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JAL-629 example files from nf-core
[jalview.git] / src /
2020-08-31 gmungocJAL-1191 reduce logging level for warnings tree | commitdiff
2020-08-27 Ben SoaresMerge branch 'releases/Release_2_11_1_Branch' into... merge/JAL_1842+JAL-3509+releases_Release_2_11_1_Branch tree | commitdiff
2020-08-25 Jim ProcterJAL-3671 hardwire log4j.root logger to INFO to supress... tree | commitdiff
2020-08-24 gmungocJAL-3018 updated reviewed REST version to 12.0 tree | commitdiff
2020-08-21 Jim ProcterJAL-3675 2.11.1.1 java 8 compatible patch for JAL-3615... tree | commitdiff
2020-08-21 Jim ProcterJAL-3615 code tidy, improve unit test tree | commitdiff
2020-08-20 Ben SoaresJAL-2656 better read of (potential) gzip magic bytes tree | commitdiff
2020-08-18 gmungocJAL-2656 Java 8 compatible test for gzipped, refactored... tree | commitdiff
2020-08-18 gmungocJAL-3692 parse multiline CDS location correctly tree | commitdiff
2020-08-17 Jim ProcterMerge branch 'patch/JAL-3691_No_score_models_available... tree | commitdiff
2020-08-17 Jim ProcterMerge branch 'patch/JAL-3561_JAL-3660_fileformatexport_... tree | commitdiff
2020-08-17 Jim ProcterJAL-3490 don't init the combo box's history cache for... tree | commitdiff
2020-08-17 Jim ProcterJAL-3490 merged with 2.11.2 develop tree | commitdiff
2020-08-17 Jim ProcterMerge branch 'patch/Release_2_11_1_Branch_patch_JAL... tree | commitdiff
2020-08-17 Jim ProcterMerge branch 'task/JAL-3597memoryLeakTest' into develop tree | commitdiff
2020-08-17 Jim ProcterMerge branch 'patch/JAL-3597_for_Release_2_11_1_Branch... tree | commitdiff
2020-08-14 Ben SoaresJAL-3676 More explicit tooltip about resetting log... tree | commitdiff
2020-08-13 gmungocJAL-3597 additional references nulled, bug in test... tree | commitdiff
2020-08-12 Ben SoaresJAL-3676 Removed BACKUPFILESPRESETENTRY logging for... tree | commitdiff
2020-08-12 Ben SoaresMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2020-08-12 Jim ProcterMerge branch 'task/JAL-3608_property_set_laf_and_tests... tree | commitdiff
2020-08-12 Ben SoaresJAL-3608 Changes from code review CR-JAL-236 tree | commitdiff
2020-08-11 Jim ProcterJAL-3673 make sure font metrics are updated if dealing... tree | commitdiff
2020-08-11 Jim ProcterMerge branch 'bug/JAL-2983negativeSliderMin' into relea... tree | commitdiff
2020-08-11 gmungocJAL-3371 more fine-grained slider; set Param slider... tree | commitdiff
2020-08-10 gmungocJAL-3490 match count independent of contiguous matches... patch/Release_2_11_1_Branch_patch_JAL-3490 tree | commitdiff
2020-08-10 Jim ProcterJAL-3691 toUpperCase(Locale.ROOT) for all standard... tree | commitdiff
2020-08-10 Jim ProcterMerge branch 'releases/Release_2_11_1_Branch' into... tree | commitdiff
2020-08-10 Jim ProcterJAL-3628 JAL-3708 call Cache.initLogger() before using... tree | commitdiff
2020-08-09 Ben SoaresJAL-3691 Changed .toUppoerCase().startsWith(...) to... tree | commitdiff
2020-08-05 Ben SoaresJAL-3691 Changed .toUppoerCase().startsWith(...) to... tree | commitdiff
2020-08-05 Jim ProcterMerge branch 'patch/JAL-3692enaEndpointFlatfile' into... tree | commitdiff
