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JAL-4356 release notes
[jalview.git] / src / jalview /
2023-10-17 James ProcterJAL-4134 TODO printNode update for columnTrees tree | commitdiff
2023-10-17 James ProcterJAL-4134 JAL-4302 remove unnecessary casts tree | commitdiff
2023-10-17 James ProcterJAL-4089 selected columns are reported in absolute... tree | commitdiff
2023-10-13 Ben SoaresJAL-3783 Updated groovy jars. Requires javaparser... tree | commitdiff
2023-10-13 James ProcterJAL-4295 concatenate all mouseover highlights into... tree | commitdiff
2023-10-12 Ben SoaresJAL-3772 Fix the logic of prompt to save URL loaded... tree | commitdiff
2023-10-12 Ben SoaresJAL-629 null check and neatening code tree | commitdiff
2023-10-11 Ben SoaresJAL-629 correct a timeout. Correct passing html flag. tree | commitdiff
2023-10-11 Ben SoaresJAL-629 Add a timeout to modal dialogs for command... tree | commitdiff
2023-10-11 Ben SoaresJAL-629 Remove argfiles from the hashset of used argfil... tree | commitdiff
2023-10-11 Ben SoaresJAL-3772 Preference to NOT prompt to save remotely... tree | commitdiff
2023-10-11 Ben SoaresJAL-4298 Added diagnostics and minor dimension changes... tree | commitdiff
2023-10-05 Ben SoaresJAL-4298 Fixed initial log level to see .jalview_proper... tree | commitdiff
2023-10-03 Ben SoaresJAL-4001 Only use acquireDialogQueue and releaseDialogQ... bug/JAL-4001_fix_About_Jalview_not_appearing tree | commitdiff
2023-10-03 Ben SoaresMerge branch 'develop' into bug/JAL-4289_group_boundary... tree | commitdiff
2023-10-03 James ProcterMerge branch 'patch/JAL-4062_sort_and_merge_contiguousr... tree | commitdiff
2023-10-02 Ben SoaresJAL-4289 In fastPaint(), don't render one more than... tree | commitdiff
2023-10-01 James ProcterJAL-244 ensure background is completely filled with... tree | commitdiff
2023-10-01 James ProcterJAL-244 export image with full width IDs regardless... tree | commitdiff
2023-10-01 James ProcterJAL-244 JAL-4091 allow calculation of label id width... tree | commitdiff
2023-10-01 James ProcterJAL-244 JAL-4091 FIXME for JAL-3362 patch testCalculate... tree | commitdiff
2023-09-29 James ProcterJAL-629 JAL-4265 JAL-4286 report the filename for the... tree | commitdiff
2023-09-29 James ProcterJAL-244 JAL-4090 use current IdWidth when exporting... tree | commitdiff
2023-09-29 James ProcterJAL-3858 fix check annotation row and column positionin... tree | commitdiff
2023-09-28 James ProcterJAL-3858 don’t divide if we only had one value to count tree | commitdiff
2023-09-28 James ProcterJAL-3858 check annotation row and column positioning... tree | commitdiff
2023-09-28 James ProcterJAL-3858 improved contactInterval computation and added... tree | commitdiff
2023-09-26 James ProcterJAL-3858 JAL-4090 avoid NPE when given out of bound... tree | commitdiff
2023-09-25 James ProcterJAL-3858 minimum value for a range is used to shade... tree | commitdiff
2023-09-25 James ProcterJAL-3858 javadoc and slightly revised green linear... tree | commitdiff
2023-09-25 James ProcterJAL-3858 report PAE range with sensible precision tree | commitdiff
2023-09-21 James ProcterJAL-1551 javadoc for mapUtils tree | commitdiff
2023-09-21 James ProcterJAL-3855 disable the AlphaFold DB entry in Sequence... tree | commitdiff
2023-09-21 Ben SoaresJAL-4265 Use ColourUtils.parseColourString() for consis... merge/JAL-4262+JAL-4265+JAL-4269+JAL-4274+JAL-4277+JAL-4285 tree | commitdiff
