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 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>Show All Annotations</strong><em><br>
- Show all available annotations on the alignment. You can selectively hide these from the <a href="./popupMenu.html">Popup</a>
- or <a href="../features/annotation.html">Annotation</a> menus. (Since Jalview 2.8.2)</em></li>
- <li><strong>Hide All Annotations</strong><em><br>
- Hide all annotations on the alignment. (Since Jalview 2.8.2)</em></li>
- <li><strong>Autocalculated Annotation<br> </strong><em>Settings
- for the display of autocalculated annotation.</em>
- <ul>
- <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>Apply to all groups<br> </strong><em> When
- ticked, display a consensus row for all groups.</em></li>
- </ul></li>
<li><strong>Show Sequence Features</strong><br> <em>Show
or hide sequence features on this alignment.</em>
</li>
using the mouse. </em>
</li>
</ul></li>
+ <li><strong>Annotations</strong><em> (Since Jalview 2.8.2)</em>
+ <ul>
+ <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>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><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>
+ </li>
<li><strong>Alignment Window Format Menu</strong>
<ul>
<li><strong>Font...<br> </strong><em>Opens the
git://source.jalview.org / jalview.git / blobdiff