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Merge branch 'JAL-3878_ws-overhaul-3' into mmw/Release_2_12_ws_merge
[jalview.git]
/
src
/
2022-02-11
Jim Procter
JAL-3949 - refactor logging from jalview.bin.Cache...
tree
|
commitdiff
2022-02-11
Ben Soares
JAL-3949 read ~/.jalview_properties before initialising...
tree
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commitdiff
2022-02-11
Ben Soares
Merge branch 'develop' into update/JAL-3949_abstracted_...
tree
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commitdiff
2022-02-11
Ben Soares
JAL-3949 Complete new abstracted logging framework...
tree
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commitdiff
2022-02-07
Jim Procter
JAL-3186 remove ‘Variable Colour’ from the sequence...
tree
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commitdiff
2022-02-04
Ben Soares
JAL-3949 An attempt at converting to Log4j 2 -- no...
tree
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commitdiff
2022-02-04
Jim Procter
Merge branch 'bug/JAL-3806_mappingCoversSequence_for211...
bug/JAL-3806_without_shared_DS_for_2_11_2
tree
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commitdiff
2022-02-04
Jim Procter
JAL-3806 require mapping extent covers both sequence...
tree
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commitdiff
2022-02-03
Jim Procter
JAL-3806 use the covers() test for each selected sequen...
tree
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commitdiff
2022-02-03
Jim Procter
JAL-3806 use same logic as for mouse over highlighting...
tree
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commitdiff
2022-02-03
Jim Procter
JAL-3806 todo - problem seems to be Protein:Many CDS...
tree
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commitdiff
2022-02-03
Jim Procter
JAL-2305 comments re testFindXrefSequences_withFetch...
tree
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commitdiff
2022-01-28
Jim Procter
Merge branch 'merge/develop_JAL-3725' into develop
tree
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commitdiff
2022-01-28
Ben Soares
Merge branch 'develop' into JAL-3416_different_look_and...
tree
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commitdiff
2022-01-27
Jim Procter
Merge branch 'bug/JAL-3633_read_proxy_settings_from_jal...
tree
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commitdiff
2022-01-26
Jim Procter
Merge branch 'task/JAL-3763_newDatasetForCds' into...
tree
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commitdiff
2022-01-26
gmungoc
JAL-3806 (2.11.2 version) more lax allowance (3 positio...
tree
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commitdiff
2022-01-26
Jim Procter
JAL-3806 JAL-3725 propagate relaxed criteria for stop...
tree
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commitdiff
2022-01-26
gmungoc
JAL-3725 restrict mapped virtual feature location to...
tree
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commitdiff
2022-01-26
gmungoc
JAL-3725 helper methods for computing mapped feature...
tree
|
commitdiff
2022-01-26
gmungoc
JAL-3725 exclude stop codon from CDS-to-protein mapping
tree
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commitdiff
2022-01-17
Ben Soares
JAL-3703 fix Gff3 shared InputStream with embedded...
tree
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commitdiff
2022-01-17
Ben Soares
close filehandles straight after parse, without setting...
tree
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commitdiff
2022-01-11
Ben Soares
JAL-3703 fix Gff3 shared InputStream with embedded...
tree
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commitdiff
2022-01-11
Ben Soares
close filehandles straight after parse, without setting...
tree
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commitdiff
2022-01-10
Ben Soares
JAL-3937 enable AIA download of intermediate certificat...
tree
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commitdiff
2022-01-10
Ben Soares
JAL-3937 enable AIA download of intermediate certificat...
tree
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commitdiff
2021-12-22
Ben Soares
Merge branch 'develop' into critical/JAL-3933_log4j_upd...
tree
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commitdiff
2021-12-15
Jim Procter
JAL-3933 remove obsolete Castor logging configuration
tree
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commitdiff
2021-12-15
Jim Procter
JAL-3933 configure root logger console appender to...
tree
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commitdiff
2021-12-15
Jim Procter
JAL-3933 remove obsolete Castor logging configuration
tree
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commitdiff
2021-12-15
Jim Procter
JAL-3933 configure root logger console appender to...
tree
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commitdiff
2021-12-14
Ben Soares
JAL-3933 updated log4j and slf4j jars with log4j1.2...
