JAL-3989 Code tidying, added JVL_HEADER for older versions of Jalview, allow time...
[jalview.git] / src / jalview / util /
2022-03-18 Ben SoaresJAL-3978 New tasks to build archive 'old' dir with...
2022-03-08 Jim ProcterJAL-3746 apply copyright to source
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0
2022-03-08 Ben SoaresJAL-3103 Remove BrowserLauncher2 and use Desktop.browse...
2022-03-08 Ben SoaresJAL-3103 Put jalview.jar first in getdown for .properti...
2022-03-07 Ben SoaresJAL-3103 Switched to (a wrapper around) BrowserLauncher2
2022-02-17 Jim ProcterJAL-3691 patch toUpper/toLower to use Locale.ROOT for...
2022-02-11 Jim ProcterJAL-3949 - refactor logging from jalview.bin.Cache...
2022-02-11 Ben SoaresMerge branch 'develop' into update/JAL-3949_abstracted_...
2022-02-11 Ben SoaresJAL-3949 Complete new abstracted logging framework...
2022-02-04 Ben SoaresJAL-3949 An attempt at converting to Log4j 2 -- no...
2022-02-04 Jim ProcterMerge branch 'bug/JAL-3806_mappingCoversSequence_for211... bug/JAL-3806_without_shared_DS_for_2_11_2
2022-02-04 Jim ProcterJAL-3806 require mapping extent covers both sequence...
2022-02-03 Jim ProcterJAL-3806 use the covers() test for each selected sequen...
2022-02-03 Jim ProcterJAL-3806 use same logic as for mouse over highlighting...
2022-02-03 Jim ProcterJAL-3806 todo - problem seems to be Protein:Many CDS...
2022-01-28 Jim ProcterMerge branch 'merge/develop_JAL-3725' into develop
2022-01-27 Jim ProcterMerge branch 'bug/JAL-3633_read_proxy_settings_from_jal...
2022-01-26 Jim ProcterMerge branch 'task/JAL-3763_newDatasetForCds' into...
2022-01-26 gmungocJAL-3725 helper methods for computing mapped feature...
2021-10-01 gmungocJAL-3725 helper methods for computing mapped feature...
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC...
2021-09-17 gmungocJAL-1260 refactored GenBank (and EMBL) flat file parser
2021-09-16 Jim ProcterJAL-3794 X and N are counted as DNA characters, but...
2021-09-16 gmungocJAL-3761 more consistent parameter naming
2021-09-16 gmungocJAL-3761 helper method reinstated to avoid code duplication
2021-09-16 gmungocJAL-3761 locateInFrom/To revised with tests; unused...
2021-09-16 gmungocJAL-3761 debugged and working (but not tidied) locateIn...
2021-09-16 gmungocJAL-3761 locateInFrom2 work in progress commit
2021-09-15 gmungocJAL-3761 failing test, formatting, method renamed
2021-09-15 gmungocJAL-3751 only merge strictly contiguous ranges of mappings
2021-09-15 Ben SoaresMerge branch 'develop' into merge/develop_ben2
2021-09-15 Jim ProcterMerge branch 'Jalview-JS/bug/JAL-3762_URLparamsOverride...
2021-09-15 Ben SoaresMerge branch 'develop' into merge/develop_ben2
2021-09-12 Jim ProcterJAL-3829 JalviewJS workarounds/patches
2021-07-27 Jim ProcterJAL-3855 convenience method to check a URL will return...
2021-03-25 Ben SoaresJAL-3633 refactored/simplified LaunchUtils code
2021-03-19 Ben SoaresJAL-3503 Added a Startup tab in Preferences, with gui...
2021-03-04 Ben SoaresJAL-3594 Allow a channel to use a different preferences...
2021-03-04 Jim ProcterRevert "Merge branch 'bug/JAL-3806_mappingCoversSequenc...
2021-02-17 Jim ProcterMerge branch 'feature/JAL-3692enaEndpoint' into patch...
2021-02-04 gmungocJAL-3806 fix and test for one-to-many sequence mapping... bug/JAL-3806_mappingCoversCDS_reprise
2020-12-11 Ben SoaresJAL-3594 Adjustments to allow JalviewJS to use ChannelP...
2020-12-09 Ben SoaresJAL-3594 Images for splash screen
2020-12-09 Ben SoaresJAL-3594 JAL-3728 Added taskbar icons to desktop and...
2020-12-08 Ben SoaresMerge branch 'merge/develop_and_rebase_squashed_merge_J...
2020-12-07 Ben SoaresJAL-3594 added BG logo. Changed some named Jalviews...
2020-12-05 Ben SoaresJAL-3594 Default values for channel properties defined...
