+ <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.schemes.ResidueProperties.BLOSUM62[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>
+ </ul>
+ <em>Application</em>
+ <ul>
+ <li><!-- JAL-2401 -->Easier creation of colours for all 'Lower case' residues (button in colourscheme editor debugged and new documentation and tooltips added)</li>
+ <li><!-- JAL-2399-->Text colour threshold's 'Cancel' button doesn't restore group-specific text colour thresholds</li>
+ <li><!-- JAL-2243 -->Feature settings panel does not update as new features are added to alignment</li>
+ <li><!-- JAL-2436 -->Structure viewer's View -> Colour By view selection menu changes colours of alignment views</li>
+ <li><!-- JAL-2366 -->Proxy server address and port always appear enabled in Preferences->Connections</li>
+ <li><!-- JAL-2426 -->Spurious exceptions in console raised from alignment calculation workers after alignment has been closed</li>
+ <li><!-- JAL-1608 -->Typo in selection popup menu - Create groups now 'Create Group'</li>
+ <li><!-- JAL-1608 -->CMD/CTRL and G or Shift G for Create/Undefine group doesn't always work</li>
+ <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>