</td>
<td><em>General</em>
<ul>
- <li><!-- --></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL-192 --->Alignment ruler shows positions relative to reference sequence</li>
</ul> <em>Application</em>
<ul>
- <li><!-- --></li>
+ <li><!-- JAL---></li>
+ <li><!-- JAL-2027-->Support for reverse-complement coding regions in ENA and EMBL</li>
+ <li><!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2 for ENA record retrieval</li>
+ <li><!-- JAL 1812 -->New 'execute Groovy script' option in an alignment window's Calculate menu</li>
+ <li><!-- JAL 1812 -->Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode</li>
+ <li><!-- JAL-1369 --->Store/restore reference sequence in Jalview projects</li>
+
</ul> <em>Applet</em>
<ul>
- <li><!-- --></li>
+ <li><!-- JAL---></li>
</ul></td>
<td>
<div align="left">
<li><!-- JAL-2018-->Export features in Jalview format (again) includes graduated colourschemes</li>
<li><!-- JAL-1722, JAL-2001-->More responsive when working with big alignments and lots of hidden columns</li>
<li><!-- JAL-2053-->hidden column markers not always rendered at right of alignment window</li>
- <li><!-- --></li>
+ <li><!-- JAL-2067, JAL- -->Tidied up links in help file table of contents</li>
+ <li><!-- JAL-2072 -->Feature based tree calculation not shown for DNA alignments</li>
+ <li><!-- JAL-2075 -->Hidden columns ignored during feature based tree calculation</li>
+ <li><!-- JAL-2065 -->Alignment view stops updating when show unconserved enabled for group on alignment</li>
+ <li><!-- JAL-2086 -->Cannot insert gaps into sequence when set as reference</li>
+
</ul>
<em>Application</em>
<ul>
<li><!-- JAL-1944 not yet fixed Error thrown when exporting a view with hidden sequences as flat-file alignment--></li>
<li><!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms</li>
<li><!-- JAL-1552-->URLs and links can imported by drag'n'drop on OSX webstart</li>
+ <li><!-- JAL-2030-->InstallAnywhere distribution fails when launching Chimera</li>
+ <li><!-- JAL-2080-->Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)</li>
+ <li><!-- JAL-2085 -->Cannot save project when view has a reference sequence defined</li>
+ <li><!-- JAL-1011 -->Columns are suddenly selected in other alignments and views when revealing hidden columns</li>
+ <li><!-- JAL-1989 -->Hide columns not mirrored in complement view in a cDNA/Protein splitframe</li>
+ <li><!-- JAL-1369 -->Cannot save/restore representative sequence from project when only one sequence is represented</li>
+ <!-- may exclude, this is an external service stability issue JAL-1941 /> RNA 3D structure not added via DSSR service</li> -->
</ul>
<em>Applet</em>
<ul>
region export in flat file generation</li>
<li>Export alignment views for display with the <a
- href="http://biojs.io/d/msa">BioJS MSAViewer</a></li>
+ href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
<li>Export scrollable SVG in HTML page</li>
<li>Optional embedding of BioJSON data when exporting