2020-12-04 Ben SoaresJAL-3594 New jalview.util.ChannelProperties to get...
2020-11-12 Ben SoaresJAL-3633 ensure check both or https:// for urls
2020-10-29 Jim ProcterMerge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11...
2020-10-29 gmungocJAL-3700 mapped sequence group includes short (or all... patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3
2020-10-28 gmungocJAL-3725 helper methods for computing mapped feature...
2020-10-28 Jim ProcterJAL-3760 refactor nucleotide proportion test to per...
2020-10-22 gmungocJAL-3751 only merge strictly contiguous ranges of mappings
2020-10-22 gmungocJAL-3751 only merge strictly contiguous ranges of mappings
2020-10-02 Jim ProcterJAL-3762 check for !args || args=="" before overwriting Jalview-JS/bug/JAL-3762_URLparamsOverrideInfoArg
2020-10-02 Jim ProcterJAL-3762 more typo fixing :q
2020-10-02 Jim ProcterJAL-3762 syntax error typo
2020-10-02 Jim ProcterJAL-3762 check if Info.args already defined before...
2020-09-29 Jim ProcterJAL-3760 refactor nucleotide proportion test to per...
2020-09-23 Ben SoaresJAL-3633 ensure check both or https:// for urls
2020-09-16 gmungocJAL-3700 fix for propagation of sort commands
2020-09-16 gmungocJAL-3700 check for 'covering' mapping when matching...
2020-08-12 Jim ProcterMerge branch 'task/JAL-3608_property_set_laf_and_tests...
2020-08-05 gmungocJAL-3700 fix for propagation of sort commands
2020-08-03 gmungocJAL-3700 check for 'covering' mapping when matching...
2020-08-03 gmungocJAL-3692 EMBL flatfile fetcher / parser (todo: CDS...
2020-07-21 gmungocJAL-3692 EMBL flatfile fetcher / parser (todo: CDS...
2020-06-16 Ben SoaresJAL-3608 non-JS cherry-pick
2020-06-16 Ben SoaresJAL-3608 formatting save only
2020-05-18 gmungocMerge branch 'Jalview-JS/develop' into develop
2020-05-18 gmungocJAL-3613 remove debug code committed in error
2020-05-18 gmungocJAL-3613 remove debug code committed in error
2020-05-01 gmungocJAL-3613 check sequence overlap when matching search...
2020-04-30 Ben SoaresJAL-3608 Enforcing MetalLookAndFeel as default on linux...
2020-04-21 Jim ProcterJAL-3407 add GPL license to Jalview source files
2020-04-21 Jim ProcterMerge branch 'bug/JAL-3574filterByPOS' into documentati...
2020-04-14 Jim ProcterMerge branch 'bug/JAL-3529_uniprotidsinstockholm' into...
2020-04-13 gmungocJAL-3574 Matcher with integer/long value pattern (e...
2020-04-07 BobHansonJAL-3589 (old Platform) fix for Jalvew-JS/develop only.
2020-03-30 gmungocMerge branch 'develop' into Jalview-JS/develop
2020-03-09 gmungocJAL-3528 unit tests added for failed lookup, Javadoc
2020-02-14 Jim Procterfix for JAL-3529
2020-02-14 Jim ProcterJAL-1354 JAL-3528 fix bug from b594d516dac69eebcccdc743...
2020-02-12 Jim ProcterJAL-1354 JAL-3528 report missing keys for MessageManage...
2020-01-28 gmungocMerge branch 'feature/JAL-3121gffAttributeMap' into...
2019-11-19 gmungocJAL-3210 use JSUtil methods getFileBytes, getApplet
2019-11-12 gmungocJAL-3274 resource path correction, code tidying (consta...
2019-11-05 gmungocJAL-3120 JAL-3130 can't read "java.specification.versio...
2019-11-05 gmungocJAL-3210 JAL-3263 redo 'Mandarin' character for JS...
2019-11-01 Ben SoaresJAL-3474 removed all .cvsignore files stored in the... improvement/JAL-3474_lots_of_.cvsignore_files
2019-10-08 gmungocMerge branch 'develop' into Jalview-JS/develop
2019-08-22 gmungocJAL-3121 round trip GFF attributes including map-valued...
2019-07-16 gmungocJAL-3210 Merge branch 'develop' into trialMerge
2019-07-10 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures
2019-06-18 Ben SoaresJAL-3312 Fixed SHIFT-CMD/SHIFT-CTRL Key combinations...
2019-06-12 Ben SoaresJAL-3295 Fixed CMD-select of sequences in alignment...
2019-06-11 gmungocJAL-3187 CDS has same dataset sequence as transcript
2019-05-02 gmungocJAL-3244 renamed Platform method for clarity bug/JAL-3244jmolWindows
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