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JAL-4090 fix url to new cli docs
[jalview.git] / src /
2023-09-29 James ProcterJAL-3858 fix check annotation row and column positionin... tree | commitdiff
2023-09-28 James ProcterJAL-3858 don’t divide if we only had one value to count tree | commitdiff
2023-09-28 James ProcterJAL-3858 check annotation row and column positioning... tree | commitdiff
2023-09-28 James ProcterJAL-3858 improved contactInterval computation and added... tree | commitdiff
2023-09-26 James ProcterJAL-3858 JAL-4090 avoid NPE when given out of bound... tree | commitdiff
2023-09-25 James ProcterJAL-3858 minimum value for a range is used to shade... tree | commitdiff
2023-09-25 James ProcterJAL-3858 javadoc and slightly revised green linear... tree | commitdiff
2023-09-25 James ProcterJAL-3858 report PAE range with sensible precision tree | commitdiff
2023-09-21 James ProcterJAL-1551 javadoc for mapUtils tree | commitdiff
2023-09-21 James ProcterJAL-3855 disable the AlphaFold DB entry in Sequence... tree | commitdiff
2023-09-21 Ben SoaresJAL-4265 Use ColourUtils.parseColourString() for consis... merge/JAL-4262+JAL-4265+JAL-4269+JAL-4274+JAL-4277+JAL-4285 tree | commitdiff
2023-09-21 Ben SoaresMerge branch 'develop' into merge/JAL-4262+JAL-4265... tree | commitdiff
2023-09-20 Ben SoaresJAL-4265 Use ColorUtils.parseColourString() and adjust... tree | commitdiff
2023-09-20 James ProcterJAL-4285 don’t say you are reporting warnings/errors... tree | commitdiff
2023-09-20 James ProcterJAL-4265 JAL-4286 reinstated explicit restoreSession... tree | commitdiff
2023-09-20 James ProcterJAL-4265 JAL-4267 added a ‘restoreSession’ StructureVie... tree | commitdiff
2023-09-20 James ProcterJAL-4195 JAL-1069 JAL-4160 errors in Cache should go... tree | commitdiff
2023-09-20 James ProcterJAL-4265 bail early when attempting to export a view... tree | commitdiff
2023-09-20 James ProcterJAL-4265 JAL-4267 allow injection of custom commands... tree | commitdiff
2023-09-20 James ProcterJAL-4265 back out redundant ‘saveState’ and ‘restoreSta... tree | commitdiff
2023-09-20 Ben SoaresJAL-4265 Added saveState and restoreState to interface... tree | commitdiff
2023-09-19 Ben SoaresJAL-4265 Change to use JmolCommands tree | commitdiff
2023-09-19 Ben SoaresJAL-629 Allow multiple structure images for multiple... tree | commitdiff
2023-09-16 Ben SoaresJAL-4250 Fixed blue arrows in drawStemAnnot() tree | commitdiff
2023-09-16 Ben SoaresJAL-629 Fix a test and omit an incorrect error message... improvement/JAL-4269_reduce_variants_of_common_subvalue_parameters tree | commitdiff
2023-09-16 Ben SoaresJAL-4265 Added --bgcolour for --structureimage output... tree | commitdiff
2023-09-16 Ben SoaresJAL-4269 Now using --width, --height, --scale for both... tree | commitdiff
2023-09-14 Ben SoaresMerge branch 'develop' into feature/JAL-4274_configurab... tree | commitdiff
2023-09-13 Ben SoaresJAL-4274 Use Cache BITMAP_* if no other image restricti... tree | commitdiff
2023-09-13 Ben SoaresJAL-4262 Made deprecation warning properly modal bug/JAL-4277_dirname_substitution_always_absolute tree | commitdiff
2023-09-12 Ben SoaresJAL-4262 Allow HTML in the dialog box for link to CLI... tree | commitdiff
2023-09-12 Ben SoaresJAL-4285 Better checkFiles processing. Better dialog. tree | commitdiff
2023-09-12 Ben SoaresJAL-4285 JAL-4262 Added a scrollable dialog to display... tree | commitdiff
