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JAL-4356 release date for 2.11.3.3 is 22nd May 2025
[jalview.git]
/
src
/
2023-10-19
Ben Soares
JAL-629 Fix --nodebug turning off debug mode from prope...
tree
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commitdiff
2023-10-19
Ben Soares
JAL-4298 comment markers
tree
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commitdiff
2023-10-19
Ben Soares
Merge branch 'improvement/JAL-3783_upgrade_to_groovy...
tree
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commitdiff
2023-10-19
James Procter
JAL-4298 avoid deadlock waiting to update doc when...
tree
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commitdiff
2023-10-19
Ben Soares
JAL-4305 Isolate and unify the Jalview object from...
tree
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commitdiff
2023-10-19
James Procter
JAL-4307 View->Ligands submenu, implementation for...
tree
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commitdiff
2023-10-19
Ben Soares
Merge branch 'improvement/JAL-3783_upgrade_to_groovy...
tree
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commitdiff
2023-10-18
Ben Soares
JAL-629 Run non-alignframe linked groovy scripts. ...
tree
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commitdiff
2023-10-18
Ben Soares
JAL-4262 Fix the nonblockingdialog so that Jalview...
tree
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commitdiff
2023-10-17
James Procter
JAL-4134 TODO printNode update for columnTrees
tree
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commitdiff
2023-10-17
James Procter
JAL-4134 JAL-4302 remove unnecessary casts
tree
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commitdiff
2023-10-17
James Procter
JAL-4089 selected columns are reported in absolute...
tree
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commitdiff
2023-10-13
Ben Soares
JAL-3783 Updated groovy jars. Requires javaparser...
tree
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commitdiff
2023-10-13
James Procter
JAL-4295 concatenate all mouseover highlights into...
tree
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commitdiff
2023-10-12
Ben Soares
JAL-3772 Fix the logic of prompt to save URL loaded...
tree
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commitdiff
2023-10-12
Ben Soares
JAL-629 null check and neatening code
tree
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commitdiff
2023-10-11
Ben Soares
JAL-629 correct a timeout. Correct passing html flag.
tree
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commitdiff
2023-10-11
Ben Soares
JAL-629 Add a timeout to modal dialogs for command...
tree
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commitdiff
2023-10-11
Ben Soares
JAL-629 Remove argfiles from the hashset of used argfil...
tree
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commitdiff
2023-10-11
Ben Soares
JAL-3772 Preference to NOT prompt to save remotely...
tree
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commitdiff
2023-10-11
Ben Soares
JAL-4298 Added diagnostics and minor dimension changes...
tree
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commitdiff
2023-10-05
Ben Soares
JAL-4298 Fixed initial log level to see .jalview_proper...
tree
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commitdiff
2023-10-03
Ben Soares
JAL-4001 Only use acquireDialogQueue and releaseDialogQ...
bug/JAL-4001_fix_About_Jalview_not_appearing
tree
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commitdiff
2023-10-03
Ben Soares
Merge branch 'develop' into bug/JAL-4289_group_boundary...
tree
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commitdiff
2023-10-03
James Procter
Merge branch 'patch/JAL-4062_sort_and_merge_contiguousr...
tree
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commitdiff
2023-10-02
Ben Soares
JAL-4289 In fastPaint(), don't render one more than...
tree
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commitdiff
2023-10-01
James Procter
JAL-244 ensure background is completely filled with...
tree
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commitdiff
2023-10-01
James Procter
JAL-244 export image with full width IDs regardless...
tree
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commitdiff
2023-10-01
James Procter
JAL-244 JAL-4091 allow calculation of label id width...
tree
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commitdiff
2023-10-01
James Procter
JAL-244 JAL-4091 FIXME for JAL-3362 patch testCalculate...
tree
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commitdiff
2023-09-29
James Procter
JAL-629 JAL-4265 JAL-4286 report the filename for the...
tree
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commitdiff
2023-09-29
James Procter
JAL-244 JAL-4090 use current IdWidth when exporting...
tree
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commitdiff
2023-09-29
James Procter
JAL-3858 fix check annotation row and column positionin...
tree
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commitdiff
2023-09-28
James Procter
JAL-3858 don’t divide if we only had one value to count
tree
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commitdiff
2023-09-28
James Procter
JAL-3858 check annotation row and column positioning...
