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2023-09-01	James Procter	JAL-4124 need to repaint alignFrames imported from...	commit \| commitdiff \| tree
2023-09-01	James Procter	JAL-4124 matrix is saved in dataset, with forward references...	commit \| commitdiff \| tree
2023-09-01	James Procter	JAL-4124 add strategic newlines in matrix stringified...	commit \| commitdiff \| tree
2023-08-31	James Procter	JAL-4124 comment out incomplete test bits.. for now	commit \| commitdiff \| tree
2023-08-31	James Procter	JAL-4124 MappableContactMatrix equivalence and hashCode...	commit \| commitdiff \| tree
2023-08-29	James Procter	JAL-4124 Dataset holds list of MatrixType instances...	commit \| commitdiff \| tree
2023-08-29	James Procter	JAL-4124 decouple mappable contact matrix mapping logic...	commit \| commitdiff \| tree
2023-08-28	James Procter	Merge branch 'develop' into more_efficient_PAE	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	exploring making PAE storage in projects more efficient	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
2023-07-07	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
2023-06-30	James Procter	JAL-4216 release notes	commit \| commitdiff \| tree
2023-06-30	James Procter	JAL-4216 compute size of annotation using start/end...	commit \| commitdiff \| tree
2023-06-30	James Procter	Merge branch 'task/JAL-4001_Plausible_API' into develop	commit \| commitdiff \| tree
2023-06-29	James Procter	Merge branch 'task/JAL-4001_Plausible_API' into develop	commit \| commitdiff \| tree
2023-06-29	James Procter	JAL-4117 JAL-4001 plausible analytics release notes...	commit \| commitdiff \| tree
2023-06-29	James Procter	JAL-4090 update from 2.11.2.7 JAL-4117 - version bump...	commit \| commitdiff \| tree
2023-06-29	James Procter	JAL-4001 analytics url provided by https://www.jalview...	commit \| commitdiff \| tree
2023-06-22	James Procter	JAL-4213 don’t pass active selection when actioning...	commit \| commitdiff \| tree
2023-06-22	James Procter	JAL-4213 - document the addReferenceAnnotations method...	commit \| commitdiff \| tree
2023-06-22	James Procter	JAL-2292 - ensure mapping is built for equal symbols...	commit \| commitdiff \| tree
2023-06-21	James Procter	Merge branch 'patch/JAL-4196_structure_viewer_synchronising...	commit \| commitdiff \| tree
2023-06-08	James Procter	Merge branch 'develop' into patch/JAL-4196_structure_viewer_...	commit \| commitdiff \| tree
2023-06-08	James Procter	JAL-4196 make very sure we avoid CME by defensively...	commit \| commitdiff \| tree
2023-06-08	James Procter	JAL-4196 report an error if structure view doesn’t...	commit \| commitdiff \| tree
2023-06-08	James Procter	JAL-4196 structure view cli tests wait using new jalview...	commit \| commitdiff \| tree
2023-06-08	James Procter	Merge branch 'patch/JAL-4195_cli_eps_export_npe' into...	commit \| commitdiff \| tree
2023-06-07	James Procter	JAL-4195 add exception handling for all image output...	commit \| commitdiff \| tree
2023-06-07	James Procter	Merge branch 'patch/JAL-4195_cli_eps_export_npe' into...	commit \| commitdiff \| tree
2023-06-07	James Procter	JAL-4195 catch thrown exceptions (if any) during image...	commit \| commitdiff \| tree
2023-06-07	James Procter	JAL-4195 tidy up desktop instances after creating them	commit \| commitdiff \| tree
2023-06-06	James Procter	JAL-4195 report full stack trace for exceptions raised...	commit \| commitdiff \| tree
2023-06-06	James Procter	JAL-4160 --colour can now take user defined scheme...	commit \| commitdiff \| tree
2023-06-06	James Procter	JAL-4160 JAL-4195 wait around until alignFrame calculators...	commit \| commitdiff \| tree
2023-06-06	James Procter	JAL-1551 formatting and javadoc for ArgParser rather...	commit \| commitdiff \| tree
2023-06-06	James Procter	JAL-629 - remove TODO from jalview.bin.Jalview since...	commit \| commitdiff \| tree
2023-06-06	James Procter	JAL-4195 Debug message indicating creation of an image...	commit \| commitdiff \| tree
2023-06-06	James Procter	JAL-1551 a bit of javadoc for Jalview.testoutput methods	commit \| commitdiff \| tree
2023-06-02	James Procter	JAL-4090 update 2.11.3.0 release notes for recent merges	commit \| commitdiff \| tree
2023-06-01	James Procter	Merge branch 'features/JAL-4134_use_annotation_row_for_colou...	commit \| commitdiff \| tree
2023-06-01	James Procter	Merge branch 'develop' into features/JAL-4134_use_annotation...	commit \| commitdiff \| tree
2023-06-01	James Procter	JAL-4134 properly resolve positions in associated aligned...	commit \| commitdiff \| tree
2023-05-30	James Procter	JAL-4134 repaint the tree or alignment view(s) when...	commit \| commitdiff \| tree
2023-05-30	James Procter	JAL-4134 highlight selected column nodes on the linked...	commit \| commitdiff \| tree
2023-05-29	James Procter	JAL-4190 - escape clears selected nodes	commit \| commitdiff \| tree
2023-05-29	James Procter	JAL-4134 JAL-2349 test & fixed implementation(ish)...	commit \| commitdiff \| tree
2023-05-29	James Procter	Merge branch 'develop' into features/JAL-4134_use_annotation...	commit \| commitdiff \| tree
2023-05-26	James Procter	JAL-4134 internationalise popup menu entries and show...	commit \| commitdiff \| tree
2023-05-26	James Procter	JAL-1556 fix bad import	commit \| commitdiff \| tree
2023-05-26	James Procter	Merge branch 'develop' into features/JAL-4134_use_annotation...	commit \| commitdiff \| tree
2023-05-26	James Procter	JAL-1556 initial implementation - no tests as yet but...	commit \| commitdiff \| tree
2023-05-25	James Procter	JAL-4134 popup menu and annotation row property to...	commit \| commitdiff \| tree
2023-05-25	James Procter	JAL-2381 don’t need to set description, dbrefs etc...	commit \| commitdiff \| tree
2023-05-25	James Procter	JAL-2381 copy and paste sequence also copies contact...	commit \| commitdiff \| tree
2023-05-25	James Procter	Merge branch 'bug/JAL-4186_space_in_sequence_name_causes_emp...	commit \| commitdiff \| tree
2023-05-22	James Procter	JAL-4134 map between column and node selections better...	commit \| commitdiff \| tree
2023-05-22	James Procter	JAL-4134 efficiency improvement	commit \| commitdiff \| tree
2023-05-22	James Procter	JAL-629 javadoc on StructureSelectionManager.computeMapping	commit \| commitdiff \| tree
2023-05-22	James Procter	JAL-4134 only build tree when showing it in the tree...	commit \| commitdiff \| tree
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