2023-09-11 Ben SoaresJAL-4001 corrected analytics message labels tree | commitdiff
2023-09-11 Ben SoaresMerge branch 'improvement/JAL-4262_deprecation_warning_... tree | commitdiff
2023-09-11 Ben SoaresJAL-4277 --mkdirs with cautious refusal for paths with .. tree | commitdiff
2023-09-11 Ben SoaresJAL-4284 JAL-4285 Deal with output files/images consist... tree | commitdiff
2023-09-08 Ben SoaresJAL-4262 Make an excepetion for STDOUT filename in... improvement/JAL-4262_deprecation_warning_when_old_CLI_arguments_are_processed tree | commitdiff
2023-09-08 Ben SoaresMerge branch 'bug/JAL-4277_dirname_substitution_always_... tree | commitdiff
2023-09-08 Ben SoaresJAL-4262 Dialog for GUI and WARN for CLI of old style... tree | commitdiff
2023-09-07 Ben SoaresMerge branch 'develop' into bug/JAL-4277_dirname_substi... tree | commitdiff
2023-09-07 Ben SoaresJAL-4277 Corrected choice of all or last opened linkedI... tree | commitdiff
2023-09-07 James ProcterJAL-4279 suppress error dialogs raised by file loader... improvement/JAL-4279_gracefully_handle_failure_to_openviaCLI tree | commitdiff
2023-09-07 James ProcterJAL-4279 move on if the file doesn't exist, or Identify... tree | commitdiff
2023-09-07 James ProcterJAL-4279 catch exceptions with fileLoader and report... tree | commitdiff
2023-09-07 James ProcterJAL-4090 JAL-4160 JAL-4274 image export dimensions... tree | commitdiff
2023-09-07 Ben SoaresJAL-629 Change names of Opt.ALLOWALL to Opt.ALLOWMULTII... improvement/JAL-629_Apply_alignment_options_to_all_globbed_files tree | commitdiff
2023-09-07 James ProcterJAL-4273 release notes for visible adjuster marks,... tree | commitdiff
2023-09-06 James ProcterJAL-4260 attempt to rejig paging when id width is adjus... tree | commitdiff
2023-09-06 James ProcterJAL-4258 remove unnecessary ‘this’ tree | commitdiff
2023-09-06 James ProcterJAL-4259 construct a new SequenceRenderer when renderin... tree | commitdiff
2023-09-06 James ProcterJAL-629 javadoc on new setMapping variant for structure... tree | commitdiff
2023-09-06 James ProcterJAL-629 reinstate INFO level stack trace from Structure... tree | commitdiff
2023-09-06 James ProcterJAL-629 javadoc tree | commitdiff
2023-09-05 James ProcterJAL-629 remove structure viewer from the list of struct... tree | commitdiff
2023-09-05 James ProcterJAL-629 use JalviewStructureDisplayI in place of Struct... tree | commitdiff
2023-09-02 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t... tree | commitdiff
2023-09-02 Ben SoaresJAL-629 Add accessors for argParser and bootstrapArgs feature/JAL-629_--output_-_means_output_to_STDOUT tree | commitdiff
2023-09-01 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t... tree | commitdiff
2023-09-01 Ben SoaresJAL-629 Save structure frames in project files when... tree | commitdiff
2023-09-01 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t... tree | commitdiff
2023-09-01 Ben SoaresJAL-629 Fix --structureimage and options tree | commitdiff
2023-08-31 Ben SoaresMerge branch 'features/r2_11_2_alphafold/JAL-629' into... tree | commitdiff
2023-08-31 Ben SoaresJAL-629 Small buglet with getting --seqid features/r2_11_2_alphafold/JAL-629 tree | commitdiff
2023-08-31 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-08-28 Ben SoaresMerge branch 'develop' into merge/big_merge_of_bens_stu... tree | commitdiff
