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Merge branch 'develop' into bug/JAL-4235_gradle_task_jalviewjsTranspile_does_not_fail...
[jalview.git]
/
src
/
2023-09-13
Ben Soares
JAL-4262 Made deprecation warning properly modal
bug/JAL-4277_dirname_substitution_always_absolute
tree
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commitdiff
2023-09-12
Ben Soares
JAL-4262 Allow HTML in the dialog box for link to CLI...
tree
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commitdiff
2023-09-12
Ben Soares
JAL-4285 Better checkFiles processing. Better dialog.
tree
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commitdiff
2023-09-12
Ben Soares
JAL-4285 JAL-4262 Added a scrollable dialog to display...
tree
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commitdiff
2023-09-11
Ben Soares
JAL-4001 corrected analytics message labels
tree
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commitdiff
2023-09-11
Ben Soares
Merge branch 'improvement/JAL-4262_deprecation_warning_...
tree
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commitdiff
2023-09-11
Ben Soares
JAL-4277 --mkdirs with cautious refusal for paths with ..
tree
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commitdiff
2023-09-11
Ben Soares
JAL-4284 JAL-4285 Deal with output files/images consist...
tree
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commitdiff
2023-09-08
James Procter
JAL-4281 store/restore ID width and manual adjustment...
tree
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commitdiff
2023-09-08
James Procter
JAL-4281 reinstate access to legacy id width calculatio...
tree
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commitdiff
2023-09-08
James Procter
JAL-4282 make sure font is updated in alignPanel before...
tree
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commitdiff
2023-09-08
Ben Soares
JAL-4262 Make an excepetion for STDOUT filename in...
improvement/JAL-4262_deprecation_warning_when_old_CLI_arguments_are_processed
tree
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commitdiff
2023-09-08
Ben Soares
Merge branch 'bug/JAL-4277_dirname_substitution_always_...
tree
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commitdiff
2023-09-08
Ben Soares
JAL-4262 Dialog for GUI and WARN for CLI of old style...
tree
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commitdiff
2023-09-07
Ben Soares
Merge branch 'develop' into bug/JAL-4277_dirname_substi...
tree
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commitdiff
2023-09-07
Ben Soares
JAL-4277 Corrected choice of all or last opened linkedI...
tree
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commitdiff
2023-09-07
James Procter
JAL-4279 suppress error dialogs raised by file loader...
improvement/JAL-4279_gracefully_handle_failure_to_openviaCLI
tree
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commitdiff
2023-09-07
James Procter
JAL-4279 move on if the file doesn't exist, or Identify...
tree
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commitdiff
2023-09-07
James Procter
JAL-4279 catch exceptions with fileLoader and report...
tree
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commitdiff
2023-09-07
James Procter
JAL-4090 JAL-4160 JAL-4274 image export dimensions...
tree
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commitdiff
2023-09-07
Ben Soares
JAL-629 Change names of Opt.ALLOWALL to Opt.ALLOWMULTII...
improvement/JAL-629_Apply_alignment_options_to_all_globbed_files
tree
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commitdiff
2023-09-07
James Procter
JAL-4273 release notes for visible adjuster marks,...
tree
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commitdiff
2023-09-06
James Procter
JAL-4260 attempt to rejig paging when id width is adjus...
tree
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commitdiff
2023-09-06
James Procter
JAL-4258 remove unnecessary ‘this’
tree
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commitdiff
2023-09-06
James Procter
JAL-4259 construct a new SequenceRenderer when renderin...
tree
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commitdiff
2023-09-06
James Procter
JAL-629 javadoc on new setMapping variant for structure...
tree
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commitdiff
2023-09-06
James Procter
JAL-629 reinstate INFO level stack trace from Structure...
tree
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commitdiff
2023-09-06
James Procter
JAL-629 javadoc
tree
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commitdiff
2023-09-05
James Procter
JAL-629 remove structure viewer from the list of struct...
tree
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commitdiff
2023-09-05
James Procter
JAL-629 use JalviewStructureDisplayI in place of Struct...
tree
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commitdiff
2023-09-02
Ben Soares
Merge branch 'feature/JAL-629_--output_-_means_output_t...
