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jalview.git
2021-09-24 Jim ProcterJAL-3829 abstract essential TDB metadata from the user... commit | commitdiff | tree | snapshot
2021-09-23 Jim ProcterMerge branch 'features/r2_11_2/JAL-3821_reinstate_patch... commit | commitdiff | tree | snapshot
2021-09-23 Jim ProcterJAL-3821 less ambiguous base class name for EMBL and... commit | commitdiff | tree | snapshot
2021-09-23 Jim ProcterJAL-3821 ported to refactored FlatFile parser commit | commitdiff | tree | snapshot
2021-09-23 Jim ProcterJAL-3821 failing test commit | commitdiff | tree | snapshot
2021-09-23 Jim ProcterJAL-3692 JAL-3861 remove extra call to .parse() so... commit | commitdiff | tree | snapshot
2021-09-23 Jim ProcterMerge branch 'patch/JAL-3874_newJmolAndGradleDedup... commit | commitdiff | tree | snapshot
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC... commit | commitdiff | tree | snapshot
2021-09-21 Jim ProcterJAL-3746 release notes and what’s new for 2.11.2 -... doc/JAL-3746_Release_2_11_2 commit | commitdiff | tree | snapshot
2021-09-21 Jim ProcterMerge branch 'doc/JAL-3746_Release_2_11_2' into develop commit | commitdiff | tree | snapshot
2021-09-21 Jim ProcterMerge branch 'features/r2_11_2/JAL-3829_3dbeacons'... commit | commitdiff | tree | snapshot
2021-09-21 Jim ProcterJAL-3829 - callback finessing - leave DBRefFetcher... commit | commitdiff | tree | snapshot
2021-09-21 Jim ProcterJAL-3829 prefix PDBe filters with PDBe to make clear... commit | commitdiff | tree | snapshot
2021-09-21 Jim ProcterJAL-3829 alternative UX: need to select 3d-beacons... commit | commitdiff | tree | snapshot
2021-09-21 Jim ProcterJAL-3829 ignore the fake ID generated when a PDB format... commit | commitdiff | tree | snapshot
2021-09-21 Ben SoaresJAL-3521 'Debian-safe' version of minimal build.gradle... commit | commitdiff | tree | snapshot
2021-09-20 Ben SoaresJAL-3521 Created a patch file to transform build.gradle... commit | commitdiff | tree | snapshot
2021-09-20 Jim ProcterJAL-3829 updated response for P01308 commit | commitdiff | tree | snapshot
2021-09-20 Jim ProcterJAL-3829 tests need to wait for dialog to be closed... commit | commitdiff | tree | snapshot
2021-09-20 Jim ProcterJAL-3829 TDBeacons fetcher needs a sequence with at... commit | commitdiff | tree | snapshot
2021-09-20 Jim ProcterJAL-3829 throw the exception even if it has no message commit | commitdiff | tree | snapshot
2021-09-20 Jim ProcterJAL-3829 ensure nulls are not wildcards when retrieving... commit | commitdiff | tree | snapshot
2021-09-20 Ben SoaresJAL-3521 working minimal build.gradle for debian and... merge/develop_JAL-3521_minimal_build.gradle_file commit | commitdiff | tree | snapshot
2021-09-20 Ben SoaresJAL-3521 not quite working minimal build.gradle for... commit | commitdiff | tree | snapshot
2021-09-20 Jim ProcterJAL-3829 do better at detecting structure type, prompt... commit | commitdiff | tree | snapshot
2021-09-20 Jim ProcterJAL-3829 make sure structure data type reflects actual... commit | commitdiff | tree | snapshot
2021-09-20 Jim ProcterJAL-3829 store 3db metadata on PDBEntry so it can be... commit | commitdiff | tree | snapshot
2021-09-20 Jim ProcterJAL-3829 allow PDBEntry with file and ID with mismatchi... commit | commitdiff | tree | snapshot
2021-09-17 Ben SoaresMerge branch 'merge/develop_JAL-1260' into develop commit | commitdiff | tree | snapshot
2021-09-17 Ben SoaresJAL-1260 rudimentary parsing of LOCUS line to at least... commit | commitdiff | tree | snapshot
2021-09-17 Jim ProcterMerge branch 'develop' into features/r2_11_2/JAL-3829_3... commit | commitdiff | tree | snapshot
2021-09-17 Jim ProcterJAL-3079 JAL-3055 remember to reset font transform... commit | commitdiff | tree | snapshot
