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jalview.git
2022-02-14 Jim ProcterJAL-3956 - PDBEntry objects constructed from 3D-Beacons... commit | commitdiff | tree | snapshot
2022-02-12 Jim ProcterMerge branch 'update/JAL-3949_jalview_bin_Console_to_cu... commit | commitdiff | tree | snapshot
2022-02-12 Ben SoaresJAL-3949 fix testProps path and make line count more... update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more commit | commitdiff | tree | snapshot
2022-02-11 Jim ProcterJAL-3949 increase command line ops test timeout commit | commitdiff | tree | snapshot
2022-02-11 Jim ProcterJAL-3949 ensure Jalview command line ops setup actually... commit | commitdiff | tree | snapshot
2022-02-11 Jim ProcterMerge branch 'update/JAL-3949_jalview_bin_Console_to_cu... commit | commitdiff | tree | snapshot
2022-02-11 Jim ProcterJAL-3931 fix - escape % symbols after urlencoding commit | commitdiff | tree | snapshot
2022-02-11 Ben SoaresMerge branch 'update/JAL-3949_jalview_bin_Console_to_cu... commit | commitdiff | tree | snapshot
2022-02-11 Ben SoaresJLogger loglevel check on whether to call the actual... commit | commitdiff | tree | snapshot
2022-02-11 Jim ProcterJAL-3949 - refactor logging from jalview.bin.Cache... commit | commitdiff | tree | snapshot
2022-02-11 Ben SoaresJAL-3949 fixed failing commandlinetests due to more... commit | commitdiff | tree | snapshot
2022-02-11 Ben SoaresJAL-3949 added Java Console autoscrolling help paragraph commit | commitdiff | tree | snapshot
2022-02-11 Ben SoaresJAL-3949 read ~/.jalview_properties before initialising... commit | commitdiff | tree | snapshot
2022-02-11 Ben SoaresMerge branch 'develop' into update/JAL-3949_abstracted_... commit | commitdiff | tree | snapshot
2022-02-11 Ben SoaresJAL-3949 Complete new abstracted logging framework... commit | commitdiff | tree | snapshot
2022-02-10 Jim ProcterMerge branch 'bug/JAL-3523_cwd_not_preserved' into... commit | commitdiff | tree | snapshot
2022-02-07 Jim ProcterJAL-3186 remove ‘Variable Colour’ from the sequence... commit | commitdiff | tree | snapshot
2022-02-04 Ben SoaresJAL-3949 An attempt at converting to Log4j 2 -- no... commit | commitdiff | tree | snapshot
2022-02-04 Jim ProcterMerge branch 'bug/JAL-3806_mappingCoversSequence_for211... bug/JAL-3806_without_shared_DS_for_2_11_2 commit | commitdiff | tree | snapshot
2022-02-04 Jim ProcterJAL-3806 JAL-3725 update tests since CDS mappings now... commit | commitdiff | tree | snapshot
2022-02-04 Jim ProcterJAL-3806 require mapping extent covers both sequence... commit | commitdiff | tree | snapshot
2022-02-03 Ben SoaresJAL-3949 upgraded log4j to 2.17.1 (no actual known... commit | commitdiff | tree | snapshot
2022-02-03 Jim ProcterJAL-3806 use the covers() test for each selected sequen... commit | commitdiff | tree | snapshot
2022-02-03 Jim ProcterJAL-3806 use same logic as for mouse over highlighting... commit | commitdiff | tree | snapshot
2022-02-03 Jim ProcterJAL-3806 todo - problem seems to be Protein:Many CDS... commit | commitdiff | tree | snapshot
2022-02-03 Jim ProcterJAL-2305 comments re testFindXrefSequences_withFetch... commit | commitdiff | tree | snapshot
2022-01-28 Ben SoaresMerge branch 'develop' into improvement/JAL-3420_match_... commit | commitdiff | tree | snapshot
2022-01-28 Ben Soaresnew jvl_file svg, png, ico and icns files, and changed... commit | commitdiff | tree | snapshot
2022-01-28 Jim ProcterJAL-3137 tests are for linux only commit | commitdiff | tree | snapshot
2022-01-28 Jim ProcterMerge branch 'merge/develop_JAL-3725' into develop commit | commitdiff | tree | snapshot
2022-01-27 Jim ProcterMerge branch 'bug/JAL-3633_read_proxy_settings_from_jal... commit | commitdiff | tree | snapshot
2022-01-26 Jim ProcterJAL-3763 (for whatever reason) need to increase timeout... commit | commitdiff | tree | snapshot
2022-01-26 Jim ProcterJAL-3746 note about adding JAL-3700,JAL-3751,JAL-3763... commit | commitdiff | tree | snapshot
2022-01-26 Jim ProcterMerge branch 'merge/develop_task/JAL-3763_newDatasetFor... commit | commitdiff | tree | snapshot
2022-01-26 Jim ProcterJAL-3763 (for whatever reason) need to increase timeout... merge/develop_task/JAL-3763_newDatasetForCds commit | commitdiff | tree | snapshot
