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jalview.git
2023-05-18 James ProcterJAL-4134 colour by annotation needs distinct annotation... commit | commitdiff | tree | snapshot
2023-05-18 James ProcterJAL-4134 column grouping model and methods moved to... commit | commitdiff | tree | snapshot
2023-05-18 James ProcterJAL-4134 formatting commit | commitdiff | tree | snapshot
2023-05-18 James ProcterJAL-4134 properly specify BinaryNode as a typed generic... commit | commitdiff | tree | snapshot
2023-05-16 James ProcterJAL-4089 - if no centerViewOn commands are given, don... commit | commitdiff | tree | snapshot
2023-05-15 James ProcterJAL-4182 patch - map selection group onto sequence... commit | commitdiff | tree | snapshot
2023-05-15 James ProcterJAL-4182 failing test commit | commitdiff | tree | snapshot
2023-05-14 James ProcterJAL-2349 fix up tests for Java 11 compatibility and... commit | commitdiff | tree | snapshot
2023-05-14 James ProcterJAL-4134 add tree distance engine test to functional commit | commitdiff | tree | snapshot
2023-05-14 James ProcterJAL-2349 store/restore mappable contact matrix in proje... commit | commitdiff | tree | snapshot
2023-05-13 James ProcterJAL-2349 JAL-3855 PAE tests covers ContactListI.getMapp... commit | commitdiff | tree | snapshot
2023-05-13 James ProcterJAL-2349 JAL-3855 helper method to make it easy to... commit | commitdiff | tree | snapshot
2023-05-12 James ProcterJAL-2349 allow PAE or other contact matrices to hold... commit | commitdiff | tree | snapshot
2023-05-01 James ProcterMerge branch 'features/JAL-4134_treeviewerforcolumns... commit | commitdiff | tree | snapshot
2023-05-01 James ProcterJAL-4177 disable ‘Cancel’ as well - since we as yet... features/JAL-4134_treeviewerforcolumns commit | commitdiff | tree | snapshot
2023-05-01 James ProcterJAL-4177 disable add/new view when an import is started. commit | commitdiff | tree | snapshot
2023-05-01 James ProcterJAL-4123 JAL-3914 JAL-3858 tweak wording and layout... commit | commitdiff | tree | snapshot
2023-05-01 James ProcterJAL-4134 double click to select column groups commit | commitdiff | tree | snapshot
2023-05-01 James ProcterJAL-3858 report errors when trying to parse JSON to... commit | commitdiff | tree | snapshot
2023-05-01 James ProcterMerge branch 'features/JAL-4134_treeviewerforcolumns... commit | commitdiff | tree | snapshot
2023-03-24 James ProcterMerge branch 'develop' into features/JAL-4134_treeviewe... commit | commitdiff | tree | snapshot
2023-03-24 James ProcterJAL-4134 - store colours in annotation row, so colour... commit | commitdiff | tree | snapshot
2023-03-24 James ProcterJAL-4158 first attempt at stashing colours for contact... commit | commitdiff | tree | snapshot
2023-03-23 James ProcterMerge branch 'patch/JAL-4153_flakyJvCacheableInputBoxTe... commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-4134 override default hasTree so PAE tree is saved! commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-4153 longer Thread.sleep() calls in the hope that... commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-4134 - missing Jalview project JAXB class - st... commit | commitdiff | tree | snapshot
2023-03-20 James ProcterMerge branch 'develop' into features/JAL-4134_treeviewe... commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-4150 test and quick patch copying code from AlignFr... commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-2349 JAL-4134 Console log messages for contact... commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-4134 propagate column selection changes in tree... commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-4134 fix off-by-one in selection commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-4134 fix NPEs when matrix not resolved or alignment... commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-4134 better popup menu name ‘Tree for Contact Matrix’ commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-2349 test TODOs commit | commitdiff | tree | snapshot
