git://source.jalview.org
/
jalview.git
/ history
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
first
⋅
prev
⋅
next
Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git]
/ src
2023-09-28
James Procter
JAL-3858 improved contactInterval computation and added...
commit
|
commitdiff
2023-09-26
James Procter
JAL-3858 JAL-4090 avoid NPE when given out of bound...
commit
|
commitdiff
2023-09-25
James Procter
JAL-3858 minimum value for a range is used to shade...
commit
|
commitdiff
2023-09-25
James Procter
JAL-3858 javadoc and slightly revised green linear...
commit
|
commitdiff
2023-09-25
James Procter
JAL-3858 report PAE range with sensible precision
commit
|
commitdiff
2023-09-21
James Procter
JAL-1551 javadoc for mapUtils
commit
|
commitdiff
2023-09-21
James Procter
JAL-3855 disable the AlphaFold DB entry in Sequence...
commit
|
commitdiff
2023-09-21
Ben Soares
JAL-4265 Use ColourUtils.parseColourString() for consis...
merge/JAL-4262+JAL-4265+JAL-4269+JAL-4274+JAL-4277+JAL-4285
commit
|
commitdiff
2023-09-21
Ben Soares
Merge branch 'develop' into merge/JAL-4262+JAL-4265...
commit
|
commitdiff
2023-09-20
Ben Soares
JAL-4265 Use ColorUtils.parseColourString() and adjust...
commit
|
commitdiff
2023-09-20
James Procter
JAL-4285 don’t say you are reporting warnings/errors...
commit
|
commitdiff
2023-09-20
James Procter
JAL-4265 JAL-4286 reinstated explicit restoreSession...
commit
|
commitdiff
2023-09-20
James Procter
JAL-4265 JAL-4267 added a ‘restoreSession’ StructureVie...
commit
|
commitdiff
2023-09-20
James Procter
JAL-4195 JAL-1069 JAL-4160 errors in Cache should go...
commit
|
commitdiff
2023-09-20
James Procter
JAL-4265 bail early when attempting to export a view...
commit
|
commitdiff
2023-09-20
James Procter
JAL-4265 JAL-4267 allow injection of custom commands...
commit
|
commitdiff
2023-09-20
James Procter
JAL-4265 back out redundant ‘saveState’ and ‘restoreSta...
commit
|
commitdiff
2023-09-20
Ben Soares
JAL-4265 Added saveState and restoreState to interface...
commit
|
commitdiff
2023-09-19
Ben Soares
JAL-4265 Change to use JmolCommands
commit
|
commitdiff
2023-09-19
Ben Soares
JAL-629 Allow multiple structure images for multiple...
commit
|
commitdiff
2023-09-18
MorellThomas
Fix buttons on the PaSiMap plot window
commit
|
commitdiff
2023-09-16
Ben Soares
JAL-4250 Fixed blue arrows in drawStemAnnot()
commit
|
commitdiff
2023-09-16
Ben Soares
JAL-629 Fix a test and omit an incorrect error message...
improvement/JAL-4269_reduce_variants_of_common_subvalue_parameters
commit
|
commitdiff
2023-09-16
Ben Soares
JAL-4265 Added --bgcolour for --structureimage output...
commit
|
commitdiff
2023-09-16
MorellThomas
Correctly working implementation of the PaSiMap pipeline
commit
|
commitdiff
2023-09-16
Ben Soares
JAL-4269 Now using --width, --height, --scale for both...
commit
|
commitdiff
2023-09-16
MorellThomas
Almost working
commit
|
commitdiff
2023-09-14
Ben Soares
Merge branch 'develop' into feature/JAL-4274_configurab...
commit
|
commitdiff
2023-09-13
Ben Soares
JAL-4274 Use Cache BITMAP_* if no other image restricti...
commit
|
commitdiff
2023-09-13
Ben Soares
JAL-4262 Made deprecation warning properly modal
bug/JAL-4277_dirname_substitution_always_absolute
commit
|
commitdiff
2023-09-12
Ben Soares
JAL-4262 Allow HTML in the dialog box for link to CLI...
commit
|
commitdiff
2023-09-12
Ben Soares
JAL-4285 Better checkFiles processing. Better dialog.