2021-09-17 gmungocJAL-1260 refactored multi-line qualifier separators commit | commitdiff | tree | snapshot
2021-09-17 gmungocJAL-1260 unit test for FileFormats updated for GenBank/ENA commit | commitdiff | tree | snapshot
2021-09-17 gmungocJAL-1260 file formats and IdentifyFile updates for... commit | commitdiff | tree | snapshot
2021-09-17 gmungocJAL-1260 refactored GenBank (and EMBL) flat file parser commit | commitdiff | tree | snapshot
2021-09-17 Jim ProcterJAL-1260 FileFormat entry for EMBL/GENBANK: TODO: creat... commit | commitdiff | tree | snapshot
2021-09-17 Jim ProcterJAL-3874 - replace Jmol with custom build of 14.31... patch/JAL-3874_newJmolAndGradleDedup commit | commitdiff | tree | snapshot
2021-09-17 Jim ProcterJAL-2226 transfer chain annotation when calcId, label... commit | commitdiff | tree | snapshot
2021-09-17 Jim ProcterJAL-2226 new method to search for annotation matching... commit | commitdiff | tree | snapshot
2021-09-17 Jim ProcterJAL-3829 belt and braces check to make sure there is... commit | commitdiff | tree | snapshot
2021-09-16 Ben SoaresJAL-3779 Added to documentation commit | commitdiff | tree | snapshot
2021-09-16 gmungocJAL-3779 apply properties to all groups with given... commit | commitdiff | tree | snapshot
2021-09-16 Ben SoaresJAL-3774 combined changes from bug/JAL-3774_splitFrameF... commit | commitdiff | tree | snapshot
2021-09-16 Jim ProcterMerge branch 'develop' into doc/JAL-3746_Release_2_11_2 commit | commitdiff | tree | snapshot
2021-09-16 Ben SoaresJAL-3739 (combined) commits from feature/JAL-3739_useFo... commit | commitdiff | tree | snapshot
2021-09-16 Jim ProcterJAL-3794 X and N are counted as DNA characters, but... commit | commitdiff | tree | snapshot
2021-09-16 Jim ProcterJAL-3794 new test for recognition of protein or DNA... commit | commitdiff | tree | snapshot
2021-09-16 Ben SoaresJAL-3761 listToArray became rangeListToArray commit | commitdiff | tree | snapshot
2021-09-16 gmungocJAL-3761 more consistent parameter naming commit | commitdiff | tree | snapshot
2021-09-16 gmungocJAL-3761 helper method reinstated to avoid code duplication commit | commitdiff | tree | snapshot
2021-09-16 gmungocJAL-3761 locateInFrom/To revised with tests; unused... commit | commitdiff | tree | snapshot
2021-09-16 gmungocJAL-3761 extra check that VCF feature is fully mappable... commit | commitdiff | tree | snapshot
2021-09-16 gmungocJAL-3761 debugged and working (but not tidied) locateIn... commit | commitdiff | tree | snapshot
2021-09-16 Ben SoaresJAL-3761 listToArray became rangeListToArray commit | commitdiff | tree | snapshot
2021-09-16 gmungocJAL-3761 locateInFrom2 work in progress commit commit | commitdiff | tree | snapshot
2021-09-15 gmungocJAL-3761 unit test for MapList.countPos() commit | commitdiff | tree | snapshot
2021-09-15 gmungocJAL-3761 failing test, formatting, method renamed commit | commitdiff | tree | snapshot
2021-09-15 gmungocJAL-3761 failing tests for locateInFrom/To with overlap... commit | commitdiff | tree | snapshot
2021-09-15 gmungocJAL-3751 only merge strictly contiguous ranges of mappings commit | commitdiff | tree | snapshot
2021-09-15 gmungocJAL-3788 synchronize concurrent findColour() and alignm... commit | commitdiff | tree | snapshot
2021-09-15 Ben SoaresJAL-3818 formatting commit | commitdiff | tree | snapshot
2021-09-15 gmungocJAL-3818 process Jmol callbacks in AWT thread commit | commitdiff | tree | snapshot
2021-09-15 Ben SoaresMerge branch 'develop' into merge/develop_ben2 commit | commitdiff | tree | snapshot
2021-09-15 Ben SoaresMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2021-09-15 Ben SoaresJAL-3829 Fixed Jmol jar -- duplicates of other classes... commit | commitdiff | tree | snapshot
2021-09-15 Jim ProcterMerge branch 'Jalview-JS/bug/JAL-3762_URLparamsOverride... commit | commitdiff | tree | snapshot
