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jalview.git
2023-09-13 James ProcterJAL-4225 failed attempts to force MFE structure to... bug/JAL-4225_rnaalifold_structure_not_recognised_as_such commit | commitdiff | tree | snapshot
2023-09-12 Ben SoaresJAL-4262 Allow HTML in the dialog box for link to CLI... commit | commitdiff | tree | snapshot
2023-09-12 Ben SoaresJAL-4277 No longer using getCanonicalPath() for parent... commit | commitdiff | tree | snapshot
2023-09-12 Ben SoaresJAL-4285 Better checkFiles processing. Better dialog. commit | commitdiff | tree | snapshot
2023-09-12 Ben SoaresJAL-629 updated tests commit | commitdiff | tree | snapshot
2023-09-12 Ben SoaresJAL-4285 JAL-4262 Added a scrollable dialog to display... commit | commitdiff | tree | snapshot
2023-09-11 Ben SoaresMerge branch 'improvement/JAL-4262_deprecation_warning_... commit | commitdiff | tree | snapshot
2023-09-11 Ben SoaresJAL-4277 --mkdirs with cautious refusal for paths with .. commit | commitdiff | tree | snapshot
2023-09-11 Ben SoaresJAL-4284 JAL-4285 Deal with output files/images consist... commit | commitdiff | tree | snapshot
2023-09-08 Ben SoaresJAL-4262 Make an excepetion for STDOUT filename in... improvement/JAL-4262_deprecation_warning_when_old_CLI_arguments_are_processed commit | commitdiff | tree | snapshot
2023-09-08 Ben SoaresMerge branch 'bug/JAL-4277_dirname_substitution_always_... commit | commitdiff | tree | snapshot
2023-09-08 Ben SoaresJAL-4262 Dialog for GUI and WARN for CLI of old style... commit | commitdiff | tree | snapshot
2023-09-07 Ben SoaresMerge branch 'develop' into bug/JAL-4277_dirname_substi... commit | commitdiff | tree | snapshot
2023-09-07 Ben SoaresJAL-4277 fixed and improved tests commit | commitdiff | tree | snapshot
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 commit | commitdiff | tree | snapshot
2023-09-07 Ben SoaresJAL-4277 Corrected choice of all or last opened linkedI... commit | commitdiff | tree | snapshot
2023-09-07 James ProcterJAL-4279 suppress error dialogs raised by file loader... improvement/JAL-4279_gracefully_handle_failure_to_openviaCLI commit | commitdiff | tree | snapshot
2023-09-07 James ProcterJAL-4279 move on if the file doesn't exist, or Identify... commit | commitdiff | tree | snapshot
2023-09-07 James ProcterJAL-4279 catch exceptions with fileLoader and report... commit | commitdiff | tree | snapshot
2023-09-07 James ProcterJAL-4090 JAL-4160 JAL-4274 image export dimensions... commit | commitdiff | tree | snapshot
2023-09-07 Ben SoaresJAL-629 Change names of Opt.ALLOWALL to Opt.ALLOWMULTII... improvement/JAL-629_Apply_alignment_options_to_all_globbed_files commit | commitdiff | tree | snapshot
2023-09-07 James ProcterJAL-4273 release notes for visible adjuster marks,... commit | commitdiff | tree | snapshot
2023-09-07 James ProcterJAL-4090 report JAL-4261 known issue commit | commitdiff | tree | snapshot
2023-09-06 James ProcterJAL-4260 attempt to rejig paging when id width is adjus... commit | commitdiff | tree | snapshot
2023-09-06 James ProcterJAL-4258 remove unnecessary ‘this’ commit | commitdiff | tree | snapshot
2023-09-06 James ProcterJAL-4259 construct a new SequenceRenderer when renderin... commit | commitdiff | tree | snapshot
2023-09-06 James ProcterJAL-629 javadoc on new setMapping variant for structure... commit | commitdiff | tree | snapshot
2023-09-06 James ProcterJAL-629 reinstate INFO level stack trace from Structure... commit | commitdiff | tree | snapshot
2023-09-06 James ProcterJAL-629 javadoc commit | commitdiff | tree | snapshot
2023-09-05 James ProcterJAL-629 remove structure viewer from the list of struct... commit | commitdiff | tree | snapshot
2023-09-05 James ProcterJAL-629 use JalviewStructureDisplayI in place of Struct... commit | commitdiff | tree | snapshot
2023-09-02 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t... commit | commitdiff | tree | snapshot
2023-09-02 Ben SoaresJAL-629 Add accessors for argParser and bootstrapArgs feature/JAL-629_--output_-_means_output_to_STDOUT commit | commitdiff | tree | snapshot
