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Merge branch 'bug/JAL-3980_JAL-3981_tooltips_sequence_details' into develop
[jalview.git] / src /
2022-04-05 Jim ProcterMerge branch 'bug/JAL-3980_JAL-3981_tooltips_sequence_d... tree | commitdiff
2022-03-31 Jim ProcterJAL-3985 formatting tree | commitdiff
2022-03-31 Jim ProcterJAL-3985 split PDB id queries into multiple queries... tree | commitdiff
2022-03-30 Jim ProcterMerge branch 'patch/JAL-3976_3dbeaconsnull' into develop tree | commitdiff
2022-03-30 Jim ProcterJAL-360 JAL-3975 update parent for text colour dialog... tree | commitdiff
2022-03-30 Ben SoaresJAL-360 JAL-3975 make AlignFrame the parent of FeatureE... tree | commitdiff
2022-03-25 Jim ProcterJAL-3980 JAL-3979 TODOs bug/JAL-3980_JAL-3981_tooltips_sequence_details tree | commitdiff
2022-03-25 Jim ProcterJAL-3980 defensive copy - inefficient but fixes bug tree | commitdiff
2022-03-25 Jim ProcterJAL-3981 Additional line breaks - sort of helps tree | commitdiff
2022-03-24 Jim ProcterJAL-3981 strategic newlines to help speed up Java's... tree | commitdiff
2022-03-23 Jim ProcterJAL-3976 skip entries with null values when analyzing tree | commitdiff
2022-03-08 Jim ProcterJAL-3746 apply copyright to source tree | commitdiff
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0 tree | commitdiff
2022-03-08 Jim ProcterJAL-3108 updated Ensembl client and model species names tree | commitdiff
2022-03-08 Ben SoaresJAL-3103 Removed code and unused widgets for defaultBrowser tree | commitdiff
2022-03-08 Ben SoaresJAL-3103 Remove BrowserLauncher2 and use Desktop.browse... tree | commitdiff
2022-03-08 Ben SoaresJAL-3103 Put jalview.jar first in getdown for .properti... tree | commitdiff
2022-03-07 Ben SoaresJAL-3103 Switched to (a wrapper around) BrowserLauncher2 tree | commitdiff
2022-03-04 Jim ProcterJAL-3746 JAL-3811 document SHOW_JWS2_SERVICES user... tree | commitdiff
2022-03-04 Jim ProcterJAL-3746 JAL-3812 new argument ‘-nohtmltemplates’ and... tree | commitdiff
2022-03-04 Jim ProcterJAL-3746 JAL-3813 NOIDENTIFIERSSERVICE preference disab... tree | commitdiff
2022-03-04 Jim ProcterJAL-3746 JAL-3814 don’t automatically launch the news... tree | commitdiff
2022-03-04 Jim ProcterJAL-3746 JAL-3814 NONEWS property tree | commitdiff
2022-03-02 Jim ProcterMerge branch 'benreview/JAL-3691_for_2_11_2_getdownrebu... tree | commitdiff
2022-03-02 Jim ProcterJAL-3619 fix up error messages and try to bail quietly... tree | commitdiff
2022-03-02 Jim ProcterJAL-3619 fix up warning message and minimal patch to... tree | commitdiff
2022-02-17 Jim ProcterJAL-3959 add key retrieval urls that support CORS neede... tree | commitdiff
2022-02-17 Jim ProcterJAL-3691 patch toUpper/toLower to use Locale.ROOT for... tree | commitdiff
2022-02-16 Jim ProcterJAL-3551 - wrap pair_fit with undo_disable and undo_enable tree | commitdiff
2022-02-16 Jim ProcterJAL-3837 GPL license on splashscreen (finally !) and... tree | commitdiff
2022-02-16 Jim ProcterJAL-3949 report Pymol XMLRPC port via log.info tree | commitdiff
2022-02-15 Jim ProcterJAL-1761 backbone type parameter for configuring which... tree | commitdiff
2022-02-15 Jim ProcterJAL-1761 need to pass molecule type when generating... tree | commitdiff
2022-02-15 Jim ProcterJAL-3906 use indicate to highlight current mousedOver... tree | commitdiff
2022-02-14 Jim ProcterMerge branch 'task/r_2_11_2/JAL-3956_alphaFill_authorit... tree | commitdiff
2022-02-14 Jim ProcterJAL-3551 tree | commitdiff
2022-02-14 Jim ProcterJAL-3956 - PDBEntry objects constructed from 3D-Beacons... tree | commitdiff
2022-02-11 Jim ProcterMerge branch 'update/JAL-3949_jalview_bin_Console_to_cu... tree | commitdiff
2022-02-11 Jim ProcterJAL-3931 fix - escape % symbols after urlencoding tree | commitdiff
2022-02-11 Ben SoaresMerge branch 'update/JAL-3949_jalview_bin_Console_to_cu... tree | commitdiff
2022-02-11 Ben SoaresJLogger loglevel check on whether to call the actual... tree | commitdiff
2022-02-11 Jim ProcterJAL-3949 - refactor logging from jalview.bin.Cache... tree | commitdiff
2022-02-11 Ben SoaresJAL-3949 read ~/.jalview_properties before initialising... tree | commitdiff
