jalview.git
2022-02-14 Jim ProcterJAL-3956 - PDBEntry objects constructed from 3D-Beacons...
2022-02-12 Jim ProcterMerge branch 'update/JAL-3949_jalview_bin_Console_to_cu...
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
2022-02-11 Jim ProcterJAL-3949 increase command line ops test timeout
2022-02-11 Jim ProcterJAL-3949 ensure Jalview command line ops setup actually...
2022-02-11 Jim ProcterMerge branch 'update/JAL-3949_jalview_bin_Console_to_cu...
2022-02-11 Jim ProcterJAL-3931 fix - escape % symbols after urlencoding
2022-02-11 Ben SoaresMerge branch 'update/JAL-3949_jalview_bin_Console_to_cu...
2022-02-11 Ben SoaresJLogger loglevel check on whether to call the actual...
2022-02-11 Jim ProcterJAL-3949 - refactor logging from jalview.bin.Cache...
2022-02-11 Ben SoaresJAL-3949 fixed failing commandlinetests due to more...
2022-02-11 Ben SoaresJAL-3949 added Java Console autoscrolling help paragraph
2022-02-11 Ben SoaresJAL-3949 read ~/.jalview_properties before initialising...
2022-02-11 Ben SoaresMerge branch 'develop' into update/JAL-3949_abstracted_...
2022-02-11 Ben SoaresJAL-3949 Complete new abstracted logging framework...
2022-02-10 Jim ProcterMerge branch 'bug/JAL-3523_cwd_not_preserved' into...
2022-02-07 Jim ProcterJAL-3186 remove ‘Variable Colour’ from the sequence...
2022-02-04 Ben SoaresJAL-3949 An attempt at converting to Log4j 2 -- no...
2022-02-04 Jim ProcterMerge branch 'bug/JAL-3806_mappingCoversSequence_for211... bug/JAL-3806_without_shared_DS_for_2_11_2
2022-02-04 Jim ProcterJAL-3806 JAL-3725 update tests since CDS mappings now...
2022-02-04 Jim ProcterJAL-3806 require mapping extent covers both sequence...
2022-02-03 Ben SoaresJAL-3949 upgraded log4j to 2.17.1 (no actual known...
2022-02-03 Jim ProcterJAL-3806 use the covers() test for each selected sequen...
2022-02-03 Jim ProcterJAL-3806 use same logic as for mouse over highlighting...
2022-02-03 Jim ProcterJAL-3806 todo - problem seems to be Protein:Many CDS...
2022-02-03 Jim ProcterJAL-2305 comments re testFindXrefSequences_withFetch...
2022-01-28 Ben SoaresMerge branch 'develop' into improvement/JAL-3420_match_...
2022-01-28 Ben Soaresnew jvl_file svg, png, ico and icns files, and changed...
2022-01-28 Jim ProcterJAL-3137 tests are for linux only
2022-01-28 Jim ProcterMerge branch 'merge/develop_JAL-3725' into develop
2022-01-27 Jim ProcterMerge branch 'bug/JAL-3633_read_proxy_settings_from_jal...
2022-01-26 Jim ProcterJAL-3763 (for whatever reason) need to increase timeout...
2022-01-26 Jim ProcterJAL-3746 note about adding JAL-3700,JAL-3751,JAL-3763...
2022-01-26 Jim ProcterMerge branch 'merge/develop_task/JAL-3763_newDatasetFor...
2022-01-26 Jim ProcterJAL-3763 (for whatever reason) need to increase timeout... merge/develop_task/JAL-3763_newDatasetForCds
2022-01-26 Jim ProcterMerge branch 'task/JAL-3763_newDatasetForCds' into...
2022-01-26 gmungocJAL-3806 (2.11.2 version) more lax allowance (3 positio...
2022-01-26 Jim ProcterJAL-3806 JAL-3725 propagate relaxed criteria for stop...
2022-01-26 gmungocJAL-3725 restrict mapped virtual feature location to...
2022-01-26 gmungocJAL-3725 helper methods for computing mapped feature...
2022-01-26 gmungocJAL-3725 exclude stop codon from CDS-to-protein mapping
2022-01-18 Jim ProcterJAL-3940 update 2.11.2 release notes for 2.11.1.7 patch...
2022-01-17 Jim ProcterJAL-3940 update 2.11.2 release notes for 2.11.1.7 patch...
2022-01-17 Jim ProcterJAL-3746 possible release date 1st Feb 2022
2022-01-17 Jim ProcterJAL-3746 Release notes for patch JAL-3702 JAL-3915
2022-01-17 Jim ProcterMerge branch 'bug/JAL-3703_saving_a_file_in_Windows_10_...
2022-01-12 Ben SoaresJAL-3703 Test that fails in Windows only, and only...
2022-01-11 Ben SoaresJAL-3703 fix Gff3 shared InputStream with embedded...
2022-01-11 Ben Soaresclose filehandles straight after parse, without setting...
