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JAL-4004 add the autogenerated whatsNew.html and releases.html to .gitignore
[jalview.git] / src /
2021-11-19 Jim ProcterJAL-3926 disable autosearch by default tree | commitdiff
2021-11-08 Jim ProcterJAL-3855 JAL-1731 reuse the StructureViewer.fetchPdbFil... tree | commitdiff
2021-11-08 Jim ProcterJAL-3855 try harder to ignore DNA/RNA only structures... tree | commitdiff
2021-11-08 Jim ProcterJAL-3921 wait around until session file has been written tree | commitdiff
2021-11-05 Jim ProcterJAL-3829 remove duplicate IDs in 3DBeacons generated... tree | commitdiff
2021-11-05 Jim ProcterJAL-3829 format and tidy up unused code tree | commitdiff
2021-11-05 Jim ProcterJAL-3919 use model format field to ensure we get the... tree | commitdiff
2021-11-05 Jim ProcterJAL-3875 fully reset filter combo-box when fetch 3d... tree | commitdiff
2021-11-03 Jim ProcterJAL-3916 TODO for improved selection of covering structures tree | commitdiff
2021-11-03 Jim ProcterJAL-3915 remove RNAview opts from preferences. Still... tree | commitdiff
2021-11-02 Jim ProcterJAL-3875 test case and patch to verify the query 3d... tree | commitdiff
2021-10-18 Jim ProcterJAL-3905 Fix: wait for response when sending mouseovers... bug/r2_11_2/JAL-3904_structureviewermenu tree | commitdiff
2021-10-18 Jim ProcterJAL-3904 override buildActionMenu to add in additional... tree | commitdiff
2021-10-18 Jim ProcterJAL-3904 failing test tree | commitdiff
2021-10-01 gmungocJAL-3725 restrict mapped virtual feature location to... tree | commitdiff
2021-10-01 gmungocJAL-3725 helper methods for computing mapped feature... tree | commitdiff
2021-10-01 gmungocJAL-3725 exclude stop codon from CDS-to-protein mapping tree | commitdiff
2021-10-01 Jim ProcterJAL-3616 show name of structure viewer in ‘new view... tree | commitdiff
2021-10-01 Jim ProcterJAL-3616 explicit configure external viewer config tree | commitdiff
2021-10-01 Jim ProcterJAL-3829 fetch 3D beacons now started by clicking butto... tree | commitdiff
2021-10-01 Jim ProcterMerge branch 'develop' into features/r2_11_2/JAL-3829_3... tree | commitdiff
2021-09-30 Ben SoaresJAL-1260 Added .gbk to GenBank extensions. Added GenBa... tree | commitdiff
2021-09-30 gmungocJAL-3371 more fine-grained slider; set Param slider... tree | commitdiff
2021-09-29 Ben SoaresJAL-3885 Made the database JComboBox have StringPair... tree | commitdiff
2021-09-29 Jim ProcterJAL-3884 squish alarming but harmless errors when unipr... tree | commitdiff
2021-09-29 Jim ProcterJAL-3881 split on any nonalphanumeric symbol (plus... tree | commitdiff
2021-09-29 Jim ProcterJAL-3829 report when 3d-beacons doesn’t provide any... tree | commitdiff
2021-09-24 Jim ProcterJAL-3829 open web page for 3d beacons structure by... features/r2_11_2/JAL-3829_3dbeacons tree | commitdiff
2021-09-24 Jim ProcterJAL-3829 right click to view popup menu to show link... tree | commitdiff
2021-09-24 Jim ProcterJAL-3829 abstract essential TDB metadata from the user... tree | commitdiff
2021-09-23 Jim ProcterJAL-3821 less ambiguous base class name for EMBL and... tree | commitdiff
2021-09-23 Jim ProcterJAL-3821 ported to refactored FlatFile parser tree | commitdiff
2021-09-23 Jim ProcterJAL-3692 JAL-3861 remove extra call to .parse() so... tree | commitdiff
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC... tree | commitdiff
2021-09-21 Jim ProcterMerge branch 'doc/JAL-3746_Release_2_11_2' into develop tree | commitdiff
2021-09-21 Jim ProcterMerge branch 'features/r2_11_2/JAL-3829_3dbeacons'... tree | commitdiff
2021-09-21 Jim ProcterJAL-3829 - callback finessing - leave DBRefFetcher... tree | commitdiff
2021-09-21 Jim ProcterJAL-3829 prefix PDBe filters with PDBe to make clear... tree | commitdiff
2021-09-21 Jim ProcterJAL-3829 alternative UX: need to select 3d-beacons... tree | commitdiff
2021-09-21 Jim ProcterJAL-3829 ignore the fake ID generated when a PDB format... tree | commitdiff
2021-09-20 Jim ProcterJAL-3829 tests need to wait for dialog to be closed... tree | commitdiff
2021-09-20 Jim ProcterJAL-3829 TDBeacons fetcher needs a sequence with at... tree | commitdiff
2021-09-20 Jim ProcterJAL-3829 throw the exception even if it has no message tree | commitdiff
2021-09-20 Jim ProcterJAL-3829 ensure nulls are not wildcards when retrieving... tree | commitdiff
2021-09-20 Jim ProcterJAL-3829 do better at detecting structure type, prompt... tree | commitdiff
2021-09-20 Jim ProcterJAL-3829 make sure structure data type reflects actual... tree | commitdiff
2021-09-20 Jim ProcterJAL-3829 store 3db metadata on PDBEntry so it can be... tree | commitdiff
2021-09-20 Jim ProcterJAL-3829 allow PDBEntry with file and ID with mismatchi... tree | commitdiff
