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