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2022-03-08	Ben Soares	JAL-3103 Removed code and unused widgets for defaultBrowser	commit \| commitdiff \| tree
2022-03-08	Ben Soares	JAL-3103 Remove BrowserLauncher2 and use Desktop.browse...	commit \| commitdiff \| tree
2022-03-08	Ben Soares	JAL-3103 add BrowserLauncher2 LGPLv2.1 to THIRDPARTYLIBS	commit \| commitdiff \| tree
2022-03-08	Ben Soares	JAL-3103 Put jalview.jar first in getdown for .properties...	commit \| commitdiff \| tree
2022-03-07	Ben Soares	JAL-3103 Switched to (a wrapper around) BrowserLauncher2	commit \| commitdiff \| tree
2022-03-04	Ben Soares	JAL-3830 added command line to whatsnew and releases	commit \| commitdiff \| tree
2022-03-04	Ben Soares	JAL-3830 Added new command line usage to docs	commit \| commitdiff \| tree
2022-03-04	Ben Soares	JAL-3608 added to LaF documentation	commit \| commitdiff \| tree
2022-03-03	Ben Soares	JAL-3830 fix broken/buggy install4j9 setting of executeSetup...	commit \| commitdiff \| tree
2022-03-02	Ben Soares	JAL-3691 bumped the version to 1.8.3-1.2.12 in source...	commit \| commitdiff \| tree
2022-03-02	Ben Soares	JAL-3962 Added jre/bin and dist folders to the native...	commit \| commitdiff \| tree
2022-03-02	Ben Soares	JAL-3130 updated download_jres.sh	commit \| commitdiff \| tree
2022-02-12	Ben Soares	JAL-3949 fix testProps path and make line count more...	commit \| commitdiff \| tree
2022-02-11	Ben Soares	Merge branch 'update/JAL-3949_jalview_bin_Console_to_cure_sa...	commit \| commitdiff \| tree
2022-02-11	Ben Soares	JLogger loglevel check on whether to call the actual...	commit \| commitdiff \| tree
2022-02-11	Ben Soares	JAL-3949 fixed failing commandlinetests due to more...	commit \| commitdiff \| tree
2022-02-11	Ben Soares	JAL-3949 added Java Console autoscrolling help paragraph	commit \| commitdiff \| tree
2022-02-11	Ben Soares	JAL-3949 read ~/.jalview_properties before initialising...	commit \| commitdiff \| tree
2022-02-11	Ben Soares	Merge branch 'develop' into update/JAL-3949_abstracted_loggi...	commit \| commitdiff \| tree
2022-02-11	Ben Soares	JAL-3949 Complete new abstracted logging framework...	commit \| commitdiff \| tree
2022-02-04	Ben Soares	JAL-3949 An attempt at converting to Log4j 2 -- no...	commit \| commitdiff \| tree
2022-02-03	Ben Soares	JAL-3949 upgraded log4j to 2.17.1 (no actual known...	commit \| commitdiff \| tree
2022-01-29	Ben Soares	JAL-3830 JAL-3420 added new jvl_file to install4j9...	commit \| commitdiff \| tree
2022-01-29	Ben Soares	Merge branch 'develop' into improvement/JAL-3830_install4j9_...	commit \| commitdiff \| tree
2022-01-28	Ben Soares	Merge branch 'develop' into improvement/JAL-3420_match_jvl_i...	commit \| commitdiff \| tree
2022-01-28	Ben Soares	new jvl_file svg, png, ico and icns files, and changed...	commit \| commitdiff \| tree
2022-01-12	Ben Soares	JAL-3703 Test that fails in Windows only, and only...	commit \| commitdiff \| tree
2022-01-11	Ben Soares	JAL-3703 fix Gff3 shared InputStream with embedded...	commit \| commitdiff \| tree
2022-01-11	Ben Soares	close filehandles straight after parse, without setting...	commit \| commitdiff \| tree
2022-01-10	Ben Soares	JAL-3937 enable AIA download of intermediate certificates...	commit \| commitdiff \| tree
2021-12-22	Ben Soares	Merge branch 'develop' into critical/JAL-3933_log4j_update_f...	commit \| commitdiff \| tree
2021-12-22	Ben Soares	JAL-3934 updated log4j from 2.16.0 to 2.17.0	commit \| commitdiff \| tree