2023-09-21 Ben SoaresMerge branch 'develop' into merge/JAL-4262+JAL-4265... tree | commitdiff
2023-09-20 Ben SoaresJAL-4265 Use ColorUtils.parseColourString() and adjust... tree | commitdiff
2023-09-20 James ProcterJAL-4285 don’t say you are reporting warnings/errors... tree | commitdiff
2023-09-20 James ProcterJAL-4265 JAL-4286 reinstated explicit restoreSession... tree | commitdiff
2023-09-20 James ProcterJAL-4265 JAL-4267 added a ‘restoreSession’ StructureVie... tree | commitdiff
2023-09-20 James ProcterJAL-4195 JAL-1069 JAL-4160 errors in Cache should go... tree | commitdiff
2023-09-20 James ProcterJAL-4265 bail early when attempting to export a view... tree | commitdiff
2023-09-20 James ProcterJAL-4265 JAL-4267 allow injection of custom commands... tree | commitdiff
2023-09-20 James ProcterJAL-4265 back out redundant ‘saveState’ and ‘restoreSta... tree | commitdiff
2023-09-20 Ben SoaresJAL-4265 Added saveState and restoreState to interface... tree | commitdiff
2023-09-19 Ben SoaresJAL-4265 Change to use JmolCommands tree | commitdiff
2023-09-19 Ben SoaresJAL-629 Allow multiple structure images for multiple... tree | commitdiff
2023-09-16 Ben SoaresJAL-4250 Fixed blue arrows in drawStemAnnot() tree | commitdiff
2023-09-16 Ben SoaresJAL-629 Fix a test and omit an incorrect error message... improvement/JAL-4269_reduce_variants_of_common_subvalue_parameters tree | commitdiff
2023-09-16 Ben SoaresJAL-4265 Added --bgcolour for --structureimage output... tree | commitdiff
2023-09-16 Ben SoaresJAL-4269 Now using --width, --height, --scale for both... tree | commitdiff
2023-09-14 Ben SoaresMerge branch 'develop' into feature/JAL-4274_configurab... tree | commitdiff
2023-09-13 Ben SoaresJAL-4274 Use Cache BITMAP_* if no other image restricti... tree | commitdiff
2023-09-13 Ben SoaresJAL-4262 Made deprecation warning properly modal bug/JAL-4277_dirname_substitution_always_absolute tree | commitdiff
2023-09-12 Ben SoaresJAL-4262 Allow HTML in the dialog box for link to CLI... tree | commitdiff
2023-09-12 Ben SoaresJAL-4285 Better checkFiles processing. Better dialog. tree | commitdiff
2023-09-12 Ben SoaresJAL-4285 JAL-4262 Added a scrollable dialog to display... tree | commitdiff
2023-09-11 Ben SoaresJAL-4001 corrected analytics message labels tree | commitdiff
2023-09-11 Ben SoaresMerge branch 'improvement/JAL-4262_deprecation_warning_... tree | commitdiff
2023-09-11 Ben SoaresJAL-4277 --mkdirs with cautious refusal for paths with .. tree | commitdiff
2023-09-11 Ben SoaresJAL-4284 JAL-4285 Deal with output files/images consist... tree | commitdiff
2023-09-08 James ProcterJAL-4281 store/restore ID width and manual adjustment... tree | commitdiff
2023-09-08 James ProcterJAL-4281 reinstate access to legacy id width calculatio... tree | commitdiff
2023-09-08 James ProcterJAL-4282 make sure font is updated in alignPanel before... tree | commitdiff
2023-09-08 Ben SoaresJAL-4262 Make an excepetion for STDOUT filename in... improvement/JAL-4262_deprecation_warning_when_old_CLI_arguments_are_processed tree | commitdiff
2023-09-08 Ben SoaresMerge branch 'bug/JAL-4277_dirname_substitution_always_... tree | commitdiff
2023-09-08 Ben SoaresJAL-4262 Dialog for GUI and WARN for CLI of old style... tree | commitdiff
2023-09-07 Ben SoaresMerge branch 'develop' into bug/JAL-4277_dirname_substi... tree | commitdiff
