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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
2023-05-16	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
2023-03-24	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
2023-02-27	James Procter	Merge branch 'develop' into features/JAL-4134_treeviewerforc...	commit \| commitdiff \| tree
2023-02-24	James Procter	JAL-629 JAL-4124 JAL-3855 test to check we can import...	commit \| commitdiff \| tree
2023-02-24	James Procter	JAL-629 JAL-4124 JAL-3855 test to check we can import...	commit \| commitdiff \| tree
2023-02-24	James Procter	Merge branch 'features/JAL-3858_PAEsInProjects' into...	commit \| commitdiff \| tree
2023-02-24	James Procter	Merge branch 'features/r2_11_2_alphafold/JAL-629' into...	commit \| commitdiff \| tree
2023-02-23	James Procter	JAL-4134 group columns using a tree cut - seems to...	commit \| commitdiff \| tree
2023-02-23	James Procter	JAL-4134 - brutal hack to build a tree clustering columns...	commit \| commitdiff \| tree
2023-02-23	James Procter	JAL-4134 tidied up refactoring and fix compilation...	commit \| commitdiff \| tree
2023-02-23	James Procter	Merge branch 'features/JAL-3858_PAEsInProjects' into...	commit \| commitdiff \| tree
2023-02-23	James Procter	JAL-3858 new MatrixType JAX-RI POJO	commit \| commitdiff \| tree
2023-02-23	James Procter	JAL-4134 - refactor tree calculation code to work with...	commit \| commitdiff \| tree
2023-02-23	James Procter	JAL-4133 update validChar width when font is changed...	commit \| commitdiff \| tree
2023-02-22	James Procter	JAL-4133 store/restore alignment view’s charWidth and...	commit \| commitdiff \| tree
2023-02-22	James Procter	JAL-3858 persist PAE matrix (only so far) as serialised...	commit \| commitdiff \| tree
2023-02-22	James Procter	JAL-1551 source formatting	commit \| commitdiff \| tree
2023-02-22	James Procter	JAL-3858 simple test for PAE matrix recovery	commit \| commitdiff \| tree
2023-02-22	James Procter	JAL-3858 construct a PAE direct from float array	commit \| commitdiff \| tree
2023-02-22	James Procter	JAL-629 make sure we show GUI when not driven programmatically	commit \| commitdiff \| tree
2023-02-22	James Procter	JAL-4095 slightly better threshold setting and todos...	commit \| commitdiff \| tree
2023-02-22	James Procter	JAL-4095 magic fill behaviour is PAE specific	commit \| commitdiff \| tree
2023-02-22	James Procter	JAL-3858 JAL-2381 allow different linear shading schemes...	commit \| commitdiff \| tree
2023-02-22	James Procter	JAL-4027 JAL-3858 rename CUSTOM_RENDERER to CONTACT_MATRIX...	commit \| commitdiff \| tree
2023-02-16	James Procter	Merge branch 'features/r2_11_2_alphafold/JAL-629' into...	commit \| commitdiff \| tree
2023-02-16	James Procter	JAL-1713 don’t close an automatically created overview...	commit \| commitdiff \| tree
2023-02-15	James Procter	Merge branch 'develop' into feature/JAL-1713_overviewInProject	commit \| commitdiff \| tree
2023-02-15	James Procter	Passing test for JAL-4127 failing on the JAL-1713 branch	commit \| commitdiff \| tree
2023-02-15	James Procter	JAL-4090 move 2.11.3 series release notes to 2.11.3...	commit \| commitdiff \| tree
2023-02-13	James Procter	Merge branch 'develop' into feature/JAL-1713_overviewInProject	commit \| commitdiff \| tree
2023-02-10	James Procter	JAL-3077 broken conflict resolve resulted in failing...	commit \| commitdiff \| tree
2023-02-10	James Procter	Fix for JAL-4126 - don’t automatically create a threshold...	commit \| commitdiff \| tree
2023-02-10	James Procter	JAL-4126 comment out closeAll - so we can visually...	commit \| commitdiff \| tree
2023-02-10	James Procter	JAL-4126 failing test - colour scheme appears to be...	commit \| commitdiff \| tree
2023-02-03	James Procter	JAL-1551 remove temp file in src	commit \| commitdiff \| tree
2023-02-03	James Procter	Merge branch 'develop' into features/r2_11_2_alphafold...	commit \| commitdiff \| tree
2023-01-31	James Procter	JAL-1713 update from Jalview 2.11.3 develop	commit \| commitdiff \| tree
2023-01-25	James Procter	JAL-4116 relegate the failed to promote warning to...	commit \| commitdiff \| tree
2023-01-25	James Procter	Merge branch 'new_feature/JAL-4019_ambiguous_base_coloursche...	commit \| commitdiff \| tree
2023-01-24	James Procter	JAL-4090 Release 2.11.3.0 release notes and version...	commit \| commitdiff \| tree
2023-01-24	James Procter	Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL...	commit \| commitdiff \| tree
2023-01-24	James Procter	JAL-629 hacked in --tempfac-shading - hardcoded to...	commit \| commitdiff \| tree
2023-01-24	James Procter	JAL-629 suggest not breaking out of the structure processing...	commit \| commitdiff \| tree
2023-01-24	James Procter	JAL-629 need to delay call to AlignFile.parse() if...	commit \| commitdiff \| tree
2023-01-24	James Procter	JAL-629 don’t carry on Jalview.main if we’ve already...	commit \| commitdiff \| tree
2023-01-24	James Procter	JAL-629 don’t trash user’s system property file when...	commit \| commitdiff \| tree
2023-01-24	James Procter	JAL-629 don’t complain for Unary args	commit \| commitdiff \| tree
2023-01-24	James Procter	JAL-629 labelled breaks are frowned upon by everyone	commit \| commitdiff \| tree
2023-01-24	James Procter	Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL...	commit \| commitdiff \| tree
2023-01-24	James Procter	Merge branch 'develop' (JAL-4102 2.11.2.6 patch release...	commit \| commitdiff \| tree
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