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JAL-4135 replace stream.toString(Charset) calls with stream.toString(String)
[jalview.git]
/
src
/
jalview
/
util
/
2023-02-06
Mateusz Warowny
Merge branch 'JAL-3878_ws-overhaul-3' into mmw/Release_...
tree
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commitdiff
2023-01-20
Jim Procter
JAL-4102 update 2.12 from 2.11.2.6 patch release -...
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
2022-12-14
Jim Procter
Merge branch 'develop' into update_212_Dec_merge_with_2...
tree
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commitdiff
2022-11-21
Jim Procter
Merge commit 'alpha/update_2_12_for_2_11_2_series_merge...
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
2022-04-07
Mateusz Warowny
JAL-3878 Add action and task for annotation services
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
2022-03-14
Mateusz Warowny
JAL-3878 Move array index search to ArrayUtils
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
2022-02-15
Mateusz Warowny
JAL-3878 Add universal id generator to MathUtils.
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
2021-07-27
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
2020-12-14
Jim Procter
Merge branch 'Jalview-JS/develop' into merge_js_develop
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
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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
|
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
2020-06-30
gmungoc
JAL-3446 unused imports removed
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
2020-06-16
BobHanson
JAL-3446 proper call for headless state
tree
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commitdiff
2020-06-16
BobHanson
JAL-3446 CTRL-DOWN check for headless operation
tree
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commitdiff
2020-06-12
soares
JAL-3446 fixing a bad merge, sorry
tree
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commitdiff
2020-06-12
soares
JAL-3446 separated out potential exceptions for simplif...
tree
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commitdiff
2020-06-12
BobHanson
JAL-3446 removing mouse button test debug
tree
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commitdiff
2020-06-12
BobHanson
JAL-3446 from applet -- reload; also fixes some repaint...
tree
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commitdiff
2020-06-11
BobHanson
JAL-3446 no need for SHIFT_DOWN or ALT_DOWN masks
tree
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commitdiff
2020-06-11
BobHanson
First try at merging didn't go so well.
tree
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commitdiff
2020-06-11
BobHanson
Merge branch 'Jalview-JS/develop.JAL-3446.ctrlDown...
tree
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commitdiff
2020-06-07
BobHanson
JAL-3446 JavaScript interface
tree
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commitdiff
2020-06-05
BobHanson
JAL-3446 UrlDownloadClient and Test
tree
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commitdiff
2020-06-05
BobHanson
JAL-3446 forgot to escape Java in modified Platform...
tree
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commitdiff
2020-06-05
BobHanson
JAL-3446 new Locale("") moved to Platform for review.
tree
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commitdiff
2020-06-05
BobHanson
JAL-3446 removes all JalviewJSApp dependency from jalvi...
tree
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commitdiff
2020-06-05
BobHanson
Refactoring of Jalview, JalviewAppLoader, JalviewApp...
tree
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commitdiff
2020-06-03
BobHanson
JAL-3664 support for new Locale(""), meaning "not actua...
tree
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commitdiff
2020-06-03
BobHanson
JAL-3446 adds SIFTs JAL-3625 SiftsClient
tree
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commitdiff
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