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jalview.git
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 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
2022-01-26 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 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
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