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Merge branch 'bug/JAL-3365_extendedDSSP_via_stockholm' into develop
[jalview.git]
/
src
/
2022-04-16
Jim Procter
JAL-3365 expand range of allowed DSSP secondary structu...
tree
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commitdiff
2022-04-05
Jim Procter
JAL-3981 patch tests and remove errant imports
tree
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commitdiff
2022-04-05
Jim Procter
JAL-3990 gradle spotlessApply
tree
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commitdiff
2022-04-05
Jim Procter
Merge branch 'bug/JAL-3980_JAL-3981_tooltips_sequence_d...
tree
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commitdiff
2022-03-31
Jim Procter
JAL-3985 formatting
tree
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commitdiff
2022-03-31
Jim Procter
JAL-3985 split PDB id queries into multiple queries...
tree
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commitdiff
2022-03-30
Jim Procter
Merge branch 'patch/JAL-3976_3dbeaconsnull' into develop
tree
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commitdiff
2022-03-30
Jim Procter
JAL-360 JAL-3975 update parent for text colour dialog...
tree
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commitdiff
2022-03-30
Ben Soares
JAL-360 JAL-3975 make AlignFrame the parent of FeatureE...
tree
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commitdiff
2022-03-25
Jim Procter
JAL-3980 JAL-3979 TODOs
bug/JAL-3980_JAL-3981_tooltips_sequence_details
tree
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commitdiff
2022-03-25
Jim Procter
JAL-3980 defensive copy - inefficient but fixes bug
tree
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commitdiff
2022-03-25
Jim Procter
JAL-3981 Additional line breaks - sort of helps
tree
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commitdiff
2022-03-24
Jim Procter
JAL-3981 strategic newlines to help speed up Java's...
tree
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commitdiff
2022-03-23
Jim Procter
JAL-3976 skip entries with null values when analyzing
tree
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commitdiff
2022-03-08
Jim Procter
JAL-3746 apply copyright to source
tree
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commitdiff
2022-03-08
Jim Procter
JAL-3438 spotless for 2.11.2.0
tree
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commitdiff
2022-03-08
Jim Procter
JAL-3108 updated Ensembl client and model species names
tree
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commitdiff
2022-03-08
Ben Soares
JAL-3103 Removed code and unused widgets for defaultBrowser
tree
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commitdiff
2022-03-08
Ben Soares
JAL-3103 Remove BrowserLauncher2 and use Desktop.browse...
tree
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commitdiff
2022-03-08
Ben Soares
JAL-3103 Put jalview.jar first in getdown for .properti...
tree
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commitdiff
2022-03-07
Ben Soares
JAL-3103 Switched to (a wrapper around) BrowserLauncher2
tree
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commitdiff
2022-03-04
Jim Procter
JAL-3746 JAL-3811 document SHOW_JWS2_SERVICES user...
tree
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commitdiff
2022-03-04
Jim Procter
JAL-3746 JAL-3812 new argument ‘-nohtmltemplates’ and...
tree
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commitdiff
2022-03-04
Jim Procter
JAL-3746 JAL-3813 NOIDENTIFIERSSERVICE preference disab...
tree
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commitdiff
2022-03-04
Jim Procter
JAL-3746 JAL-3814 don’t automatically launch the news...
tree
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commitdiff
2022-03-04
Jim Procter
JAL-3746 JAL-3814 NONEWS property
tree
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commitdiff
2022-03-02
Jim Procter
Merge branch 'benreview/JAL-3691_for_2_11_2_getdownrebu...
tree
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commitdiff
2022-03-02
Jim Procter
JAL-3619 fix up error messages and try to bail quietly...
tree
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commitdiff
2022-03-02
Jim Procter
JAL-3619 fix up warning message and minimal patch to...
tree
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commitdiff
2022-02-17
Jim Procter
JAL-3959 add key retrieval urls that support CORS neede...
tree
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commitdiff
2022-02-17
Jim Procter
JAL-3691 patch toUpper/toLower to use Locale.ROOT for...
tree
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commitdiff
2022-02-16
Jim Procter
JAL-3551 - wrap pair_fit with undo_disable and undo_enable
tree
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commitdiff
2022-02-16
Jim Procter
JAL-3837 GPL license on splashscreen (finally !) and...
tree
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commitdiff
2022-02-16
Jim Procter
JAL-3949 report Pymol XMLRPC port via log.info
tree
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commitdiff
2022-02-15
Jim Procter
JAL-1761 backbone type parameter for configuring which...
tree
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commitdiff
2022-02-15
Jim Procter
JAL-1761 need to pass molecule type when generating...
tree
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commitdiff
2022-02-15
Jim Procter
JAL-3906 use indicate to highlight current mousedOver...
tree
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commitdiff
2022-02-14
Jim Procter
Merge branch 'task/r_2_11_2/JAL-3956_alphaFill_authorit...
tree
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commitdiff
2022-02-14
Jim Procter
JAL-3551
tree
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commitdiff
2022-02-14
Jim Procter
JAL-3956 - PDBEntry objects constructed from 3D-Beacons...
tree
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commitdiff
2022-02-11
Jim Procter
Merge branch 'update/JAL-3949_jalview_bin_Console_to_cu...
tree
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commitdiff
2022-02-11
Jim Procter
JAL-3931 fix - escape % symbols after urlencoding
tree
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commitdiff
2022-02-11
Ben Soares
Merge branch 'update/JAL-3949_jalview_bin_Console_to_cu...
tree
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commitdiff
2022-02-11
Ben Soares
JLogger loglevel check on whether to call the actual...
tree
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commitdiff
2022-02-11
Jim Procter
JAL-3949 - refactor logging from jalview.bin.Cache...
tree
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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
2022-01-27
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
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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
2021-11-19
Jim Procter
JAL-3926 disable autosearch by default
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
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