2023-09-01 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t... commit | commitdiff | tree | snapshot
2023-09-01 Ben SoaresJAL-629 Save structure frames in project files when... commit | commitdiff | tree | snapshot
2023-09-01 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t... commit | commitdiff | tree | snapshot
2023-09-01 Ben SoaresJAL-629 Fix --structureimage and options commit | commitdiff | tree | snapshot
2023-08-31 Ben SoaresMerge branch 'improvement/JAL-3830_remove_dock_icon_in_... commit | commitdiff | tree | snapshot
2023-08-31 Ben SoaresJAL-3830 Remove dock icon for -h too improvement/JAL-3830_remove_dock_icon_in_headless_mode commit | commitdiff | tree | snapshot
2023-08-31 Ben SoaresMerge branch 'features/r2_11_2_alphafold/JAL-629' into... commit | commitdiff | tree | snapshot
2023-08-31 Ben SoaresJAL-629 Small buglet with getting --seqid features/r2_11_2_alphafold/JAL-629 commit | commitdiff | tree | snapshot
2023-08-31 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... commit | commitdiff | tree | snapshot
2023-08-29 Ben SoaresMerge branch 'bug/JAL-4255_slf4j_missing_StaticLoggerBi... commit | commitdiff | tree | snapshot
2023-08-29 Ben SoaresJAL-4255 better grammar bug/JAL-4255_slf4j_missing_StaticLoggerBinder_error_message commit | commitdiff | tree | snapshot
2023-08-29 Ben SoaresJAL-4255 Updated THIRDPARTYLIBS commit | commitdiff | tree | snapshot
2023-08-29 Ben SoaresMerge branch 'bug/JAL-4255_slf4j_missing_StaticLoggerBi... commit | commitdiff | tree | snapshot
2023-08-29 Ben SoaresJAL-4255 Added slf4j-nop jar and upgraded to last 1... commit | commitdiff | tree | snapshot
2023-08-28 Ben SoaresMerge branch 'develop' into merge/big_merge_of_bens_stu... commit | commitdiff | tree | snapshot
2023-08-28 James ProcterJAL-4090 JAL-4250 JAL-4253 JAL-325 release notes and... commit | commitdiff | tree | snapshot
2023-08-28 James ProcterMerge branch 'improvement/JAL-4250_secondary_structure_... commit | commitdiff | tree | snapshot
2023-08-28 James ProcterJAL-4253 drop the bottom line so it lines up with the... commit | commitdiff | tree | snapshot
2023-08-24 Ben SoaresMerge branch 'develop' into merge/big_merge_of_bens_stu... commit | commitdiff | tree | snapshot
2023-08-24 Ben SoaresMerge branch 'features/r2_11_2_alphafold/JAL-629' into... commit | commitdiff | tree | snapshot
2023-08-24 Ben SoaresJAL-629 Avoid hidden options dialog when saving in... commit | commitdiff | tree | snapshot
2023-08-24 Ben SoaresMerge branch 'bug/JAL-4214_system_freeze_when_opening_f... commit | commitdiff | tree | snapshot
2023-08-24 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_... commit | commitdiff | tree | snapshot
2023-08-24 Ben SoaresJAL-4250 Fix bug in vector rendition where more than... improvement/JAL-4250_secondary_structure_annotation_antialias commit | commitdiff | tree | snapshot
2023-08-24 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_... commit | commitdiff | tree | snapshot
2023-08-24 Ben SoaresJAL-4250 Much simplified glyph creation removing most... commit | commitdiff | tree | snapshot
2023-08-23 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_... commit | commitdiff | tree | snapshot
2023-08-23 Ben SoaresJAL-4250 Fix one word bug for 'af.createEPS(file, rende... commit | commitdiff | tree | snapshot
2023-08-23 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_... commit | commitdiff | tree | snapshot
2023-08-23 Ben SoaresJAL-4250 Updated jfreesvg to fix round stroke in linegraph. commit | commitdiff | tree | snapshot
2023-08-23 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_... commit | commitdiff | tree | snapshot
2023-08-23 Ben SoaresJAL-4250 Simplification of polygons and adjustments... commit | commitdiff | tree | snapshot
2023-08-21 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_... commit | commitdiff | tree | snapshot
2023-08-21 Ben SoaresJAL-4250 revert green to bright green commit | commitdiff | tree | snapshot
