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2023-10-01	James Procter	JAL-244 JAL-4091 FIXME for JAL-3362 patch testCalculateIdWid...	commit \| commitdiff \| tree
2023-10-01	James Procter	JAL-4160 update args used in test suite for new CLI...	commit \| commitdiff \| tree
2023-09-29	James Procter	Merge branch 'bug/JAL-244_interactingpngexportnotwysiwig...	commit \| commitdiff \| tree
2023-09-29	James Procter	JAL-629 JAL-4265 JAL-4286 report the filename for the...	commit \| commitdiff \| tree
2023-09-29	James Procter	JAL-4090 JAL-629 FER1+SPIOL -> FER1_SPIOL in command...	commit \| commitdiff \| tree
2023-09-29	James Procter	JAL-244 JAL-4090 use current IdWidth when exporting...	commit \| commitdiff \| tree
2023-09-29	James Procter	JAL-4090 figures in paematrix doc	commit \| commitdiff \| tree
2023-09-29	James Procter	JAL-4288 fix up gradle generated getdown launch jvl...	commit \| commitdiff \| tree
2023-09-29	James Procter	JAL-4090 fix url to new cli docs	commit \| commitdiff \| tree
2023-09-29	James Procter	JAL-4153 move JvCacheableInputBoxTest to testTask2	commit \| commitdiff \| tree
2023-09-29	James Procter	JAL-3858 fix check annotation row and column positioning...	commit \| commitdiff \| tree
2023-09-28	James Procter	JAL-4090 JAL-3855 figure showing PAEs for epas1 homolog...	commit \| commitdiff \| tree
2023-09-28	James Procter	JAL-1556 JAL-4090 colour by annotation options on annotation...	commit \| commitdiff \| tree
2023-09-28	James Procter	JAL-3858 don’t divide if we only had one value to count	commit \| commitdiff \| tree
2023-09-28	James Procter	JAL-3858 check annotation row and column positioning...	commit \| commitdiff \| tree
2023-09-28	James Procter	JAL-3858 improved contactInterval computation and added...	commit \| commitdiff \| tree
2023-09-26	James Procter	JAL-3858 JAL-4090 pae matrix docs. WIP	commit \| commitdiff \| tree
2023-09-26	James Procter	JAL-3858 JAL-4090 avoid NPE when given out of bound...	commit \| commitdiff \| tree
2023-09-25	James Procter	JAL-3858 JAL-4090 PAE documentation..	commit \| commitdiff \| tree
2023-09-25	James Procter	JAL-3858 minimum value for a range is used to shade...	commit \| commitdiff \| tree
2023-09-25	James Procter	JAL-3858 javadoc and slightly revised green linear...	commit \| commitdiff \| tree
2023-09-25	James Procter	JAL-3858 report PAE range with sensible precision	commit \| commitdiff \| tree
2023-09-25	James Procter	JAL-4090 fix link...	commit \| commitdiff \| tree
2023-09-22	James Procter	JAL-4090 smaller associate PDB file panel image in...	commit \| commitdiff \| tree
2023-09-21	James Procter	JAL-4090 what’s new and additional help docs for JAL...	commit \| commitdiff \| tree
2023-09-21	James Procter	JAL-4090 JAL-4262 JAL-4265 release notes	commit \| commitdiff \| tree
2023-09-21	James Procter	JAL-1551 javadoc for mapUtils	commit \| commitdiff \| tree
2023-09-21	James Procter	JAL-3855 disable the AlphaFold DB entry in Sequence...	commit \| commitdiff \| tree
2023-09-21	James Procter	JAL-3858 JAL-3855 documentation for import and display...	commit \| commitdiff \| tree
2023-09-21	James Procter	Merge branch 'merge/JAL-4262+JAL-4265+JAL-4269+JAL...	commit \| commitdiff \| tree
2023-09-20	James Procter	JAL-4285 don’t say you are reporting warnings/errors...	commit \| commitdiff \| tree
2023-09-20	James Procter	JAL-4265 JAL-4286 reinstated explicit restoreSession...	commit \| commitdiff \| tree
2023-09-20	James Procter	JAL-4265 JAL-4267 added a ‘restoreSession’ StructureViewer...	commit \| commitdiff \| tree
2023-09-20	James Procter	JAL-4195 JAL-1069 JAL-4160 errors in Cache should go...	commit \| commitdiff \| tree