2022-02-11 Ben SoaresMerge branch 'develop' into update/JAL-3949_abstracted_... tree | commitdiff
2022-02-11 Ben SoaresJAL-3949 Complete new abstracted logging framework... tree | commitdiff
2022-02-07 Jim ProcterJAL-3186 remove ‘Variable Colour’ from the sequence... tree | commitdiff
2022-02-04 Ben SoaresJAL-3949 An attempt at converting to Log4j 2 -- no... tree | commitdiff
2022-02-04 Jim ProcterMerge branch 'bug/JAL-3806_mappingCoversSequence_for211... bug/JAL-3806_without_shared_DS_for_2_11_2 tree | commitdiff
2022-02-04 Jim ProcterJAL-3806 require mapping extent covers both sequence... tree | commitdiff
2022-02-03 Jim ProcterJAL-3806 use the covers() test for each selected sequen... tree | commitdiff
2022-02-03 Jim ProcterJAL-3806 use same logic as for mouse over highlighting... tree | commitdiff
2022-02-03 Jim ProcterJAL-3806 todo - problem seems to be Protein:Many CDS... tree | commitdiff
2022-02-03 Jim ProcterJAL-2305 comments re testFindXrefSequences_withFetch... tree | commitdiff
2022-01-28 Jim ProcterMerge branch 'merge/develop_JAL-3725' into develop tree | commitdiff
2022-01-27 Jim ProcterMerge branch 'bug/JAL-3633_read_proxy_settings_from_jal... tree | commitdiff
2022-01-26 Jim ProcterMerge branch 'task/JAL-3763_newDatasetForCds' into... tree | commitdiff
2022-01-26 gmungocJAL-3806 (2.11.2 version) more lax allowance (3 positio... tree | commitdiff
2022-01-26 Jim ProcterJAL-3806 JAL-3725 propagate relaxed criteria for stop... tree | commitdiff
2022-01-26 gmungocJAL-3725 restrict mapped virtual feature location to... tree | commitdiff
2022-01-26 gmungocJAL-3725 helper methods for computing mapped feature... tree | commitdiff
2022-01-26 gmungocJAL-3725 exclude stop codon from CDS-to-protein mapping tree | commitdiff
2022-01-17 Ben SoaresJAL-3703 fix Gff3 shared InputStream with embedded... tree | commitdiff
2022-01-17 Ben Soaresclose filehandles straight after parse, without setting... tree | commitdiff
2022-01-11 Ben SoaresJAL-3703 fix Gff3 shared InputStream with embedded... tree | commitdiff
2022-01-11 Ben Soaresclose filehandles straight after parse, without setting... tree | commitdiff
2022-01-10 Ben SoaresJAL-3937 enable AIA download of intermediate certificat... tree | commitdiff
2022-01-10 Ben SoaresJAL-3937 enable AIA download of intermediate certificat... tree | commitdiff
2021-12-22 Ben SoaresMerge branch 'develop' into critical/JAL-3933_log4j_upd... tree | commitdiff
2021-12-15 Jim ProcterJAL-3933 remove obsolete Castor logging configuration tree | commitdiff
2021-12-15 Jim ProcterJAL-3933 configure root logger console appender to... tree | commitdiff
2021-12-15 Jim ProcterJAL-3933 remove obsolete Castor logging configuration tree | commitdiff
2021-12-15 Jim ProcterJAL-3933 configure root logger console appender to... tree | commitdiff
2021-12-14 Ben SoaresJAL-3933 updated log4j and slf4j jars with log4j1.2... tree | commitdiff
2021-12-14 Ben SoaresJAL-3933 Updated log4j jars with log4j-2.16.0 and compa... tree | commitdiff
2021-12-13 Jim ProcterJAL-3829 isCanonical should by default be false - ensur... tree | commitdiff
2021-12-13 Jim ProcterJAL-3855 JAL-3829 don’t need to make up alphafold model... tree | commitdiff
2021-12-13 Jim ProcterJAL-3929 preserve lowercase pdbid in group name for... tree | commitdiff
2021-12-08 Jim ProcterJAL-3929 don’t use the url encoded pdbId in feature... tree | commitdiff
2021-12-08 Jim ProcterJAL-3616 update messages/tooltips/menu items to use... tree | commitdiff
2021-12-08 Jim ProcterJAL-3551 JAL-3931 view pymol commands/responses in... tree | commitdiff
2021-12-08 Jim ProcterJAL-3931 remove % and - from ids so Pymol doesn’t strip... tree | commitdiff
2021-12-08 Jim ProcterJAL-3929 URLencode pdbid to remove problematic characte... tree | commitdiff
2021-12-02 Jim ProcterJAL-3904 use new AlignPanel API method tree | commitdiff
2021-12-02 Jim ProcterJAL-3904 simple method to make an alignPanel the curren... tree | commitdiff
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
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