+ </ul>
+ <em>Test Suite</em>
+ <li><!-- JAL-2474 -->Added PrivilegedAccessor to test suite</li>
+ <li><!-- JAL-2326 -->Prevent or clear modal dialogs raised during tests</li>
+ <li><!-- -->
+ </ul>
+ </div></td><td><div align="left">
+ <em>General</em>
+ <ul>
+ <li>
+ <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
+ matrix - C->R should be '3'<br />Old matrix restored with
+ this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
+ </li>
+ <li>
+ <!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
+ and substitution matrix based Tree calculations.<br />In
+ earlier versions of Jalview, gaps matching gaps were
+ penalised, and gaps matching non-gaps penalised even more.
+ In the PCA calculation, gaps were actually treated as
+ non-gaps - so different costs were applied, which mean't
+ Jalview's PCAs were different to those produced by
+ SeqSpace.<br />Jalview now treats gaps in the same way as
+ SeqSpace (ie it scores them as 0). To restore pre-2.10.2
+ behaviour<br />
+ jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
+ 2.10.1 mode<br />
+ jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
+ restore 2.10.2 mode
+ </li>
+ <li><!-- JAL-2346 -->Reopening Colour by annotation dialog doesn't reselect a specific sequence's associated annotation after it was used for colouring a view</li>
+ <li><!-- JAL-2430 -->Hidden regions in alignment views are not coloured in linked structure views</li>
+ <li><!-- JAL-2419 -->Current selection lost if popup menu opened on a region of alignment without groups</li>
+ <li><!-- JAL-2374 -->Popup menu not always shown for regions of an alignment with overlapping groups</li>
+ <li><!-- JAL-2310 -->Finder double counts if both a sequence's name and description match</li>
+ <li><!-- JAL-2370 -->Hiding column selection containing two hidden regions results in incorrect hidden regions</li>
+ <li><!-- JAL-2377 -->PCA calculation could hang when generating output report when working with highly redundant alignments</li>
+ <li><!-- JAL-2365 -->Cannot configure feature colours with lightGray or darkGray via features file</li>
+ <li><!-- JAL-2421 -->Overview window visible region moves erratically when hidden rows or columns are present</li>
+ <li><!-- JAL-2362 -->Per-residue colourschemes applied via the Structure Viewer's colour menu don't correspond to sequence colouring</li>
+ <li><!-- JAL-2405 -->Protein specific colours only offered in colour and group colour menu for protein alignments</li>
+ <li><!-- JAL-2386 -->'Apply to all groups' setting when changing colour does not apply Conservation slider value to all groups</li>
+ <li><!-- JAL-2385 -->Colour threshold slider doesn't update to reflect currently selected view or group's shading thresholds</li>
+ <li><!-- JAL-2373 -->Percentage identity and conservation menu items do not show a tick or allow shading to be disabled</li>
+ <li><!-- JAL-2385 -->Conservation shading or PID threshold lost when base colourscheme changed if slider not visible</li>
+ <li><!-- JAL-2547 -->Sequence features shown in tooltip for gaps before start of features</li>
+ <li><!-- JAL-2576 -->Very large alignments take a long time to load</li>
+ <li><!-- JAL-2590 -->Cannot load Newick trees from eggnog ortholog database</li>