Merge branch 'spotless_2' into JAL-1551_2_11_3_spotlett
[jalview.git] / src / jalview / util /
2023-05-19 Ben SoaresJAL-629 Added Arg.Types and additional --help-type...
2023-05-14 Ben SoaresJAL-629 add an {extension} substitution
2023-05-11 Ben SoaresJAL-629 Fix --tempfac. Hide non-working --notempfac...
2023-04-23 Ben SoaresJAL-629 Change --open to --append and --opennew to...
2023-04-12 Ben SoaresJAL-629 Add substituteHomeDir to getDirname(). Tighten...
2023-04-03 Ben SoaresJAL-629 sort files from java glob for predictability...
2023-04-03 Ben SoaresJAL-629 added setprop. More filename based substitution...
2023-03-30 Ben SoaresJAL-629 More extensive tests with real files being...
2023-03-29 Ben SoaresJAL-629 Added --opennew --nonews --nosplash. Added...
2023-03-17 Ben SoaresJAL-629 All applications System.exits going through...
2023-03-15 Ben SoaresJAL-629 Commands more objecty, less classy. FileLoader...
2023-03-10 Ben SoaresJAL-629 start of tests and more examples
2023-03-09 Ben SoaresJAL-629 --argfile=glob implemented. Remove reference...
2023-03-08 Ben SoaresJAL-629 improved comment and return speed of StringUtil...
2023-02-26 Ben SoaresJAL-629 PAE matrix file guesstimate from filename
2023-02-22 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold...
2023-02-16 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into...
2023-02-03 Ben SoaresJAL-629 Fasta sequence id reading whitespace fix. Flexi...
2023-02-03 James ProcterJAL-1551 remove temp file in src
2023-02-03 James ProcterMerge branch 'develop' into features/r2_11_2_alphafold...
2023-01-25 James ProcterJAL-4116 relegate the failed to promote warning to...
2023-01-25 James ProcterMerge branch 'new_feature/JAL-4019_ambiguous_base_colou...
2023-01-24 James ProcterMerge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL...
2023-01-24 James ProcterMerge branch 'develop' (JAL-4102 2.11.2.6 patch release... features/r2_11_2_alphafold/JAL-2349_JAL-3855
2023-01-20 Jim ProcterJAL-2353 primary ref candidates that should be promoted... patch/Release_2_11_2_6_Branch
2022-11-16 Ben SoaresJAL-4019 finalised a boolean option and tidied some...
2022-11-14 Ben SoaresJAL-4019 Make diagnostic message debug level
2022-11-13 Ben SoaresJAL-4019 improvement to short sequence nucleotide detec...
2022-11-10 Ben SoaresJAL-4019 Nucleotide Ambiguity Colour Scheme added....
2022-11-03 Ben SoaresJAL-1988 JAL-3772 Tidying of unspecified Callable decla...
2022-10-24 Ben SoaresJAL-1988 JAL-3772 Non-blocking modal dialogs for unsave...
2022-10-14 Jim ProcterMerge branch 'features/JAL-3895_alphafoldcolours' into...
2022-08-08 Jim ProcterMerge branch 'task/JAL-3991_check_actual_JAVA_VERSION_a...
2022-06-10 Jim ProcterMerge branch 'features/r2_11_2_alphafold/JAL-2349_JAL...
2022-04-06 Ben SoaresJAL-3991 JAVA_COMPILE_VERSION put into build_properties...
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...
2022-02-16 Jim ProcterMerge branch 'develop' into features/r2_11_2_alphafold...
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
2021-08-13 Jim ProcterMerge branch 'feature/JAL-3855_ebi_alphafold_import...
2021-08-11 Jim ProcterMerge branch 'features/JAL-2349_matrixvis' into feature...
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
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