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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
2021-09-14	Ben Soares	JAL-2422 More helpful highlighting/user guidance of...	commit \| commitdiff \| tree
2021-09-14	Ben Soares	JAL-2422 Fixed URL encoding of REST calls (broken paths...	commit \| commitdiff \| tree
2021-09-13	Ben Soares	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2021-09-13	Ben Soares	JAL-2422 Fixed URL encoding of REST calls (broken paths...	commit \| commitdiff \| tree
2021-09-13	Ben Soares	Merge branch 'develop' into feature/JAL-2422ChimeraX	commit \| commitdiff \| tree
2021-09-13	Ben Soares	JAL-2422 Added linux rpm and deb install locations...	commit \| commitdiff \| tree
2021-07-21	Ben Soares	JAL-3850 fixed full class name	commit \| commitdiff \| tree
2021-07-21	Ben Soares	JAL-3850 using reflection for SimpleHttpFileServerFactory	commit \| commitdiff \| tree
2021-06-18	Ben Soares	JAL-3594 Updated the Jalview Develop getdown splashscreen...	commit \| commitdiff \| tree
2021-06-08	Ben Soares	Merge branch 'develop' into improvement/JAL-3830_macOS_bundl...	commit \| commitdiff \| tree
2021-04-26	Ben Soares	JAL-3248 Moved old README to doc/old_README and put...	commit \| commitdiff \| tree
2021-04-26	Ben Soares	JAL-3743 JAL-3745 Fixed NullPointerExceptions happening...	commit \| commitdiff \| tree
2021-04-22	Ben Soares	JAL-3833 Allow setHiDPI and setHiDPIScale to work more...	commit \| commitdiff \| tree
2021-04-18	Ben Soares	JAL-3833 cap the scaling used by HiDPISetting for incorrect...	commit \| commitdiff \| tree
2021-04-13	Ben Soares	JAL-3830 Improved jalview.bat to find either pwsh.exe...	commit \| commitdiff \| tree
2021-03-31	Ben Soares	JAL-3830 BAT file wrapper around powershell, so jalview...	commit \| commitdiff \| tree
2021-03-30	Ben Soares	JAL-3830 Follow all SymbolicLinks in Windows powershell...	commit \| commitdiff \| tree
2021-03-26	Ben Soares	JAL-3830 delete channel.props and channel.propsv when...	commit \| commitdiff \| tree
2021-03-24	Ben Soares	JAL-3830 Moved wrappers to bin/jalview.* and make a...	commit \| commitdiff \| tree
2021-03-17	Ben Soares	JAL-3830 Allow paths to start with '~'. Make path check...	commit \| commitdiff \| tree
2021-03-17	Ben Soares	JAL-3830 Now using a single universal bash script ...	commit \| commitdiff \| tree
2021-03-17	Ben Soares	JAL-3830 add the windows bash script to getdown files...	commit \| commitdiff \| tree
2021-03-17	Ben Soares	JAL-3830 bash script that works in both cygwin and...	commit \| commitdiff \| tree
2021-03-15	Ben Soares	JAL-3830 Delete wrapper scripts and getdown *v files...	commit \| commitdiff \| tree
2021-03-15	Ben Soares	JAL-3830 powershell wrapper tested on linux, macos...	commit \| commitdiff \| tree
2021-03-14	Ben Soares	JAL-3830 minor fix in powershell wrapper	commit \| commitdiff \| tree
2021-03-14	Ben Soares	JAL-3830 powershell follows symlinks as they do exist...	commit \| commitdiff \| tree
2021-03-14	Ben Soares	JAL-3830 Powershell wrapper now works cross-platform...	commit \| commitdiff \| tree
2021-03-14	Ben Soares	JAL-3830 Make wrapper scripts executable	commit \| commitdiff \| tree
2021-03-12	Ben Soares	JAL-3830 powershell wrapper tested and fixed	commit \| commitdiff \| tree
2021-03-12	Ben Soares	JAL-3830 improved bash scripts. Added powershell script...	commit \| commitdiff \| tree
2021-03-12	Ben Soares	JAL-3830 unix and macos wrappers. Symbolic link to...	commit \| commitdiff \| tree
2021-03-11	Ben Soares	JAL-3830 Improved for .app dir name with spaces, e...	commit \| commitdiff \| tree
