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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... tree | commitdiff
2023-05-14 Ben SoaresJAL-629 add an {extension} substitution tree | commitdiff
2023-05-11 Ben SoaresJAL-629 Fix --tempfac. Hide non-working --notempfac... tree | commitdiff
2023-04-23 Ben SoaresJAL-629 Change --open to --append and --opennew to... tree | commitdiff
2023-04-12 Ben SoaresJAL-629 Add substituteHomeDir to getDirname(). Tighten... tree | commitdiff
2023-04-03 Ben SoaresJAL-629 sort files from java glob for predictability... tree | commitdiff
2023-04-03 Ben SoaresJAL-629 added setprop. More filename based substitution... tree | commitdiff
2023-03-30 Ben SoaresJAL-629 More extensive tests with real files being... tree | commitdiff
2023-03-29 Ben SoaresJAL-629 Added --opennew --nonews --nosplash. Added... tree | commitdiff
2023-03-17 Ben SoaresJAL-629 All applications System.exits going through... tree | commitdiff
2023-03-15 Ben SoaresJAL-629 Commands more objecty, less classy. FileLoader... tree | commitdiff
2023-03-10 Ben SoaresJAL-629 start of tests and more examples tree | commitdiff
2023-03-09 Ben SoaresJAL-629 --argfile=glob implemented. Remove reference... tree | commitdiff
2023-03-08 Ben SoaresJAL-629 improved comment and return speed of StringUtil... tree | commitdiff
2023-02-26 Ben SoaresJAL-629 PAE matrix file guesstimate from filename tree | commitdiff
2023-02-22 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-02-16 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... tree | commitdiff
2023-02-03 Ben SoaresJAL-629 Fasta sequence id reading whitespace fix. Flexi... tree | commitdiff
2023-02-03 James ProcterJAL-1551 remove temp file in src tree | commitdiff
2023-02-03 James ProcterMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2023-01-25 James ProcterJAL-4116 relegate the failed to promote warning to... tree | commitdiff
2023-01-25 James ProcterMerge branch 'new_feature/JAL-4019_ambiguous_base_colou... tree | commitdiff
2023-01-24 James ProcterMerge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL... tree | commitdiff
2023-01-24 James ProcterMerge branch 'develop' (JAL-4102 2.11.2.6 patch release... features/r2_11_2_alphafold/JAL-2349_JAL-3855 tree | commitdiff
2023-01-20 Jim ProcterJAL-2353 primary ref candidates that should be promoted... patch/Release_2_11_2_6_Branch tree | commitdiff
2022-11-16 Ben SoaresJAL-4019 finalised a boolean option and tidied some... tree | commitdiff
2022-11-14 Ben SoaresJAL-4019 Make diagnostic message debug level tree | commitdiff
2022-11-13 Ben SoaresJAL-4019 improvement to short sequence nucleotide detec... tree | commitdiff
2022-11-10 Ben SoaresJAL-4019 Nucleotide Ambiguity Colour Scheme added.... tree | commitdiff
2022-11-03 Ben SoaresJAL-1988 JAL-3772 Tidying of unspecified Callable decla... tree | commitdiff
2022-10-24 Ben SoaresJAL-1988 JAL-3772 Non-blocking modal dialogs for unsave... tree | commitdiff
2022-10-14 Jim ProcterMerge branch 'features/JAL-3895_alphafoldcolours' into... tree | commitdiff
2022-08-08 Jim ProcterMerge branch 'task/JAL-3991_check_actual_JAVA_VERSION_a... tree | commitdiff
2022-06-10 Jim ProcterMerge branch 'features/r2_11_2_alphafold/JAL-2349_JAL... tree | commitdiff
2022-04-06 Ben SoaresJAL-3991 JAVA_COMPILE_VERSION put into build_properties... tree | commitdiff
2022-03-18 Ben SoaresJAL-3978 New tasks to build archive 'old' dir with... tree | commitdiff
2022-03-08 Jim ProcterJAL-3746 apply copyright to source tree | commitdiff
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0 tree | commitdiff
2022-03-08 Ben SoaresJAL-3103 Remove BrowserLauncher2 and use Desktop.browse... tree | commitdiff
2022-03-08 Ben SoaresJAL-3103 Put jalview.jar first in getdown for .properti... tree | commitdiff
2022-03-07 Ben SoaresJAL-3103 Switched to (a wrapper around) BrowserLauncher2 tree | commitdiff
2022-02-17 Jim ProcterJAL-3691 patch toUpper/toLower to use Locale.ROOT for... tree | commitdiff
2022-02-16 Jim ProcterMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2022-02-11 Jim ProcterJAL-3949 - refactor logging from jalview.bin.Cache... tree | commitdiff
2022-02-11 Ben SoaresMerge branch 'develop' into update/JAL-3949_abstracted_... tree | commitdiff
2022-02-11 Ben SoaresJAL-3949 Complete new abstracted logging framework... tree | commitdiff
2022-02-04 Ben SoaresJAL-3949 An attempt at converting to Log4j 2 -- no... tree | commitdiff
2022-02-04 Jim ProcterMerge branch 'bug/JAL-3806_mappingCoversSequence_for211... bug/JAL-3806_without_shared_DS_for_2_11_2 tree | commitdiff
2022-02-04 Jim ProcterJAL-3806 require mapping extent covers both sequence... tree | commitdiff
2022-02-03 Jim ProcterJAL-3806 use the covers() test for each selected sequen... tree | commitdiff