2023-08-28 James ProcterJAL-4253 drop the bottom line so it lines up with the... tree | commitdiff
2023-08-24 Ben SoaresMerge branch 'develop' into merge/big_merge_of_bens_stu... tree | commitdiff
2023-08-24 Ben SoaresMerge branch 'features/r2_11_2_alphafold/JAL-629' into... tree | commitdiff
2023-08-24 Ben SoaresJAL-629 Avoid hidden options dialog when saving in... tree | commitdiff
2023-08-24 Ben SoaresMerge branch 'bug/JAL-4214_system_freeze_when_opening_f... tree | commitdiff
2023-08-24 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_... tree | commitdiff
2023-08-24 Ben SoaresJAL-4250 Fix bug in vector rendition where more than... improvement/JAL-4250_secondary_structure_annotation_antialias tree | commitdiff
2023-08-24 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_... tree | commitdiff
2023-08-24 Ben SoaresJAL-4250 Much simplified glyph creation removing most... tree | commitdiff
2023-08-23 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_... tree | commitdiff
2023-08-23 Ben SoaresJAL-4250 Fix one word bug for 'af.createEPS(file, rende... tree | commitdiff
2023-08-23 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_... tree | commitdiff
2023-08-23 Ben SoaresJAL-4250 Updated jfreesvg to fix round stroke in linegraph. tree | commitdiff
2023-08-23 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_... tree | commitdiff
2023-08-23 Ben SoaresJAL-4250 Simplification of polygons and adjustments... tree | commitdiff
2023-08-21 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_... tree | commitdiff
2023-08-21 Ben SoaresJAL-4250 revert green to bright green tree | commitdiff
2023-08-21 Ben SoaresMerge branch 'improvement/JAL-4250_secondary_structure_... tree | commitdiff
2023-08-21 Ben SoaresJAL-4250 Conservative setting of ANTIALIAS and readjust... tree | commitdiff
2023-08-18 Ben SoaresJAL-4250 Make secondary structure annotation shapes... tree | commitdiff
2023-08-18 Ben SoaresMerge branch 'improvement/JAL-4206_improve_JalviewFileC... tree | commitdiff
2023-08-18 Ben SoaresMerge branch 'bug/JAL-4214_system_freeze_when_opening_f... tree | commitdiff
2023-08-18 Ben SoaresMerge branch 'feature/JAL-244_Automatically_adjust_left... tree | commitdiff
2023-08-18 Ben SoaresMerge branch 'improvement/JAL-3830_remove_dock_icon_in_... tree | commitdiff
2023-08-18 Ben SoaresMerge branch 'bug/JAL-4242_exception_when_pressing_esca... tree | commitdiff
2023-08-18 Ben SoaresJAL-3416 Remove full height separators between new... improvement/JAL-3416_FlatLaf_3.2 tree | commitdiff
2023-08-18 Ben SoaresJAL-4242 null check on getValue() return bug/JAL-4242_exception_when_pressing_escape_in_fetch_from_URL_dialog tree | commitdiff
2023-08-17 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t... tree | commitdiff
2023-08-17 Ben SoaresJAL-3830 JAL-4160 Remove --noheadless as --gui does... tree | commitdiff
2023-08-16 Ben SoaresMerge branch 'develop' into improvement/JAL-3830_remove... tree | commitdiff
2023-08-16 Ben SoaresJAL-3820 JAL-4189 Move checks for java executable symli... tree | commitdiff
2023-08-11 Ben SoaresJAL-629 Much better way of dealing with list of filenam... tree | commitdiff
2023-08-10 Ben SoaresJAL-629 STDOUT documentation. Opt.STDOUT narrower... tree | commitdiff
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use... tree | commitdiff
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