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- JAL-4336
jvCacheableInputBox isn't getting minimum default width in JalviewJS - JAL-4334
Uniprot parser does not support sequence features with 'unknown' start or end - JAL-4331
overview window doesn't get a title in desktop windows menu - JAL-4319
stop clover instrumentation tasks being triggered during shadowJar build - JAL-4317
feature should be displayed when its rendering and filtering settings are adjusted - JAL-4315
drag and drop feature colours file to quickly apply feature settings - JAL-4312
concurrent modification exceptions during CLI tests - JAL-4310
don't offer View model page for sources that do not have model pages - JAL-4308
Reduce number of database crossreferences shown in tooltip - JAL-4307
menu options to show or hide HETATM groups in structure view - JAL-4305
unify behaviour of groovy scripts when called via CLI, run from Groovy console and calculate 'run script' menu - JAL-4304
upgrade groovy to v4 - JAL-4298
Java Console opening at startup with the exampleFile.jvp opening (nearly always) causes Jalview to hang - JAL-4295
Application hangs when Jalview sends Jmol commands whilst Jmol is acting on commands from Jalview - JAL-4293
overhang of 1 pixel on bottom left vertical for group boundaries - JAL-4289
Group boundary not drawn properly in fastPaint or paint - JAL-4288
check and verify channel launch build jvl files produced by bamboo getdown build are launchable - JAL-4285
User should be able to see a collected list of warnings/errors after a batch open. - JAL-4284
--image and --structureimage should require --overwrite if file exists - JAL-4282
ID width for imported project is affected by changes in font size in User preferences - JAL-4281
store and restore adjustable ID margin and annotation panel height in Jalview projects - JAL-4279
gracefully handle failures to load files during CLI based processing - JAL-4277
{dirname} substitution always substitutes the absolute dirname - JAL-4274
Configurable bitmap export preferences for height, width and scale factor - JAL-4273
Visible adjuster marks to grab and adjust annotation panel height and id width - JAL-4269
Reduce number of specific variants of common sub-value parameters in next generation command line interface - JAL-4265
Command line option allowing the background colour for a structure view to be configured - JAL-4262
Deprecation warning when pre 2.11.3.0 CLI arguments are processed - JAL-4260
Adjustable ID margin in wrapped mode - JAL-4259
HTML Export sometimes doesn't include all rows of sequence alignment - JAL-4258
review bens big merge for 2.11.3.0 - JAL-4256
RNA secondary structure glyph renderings still a little skew - JAL-4255
SLF4J produces an error to STDERR at Jalview startup due to missing class - JAL-4253
bottom line of a sequence group's border misaligned with vertical and colour box - JAL-4252
enable antialiasdisplay in Jmol - JAL-4250
Secondary Structure annotation is clunkily pixellated on HiDPI screens - JAL-4243
bio.tools record accompanying Jalview source code - JAL-4242
exception when pressing escape in fetch from URL dialog - JAL-4237
sun.management.ManagementFactoryHelper not found when Opening preferences - JAL-4236
2.11.3 version Uniprot FTS doesn't work in JalviewJS - JAL-4223
rnaml import missing terminal residue - JAL-4222
Structure viewer image export can hang when run from command line - JAL-4221
sequence descriptions are updated from database reference sources if not already defined - JAL-4218
remove build artefacts to reduce source distribution tarball size - JAL-4217
2.11.3 develop build hanging in tests.. - JAL-4216
chains in PDB or mmCIF files with negative RESNUMs for their whole sequence extent throw exceptions - JAL-4214
System freeze when opening file using gui (not `Ctrl+O`) while a dialog is open - JAL-4213
"add reference annotation" should ignore when a selection is active and not only add positions for currently highlighted columns/selection range - JAL-4212
Prevent gradle test on macOS continuously grabbing focus - JAL-4208
Structures imported directly via PDB sequence fetcher have alphafold reliability instead of temperature factor
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