--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * 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.
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+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Alignment Window Menus</title>
+</head>
+
+<body>
+ <p>
+ <strong>Alignment Window Annotations Menu</strong> <em>Since
+ Jalview 2.8.2</em>
+ </p>
+ <ul>
+ <li><strong>Show Alignment Related</strong><em><br>
+ Show all annotations that are for the alignment as a whole (for
+ example, Consensus, or secondary structure prediction from
+ alignment)).</em></li>
+ <li><strong>Hide Alignment Related</strong><em><br>
+ Hide all annotations that are for the alignment as a whole.</em></li>
+ <li><strong>Show Sequence Related</strong><em><br>
+ Show all annotations that are for individual sequences.</em></li>
+ <li><strong>Hide Sequence Related</strong><em><br>
+ Hide all annotations that are for individual sequences.</em></li>
+ <li><strong>Show Alignment Related</strong><em><br>
+ Show all annotations that are for the alignment as a whole (for
+ example, Consensus).</em></li>
+ <li><em>You can also selectively show or hide annotations
+ from the <a href="./popupMenu.html">Popup</a> or <a
+ href="../features/annotation.html">Annotation</a> menus.
+ </em></li>
+ <li><strong>Sort by Sequence</strong><em><br>Sort
+ sequence-specific annotations by sequence order in the alignment
+ (and within that, by label).</em></li>
+ <li><strong>Sort by Label</strong><em><br>Sort
+ sequence-specific annotations by label (and within that, by
+ sequence order). If neither sort order is selected, no sorting
+ is applied, allowing you to make a manual ordering of the
+ annotations.</em></li>
+ <li><strong>Autocalculated Annotation<br>
+ </strong><em>Settings for the display of autocalculated annotation.</em>
+ <ul>
+ <li><strong>Show first<br></strong><em> Show
+ autocalculated annotations above sequence-specific
+ annotations. Note this also applies to other annotations for
+ the alignment, for example secondary structure prediction
+ from alignment.</em></li>
+ <li><strong>Show last<br></strong><em> Show
+ autocalculated / alignment annotations below
+ sequence-specific annotations.</em></li>
+ <li><strong>Apply to all groups<br>
+ </strong><em> When ticked, any modification to the current settings
+ will be applied to all autocalculated annotation.</em></li>
+ <li><strong>Show Consensus Histogram<br>
+ </strong><em> Enable or disable the display of the histogram above
+ the consensus sequence.</em></li>
+ <li><strong>Show Consensus Logo<br>
+ </strong><em> Enable or disable the display of the Consensus Logo
+ above the consensus sequence.</em></li>
+ <li><strong>Normalise Consensus Logo<br>
+ </strong><em>When enabled, scales all logo stacks to the same
+ height, making it easier to compare symbol diversity in
+ highly variable regions.</em></li>
+ <li><strong>Group Conservation<br>
+ </strong><em> When ticked, display a conservation row for all groups
+ (only available for protein alignments).</em></li>
+ <li><strong>Group Consensus<br>
+ </strong><em> When ticked, display a consensus row for all groups.</em></li>
+ </ul></li>
+ </ul>
+ <p> </p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff