<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
<head>
<title>Popup Menu</title>
</head>
</strong><em>Selecting this will display a "Colour Chooser"
window. Select a colour than press OK to set the border colour of
a group.</em></li>
- </ul>
+ <li><strong>Show Unconserved<br>
+ </strong><em>When this is selected, all symbols in the group matching the consensus sequence at that column will be rendered as a '.', highlighting mutations in the group area.
+ </em></li>
+ </ul>
</li>
+<!-- not available in 2.5 yet
+ <li><strong>Group Links<br>
+ </strong><em>This menu is only visible if there are group links available for the current selection.
+ </em>
+ <ul>
+ <li><em>ID links</em> allow you to send IDs associated with the current selection to a web server.</li>
+ <li><em>Sequence links</em> allow you to send the sequences in the currently selected region to a web server.</li>
+ <li><em>Sequence and ID links</em> allow you to send sets of IDs and sequences associated with the current selection to a web server.</li>
</ul>
+ <em>Group Links were added in Jalview 2.5</em></li>
+--> </ul>
</li>
<li><strong>Sequence Id<br>
</strong><em>This menu is only visible if you right-click on a sequence name.
<em>All sequences in the current selection group will be hidden, apart
from (Sequence Id). Any edits performed on the visible representative
sequence will be propagated to the hidden sequences. </em></li>
- <li><strong>Link</strong><br>
+ <li><a name="sqid.popup"><strong>Link</strong><br>
<em>This menu item lists all links which have been set up in the <a href="../features/preferences.html">Preferences</a>
- Connections tab.</em><strong><br>
+ Connections tab.<br>
+ Since Jalview 2.4, links will also be made for database cross
+ references (where the database name exactly matches the link name set up in <a href="../features/preferences.html">Preferences</a>).
+ <br>Since Jalview 2.5, links are also shown for non-positional sequence features attached to
+ the sequence, and any regular-expression based URL links that
+ matched the description line.
+ </em><strong><br>
</strong></li>
</ul>
</li>