2023-09-20	James Procter	Merge branch 'reviews/merge/JAL-4262+JAL-4265+JAL-4269...	commit \| commitdiff \| tree
2023-09-20	James Procter	JAL-4217 - try to invokeAndWait on Desktop.closeAll...	commit \| commitdiff \| tree
2023-09-20	James Procter	JAL-4274 fix test failure message typo	commit \| commitdiff \| tree
2023-09-20	James Procter	JAL-4265 bail early when attempting to export a view...	commit \| commitdiff \| tree
2023-09-20	James Procter	JAL-4265 JAL-4267 allow injection of custom commands...	commit \| commitdiff \| tree
2023-09-20	James Procter	JAL-4265 back out redundant ‘saveState’ and ‘restoreState...	commit \| commitdiff \| tree
2023-09-07	James Procter	JAL-4090 release notes for JAL-244 JAL-901 JAL-4260...	commit \| commitdiff \| tree
2023-09-07	James Procter	JAL-4279 suppress error dialogs raised by file loader...	commit \| commitdiff \| tree
2023-09-07	James Procter	JAL-4279 move on if the file doesn't exist, or Identify...	commit \| commitdiff \| tree
2023-09-07	James Procter	JAL-4279 catch exceptions with fileLoader and report...	commit \| commitdiff \| tree
2023-09-07	James Procter	JAL-4090 JAL-4160 JAL-4274 image export dimensions...	commit \| commitdiff \| tree
2023-09-07	James Procter	JAL-4273 release notes for visible adjuster marks,...	commit \| commitdiff \| tree
2023-09-07	James Procter	JAL-4090 report JAL-4261 known issue	commit \| commitdiff \| tree
2023-09-06	James Procter	JAL-4260 attempt to rejig paging when id width is adjusted...	commit \| commitdiff \| tree
2023-09-06	James Procter	JAL-4258 remove unnecessary ‘this’	commit \| commitdiff \| tree
2023-09-06	James Procter	JAL-4259 construct a new SequenceRenderer when rendering...	commit \| commitdiff \| tree
2023-09-06	James Procter	JAL-629 javadoc on new setMapping variant for structureselec...	commit \| commitdiff \| tree
2023-09-06	James Procter	JAL-629 reinstate INFO level stack trace from StructureChoos...	commit \| commitdiff \| tree
2023-09-06	James Procter	JAL-629 javadoc	commit \| commitdiff \| tree
2023-09-05	James Procter	JAL-629 remove structure viewer from the list of structure...	commit \| commitdiff \| tree
2023-09-05	James Procter	JAL-629 use JalviewStructureDisplayI in place of StructureVi...	commit \| commitdiff \| tree
2023-08-28	James Procter	JAL-4090 JAL-4250 JAL-4253 JAL-325 release notes and...	commit \| commitdiff \| tree
2023-08-28	James Procter	Merge branch 'improvement/JAL-4250_secondary_structure_annot...	commit \| commitdiff \| tree
2023-08-28	James Procter	JAL-4253 drop the bottom line so it lines up with the...	commit \| commitdiff \| tree
2023-08-17	James Procter	JAL-4090 JAL-4243 bio.tools json file release notes	commit \| commitdiff \| tree
2023-07-22	James Procter	JAL-4243 Jalview 2.11.2.7’s biotool record as JSON...	commit \| commitdiff \| tree
2023-07-20	James Procter	JAL-3855 tree title for PAE matrix tree is PAE Matrix...	commit \| commitdiff \| tree
2023-07-20	James Procter	JAL-3855 auto select clusters and fix up colouring...	commit \| commitdiff \| tree
2023-07-19	James Procter	Merge branch 'patch/JAL-3855_fixup_pae' into develop	commit \| commitdiff \| tree
2023-07-18	James Procter	Merge branch 'develop' into patch/JAL-3855_fixup_pae	commit \| commitdiff \| tree
2023-07-18	James Procter	JAL-4153 comments re patch incorrectly committed under...	commit \| commitdiff \| tree
2023-07-18	James Procter	JAL-3855 PAE matrices are transposed on import from...	commit \| commitdiff \| tree
2023-07-18	James Procter	JAL-3855 JAL-4124 test checks asymmetric matrices are...	commit \| commitdiff \| tree
