build.gradle

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JAL-3874 - replace Jmol with custom build of 14.31.53 from Jmol-SwingJS GitHub repo

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JAL-3874 attempt to add source jars to eclipse through buildship

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JAL-3871 replaced Jmol with zip -F version fo Jmol and added excludeDuplicates flags to build.gradle

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JAL-3850 fixed full class name

JAL-3850 using reflection for SimpleHttpFileServerFactory

JAL-3847 set default behaviour as exclude when dealing with duplicate entries in jars and zips

JAL-3847 set default behaviour as exclude when dealing with duplicate entries in jars and zips

Merge branch 'develop' into improvement/JAL-3830_macOS_bundle_wrapper

JAL-3743 Fixed NullPointerExceptions happening with linkCheck task when gradle >= 6.6

JAL-3743 JAL-3745 Fixed NullPointerExceptions happening with linkCheck and jalviewjsTranspile tasks when gradle >= 6.6

JAL-3743 JAL-3745 Fixed NullPointerExceptions happening with linkCheck and jalviewjsTranspile tasks when gradle >= 6.6

JAL-3830 BAT file wrapper around powershell, so jalview works in command prompt. Added install4j option for installer to add Jalview's bin dir to Path in Windows. Added install4j option to create symlink to bash script to user's local bin (first of ~/bin, ~/.local/bin, ~/local/bin, ~/opt/bin that exists. First two of these usually automatically in PATH).

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JAL-3633 getdown reads jalview_properties for proxy settings

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JAL-3830 Moved wrappers to bin/jalview.* and make a symlink bin/jalview. Install4j script now jalviewg

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JAL-3503 Added a Startup tab in Preferences, with gui for JVMMEMMAX and JVMMEMPC settings. Allowed jalview.bin.Launcher and getdown to read/use these memory settings at launch. Added channel.props to getdown appdir, used to determing correct .jalview_properties file. Refactored MemorySetting a bit, with more helper methods for the Preferences tab.

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JAL-3830 Now using a single universal bash script (jalviewc) for bash in linux, macos, cygwin and WSL. It keeps things together.

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JAL-3830 add the windows bash script to getdown files and install4j installers

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JAL-3830 improved bash scripts. Added powershell script. Needs testing

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JAL-3830 unix and macos wrappers. Symbolic link to jalviewc-macos in Contents/MacOS/jalviewc.

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JAL-3830 install4j adds script to Jalview.app/Contents/MacOS/jalview but we need install4j9 to make it executable

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JAL-3826 Simple configuration with CodeStyle implemented in .editorconfig file

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JAL-3521 Changed wording of INSTALLATION in source tarball build_properties

JAL-3521 Changed wording of INSTALLATION in source tarball build_properties

JAL-3521 Adding a build_properties into sourceDist tarball, with INSTALLATION=SourceDist git-commit...

JAL-3521 Adding a build_properties into sourceDist tarball, with INSTALLATION=SourceDist git-commit...

JAL-3521 Moved the debian build.gradle to utils/debian/build.gradle.debian

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Merge branch 'task/JAL-3805_Remove_Uninstall_Old_Jalview_application_for_develop_branch' into task/JAL-3796_notarization_no_uninstaller

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Merge branch 'develop' into task/JAL-3796_notarization_no_uninstaller

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Merge branch 'develop' into task/JAL-3796_notarization

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