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jalview.git
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
2023-02-22 James ProcterJAL-629 make sure we show GUI when not driven programma... commit | commitdiff | tree | snapshot
2023-02-22 James ProcterJAL-4095 slightly better threshold setting and todos... commit | commitdiff | tree | snapshot
2023-02-22 James ProcterJAL-4095 magic fill behaviour is PAE specific commit | commitdiff | tree | snapshot
2023-02-22 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... commit | commitdiff | tree | snapshot
2023-02-22 James ProcterJAL-3858 JAL-2381 allow different linear shading scheme... commit | commitdiff | tree | snapshot
2023-02-22 James ProcterJAL-4027 JAL-3858 rename CUSTOM_RENDERER to CONTACT_MAT... commit | commitdiff | tree | snapshot
2023-02-21 Ben SoaresJAL-4088 Updated j8libs/*.jar in THIRDPARTYLIBS commit | commitdiff | tree | snapshot
2023-02-20 Ben SoaresJAL-3416 Turn off (partial) flatlaf scaling for HiDPI... commit | commitdiff | tree | snapshot
2023-02-20 Ben SoaresJAL-4064 JAL-4054 Correct names of mac arch installer... commit | commitdiff | tree | snapshot
2023-02-20 Ben SoaresMerge branch 'develop' into improvement/JAL-4111_suffix... improvement/JAL-4111_suffixed_DEVELOP_channels commit | commitdiff | tree | snapshot
2023-02-20 Ben SoaresJAL-4128 Catch RasterFormatException caused whilst... bug/JAL-4128_resizing_overview_with_solid_drags_causes_exception commit | commitdiff | tree | snapshot
2023-02-20 Ben SoaresMerge branch 'develop' into bug/JAL-4125_flatlaf_quitha... bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly commit | commitdiff | tree | snapshot
2023-02-16 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... commit | commitdiff | tree | snapshot
2023-02-16 James ProcterJAL-1713 don’t close an automatically created overview... commit | commitdiff | tree | snapshot
2023-02-15 James ProcterMerge branch 'develop' into feature/JAL-1713_overviewIn... commit | commitdiff | tree | snapshot
2023-02-15 James ProcterPassing test for JAL-4127 failing on the JAL-1713 branch commit | commitdiff | tree | snapshot
2023-02-15 James ProcterJAL-4090 move 2.11.3 series release notes to 2.11.3... commit | commitdiff | tree | snapshot
2023-02-13 Ben SoaresMerge branch 'develop' into bug/JAL-4125_flatlaf_quitha... commit | commitdiff | tree | snapshot
2023-02-13 Ben SoaresJAL-4125 Spanish translations commit | commitdiff | tree | snapshot
2023-02-13 Ben SoaresMerge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL... commit | commitdiff | tree | snapshot
2023-02-13 Ben SoaresJAL-4125 Move confirmation of closing external viewer... commit | commitdiff | tree | snapshot
2023-02-13 James ProcterMerge branch 'develop' into feature/JAL-1713_overviewIn... commit | commitdiff | tree | snapshot
2023-02-10 James ProcterJAL-3077 broken conflict resolve resulted in failing... commit | commitdiff | tree | snapshot
2023-02-10 James ProcterFix for JAL-4126 - don’t automatically create a thresho... commit | commitdiff | tree | snapshot
2023-02-10 James ProcterJAL-4126 comment out closeAll - so we can visually... commit | commitdiff | tree | snapshot
2023-02-10 James ProcterJAL-4126 failing test - colour scheme appears to be... commit | commitdiff | tree | snapshot
2023-02-09 Ben SoaresJAL-4125 Additions to JvOptionPane and QuitHandler... commit | commitdiff | tree | snapshot
2023-02-03 Ben SoaresJAL-629 Fasta sequence id reading whitespace fix. Flexi... commit | commitdiff | tree | snapshot
2023-02-03 Ben SoaresJAL-629 "updated" json-simple commit | commitdiff | tree | snapshot
2023-02-03 James ProcterJAL-1551 remove temp file in src commit | commitdiff | tree | snapshot
2023-02-03 James ProcterMerge branch 'develop' into features/r2_11_2_alphafold... commit | commitdiff | tree | snapshot
2023-01-31 James ProcterJAL-1713 update from Jalview 2.11.3 develop commit | commitdiff | tree | snapshot
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