2021-09-17 Ben SoaresMerge branch 'merge/develop_JAL-1260' into develop tree | commitdiff
2021-09-17 Ben SoaresJAL-1260 rudimentary parsing of LOCUS line to at least... tree | commitdiff
2021-09-17 Jim ProcterMerge branch 'develop' into features/r2_11_2/JAL-3829_3... tree | commitdiff
2021-09-17 Jim ProcterJAL-3079 JAL-3055 remember to reset font transform... tree | commitdiff
2021-09-17 gmungocJAL-1260 refactored multi-line qualifier separators tree | commitdiff
2021-09-17 gmungocJAL-1260 file formats and IdentifyFile updates for... tree | commitdiff
2021-09-17 gmungocJAL-1260 refactored GenBank (and EMBL) flat file parser tree | commitdiff
2021-09-17 Jim ProcterJAL-1260 FileFormat entry for EMBL/GENBANK: TODO: creat... tree | commitdiff
2021-09-17 Jim ProcterJAL-2226 transfer chain annotation when calcId, label... tree | commitdiff
2021-09-17 Jim ProcterJAL-2226 new method to search for annotation matching... tree | commitdiff
2021-09-17 Jim ProcterJAL-3829 belt and braces check to make sure there is... tree | commitdiff
2021-09-16 gmungocJAL-3779 apply properties to all groups with given... tree | commitdiff
2021-09-16 Ben SoaresJAL-3774 combined changes from bug/JAL-3774_splitFrameF... tree | commitdiff
2021-09-16 Jim ProcterMerge branch 'develop' into doc/JAL-3746_Release_2_11_2 tree | commitdiff
2021-09-16 Ben SoaresJAL-3739 (combined) commits from feature/JAL-3739_useFo... tree | commitdiff
2021-09-16 Jim ProcterJAL-3794 X and N are counted as DNA characters, but... tree | commitdiff
2021-09-16 gmungocJAL-3761 more consistent parameter naming tree | commitdiff
2021-09-16 gmungocJAL-3761 helper method reinstated to avoid code duplication tree | commitdiff
2021-09-16 gmungocJAL-3761 locateInFrom/To revised with tests; unused... tree | commitdiff
2021-09-16 gmungocJAL-3761 extra check that VCF feature is fully mappable... tree | commitdiff
2021-09-16 gmungocJAL-3761 debugged and working (but not tidied) locateIn... tree | commitdiff
2021-09-16 Ben SoaresJAL-3761 listToArray became rangeListToArray tree | commitdiff
2021-09-16 gmungocJAL-3761 locateInFrom2 work in progress commit tree | commitdiff
2021-09-15 gmungocJAL-3761 failing test, formatting, method renamed tree | commitdiff
2021-09-15 gmungocJAL-3751 only merge strictly contiguous ranges of mappings tree | commitdiff
2021-09-15 gmungocJAL-3788 synchronize concurrent findColour() and alignm... tree | commitdiff
2021-09-15 Ben SoaresJAL-3818 formatting tree | commitdiff
2021-09-15 gmungocJAL-3818 process Jmol callbacks in AWT thread tree | commitdiff
2021-09-15 Ben SoaresMerge branch 'develop' into merge/develop_ben2 tree | commitdiff
2021-09-15 Jim ProcterMerge branch 'Jalview-JS/bug/JAL-3762_URLparamsOverride... tree | commitdiff
2021-09-15 Jim ProcterJAL-3746 fix bad merge from 2.11.1.4/5 branch cherrypick tree | commitdiff
2021-09-15 Jim ProcterJAL-3741 http to https (and jar to jvp for exampleFile... tree | commitdiff
2021-09-15 Jim ProcterJAL-3638 JAL-3680 fix docs for Alt + Arrow LRUD in... tree | commitdiff
2021-09-15 Ben SoaresMerge branch 'develop' into merge/develop_ben2 tree | commitdiff
2021-09-14 Ben SoaresMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2021-09-14 Ben SoaresJAL-3521 Change grouped Jalview windows on linux taskba... tree | commitdiff
2021-09-14 Jim ProcterMerge branch 'features/r2_11_2/JAL-3829_3dbeacons'... tree | commitdiff
2021-09-14 Jim ProcterJAL-3551 - doc tweak tree | commitdiff
2021-09-14 Jim ProcterJAL-3855 JAL-3829 better checks on PDB or mmCIF file... tree | commitdiff
2021-09-14 Jim ProcterJAL-3829 JAL-3855 moved routing for retrieving structur... tree | commitdiff
2021-09-14 Jim ProcterJAL-3829 JAL-3855 ignore case when detecting alphafold ID tree | commitdiff
2021-09-14 Jim ProcterJAL-3855 detect an alphafold model and import its tempe... tree | commitdiff
2021-09-14 Jim ProcterJAL-3829 move mock query and responses to files tree | commitdiff
2021-09-14 Ben SoaresJAL-2422 Also look in ~/Applications for ChimeraX on... tree | commitdiff
2021-09-14 Jim ProcterMerge branch 'develop' into features/r2_11_2/JAL-3829_3... tree | commitdiff
2021-09-14 Jim ProcterJAL-3829 3d-beacons doesn’t work as a sequence source... tree | commitdiff
2021-09-14 Jim ProcterJAL-3829 avoid sending rubbish to PDBe search api tree | commitdiff
2021-09-14 Jim ProcterJAL-3829 some providers don’t provide model quality... tree | commitdiff
2021-09-14 Jim ProcterJAL-3829 allow multiple URL mocks and include P01308... tree | commitdiff
2021-09-14 Ben SoaresJAL-2422 More helpful highlighting/user guidance of... tree | commitdiff
2021-09-14 Ben SoaresJAL-2422 Fixed URL encoding of REST calls (broken paths... tree | commitdiff
2021-09-13 Ben SoaresMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
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