2022-01-26 Jim ProcterMerge branch 'task/JAL-3763_newDatasetForCds' into... commit | commitdiff | tree | snapshot
2022-01-26 gmungocJAL-3806 (2.11.2 version) more lax allowance (3 positio... commit | commitdiff | tree | snapshot
2022-01-26 Jim ProcterJAL-3806 JAL-3725 propagate relaxed criteria for stop... commit | commitdiff | tree | snapshot
2022-01-26 gmungocJAL-3725 restrict mapped virtual feature location to... commit | commitdiff | tree | snapshot
2022-01-26 gmungocJAL-3725 helper methods for computing mapped feature... commit | commitdiff | tree | snapshot
2022-01-26 gmungocJAL-3725 exclude stop codon from CDS-to-protein mapping commit | commitdiff | tree | snapshot
2022-01-18 Jim ProcterJAL-3940 update 2.11.2 release notes for 2.11.1.7 patch... commit | commitdiff | tree | snapshot
2022-01-17 Jim ProcterJAL-3940 update 2.11.2 release notes for 2.11.1.7 patch... commit | commitdiff | tree | snapshot
2022-01-17 Jim ProcterJAL-3746 possible release date 1st Feb 2022 commit | commitdiff | tree | snapshot
2022-01-17 Jim ProcterJAL-3746 Release notes for patch JAL-3702 JAL-3915 commit | commitdiff | tree | snapshot
2022-01-17 Jim ProcterMerge branch 'bug/JAL-3703_saving_a_file_in_Windows_10_... commit | commitdiff | tree | snapshot
2022-01-12 Ben SoaresJAL-3703 Test that fails in Windows only, and only... commit | commitdiff | tree | snapshot
2022-01-11 Ben SoaresJAL-3703 fix Gff3 shared InputStream with embedded... commit | commitdiff | tree | snapshot
2022-01-11 Ben Soaresclose filehandles straight after parse, without setting... commit | commitdiff | tree | snapshot
2022-01-10 Ben SoaresJAL-3937 enable AIA download of intermediate certificat... commit | commitdiff | tree | snapshot
2022-01-06 Jim ProcterJAL-3746 update release history for 2.11.1.5 and 2... commit | commitdiff | tree | snapshot
2022-01-06 Jim ProcterMerge branch 'critical/JAL-3933_log4j_update_for_develo... commit | commitdiff | tree | snapshot
2021-12-22 Ben SoaresMerge branch 'develop' into critical/JAL-3933_log4j_upd... commit | commitdiff | tree | snapshot
2021-12-22 Ben SoaresJAL-3934 updated log4j from 2.16.0 to 2.17.0 commit | commitdiff | tree | snapshot
2021-12-15 Ben SoaresJAL-3933 updated THIRDPARTYLIBS commit | commitdiff | tree | snapshot
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
2021-12-13 Jim ProcterJAL-3829 isCanonical should by default be false - ensur... commit | commitdiff | tree | snapshot
2021-12-13 Jim ProcterJAL-3855 JAL-3829 don’t need to make up alphafold model... commit | commitdiff | tree | snapshot
2021-12-13 Jim ProcterJAL-3929 preserve lowercase pdbid in group name for... commit | commitdiff | tree | snapshot
2021-12-08 Jim ProcterMerge branch 'to_merge/r2_11_2/JAL-3904_improved_alignp... commit | commitdiff | tree | snapshot
2021-12-08 Jim ProcterJAL-3551 pymol docs - work in progress commit | commitdiff | tree | snapshot
2021-12-08 Jim ProcterJAL-3929 don’t use the url encoded pdbId in feature... commit | commitdiff | tree | snapshot
2021-12-08 Jim ProcterJAL-3616 update messages/tooltips/menu items to use... commit | commitdiff | tree | snapshot
2021-12-08 Jim ProcterJAL-3551 JAL-3931 view pymol commands/responses in... commit | commitdiff | tree | snapshot
2021-12-08 Jim ProcterJAL-3931 remove % and - from ids so Pymol doesn’t strip... commit | commitdiff | tree | snapshot
2021-12-08 Jim ProcterJAL-3929 URLencode pdbid to remove problematic characte... commit | commitdiff | tree | snapshot
2021-12-07 Ben SoaresJAL-3930 Added a customizedId="JALVIEW" to launcher... commit | commitdiff | tree | snapshot
2021-12-02 Jim ProcterJAL-3904 use new AlignPanel API method commit | commitdiff | tree | snapshot
2021-12-02 Jim ProcterJAL-3904 simple method to make an alignPanel the curren... 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 gmungocJAL-3725 restrict mapped virtual feature location to... commit | commitdiff | tree | snapshot
2021-10-01 gmungocJAL-3725 helper methods for computing mapped feature... commit | commitdiff | tree | snapshot
2021-10-01 gmungocJAL-3725 exclude stop codon from CDS-to-protein mapping commit | commitdiff | tree | snapshot
2021-10-01 Jim ProcterJAL-3616 show name of structure viewer in ‘new view... commit | commitdiff | tree | snapshot
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