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JAL-629 Test and fix --annotation --ssannotation args. Added a viewerType arg/subval...
[jalview.git] / src /
2023-04-22 Ben SoaresJAL-629 Test and fix --annotation --ssannotation args... tree | commitdiff
2023-04-19 Ben SoaresJAL-629 Now showing temp fac and secondary structure... tree | commitdiff
2023-04-14 Ben SoaresJAL-629 Adding PAE and TFType at structure loading... tree | commitdiff
2023-04-12 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-04-12 Ben SoaresJAL-629 Add substituteHomeDir to getDirname(). Tighten... tree | commitdiff
2023-04-12 Ben SoaresJAL-629 Fix non-multi string bootstrap arg bug. tree | commitdiff
2023-04-12 Ben SoaresJAL-629 parse SubVals once with ArgValue. Ensure SubVal... tree | commitdiff
2023-04-12 Ben SoaresJAL-629 allow argfiles in argfiles, but avoid looping... tree | commitdiff
2023-04-12 Ben SoaresJAL-629 allow comments in argfiles '#' tree | commitdiff
2023-04-05 Ben SoaresJAL-629 Tests for FileUtils. Tidying counter substituti... tree | commitdiff
2023-04-04 Ben SoaresJAL-629 more info in usage statement tree | commitdiff
2023-04-04 Ben SoaresJAL-629 Start of Usage statement tree | commitdiff
2023-04-04 Ben SoaresJAL-629 More consistent printing of --arguments. Exampl... tree | commitdiff
2023-04-04 Ben SoaresJAL-629 Remove debugging comment tree | commitdiff
2023-04-04 Ben SoaresJAL-629 --initsubstitutions as a bootstrap arg, new... tree | commitdiff
2023-04-03 Ben SoaresJAL-629 sort files from java glob for predictability... tree | commitdiff
2023-04-03 Ben SoaresJAL-629 added setprop. More filename based substitution... tree | commitdiff
2023-03-30 Ben SoaresJAL-629 More extensive tests with real files being... tree | commitdiff
2023-03-30 Ben SoaresJAL-629 fix bug for opening single named file with... tree | commitdiff
2023-03-30 Ben SoaresJAL-629 Don't use new ArgParser if there are no --args... tree | commitdiff
2023-03-30 Ben SoaresJAL-629 fix SubVals npe tree | commitdiff
2023-03-29 Ben SoaresJAL-629 Added --opennew --nonews --nosplash. Added... tree | commitdiff
2023-03-28 Ben SoaresJAL-629 Opening files in new windows. not working yet tree | commitdiff
2023-03-25 Ben SoaresJAL-629 open initial non-Arg arguments as files in... tree | commitdiff
2023-03-25 Ben SoaresJAL-629 improvements to argparser toString. Improvement... tree | commitdiff
2023-03-24 James ProcterJAL-4158 first attempt at stashing colours for contact... tree | commitdiff
2023-03-24 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-03-24 Ben SoaresJAL-629 Test tidyup tree | commitdiff
2023-03-23 Ben SoaresJAL-629 refactor ArgParser and helper classes all to... tree | commitdiff
2023-03-20 James ProcterJAL-4134 override default hasTree so PAE tree is saved! tree | commitdiff
2023-03-20 James ProcterJAL-4134 - missing Jalview project JAXB class - st... tree | commitdiff
2023-03-20 James ProcterMerge branch 'develop' into features/JAL-4134_treeviewe... tree | commitdiff
2023-03-20 James ProcterJAL-4150 test and quick patch copying code from AlignFr... tree | commitdiff
2023-03-20 James ProcterJAL-2349 JAL-4134 Console log messages for contact... tree | commitdiff
2023-03-20 James ProcterJAL-4134 propagate column selection changes in tree... tree | commitdiff
2023-03-20 James ProcterJAL-4134 fix off-by-one in selection tree | commitdiff
2023-03-20 James ProcterJAL-4134 fix NPEs when matrix not resolved or alignment... tree | commitdiff
2023-03-20 James ProcterJAL-4134 better popup menu name ‘Tree for Contact Matrix’ tree | commitdiff
2023-03-20 James ProcterJAL-2349 fix off by one when resolving columns for... tree | commitdiff
2023-03-18 Ben SoaresJAL-629 Check for new commandsSuccess before quit tree | commitdiff
2023-03-18 Ben SoaresJAL-629 move getdown update to earlier stage tree | commitdiff
2023-03-17 Ben SoaresJAL-629 All applications System.exits going through... tree | commitdiff
2023-03-17 James ProcterJAL-4134 fix up column selection when hidden regions... tree | commitdiff
2023-03-17 James ProcterJAL-4134 store/restore Newick tree for PAE annotation row tree | commitdiff
2023-03-16 Ben SoaresJAL-629 revert metal laf tree | commitdiff
2023-03-16 Ben SoaresJAL-629 Set Metal as default LAF for build server tests tree | commitdiff
2023-03-15 James ProcterJAL-4091 JAL-4147 - revised annotation label display... tree | commitdiff
2023-03-15 James ProcterJAL-4091 JAL-629 ‘Add Reference Annotations’ takes... tree | commitdiff
2023-03-15 James ProcterJAL-2349 don’t clobber existing label/description... tree | commitdiff
2023-03-15 James ProcterJAL-4134 JAL-3855 store/restore groups, tree and thresh... tree | commitdiff
