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jalview.git
2021-12-15 Ben SoaresJAL-3933 updated THIRDPARTYLIBS commit | commitdiff | tree | snapshot
2021-12-15 Jim ProcterJAL-3933 remove obsolete Castor logging configuration commit | commitdiff | tree | snapshot
2021-12-15 Jim ProcterJAL-3933 configure root logger console appender to... commit | commitdiff | tree | snapshot
2021-12-14 Ben SoaresJAL-3933 updated log4j and slf4j jars with log4j1.2... commit | commitdiff | tree | snapshot
2021-12-07 Ben SoaresJAL-3930 Added a customizedId="JALVIEW" to launcher... commit | commitdiff | tree | snapshot
2021-11-29 Ben SoaresJAL-3594 correct Jalview Develop logo SVG added in... commit | commitdiff | tree | snapshot
2021-11-19 Jim ProcterJAL-3926 disable autosearch by default commit | commitdiff | tree | snapshot
2021-11-08 Jim ProcterJAL-3855 verify pdb suffix is preserved when locally... commit | commitdiff | tree | snapshot
2021-11-08 Jim ProcterJAL-3855 JAL-1731 reuse the StructureViewer.fetchPdbFil... commit | commitdiff | tree | snapshot
2021-11-08 Jim ProcterJAL-3855 try harder to ignore DNA/RNA only structures... commit | commitdiff | tree | snapshot
2021-11-08 Jim ProcterJAL-3921 wait around until session file has been written commit | commitdiff | tree | snapshot
2021-11-05 Jim ProcterJAL-3829 remove duplicate IDs in 3DBeacons generated... commit | commitdiff | tree | snapshot
2021-11-05 Jim ProcterJAL-3829 format and tidy up unused code commit | commitdiff | tree | snapshot
2021-11-05 Jim ProcterJAL-3919 use model format field to ensure we get the... commit | commitdiff | tree | snapshot
2021-11-05 Jim ProcterJAL-3875 fully reset filter combo-box when fetch 3d... commit | commitdiff | tree | snapshot
2021-11-05 Ben SoaresJAL-3746 Updated help docs for 3D-Beacons. Added and... commit | commitdiff | tree | snapshot
2021-11-03 Jim ProcterJAL-3915 JAL-3746 documentation for removed rnaview... commit | commitdiff | tree | snapshot
2021-11-03 Jim ProcterJAL-3916 TODO for improved selection of covering structures commit | commitdiff | tree | snapshot
2021-11-03 Jim ProcterJAL-3916 TODO for improved selection of covering structures commit | commitdiff | tree | snapshot
2021-11-03 Jim ProcterJAL-3915 remove RNAview opts from preferences. Still... commit | commitdiff | tree | snapshot
2021-11-02 Jim ProcterMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2021-11-02 Jim ProcterJAL-3875 test case and patch to verify the query 3d... commit | commitdiff | tree | snapshot
2021-11-01 Ben SoaresJAL-3907 changed two commented out lines to reflect... commit | commitdiff | tree | snapshot
2021-11-01 Ben SoaresJAL-3907 added creation of symbolic links to workaround... commit | commitdiff | tree | snapshot
2021-10-26 Ben SoaresJAL-3907 adjusted download_jdks.sh and download_jres... commit | commitdiff | tree | snapshot
2021-10-18 Jim ProcterMerge branch 'bug/r2_11_2/JAL-3904_structureviewermenu... commit | commitdiff | tree | snapshot
2021-10-18 Jim ProcterJAL-3905 Fix: wait for response when sending mouseovers... bug/r2_11_2/JAL-3904_structureviewermenu commit | commitdiff | tree | snapshot
2021-10-18 Jim ProcterJAL-3904 override buildActionMenu to add in additional... commit | commitdiff | tree | snapshot
2021-10-18 Jim ProcterJAL-3904 failing test commit | commitdiff | tree | snapshot
2021-10-01 Jim ProcterJAL-3616 show name of structure viewer in ‘new view... commit | commitdiff | tree | snapshot
2021-10-01 Jim ProcterJAL-3616 explicit configure external viewer config commit | commitdiff | tree | snapshot