2023-07-18	James Procter	JAL-3858 fix off-by-one in matrix visualisation and...	commit \| commitdiff \| tree
2023-07-18	James Procter	JAL-3858 flip diagonal so matrix visualisation is top...	commit \| commitdiff \| tree
2023-07-18	James Procter	JAL-3858 annotation .height is bigger than graphHeight...	commit \| commitdiff \| tree
2023-07-17	James Procter	JAL-4119 TRACE level console message reporting download...	commit \| commitdiff \| tree
2023-07-17	James Procter	JAL-4090 JAL-4165 known issue	commit \| commitdiff \| tree
2023-07-17	James Procter	JAL-4090 JAL-4165 known issue	commit \| commitdiff \| tree
2023-07-17	James Procter	JAL-4223 add testdata for test	commit \| commitdiff \| tree
2023-07-17	James Procter	JAL-4090 mark JAL-4178 and JAL-4142 as known issues	commit \| commitdiff \| tree
2023-07-17	James Procter	JAL-4217 move Commands.structureImageTest to testTask1	commit \| commitdiff \| tree
2023-07-12	James Procter	JAL-4223 - test and patch to ensure numbering matches...	commit \| commitdiff \| tree
2023-07-10	James Procter	Merge branch 'improvement/JAL-4212_remove_macos_test_java_ic...	commit \| commitdiff \| tree
2023-07-10	James Procter	Merge branch 'improvement/JAL-3830_remove_dock_icon_in_headl...	commit \| commitdiff \| tree
2023-07-07	James Procter	Merge branch 'patch/JAL-4195_cli_eps_export_npe' into...	commit \| commitdiff \| tree
2023-07-07	James Procter	JAL-4217 JAL-629 built in 25s time out waiting for...	commit \| commitdiff \| tree
2023-07-07	James Procter	JAL-4090 update 2.11.3.0 release notes (with in-progress...	commit \| commitdiff \| tree
2023-07-07	James Procter	Merge branch 'patch/JAL-4119_sifts_ftp_split' into...	commit \| commitdiff \| tree
2023-07-07	James Procter	Merge branch 'develop' into patch/JAL-4195_cli_eps_export_npe	commit \| commitdiff \| tree
2023-07-07	James Procter	JAL-4195 add exception handling for all other CommandsTest...	commit \| commitdiff \| tree
2023-07-07	James Procter	JAL-4221 update description when transferring annotation...	commit \| commitdiff \| tree
2023-07-07	James Procter	JAL-629 even more console debug for --structureviewer...	commit \| commitdiff \| tree
2023-07-06	James Procter	JAL-629 liberal defensive coding, comments about refactoring...	commit \| commitdiff \| tree
2023-07-06	James Procter	JAL-629 make —structure image work again after threading...	commit \| commitdiff \| tree
2023-07-06	James Procter	JAL-4217 catch case when the structure viewer doesn...	commit \| commitdiff \| tree
2023-07-06	James Procter	JAL-4217 interruptedExceptions should also break any...	commit \| commitdiff \| tree
2023-07-06	James Procter	JAL-2292 verify mixed case alignment actually aligns	commit \| commitdiff \| tree
2023-07-06	James Procter	JAL-4217 wrap imageExport CLI method's call to imageExport...	commit \| commitdiff \| tree
2023-07-06	James Procter	JAL-4217 wrap imageExport CLI method's call to imageExport...	commit \| commitdiff \| tree
2023-07-05	James Procter	Merge branch 'patch/JAL-2292_caseSensitivePAE' into...	commit \| commitdiff \| tree
2023-07-05	James Procter	Merge branch 'patch/JAL-4213_addref_with_selection...	commit \| commitdiff \| tree
2023-07-04	James Procter	Merge branch 'merge/from_2_11_2_7_to_2_11_3_0' into...	commit \| commitdiff \| tree
2023-07-04	James Procter	JAL-4117 JAL-1551 source licensing	commit \| commitdiff \| tree
2023-07-04	James Procter	JAL-4117 Fri June 30th release of 2.11.2.7 with Jalview...	commit \| commitdiff \| tree
2023-06-30	James Procter	JAL-4217 try really hard to shut down and dispose of...	commit \| commitdiff \| tree
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