2022-02-03 Jim ProcterJAL-3806 use same logic as for mouse over highlighting... tree | commitdiff
2022-02-03 Jim ProcterJAL-3806 todo - problem seems to be Protein:Many CDS... tree | commitdiff
2022-01-28 Jim ProcterMerge branch 'merge/develop_JAL-3725' into develop tree | commitdiff
2022-01-27 Jim ProcterMerge branch 'bug/JAL-3633_read_proxy_settings_from_jal... tree | commitdiff
2022-01-26 Jim ProcterMerge branch 'task/JAL-3763_newDatasetForCds' into... tree | commitdiff
2022-01-26 gmungocJAL-3725 helper methods for computing mapped feature... tree | commitdiff
2021-10-01 gmungocJAL-3725 helper methods for computing mapped feature... tree | commitdiff
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC... tree | commitdiff
2021-09-17 gmungocJAL-1260 refactored GenBank (and EMBL) flat file parser tree | commitdiff
2021-09-16 Jim ProcterJAL-3794 X and N are counted as DNA characters, but... tree | commitdiff
2021-09-16 gmungocJAL-3761 more consistent parameter naming tree | commitdiff
2021-09-16 gmungocJAL-3761 helper method reinstated to avoid code duplication tree | commitdiff
2021-09-16 gmungocJAL-3761 locateInFrom/To revised with tests; unused... tree | commitdiff
2021-09-16 gmungocJAL-3761 debugged and working (but not tidied) locateIn... tree | commitdiff
2021-09-16 gmungocJAL-3761 locateInFrom2 work in progress commit tree | commitdiff
2021-09-15 gmungocJAL-3761 failing test, formatting, method renamed tree | commitdiff
2021-09-15 gmungocJAL-3751 only merge strictly contiguous ranges of mappings tree | commitdiff
2021-09-15 Ben SoaresMerge branch 'develop' into merge/develop_ben2 tree | commitdiff
2021-09-15 Jim ProcterMerge branch 'Jalview-JS/bug/JAL-3762_URLparamsOverride... tree | commitdiff
2021-09-15 Ben SoaresMerge branch 'develop' into merge/develop_ben2 tree | commitdiff
2021-09-12 Jim ProcterJAL-3829 JalviewJS workarounds/patches tree | commitdiff
2021-08-13 Jim ProcterMerge branch 'feature/JAL-3855_ebi_alphafold_import... tree | commitdiff
2021-08-11 Jim ProcterMerge branch 'features/JAL-2349_matrixvis' into feature... tree | commitdiff
2021-07-27 Jim ProcterJAL-3855 convenience method to check a URL will return... tree | commitdiff
2021-03-25 Ben SoaresJAL-3633 refactored/simplified LaunchUtils code tree | commitdiff
2021-03-19 Ben SoaresJAL-3503 Added a Startup tab in Preferences, with gui... tree | commitdiff
2021-03-04 Ben SoaresJAL-3594 Allow a channel to use a different preferences... tree | commitdiff
2021-03-04 Jim ProcterRevert "Merge branch 'bug/JAL-3806_mappingCoversSequenc... tree | commitdiff
2021-02-17 Jim ProcterMerge branch 'feature/JAL-3692enaEndpoint' into patch... tree | commitdiff
2021-02-04 gmungocJAL-3806 fix and test for one-to-many sequence mapping... bug/JAL-3806_mappingCoversCDS_reprise tree | commitdiff
2020-12-11 Ben SoaresJAL-3594 Adjustments to allow JalviewJS to use ChannelP... tree | commitdiff
2020-12-09 Ben SoaresJAL-3594 Images for splash screen tree | commitdiff
2020-12-09 Ben SoaresJAL-3594 JAL-3728 Added taskbar icons to desktop and... tree | commitdiff
2020-12-08 Ben SoaresMerge branch 'merge/develop_and_rebase_squashed_merge_J... tree | commitdiff
2020-12-07 Ben SoaresJAL-3594 added BG logo. Changed some named Jalviews... tree | commitdiff
2020-12-05 Ben SoaresJAL-3594 Default values for channel properties defined... tree | commitdiff
2020-12-04 Ben SoaresJAL-3594 New jalview.util.ChannelProperties to get... tree | commitdiff
2020-11-12 Ben SoaresJAL-3633 ensure check both or https:// for urls tree | commitdiff
2020-10-29 Jim ProcterMerge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11... tree | commitdiff
2020-10-29 gmungocJAL-3700 mapped sequence group includes short (or all... patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3 tree | commitdiff
2020-10-28 gmungocJAL-3725 helper methods for computing mapped feature... tree | commitdiff
2020-10-28 Jim ProcterJAL-3760 refactor nucleotide proportion test to per... tree | commitdiff
2020-10-22 gmungocJAL-3751 only merge strictly contiguous ranges of mappings tree | commitdiff
2020-10-22 gmungocJAL-3751 only merge strictly contiguous ranges of mappings tree | commitdiff
2020-10-02 Jim ProcterJAL-3762 check for !args || args=="" before overwriting Jalview-JS/bug/JAL-3762_URLparamsOverrideInfoArg tree | commitdiff
2020-10-02 Jim ProcterJAL-3762 more typo fixing :q tree | commitdiff
2020-10-02 Jim ProcterJAL-3762 syntax error typo tree | commitdiff
2020-10-02 Jim ProcterJAL-3762 check if Info.args already defined before... tree | commitdiff
2020-09-29 Jim ProcterJAL-3760 refactor nucleotide proportion test to per... tree | commitdiff
2020-09-23 Ben SoaresJAL-3633 ensure check both or https:// for urls tree | commitdiff
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