2021-10-01 Jim ProcterMerge branch 'develop' into releases/Release_2_11_2_Branch commit | commitdiff | tree | snapshot
2021-10-01 Jim ProcterMerge branch 'features/r2_11_2/JAL-3829_3dbeacons'... commit | commitdiff | tree | snapshot
2021-10-01 Jim ProcterJAL-3829 3d beacons logo - misi varadi gave permission... commit | commitdiff | tree | snapshot
2021-10-01 Ben SoaresMerge branch 'improvement/JAL-3594_logos_for_jalview_te... commit | commitdiff | tree | snapshot
2021-10-01 Jim ProcterMerge branch 'develop' into releases/Release_2_11_2_Branch commit | commitdiff | tree | snapshot
2021-10-01 Jim ProcterMerge branch 'features/r2_11_2/JAL-3829_3dbeacons'... commit | commitdiff | tree | snapshot
2021-10-01 Jim ProcterJAL-3829 fetch 3D beacons now started by clicking butto... commit | commitdiff | tree | snapshot
2021-10-01 Ben SoaresMerge branch 'develop' into improvement/JAL-3594_logos_... improvement/JAL-3594_logos_for_jalview_test commit | commitdiff | tree | snapshot
2021-10-01 Ben SoaresJAL-3594 New Jalview Test logos and .icns/.ico creation... commit | commitdiff | tree | snapshot
2021-10-01 Jim ProcterMerge branch 'develop' into features/r2_11_2/JAL-3829_3... commit | commitdiff | tree | snapshot
2021-09-30 Ben SoaresJAL-3594 Changed logo for Jalview Test commit | commitdiff | tree | snapshot
2021-09-30 Ben SoaresJAL-1260 Added .gbk to GenBank extensions. Added GenBa... commit | commitdiff | tree | snapshot
2021-09-30 gmungocJAL-3371 more fine-grained slider; set Param slider... commit | commitdiff | tree | snapshot
2021-09-30 Jim ProcterMerge branch 'bug/JAL-3885_sequence_fetched_not_display... commit | commitdiff | tree | snapshot
2021-09-29 Ben SoaresJAL-3885 Made the database JComboBox have StringPair... commit | commitdiff | tree | snapshot
2021-09-29 Jim ProcterJAL-3884 squish alarming but harmless errors when unipr... commit | commitdiff | tree | snapshot
2021-09-29 Jim ProcterJAL-3881 split on any nonalphanumeric symbol (plus... commit | commitdiff | tree | snapshot
2021-09-29 Jim ProcterJAL-3829 report when 3d-beacons doesn’t provide any... commit | commitdiff | tree | snapshot
2021-09-28 Ben SoaresJAL-3783 Updated groovy-all-2.4. Currently newer stable... commit | commitdiff | tree | snapshot
2021-09-27 Jim ProcterJAL-3746 update the example corefile for jalviewjs commit | commitdiff | tree | snapshot
2021-09-24 Jim ProcterJAL-3829 open web page for 3d beacons structure by... features/r2_11_2/JAL-3829_3dbeacons commit | commitdiff | tree | snapshot
2021-09-24 Jim ProcterMerge branch 'develop' into features/r2_11_2/JAL-3829_3... commit | commitdiff | tree | snapshot
2021-09-24 Jim ProcterMerge branch 'develop' into releases/Release_2_11_2_Branch commit | commitdiff | tree | snapshot
2021-09-24 Jim ProcterJAL-3821 data file for failing test commit | commitdiff | tree | snapshot
2021-09-24 Jim ProcterJAL-3829 right click to view popup menu to show link... commit | commitdiff | tree | snapshot
2021-09-24 Jim ProcterJAL-3829 abstract essential TDB metadata from the user... commit | commitdiff | tree | snapshot
2021-09-23 Jim ProcterMerge branch 'develop' into releases/Release_2_11_2_Branch 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 'develop' into releases/Release_2_11_2_Branch commit | commitdiff | tree | snapshot
2021-09-23 Jim ProcterMerge branch 'patch/JAL-3874_newJmolAndGradleDedup... commit | commitdiff | tree | snapshot
2021-09-23 Jim ProcterMerge branch 'develop' into releases/Release_2_11_2_Branch 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
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