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2023-07-07	James Procter	JAL-4195 add exception handling for all other CommandsTest...	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
2023-05-22	James Procter	JAL-4134 catch NPE - though in principle this should...	commit \| commitdiff \| tree
2023-05-22	James Procter	Merge branch 'JAL-1551_2_11_3_spotlett' into features...	commit \| commitdiff \| tree
2023-05-22	James Procter	Merge branch 'spotless_2' into JAL-1551_2_11_3_spotlett	commit \| commitdiff \| tree
2023-05-22	James Procter	JAL-1551 spotless	commit \| commitdiff \| tree
2023-05-19	James Procter	Merge branch 'develop' into features/JAL-4134_use_annotation...	commit \| commitdiff \| tree
2023-05-19	James Procter	JAL-1551 spotlessApply	commit \| commitdiff \| tree
2023-05-19	James Procter	JAL-1551 spotlessApply	commit \| commitdiff \| tree
2023-05-18	James Procter	JAL-4134 support recovery of mapped positions for raw...	commit \| commitdiff \| tree
2023-05-18	James Procter	JAL-4134 colour by annotation needs distinct annotation...	commit \| commitdiff \| tree
2023-05-18	James Procter	JAL-4134 column grouping model and methods moved to...	commit \| commitdiff \| tree
2023-05-18	James Procter	JAL-4134 formatting	commit \| commitdiff \| tree
2023-05-18	James Procter	JAL-4134 properly specify BinaryNode as a typed generic...	commit \| commitdiff \| tree
2023-05-17	James Procter	JAL-4184 release notes	commit \| commitdiff \| tree
2023-05-17	James Procter	Merge branch 'patch/JAL-4184_description_stockholm...	commit \| commitdiff \| tree
2023-05-17	James Procter	JAL-4184 export description line in stockholm	commit \| commitdiff \| tree
2023-05-17	James Procter	JAL-4184 failing test for description export and re...	commit \| commitdiff \| tree
2023-05-16	James Procter	JAL-4089 - if no centerViewOn commands are given, don...	commit \| commitdiff \| tree
2023-05-15	James Procter	JAL-4182 patch - map selection group onto sequence...	commit \| commitdiff \| tree
2023-05-15	James Procter	JAL-4182 failing test	commit \| commitdiff \| tree
2023-05-14	James Procter	JAL-2349 fix up tests for Java 11 compatibility and...	commit \| commitdiff \| tree
2023-05-14	James Procter	JAL-4134 add tree distance engine test to functional	commit \| commitdiff \| tree
2023-05-14	James Procter	JAL-2349 store/restore mappable contact matrix in project...	commit \| commitdiff \| tree
2023-05-13	James Procter	JAL-2349 JAL-3855 PAE tests covers ContactListI.getMappedPos...	commit \| commitdiff \| tree
2023-05-13	James Procter	JAL-2349 JAL-3855 helper method to make it easy to...	commit \| commitdiff \| tree
2023-05-12	James Procter	JAL-2349 allow PAE or other contact matrices to hold...	commit \| commitdiff \| tree
2023-05-01	James Procter	Merge branch 'features/JAL-4134_treeviewerforcolumns...	commit \| commitdiff \| tree
2023-05-01	James Procter	JAL-4177 disable ‘Cancel’ as well - since we as yet...	commit \| commitdiff \| tree
2023-05-01	James Procter	JAL-4177 disable add/new view when an import is started.	commit \| commitdiff \| tree
2023-05-01	James Procter	JAL-4123 JAL-3914 JAL-3858 tweak wording and layout...	commit \| commitdiff \| tree
2023-05-01	James Procter	JAL-4134 double click to select column groups	commit \| commitdiff \| tree
2023-05-01	James Procter	JAL-3858 report errors when trying to parse JSON to...	commit \| commitdiff \| tree
2023-05-01	James Procter	Merge branch 'features/JAL-4134_treeviewerforcolumns...	commit \| commitdiff \| tree
2023-03-31	James Procter	Merge branch 'features/JAL-4134_treeviewerforcolumns...	commit \| commitdiff \| tree
2023-03-24	James Procter	Merge branch 'develop' into features/JAL-4134_treeviewerforc...	commit \| commitdiff \| tree
