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Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629
[jalview.git]
/
src
/
jalview
/
util
/
2023-02-22
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-02-03
Ben Soares
JAL-629 Fasta sequence id reading whitespace fix. Flexi...
tree
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commitdiff
2023-02-03
James Procter
JAL-1551 remove temp file in src
tree
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commitdiff
2023-02-03
James Procter
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-01-25
James Procter
JAL-4116 relegate the failed to promote warning to...
tree
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commitdiff
2023-01-25
James Procter
Merge branch 'new_feature/JAL-4019_ambiguous_base_colou...
tree
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commitdiff
2023-01-24
James Procter
Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL...
tree
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commitdiff
2023-01-24
James Procter
Merge branch 'develop' (JAL-4102 2.11.2.6 patch release...
features/r2_11_2_alphafold/JAL-2349_JAL-3855
tree
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commitdiff
2023-01-20
Jim Procter
JAL-2353 primary ref candidates that should be promoted...
patch/Release_2_11_2_6_Branch
tree
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commitdiff
2022-11-16
Ben Soares
JAL-4019 finalised a boolean option and tidied some...
tree
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commitdiff
2022-11-14
Ben Soares
JAL-4019 Make diagnostic message debug level
tree
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commitdiff
2022-11-13
Ben Soares
JAL-4019 improvement to short sequence nucleotide detec...
tree
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commitdiff
2022-11-10
Ben Soares
JAL-4019 Nucleotide Ambiguity Colour Scheme added....
tree
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commitdiff
2022-11-03
Ben Soares
JAL-1988 JAL-3772 Tidying of unspecified Callable decla...
tree
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commitdiff
2022-10-24
Ben Soares
JAL-1988 JAL-3772 Non-blocking modal dialogs for unsave...
tree
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commitdiff
2022-10-14
Jim Procter
Merge branch 'features/JAL-3895_alphafoldcolours' into...
tree
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commitdiff
2022-08-08
Jim Procter
Merge branch 'task/JAL-3991_check_actual_JAVA_VERSION_a...
tree
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commitdiff
2022-06-10
Jim Procter
Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL...
tree
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commitdiff
2022-04-06
Ben Soares
JAL-3991 JAVA_COMPILE_VERSION put into build_properties...
tree
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commitdiff
2022-03-18
Ben Soares
JAL-3978 New tasks to build archive 'old' dir with...
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
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
2022-02-17
Jim Procter
JAL-3691 patch toUpper/toLower to use Locale.ROOT for...
tree
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commitdiff
2022-02-16
Jim Procter
Merge branch 'develop' into features/r2_11_2_alphafold...
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
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
2022-02-04
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
2022-01-28
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-3725 helper methods for computing mapped feature...
tree
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commitdiff
2021-10-01
gmungoc
JAL-3725 helper methods for computing mapped feature...
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
2021-09-17
gmungoc
JAL-1260 refactored GenBank (and EMBL) flat file parser
tree
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commitdiff
2021-09-16
Jim Procter
JAL-3794 X and N are counted as DNA characters, but...
tree
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commitdiff
2021-09-16
gmungoc
JAL-3761 more consistent parameter naming
tree
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commitdiff
2021-09-16
gmungoc
JAL-3761 helper method reinstated to avoid code duplication
tree
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commitdiff
2021-09-16
gmungoc
JAL-3761 locateInFrom/To revised with tests; unused...
tree
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commitdiff
2021-09-16
gmungoc
JAL-3761 debugged and working (but not tidied) locateIn...
tree
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commitdiff
2021-09-16
gmungoc
JAL-3761 locateInFrom2 work in progress commit
tree
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commitdiff
2021-09-15
gmungoc
JAL-3761 failing test, formatting, method renamed
tree
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commitdiff
2021-09-15
gmungoc
JAL-3751 only merge strictly contiguous ranges of mappings
tree
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commitdiff
2021-09-15
Ben Soares
Merge branch 'develop' into merge/develop_ben2
tree
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commitdiff
2021-09-15
Jim Procter
Merge branch 'Jalview-JS/bug/JAL-3762_URLparamsOverride...
tree
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commitdiff
2021-09-15
Ben Soares
Merge branch 'develop' into merge/develop_ben2
tree
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commitdiff
2021-09-12
Jim Procter
JAL-3829 JalviewJS workarounds/patches
tree
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commitdiff
2021-08-13
Jim Procter
Merge branch 'feature/JAL-3855_ebi_alphafold_import...
tree
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commitdiff
2021-08-11
Jim Procter
Merge branch 'features/JAL-2349_matrixvis' into feature...
tree
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commitdiff
2021-07-27
Jim Procter
JAL-3855 convenience method to check a URL will return...
tree
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commitdiff
2021-03-25
Ben Soares
JAL-3633 refactored/simplified LaunchUtils code
tree
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commitdiff
2021-03-19
Ben Soares
JAL-3503 Added a Startup tab in Preferences, with gui...
