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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
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+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
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+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
<head>
<title>Alignment Window Menus</title>
</head>
<li><strong>Gather Views (G)</strong><em><br>
Each view associated with the alignment will be displayed within its own tab
on the current alignment window. </em></li>
- <li><strong>Show→(all Columns / Sequences)</strong><em><br>
- All hidden Columns / Sequences will be revealed. </em></li>
- <li><strong>Hide→(all Columns / Sequences)</strong><em><br>
- Hides the currently selected Columns / Sequences</em></li>
+ <li><strong>Show→(all Columns / Sequences / Sequences and Columns</strong> )</strong><em><br>
+ All hidden Columns / Sequences / Sequences and Columns will be revealed. </em></li>
+ <li><strong>Hide→(all Columns / Sequences / Selected Region / All but Selected Region)</strong><em><br>
+ Hides the currently selected Columns / Sequences / Region or everything but the selected Region.</em></li>
<li><strong>Show Annotations<br>
</strong><em>If this is selected the "Annotation Panel" will be
displayed below the alignment. The default setting is to display the conservation
calculation, quality calculation and consensus values as bar charts. </em></li>
+ <li><strong>Autocalculated Annotation<br></strong>Settings for the display of autocalculated annotation.
+ <ul><li>
+ <strong>Apply to all groups<br></strong>
+ When ticked, any modification to the current settings will be applied to all autocalculated annotation.
+ </li>
+ <li>
+ <strong>Show Consensus Histogram<br></strong>
+ Enable or disable the display of the histogram above the consensus sequence.
+ </li>
+ <li>
+ <strong>Show Consensus Logo<br></strong>
+ Enable or disable the display of the sequence logo above the consensus sequence.
+ </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>
+ When ticked, display a conservation row for all groups (only available for protein alignments).
+ </li>
+ <li>
+ <strong>Apply to all groups<br></strong>
+ When ticked, display a consensus row for all groups.
+ </li>
+ </ul>
+ </li>
+ <li><strong>Automatic Scrolling<br>
+ </strong><em>When selected, the view will automatically scroll to display the
+ highlighted sequence position corresponding to the position under the mouse
+ pointer in a linked alignment or structure view.</em>
+ </li>
<li><strong>Show Sequence Features</strong><br>
<em>Show or hide sequence features on this alignment.</em></li>
<li><strong><a href="../features/featuresettings.html">Seqence Feature Settings...</a></strong><em><br>
Opens the Sequence Feature Settings dialog box to control the colour and display
of sequence features on the alignment, and configure and retrieve features
from DAS annotation servers.</em></li>
+ <li><strong>Sequence ID Tooltip</strong><em> (application only)
+ <br>This submenu's options allow the inclusion or exclusion of
+ non-positional sequence features or database cross references
+ from the tooltip shown when the mouse hovers over the sequence ID panel.</em></li>
<li><strong>Alignment Properties...<br>
</strong><em>Displays some simple statistics computed for the
current alignment view and any named properties defined on the
git://source.jalview.org / jalview.git / blobdiff