tree
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commitdiff
2023-09-02
Ben Soares
JAL-629 Add accessors for argParser and bootstrapArgs
feature/JAL-629_--output_-_means_output_to_STDOUT
tree
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commitdiff
2023-09-01
Ben Soares
Merge branch 'feature/JAL-629_--output_-_means_output_t...
tree
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commitdiff
2023-09-01
Ben Soares
JAL-629 Save structure frames in project files when...
tree
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commitdiff
2023-09-01
Ben Soares
Merge branch 'feature/JAL-629_--output_-_means_output_t...
tree
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commitdiff
2023-09-01
Ben Soares
JAL-629 Fix --structureimage and options
tree
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commitdiff
2023-09-01
James Procter
JAL-4124 need to repaint alignFrames imported from...
tree
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commitdiff
2023-09-01
James Procter
JAL-4124 matrix is saved in dataset, with forward refer...
tree
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commitdiff
2023-09-01
James Procter
JAL-4124 add strategic newlines in matrix stringified...
tree
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commitdiff
2023-08-31
Ben Soares
Merge branch 'features/r2_11_2_alphafold/JAL-629' into...
tree
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commitdiff
2023-08-31
Ben Soares
JAL-629 Small buglet with getting --seqid
features/r2_11_2_alphafold/JAL-629
tree
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commitdiff
2023-08-31
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-08-31
James Procter
JAL-4124 MappableContactMatrix equivalence and hashCode...
tree
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commitdiff
2023-08-29
James Procter
JAL-4124 Dataset holds list of MatrixType instances...
tree
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commitdiff
2023-08-29
James Procter
JAL-4124 decouple mappable contact matrix mapping logic...
tree
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commitdiff
2023-08-28
Ben Soares
Merge branch 'develop' into merge/big_merge_of_bens_stu...
tree
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commitdiff
2023-08-28
James Procter
Merge branch 'develop' into more_efficient_PAE
tree
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commitdiff
2023-08-28
James Procter
JAL-4253 drop the bottom line so it lines up with the...
tree
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commitdiff
2023-08-24
Ben Soares
Merge branch 'develop' into merge/big_merge_of_bens_stu...
tree
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commitdiff
2023-08-24
Ben Soares
Merge branch 'features/r2_11_2_alphafold/JAL-629' into...
tree
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commitdiff
2023-08-24
Ben Soares
JAL-629 Avoid hidden options dialog when saving in...
tree
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commitdiff
2023-08-24
Ben Soares
Merge branch 'bug/JAL-4214_system_freeze_when_opening_f...
tree
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commitdiff
2023-08-24
Ben Soares
Merge branch 'improvement/JAL-4250_secondary_structure_...
tree
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commitdiff
2023-08-24
Ben Soares
JAL-4250 Fix bug in vector rendition where more than...
improvement/JAL-4250_secondary_structure_annotation_antialias
tree
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commitdiff
2023-08-24
Ben Soares
Merge branch 'improvement/JAL-4250_secondary_structure_...
tree
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commitdiff
2023-08-24
Ben Soares
JAL-4250 Much simplified glyph creation removing most...
tree
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commitdiff
2023-08-23
Ben Soares
Merge branch 'improvement/JAL-4250_secondary_structure_...
tree
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commitdiff
2023-08-23
Ben Soares
JAL-4250 Fix one word bug for 'af.createEPS(file, rende...
tree
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commitdiff
2023-08-23
Ben Soares
Merge branch 'improvement/JAL-4250_secondary_structure_...
tree
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commitdiff
2023-08-23
Ben Soares
JAL-4250 Updated jfreesvg to fix round stroke in linegraph.
tree
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commitdiff
2023-08-23
Ben Soares
Merge branch 'improvement/JAL-4250_secondary_structure_...
tree
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commitdiff
2023-08-23
Ben Soares
JAL-4250 Simplification of polygons and adjustments...
tree
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commitdiff
2023-08-21
James Procter
JAL-4062 revert to ArrayList and integrate check for...
tree
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commitdiff
2023-08-21
James Procter
JAL-4062 fix up imports
tree
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commitdiff
2023-08-21
James Procter
JAL-4062 appendResult(seq,start,end) called by structur...
tree
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commitdiff
2023-08-21
Ben Soares
Merge branch 'improvement/JAL-4250_secondary_structure_...