2023-03-20 James ProcterJAL-2349 fix off by one when resolving columns for... commit | commitdiff | tree | snapshot
2023-03-17 James ProcterJAL-4134 fix up column selection when hidden regions... commit | commitdiff | tree | snapshot
2023-03-17 James ProcterJAL-4134 store/restore Newick tree for PAE annotation row commit | commitdiff | tree | snapshot
2023-03-15 James ProcterJAL-4091 JAL-4147 - revised annotation label display... commit | commitdiff | tree | snapshot
2023-03-15 James ProcterJAL-4091 JAL-629 ‘Add Reference Annotations’ takes... commit | commitdiff | tree | snapshot
2023-03-15 James ProcterJAL-2349 don’t clobber existing label/description... commit | commitdiff | tree | snapshot
2023-03-15 James ProcterJAL-4134 JAL-3855 store/restore groups, tree and thresh... commit | commitdiff | tree | snapshot
2023-03-08 James ProcterJAL-2349 handle matrix_clicked on mouse_release rather... commit | commitdiff | tree | snapshot
2023-03-08 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... commit | commitdiff | tree | snapshot
2023-03-08 Ben SoaresJAL-629 Fix --headless for new args. Fix progressbar... commit | commitdiff | tree | snapshot
2023-03-08 Ben SoaresJAL-629 stash some TFType and PAEFile info into a PDBEntry commit | commitdiff | tree | snapshot
2023-03-06 Ben SoaresJAL-629 Fix null AlignPanel. More descriptive label... commit | commitdiff | tree | snapshot
2023-03-03 Ben SoaresJAL-629 Improved consistency of ArgParser classes ... commit | commitdiff | tree | snapshot
2023-03-02 Ben SoaresJAL-629 slight tidy up commit | commitdiff | tree | snapshot
2023-03-02 Ben SoaresJAL-629 Removal of unnecessary methods. Set pLTTD tempf... commit | commitdiff | tree | snapshot
2023-03-02 Ben SoaresJAL-629 Some refactoring to allow more flexible use... commit | commitdiff | tree | snapshot
2023-03-01 James ProcterJAL-4134 hold ctrl to select groups containing rows... commit | commitdiff | tree | snapshot
2023-02-28 Ben SoaresJAL-629 Firm up bootstrapArgs. Correct '-colour' in... commit | commitdiff | tree | snapshot
2023-02-27 Ben SoaresJAL-629 add AF examples for FER1_SPIOL. Link and displa... commit | commitdiff | tree | snapshot
2023-02-27 James ProcterJAL-2349 TODO consider caching contactRanges from getCo... commit | commitdiff | tree | snapshot
2023-02-27 James ProcterJAL-4134 tree panel shouldn’t try to redraw before... commit | commitdiff | tree | snapshot
2023-02-27 James ProcterJAL-4134 fix more of the egregious SeqNode/BinaryNode... commit | commitdiff | tree | snapshot
2023-02-27 James ProcterJAL-4134 leaves marked when columns are selected -... commit | commitdiff | tree | snapshot
2023-02-27 James ProcterJAL-4134 TODO: alternative way of performing interactiv... commit | commitdiff | tree | snapshot
2023-02-27 James ProcterJAL-4134 use average distance between PAE elements... commit | commitdiff | tree | snapshot
2023-02-27 James ProcterJAL-4134 display tree for columns - selecting an intern... commit | commitdiff | tree | snapshot
2023-02-27 James ProcterJAL-4134 compute normalised dot product for contact... commit | commitdiff | tree | snapshot
2023-02-27 James ProcterJAL-4134 allow tree groups to be stored/recovered on... commit | commitdiff | tree | snapshot
2023-02-27 Ben SoaresJAL-629 Fix Exceptions when running with CLI not headless commit | commitdiff | tree | snapshot
2023-02-27 Ben SoaresJAL-629 Guesstimate whether to set pLDDT with PDB file commit | commitdiff | tree | snapshot
2023-02-27 Ben SoaresJAL-629 JAL-4124 JAL-3855 remove deleted debugging... commit | commitdiff | tree | snapshot
