3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
4 * Copyright (C) 2015 The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Alignment Window Menus</title>
28 <strong>Alignment Window Annotations Menu</strong> <em>Since
32 <li><strong>Show Alignment Related</strong><em><br>
33 Show all annotations that are for the alignment as a whole (for
34 example, Consensus, or secondary structure prediction from
35 alignment)).</em></li>
36 <li><strong>Hide Alignment Related</strong><em><br>
37 Hide all annotations that are for the alignment as a whole.</em></li>
38 <li><strong>Show Sequence Related</strong><em><br>
39 Show all annotations that are for individual sequences.</em></li>
40 <li><strong>Hide Sequence Related</strong><em><br>
41 Hide all annotations that are for individual sequences.</em></li>
42 <li><strong>Show Alignment Related</strong><em><br>
43 Show all annotations that are for the alignment as a whole (for
44 example, Consensus).</em></li>
45 <li><em>You can also selectively show or hide annotations
46 from the <a href="./popupMenu.html">Popup</a> or <a
47 href="../features/annotation.html">Annotation</a> menus.
49 <li><strong>Sort by Sequence</strong><em><br>Sort
50 sequence-specific annotations by sequence order in the alignment
51 (and within that, by label).</em></li>
52 <li><strong>Sort by Label</strong><em><br>Sort
53 sequence-specific annotations by label (and within that, by
54 sequence order). If neither sort order is selected, no sorting
55 is applied, allowing you to make a manual ordering of the
56 annotations.</em></li>
57 <li><strong>Autocalculated Annotation<br>
58 </strong><em>Settings for the display of autocalculated annotation.</em>
60 <li><strong>Show first<br></strong><em> Show
61 autocalculated annotations above sequence-specific
62 annotations. Note this also applies to other annotations for
63 the alignment, for example secondary structure prediction
64 from alignment.</em></li>
65 <li><strong>Show last<br></strong><em> Show
66 autocalculated / alignment annotations below
67 sequence-specific annotations.</em></li>
68 <li><strong>Apply to all groups<br>
69 </strong><em> When ticked, any modification to the current settings
70 will be applied to all autocalculated annotation.</em></li>
71 <li><strong>Show Consensus Histogram<br>
72 </strong><em> Enable or disable the display of the histogram above
73 the consensus sequence.</em></li>
74 <li><strong>Show Consensus Logo<br>
75 </strong><em> Enable or disable the display of the Consensus Logo
76 above the consensus sequence.</em></li>
77 <li><strong>Normalise Consensus Logo<br>
78 </strong><em>When enabled, scales all logo stacks to the same
79 height, making it easier to compare symbol diversity in
80 highly variable regions.</em></li>
81 <li><strong>Group Conservation<br>
82 </strong><em> When ticked, display a conservation row for all groups
83 (only available for protein alignments).</em></li>
84 <li><strong>Group Consensus<br>
85 </strong><em> When ticked, display a consensus row for all groups.</em></li>