<td><div align="left">
<em>General</em>
<ul>
- <li><!-- JAL-2360,JAL-2371, -->More robust colours and shader model for alignments and groups</li>
+ <li><!-- JAL-2379 -->Revised implementation of PCA for speed and memory efficiency (~30x faster)</li>
+ <li><!-- JAL-2500 -->Trees computed on Sequence Feature Similarity may have different topology due to increased precision</li>
+ <li><!-- JAL-2360,JAL-2371, -->More robust colours and shader model for alignments and groups</li>
<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>
</ul>
<em>Test Suite</em>
+ <ul>
<li><!-- JAL-2474 -->Added PrivilegedAccessor to test suite</li>
<li><!-- JAL-2326 -->Prevent or clear modal dialogs raised during tests</li>
<li><!-- -->
+ <em>Scripting</em>
+ <ul>
+ <li><!-- JAL-2344 -->FileFormatI interface for describing and identifying file formats (instead of String constants)</li>
+ </ul>
</ul>
</div></td><td><div align="left">
<em>General</em>
<li><!-- JAL-2034 -->Overview window doesn't always update when a group defined on the alignment is resized</li>
<li><!-- JAL-2605 -->Mouseovers on left/right scale region in wrapped view result in positional status updates</li>
<li><!-- JAL-2563 -->Status bar shows position for ambiguous amino acid and nucleotide symbols</li>
+ <li><!-- JAL-2602 -->Copy consensus sequence failed if alignment included gapped columns</li>
+ <li><!-- JAL-2589 -->User defined gap colour not shown in overview when features overlaid on alignment</li>
+ </ul>
+ <strong>Documentation</strong>
+ <ul>
+ <li><!-- JAL-2339 -->Release notes reformatted for readibility with the built-in Java help viewer</li>
</ul>
<em>Application</em>
<ul>
<li><!-- JAL-2563 -->Status bar doesn't show positions for ambiguous amino acids</li>
<li><!-- JAL-2291 -->Hide insertions in PopUp menu excludes gaps in selection, current sequence and only within selected columns</li>
<li><!-- JAL-2582 -->Cannot retrieve protein products from Ensembl by Peptide ID</li>
+ <li><!-- JAL-2431 -->cDNA Consensus annotation not shown in CDS/Protein view after CDS sequences added for aligned proteins</li>
</ul>
<em>Applet</em>
<ul>
+ <li><!-- JAL-2468 -->Switching between Nucleotide and Protein score models doesn't always result in an updated PCA plot</li>
<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>
<li><!-- JAL-2550 -->Importing annotation file with rows containing just upper and lower case letters are interpreted as WUSS rna secondary structure symbols</li>
<li><!-- JAL-2590 -->Cannot load Newick trees from eggnog ortholog database</li>
</ul>
-
+ <em>Test Suite</em>
+ <ul><li><!-- JAL-2314 -->Unit test failure: jalview.ws.jabaws.RNAStructExportImport setup fails</li>
+ <li><!-- JAL- --></li>
+ </ul>
</div>
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