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JAL-3949 Complete new abstracted logging framework in jalview.log. Updated log calls...
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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2022-01-28 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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2022-01-10 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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2021-12-15 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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2021-12-07 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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2021-11-05 Ben SoaresJAL-3746 Updated help docs for 3D-Beacons. Added and...
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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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2021-10-26 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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2021-09-15 gmungocJAL-3818 process Jmol callbacks in AWT thread
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2021-09-15 Ben SoaresMerge branch 'develop' into merge/develop_ben2
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2021-09-15 Ben SoaresMerge branch 'develop' of https://source.jalview.org...
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2021-09-15 Ben SoaresJAL-3829 Fixed Jmol jar -- duplicates of other classes...
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2021-09-15 Ben SoaresMerge branch 'develop' into merge/develop_ben2
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2021-09-14 Jim ProcterJAL-3815 default /etc/jalview_properties under utils...
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2021-09-14 Ben SoaresMerge branch 'develop' of https://source.jalview.org...
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2021-09-14 Ben SoaresJAL-3521 Adjusted wrapper shell script and .desktop...
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2021-09-14 Ben SoaresJAL-3521 High quality file icons for jalview associated...
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2021-09-14 Ben SoaresJAL-3521 Change grouped Jalview windows on linux taskbar...
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2021-09-14 Ben SoaresJAL-2422 Also look in ~/Applications for ChimeraX on...
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2021-09-14 Ben SoaresJAL-2422 More helpful highlighting/user guidance of...
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2021-09-14 Ben SoaresJAL-2422 Fixed URL encoding of REST calls (broken paths...
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2021-09-13 Ben SoaresMerge branch 'develop' of https://source.jalview.org...
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2021-09-13 Ben SoaresJAL-2422 Fixed URL encoding of REST calls (broken paths...
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2021-09-13 Ben SoaresMerge branch 'develop' into feature/JAL-2422ChimeraX
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2021-09-13 Ben SoaresJAL-2422 Added linux rpm and deb install locations...
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2021-07-21 Ben SoaresJAL-3850 fixed full class name
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2021-07-21 Ben SoaresJAL-3850 using reflection for SimpleHttpFileServerFactory
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2021-06-18 Ben SoaresJAL-3594 Updated the Jalview Develop getdown splashscreen...
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2021-06-08 Ben SoaresMerge branch 'develop' into improvement/JAL-3830_macOS_bundl...
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2021-04-26 Ben SoaresJAL-3248 Moved old README to doc/old_README and put...
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2021-04-26 Ben SoaresJAL-3743 JAL-3745 Fixed NullPointerExceptions happening...
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2021-04-22 Ben SoaresJAL-3833 Allow setHiDPI and setHiDPIScale to work more...
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2021-04-18 Ben SoaresJAL-3833 cap the scaling used by HiDPISetting for incorrect...
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2021-04-13 Ben SoaresJAL-3830 Improved jalview.bat to find either pwsh.exe...
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2021-03-31 Ben SoaresJAL-3830 BAT file wrapper around powershell, so jalview...
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2021-03-30 Ben SoaresJAL-3830 Follow all SymbolicLinks in Windows powershell...
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2021-03-26 Ben SoaresJAL-3830 delete channel.props and channel.propsv when...
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2021-03-25 Ben SoaresJAL-3633 new getdown jars
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2021-03-25 Ben SoaresJAL-3633 refactored/simplified LaunchUtils code
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2021-03-25 Ben SoaresJAL-3633 new getdown jars
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2021-03-25 Ben SoaresJAL-3633 getdown reads jalview_properties for proxy...
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2021-03-24 Ben SoaresJAL-3830 Moved wrappers to bin/jalview.* and make a...
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2021-03-20 Ben SoaresJAL-3503 Changed decimal display of memory in Prefences
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2021-03-19 Ben SoaresJAL-3594 Making default .jalview_properties file separate...
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2021-03-19 Ben SoaresJAL-3503 missed a widget being disabled
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