tree
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commitdiff
2023-09-28
James Procter
JAL-3858 improved contactInterval computation and added...
tree
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commitdiff
2023-09-26
James Procter
JAL-3858 JAL-4090 avoid NPE when given out of bound...
tree
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commitdiff
2023-09-25
James Procter
JAL-3858 minimum value for a range is used to shade...
tree
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commitdiff
2023-09-25
James Procter
JAL-3858 javadoc and slightly revised green linear...
tree
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commitdiff
2023-09-25
James Procter
JAL-3858 report PAE range with sensible precision
tree
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commitdiff
2023-09-21
James Procter
JAL-1551 javadoc for mapUtils
tree
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commitdiff
2023-09-21
James Procter
JAL-3855 disable the AlphaFold DB entry in Sequence...
tree
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commitdiff
2023-09-21
Ben Soares
JAL-4265 Use ColourUtils.parseColourString() for consis...
merge/JAL-4262+JAL-4265+JAL-4269+JAL-4274+JAL-4277+JAL-4285
tree
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commitdiff
2023-09-21
Ben Soares
Merge branch 'develop' into merge/JAL-4262+JAL-4265...
tree
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commitdiff
2023-09-20
Ben Soares
JAL-4265 Use ColorUtils.parseColourString() and adjust...
tree
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commitdiff
2023-09-20
James Procter
JAL-4285 don’t say you are reporting warnings/errors...
tree
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commitdiff
2023-09-20
James Procter
JAL-4265 JAL-4286 reinstated explicit restoreSession...
tree
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commitdiff
2023-09-20
James Procter
JAL-4265 JAL-4267 added a ‘restoreSession’ StructureVie...
tree
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commitdiff
2023-09-20
James Procter
JAL-4195 JAL-1069 JAL-4160 errors in Cache should go...
tree
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commitdiff
2023-09-20
James Procter
JAL-4265 bail early when attempting to export a view...
tree
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commitdiff
2023-09-20
James Procter
JAL-4265 JAL-4267 allow injection of custom commands...
tree
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commitdiff
2023-09-20
James Procter
JAL-4265 back out redundant ‘saveState’ and ‘restoreSta...
tree
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commitdiff
2023-09-20
Ben Soares
JAL-4265 Added saveState and restoreState to interface...
tree
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commitdiff
2023-09-19
Ben Soares
JAL-4265 Change to use JmolCommands
tree
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commitdiff
2023-09-19
Ben Soares
JAL-629 Allow multiple structure images for multiple...
tree
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commitdiff
2023-09-16
Ben Soares
JAL-4250 Fixed blue arrows in drawStemAnnot()
tree
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commitdiff
2023-09-16
Ben Soares
JAL-629 Fix a test and omit an incorrect error message...
improvement/JAL-4269_reduce_variants_of_common_subvalue_parameters
tree
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commitdiff
2023-09-16
Ben Soares
JAL-4265 Added --bgcolour for --structureimage output...
tree
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commitdiff
2023-09-16
Ben Soares
JAL-4269 Now using --width, --height, --scale for both...
tree
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commitdiff
2023-09-14
Ben Soares
Merge branch 'develop' into feature/JAL-4274_configurab...
tree
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commitdiff
2023-09-13
Ben Soares
JAL-4274 Use Cache BITMAP_* if no other image restricti...
tree
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commitdiff
2023-09-13
Ben Soares
JAL-4262 Made deprecation warning properly modal
bug/JAL-4277_dirname_substitution_always_absolute
tree
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commitdiff
2023-09-12
Ben Soares
JAL-4262 Allow HTML in the dialog box for link to CLI...
tree
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commitdiff
2023-09-12
Ben Soares
JAL-4285 Better checkFiles processing. Better dialog.
tree
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commitdiff
2023-09-12
Ben Soares
JAL-4285 JAL-4262 Added a scrollable dialog to display...
tree
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commitdiff
2023-09-11
Ben Soares
JAL-4001 corrected analytics message labels
tree
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commitdiff
2023-09-11
Ben Soares
Merge branch 'improvement/JAL-4262_deprecation_warning_...
