JAL-3858 improved contactInterval computation and added detailed test coverage for...
[jalview.git] / src /
2023-09-28 James ProcterJAL-3858 improved contactInterval computation and added...
2023-09-26 James ProcterJAL-3858 JAL-4090 avoid NPE when given out of bound...
2023-09-25 James ProcterJAL-3858 minimum value for a range is used to shade...
2023-09-25 James ProcterJAL-3858 javadoc and slightly revised green linear...
2023-09-25 James ProcterJAL-3858 report PAE range with sensible precision
2023-09-21 James ProcterJAL-1551 javadoc for mapUtils
2023-09-21 James ProcterJAL-3855 disable the AlphaFold DB entry in Sequence...
2023-09-21 Ben SoaresJAL-4265 Use ColourUtils.parseColourString() for consis... merge/JAL-4262+JAL-4265+JAL-4269+JAL-4274+JAL-4277+JAL-4285
2023-09-21 Ben SoaresMerge branch 'develop' into merge/JAL-4262+JAL-4265...
2023-09-20 Ben SoaresJAL-4265 Use ColorUtils.parseColourString() and adjust...
2023-09-20 James ProcterJAL-4285 don’t say you are reporting warnings/errors...
2023-09-20 James ProcterJAL-4265 JAL-4286 reinstated explicit restoreSession...
2023-09-20 James ProcterJAL-4265 JAL-4267 added a ‘restoreSession’ StructureVie...
2023-09-20 James ProcterJAL-4195 JAL-1069 JAL-4160 errors in Cache should go...
2023-09-20 James ProcterJAL-4265 bail early when attempting to export a view...
2023-09-20 James ProcterJAL-4265 JAL-4267 allow injection of custom commands...
2023-09-20 James ProcterJAL-4265 back out redundant ‘saveState’ and ‘restoreSta...
2023-09-20 Ben SoaresJAL-4265 Added saveState and restoreState to interface...
2023-09-19 Ben SoaresJAL-4265 Change to use JmolCommands
2023-09-19 Ben SoaresJAL-629 Allow multiple structure images for multiple...
2023-09-16 Ben SoaresJAL-4250 Fixed blue arrows in drawStemAnnot()
2023-09-16 Ben SoaresJAL-629 Fix a test and omit an incorrect error message... improvement/JAL-4269_reduce_variants_of_common_subvalue_parameters
2023-09-16 Ben SoaresJAL-4265 Added --bgcolour for --structureimage output...
2023-09-16 Ben SoaresJAL-4269 Now using --width, --height, --scale for both...
2023-09-14 Ben SoaresMerge branch 'develop' into feature/JAL-4274_configurab...
2023-09-13 Ben SoaresJAL-4274 Use Cache BITMAP_* if no other image restricti...
2023-09-13 Ben SoaresJAL-4262 Made deprecation warning properly modal bug/JAL-4277_dirname_substitution_always_absolute
2023-09-12 Ben SoaresJAL-4262 Allow HTML in the dialog box for link to CLI...
2023-09-12 Ben SoaresJAL-4285 Better checkFiles processing. Better dialog.
2023-09-12 Ben SoaresJAL-4285 JAL-4262 Added a scrollable dialog to display...
2023-09-11 Ben SoaresJAL-4001 corrected analytics message labels
2023-09-11 Ben SoaresMerge branch 'improvement/JAL-4262_deprecation_warning_...
2023-09-11 Ben SoaresJAL-4277 --mkdirs with cautious refusal for paths with ..
2023-09-11 Ben SoaresJAL-4284 JAL-4285 Deal with output files/images consist...
2023-09-08 Ben SoaresJAL-4262 Make an excepetion for STDOUT filename in... improvement/JAL-4262_deprecation_warning_when_old_CLI_arguments_are_processed
2023-09-08 Ben SoaresMerge branch 'bug/JAL-4277_dirname_substitution_always_...
2023-09-08 Ben SoaresJAL-4262 Dialog for GUI and WARN for CLI of old style...
2023-09-07 Ben SoaresMerge branch 'develop' into bug/JAL-4277_dirname_substi...
2023-09-07 Ben SoaresJAL-4277 Corrected choice of all or last opened linkedI...
2023-09-07 James ProcterJAL-4279 suppress error dialogs raised by file loader... improvement/JAL-4279_gracefully_handle_failure_to_openviaCLI
2023-09-07 James ProcterJAL-4279 move on if the file doesn't exist, or Identify...
2023-09-07 James ProcterJAL-4279 catch exceptions with fileLoader and report...
2023-09-07 James ProcterJAL-4090 JAL-4160 JAL-4274 image export dimensions...
2023-09-07 Ben SoaresJAL-629 Change names of Opt.ALLOWALL to Opt.ALLOWMULTII... improvement/JAL-629_Apply_alignment_options_to_all_globbed_files
2023-09-07 James ProcterJAL-4273 release notes for visible adjuster marks,...
