utils

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JAL-3225 tasks to create extra desired settings for eclipse

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    ./eclipse/org.eclipse.jdt.groovy.core.prefs
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    ./eclipse/org.eclipse.jdt.ui.prefs
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JAL-3393 Don't need PDF file using Illustrator. Replaced with SVG using Inkscape

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    ./install4j/jalview_dmg_background_layers.pdf
Merge branch 'develop' into Jalview-JS/develop

Conflicts:

.gitignore

build.gradle

gradle.properties

src/jalview/gui/AlignFrame.java

src/jalview/gui/Desktop.java

src/jalview/gui/FeatureSettings.java

src/jalview/gui/JvSwingUtils.java

src/jalview/util/MessageManager.java

test/jalview/gui/AlignmentPanelTest.java

test/jalview/gui/JvSwingUtilsTest.java

test/jalview/gui/PopupMenuTest.java

utils/eclipse/org.eclipse.jdt.core.jalview.prefs

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    ./install4j/jalview_dmg_background_layers.pdf
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JAL-3225 updated essential files for eclipse project if buildship fails

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    ./eclipse/eclipse_startup_files.zip
JAL-3225 updated essential files for eclipse project if buildship fails

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    ./eclipse/eclipse_startup_files.zip
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    ./jalviewjs/eclipse/eclipse_files.zip
JAL-3225 All of .settings now gitignored. org.eclipse...prefs made by buildship or gradle eclipse. Jalview specific prefs pulled in from utils/eclipse/org.eclipse.jdt.core.jalview.prefs

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    ./eclipse/org.eclipse.jdt.core.jalview.prefs
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JAL-3225 All of .settings now gitignored. org.eclipse...prefs made by buildship or gradle eclipse. Jalview specific prefs pulled in from utils/eclipse/org.eclipse.jdt.core.jalview.prefs

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    ./eclipse/org.eclipse.jdt.core.jalview.prefs
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JAL-3210 New site-resources dir too

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    ./jalviewjs/site-resources/applets-nocore.html
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    ./jalviewjs/site-resources/applets.html
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    ./jalviewjs/site-resources/css/ie6.css
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    ./jalviewjs/site-resources/css/ie7.css
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    ./jalviewjs/site-resources/css/reset.css
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    ./jalviewjs/site-resources/css/style.css
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    ./jalviewjs/site-resources/examples/1gaq.txt
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    ./jalviewjs/site-resources/examples/2GIS.pdb
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    ./jalviewjs/site-resources/examples/3W5V.pdb
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    ./jalviewjs/site-resources/examples/backupfilestest.fa
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    ./jalviewjs/site-resources/examples/biojsonschema.json
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    ./jalviewjs/site-resources/examples/dna_interleaved.phy
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    ./jalviewjs/site-resources/examples/dna_sequential.phy
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JAL-3210 New version of swingjs and supporting .zip libraries. Swing-JS version 3.2.9.v1e

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    ./jalviewjs/libjs/MiGLayout-site.zip
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    ./jalviewjs/libjs/intervalstore-site.zip
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JAL-3227 slightly adapted download_jres.sh to make it easier to specify GNU tar on macos. 'TAR=gtar'

JAL-3394 Made Categories line configurable/readable in gradle.properties as will be used more generically in future

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    ./install4j/install4j8_template.install4j
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JAL-3394 Added Categories=Science;Biology;Java; to unix shell installer .desktop file

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    ./install4j/install4j8_template.install4j
JAL-3289 Improved the name of the channel_launch.jvl file to channel_launch-CHANNELNAMEWITHPLANKEY.jvl

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    ./install4j/install4j8_template.install4j
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JAL-3252 download-jres.sh helper script for keeping JREs for all platforms up to date changed to create .zip files for getdown OTA updates

JAL-3394 A little streamlining and fixing of helper script

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    ./install4j/install4j8_template.install4j
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JAL-3394 remove no longer used files

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    ./install4j/Jalview-Version-Locator.icns
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    ./install4j/Jalview-Version-Locator.ico
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    ./install4j/Jalview-Version-Locator.png
JAL-3449 getdown resilience change to launcher classpath, includes the backup getdown-launcher.jar

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    ./install4j/install4j8_template.install4j
JAL-3227 helper shell scripts for setting up a build environment

JAL-3523 No longer change CWD of getdown when invoked by install4j launcher

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    ./install4j/install4j8_template.install4j
JAL-3447 MSI installer for windows

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    ./install4j/install4j8_template.install4j
JAL-3393 Trying out a beta strand arrow in the DMG background

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    ./install4j/beta-strand2.png
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    ./install4j/jalview_dmg_background.png
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    ./install4j/jalview_dmg_background_blur_layers_beta_strand.png
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    ./install4j/jalview_dmg_background_blur_layers_beta_strand.svg
JAL-3394 Removed libjli.dylib symbolic link from embedded macOS JRE, works in 8 and 11. Preparation for non-linked Uninstall.app in DMG

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    ./install4j/DS_Store_no_link
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    ./install4j/dmg_nolink_install4j8_template.install4j
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    ./install4j/install4j8_template.install4j
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JAL-3394 Variable-ise output folders -- will work better with sub-project/modularised gradle build

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    ./install4j/install4j8_template.install4j
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JAL-3130 Improved locations of AdoptOpenJDK JRE downloads \(locally and on build server\) and helper script download_jres.sh to update them using AdoptOpenJDK API.

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    ./install4j/download_jres.sh
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    ./install4j/install4j8_template.install4j
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JAL-3447 Minor improvement on file association creation

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    ./install4j/auto_file_associations-i4j8.pl
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    ./install4j/file_associations_auto-install4j8.xml
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    ./install4j/file_associations_template-install4j8.xml
JAL-3393 Improved background image, SVG file, and added instructions on how the image is made

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    ./install4j/DMG_background_image_creation_README.md
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    ./install4j/jalview_dmg_background_blur_72dpi.png
JAL-3393 Improved background image, SVG file, and added instructions on how the image is made

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    ./install4j/DMG_background_image_creation_README.md
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    ./install4j/jalview_dmg_background.png
JAL-3393 Improved background image, and generating SVG file

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    ./install4j/jalview_dmg_background-old.png
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    ./install4j/jalview_dmg_background.png
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    ./install4j/jalview_dmg_background_blur.png
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    ./install4j/jalview_dmg_background_blur_layers.svg
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    ./install4j/jalview_dmg_background_layers.svg
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    ./install4j/jalview_dmg_background_pale.png
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    ./install4j/jalview_dmg_background_plain.png
JAL-3447 minor corrections to cif and mmcif file associations

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    ./install4j/auto_file_associations-i4j8.pl
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    ./install4j/file_associations_auto-Info_plist.xml
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    ./install4j/file_associations_auto-install4j8.xml
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    ./install4j/install4j8_template.install4j
JAL-3210 Bringing in improvements to build.gradle

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    ./install4j/file_associations_auto-Info_plist.xml
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    ./install4j/file_associations_auto-install4j8.xml
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    ./install4j/install4j8_template.install4j
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