tree
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commitdiff
2021-03-04
Ben Soares
JAL-3594 Allow a channel to use a different preferences...
tree
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commitdiff
2021-03-04
Jim Procter
Revert "Merge branch 'bug/JAL-3806_mappingCoversSequenc...
tree
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commitdiff
2021-02-17
Jim Procter
Merge branch 'feature/JAL-3692enaEndpoint' into patch...
tree
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commitdiff
2021-02-04
gmungoc
JAL-3806 fix and test for one-to-many sequence mapping...
bug/JAL-3806_mappingCoversCDS_reprise
tree
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commitdiff
2020-12-11
Ben Soares
JAL-3594 Adjustments to allow JalviewJS to use ChannelP...
tree
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commitdiff
2020-12-09
Ben Soares
JAL-3594 Images for splash screen
tree
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commitdiff
2020-12-09
Ben Soares
JAL-3594 JAL-3728 Added taskbar icons to desktop and...
tree
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commitdiff
2020-12-08
Ben Soares
Merge branch 'merge/develop_and_rebase_squashed_merge_J...
tree
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commitdiff
2020-12-07
Ben Soares
JAL-3594 added BG logo. Changed some named Jalviews...
tree
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commitdiff
2020-12-05
Ben Soares
JAL-3594 Default values for channel properties defined...
tree
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commitdiff
2020-12-04
Ben Soares
JAL-3594 New jalview.util.ChannelProperties to get...
tree
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commitdiff
2020-11-12
Ben Soares
JAL-3633 ensure check both or https:// for urls
tree
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commitdiff
2020-10-29
Jim Procter
Merge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11...
tree
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commitdiff
2020-10-29
gmungoc
JAL-3700 mapped sequence group includes short (or all...
patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3
tree
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commitdiff
2020-10-28
gmungoc
JAL-3725 helper methods for computing mapped feature...
tree
|
commitdiff
2020-10-28
Jim Procter
JAL-3760 refactor nucleotide proportion test to per...
tree
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commitdiff
2020-10-22
gmungoc
JAL-3751 only merge strictly contiguous ranges of mappings
tree
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commitdiff
2020-10-22
gmungoc
JAL-3751 only merge strictly contiguous ranges of mappings
tree
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commitdiff
2020-10-02
Jim Procter
JAL-3762 check for !args || args=="" before overwriting
Jalview-JS/bug/JAL-3762_URLparamsOverrideInfoArg
tree
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commitdiff
2020-10-02
Jim Procter
JAL-3762 more typo fixing :q
tree
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commitdiff
2020-10-02
Jim Procter
JAL-3762 syntax error typo
tree
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commitdiff
2020-10-02
Jim Procter
JAL-3762 check if Info.args already defined before...
tree
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commitdiff
2020-09-29
Jim Procter
JAL-3760 refactor nucleotide proportion test to per...
tree
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commitdiff
2020-09-23
Ben Soares
JAL-3633 ensure check both or https:// for urls
tree
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commitdiff
2020-09-16
gmungoc
JAL-3700 fix for propagation of sort commands
tree
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commitdiff
2020-09-16
gmungoc
JAL-3700 check for 'covering' mapping when matching...
tree
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commitdiff
2020-08-12
Jim Procter
Merge branch 'task/JAL-3608_property_set_laf_and_tests...
tree
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commitdiff
2020-08-05
gmungoc
JAL-3700 fix for propagation of sort commands
tree
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commitdiff
2020-08-03
gmungoc
JAL-3700 check for 'covering' mapping when matching...
tree
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commitdiff
2020-08-03
gmungoc
JAL-3692 EMBL flatfile fetcher / parser (todo: CDS...
tree
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commitdiff
2020-07-21
gmungoc
JAL-3692 EMBL flatfile fetcher / parser (todo: CDS...
tree
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commitdiff
2020-06-16
Ben Soares
JAL-3608 non-JS cherry-pick
tree
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commitdiff
2020-06-16
Ben Soares
JAL-3608 formatting save only
tree
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commitdiff
2020-05-18
gmungoc
Merge branch 'Jalview-JS/develop' into develop
tree
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commitdiff
2020-05-18
gmungoc
JAL-3613 remove debug code committed in error
tree
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commitdiff
2020-05-18
gmungoc
JAL-3613 remove debug code committed in error
tree
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commitdiff
2020-05-01
gmungoc
JAL-3613 check sequence overlap when matching search...
tree
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commitdiff
2020-04-30
Ben Soares
JAL-3608 Enforcing MetalLookAndFeel as default on linux...
tree
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commitdiff
2020-04-21
Jim Procter
JAL-3407 add GPL license to Jalview source files
tree
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commitdiff
2020-04-21
Jim Procter
Merge branch 'bug/JAL-3574filterByPOS' into documentati...
tree
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commitdiff
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