2020-08-05 gmungocJAL-3692 parse multiline feature qualifiers and escaped... tree | commitdiff
2020-08-05 gmungocJAL-3692 parse multiline feature qualifiers and escaped... tree | commitdiff
2020-08-05 Jim ProcterMerge branch 'merge/JAL-3628+JAL-3608+JAL-3609+JAL... tree | commitdiff
2020-08-05 gmungocJAL-3700 fix for propagation of sort commands tree | commitdiff
2020-08-04 Ben SoaresJAL-3477 Added -help text for jvmmempc and jvmmemmax... tree | commitdiff
2020-08-04 Ben SoaresJAL-3477 Added -help text for jvmmempc and jvmmemmax... tree | commitdiff
2020-08-03 gmungocJAL-3700 check for 'covering' mapping when matching... tree | commitdiff
2020-08-03 gmungocJAL-3692 set CDS /product as EMBLCDSPROTEIN description tree | commitdiff
2020-08-03 gmungocJAL-3692 refactor/complete parsing, more unit test... tree | commitdiff
2020-08-03 gmungocJAL-3692 parse DE for description, and other refactoring... tree | commitdiff
2020-08-03 gmungocJAL-3692 unit test (J03321), fixes, dbrefs; todo: prote... tree | commitdiff
2020-08-03 gmungocJAL-3692 EMBL flatfile fetcher / parser (todo: CDS... tree | commitdiff
2020-08-03 Jim ProcterMerge branch 'bug/JAL-2983negativeSliderMin' into develop tree | commitdiff
2020-07-31 Ben SoaresMerge branch 'releases/Release_2_11_1_Branch' into... tree | commitdiff
2020-07-29 Jim ProcterMerge branch 'bug/JAL-2983negativeSliderMin' into relea... tree | commitdiff
2020-07-29 Jim ProcterJAL-3371 JAL-2983 don't modify 'extent' of slider ... tree | commitdiff
2020-07-28 Jim ProcterMerge branch 'feature/JAL-3615gzipXfam' into develop tree | commitdiff
2020-07-28 Jim ProcterJAL-3615 JAL-2656 missing import after cherrypick tree | commitdiff
2020-07-28 Jim ProcterJAL-2656 recognise non-HTTP URI input streams as gzippe... tree | commitdiff
2020-07-28 Jim ProcterJAL-2656 recognise Gzipped file input streams by their... tree | commitdiff
2020-07-28 Jim ProcterJAL-2656 recognise non-HTTP URI input streams as gzippe... tree | commitdiff
2020-07-28 Jim ProcterJAL-2656 recognise Gzipped file input streams by their... tree | commitdiff
2020-07-27 gmungocJAL-2656 JAL-3615 check response headers to test for... tree | commitdiff
2020-07-27 gmungocJAL-3615 used gzip endpoints for Pfam and Rfam tree | commitdiff
2020-07-27 Jim ProcterMerge branch 'bug/JAL-2983negativeSliderMin' into relea... tree | commitdiff
2020-07-27 gmungocJAL-3692 set CDS /product as EMBLCDSPROTEIN description tree | commitdiff
2020-07-27 gmungocJAL-3692 refactor/complete parsing, more unit test... tree | commitdiff
2020-07-27 gmungocJAL-3621 corrected sequence feature sort and test tree | commitdiff
2020-07-27 gmungocJAL-3621 update to intervalstore v1.1 tree | commitdiff
2020-07-27 Jim ProcterJAL-3697 show total number of features not shown tree | commitdiff
2020-07-27 Jim ProcterJAL-3696 log the error message from the exception to... tree | commitdiff
2020-07-27 Jim ProcterJAL-3697 show total number of features not shown tree | commitdiff
2020-07-27 Jim ProcterJAL-3696 log the error message from the exception to... tree | commitdiff
2020-07-24 gmungocJAL-3692 parse DE for description, and other refactoring... tree | commitdiff
