- <li>
- <!-- JAL-247 -->Hidden sequence markers and representative
- sequence bolding included when exporting alignment as EPS,
- SVG, PNG or HTML. <em>Display of these can be
- configured via the Format menu or in batch mode with a
- jalview properties file.</em>
- </li>
- <li>
- <!-- JAL-3003 -->Alignment is black in exported EPS file
- when sequences are selected in exported view.</em>
- </li>
- <li>
- <!-- JAL-3059 -->Groups with different coloured borders
- aren't rendered with correct colour.
- </li>
- <li>
- <!-- JAL-3092 -->Jalview could hang when importing certain types of knotted RNA secondary structure
- </li>
- <li>
- <!-- JAL-3095 -->Sequence highlight in trimmed VARNA 2D structure is incorrect for sequences that do not start at 1
- </li>
- </ul>
- </div>
+ <li>
+ <!-- JAL-3104 -->Poorly scaled bar in quality annotation
+ row shown in Feredoxin Structure alignment view of example
+ alignment.
+ </li>
+ <li>
+ <!-- JAL-2854 -->Annotation obscures sequences if lots of
+ annotation displayed.
+ </li>
+ <li>
+ <!-- JAL-3107 -->Group conservation/consensus not shown
+ for newly created group when 'Apply to all groups'
+ selected
+ </li>
+ <li>
+ <!-- JAL-3087 -->Corrupted display when switching to
+ wrapped mode when sequence panel's vertical scrollbar is
+ visible.
+ </li>
+ <li>
+ <!-- JAL-3003 -->Alignment is black in exported EPS file
+ when sequences are selected in exported view.</em>
+ </li>
+ <li>
+ <!-- JAL-3059 -->Groups with different coloured borders
+ aren't rendered with correct colour.
+ </li>
+ <li>
+ <!-- JAL-3092 -->Jalview could hang when importing certain
+ types of knotted RNA secondary structure.
+ </li>
+ <li>
+ <!-- JAL-3095 -->Sequence highlight and selection in
+ trimmed VARNA 2D structure is incorrect for sequences that
+ do not start at 1.
+ </li>
+ <li>
+ <!-- JAL-3061 -->'.' inserted into RNA secondary structure
+ annotation when columns are inserted into an alignment,
+ and when exporting as Stockholm flatfile.
+ </li>
+ <li>
+ <!-- JAL-3053 -->Jalview annotation rows containing upper
+ and lower-case 'E' and 'H' do not automatically get
+ treated as RNA secondary structure.
+ </li>
+ <li>
+ <!-- JAL-3106 -->.jvp should be used as default extension
+ (not .jar) when saving a jalview project file.
+ </li>
+ <li>
+ <!-- JAL-3105 -->Mac Users: closing a window correctly
+ transfers focus to previous window on OSX
+ </li>
+ </ul>
+ <em>Java 10 Issues Resolved</em>
+ <ul>
+ <li>
+ <!-- JAL-2988 -->OSX - Can't save new files via the File
+ or export menus by typing in a name into the Save dialog
+ box.
+ </li>
+ <li>
+ <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
+ of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
+ 'look and feel' which has improved compatibility with the
+ latest version of OSX.
+ </li>
+ </ul>
+ </div>