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jalview.git
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
2023-09-02 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
2023-08-02 Ben SoaresJAL-244 Fix buglet with automatic change in id column... commit | commitdiff | tree | snapshot
2023-08-01 Ben SoaresJAL-244 More control of automatic idWidth adjustments... commit | commitdiff | tree | snapshot
2023-08-01 Ben SoaresMerge branch 'develop' into feature/JAL-244_Automatical... commit | commitdiff | tree | snapshot
2023-07-28 Ben SoaresJAL-4064 Added more recognisable display names to macOS... commit | commitdiff | tree | snapshot
2023-07-27 Ben SoaresMerge branch 'develop' into feature/JAL-244_Automatical... commit | commitdiff | tree | snapshot
2023-07-27 Ben SoaresJAL-244 Allow wrap manual adjustments to be smaller... commit | commitdiff | tree | snapshot
2023-07-27 Ben SoaresJAL-244 Allow adjusting Id column width in wrap mode... commit | commitdiff | tree | snapshot
2023-07-25 Ben SoaresJAL-244 testing without AlignFrame for --wrap commit | commitdiff | tree | snapshot
2023-07-22 James ProcterJAL-4243 Jalview 2.11.2.7’s biotool record as JSON... commit | commitdiff | tree | snapshot
2023-07-21 Ben SoaresJAL-244 Fixed idWidth labels in headless mode for non... commit | commitdiff | tree | snapshot
2023-07-20 Ben SoaresJAL-244 More accurate width calculation, allow increase... commit | commitdiff | tree | snapshot
2023-07-20 Ben SoaresJAL-244 test files commit | commitdiff | tree | snapshot
2023-07-20 James ProcterJAL-3855 tree title for PAE matrix tree is PAE Matrix... patch/JAL-3855_fixup_pae commit | commitdiff | tree | snapshot
2023-07-20 James ProcterJAL-3855 auto select clusters and fix up colouring... commit | commitdiff | tree | snapshot
2023-07-19 Ben SoaresJAL-244 Changes to Annotation labels width now adjusts... commit | commitdiff | tree | snapshot
2023-07-19 James ProcterMerge branch 'patch/JAL-3855_fixup_pae' into develop commit | commitdiff | tree | snapshot
2023-07-18 James ProcterMerge branch 'develop' into patch/JAL-3855_fixup_pae commit | commitdiff | tree | snapshot
2023-07-18 James ProcterJAL-4153 comments re patch incorrectly committed under... commit | commitdiff | tree | snapshot
2023-07-18 Ben SoaresJAL-4513 move comments commit | commitdiff | tree | snapshot
2023-07-18 Ben SoaresJAL-4513 now re-add the SwingUtilities.invokeAndWait... bug/JAL-4513_JvCacheableInputBoxTest_flaky_on_build_server commit | commitdiff | tree | snapshot
2023-07-18 James ProcterJAL-3855 PAE matrices are transposed on import from... commit | commitdiff | tree | snapshot
2023-07-18 James ProcterJAL-3855 JAL-4124 test checks asymmetric matrices are... commit | commitdiff | tree | snapshot
2023-07-18 James ProcterJAL-3858 fix off-by-one in matrix visualisation and... commit | commitdiff | tree | snapshot
2023-07-18 James ProcterJAL-3858 flip diagonal so matrix visualisation is top... commit | commitdiff | tree | snapshot
2023-07-18 James ProcterJAL-3858 annotation .height is bigger than graphHeight... commit | commitdiff | tree | snapshot
2023-07-18 Ben SoaresJAL-4513 reduce wait to invoke fail commit | commitdiff | tree | snapshot
2023-07-18 Ben SoaresJAL-4513 add a SwingUtilities.invokeAndWait() to see... commit | commitdiff | tree | snapshot
2023-07-17 Ben SoaresJAL-3599 Updated default eclipse to 'latest' and made... commit | commitdiff | tree | snapshot
2023-07-17 James ProcterJAL-4119 TRACE level console message reporting download... commit | commitdiff | tree | snapshot
2023-07-17 James ProcterJAL-4090 JAL-4165 known issue commit | commitdiff | tree | snapshot
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