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Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
[jalview.git]
/
src
/
2023-10-31
Ben Soares
Merge branch 'develop' into bug/JAL-4059_update_swingJS...
tree
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commitdiff
2023-10-31
Ben Soares
JAL-4059 Converting Pattern/Matcher methods that are...
tree
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commitdiff
2023-10-26
James Procter
Merge branch 'bug/JAL-4313_cme_in_tests' into patch...
tree
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commitdiff
2023-10-25
James Procter
JAL-4312 defend against ConcurrentModificationException
bug/JAL-4313_cme_in_tests
tree
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commitdiff
2023-10-25
James Procter
JAL-4312 call AlignFrame.setAnnotationsVisibility on...
tree
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commitdiff
2023-10-23
James Procter
JAL-4311 fix ranking so models with like scores are...
improvement/JAL-4124_dont_duplacate_PAE_data_acrossviews
tree
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commitdiff
2023-10-23
James Procter
JAL-4311 failing test case for 3d-beacons epas1_human...
tree
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commitdiff
2023-10-23
Ben Soares
Merge branch 'develop' into bug/JAL-4059_update_swingJS...
tree
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commitdiff
2023-10-23
James Procter
JAL-4310 let the user know when model pages are not...
tree
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commitdiff
2023-10-23
James Procter
Merge branch 'develop' into improvement/JAL-4124_dont_d...
tree
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commitdiff
2023-10-23
James Procter
Merge branch 'feature/JAL-4307_hetatm_showhide' into...
tree
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commitdiff
2023-10-23
James Procter
JAL-4090 defensive check for featureSettings redraws...
improvement/JAL-4308_smalleridtooltip
tree
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commitdiff
2023-10-23
James Procter
JAL-4308 reduce number of refs to 5, always have canoni...
tree
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commitdiff
2023-10-22
James Procter
JAL-1551 errant tab and import
tree
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commitdiff
2023-10-22
James Procter
Merge branch 'patch/JAL-4298_synchronize_consoledoc...
tree
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commitdiff
2023-10-21
James Procter
JAL-1332 JAL-4298 JAL-3772 rejig the quit handler so...
jims/bug/JAL-4298_java_console_causing_hang_at_startup
tree
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commitdiff
2023-10-20
James Procter
Merge branch 'improvement/JAL-3783_upgrade_to_groovy...
tree
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commitdiff
2023-10-20
Ben Soares
JAL-4298 Remove a stray return in the processGroovyScri...
tree
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commitdiff
2023-10-20
James Procter
JAL-4298 reuse existing log level preference method
tree
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commitdiff
2023-10-20
James Procter
JAL-4307 also report molecule name in tooltip for show...
feature/JAL-4307_hetatm_showhide
tree
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commitdiff
2023-10-20
Ben Soares
JAL-4298 another implicated line
bug/JAL-4298_java_console_causing_hang_at_startup
tree
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commitdiff
2023-10-20
James Procter
Merge branch 'feature/JAL-4307_hetatm_showhide' into...
tree
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commitdiff
2023-10-20
James Procter
JAL-4307 some models return null for hetatm list
tree
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commitdiff
2023-10-20
James Procter
JAL-4298 try much harder to avoid modifying console...
patch/JAL-4298_synchronize_consoledoc
tree
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commitdiff
2023-10-19
Ben Soares
Merge branch 'patch/JAL-4298_synchronize_consoledoc...
tree
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commitdiff
2023-10-19
Ben Soares
JAL-629 Fix --nodebug turning off debug mode from prope...
tree
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commitdiff
2023-10-19
Ben Soares
JAL-4298 comment markers
tree
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commitdiff
2023-10-19
Ben Soares
Merge branch 'improvement/JAL-3783_upgrade_to_groovy...
tree
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commitdiff
2023-10-19
James Procter
JAL-4298 avoid deadlock waiting to update doc when...
tree
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commitdiff
2023-10-19
Ben Soares
JAL-4305 Isolate and unify the Jalview object from...
tree
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commitdiff
2023-10-19
James Procter
JAL-4307 View->Ligands submenu, implementation for...
tree
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commitdiff
2023-10-19
Ben Soares
Merge branch 'improvement/JAL-3783_upgrade_to_groovy...
tree
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commitdiff
2023-10-18
Ben Soares
JAL-629 Run non-alignframe linked groovy scripts. ...
tree
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commitdiff
2023-10-18
Ben Soares
JAL-4262 Fix the nonblockingdialog so that Jalview...
tree
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commitdiff
2023-10-17
James Procter
JAL-4134 TODO printNode update for columnTrees
tree
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commitdiff
2023-10-17
James Procter
JAL-4134 JAL-4302 remove unnecessary casts
tree
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commitdiff
2023-10-17
James Procter
JAL-4089 selected columns are reported in absolute...
tree
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commitdiff
2023-10-13
Ben Soares
JAL-3783 Updated groovy jars. Requires javaparser...
tree
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commitdiff
2023-10-13
James Procter
JAL-4295 concatenate all mouseover highlights into...
tree
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commitdiff
2023-10-12
Ben Soares
JAL-3772 Fix the logic of prompt to save URL loaded...
tree
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commitdiff
2023-10-12
Ben Soares
JAL-629 null check and neatening code
tree
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commitdiff
2023-10-11
Ben Soares
JAL-629 correct a timeout. Correct passing html flag.