tree
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commitdiff
2023-09-11
Ben Soares
JAL-4277 --mkdirs with cautious refusal for paths with ..
tree
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commitdiff
2023-09-11
Ben Soares
JAL-4284 JAL-4285 Deal with output files/images consist...
tree
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commitdiff
2023-09-08
James Procter
JAL-4281 store/restore ID width and manual adjustment...
tree
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commitdiff
2023-09-08
James Procter
JAL-4281 reinstate access to legacy id width calculatio...
tree
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commitdiff
2023-09-08
James Procter
JAL-4282 make sure font is updated in alignPanel before...
tree
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commitdiff
2023-09-08
Ben Soares
JAL-4262 Make an excepetion for STDOUT filename in...
improvement/JAL-4262_deprecation_warning_when_old_CLI_arguments_are_processed
tree
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commitdiff
2023-09-08
Ben Soares
Merge branch 'bug/JAL-4277_dirname_substitution_always_...
tree
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commitdiff
2023-09-08
Ben Soares
JAL-4262 Dialog for GUI and WARN for CLI of old style...
tree
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commitdiff
2023-09-07
Ben Soares
Merge branch 'develop' into bug/JAL-4277_dirname_substi...
tree
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commitdiff
2023-09-07
Ben Soares
JAL-4277 Corrected choice of all or last opened linkedI...
tree
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commitdiff
2023-09-07
James Procter
JAL-4279 suppress error dialogs raised by file loader...
improvement/JAL-4279_gracefully_handle_failure_to_openviaCLI
tree
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commitdiff
2023-09-07
James Procter
JAL-4279 move on if the file doesn't exist, or Identify...
tree
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commitdiff
2023-09-07
James Procter
JAL-4279 catch exceptions with fileLoader and report...
tree
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commitdiff
2023-09-07
James Procter
JAL-4090 JAL-4160 JAL-4274 image export dimensions...
tree
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commitdiff
2023-09-07
Ben Soares
JAL-629 Change names of Opt.ALLOWALL to Opt.ALLOWMULTII...
improvement/JAL-629_Apply_alignment_options_to_all_globbed_files
tree
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commitdiff
2023-09-07
James Procter
JAL-4273 release notes for visible adjuster marks,...
tree
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commitdiff
2023-09-06
James Procter
JAL-4260 attempt to rejig paging when id width is adjus...
tree
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commitdiff
2023-09-06
James Procter
JAL-4258 remove unnecessary ‘this’
tree
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commitdiff
2023-09-06
James Procter
JAL-4259 construct a new SequenceRenderer when renderin...
tree
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commitdiff
2023-09-06
James Procter
JAL-629 javadoc on new setMapping variant for structure...
tree
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commitdiff
2023-09-06
James Procter
JAL-629 reinstate INFO level stack trace from Structure...
tree
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commitdiff
2023-09-06
James Procter
JAL-629 javadoc
tree
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commitdiff
2023-09-05
James Procter
JAL-629 remove structure viewer from the list of struct...
tree
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commitdiff
2023-09-05
James Procter
JAL-629 use JalviewStructureDisplayI in place of Struct...
tree
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commitdiff
2023-09-04
James Procter
JAL-3088 check for validEnd when working out whether...
tree
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commitdiff
2023-09-04
James Procter
JAL-4250 fix location and height for RNA secondary...
tree
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commitdiff
2023-09-04
James Procter
JAL-4250 rendition is way too obscure for me
tree
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commitdiff
2023-09-02
Ben Soares
Merge branch 'feature/JAL-629_--output_-_means_output_t...
tree
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commitdiff
2023-09-02
Ben Soares
JAL-629 Add accessors for argParser and bootstrapArgs
feature/JAL-629_--output_-_means_output_to_STDOUT
tree
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commitdiff
2023-09-01
Ben Soares
Merge branch 'feature/JAL-629_--output_-_means_output_t...
tree
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commitdiff
2023-09-01
Ben Soares
JAL-629 Save structure frames in project files when...
tree
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commitdiff
2023-09-01
Ben Soares
Merge branch 'feature/JAL-629_--output_-_means_output_t...
tree
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commitdiff
2023-09-01
Ben Soares
JAL-629 Fix --structureimage and options
tree
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commitdiff
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