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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
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<body>
-<p><strong>Alignment Window Annotations Menu</strong> (Since Jalview 2.8.2)</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>
+ <p>
+ <strong>Alignment Window Annotations Menu</strong> (Since Jalview
+ 2.8.2)
+ </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>
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</html>
git://source.jalview.org / jalview.git / blobdiff