commit
|
commitdiff
2023-09-12
Ben Soares
JAL-4285 JAL-4262 Added a scrollable dialog to display...
commit
|
commitdiff
2023-09-11
Ben Soares
JAL-4001 corrected analytics message labels
commit
|
commitdiff
2023-09-11
Ben Soares
Merge branch 'improvement/JAL-4262_deprecation_warning_...
commit
|
commitdiff
2023-09-11
Ben Soares
JAL-4277 --mkdirs with cautious refusal for paths with ..
commit
|
commitdiff
2023-09-11
Ben Soares
JAL-4284 JAL-4285 Deal with output files/images consist...
commit
|
commitdiff
2023-09-08
James Procter
JAL-4281 store/restore ID width and manual adjustment...
commit
|
commitdiff
2023-09-08
James Procter
JAL-4281 reinstate access to legacy id width calculatio...
commit
|
commitdiff
2023-09-08
James Procter
JAL-4282 make sure font is updated in alignPanel before...
commit
|
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
commit
|
commitdiff
2023-09-08
Ben Soares
Merge branch 'bug/JAL-4277_dirname_substitution_always_...
commit
|
commitdiff
2023-09-08
Ben Soares
JAL-4262 Dialog for GUI and WARN for CLI of old style...
commit
|
commitdiff
2023-09-08
MorellThomas
Properly integrated endGaps option for AlignSeq.traceAl...
commit
|
commitdiff
2023-09-07
Ben Soares
Merge branch 'develop' into bug/JAL-4277_dirname_substi...
commit
|
commitdiff
2023-09-07
Ben Soares
JAL-4277 Corrected choice of all or last opened linkedI...
commit
|
commitdiff
2023-09-07
James Procter
JAL-4279 suppress error dialogs raised by file loader...
improvement/JAL-4279_gracefully_handle_failure_to_openviaCLI
commit
|
commitdiff
2023-09-07
James Procter
JAL-4279 move on if the file doesn't exist, or Identify...
commit
|
commitdiff
2023-09-07
James Procter
JAL-4279 catch exceptions with fileLoader and report...
commit
|
commitdiff
2023-09-07
James Procter
JAL-4090 JAL-4160 JAL-4274 image export dimensions...
commit
|
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
commit
|
commitdiff
2023-09-07
James Procter
JAL-4273 release notes for visible adjuster marks,...
commit
|
commitdiff
2023-09-07
MorellThomas
Merge branch 'hardcode'
commit
|
commitdiff
2023-09-07
MorellThomas
Implemented least-squares optimisation in ccAnalysis
commit
|
commitdiff
2023-09-06
James Procter
JAL-4260 attempt to rejig paging when id width is adjus...
commit
|
commitdiff
2023-09-06
James Procter
JAL-4258 remove unnecessary ‘this’
commit
|
commitdiff
2023-09-06
James Procter
JAL-4259 construct a new SequenceRenderer when renderin...
commit
|
commitdiff
2023-09-06
James Procter
JAL-629 javadoc on new setMapping variant for structure...
commit
|
commitdiff
2023-09-06
James Procter
JAL-629 reinstate INFO level stack trace from Structure...
commit
|
commitdiff
2023-09-06
James Procter
JAL-629 javadoc
commit
|
commitdiff
2023-09-05
James Procter
JAL-629 remove structure viewer from the list of struct...
commit
|
commitdiff
2023-09-05
James Procter
JAL-629 use JalviewStructureDisplayI in place of Struct...
commit
|
commitdiff
2023-09-04
James Procter
JAL-3088 check for validEnd when working out whether...
commit
|
commitdiff
2023-09-04
James Procter
JAL-4250 fix location and height for RNA secondary...
commit
|
commitdiff
2023-09-04
James Procter
JAL-4250 rendition is way too obscure for me
commit
|
commitdiff
2023-09-04
James Procter
JAL-4159 JAL-4257 simple test for default gap parameter...
features/JAL-4257_adjustablegapparams_nw
commit
|
commitdiff
2023-09-02
Ben Soares
Merge branch 'feature/JAL-629_--output_-_means_output_t...
