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+<!--
+ * 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>Annotation Panel Menus</title>
</head>
<body>
<p><strong>Annotation Panel Menus</strong></p>
<ul>
-<li>
-<strong>Annotation Label Popup Menu</strong><br>
-<em>This menu is opened by clicking anywhere on the annotation row labels
-area (below the sequence ID area).</em>
-<ul>
-<li><strong>
-Add New Row</strong><br>
-<em>Adds a new, named annotation row (a dialog box will pop up for you
-to enter the label for the new row). </em>
-</li><li><strong>Hide Row</strong><br>
-<em>Hides the annotation row whose label was clicked in order to bring
-up the menu.</em>
-</li><li><strong>Delete Row</strong><br>
-<em>Deletes the annotation row whose label was clicked in order to bring
-up the menu.</em>
-</li><li><strong>Show All Hidden Rows</strong><br>
-<em>Shows all hidden annotation rows.</em>
-</li><li><strong>Show Values in Text Box</strong><br>
-<em>Opens a text box with a list of comma-separated values
-corresponding to the annotation (numerical or otherwise) at each
-position in the row. This is useful to export alignment quality
-measurements for further analysis.</em>
-</li>
-</ul>
-</li>
-<li><strong>Annotation Popup Menu<br></strong><em>This menu is opened when
-right-clicking on the selected positions of an annotation.</em>
-<ul>
-<li><strong>Helix</strong><br><em>Mark selected positions with a helix glyph (a red
-oval), and optional text label (see below). Consecutive ovals
-will be rendered as an unbroken red line.</em>
-</li>
-<li><strong>Sheet</strong><br><em>Mark selected positions with a sheet glyph (a green
-arrow oriented from left to right), and optional text label (see
-below). Consecutive arrows will be joined together to form a single
-green arrow.</em>
-</li>
-<li><strong>Label</strong><br><em>Sets the text label at the selected positions. If
-more that one consecutive position is marked with the same label, only
-the first position's label will be rendered.</em>
-</li>
-<li><strong>Colour</strong><br><em>Changes the colour of the annotation text label.</em>
-</li>
-<li><strong>Remove Annotation</strong><br><em>Blanks any annotation at the selected positions on
-the row. Note: <strong>This cannot be undone</strong></em>
-</li>
-</ul>
-</li>
+ <li> <strong>Annotation Label Popup Menu</strong><br>
+ <em>This menu is opened by clicking anywhere on the annotation row labels
+ area (below the sequence ID area).</em>
+ <ul>
+ <li><strong> Add New Row</strong><br>
+ <em>Adds a new, named annotation row (a dialog box will pop up for you
+ to enter the label for the new row). </em> </li>
+ <li><strong>Hide Row</strong><br>
+ <em>Hides the annotation row whose label was clicked in order to bring
+ up the menu.</em> </li>
+ <li><strong>Delete Row</strong><br>
+ <em>Deletes the annotation row whose label was clicked in order to bring
+ up the menu.</em> </li>
+ <li><strong>Show All Hidden Rows</strong><br>
+ <em>Shows all hidden annotation rows.</em> </li>
+ <li><strong>Export Annotation</strong> <em>(Application only)</em><br>
+ <em>Annotations can be saved to file or output to a text window in either the
+ Jalview annotations format or as a spreadsheet style set of comma separated values (CSV). </em> </li>
+ <li><strong>Show Values in Text Box</strong> <em>(applet only)</em><br>
+ <em>Opens a text box with a list of comma-separated values corresponding
+ to the annotation (numerical or otherwise) at each position in the row.
+ This is useful to export alignment quality measurements for further analysis.</em>
+ </li>
+ </ul>
+ <em>The following additional entries are avalable when the popup menu is opened on a consensus sequence annotation row:</em>
+ <ul>
+ <li><strong>Ignore Gaps in Consensus</strong><br>
+ If this checkbox is selected, all consensus calculations performed in
+ the current Alignment window will be done without counting gaps as a consensus
+ character.</li>
+ <li><strong>Copy Consensus Sequence</strong><br>
+ Copies the consensus sequence to the clipboard in Fasta format, to allow
+ the consensus sequence to be added to an alignment. Note the copied sequence
+ is not accessible to other programs if Jalview is running as an applet
+ in a web page.</li>
+ </ul>
+ </li>
+ <li><strong>Annotation Popup Menu<br>
+ </strong><em>This menu is opened when right-clicking on the selected positions
+ of an annotation.</em>
+ <ul>
+ <li><strong>Helix</strong><br>
+ <em>Mark selected positions with a helix glyph (a red oval), and optional
+ text label (see below). Consecutive ovals will be rendered as an unbroken
+ red line.</em> </li>
+ <li><strong>Sheet</strong><br>
+ <em>Mark selected positions with a sheet glyph (a green arrow oriented
+ from left to right), and optional text label (see below). Consecutive
+ arrows will be joined together to form a single green arrow.</em> </li>
+ <li><strong>Label</strong><br>
+ <em>Sets the text label at the selected positions. If more that one consecutive
+ position is marked with the same label, only the first position's label
+ will be rendered.</em> </li>
+ <li><strong>Colour</strong><br>
+ <em>Changes the colour of the annotation text label.</em> </li>
+ <li><strong>Remove Annotation</strong><br>
+ <em>Blanks any annotation at the selected positions on the row. Note:
+ <strong>This cannot be undone</strong></em> </li>
+ </ul>
+ </li>
</ul>
</body>
</html>
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