2023-02-27 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... commit | commitdiff | tree | snapshot
2023-02-27 Ben SoaresJAL-629 removed debug prints. added .cif. added some... commit | commitdiff | tree | snapshot
2023-02-27 James ProcterMerge branch 'develop' into features/JAL-4134_treeviewe... commit | commitdiff | tree | snapshot
2023-02-26 Ben SoaresJAL-629 PAE matrix file guesstimate from filename commit | commitdiff | tree | snapshot
2023-02-24 Ben SoaresJAL-629 Position GUI widgets for PDF file options.... commit | commitdiff | tree | snapshot
2023-02-24 James ProcterJAL-629 JAL-4124 JAL-3855 test to check we can import... commit | commitdiff | tree | snapshot
2023-02-24 James ProcterJAL-629 JAL-4124 JAL-3855 test to check we can import... commit | commitdiff | tree | snapshot
2023-02-24 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... commit | commitdiff | tree | snapshot
2023-02-24 Ben SoaresJAL-629 add widgets to StructureChooser for tempfac... commit | commitdiff | tree | snapshot
2023-02-24 James ProcterMerge branch 'features/JAL-3858_PAEsInProjects' into... commit | commitdiff | tree | snapshot
2023-02-24 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... features/JAL-3858_PAEsInProjects commit | commitdiff | tree | snapshot
2023-02-24 Ben SoaresJAL-629 helper function for getting sensible structure... commit | commitdiff | tree | snapshot
2023-02-24 Ben SoaresJAL-629 better test fixes. --props=... instead of ... commit | commitdiff | tree | snapshot
2023-02-24 Ben SoaresJAL-629 Made ArgValuesMap helper class, simplifies... commit | commitdiff | tree | snapshot
2023-02-23 Ben SoaresJAL-629 test fixing commit | commitdiff | tree | snapshot
2023-02-23 James ProcterJAL-4134 group columns using a tree cut - seems to... commit | commitdiff | tree | snapshot
2023-02-23 Ben SoaresJAL-629 Add debug messages for more failing tests commit | commitdiff | tree | snapshot
2023-02-23 James ProcterJAL-4134 - brutal hack to build a tree clustering colum... commit | commitdiff | tree | snapshot
2023-02-23 Ben SoaresJAL-629 fixed a Log4j test by adding --debug arg commit | commitdiff | tree | snapshot
2023-02-23 Ben SoaresJAL-629 bootstrap args and properties. Remember index... commit | commitdiff | tree | snapshot
2023-02-23 Ben SoaresJAL-629 nf-core sample alignment files and a2m versions commit | commitdiff | tree | snapshot
2023-02-23 Ben SoaresJAL-629 fix a PAEMatrix casting error commit | commitdiff | tree | snapshot
2023-02-23 James ProcterJAL-4134 tidied up refactoring and fix compilation... commit | commitdiff | tree | snapshot
2023-02-23 James ProcterMerge branch 'features/JAL-3858_PAEsInProjects' into... commit | commitdiff | tree | snapshot
2023-02-23 James ProcterJAL-3858 new MatrixType JAX-RI POJO commit | commitdiff | tree | snapshot
2023-02-23 James ProcterJAL-4134 - refactor tree calculation code to work with... commit | commitdiff | tree | snapshot
2023-02-23 James ProcterJAL-4133 update validChar width when font is changed... commit | commitdiff | tree | snapshot
2023-02-22 James ProcterJAL-4133 store/restore alignment view’s charWidth and... commit | commitdiff | tree | snapshot
2023-02-22 James ProcterJAL-3858 persist PAE matrix (only so far) as serialised... commit | commitdiff | tree | snapshot
2023-02-22 James ProcterJAL-1551 source formatting commit | commitdiff | tree | snapshot
2023-02-22 James ProcterJAL-3858 simple test for PAE matrix recovery commit | commitdiff | tree | snapshot
2023-02-22 James ProcterJAL-3858 construct a PAE direct from float array commit | commitdiff | tree | snapshot
2023-02-22 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... commit | commitdiff | tree | snapshot
2023-02-22 Ben SoaresJAL-4064 JAL-4054 Corrected the tgz top-level dir from... commit | commitdiff | tree | snapshot
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