2023-03-24	James Procter	JAL-4134 - store colours in annotation row, so colour...	commit \| commitdiff \| tree
2023-03-24	James Procter	JAL-4158 first attempt at stashing colours for contact...	commit \| commitdiff \| tree
2023-03-23	James Procter	Merge branch 'patch/JAL-4153_flakyJvCacheableInputBoxTest...	commit \| commitdiff \| tree
2023-03-20	James Procter	JAL-4134 override default hasTree so PAE tree is saved!	commit \| commitdiff \| tree
2023-03-20	James Procter	JAL-4153 longer Thread.sleep() calls in the hope that...	commit \| commitdiff \| tree
2023-03-20	James Procter	JAL-4134 - missing Jalview project JAXB class - st...	commit \| commitdiff \| tree
2023-03-20	James Procter	Merge branch 'develop' into features/JAL-4134_treeviewerforc...	commit \| commitdiff \| tree
2023-03-20	James Procter	JAL-4150 test and quick patch copying code from AlignFrame...	commit \| commitdiff \| tree
2023-03-20	James Procter	JAL-2349 JAL-4134 Console log messages for contact...	commit \| commitdiff \| tree
2023-03-20	James Procter	JAL-4134 propagate column selection changes in tree...	commit \| commitdiff \| tree
2023-03-20	James Procter	JAL-4134 fix off-by-one in selection	commit \| commitdiff \| tree
2023-03-20	James Procter	JAL-4134 fix NPEs when matrix not resolved or alignment...	commit \| commitdiff \| tree
2023-03-20	James Procter	JAL-4134 better popup menu name ‘Tree for Contact Matrix’	commit \| commitdiff \| tree
2023-03-20	James Procter	JAL-2349 test TODOs	commit \| commitdiff \| tree
2023-03-20	James Procter	JAL-2349 fix off by one when resolving columns for...	commit \| commitdiff \| tree
2023-03-17	James Procter	JAL-4134 fix up column selection when hidden regions...	commit \| commitdiff \| tree
2023-03-17	James Procter	JAL-4134 store/restore Newick tree for PAE annotation row	commit \| commitdiff \| tree
2023-03-15	James Procter	JAL-4091 JAL-4147 - revised annotation label display...	commit \| commitdiff \| tree
2023-03-15	James Procter	JAL-4091 JAL-629 ‘Add Reference Annotations’ takes...	commit \| commitdiff \| tree
2023-03-15	James Procter	JAL-2349 don’t clobber existing label/description...	commit \| commitdiff \| tree
2023-03-15	James Procter	JAL-4134 JAL-3855 store/restore groups, tree and threshold...	commit \| commitdiff \| tree
2023-03-08	James Procter	JAL-2349 handle matrix_clicked on mouse_release rather...	commit \| commitdiff \| tree
2023-03-08	James Procter	Merge branch 'features/r2_11_2_alphafold/JAL-629' into...	commit \| commitdiff \| tree
2023-03-01	James Procter	JAL-4134 hold ctrl to select groups containing rows...	commit \| commitdiff \| tree
2023-02-27	James Procter	JAL-2349 TODO consider caching contactRanges from getContact...	commit \| commitdiff \| tree
2023-02-27	James Procter	JAL-4134 tree panel shouldn’t try to redraw before...	commit \| commitdiff \| tree
2023-02-27	James Procter	JAL-4134 fix more of the egregious SeqNode/BinaryNode...	commit \| commitdiff \| tree
2023-02-27	James Procter	JAL-4134 leaves marked when columns are selected -...	commit \| commitdiff \| tree
2023-02-27	James Procter	JAL-4134 TODO: alternative way of performing interactive...	commit \| commitdiff \| tree
2023-02-27	James Procter	JAL-4134 use average distance between PAE elements...	commit \| commitdiff \| tree
2023-02-27	James Procter	JAL-4134 display tree for columns - selecting an internal...	commit \| commitdiff \| tree
2023-02-27	James Procter	JAL-4134 compute normalised dot product for contact...	commit \| commitdiff \| tree
2023-02-27	James Procter	JAL-4134 allow tree groups to be stored/recovered on...	commit \| commitdiff \| tree
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