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Merge branch 'merge/develop_JAL-1260' into develop
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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2021-03-24 Ben SoaresJAL-3830 Moved wrappers to bin/jalview.* and make a...
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2021-03-17 Ben SoaresJAL-3830 Allow paths to start with '~'. Make path check...
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2021-03-17 Ben SoaresJAL-3830 Now using a single universal bash script ...
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2021-03-17 Ben SoaresJAL-3830 add the windows bash script to getdown files...
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2021-03-17 Ben SoaresJAL-3830 bash script that works in both cygwin and...
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2021-03-15 Ben SoaresJAL-3830 Delete wrapper scripts and getdown *v files...
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2021-03-15 Ben SoaresJAL-3830 powershell wrapper tested on linux, macos...
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2021-03-14 Ben SoaresJAL-3830 minor fix in powershell wrapper
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2021-03-14 Ben SoaresJAL-3830 powershell follows symlinks as they do exist...
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2021-03-14 Ben SoaresJAL-3830 Powershell wrapper now works cross-platform...
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2021-03-14 Ben SoaresJAL-3830 Make wrapper scripts executable
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2021-03-12 Ben SoaresJAL-3830 powershell wrapper tested and fixed
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2021-03-12 Ben SoaresJAL-3830 improved bash scripts. Added powershell script...
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2021-03-12 Ben SoaresJAL-3830 unix and macos wrappers. Symbolic link to...
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2021-03-11 Ben SoaresJAL-3830 Improved for .app dir name with spaces, e...
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2021-03-10 Ben SoaresJAL-3830 install4j adds script to Jalview.app/Contents...
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2021-03-10 Ben SoaresJAL-3830 first draft of wrapper script to go in macOS...
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2021-03-05 Ben SoaresJAL-3618 Enable appBundleIsTraversable in JFileChooser...
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2021-03-04 Ben SoaresJAL-3594 Allow a channel to use a different preferences...
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2021-02-10 Ben SoaresJAL-3251 On linux set (sun.awt.X11.XToolkit.)awtAppClassName...
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2021-02-10 Ben SoaresJAL-3521 Changed wording of INSTALLATION in source...
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2021-02-08 Ben SoaresJAL-3521 Adding a build_properties into sourceDist...
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2021-01-26 Ben SoaresJAL-3521 Updating file opening marker to %u
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2021-01-26 Ben SoaresJAL-3521 Debian mime-type and desktop helper files...
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2021-01-22 Ben SoaresJAL-3805 Smaller DMG Finder windows for all DS_Store...
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2021-01-22 Ben SoaresJAL-3805 New DS_Store for smaller DMG Finder window
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2021-01-22 Ben SoaresJAL-3805 Remove Uninstall Old Jalview.app in Release_2_11_1_...
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2021-01-11 Ben SoaresJAL-3789 Use j2s.config.altfileproperty in .j2s for...
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2021-01-11 Ben SoaresJAL-3789 New swingjs for Java2Script 3.2.10 with j2s...
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2020-12-14 Ben SoaresJAL-3280 Fixed the version checking URL formulation...
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2020-12-14 Ben SoaresJAL-3783 Reverting to using groovy-all-2.4.12-indy...
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2020-12-14 Ben SoaresJAL-3628 Test for doubly saved single backup file scheme
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2020-12-14 Ben SoaresJAL-3594 Allow setting of getdownappbase and getdowndistdir...
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2020-12-14 Ben SoaresJAL-3280 Test for remote release build_properties file...
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2020-12-14 Ben SoaresJAL-3280 fixes after CR-JAL-241. Now only checking...
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2020-12-14 Ben SoaresJAL-3280 Pass appbase and appdir from getdown to jalvew...
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2020-12-11 Ben SoaresJAL-3594 Defintely want SplashScreen to appear in the...
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2020-12-11 Ben SoaresJAL-3594 Changed building.md to describe -PCHANNEL...
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2020-12-11 Ben SoaresJAL-3594 Changed building.md to reflect change of name...
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2020-12-11 Ben SoaresJAL-3594 Adjustments to allow JalviewJS to use ChannelProper...
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2020-12-11 Ben SoaresJAL-3775 JAL-3633 Make java.net.Authenticator code...
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2020-12-10 Ben SoaresMerge branch 'task/JAL-3594_updated--CHANNEL_cosmetics...
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2020-12-10 Ben SoaresJAL-3594 Better Jalview Develop banner
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2020-12-10 Ben SoaresJAL-3594 Documentation added to building.md for using...
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