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Merge branch 'bug/JAL-4397_failing_idWidth_tests' into improvement/JAL-4409_implement...
[jalview.git]
/
src
/
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
2023-07-20
Ben Soares
JAL-244 More accurate width calculation, allow increase...
tree
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commitdiff
2023-07-20
James Procter
JAL-3855 tree title for PAE matrix tree is PAE Matrix...
patch/JAL-3855_fixup_pae
tree
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commitdiff
2023-07-20
James Procter
JAL-3855 auto select clusters and fix up colouring...
tree
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commitdiff
2023-07-19
Ben Soares
JAL-244 Changes to Annotation labels width now adjusts...
tree
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commitdiff
2023-07-18
James Procter
exploring making PAE storage in projects more efficient
tree
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commitdiff
2023-07-18
James Procter
JAL-3855 PAE matrices are transposed on import from...
tree
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commitdiff
2023-07-18
James Procter
JAL-3858 fix off-by-one in matrix visualisation and...
tree
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commitdiff
2023-07-18
James Procter
JAL-3858 flip diagonal so matrix visualisation is top...
tree
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commitdiff
2023-07-18
James Procter
JAL-3858 annotation .height is bigger than graphHeight...
tree
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commitdiff
2023-07-17
James Procter
JAL-4119 TRACE level console message reporting download...
tree
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commitdiff
2023-07-12
James Procter
JAL-4223 - test and patch to ensure numbering matches...
tree
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commitdiff
2023-07-10
James Procter
Merge branch 'improvement/JAL-3830_remove_dock_icon_in_...
tree
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commitdiff
2023-07-07
James Procter
JAL-4217 JAL-629 built in 25s time out waiting for...
tree
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commitdiff
2023-07-07
James Procter
Merge branch 'patch/JAL-4119_sifts_ftp_split' into...
tree
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commitdiff
2023-07-07
James Procter
JAL-4221 update description when transferring annotatio...
tree
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commitdiff
2023-07-07
James Procter
JAL-629 even more console debug for --structureviewer...
tree
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commitdiff
2023-07-06
James Procter
JAL-629 liberal defensive coding, comments about refact...
tree
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commitdiff
2023-07-06
James Procter
JAL-629 make —structure image work again after threadin...
tree
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commitdiff
2023-07-06
James Procter
JAL-4217 catch case when the structure viewer doesn...
tree
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commitdiff
2023-07-06
James Procter
JAL-4217 interruptedExceptions should also break any...
tree
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commitdiff
2023-07-06
James Procter
JAL-4217 wrap imageExport CLI method's call to imageExp...
tree
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commitdiff
2023-07-06
James Procter
JAL-4217 wrap imageExport CLI method's call to imageExp...
tree
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commitdiff
2023-07-05
James Procter
Merge branch 'patch/JAL-2292_caseSensitivePAE' into...
tree
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commitdiff
2023-07-05
James Procter
Merge branch 'patch/JAL-4213_addref_with_selection...
tree
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commitdiff
2023-07-04
James Procter
JAL-4117 JAL-1551 source licensing
tree
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commitdiff
2023-06-30
James Procter
JAL-4217 try really hard to shut down and dispose of...
tree
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commitdiff
2023-06-30
James Procter
JAL-4216 compute size of annotation using start/end...
tree
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commitdiff
2023-06-30
Ben Soares
JAL-4001 Added a random id to User-Agent to ensure...
task/JAL-4001_Plausible_API
tree
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commitdiff
2023-06-29
Ben Soares
JAL-4214 Linux only: Disable menus when internal modal...
bug/JAL-4214_system_freeze_when_opening_file_using_gui_in_linux
tree
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commitdiff
2023-06-29
James Procter
JAL-4001 analytics url provided by https://jalview...
tree
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commitdiff
2023-06-28
Ben Soares
JAL-4214 Make modal internal frame disappear when main...
tree
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commitdiff
2023-06-28
Ben Soares
JAL-4001 change Plausible discovery URL
tree
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commitdiff
2023-06-28
Ben Soares
JAL-4001 remove stray --headless mode analytic
tree
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commitdiff
2023-06-28
Ben Soares
Merge branch 'task/JAL-4001_Plausible_API' into improve...
tree
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commitdiff
2023-06-28
Ben Soares
JAL-3820 add java and java.exe from JAVAHOME to list...
tree
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commitdiff
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