2023-08-21 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_... commit | commitdiff | tree | snapshot
2023-08-21 Ben SoaresJAL-4250 Conservative setting of ANTIALIAS and readjust... commit | commitdiff | tree | snapshot
2023-08-18 Ben SoaresJAL-4250 Make secondary structure annotation shapes... commit | commitdiff | tree | snapshot
2023-08-18 Ben SoaresMerge branch 'improvement/JAL-4206_improve_JalviewFileC... commit | commitdiff | tree | snapshot
2023-08-18 Ben SoaresMerge branch 'bug/JAL-4214_system_freeze_when_opening_f... commit | commitdiff | tree | snapshot
2023-08-18 Ben SoaresMerge branch 'improvement/JAL-4212_remove_macos_test_ja... commit | commitdiff | tree | snapshot
2023-08-18 Ben SoaresMerge branch 'feature/JAL-244_Automatically_adjust_left... commit | commitdiff | tree | snapshot
2023-08-18 Ben SoaresMerge branch 'improvement/JAL-3830_remove_dock_icon_in_... commit | commitdiff | tree | snapshot
2023-08-18 Ben SoaresMerge branch 'bug/JAL-4242_exception_when_pressing_esca... commit | commitdiff | tree | snapshot
2023-08-18 Ben SoaresJAL-3416 Remove full height separators between new... improvement/JAL-3416_FlatLaf_3.2 commit | commitdiff | tree | snapshot
2023-08-18 Ben SoaresJAL-3416 flatlaf and flatlaf-extras 3.2 jars commit | commitdiff | tree | snapshot
2023-08-18 Ben SoaresJAL-4242 null check on getValue() return bug/JAL-4242_exception_when_pressing_escape_in_fetch_from_URL_dialog commit | commitdiff | tree | snapshot
2023-08-17 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t... commit | commitdiff | tree | snapshot
2023-08-17 Ben SoaresJAL-3830 JAL-4160 Remove --noheadless as --gui does... commit | commitdiff | tree | snapshot
2023-08-17 James ProcterJAL-4090 JAL-4243 bio.tools json file release notes commit | commitdiff | tree | snapshot
2023-08-16 Ben SoaresJAL-3830 JAL-3421 Conda launch script for 2.11.3 and... commit | commitdiff | tree | snapshot
2023-08-16 Ben SoaresMerge branch 'develop' into improvement/JAL-3830_remove... commit | commitdiff | tree | snapshot
2023-08-16 Ben SoaresJAL-4160 JAL-3830 Improvements to the jalview.sh bash... commit | commitdiff | tree | snapshot
2023-08-16 Ben SoaresJAL-3820 JAL-4189 Use the same LaunchUtils methods... commit | commitdiff | tree | snapshot
2023-08-16 Ben SoaresJAL-3820 JAL-4189 Move checks for java executable symli... commit | commitdiff | tree | snapshot
2023-08-11 Ben SoaresJAL-629 Much better way of dealing with list of filenam... commit | commitdiff | tree | snapshot
2023-08-10 Ben SoaresJAL-629 more tests for stdout commit | commitdiff | tree | snapshot
2023-08-10 Ben SoaresJAL-629 STDOUT documentation. Opt.STDOUT narrower... commit | commitdiff | tree | snapshot
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use... commit | commitdiff | tree | snapshot
2023-08-10 Ben SoaresJAL-629 Method to use for printStackTrace commit | commitdiff | tree | snapshot
2023-08-09 Ben SoaresJAL-629 Move more stdout messages to stderr when output... commit | commitdiff | tree | snapshot
2023-08-09 Ben SoaresJAL-629 Default to FASTA if no format given for output... commit | commitdiff | tree | snapshot
2023-08-09 Ben SoaresJAL-629 Enable output to STDOUT when specifying output... commit | commitdiff | tree | snapshot
2023-08-09 Ben SoaresJAL-244 Fix window size narrow adjustment not becoming... feature/JAL-244_Automatically_adjust_left_margin_to_avoid_cropping_annotation_labels commit | commitdiff | tree | snapshot
2023-08-08 Ben SoaresJAL-244 Added light grey marks to indicate regions... commit | commitdiff | tree | snapshot
2023-08-08 Ben SoaresJAL-244 Fix mismatched vertical positioning of sequence... commit | commitdiff | tree | snapshot
2023-08-07 Ben SoaresJAL-244 Avoid working on the Ids Graphics object when... commit | commitdiff | tree | snapshot
2023-08-04 Ben SoaresJAL-244 Adjust wrapped alignment widths to always maint... commit | commitdiff | tree | snapshot
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