2021-09-15 Jim ProcterJAL-3746 fix bad merge from 2.11.1.4/5 branch cherrypick commit | commitdiff | tree | snapshot
2021-09-15 Jim ProcterJAL-3842 fix automatic what's new link for custom versi... commit | commitdiff | tree | snapshot
2021-09-15 Jim ProcterJAL-3842 2.11.1.5 what’s new, release notes, and versio... commit | commitdiff | tree | snapshot
2021-09-15 Jim ProcterJAL-3816 bump version number and cut release notes commit | commitdiff | tree | snapshot
2021-09-15 Jim ProcterJAL-3766 cut new patch release commit | commitdiff | tree | snapshot
2021-09-15 Jim ProcterJAL-3758 2.11.1.2 patch release notes and version bump commit | commitdiff | tree | snapshot
2021-09-15 Jim ProcterJAL-3741 http to https (and jar to jvp for exampleFile... commit | commitdiff | tree | snapshot
2021-09-15 Jim ProcterJAL-3477 added help documentation for executable jar... commit | commitdiff | tree | snapshot
2021-09-15 Jim ProcterJAL-3675 version update and documentation for JAL-3493... commit | commitdiff | tree | snapshot
2021-09-15 Jim ProcterJAL-3638 JAL-3680 fix docs for Alt + Arrow LRUD in... commit | commitdiff | tree | snapshot
2021-09-15 Ben SoaresMerge branch 'develop' into merge/develop_ben2 commit | commitdiff | tree | snapshot
2021-09-15 Jim ProcterMerge branch 'features/r2_11_2/JAL-3829_3dbeacons'... commit | commitdiff | tree | snapshot
2021-09-14 Jim ProcterJAL-3815 default /etc/jalview_properties under utils... commit | commitdiff | tree | snapshot
2021-09-14 Jim ProcterJAL-3829 parallel not welcome here commit | commitdiff | tree | snapshot
2021-09-14 Jim ProcterJAL-3829 test flakiness and human flakiness commit | commitdiff | tree | snapshot
2021-09-14 Jim ProcterJAL-3829 more info on test fail - seems to be flaky commit | commitdiff | tree | snapshot
2021-09-14 Ben SoaresMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2021-09-14 Ben SoaresJAL-3521 Adjusted wrapper shell script and .desktop... commit | commitdiff | tree | snapshot
2021-09-14 Ben SoaresJAL-3521 High quality file icons for jalview associated... commit | commitdiff | tree | snapshot
2021-09-14 Ben SoaresJAL-3521 Change grouped Jalview windows on linux taskba... commit | commitdiff | tree | snapshot
2021-09-14 Jim ProcterMerge branch 'features/r2_11_2/JAL-3829_3dbeacons'... commit | commitdiff | tree | snapshot
2021-09-14 Jim ProcterJAL-3551 - doc tweak commit | commitdiff | tree | snapshot
2021-09-14 Jim ProcterJAL-3855 JAL-3829 better checks on PDB or mmCIF file... commit | commitdiff | tree | snapshot
2021-09-14 Jim ProcterJAL-3829 JAL-3855 moved routing for retrieving structur... commit | commitdiff | tree | snapshot
2021-09-14 Jim ProcterJAL-3829 JAL-3855 ignore case when detecting alphafold ID commit | commitdiff | tree | snapshot
2021-09-14 Jim ProcterJAL-3855 detect an alphafold model and import its tempe... commit | commitdiff | tree | snapshot
2021-09-14 Jim ProcterJAL-3829 move mock query and responses to files commit | commitdiff | tree | snapshot
2021-09-14 Ben SoaresJAL-2422 Also look in ~/Applications for ChimeraX on... commit | commitdiff | tree | snapshot
2021-09-14 Jim ProcterMerge branch 'develop' into features/r2_11_2/JAL-3829_3... commit | commitdiff | tree | snapshot
2021-09-14 Jim ProcterMerge branch 'feature/JAL-2422ChimeraX' into develop commit | commitdiff | tree | snapshot
2021-09-14 Jim ProcterJAL-3829 3d-beacons doesn’t work as a sequence source... commit | commitdiff | tree | snapshot
2021-09-14 Jim ProcterJAL-3829 avoid sending rubbish to PDBe search api commit | commitdiff | tree | snapshot
2021-09-14 Jim ProcterJAL-3829 some providers don’t provide model quality... commit | commitdiff | tree | snapshot
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