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Merge branch 'develop' into bug/JAL-4277_dirname_substitution_always_absolute
[jalview.git] / src /
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
2023-09-02 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
2023-08-31 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
2023-08-28 Ben SoaresMerge branch 'develop' into merge/big_merge_of_bens_stu... tree | commitdiff
2023-08-28 James ProcterJAL-4253 drop the bottom line so it lines up with the... tree | commitdiff
2023-08-24 Ben SoaresMerge branch 'develop' into merge/big_merge_of_bens_stu... tree | commitdiff
2023-08-24 Ben SoaresMerge branch 'features/r2_11_2_alphafold/JAL-629' into... tree | commitdiff
2023-08-24 Ben SoaresJAL-629 Avoid hidden options dialog when saving in... tree | commitdiff
2023-08-24 Ben SoaresMerge branch 'bug/JAL-4214_system_freeze_when_opening_f... tree | commitdiff
2023-08-24 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_... tree | commitdiff
2023-08-24 Ben SoaresJAL-4250 Fix bug in vector rendition where more than... improvement/JAL-4250_secondary_structure_annotation_antialias tree | commitdiff
2023-08-24 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_... tree | commitdiff
2023-08-24 Ben SoaresJAL-4250 Much simplified glyph creation removing most... tree | commitdiff
2023-08-23 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_... tree | commitdiff
2023-08-23 Ben SoaresJAL-4250 Fix one word bug for 'af.createEPS(file, rende... tree | commitdiff
2023-08-23 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_... tree | commitdiff
2023-08-23 Ben SoaresJAL-4250 Updated jfreesvg to fix round stroke in linegraph. tree | commitdiff
2023-08-23 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_... tree | commitdiff
2023-08-23 Ben SoaresJAL-4250 Simplification of polygons and adjustments... tree | commitdiff
2023-08-21 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_... tree | commitdiff
2023-08-21 Ben SoaresJAL-4250 revert green to bright green tree | commitdiff
2023-08-21 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_... tree | commitdiff
2023-08-21 Ben SoaresJAL-4250 Conservative setting of ANTIALIAS and readjust... tree | commitdiff
2023-08-18 Ben SoaresJAL-4250 Make secondary structure annotation shapes... tree | commitdiff
2023-08-18 Ben SoaresMerge branch 'improvement/JAL-4206_improve_JalviewFileC... tree | commitdiff
2023-08-18 Ben SoaresMerge branch 'bug/JAL-4214_system_freeze_when_opening_f... tree | commitdiff
2023-08-18 Ben SoaresMerge branch 'feature/JAL-244_Automatically_adjust_left... tree | commitdiff
2023-08-18 Ben SoaresMerge branch 'improvement/JAL-3830_remove_dock_icon_in_... tree | commitdiff
2023-08-18 Ben SoaresMerge branch 'bug/JAL-4242_exception_when_pressing_esca... tree | commitdiff
2023-08-18 Ben SoaresJAL-3416 Remove full height separators between new... improvement/JAL-3416_FlatLaf_3.2 tree | commitdiff
2023-08-18 Ben SoaresJAL-4242 null check on getValue() return bug/JAL-4242_exception_when_pressing_escape_in_fetch_from_URL_dialog tree | commitdiff
2023-08-17 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t... tree | commitdiff
2023-08-17 Ben SoaresJAL-3830 JAL-4160 Remove --noheadless as --gui does... tree | commitdiff
2023-08-16 Ben SoaresMerge branch 'develop' into improvement/JAL-3830_remove... tree | commitdiff
2023-08-16 Ben SoaresJAL-3820 JAL-4189 Move checks for java executable symli... tree | commitdiff
2023-08-11 Ben SoaresJAL-629 Much better way of dealing with list of filenam... tree | commitdiff
2023-08-10 Ben SoaresJAL-629 STDOUT documentation. Opt.STDOUT narrower... tree | commitdiff
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use... tree | commitdiff
2023-08-10 Ben SoaresJAL-629 Method to use for printStackTrace tree | commitdiff