2021-12-15	Ben Soares	JAL-3933 updated THIRDPARTYLIBS	commit \| commitdiff \| tree
2021-12-15	Ben Soares	JAL-3933 updated THIRDPARTYLIBS	commit \| commitdiff \| tree
2021-12-14	Ben Soares	JAL-3933 updated log4j and slf4j jars with log4j1.2...	commit \| commitdiff \| tree
2021-12-07	Ben Soares	JAL-3930 Added a customizedId="JALVIEW" to launcher...	commit \| commitdiff \| tree
2021-12-07	Ben Soares	JAL-3930 Added a customizedId="JALVIEW" to launcher...	commit \| commitdiff \| tree
2021-11-29	Ben Soares	JAL-3594 correct Jalview Develop logo SVG added in...	commit \| commitdiff \| tree
2021-11-16	Ben Soares	JAL-3553 added customized labels for install4j output.txt	commit \| commitdiff \| tree
2021-11-01	Ben Soares	JAL-3907 changed two commented out lines to reflect...	commit \| commitdiff \| tree
2021-11-01	Ben Soares	JAL-3907 added creation of symbolic links to workaround...	commit \| commitdiff \| tree
2021-10-28	Ben Soares	JAL-3830 forgot to uncheck this	commit \| commitdiff \| tree
2021-10-27	Ben Soares	JAL-3830 quick fix to installer text	commit \| commitdiff \| tree
2021-10-27	Ben Soares	JAL-3830 install4j9 tries to parse and can't cope with...	commit \| commitdiff \| tree
2021-10-26	Ben Soares	JAL-3830 Added steps for install4j9 to create macOS...	commit \| commitdiff \| tree
2021-10-26	Ben Soares	JAL-3907 adjusted download_jdks.sh and download_jres...	commit \| commitdiff \| tree
2021-10-01	gmungoc	JAL-3725 restrict mapped virtual feature location to...	commit \| commitdiff \| tree
2021-10-01	gmungoc	JAL-3725 helper methods for computing mapped feature...	commit \| commitdiff \| tree
2021-10-01	gmungoc	JAL-3725 exclude stop codon from CDS-to-protein mapping	commit \| commitdiff \| tree
2021-10-01	Ben Soares	Merge branch 'improvement/JAL-3594_logos_for_jalview_test...	commit \| commitdiff \| tree
2021-10-01	Ben Soares	Merge branch 'develop' into improvement/JAL-3594_logos_for_j...	commit \| commitdiff \| tree
2021-10-01	Ben Soares	JAL-3594 New Jalview Test logos and .icns/.ico creation...	commit \| commitdiff \| tree
2021-09-30	Ben Soares	JAL-3594 Changed logo for Jalview Test	commit \| commitdiff \| tree
2021-09-30	Ben Soares	JAL-1260 Added .gbk to GenBank extensions. Added GenBank...	commit \| commitdiff \| tree
2021-09-30	gmungoc	JAL-3371 more fine-grained slider; set Param slider...	commit \| commitdiff \| tree
2021-09-29	Ben Soares	JAL-3885 Made the database JComboBox have StringPair...	commit \| commitdiff \| tree
2021-09-28	Ben Soares	JAL-3783 Updated groovy-all-2.4. Currently newer stable...	commit \| commitdiff \| tree
2021-09-21	Ben Soares	JAL-3691 automatic insertion of Locale.ROOT to toUpperCase...	commit \| commitdiff \| tree
2021-09-21	Ben Soares	JAL-3521 'Debian-safe' version of minimal build.gradle...	commit \| commitdiff \| tree
2021-09-20	Ben Soares	JAL-3521 Created a patch file to transform build.gradle...	commit \| commitdiff \| tree
2021-09-20	Ben Soares	JAL-3521 working minimal build.gradle for debian and...	commit \| commitdiff \| tree
2021-09-20	Ben Soares	JAL-3521 not quite working minimal build.gradle for...	commit \| commitdiff \| tree
2021-09-17	Ben Soares	Merge branch 'merge/develop_JAL-1260' into develop	commit \| commitdiff \| tree
2021-09-17	Ben Soares	JAL-1260 rudimentary parsing of LOCUS line to at least...	commit \| commitdiff \| tree
2021-09-17	gmungoc	JAL-1260 refactored multi-line qualifier separators	commit \| commitdiff \| tree
2021-09-17	gmungoc	JAL-1260 unit test for FileFormats updated for GenBank/ENA	commit \| commitdiff \| tree