tree
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commitdiff
2021-12-14
Ben Soares
JAL-3933 Updated log4j jars with log4j-2.16.0 and compa...
tree
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commitdiff
2021-12-13
Jim Procter
JAL-3829 isCanonical should by default be false - ensur...
tree
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commitdiff
2021-12-13
Jim Procter
JAL-3855 JAL-3829 don’t need to make up alphafold model...
tree
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commitdiff
2021-12-13
Jim Procter
JAL-3929 preserve lowercase pdbid in group name for...
tree
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commitdiff
2021-12-08
Jim Procter
JAL-3929 don’t use the url encoded pdbId in feature...
tree
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commitdiff
2021-12-08
Jim Procter
JAL-3616 update messages/tooltips/menu items to use...
tree
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commitdiff
2021-12-08
Jim Procter
JAL-3551 JAL-3931 view pymol commands/responses in...
tree
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commitdiff
2021-12-08
Jim Procter
JAL-3931 remove % and - from ids so Pymol doesn’t strip...
tree
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commitdiff
2021-12-08
Jim Procter
JAL-3929 URLencode pdbid to remove problematic characte...
tree
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commitdiff
2021-12-02
Jim Procter
JAL-3904 use new AlignPanel API method
tree
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commitdiff
2021-12-02
Jim Procter
JAL-3904 simple method to make an alignPanel the curren...
tree
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commitdiff
2021-11-25
Mateusz Warowny
JAL-3927 Make url checks asynchronous in preferences...
tree
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commitdiff
2021-11-19
Jim Procter
JAL-3926 disable autosearch by default
tree
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commitdiff
2021-11-18
Mateusz Warowny
JAL-3066 Remove redundant throws declaration from Slivk...
tree
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commitdiff
2021-11-16
Mateusz Warowny
Merge branch 'JAL-3866_RNAalifold-slivka-client' into...
tree
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commitdiff
2021-11-08
Jim Procter
JAL-3855 JAL-1731 reuse the StructureViewer.fetchPdbFil...
tree
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commitdiff
2021-11-08
Jim Procter
JAL-3855 try harder to ignore DNA/RNA only structures...
tree
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commitdiff
2021-11-08
Jim Procter
JAL-3921 wait around until session file has been written
tree
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commitdiff
2021-11-05
Jim Procter
JAL-3829 remove duplicate IDs in 3DBeacons generated...
tree
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commitdiff
2021-11-05
Jim Procter
JAL-3829 format and tidy up unused code
tree
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commitdiff
2021-11-05
Jim Procter
JAL-3919 use model format field to ensure we get the...
tree
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commitdiff
2021-11-05
Jim Procter
JAL-3875 fully reset filter combo-box when fetch 3d...
tree
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commitdiff
2021-11-03
Jim Procter
JAL-3916 TODO for improved selection of covering structures
tree
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commitdiff
2021-11-03
Jim Procter
JAL-3915 remove RNAview opts from preferences. Still...
tree
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commitdiff
2021-11-02
Jim Procter
JAL-3875 test case and patch to verify the query 3d...
tree
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commitdiff
2021-10-18
Jim Procter
JAL-3905 Fix: wait for response when sending mouseovers...
bug/r2_11_2/JAL-3904_structureviewermenu
tree
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commitdiff
2021-10-18
Jim Procter
JAL-3904 override buildActionMenu to add in additional...
tree
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commitdiff
2021-10-18
Jim Procter
JAL-3904 failing test
tree
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commitdiff
2021-10-07
Mateusz Warowny
JAL-3899 Replace prints with logger messages.
alpha/JAL-3899_deuniquify_refactor
tree
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commitdiff
2021-10-06
Mateusz Warowny
JAL-3899 Update usages of uniquify and deuniquify.
tree
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commitdiff
2021-10-06
Mateusz Warowny
JAL-3899 Refactor sequence de/uniquification.
tree
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commitdiff
2021-10-05
Ben Soares
JAL-3416 make flat default laf for linux
tree
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commitdiff
2021-10-04
Ben Soares
JAL-3416 updated FlatLaf to 1.6 and added some tabbed...
tree
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commitdiff
2021-10-04
Ben Soares
Merge branch 'develop' into JAL-3416_different_look_and...
