<li><!-- JAL-384 -->Custom shading schemes created via groovy scripts</li>
<li><!-- JAL-2491 -->linked scrolling of CDS/Protein views via Overview or sequence motif search operations</li>
<li><!-- JAL-2526 -->Efficiency improvements for interacting with alignment and overview windows</li>
- <li><!-- --></li>
+ <li>
+ <!-- JAL-2535 -->Posterior probability annotation from
+ Stockholm files imported as sequence associated annotation
+ </li>
+ <li>
+ <!-- JAL-2533 -->Sequence names don't include file
+ extension when importing structure files without embedded
+ names or PDB accessions
+ </li>
</ul>
<em>Application</em>
<ul>
<li><!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get shown again after pressing 'Cancel'</li>
<li><!-- JAL-2461 -->DAS registry not found exceptions removed from console output</li>
<li><!-- JAL-2383 -->Above PID colour threshold not recovered when alignment view imported from project</li>
-
+ <li><!-- JAL-2465 -->No mappings generated between structure and sequences extracted from structure files imported via URL</li>
+ <li>
+ <!-- JAL-2520 -->Structures loaded via URL are saved in
+ Jalview Projects rather than fetched via URL again when
+ the project is loaded and the structure viewed
+ </li>
</ul>
<em>Applet</em>
<ul>
<li><!-- JAL-2442 -->Features not rendered as transparent on overview or linked structure view</li>
<li><!-- JAL-2372 -->Colour group by conservation doesn't work (since 2.8)</li>
+ <li><!-- JAL-2517 -->Hitting Cancel after applying user-defined colourscheme doesn't restore original colourscheme</li>
</ul>
<em>New Known Issues</em>
<ul>
<li><!-- JAL-2566 -->Protein/CDS view scrolling not always in phase after a sequence motif find operation</li>
<li><!-- JAL-2563 -->Status bar doesn't show positions for ambiguous amino acids</li>
+ <li><!-- JAL-2550 -->Importing annotation file with rows containing just upper and lower case letters are interpreted as WUSS rna secondary structure symbols</li>
</ul>
</div>