3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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23 <title>Alignment Window Menus</title>
27 <p><strong>Alignment Window Annotations Menu</strong> (Since Jalview 2.8.2)</p>
29 <li><strong>Show Alignment Related</strong><em><br>
30 Show all annotations that are for the alignment as a whole (for example, Consensus,
31 or secondary structure prediction from alignment)).</em></li>
32 <li><strong>Hide Alignment Related</strong><em><br>
33 Hide all annotations that are for the alignment as a whole.</em></li>
34 <li><strong>Show Sequence Related</strong><em><br>
35 Show all annotations that are for individual sequences.</em></li>
36 <li><strong>Hide Sequence Related</strong><em><br>
37 Hide all annotations that are for individual sequences.</em></li>
38 <li><strong>Show Alignment Related</strong><em><br>
39 Show all annotations that are for the alignment as a whole (for example, Consensus).</em></li>
40 <li><em>You can also selectively show or hide annotations from the <a href="./popupMenu.html">Popup</a>
41 or <a href="../features/annotation.html">Annotation</a> menus.</em></li>
42 <li><strong>Sort by Sequence</strong><em><br>Sort sequence-specific annotations by sequence order in the alignment
43 (and within that, by label).</em></li>
44 <li><strong>Sort by Label</strong><em><br>Sort sequence-specific annotations by label
45 (and within that, by sequence order). If neither sort order is selected, no sorting is applied,
46 allowing you to make a manual ordering of the annotations.</em></li>
47 <li><strong>Autocalculated Annotation<br> </strong><em>Settings
48 for the display of autocalculated annotation.</em>
50 <li><strong>Show first<br></strong><em>
51 Show autocalculated annotations above sequence-specific annotations.
52 Note this also applies to other annotations for the alignment, for example secondary
53 structure prediction from alignment.</em></li>
54 <li><strong>Show last<br></strong><em>
55 Show autocalculated / alignment annotations below sequence-specific annotations.</em></li>
56 <li><strong>Apply to all groups<br> </strong><em> When
57 ticked, any modification to the current settings will be applied
58 to all autocalculated annotation.</em></li>
59 <li><strong>Show Consensus Histogram<br> </strong><em>
60 Enable or disable the display of the histogram above the
61 consensus sequence.</em></li>
62 <li><strong>Show Consensus Logo<br> </strong><em> Enable
63 or disable the display of the Consensus Logo above the consensus
65 <li><strong>Normalise Consensus Logo<br>
66 </strong><em>When enabled, scales all logo stacks to the same height,
67 making it easier to compare symbol diversity in highly variable
69 <li><strong>Group Conservation<br> </strong><em> When
70 ticked, display a conservation row for all groups (only available
71 for protein alignments).</em></li>
72 <li><strong>Group Consensus<br> </strong><em> When
73 ticked, display a consensus row for all groups.</em></li>