jalview.git
2023-09-28 James ProcterJAL-3858 improved contactInterval computation and added...
2023-09-26 James ProcterJAL-3858 JAL-4090 pae matrix docs. WIP
2023-09-26 James ProcterJAL-3858 JAL-4090 avoid NPE when given out of bound...
2023-09-25 James ProcterJAL-3858 JAL-4090 PAE documentation..
2023-09-25 James ProcterJAL-3858 minimum value for a range is used to shade...
2023-09-25 James ProcterJAL-3858 javadoc and slightly revised green linear...
2023-09-25 James ProcterJAL-3858 report PAE range with sensible precision
2023-09-25 James ProcterJAL-4090 fix link...
2023-09-22 James ProcterJAL-4090 smaller associate PDB file panel image in...
2023-09-21 James ProcterJAL-4090 what’s new and additional help docs for JAL...
2023-09-21 James ProcterJAL-4090 JAL-4262 JAL-4265 release notes
2023-09-21 James ProcterJAL-1551 javadoc for mapUtils
2023-09-21 James ProcterJAL-3855 disable the AlphaFold DB entry in Sequence...
2023-09-21 James ProcterJAL-3858 JAL-3855 documentation for import and display...
2023-09-21 James ProcterMerge branch 'merge/JAL-4262+JAL-4265+JAL-4269+JAL...
2023-09-21 Ben SoaresJAL-4265 Use ColourUtils.parseColourString() for consis... merge/JAL-4262+JAL-4265+JAL-4269+JAL-4274+JAL-4277+JAL-4285
2023-09-21 Ben SoaresMerge branch 'develop' into merge/JAL-4262+JAL-4265...
2023-09-20 Ben SoaresJAL-4265 Use ColorUtils.parseColourString() and adjust...
2023-09-20 James ProcterJAL-4285 don’t say you are reporting warnings/errors...
2023-09-20 James ProcterJAL-4265 JAL-4286 reinstated explicit restoreSession...
2023-09-20 James ProcterJAL-4265 JAL-4267 added a ‘restoreSession’ StructureVie...
2023-09-20 James ProcterJAL-4195 JAL-1069 JAL-4160 errors in Cache should go...
2023-09-20 James ProcterMerge branch 'reviews/merge/JAL-4262+JAL-4265+JAL-4269...
2023-09-20 James ProcterJAL-4217 - try to invokeAndWait on Desktop.closeAll... reviews/merge/JAL-4262+JAL-4265+JAL-4269+JAL-4274+JAL-4277+JAL-4285
2023-09-20 James ProcterJAL-4274 fix test failure message typo
2023-09-20 James ProcterJAL-4265 bail early when attempting to export a view...
2023-09-20 James ProcterJAL-4265 JAL-4267 allow injection of custom commands...
2023-09-20 James ProcterJAL-4265 back out redundant ‘saveState’ and ‘restoreSta...
2023-09-20 Ben SoaresJAL-4265 Added saveState and restoreState to interface...
2023-09-20 Ben SoaresJAL-629 Explanation of \{m\} in case anyone actually...
2023-09-20 Ben SoaresJAL-629 Add link and example for BioJS image output
2023-09-20 Ben SoaresJAL-629 Make arguments appear correctly using all non...
2023-09-20 Ben SoaresJAL-629 Added/corrected/tidied documentation
2023-09-19 Ben SoaresJAL-629 JAL-4265 JAL-4269 Updated help Documentation
2023-09-19 Ben SoaresJAL-629 JAL-4265 JAL-4269 Updated help Documentation
2023-09-19 Ben SoaresJAL-4265 Change to use JmolCommands
2023-09-19 Ben SoaresJAL-629 Allow multiple structure images for multiple...
2023-09-16 Ben SoaresJAL-4250 Fixed blue arrows in drawStemAnnot()
2023-09-16 Ben SoaresJAL-629 Fix a test and omit an incorrect error message... improvement/JAL-4269_reduce_variants_of_common_subvalue_parameters
2023-09-16 Ben SoaresJAL-4265 Added --bgcolour for --structureimage output...
2023-09-16 Ben SoaresJAL-4269 Now using --width, --height, --scale for both...
2023-09-14 Ben SoaresMerge branch 'develop' into feature/JAL-4274_configurab...
2023-09-13 Ben SoaresJAL-4274 comments to help follow the tests feature/JAL-4274_configurable_bitmap_export_preferences
2023-09-13 Ben SoaresJAL-4274 Tests for BIS defaults and overrides
2023-09-13 Ben SoaresJAL-4274 Use Cache BITMAP_* if no other image restricti...
2023-09-13 Ben SoaresJAL-4262 Made deprecation warning properly modal bug/JAL-4277_dirname_substitution_always_absolute
2023-09-12 Ben SoaresJAL-4262 Allow HTML in the dialog box for link to CLI...
2023-09-12 Ben SoaresJAL-4277 No longer using getCanonicalPath() for parent...
2023-09-12 Ben SoaresJAL-4285 Better checkFiles processing. Better dialog.
2023-09-12 Ben SoaresJAL-629 updated tests
2023-09-12 Ben SoaresJAL-4285 JAL-4262 Added a scrollable dialog to display...