2023-08-09 Ben SoaresJAL-629 Move more stdout messages to stderr when output... tree | commitdiff
2023-08-09 Ben SoaresJAL-629 Default to FASTA if no format given for output... tree | commitdiff
2023-08-09 Ben SoaresJAL-629 Enable output to STDOUT when specifying output... tree | commitdiff
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 tree | commitdiff
2023-08-08 Ben SoaresJAL-244 Added light grey marks to indicate regions... tree | commitdiff
2023-08-08 Ben SoaresJAL-244 Fix mismatched vertical positioning of sequence... tree | commitdiff
2023-08-07 Ben SoaresJAL-244 Avoid working on the Ids Graphics object when... tree | commitdiff
2023-08-04 Ben SoaresJAL-244 Adjust wrapped alignment widths to always maint... tree | commitdiff
2023-08-02 Ben SoaresJAL-244 Fix buglet with automatic change in id column... tree | commitdiff
2023-08-01 Ben SoaresJAL-244 More control of automatic idWidth adjustments... tree | commitdiff
2023-07-27 Ben SoaresMerge branch 'develop' into feature/JAL-244_Automatical... tree | commitdiff
2023-07-27 Ben SoaresJAL-244 Allow wrap manual adjustments to be smaller... tree | commitdiff
2023-07-27 Ben SoaresJAL-244 Allow adjusting Id column width in wrap mode... tree | commitdiff
2023-07-25 Ben SoaresJAL-244 testing without AlignFrame for --wrap tree | commitdiff
2023-07-21 Ben SoaresJAL-244 Fixed idWidth labels in headless mode for non... tree | commitdiff
2023-07-20 Ben SoaresJAL-244 More accurate width calculation, allow increase... tree | commitdiff
2023-07-20 James ProcterJAL-3855 tree title for PAE matrix tree is PAE Matrix... patch/JAL-3855_fixup_pae tree | commitdiff
2023-07-20 James ProcterJAL-3855 auto select clusters and fix up colouring... tree | commitdiff
2023-07-19 Ben SoaresJAL-244 Changes to Annotation labels width now adjusts... tree | commitdiff
2023-07-18 James ProcterJAL-3855 PAE matrices are transposed on import from... tree | commitdiff
2023-07-18 James ProcterJAL-3858 fix off-by-one in matrix visualisation and... tree | commitdiff
2023-07-18 James ProcterJAL-3858 flip diagonal so matrix visualisation is top... tree | commitdiff
2023-07-18 James ProcterJAL-3858 annotation .height is bigger than graphHeight... tree | commitdiff
2023-07-17 James ProcterJAL-4119 TRACE level console message reporting download... tree | commitdiff
2023-07-12 James ProcterJAL-4223 - test and patch to ensure numbering matches... tree | commitdiff
2023-07-10 James ProcterMerge branch 'improvement/JAL-3830_remove_dock_icon_in_... tree | commitdiff
2023-07-07 James ProcterJAL-4217 JAL-629 built in 25s time out waiting for... tree | commitdiff
2023-07-07 James ProcterMerge branch 'patch/JAL-4119_sifts_ftp_split' into... tree | commitdiff
2023-07-07 James ProcterJAL-4221 update description when transferring annotatio... tree | commitdiff
2023-07-07 James ProcterJAL-629 even more console debug for --structureviewer... tree | commitdiff
2023-07-06 James ProcterJAL-629 liberal defensive coding, comments about refact... tree | commitdiff
2023-07-06 James ProcterJAL-629 make —structure image work again after threadin... tree | commitdiff
2023-07-06 James ProcterJAL-4217 catch case when the structure viewer doesn... tree | commitdiff
2023-07-06 James ProcterJAL-4217 interruptedExceptions should also break any... tree | commitdiff
2023-07-06 James ProcterJAL-4217 wrap imageExport CLI method's call to imageExp... tree | commitdiff
2023-07-06 James ProcterJAL-4217 wrap imageExport CLI method's call to imageExp... tree | commitdiff
2023-07-05 James ProcterMerge branch 'patch/JAL-2292_caseSensitivePAE' into... tree | commitdiff
2023-07-05 James ProcterMerge branch 'patch/JAL-4213_addref_with_selection... tree | commitdiff
2023-07-04 James ProcterJAL-4117 JAL-1551 source licensing tree | commitdiff
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