,9 +182,36 @@
   <p>
     <em>Annotation Shading Default</em> - set the default minimum and
     maximum colours used when <a
-      href="../colourSchemes/annotationColouring.html"
-    >Colour by Annotation...</a> is selected from the alignment window's
-    colours menu.
+      href="../colourSchemes/annotationColouring.html">Colour
+      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;
@@ -213,13 +250,6 @@
         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
@@ -241,6 +271,37 @@
       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>
@@ -292,11 +353,10 @@
   </p>
   <p>
     When this option is enabled, Jalview embeds <a
-      href="bioJsonFormat.html"
-    >BioJSON</a> data within HTML files exported from Jalview at
-    generation time. This enables the exported HTML files to be
-    extracted and imported back into the Jalview desktop application at
-    a later time.
+      href="bioJsonFormat.html">BioJSON</a> data within HTML files
+    exported from Jalview at generation time. This enables the exported
+    HTML files to be extracted and imported back into the Jalview
+    desktop application at a later time.
   <p>
     <em>Use Modeller Output</em>
   </p>
@@ -309,7 +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>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>
@@ -329,7 +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>
