jalview.git
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 comments to help follow the tests feature/JAL-4274_configurable_bitmap_export_preferences
2023-09-13 Ben SoaresJAL-4274 Tests for BIS defaults and overrides
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-4277 No longer using getCanonicalPath() for parent...
2023-09-12 Ben SoaresJAL-4285 Better checkFiles processing. Better dialog.
2023-09-12 Ben SoaresJAL-629 updated tests
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 fixed and improved tests
2023-09-07 James ProcterJAL-4090 release notes for JAL-244 JAL-901 JAL-4260... merge/JAL-244+JAL-629+JAL-3416+JAL-3421+JAL-3820+JAL-3830+JAL-4001+JAL-4160+JAL-4189+JAL-4214+JAL-4242+JAL-4255_Updates_to_these_issues_branches_with_merge_conflicts_resolved-bens_stuff
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,...
2023-09-07 James ProcterJAL-4090 report JAL-4261 known issue
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 'improvement/JAL-3830_remove_dock_icon_in_...
2023-08-31 Ben SoaresJAL-3830 Remove dock icon for -h too improvement/JAL-3830_remove_dock_icon_in_headless_mode
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...
2023-08-29 Ben SoaresMerge branch 'bug/JAL-4255_slf4j_missing_StaticLoggerBi...
2023-08-29 Ben SoaresJAL-4255 better grammar bug/JAL-4255_slf4j_missing_StaticLoggerBinder_error_message
2023-08-29 Ben SoaresJAL-4255 Updated THIRDPARTYLIBS
2023-08-29 Ben SoaresMerge branch 'bug/JAL-4255_slf4j_missing_StaticLoggerBi...
2023-08-29 Ben SoaresJAL-4255 Added slf4j-nop jar and upgraded to last 1...
2023-08-28 Ben SoaresMerge branch 'develop' into merge/big_merge_of_bens_stu...
2023-08-28 James ProcterJAL-4090 JAL-4250 JAL-4253 JAL-325 release notes and...
2023-08-28 James ProcterMerge branch 'improvement/JAL-4250_secondary_structure_...
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 'improvement/JAL-4212_remove_macos_test_ja...
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-3416 flatlaf and flatlaf-extras 3.2 jars
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...
2023-08-17 James ProcterJAL-4090 JAL-4243 bio.tools json file release notes
2023-08-16 Ben SoaresJAL-3830 JAL-3421 Conda launch script for 2.11.3 and...
2023-08-16 Ben SoaresMerge branch 'develop' into improvement/JAL-3830_remove...
2023-08-16 Ben SoaresJAL-4160 JAL-3830 Improvements to the jalview.sh bash...
2023-08-16 Ben SoaresJAL-3820 JAL-4189 Use the same LaunchUtils methods...
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 more tests for stdout
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