2021-09-17	gmungoc	JAL-1260 file formats and IdentifyFile updates for...	commit \| commitdiff \| tree
2021-09-17	gmungoc	JAL-1260 refactored GenBank (and EMBL) flat file parser	commit \| commitdiff \| tree
2021-09-17	Jim Procter	JAL-1260 FileFormat entry for EMBL/GENBANK: TODO: create...	commit \| commitdiff \| tree
2021-09-16	Ben Soares	JAL-3779 Added to documentation	commit \| commitdiff \| tree
2021-09-16	gmungoc	JAL-3779 apply properties to all groups with given...	commit \| commitdiff \| tree
2021-09-16	Ben Soares	JAL-3774 combined changes from bug/JAL-3774_splitFrameFinder...	commit \| commitdiff \| tree
2021-09-16	Ben Soares	JAL-3739 (combined) commits from feature/JAL-3739_useFormFie...	commit \| commitdiff \| tree
2021-09-16	Jim Procter	JAL-3794 X and N are counted as DNA characters, but...	commit \| commitdiff \| tree
2021-09-16	Jim Procter	JAL-3794 new test for recognition of protein or DNA...	commit \| commitdiff \| tree
2021-09-16	Ben Soares	JAL-3761 listToArray became rangeListToArray	commit \| commitdiff \| tree
2021-09-16	gmungoc	JAL-3761 more consistent parameter naming	commit \| commitdiff \| tree
2021-09-16	gmungoc	JAL-3761 helper method reinstated to avoid code duplication	commit \| commitdiff \| tree
2021-09-16	gmungoc	JAL-3761 locateInFrom/To revised with tests; unused...	commit \| commitdiff \| tree
2021-09-16	gmungoc	JAL-3761 extra check that VCF feature is fully mappable...	commit \| commitdiff \| tree
2021-09-16	gmungoc	JAL-3761 debugged and working (but not tidied) locateInFrom2/To2	commit \| commitdiff \| tree
2021-09-16	Ben Soares	JAL-3761 listToArray became rangeListToArray	commit \| commitdiff \| tree
2021-09-16	gmungoc	JAL-3761 locateInFrom2 work in progress commit	commit \| commitdiff \| tree
2021-09-15	gmungoc	JAL-3761 unit test for MapList.countPos()	commit \| commitdiff \| tree
2021-09-15	gmungoc	JAL-3761 failing test, formatting, method renamed	commit \| commitdiff \| tree
2021-09-15	gmungoc	JAL-3761 failing tests for locateInFrom/To with overlapping...	commit \| commitdiff \| tree
2021-09-15	gmungoc	JAL-3751 only merge strictly contiguous ranges of mappings	commit \| commitdiff \| tree
2021-09-15	gmungoc	JAL-3788 synchronize concurrent findColour() and alignmentCh...	commit \| commitdiff \| tree
2021-09-15	Ben Soares	JAL-3818 formatting	commit \| commitdiff \| tree
2021-09-15	gmungoc	JAL-3818 process Jmol callbacks in AWT thread	commit \| commitdiff \| tree
2021-09-15	Ben Soares	Merge branch 'develop' into merge/develop_ben2	commit \| commitdiff \| tree
2021-09-15	Ben Soares	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2021-09-15	Ben Soares	JAL-3829 Fixed Jmol jar -- duplicates of other classes...	commit \| commitdiff \| tree
2021-09-15	Ben Soares	Merge branch 'develop' into merge/develop_ben2	commit \| commitdiff \| tree
2021-09-14	Jim Procter	JAL-3815 default /etc/jalview_properties under utils...	commit \| commitdiff \| tree
2021-09-14	Ben Soares	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2021-09-14	Ben Soares	JAL-3521 Adjusted wrapper shell script and .desktop...	commit \| commitdiff \| tree
2021-09-14	Ben Soares	JAL-3521 High quality file icons for jalview associated...	commit \| commitdiff \| tree
2021-09-14	Ben Soares	JAL-3521 Change grouped Jalview windows on linux taskbar...	commit \| commitdiff \| tree
2021-09-14	Ben Soares	JAL-2422 Also look in ~/Applications for ChimeraX on...	commit \| commitdiff \| tree
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