tree
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commitdiff
2021-10-01
gmungoc
JAL-3725 restrict mapped virtual feature location to...
tree
|
commitdiff
2021-10-01
gmungoc
JAL-3725 helper methods for computing mapped feature...
tree
|
commitdiff
2021-10-01
gmungoc
JAL-3725 exclude stop codon from CDS-to-protein mapping
tree
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commitdiff
2021-10-01
Jim Procter
JAL-3616 show name of structure viewer in ‘new view...
tree
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commitdiff
2021-10-01
Jim Procter
JAL-3616 explicit configure external viewer config
tree
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commitdiff
2021-10-01
Jim Procter
JAL-3829 fetch 3D beacons now started by clicking butto...
tree
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commitdiff
2021-10-01
Jim Procter
Merge branch 'develop' into features/r2_11_2/JAL-3829_3...
tree
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commitdiff
2021-09-30
Ben Soares
JAL-1260 Added .gbk to GenBank extensions. Added GenBa...
tree
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commitdiff
2021-09-30
gmungoc
JAL-3371 more fine-grained slider; set Param slider...
tree
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commitdiff
2021-09-29
Ben Soares
JAL-3885 Made the database JComboBox have StringPair...
tree
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commitdiff
2021-09-29
Jim Procter
JAL-3884 squish alarming but harmless errors when unipr...
tree
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commitdiff
2021-09-29
Jim Procter
JAL-3881 split on any nonalphanumeric symbol (plus...
tree
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commitdiff
2021-09-29
Jim Procter
JAL-3829 report when 3d-beacons doesn’t provide any...
tree
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commitdiff
2021-09-24
Jim Procter
JAL-3829 open web page for 3d beacons structure by...
features/r2_11_2/JAL-3829_3dbeacons
tree
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commitdiff
2021-09-24
Jim Procter
JAL-3829 right click to view popup menu to show link...
tree
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commitdiff
2021-09-24
Jim Procter
JAL-3829 abstract essential TDB metadata from the user...
tree
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commitdiff
2021-09-23
Jim Procter
JAL-3821 less ambiguous base class name for EMBL and...
tree
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commitdiff
2021-09-23
Jim Procter
JAL-3821 ported to refactored FlatFile parser
tree
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commitdiff
2021-09-23
Jim Procter
JAL-3692 JAL-3861 remove extra call to .parse() so...
tree
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commitdiff
2021-09-21
Ben Soares
JAL-3691 automatic insertion of Locale.ROOT to toUpperC...
tree
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commitdiff
2021-09-21
Jim Procter
Merge branch 'doc/JAL-3746_Release_2_11_2' into develop
tree
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commitdiff
2021-09-21
Jim Procter
Merge branch 'features/r2_11_2/JAL-3829_3dbeacons'...
tree
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commitdiff
2021-09-21
Jim Procter
JAL-3829 - callback finessing - leave DBRefFetcher...
tree
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commitdiff
2021-09-21
Jim Procter
JAL-3829 prefix PDBe filters with PDBe to make clear...
tree
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commitdiff
2021-09-21
Jim Procter
JAL-3829 alternative UX: need to select 3d-beacons...
tree
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commitdiff
2021-09-21
Jim Procter
JAL-3829 ignore the fake ID generated when a PDB format...
tree
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commitdiff
2021-09-20
Jim Procter
JAL-3829 tests need to wait for dialog to be closed...
tree
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commitdiff
2021-09-20
Jim Procter
JAL-3829 TDBeacons fetcher needs a sequence with at...
tree
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commitdiff
2021-09-20
Jim Procter
JAL-3829 throw the exception even if it has no message
tree
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commitdiff
2021-09-20
Jim Procter
JAL-3829 ensure nulls are not wildcards when retrieving...
tree
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commitdiff
2021-09-20
Jim Procter
JAL-3829 do better at detecting structure type, prompt...
tree
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commitdiff
2021-09-20
Jim Procter
JAL-3829 make sure structure data type reflects actual...
tree
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commitdiff
2021-09-20
Jim Procter
JAL-3829 store 3db metadata on PDBEntry so it can be...
tree
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commitdiff
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