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JAL-4336
jvCacheableInputBox isn't getting minimum default width in JalviewJSJAL-4334
Uniprot parser does not support sequence features with 'unknown' start or end
overview window doesn't get a title in desktop windows menuJAL-4319
stop clover instrumentation tasks being triggered during shadowJar build
feature should be displayed when its rendering and filtering settings are adjustedJAL-4315
drag and drop feature colours file to quickly apply feature settings
concurrent modification exceptions during CLI tests
don't offer View model page for sources that do not have model pages
Reduce number of database crossreferences shown in tooltip
menu options to show or hide HETATM groups in structure view
unify behaviour of groovy scripts when called via CLI, run from Groovy console and calculate 'run script' menu
upgrade groovy to v4
Java Console opening at startup with the exampleFile.jvp opening (nearly always) causes Jalview to hang
Application hangs when Jalview sends Jmol commands whilst Jmol is acting on commands from Jalview
overhang of 1 pixel on bottom left vertical for group boundaries
Group boundary not drawn properly in fastPaint or paint
check and verify channel launch build jvl files produced by bamboo getdown build are launchable
User should be able to see a collected list of warnings/errors after a batch open.
--image and --structureimage should require --overwrite if file exists
ID width for imported project is affected by changes in font size in User preferences
store and restore adjustable ID margin and annotation panel height in Jalview projects
gracefully handle failures to load files during CLI based processing
{dirname} substitution always substitutes the absolute dirname
Exception when groovy console is opened in 2.11.3.0
Configurable bitmap export preferences for height, width and scale factor
Visible adjuster marks to grab and adjust annotation panel height and id width
Reduce number of specific variants of common sub-value parameters in next generation command line interface
Command line option allowing the background colour for a structure view to be configured
Deprecation warning when pre 2.11.3.0 CLI arguments are processed
Adjustable ID margin in wrapped mode
HTML Export sometimes doesn't include all rows of sequence alignment
review bens big merge for 2.11.3.0
RNA secondary structure glyph renderings still a little skew
SLF4J produces an error to STDERR at Jalview startup due to missing class
bottom line of a sequence group's border misaligned with vertical and colour box
enable antialiasdisplay in Jmol
Secondary Structure annotation is clunkily pixellated on HiDPI screens
bio.tools record accompanying Jalview source code
exception when pressing escape in fetch from URL dialog
sun.management.ManagementFactoryHelper not found when Opening preferences
2.11.3 version Uniprot FTS doesn't work in JalviewJS
rnaml import missing terminal residue
Structure viewer image export can hang when run from command line
sequence descriptions are updated from database reference sources if not already defined
remove build artefacts to reduce source distribution tarball size
2.11.3 develop build hanging in tests..
chains in PDB or mmCIF files with negative RESNUMs for their whole sequence extent throw exceptions
System freeze when opening file using gui (not `Ctrl+O`) while a dialog is open
"add reference annotation" should ignore when a selection is active and not only add positions for currently highlighted columns/selection range
Prevent gradle test on macOS continuously grabbing focus
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