commit
|
commitdiff
2023-09-02
Ben Soares
JAL-629 Add accessors for argParser and bootstrapArgs
feature/JAL-629_--output_-_means_output_to_STDOUT
commit
|
commitdiff
2023-09-01
Ben Soares
Merge branch 'feature/JAL-629_--output_-_means_output_t...
commit
|
commitdiff
2023-09-01
Ben Soares
JAL-629 Save structure frames in project files when...
commit
|
commitdiff
2023-09-01
Ben Soares
Merge branch 'feature/JAL-629_--output_-_means_output_t...
commit
|
commitdiff
2023-09-01
Ben Soares
JAL-629 Fix --structureimage and options
commit
|
commitdiff
2023-09-01
James Procter
JAL-4124 need to repaint alignFrames imported from...
commit
|
commitdiff
2023-09-01
James Procter
JAL-4124 matrix is saved in dataset, with forward refer...
commit
|
commitdiff
2023-09-01
James Procter
JAL-4124 add strategic newlines in matrix stringified...
commit
|
commitdiff
2023-08-31
Ben Soares
Merge branch 'features/r2_11_2_alphafold/JAL-629' into...
commit
|
commitdiff
2023-08-31
Ben Soares
JAL-629 Small buglet with getting --seqid
features/r2_11_2_alphafold/JAL-629
commit
|
commitdiff
2023-08-31
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
commit
|
commitdiff
2023-08-31
James Procter
JAL-4124 MappableContactMatrix equivalence and hashCode...
commit
|
commitdiff
2023-08-29
James Procter
JAL-4124 Dataset holds list of MatrixType instances...
commit
|
commitdiff
2023-08-29
James Procter
JAL-4124 decouple mappable contact matrix mapping logic...
commit
|
commitdiff
2023-08-28
Ben Soares
Merge branch 'develop' into merge/big_merge_of_bens_stu...
commit
|
commitdiff
2023-08-28
James Procter
Merge branch 'develop' into more_efficient_PAE
commit
|
commitdiff
2023-08-28
James Procter
JAL-4253 drop the bottom line so it lines up with the...
commit
|
commitdiff
2023-08-24
Ben Soares
Merge branch 'develop' into merge/big_merge_of_bens_stu...
commit
|
commitdiff
2023-08-24
Ben Soares
Merge branch 'features/r2_11_2_alphafold/JAL-629' into...
commit
|
commitdiff
2023-08-24
Ben Soares
JAL-629 Avoid hidden options dialog when saving in...
commit
|
commitdiff
2023-08-24
Ben Soares
Merge branch 'bug/JAL-4214_system_freeze_when_opening_f...
commit
|
commitdiff
2023-08-24
Ben Soares
Merge branch 'improvement/JAL-4250_secondary_structure_...
commit
|
commitdiff
2023-08-24
Ben Soares
JAL-4250 Fix bug in vector rendition where more than...
improvement/JAL-4250_secondary_structure_annotation_antialias
commit
|
commitdiff
2023-08-24
Ben Soares
Merge branch 'improvement/JAL-4250_secondary_structure_...
commit
|
commitdiff
2023-08-24
Ben Soares
JAL-4250 Much simplified glyph creation removing most...
commit
|
commitdiff
2023-08-23
Ben Soares
Merge branch 'improvement/JAL-4250_secondary_structure_...
commit
|
commitdiff
2023-08-23
Ben Soares
JAL-4250 Fix one word bug for 'af.createEPS(file, rende...
commit
|
commitdiff
2023-08-23
Ben Soares
Merge branch 'improvement/JAL-4250_secondary_structure_...
commit
|
commitdiff
2023-08-23
Ben Soares
JAL-4250 Updated jfreesvg to fix round stroke in linegraph.
commit
|
commitdiff
2023-08-23
Ben Soares
Merge branch 'improvement/JAL-4250_secondary_structure_...
commit
|
commitdiff
2023-08-23
Ben Soares
JAL-4250 Simplification of polygons and adjustments...
commit
|
commitdiff
2023-08-21
James Procter
JAL-4062 revert to ArrayList and integrate check for...
commit
|
commitdiff
2023-08-21
James Procter
JAL-4062 fix up imports
commit
|
commitdiff
next