- <em>The following additional entries are avalable when the popup menu is opened on a consensus sequence annotation row:</em>
- <ul>\r
- <li><strong>Ignore Gaps in Consensus</strong><br>\r
- If this checkbox is selected, all consensus calculations performed in \r
- the current Alignment window will be done without counting gaps as a consensus \r
- character.</li>\r
- <li><strong>Copy Consensus Sequence</strong><br>\r
- Copies the consensus sequence to the clipboard in Fasta format, to allow \r
- the consensus sequence to be added to an alignment. Note the copied sequence \r
- is not accessible to other programs if Jalview is running as an applet \r
- in a web page.</li>\r
- </ul>\r
- </li>\r
- <li><strong>Annotation Popup Menu<br>\r
- </strong><em>This menu is opened when right-clicking on the selected positions \r
- of an annotation.</em> \r
- <ul>\r
- <li><strong>Helix</strong><br>\r
- <em>Mark selected positions with a helix glyph (a red oval), and optional \r
- text label (see below). Consecutive ovals will be rendered as an unbroken \r
- red line.</em> </li>\r
- <li><strong>Sheet</strong><br>\r
- <em>Mark selected positions with a sheet glyph (a green arrow oriented \r
- from left to right), and optional text label (see below). Consecutive \r
- arrows will be joined together to form a single green arrow.</em> </li>\r
- <li><strong>Label</strong><br>\r
- <em>Sets the text label at the selected positions. If more that one consecutive \r
- position is marked with the same label, only the first position's label \r
- will be rendered.</em> </li>\r
- <li><strong>Colour</strong><br>\r
- <em>Changes the colour of the annotation text label.</em> </li>\r
- <li><strong>Remove Annotation</strong><br>\r
- <em>Blanks any annotation at the selected positions on the row. Note: \r
- <strong>This cannot be undone</strong></em> </li>\r
- </ul>\r
- </li>\r
-</ul>\r
-</body>\r
-</html>\r
+ <em>The following additional entries are available when the popup menu is opened on a consensus sequence annotation row:</em>
+ <ul>
+
+ <li><strong>Ignore Gaps in Consensus</strong><br>
+ If this checkbox is selected, all consensus calculations performed in
+ the current Alignment window will be done without counting gaps as a consensus
+ character.</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>
+ <li><strong>Copy Consensus Sequence</strong><br>
+ Copies the consensus sequence to the clipboard in Fasta format, to allow
+ the consensus sequence to be added to an alignment. Note the copied sequence
+ is not accessible to other programs if Jalview is running as an applet
+ in a web page.</li>
+ </ul>
+ </li>
+ <li><strong>Annotation Popup Menu<br>
+ </strong><em>This menu is opened when right-clicking on the selected positions
+ of an annotation.</em>
+ <ul>
+ <li><strong>Helix</strong><br>
+ <em>Mark selected positions with a helix glyph (a red oval), and optional
+ text label (see below). Consecutive ovals will be rendered as an unbroken
+ red line.</em> </li>
+ <li><strong>Sheet</strong><br>
+ <em>Mark selected positions with a sheet glyph (a green arrow oriented
+ from left to right), and optional text label (see below). Consecutive
+ arrows will be joined together to form a single green arrow.</em> </li>
+ <li><strong>Label</strong><br>
+ <em>Sets the text label at the selected positions. If more that one consecutive
+ position is marked with the same label, only the first position's label
+ will be rendered.</em> </li>
+ <li><strong>Colour</strong><br>
+ <em>Changes the colour of the annotation text label.</em> </li>
+ <li><strong>Remove Annotation</strong><br>
+ <em>Blanks any annotation at the selected positions on the row. Note:
+ <strong>This cannot be undone</strong></em> </li>
+ </ul>
+ </li>
+</ul>
+</body>
+</html>