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JAL-4020 class reformatting
2022-06-06 Ben SoaresJAL-4020 class reformatting
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2022-03-13 Ben SoaresAppend git.hash and git.branch to RELEASE file stored...
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2022-03-11 Ben SoaresJAL-3973 This fixes the gradle build when not in a...
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2022-03-08 Ben SoaresJAL-3103 updated help doc to remove default browser...
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2022-03-08 Ben SoaresJAL-3103 Removed code and unused widgets for defaultBrowser
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2022-03-08 Ben SoaresJAL-3103 Remove BrowserLauncher2 and use Desktop.browse...
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2022-03-08 Ben SoaresJAL-3103 add BrowserLauncher2 LGPLv2.1 to THIRDPARTYLIBS
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2022-03-08 Ben SoaresJAL-3103 Put jalview.jar first in getdown for .properties...
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2022-03-07 Ben SoaresJAL-3103 Switched to (a wrapper around) BrowserLauncher2
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2022-03-04 Ben SoaresJAL-3830 added command line to whatsnew and releases
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2022-03-04 Ben SoaresJAL-3830 Added new command line usage to docs
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2022-03-04 Ben SoaresJAL-3608 added to LaF documentation
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2022-03-03 Ben SoaresJAL-3830 fix broken/buggy install4j9 setting of executeSetup...
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2022-03-02 Ben SoaresJAL-3691 bumped the version to 1.8.3-1.2.12 in source...
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2022-03-02 Ben SoaresJAL-3962 Added jre/bin and dist folders to the native...
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2022-03-02 Ben SoaresJAL-3130 updated download_jres.sh
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2022-02-12 Ben SoaresJAL-3949 fix testProps path and make line count more...
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2022-02-11 Ben SoaresMerge branch 'update/JAL-3949_jalview_bin_Console_to_cure_sa...
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2022-02-11 Ben SoaresJLogger loglevel check on whether to call the actual...
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2022-02-11 Ben SoaresJAL-3949 fixed failing commandlinetests due to more...
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2022-02-11 Ben SoaresJAL-3949 added Java Console autoscrolling help paragraph
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2022-02-11 Ben SoaresJAL-3949 read ~/.jalview_properties before initialising...
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2022-02-11 Ben SoaresMerge branch 'develop' into update/JAL-3949_abstracted_loggi...
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2022-02-11 Ben SoaresJAL-3949 Complete new abstracted logging framework...
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2022-02-04 Ben SoaresJAL-3949 An attempt at converting to Log4j 2 -- no...
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2022-02-03 Ben SoaresJAL-3949 upgraded log4j to 2.17.1 (no actual known...
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2022-01-29 Ben SoaresJAL-3830 JAL-3420 added new jvl_file to install4j9...
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2022-01-29 Ben SoaresMerge branch 'develop' into improvement/JAL-3830_install4j9_...
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2022-01-28 Ben SoaresMerge branch 'develop' into improvement/JAL-3420_match_jvl_i...
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2022-01-28 Ben Soaresnew jvl_file svg, png, ico and icns files, and changed...
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2022-01-12 Ben SoaresJAL-3703 Test that fails in Windows only, and only...
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2022-01-11 Ben SoaresJAL-3703 fix Gff3 shared InputStream with embedded...
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2022-01-11 Ben Soaresclose filehandles straight after parse, without setting...
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2022-01-11 Ben SoaresJAL-3937 update releases.html
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2022-01-10 Ben SoaresJAL-3937 enable AIA download of intermediate certificates...
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2022-01-10 Ben SoaresJAL-3937 enable AIA download of intermediate certificates...
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2021-12-22 Ben SoaresMerge branch 'develop' into critical/JAL-3933_log4j_update_f...
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2021-12-22 Ben SoaresJAL-3934 updated log4j from 2.16.0 to 2.17.0
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2021-12-22 Ben SoaresJAL-3934 updated log4j from 2.16.0 to 2.17.0
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2021-12-15 Ben SoaresJAL-3933 updated THIRDPARTYLIBS
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2021-12-15 Ben SoaresJAL-3933 updated THIRDPARTYLIBS
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2021-12-15 Ben SoaresJAL-3933 updated THIRDPARTYLIBS
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2021-12-15 Ben SoaresJAL-3933 updated THIRDPARTYLIBS
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2021-12-14 Ben SoaresJAL-3933 updated log4j and slf4j jars with log4j1.2...
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2021-12-14 Ben SoaresJAL-3933 updated slf4j to 1.7.32
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2021-12-14 Ben SoaresJAL-3933 Updated log4j jars with log4j-2.16.0 and compatibil...
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2021-12-07 Ben SoaresJAL-3930 Added a customizedId="JALVIEW" to launcher...
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2021-12-07 Ben SoaresJAL-3930 Added a customizedId="JALVIEW" to launcher...