2023-03-15 Ben SoaresJAL-629 Commands more objecty, less classy. FileLoader... tree | commitdiff
2023-03-12 Ben SoaresJAL-629 Allow substitutions of {} = defaultCounter... tree | commitdiff
2023-03-11 Ben SoaresJAL-629 --substitutions --nosubstitutions flags, -... tree | commitdiff
2023-03-11 Ben SoaresJAL-629 Auto and Default count incrementer args. Flags... tree | commitdiff
2023-03-10 Ben SoaresJAL-629 start of tests and more examples tree | commitdiff
2023-03-09 Ben SoaresJAL-629 start of tests tree | commitdiff
2023-03-09 Ben SoaresJAL-629 --argfile=glob implemented. Remove reference... tree | commitdiff
2023-03-08 Ben SoaresJAL-629 --close individually for each AlignFrame opened... tree | commitdiff
2023-03-08 Ben SoaresJAL-629 improved comment and return speed of StringUtil... tree | commitdiff
2023-03-08 James ProcterJAL-2349 handle matrix_clicked on mouse_release rather... tree | commitdiff
2023-03-08 Ben SoaresJAL-629 --quiet [no stdout], --quiet --quiet [no stderr... tree | commitdiff
2023-03-08 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... tree | commitdiff
2023-03-08 Ben SoaresJAL-629 Fix --headless for new args. Fix progressbar... tree | commitdiff
2023-03-08 Ben SoaresJAL-629 stash some TFType and PAEFile info into a PDBEntry tree | commitdiff
2023-03-06 Ben SoaresJAL-629 Fix null AlignPanel. More descriptive label... tree | commitdiff
2023-03-03 Ben SoaresJAL-629 Improved consistency of ArgParser classes ... tree | commitdiff
2023-03-02 Ben SoaresJAL-629 slight tidy up tree | commitdiff
2023-03-02 Ben SoaresJAL-629 Removal of unnecessary methods. Set pLTTD tempf... tree | commitdiff
2023-03-02 Ben SoaresJAL-629 Some refactoring to allow more flexible use... tree | commitdiff
2023-03-01 James ProcterJAL-4134 hold ctrl to select groups containing rows... tree | commitdiff
2023-02-28 Ben SoaresJAL-629 Firm up bootstrapArgs. Correct '-colour' in... tree | commitdiff
2023-02-27 Ben SoaresJAL-629 add AF examples for FER1_SPIOL. Link and displa... tree | commitdiff
2023-02-27 James ProcterJAL-2349 TODO consider caching contactRanges from getCo... tree | commitdiff
2023-02-27 James ProcterJAL-4134 tree panel shouldn’t try to redraw before... tree | commitdiff
2023-02-27 James ProcterJAL-4134 fix more of the egregious SeqNode/BinaryNode... tree | commitdiff
2023-02-27 James ProcterJAL-4134 leaves marked when columns are selected -... tree | commitdiff
2023-02-27 James ProcterJAL-4134 TODO: alternative way of performing interactiv... tree | commitdiff
2023-02-27 James ProcterJAL-4134 use average distance between PAE elements... tree | commitdiff
2023-02-27 James ProcterJAL-4134 display tree for columns - selecting an intern... tree | commitdiff
2023-02-27 James ProcterJAL-4134 compute normalised dot product for contact... tree | commitdiff
2023-02-27 James ProcterJAL-4134 allow tree groups to be stored/recovered on... tree | commitdiff
2023-02-27 Ben SoaresJAL-629 Fix Exceptions when running with CLI not headless tree | commitdiff
2023-02-27 Ben SoaresJAL-629 Guesstimate whether to set pLDDT with PDB file tree | commitdiff
2023-02-27 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-02-27 Ben SoaresJAL-629 removed debug prints. added .cif. added some... tree | commitdiff
2023-02-27 James ProcterMerge branch 'develop' into features/JAL-4134_treeviewe... tree | commitdiff
2023-02-26 Ben SoaresJAL-629 PAE matrix file guesstimate from filename tree | commitdiff
2023-02-24 Ben SoaresJAL-629 Position GUI widgets for PDF file options.... tree | commitdiff
2023-02-24 James ProcterJAL-629 JAL-4124 JAL-3855 test to check we can import... tree | commitdiff
2023-02-24 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-02-24 Ben SoaresJAL-629 add widgets to StructureChooser for tempfac... tree | commitdiff
2023-02-24 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... features/JAL-3858_PAEsInProjects tree | commitdiff
2023-02-24 Ben SoaresJAL-629 helper function for getting sensible structure... tree | commitdiff
2023-02-24 Ben SoaresJAL-629 Made ArgValuesMap helper class, simplifies... tree | commitdiff
2023-02-23 James ProcterJAL-4134 group columns using a tree cut - seems to... tree | commitdiff
2023-02-23 James ProcterJAL-4134 - brutal hack to build a tree clustering colum... tree | commitdiff
2023-02-23 Ben SoaresJAL-629 bootstrap args and properties. Remember index... tree | commitdiff
2023-02-23 Ben SoaresJAL-629 fix a PAEMatrix casting error tree | commitdiff
2023-02-23 James ProcterJAL-4134 tidied up refactoring and fix compilation... tree | commitdiff
2023-02-23 James ProcterMerge branch 'features/JAL-3858_PAEsInProjects' into... tree | commitdiff
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