tree
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commitdiff
2023-10-11
Ben Soares
JAL-629 Add a timeout to modal dialogs for command...
tree
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commitdiff
2023-10-11
Ben Soares
JAL-629 Remove argfiles from the hashset of used argfil...
tree
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commitdiff
2023-10-11
Ben Soares
JAL-3772 Preference to NOT prompt to save remotely...
tree
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commitdiff
2023-10-11
Ben Soares
JAL-4298 Added diagnostics and minor dimension changes...
tree
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commitdiff
2023-10-05
Ben Soares
JAL-4298 Fixed initial log level to see .jalview_proper...
tree
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commitdiff
2023-10-03
Ben Soares
JAL-4001 Only use acquireDialogQueue and releaseDialogQ...
bug/JAL-4001_fix_About_Jalview_not_appearing
tree
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commitdiff
2023-10-03
James Procter
Merge branch 'patch/JAL-4062_sort_and_merge_contiguousr...
tree
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commitdiff
2023-10-01
James Procter
JAL-244 ensure background is completely filled with...
tree
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commitdiff
2023-10-01
James Procter
Merge branch 'develop' into bug/JAL-4059_update_swingJS...
tree
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commitdiff
2023-10-01
James Procter
JAL-244 export image with full width IDs regardless...
tree
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commitdiff
2023-10-01
James Procter
JAL-244 JAL-4091 allow calculation of label id width...
tree
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commitdiff
2023-10-01
James Procter
JAL-244 JAL-4091 FIXME for JAL-3362 patch testCalculate...
tree
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commitdiff
2023-09-29
James Procter
Merge branch 'develop' into bug/JAL-4059_update_swingJS...
tree
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commitdiff
2023-09-29
James Procter
JAL-629 JAL-4265 JAL-4286 report the filename for the...
tree
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commitdiff
2023-09-29
James Procter
JAL-244 JAL-4090 use current IdWidth when exporting...
tree
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commitdiff
2023-09-29
James Procter
JAL-3858 fix check annotation row and column positionin...
tree
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commitdiff
2023-09-28
James Procter
JAL-3858 don’t divide if we only had one value to count
tree
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commitdiff
2023-09-28
James Procter
JAL-3858 check annotation row and column positioning...
tree
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commitdiff
2023-09-28
James Procter
JAL-3858 improved contactInterval computation and added...
tree
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commitdiff
2023-09-28
Ben Soares
JAL-4059 Fix an incorrectly applied change of method...
tree
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commitdiff
2023-09-28
Ben Soares
JAL-4059 Try and avoid Commands Error in jalviewjs...
tree
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commitdiff
2023-09-26
James Procter
JAL-3858 JAL-4090 avoid NPE when given out of bound...
tree
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commitdiff
2023-09-25
James Procter
JAL-3858 minimum value for a range is used to shade...
tree
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commitdiff
2023-09-25
James Procter
JAL-3858 javadoc and slightly revised green linear...
tree
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commitdiff
2023-09-25
James Procter
JAL-3858 report PAE range with sensible precision
tree
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commitdiff
2023-09-21
James Procter
JAL-1551 javadoc for mapUtils
tree
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commitdiff
2023-09-21
James Procter
JAL-3855 disable the AlphaFold DB entry in Sequence...
tree
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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
tree
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commitdiff
2023-09-21
Ben Soares
Merge branch 'develop' into merge/JAL-4262+JAL-4265...
tree
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commitdiff
2023-09-20
Ben Soares
JAL-4265 Use ColorUtils.parseColourString() and adjust...
tree
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commitdiff
2023-09-20
James Procter
JAL-4285 don’t say you are reporting warnings/errors...
tree
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commitdiff
2023-09-20
James Procter
JAL-4265 JAL-4286 reinstated explicit restoreSession...
tree
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commitdiff
2023-09-20
James Procter
JAL-4265 JAL-4267 added a ‘restoreSession’ StructureVie...
tree
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commitdiff
2023-09-20
James Procter
JAL-4195 JAL-1069 JAL-4160 errors in Cache should go...
tree
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commitdiff
2023-09-20
James Procter
JAL-4265 bail early when attempting to export a view...
tree
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commitdiff
2023-09-20
James Procter
JAL-4265 JAL-4267 allow injection of custom commands...
tree
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commitdiff
2023-09-20
James Procter
JAL-4265 back out redundant ‘saveState’ and ‘restoreSta...
tree
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commitdiff
2023-09-20
Ben Soares
JAL-4265 Added saveState and restoreState to interface...
tree
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commitdiff
2023-09-19
Ben Soares
JAL-4265 Change to use JmolCommands
tree
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commitdiff
2023-09-19
Ben Soares
JAL-629 Allow multiple structure images for multiple...
tree
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commitdiff
2023-09-16
Ben Soares
JAL-4250 Fixed blue arrows in drawStemAnnot()
tree
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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
tree
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commitdiff
2023-09-16
Ben Soares
JAL-4265 Added --bgcolour for --structureimage output...
tree
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commitdiff
2023-09-16
Ben Soares
JAL-4269 Now using --width, --height, --scale for both...
tree
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commitdiff
2023-09-14
Ben Soares
Merge branch 'develop' into feature/JAL-4274_configurab...
tree
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commitdiff
2023-09-13
Ben Soares
JAL-4274 Use Cache BITMAP_* if no other image restricti...
tree
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commitdiff
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
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
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