2020-07-22 gmungocJAL-3692 unit test (J03321), fixes, dbrefs; todo: prote... tree | commitdiff
2020-07-21 gmungocJAL-3692 EMBL flatfile fetcher / parser (todo: CDS... tree | commitdiff
2020-07-14 gmungocJAL-1421 last change tidied up properly tree | commitdiff
2020-07-14 gmungocJAL-1421 types added to nameHash and nodeHash maps tree | commitdiff
2020-07-14 gmungocJAL-3597 additional references nulled, bug in test... tree | commitdiff
2020-07-08 Ben SoaresMerge branch 'releases/Release_2_11_1_Branch' into... tree | commitdiff
2020-07-08 Ben SoaresMerge branch 'task/JAL-3609_HiDPI_support_in_java'... tree | commitdiff
2020-07-07 Ben SoaresJAL-3608 Changes from code review CR-JAL-236 tree | commitdiff
2020-07-07 Ben SoaresJAL-3608 Changes from code review CR-JAL-236 tree | commitdiff
2020-07-07 Ben SoaresJAL-3608 ex stacktraces now go to Cache.log.debug tree | commitdiff
2020-07-07 Ben SoaresJAL-3628 System.out/err -> Cache.log.info/error tree | commitdiff
2020-07-07 Ben SoaresMerge branch 'bug/JAL-3628_Unable_to_save_update_to_exi... tree | commitdiff
2020-07-07 Ben SoaresJAL-3628 System.out/err -> Cache.log.info/error tree | commitdiff
2020-07-07 gmungocJAL-1424 streamlined message checker, corrected applet... tree | commitdiff
2020-07-07 Ben SoaresJAL-3628 Fixed oddly worded and non-formatted error... tree | commitdiff
2020-07-06 Ben SoaresJAL-3676 improvement for visual selection of console... tree | commitdiff
2020-07-06 gmungocJAL-3311 JAL-3141 JAL-3144 tidying obsolete message... tree | commitdiff
2020-07-06 Ben SoaresJAL-3628 improvement for visual selection of console... tree | commitdiff
2020-07-06 Ben SoaresJAL-3628 Fix for slightly incorrect boolean usage to... tree | commitdiff
2020-07-06 Ben SoaresJAL-3628 Even more Cache.log.debug statements tree | commitdiff
2020-07-04 Jim ProcterMerge branch 'merge/JAL-3609_and_JAL-3608' into release... tree | commitdiff
2020-07-04 Jim ProcterJAL-3638 don’t move cursor to next gap after moving... tree | commitdiff
2020-07-04 Jim ProcterJAL-3680 check whether a sequence selection exists... tree | commitdiff
2020-07-04 Jim ProcterJAL-3638 shift+arrow keys in cursor mode jumps cursor... tree | commitdiff
2020-07-04 Ben SoaresJAL-3628 More Cache.log.debug statements tree | commitdiff
2020-07-02 gmungocJAL-2656 JAL-3615 check response headers to test for... tree | commitdiff
2020-07-02 Ben SoaresJAL-3676 code review -- added non-listed Level into... tree | commitdiff
2020-07-02 gmungocJAL-3615 used gzip endpoints for Pfam and Rfam tree | commitdiff
2020-07-01 Ben SoaresMerge branch 'task/JAL-3608_property_set_laf_and_tests_... tree | commitdiff
2020-06-30 Ben SoaresJAL-3676 Added Log Level ComboBox and Copy to Clipboard... tree | commitdiff
2020-06-29 Jim ProcterMerge branch 'develop' of source.jalview.org/git/jalvie... tree | commitdiff
2020-06-29 Jim ProcterJAL-3493 clear search highlights when escape/deselect all tree | commitdiff
2020-06-29 Jim ProcterJAL-3493 clear search highlights when escape/deselect all tree | commitdiff
2020-06-29 gmungocJAL-3674 more finessed asynchronous structure commands tree | commitdiff
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