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2021-11-29 Ben SoaresJAL-3594 correct Jalview Develop logo SVG added in...
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2021-11-16 Ben SoaresJAL-3553 added customized labels for install4j output.txt
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2021-11-01 Ben SoaresJAL-3907 changed two commented out lines to reflect...
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2021-11-01 Ben SoaresJAL-3907 added creation of symbolic links to workaround...
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2021-10-28 Ben SoaresJAL-3830 forgot to uncheck this
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2021-10-27 Ben SoaresJAL-3830 quick fix to installer text
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2021-10-27 Ben SoaresJAL-3830 install4j9 tries to parse and can't cope with...
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2021-10-26 Ben SoaresJAL-3830 Added steps for install4j9 to create macOS...
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2021-10-26 Ben SoaresJAL-3907 adjusted download_jdks.sh and download_jres...
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2021-10-01 gmungocJAL-3725 restrict mapped virtual feature location to...
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2021-10-01 gmungocJAL-3725 helper methods for computing mapped feature...
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2021-10-01 gmungocJAL-3725 exclude stop codon from CDS-to-protein mapping
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2021-10-01 Ben SoaresMerge branch 'improvement/JAL-3594_logos_for_jalview_test...
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2021-10-01 Ben SoaresMerge branch 'develop' into improvement/JAL-3594_logos_for_j...
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2021-10-01 Ben SoaresJAL-3594 New Jalview Test logos and .icns/.ico creation...
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2021-09-30 Ben SoaresJAL-3594 Changed logo for Jalview Test
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2021-09-30 Ben SoaresJAL-1260 Added .gbk to GenBank extensions. Added GenBank...
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2021-09-30 gmungocJAL-3371 more fine-grained slider; set Param slider...
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2021-09-29 Ben SoaresJAL-3885 Made the database JComboBox have StringPair...
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2021-09-28 Ben SoaresJAL-3783 Updated groovy-all-2.4. Currently newer stable...
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2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperCase...
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2021-09-21 Ben SoaresJAL-3521 'Debian-safe' version of minimal build.gradle...
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2021-09-20 Ben SoaresJAL-3521 Created a patch file to transform build.gradle...
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2021-09-20 Ben SoaresJAL-3521 working minimal build.gradle for debian and...
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2021-09-20 Ben SoaresJAL-3521 not quite working minimal build.gradle for...
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2021-09-17 Ben SoaresMerge branch 'merge/develop_JAL-1260' into develop
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2021-09-17 Ben SoaresJAL-1260 rudimentary parsing of LOCUS line to at least...
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2021-09-17 gmungocJAL-1260 refactored multi-line qualifier separators
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2021-09-17 gmungocJAL-1260 unit test for FileFormats updated for GenBank/ENA
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2021-09-17 gmungocJAL-1260 file formats and IdentifyFile updates for...
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2021-09-17 gmungocJAL-1260 refactored GenBank (and EMBL) flat file parser
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2021-09-17 Jim ProcterJAL-1260 FileFormat entry for EMBL/GENBANK: TODO: create...
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2021-09-16 Ben SoaresJAL-3779 Added to documentation
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2021-09-16 gmungocJAL-3779 apply properties to all groups with given...
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2021-09-16 Ben SoaresJAL-3774 combined changes from bug/JAL-3774_splitFrameFinder...
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2021-09-16 Ben SoaresJAL-3739 (combined) commits from feature/JAL-3739_useFormFie...
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2021-09-16 Jim ProcterJAL-3794 X and N are counted as DNA characters, but...
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2021-09-16 Jim ProcterJAL-3794 new test for recognition of protein or DNA...
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2021-09-16 Ben SoaresJAL-3761 listToArray became rangeListToArray
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2021-09-16 gmungocJAL-3761 more consistent parameter naming
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2021-09-16 gmungocJAL-3761 helper method reinstated to avoid code duplication
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2021-09-16 gmungocJAL-3761 locateInFrom/To revised with tests; unused...
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2021-09-16 gmungocJAL-3761 extra check that VCF feature is fully mappable...
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2021-09-16 gmungocJAL-3761 debugged and working (but not tidied) locateInFrom2/To2
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2021-09-16 Ben SoaresJAL-3761 listToArray became rangeListToArray
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2021-09-16 gmungocJAL-3761 locateInFrom2 work in progress commit
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2021-09-15 gmungocJAL-3761 unit test for MapList.countPos()
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2021-09-15 gmungocJAL-3761 failing test, formatting, method renamed
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2021-09-15 gmungocJAL-3761 failing tests for locateInFrom/To with overlapping...
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2021-09-15 gmungocJAL-3751 only merge strictly contiguous ranges of mappings
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2021-09-15 gmungocJAL-3788 synchronize concurrent findColour() and alignmentCh...
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2021-09-15 Ben SoaresJAL-3818 formatting
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