+ <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-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-2386 -->'Apply to all groups' setting when
+ changing colour does not apply Conservation slider value
+ to all groups
+ </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-2623 -->Graduated feature colour threshold not
+ restored to UI when feature colour is edited
+ </li>
+ <li>
+ <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
+ a time when scrolling vertically in wrapped mode.
+ </li>
+ <li>
+ <!-- JAL-2630 -->Structure and alignment overview update
+ as graduate feature colour settings are modified via the
+ dialog box
+ </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 doesn't show position for
+ ambiguous amino acid and nucleotide symbols
+ </li>
+ <li>
+ <!-- JAL-2602 -->Copy consensus sequence failed if
+ alignment included gapped columns
+ </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-2594 -->Exception thrown if trying to create a
+ sequence feature on gaps only
+ </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-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-2291 -->Hide insertions in PopUp->Selection menu
+ only excluded gaps in current sequence and ignored
+ selection.
+ </li>
+ </ul>
+ <em>Rendering</em>
+ <ul>
+ <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-2385 -->Colour threshold slider doesn't update to
+ reflect currently selected view or group's shading
+ thresholds
+ </li>
+ <li>
+ <!-- JAL-2624 -->Feature colour thresholds not respected
+ when rendered on overview and structures when opacity at
+ 100%
+ </li>
+ <li>
+ <!-- JAL-2589 -->User defined gap colour not shown in
+ overview when features overlaid on alignment
+ </li>
+ </ul>
+ <em>Data import/export</em>
+ <ul>
+ <li>
+ <!-- JAL-2576 -->Very large alignments take a long time to
+ load
+ </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-2365,JAL-2642 -->Cannot configure feature colours
+ with lightGray or darkGray via features file (but can
+ specify lightgray)
+ </li>
+ <li>
+ <!-- JAL-2383 -->Above PID colour threshold not recovered
+ when alignment view imported from project
+ </li>
+ <li>
+ <!-- JAL-2520,JAL-2465 -->No mappings generated between
+ structure and sequences extracted from structure files
+ imported via URL and viewed in Jmol
+ </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>Web Services</em>
+ <ul>
+ <li>
+ <!-- JAL-2519 -->EnsemblGenomes example failing after
+ release of Ensembl v.88
+ </li>
+ <li>
+ <!-- JAL-2366 -->Proxy server address and port always
+ appear enabled in Preferences->Connections
+ </li>
+ <li>
+ <!-- JAL-2461 -->DAS registry not found exceptions
+ removed from console output
+ </li>
+ <li>
+ <!-- JAL-2582 -->Cannot retrieve protein products from
+ Ensembl by Peptide ID
+ </li>
+ <li>
+ <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
+ created from SIFTs, and spurious 'Couldn't open structure
+ in Chimera' errors raised after April 2017 update (problem
+ due to 'null' string rather than empty string used for
+ residues with no corresponding PDB mapping).
+ </li>
+ </ul>
+ <em>Application UI</em>
+ <ul>
+ <li>
+ <!-- JAL-2361 -->User Defined Colours not added to Colour
+ menu
+ </li>
+ <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-2532 -->Cancel in feature settings reverts
+ changes to feature colours via the Amend features dialog
+ </li>
+ <li>
+ <!-- JAL-2506 -->Null pointer exception when attempting to
+ edit graduated feature colour via amend features dialog
+ box
+ </li>
+ <li>
+ <!-- JAL-2436 -->Structure viewer's View -> Colour By view
+ selection menu changes colours of alignment views
+ </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-1256 -->Trackpad horizontal scroll gesture
+ adjusts start position in wrap mode
+ </li>
+ <li>
+ <!-- JAL-2563 -->Status bar doesn't show positions for
+ ambiguous amino acids
+ </li>
+ <li>
+ <!-- JAL-2431 -->cDNA Consensus annotation not shown in
+ CDS/Protein view after CDS sequences added for aligned
+ proteins
+ </li>
+ <li>
+ <!-- JAL-2592 -->User defined colourschemes called 'User
+ Defined' don't appear in Colours menu
+ </li>