2023-09-07 Ben SoaresJAL-4277 Corrected choice of all or last opened linkedI... tree | commitdiff
2023-09-07 James ProcterJAL-4279 suppress error dialogs raised by file loader... improvement/JAL-4279_gracefully_handle_failure_to_openviaCLI tree | commitdiff
2023-09-07 James ProcterJAL-4279 move on if the file doesn't exist, or Identify... tree | commitdiff
2023-09-07 James ProcterJAL-4279 catch exceptions with fileLoader and report... tree | commitdiff
2023-09-07 James ProcterJAL-4090 JAL-4160 JAL-4274 image export dimensions... tree | commitdiff
2023-09-07 Ben SoaresJAL-629 Change names of Opt.ALLOWALL to Opt.ALLOWMULTII... improvement/JAL-629_Apply_alignment_options_to_all_globbed_files tree | commitdiff
2023-09-07 James ProcterJAL-4273 release notes for visible adjuster marks,... tree | commitdiff
2023-09-06 James ProcterJAL-4260 attempt to rejig paging when id width is adjus... tree | commitdiff
2023-09-06 James ProcterJAL-4258 remove unnecessary ‘this’ tree | commitdiff
2023-09-06 James ProcterJAL-4259 construct a new SequenceRenderer when renderin... tree | commitdiff
2023-09-06 James ProcterJAL-629 javadoc on new setMapping variant for structure... tree | commitdiff
2023-09-06 James ProcterJAL-629 reinstate INFO level stack trace from Structure... tree | commitdiff
2023-09-06 James ProcterJAL-629 javadoc tree | commitdiff
2023-09-05 James ProcterJAL-629 remove structure viewer from the list of struct... tree | commitdiff
2023-09-05 James ProcterJAL-629 use JalviewStructureDisplayI in place of Struct... tree | commitdiff
2023-09-04 James ProcterJAL-3088 check for validEnd when working out whether... tree | commitdiff
2023-09-04 James ProcterJAL-4250 fix location and height for RNA secondary... tree | commitdiff
2023-09-04 James ProcterJAL-4250 rendition is way too obscure for me tree | commitdiff
2023-09-02 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t... tree | commitdiff
2023-09-02 Ben SoaresJAL-629 Add accessors for argParser and bootstrapArgs feature/JAL-629_--output_-_means_output_to_STDOUT tree | commitdiff
2023-09-01 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t... tree | commitdiff
2023-09-01 Ben SoaresJAL-629 Save structure frames in project files when... tree | commitdiff
2023-09-01 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t... tree | commitdiff
2023-09-01 Ben SoaresJAL-629 Fix --structureimage and options tree | commitdiff
2023-09-01 James ProcterJAL-4124 need to repaint alignFrames imported from... tree | commitdiff
2023-09-01 James ProcterJAL-4124 matrix is saved in dataset, with forward refer... tree | commitdiff
2023-09-01 James ProcterJAL-4124 add strategic newlines in matrix stringified... tree | commitdiff
2023-08-31 Ben SoaresMerge branch 'features/r2_11_2_alphafold/JAL-629' into... tree | commitdiff
2023-08-31 Ben SoaresJAL-629 Small buglet with getting --seqid features/r2_11_2_alphafold/JAL-629 tree | commitdiff
2023-08-31 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-08-31 James ProcterJAL-4124 MappableContactMatrix equivalence and hashCode... tree | commitdiff
2023-08-29 James ProcterJAL-4124 Dataset holds list of MatrixType instances... tree | commitdiff
2023-08-29 James ProcterJAL-4124 decouple mappable contact matrix mapping logic... tree | commitdiff
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