2022-01-10 Ben SoaresJAL-3937 enable AIA download of intermediate certificat...
2022-01-06 Jim ProcterJAL-3746 update release history for 2.11.1.5 and 2...
2022-01-06 Jim ProcterMerge branch 'critical/JAL-3933_log4j_update_for_develo...
2021-12-22 Ben SoaresMerge branch 'develop' into critical/JAL-3933_log4j_upd...
2021-12-22 Ben SoaresJAL-3934 updated log4j from 2.16.0 to 2.17.0
2021-12-15 Ben SoaresJAL-3933 updated THIRDPARTYLIBS
2021-12-15 Ben SoaresJAL-3933 updated THIRDPARTYLIBS
2021-12-15 Jim ProcterJAL-3933 remove obsolete Castor logging configuration
2021-12-15 Jim ProcterJAL-3933 configure root logger console appender to...
2021-12-14 Ben SoaresJAL-3933 updated log4j and slf4j jars with log4j1.2...
2021-12-13 Jim ProcterJAL-3829 isCanonical should by default be false - ensur...
2021-12-13 Jim ProcterJAL-3855 JAL-3829 don’t need to make up alphafold model...
2021-12-13 Jim ProcterJAL-3929 preserve lowercase pdbid in group name for...
2021-12-08 Jim ProcterMerge branch 'to_merge/r2_11_2/JAL-3904_improved_alignp...
2021-12-08 Jim ProcterJAL-3551 pymol docs - work in progress
2021-12-08 Jim ProcterJAL-3929 don’t use the url encoded pdbId in feature...
2021-12-08 Jim ProcterJAL-3616 update messages/tooltips/menu items to use...
2021-12-08 Jim ProcterJAL-3551 JAL-3931 view pymol commands/responses in...
2021-12-08 Jim ProcterJAL-3931 remove % and - from ids so Pymol doesn’t strip...
2021-12-08 Jim ProcterJAL-3929 URLencode pdbid to remove problematic characte...
2021-12-07 Ben SoaresJAL-3930 Added a customizedId="JALVIEW" to launcher...
2021-12-02 Jim ProcterJAL-3904 use new AlignPanel API method
2021-12-02 Jim ProcterJAL-3904 simple method to make an alignPanel the curren...
2021-11-29 Ben SoaresJAL-3594 correct Jalview Develop logo SVG added in...
2021-11-19 Jim ProcterJAL-3926 disable autosearch by default
2021-11-08 Jim ProcterJAL-3855 verify pdb suffix is preserved when locally...
2021-11-08 Jim ProcterJAL-3855 JAL-1731 reuse the StructureViewer.fetchPdbFil...
2021-11-08 Jim ProcterJAL-3855 try harder to ignore DNA/RNA only structures...
2021-11-08 Jim ProcterJAL-3921 wait around until session file has been written
2021-11-05 Jim ProcterJAL-3829 remove duplicate IDs in 3DBeacons generated...
2021-11-05 Jim ProcterJAL-3829 format and tidy up unused code
2021-11-05 Jim ProcterJAL-3919 use model format field to ensure we get the...
2021-11-05 Jim ProcterJAL-3875 fully reset filter combo-box when fetch 3d...
2021-11-05 Ben SoaresJAL-3746 Updated help docs for 3D-Beacons. Added and...
2021-11-03 Jim ProcterJAL-3915 JAL-3746 documentation for removed rnaview...
2021-11-03 Jim ProcterJAL-3916 TODO for improved selection of covering structures
2021-11-03 Jim ProcterJAL-3916 TODO for improved selection of covering structures
2021-11-03 Jim ProcterJAL-3915 remove RNAview opts from preferences. Still...
2021-11-02 Jim ProcterMerge branch 'develop' of https://source.jalview.org...
2021-11-02 Jim ProcterJAL-3875 test case and patch to verify the query 3d...
2021-11-01 Ben SoaresJAL-3907 changed two commented out lines to reflect...
2021-11-01 Ben SoaresJAL-3907 added creation of symbolic links to workaround...
2021-10-26 Ben SoaresJAL-3907 adjusted download_jdks.sh and download_jres...
2021-10-18 Jim ProcterMerge branch 'bug/r2_11_2/JAL-3904_structureviewermenu...
2021-10-18 Jim ProcterJAL-3905 Fix: wait for response when sending mouseovers... bug/r2_11_2/JAL-3904_structureviewermenu
2021-10-18 Jim ProcterJAL-3904 override buildActionMenu to add in additional...
2021-10-18 Jim ProcterJAL-3904 failing test
2021-10-01 gmungocJAL-3725 restrict mapped virtual feature location to...
2021-10-01 gmungocJAL-3725 helper methods for computing mapped feature...
2021-10-01 gmungocJAL-3725 exclude stop codon from CDS-to-protein mapping
2021-10-01 Jim ProcterJAL-3616 show name of structure viewer in ‘new view...
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