- <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-2563 -->Sequence position for ambiguous codon not shown in status bar</li>
+ <li>
+ <!-- JAL-2424 -->Fixed off-by-one bug that affected
+ scaling of branch lengths for trees computed using
+ Sequence Feature Similarity.
+ </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-2623 -->Graduated feature colour threshold not
+ restored to UI when feature colour is edited
+ </li>
+ <li>
+ <!-- JAL-2624 -->Feature colour thresholds not respected
+ when rendered on overview and structures when opacity at
+ 100%
+ </li>
+ <li>
+ <!-- JAL-2630 -->Structure and alignment overview update
+ as graduate feature colour settings are modified via the
+ dialog box
+ </li>
+ <li>
+ <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
+ a time when scrolling vertically in wrapped mode.
+ </li>
+ <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>
+ <li>
+ <!-- JAL-2473 -->Minimum size set for Jalview windows so
+ widgets don't permanently disappear
+ </li>
+ <li>
+ <!-- JAL-2503 -->Cannot select or filter quantitative
+ annotation that are shown only as column labels (e.g.
+ T-Coffee column reliability scores)
+ </li>
+ <li>
+ <!-- JAL-2589 -->Gap colours in user-defined colourschemes
+ are not shown
+ </li>
+ <li>
+ <!-- JAL-2594 -->Exception thrown if trying to create a
+ sequence feature on gaps only
+ </li>
+ <li>
+ <!-- JAL-2544 --> Sort by features includes features to
+ right of selected region when gaps present on right-hand
+ boundary
+ </li>
+ <li>
+ <!-- JAL-2504 -->Features created with 'New feature'
+ button from a Find inherit previously defined feature type
+ rather than the Find query string
+ </li>
+ <li>
+ <!-- JAL-2423 -->incorrect title in output window when
+ exporting tree calculated in Jalview
+ </li>
+ <li>
+ <!-- JAL-2507 -->Per-sequence RNA secondary structures
+ added after a sequence was imported are not written to
+ Stockholm File
+ </li>
+ <li>
+ <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
+ when importing RNA secondary structure via Stockholm
+ </li>
+ <li>
+ <!-- JAL-2509 -->Secondary structure arrows for [] and {}
+ not shown in correct direction for simple pseudoknots
+ </li>
+ <li>
+ <!-- JAL-2437 -->Hiding sequences at bottom of alignment
+ and then revealing them reorders sequences on the
+ alignment
+ </li>
+ <li>
+ <!-- JAL-964 -->Group panel in sequence feature settings
+ doesn't update to reflect available set of groups after
+ interactively adding or modifying features
+ </li>
+ <li>
+ <!-- JAL-2225 -->Sequence Database chooser unusable on
+ Linux
+ </li>
+ <li>
+ <!-- JAL -->
+ </li>
+ <li>
+ <!-- JAL -->
+ </li>
+ <li>
+ <!-- JAL -->
+ </li>
+ </ul>
+ <strong>Documentation</strong>
+ <ul>
+ <li>
+ <!-- JAL-2339 -->Release notes reformatted for readibility
+ with the built-in Java help viewer
+ </li>
+ <li>
+ <!-- JAL-1644 -->Find documentation updated with 'search
+ sequence description' option
+ </li>