tree
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commitdiff
2023-08-21
Ben Soares
JAL-4250 revert green to bright green
tree
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commitdiff
2023-08-21
Ben Soares
Merge branch 'improvement/JAL-4250_secondary_structure_...
tree
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commitdiff
2023-08-21
Ben Soares
JAL-4250 Conservative setting of ANTIALIAS and readjust...
tree
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commitdiff
2023-08-18
Ben Soares
JAL-4250 Make secondary structure annotation shapes...
tree
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commitdiff
2023-08-18
Ben Soares
Merge branch 'improvement/JAL-4206_improve_JalviewFileC...
tree
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commitdiff
2023-08-18
Ben Soares
Merge branch 'bug/JAL-4214_system_freeze_when_opening_f...
tree
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commitdiff
2023-08-18
Ben Soares
Merge branch 'feature/JAL-244_Automatically_adjust_left...
tree
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commitdiff
2023-08-18
Ben Soares
Merge branch 'improvement/JAL-3830_remove_dock_icon_in_...
tree
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commitdiff
2023-08-18
Ben Soares
Merge branch 'bug/JAL-4242_exception_when_pressing_esca...
tree
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commitdiff
2023-08-18
Ben Soares
JAL-3416 Remove full height separators between new...
improvement/JAL-3416_FlatLaf_3.2
tree
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commitdiff
2023-08-18
Ben Soares
JAL-4242 null check on getValue() return
bug/JAL-4242_exception_when_pressing_escape_in_fetch_from_URL_dialog
tree
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commitdiff
2023-08-17
Ben Soares
Merge branch 'feature/JAL-629_--output_-_means_output_t...
tree
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commitdiff
2023-08-17
Ben Soares
JAL-3830 JAL-4160 Remove --noheadless as --gui does...
tree
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commitdiff
2023-08-16
Ben Soares
Merge branch 'develop' into improvement/JAL-3830_remove...
tree
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commitdiff
2023-08-16
Ben Soares
JAL-3820 JAL-4189 Move checks for java executable symli...
tree
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commitdiff
2023-08-11
Ben Soares
JAL-629 Much better way of dealing with list of filenam...
tree
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commitdiff
2023-08-10
Ben Soares
JAL-629 STDOUT documentation. Opt.STDOUT narrower...
tree
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commitdiff
2023-08-10
Ben Soares
JAL-629 Change all stdout and stderr output to use...
tree
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commitdiff
2023-08-10
Ben Soares
JAL-629 Method to use for printStackTrace
tree
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commitdiff
2023-08-09
Ben Soares
JAL-629 Move more stdout messages to stderr when output...
tree
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commitdiff
2023-08-09
Ben Soares
JAL-629 Default to FASTA if no format given for output...
tree
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commitdiff
2023-08-09
Ben Soares
JAL-629 Enable output to STDOUT when specifying output...
tree
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commitdiff
2023-08-09
Ben Soares
JAL-244 Fix window size narrow adjustment not becoming...
feature/JAL-244_Automatically_adjust_left_margin_to_avoid_cropping_annotation_labels
tree
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commitdiff
2023-08-08
Ben Soares
JAL-244 Added light grey marks to indicate regions...
tree
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commitdiff
2023-08-08
Ben Soares
JAL-244 Fix mismatched vertical positioning of sequence...
tree
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commitdiff
2023-08-07
Ben Soares
JAL-244 Avoid working on the Ids Graphics object when...
tree
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commitdiff
2023-08-04
Ben Soares
JAL-244 Adjust wrapped alignment widths to always maint...
tree
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commitdiff
2023-08-02
Ben Soares
JAL-244 Fix buglet with automatic change in id column...
tree
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commitdiff
2023-08-01
Ben Soares
JAL-244 More control of automatic idWidth adjustments...
tree
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commitdiff
2023-07-27
Ben Soares
Merge branch 'develop' into feature/JAL-244_Automatical...
tree
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commitdiff
2023-07-27
Ben Soares
JAL-244 Allow wrap manual adjustments to be smaller...
tree
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commitdiff
2023-07-27
Ben Soares
JAL-244 Allow adjusting Id column width in wrap mode...
tree
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commitdiff
2023-07-25
Ben Soares
JAL-244 testing without AlignFrame for --wrap
tree
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commitdiff
2023-07-21
Ben Soares
JAL-244 Fixed idWidth labels in headless mode for non...
tree
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commitdiff
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