2021-03-10	Ben Soares	JAL-3830 install4j adds script to Jalview.app/Contents...	commit \| commitdiff \| tree
2021-03-10	Ben Soares	JAL-3830 first draft of wrapper script to go in macOS...	commit \| commitdiff \| tree
2021-03-05	Ben Soares	JAL-3618 Enable appBundleIsTraversable in JFileChooser...	commit \| commitdiff \| tree
2021-03-04	Ben Soares	JAL-3594 Allow a channel to use a different preferences...	commit \| commitdiff \| tree
2021-02-10	Ben Soares	JAL-3251 On linux set (sun.awt.X11.XToolkit.)awtAppClassName...	commit \| commitdiff \| tree
2021-02-10	Ben Soares	JAL-3521 Changed wording of INSTALLATION in source...	commit \| commitdiff \| tree
2021-02-08	Ben Soares	JAL-3521 Adding a build_properties into sourceDist...	commit \| commitdiff \| tree
2021-01-26	Ben Soares	JAL-3521 Updating file opening marker to %u	commit \| commitdiff \| tree
2021-01-26	Ben Soares	JAL-3521 Debian mime-type and desktop helper files...	commit \| commitdiff \| tree
2021-01-22	Ben Soares	JAL-3805 Smaller DMG Finder windows for all DS_Store...	commit \| commitdiff \| tree
2021-01-22	Ben Soares	JAL-3805 New DS_Store for smaller DMG Finder window	commit \| commitdiff \| tree
2021-01-22	Ben Soares	JAL-3805 Remove Uninstall Old Jalview.app in Release_2_11_1_...	commit \| commitdiff \| tree
2021-01-11	Ben Soares	JAL-3789 Use j2s.config.altfileproperty in .j2s for...	commit \| commitdiff \| tree
2021-01-11	Ben Soares	JAL-3789 New swingjs for Java2Script 3.2.10 with j2s...	commit \| commitdiff \| tree
2020-12-14	Ben Soares	JAL-3280 Fixed the version checking URL formulation...	commit \| commitdiff \| tree
2020-12-14	Ben Soares	JAL-3783 Reverting to using groovy-all-2.4.12-indy...	commit \| commitdiff \| tree
2020-12-14	Ben Soares	JAL-3628 Test for doubly saved single backup file scheme	commit \| commitdiff \| tree
2020-12-14	Ben Soares	JAL-3594 Allow setting of getdownappbase and getdowndistdir...	commit \| commitdiff \| tree
2020-12-14	Ben Soares	JAL-3280 Test for remote release build_properties file...	commit \| commitdiff \| tree
2020-12-14	Ben Soares	JAL-3280 fixes after CR-JAL-241. Now only checking...	commit \| commitdiff \| tree
2020-12-14	Ben Soares	JAL-3280 Pass appbase and appdir from getdown to jalvew...	commit \| commitdiff \| tree
2020-12-11	Ben Soares	JAL-3594 Defintely want SplashScreen to appear in the...	commit \| commitdiff \| tree
2020-12-11	Ben Soares	JAL-3594 Changed building.md to describe -PCHANNEL...	commit \| commitdiff \| tree
2020-12-11	Ben Soares	JAL-3594 Changed building.md to reflect change of name...	commit \| commitdiff \| tree
2020-12-11	Ben Soares	JAL-3594 Adjustments to allow JalviewJS to use ChannelProper...	commit \| commitdiff \| tree
2020-12-11	Ben Soares	JAL-3775 JAL-3633 Make java.net.Authenticator code...	commit \| commitdiff \| tree
2020-12-10	Ben Soares	Merge branch 'task/JAL-3594_updated--CHANNEL_cosmetics...	commit \| commitdiff \| tree
2020-12-10	Ben Soares	JAL-3594 Better Jalview Develop banner	commit \| commitdiff \| tree
2020-12-10	Ben Soares	JAL-3594 Documentation added to building.md for using...	commit \| commitdiff \| tree
2020-12-10	Ben Soares	Merge branch 'task/JAL-3594_updated--CHANNEL_cosmetics...	commit \| commitdiff \| tree
2020-12-10	Ben Soares	Merge branch 'merge/develop_and_rebase_squashed_merge_JAL...	commit \| commitdiff \| tree
2020-12-09	Ben Soares	JAL-3594 Improved About banners for develop and test...	commit \| commitdiff \| tree
2020-12-09	Ben Soares	JAL-3594 Images for splash screen	commit \| commitdiff \| tree
2020-12-09	Ben Soares	JAL-3594 JAL-3728 Added taskbar icons to desktop and...	commit \| commitdiff \| tree
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