2023-09-06 James ProcterJAL-4260 attempt to rejig paging when id width is adjus...
2023-09-06 James ProcterJAL-4258 remove unnecessary ‘this’
2023-09-06 James ProcterJAL-4259 construct a new SequenceRenderer when renderin...
2023-09-06 James ProcterJAL-629 javadoc on new setMapping variant for structure...
2023-09-06 James ProcterJAL-629 reinstate INFO level stack trace from Structure...
2023-09-06 James ProcterJAL-629 javadoc
2023-09-05 James ProcterJAL-629 remove structure viewer from the list of struct...
2023-09-05 James ProcterJAL-629 use JalviewStructureDisplayI in place of Struct...
2023-09-02 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t...
2023-09-02 Ben SoaresJAL-629 Add accessors for argParser and bootstrapArgs feature/JAL-629_--output_-_means_output_to_STDOUT
2023-09-01 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t...
2023-09-01 Ben SoaresJAL-629 Save structure frames in project files when...
2023-09-01 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t...
2023-09-01 Ben SoaresJAL-629 Fix --structureimage and options
2023-08-31 Ben SoaresMerge branch 'features/r2_11_2_alphafold/JAL-629' into...
2023-08-31 Ben SoaresJAL-629 Small buglet with getting --seqid features/r2_11_2_alphafold/JAL-629
2023-08-31 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold...
2023-08-28 Ben SoaresMerge branch 'develop' into merge/big_merge_of_bens_stu...
2023-08-28 James ProcterJAL-4253 drop the bottom line so it lines up with the...
2023-08-24 Ben SoaresMerge branch 'develop' into merge/big_merge_of_bens_stu...
2023-08-24 Ben SoaresMerge branch 'features/r2_11_2_alphafold/JAL-629' into...
2023-08-24 Ben SoaresJAL-629 Avoid hidden options dialog when saving in...
2023-08-24 Ben SoaresMerge branch 'bug/JAL-4214_system_freeze_when_opening_f...
2023-08-24 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_...
2023-08-24 Ben SoaresJAL-4250 Fix bug in vector rendition where more than... improvement/JAL-4250_secondary_structure_annotation_antialias
2023-08-24 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_...
2023-08-24 Ben SoaresJAL-4250 Much simplified glyph creation removing most...
2023-08-23 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_...
2023-08-23 Ben SoaresJAL-4250 Fix one word bug for 'af.createEPS(file, rende...
2023-08-23 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_...
2023-08-23 Ben SoaresJAL-4250 Updated jfreesvg to fix round stroke in linegraph.
2023-08-23 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_...
2023-08-23 Ben SoaresJAL-4250 Simplification of polygons and adjustments...
2023-08-21 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_...
2023-08-21 Ben SoaresJAL-4250 revert green to bright green
2023-08-21 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_...
2023-08-21 Ben SoaresJAL-4250 Conservative setting of ANTIALIAS and readjust...
2023-08-18 Ben SoaresJAL-4250 Make secondary structure annotation shapes...
2023-08-18 Ben SoaresMerge branch 'improvement/JAL-4206_improve_JalviewFileC...
2023-08-18 Ben SoaresMerge branch 'bug/JAL-4214_system_freeze_when_opening_f...
2023-08-18 Ben SoaresMerge branch 'feature/JAL-244_Automatically_adjust_left...
2023-08-18 Ben SoaresMerge branch 'improvement/JAL-3830_remove_dock_icon_in_...
2023-08-18 Ben SoaresMerge branch 'bug/JAL-4242_exception_when_pressing_esca...
2023-08-18 Ben SoaresJAL-3416 Remove full height separators between new... improvement/JAL-3416_FlatLaf_3.2
2023-08-18 Ben SoaresJAL-4242 null check on getValue() return bug/JAL-4242_exception_when_pressing_escape_in_fetch_from_URL_dialog
2023-08-17 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t...
2023-08-17 Ben SoaresJAL-3830 JAL-4160 Remove --noheadless as --gui does...
2023-08-16 Ben SoaresMerge branch 'develop' into improvement/JAL-3830_remove...
2023-08-16 Ben SoaresJAL-3820 JAL-4189 Move checks for java executable symli...
2023-08-11 Ben SoaresJAL-629 Much better way of dealing with list of filenam...
2023-08-10 Ben SoaresJAL-629 STDOUT documentation. Opt.STDOUT narrower...
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use...
2023-08-10 Ben SoaresJAL-629 Method to use for printStackTrace
2023-08-09 Ben SoaresJAL-629 Move more stdout messages to stderr when output...
2023-08-09 Ben SoaresJAL-629 Default to FASTA if no format given for output...
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