jalview

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JAL-3826 added root=true to editorconfig for IntelliJ

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

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    /src/.editorconfig
JAL-3822 pass panel height and width to wrapped geometry calculations

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    /test/jalview/gui/SeqPanelTest.java
JAL-2422 remove temporary patch (requires ChimeraX Daily or 1.2 build)

JAL-3251 On linux set (sun.awt.X11.XToolkit.)awtAppClassName to set the grouped application name in the taskbar

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-2422 updated unit test for ChimeraX command change

JAL-2422 a fix and a fudge for two failing ChimeraX commands

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

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

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

JAL-3521 Updating file opening marker to %u

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    /utils/debian/mime_types_for_debian.pl
JAL-3521 Debian mime-type and desktop helper files, and script to create them

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    /utils/debian/debian/jalview-file.png
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    /utils/debian/debian/jalview-icon.png
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    /utils/debian/debian/jalview-mailcap
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    /utils/debian/debian/jalview-mime.xml
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    /utils/debian/debian/jalview.desktop
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    /utils/debian/file_associations_template-mailcap.txt
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    /utils/debian/file_associations_template-shared-mime-info.xml
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    /utils/debian/mime_types_for_debian.pl
JAL-3805 Smaller DMG Finder windows for all DS_Store files in utils/channels/... . Removed no longer used DS_Store files from utils/install4j.

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    /utils/install4j/DS_Store-NON-RELEASE
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    /utils/install4j/DS_Store-TEST-RELEASE
JAL-3805 New DS_Store for smaller DMG Finder window

JAL-3805 Remove Uninstall Old Jalview.app in Release_2_11_1_Branch

JAL-3038 corrected code that reads editable JComboBox text input

JAL-3796 update to Install4j 8.0.10 and add config for code notarization

JAL-3789 Use j2s.config.altfileproperty in .j2s for alternative temporary build/jalviewjs/config/j2s settings file when running a headless build in gradle

JAL-3789 New swingjs for Java2Script 3.2.10 with j2s.config.altfileproperty

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    /swingjs/differences.txt
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    /swingjs/ver/3.2.10-j11/DEV_NOTES.txt
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    /swingjs/ver/3.2.10-j11/SwingJS-site.zip
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    /swingjs/ver/3.2.10-j11/_j2sclasslist.txt
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    /swingjs/ver/3.2.10-j11/differences.txt
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    /swingjs/ver/3.2.10-j11/net.sf.j2s.core-j11.jar
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    /swingjs/ver/3.2.10-j11/timestamp
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    /swingjs/ver/3.2.10/DEV_NOTES.txt
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    /swingjs/ver/3.2.10/SwingJS-site.zip
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    /swingjs/ver/3.2.10/_j2sclasslist.txt
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JAL-3280 Fixed the version checking URL formulation (getdown build_properties) for jalviewjs, can also use it for jalviewjs in future

JAL-3783 Reverting to using groovy-all-2.4.12-indy.jar to fix serious problem with Groovy console using shadowJar

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    /j11lib/groovy-all-2.4.12-indy.jar
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    /j11lib/groovy-cli-commons-2.5.7.jar
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    /j11lib/groovy-cli-picocli-2.5.7.jar
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    /j11lib/groovy-docgenerator-2.5.7.jar
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JAL-3628 Test for doubly saved single backup file scheme

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    /test/jalview/io/BackupFilesTest.java
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    /test/jalview/io/testProps_singlefilebackup.jvprops
JAL-3594 Allow setting of getdownappbase and getdowndistdir properties for DEVELOP channel, and change DEVELOP version to be VERSION-dDATE instead of VERSION-develop. dDATE will help users know when Jalview Develop applicaiton updated

JAL-3594 Defintely want SplashScreen to appear in the Desktop window otherwise it might not be closeable

JAL-3594 Changed building.md to describe -PCHANNEL=JALVIEWJS and JALVIEWJS-TEST

JAL-3594 Changed building.md to reflect change of name of channel_properties to channel.props

JAL-3594 Adjustments to allow JalviewJS to use ChannelProperties, and new utils/channels dir for jalviewjs and jalviewjs-release

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    /src/jalview/util/ChannelProperties.java
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    /utils/channels/default/resources/channel.props
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    /utils/channels/develop/resources/channel.props
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    /utils/channels/jalviewjs-release
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    /utils/channels/jalviewjs/channel_gradle.properties
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    /utils/channels/jalviewjs/images/UoD_banner-28.png
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    /utils/channels/jalviewjs/images/UoD_banner-32.png
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    /utils/channels/jalviewjs/images/barton_group-30.png
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    /utils/channels/jalviewjs/images/barton_group-512.png
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    /utils/channels/jalviewjs/images/barton_group-62.png
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    /utils/channels/jalviewjs/images/barton_group-white-512.png
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JAL-3775 JAL-3633 Make java.net.Authenticator code conditional on not being JalviewJS

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    /src/jalview/jbgui/GPreferences.java