2023-09-11 Ben SoaresJAL-4001 corrected analytics message labels
2023-09-11 Ben SoaresMerge branch 'improvement/JAL-4262_deprecation_warning_...
2023-09-11 Ben SoaresJAL-4277 --mkdirs with cautious refusal for paths with ..
2023-09-11 Ben SoaresJAL-4284 JAL-4285 Deal with output files/images consist...
2023-09-08 Ben SoaresJAL-4262 Make an excepetion for STDOUT filename in... improvement/JAL-4262_deprecation_warning_when_old_CLI_arguments_are_processed
2023-09-08 Ben SoaresMerge branch 'bug/JAL-4277_dirname_substitution_always_...
2023-09-08 Ben SoaresJAL-4262 Dialog for GUI and WARN for CLI of old style...
2023-09-07 Ben SoaresMerge branch 'develop' into bug/JAL-4277_dirname_substi...
2023-09-07 Ben SoaresJAL-4277 fixed and improved tests
2023-09-07 James ProcterJAL-4090 release notes for JAL-244 JAL-901 JAL-4260... merge/JAL-244+JAL-629+JAL-3416+JAL-3421+JAL-3820+JAL-3830+JAL-4001+JAL-4160+JAL-4189+JAL-4214+JAL-4242+JAL-4255_Updates_to_these_issues_branches_with_merge_conflicts_resolved-bens_stuff
2023-09-07 Ben SoaresJAL-4277 Corrected choice of all or last opened linkedI...
2023-09-07 James ProcterJAL-4279 suppress error dialogs raised by file loader... improvement/JAL-4279_gracefully_handle_failure_to_openviaCLI
2023-09-07 James ProcterJAL-4279 move on if the file doesn't exist, or Identify...
2023-09-07 James ProcterJAL-4279 catch exceptions with fileLoader and report...
2023-09-07 James ProcterJAL-4090 JAL-4160 JAL-4274 image export dimensions...
2023-09-07 Ben SoaresJAL-629 Change names of Opt.ALLOWALL to Opt.ALLOWMULTII... improvement/JAL-629_Apply_alignment_options_to_all_globbed_files
2023-09-07 James ProcterJAL-4273 release notes for visible adjuster marks,...
2023-09-07 James ProcterJAL-4090 report JAL-4261 known issue
2023-09-06 James ProcterJAL-4260 attempt to rejig paging when id width is adjus...
2023-09-06 James ProcterJAL-4258 remove unnecessary ‘this’
2023-09-06 James ProcterJAL-4259 construct a new SequenceRenderer when renderin...
2023-09-06 James ProcterJAL-629 javadoc on new setMapping variant for structure...
2023-09-06 James ProcterJAL-629 reinstate INFO level stack trace from Structure...
2023-09-06 James ProcterJAL-629 javadoc
2023-09-05 James ProcterJAL-629 remove structure viewer from the list of struct...
2023-09-05 James ProcterJAL-629 use JalviewStructureDisplayI in place of Struct...
2023-09-02 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t...
2023-09-02 Ben SoaresJAL-629 Add accessors for argParser and bootstrapArgs feature/JAL-629_--output_-_means_output_to_STDOUT
2023-09-01 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t...
2023-09-01 Ben SoaresJAL-629 Save structure frames in project files when...
2023-09-01 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t...
2023-09-01 Ben SoaresJAL-629 Fix --structureimage and options
2023-08-31 Ben SoaresMerge branch 'improvement/JAL-3830_remove_dock_icon_in_...
2023-08-31 Ben SoaresJAL-3830 Remove dock icon for -h too improvement/JAL-3830_remove_dock_icon_in_headless_mode
2023-08-31 Ben SoaresMerge branch 'features/r2_11_2_alphafold/JAL-629' into...
2023-08-31 Ben SoaresJAL-629 Small buglet with getting --seqid features/r2_11_2_alphafold/JAL-629
2023-08-31 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold...
2023-08-29 Ben SoaresMerge branch 'bug/JAL-4255_slf4j_missing_StaticLoggerBi...
2023-08-29 Ben SoaresJAL-4255 better grammar bug/JAL-4255_slf4j_missing_StaticLoggerBinder_error_message
2023-08-29 Ben SoaresJAL-4255 Updated THIRDPARTYLIBS
2023-08-29 Ben SoaresMerge branch 'bug/JAL-4255_slf4j_missing_StaticLoggerBi...
2023-08-29 Ben SoaresJAL-4255 Added slf4j-nop jar and upgraded to last 1...
2023-08-28 Ben SoaresMerge branch 'develop' into merge/big_merge_of_bens_stu...
2023-08-28 James ProcterJAL-4090 JAL-4250 JAL-4253 JAL-325 release notes and...
2023-08-28 James ProcterMerge branch 'improvement/JAL-4250_secondary_structure_...
2023-08-28 James ProcterJAL-4253 drop the bottom line so it lines up with the...
2023-08-24 Ben SoaresMerge branch 'develop' into merge/big_merge_of_bens_stu...
2023-08-24 Ben SoaresMerge branch 'features/r2_11_2_alphafold/JAL-629' into...
2023-08-24 Ben SoaresJAL-629 Avoid hidden options dialog when saving in...
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