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JAL-3446 latest jmol zip from JAL-3253-applet (commit c28e0a1)

JAL-3541 Helpers for running tests, and other commands headlessly

JAL-3541 Helpers for running tests, and other commands headlessly

JAL-3541 JavaExec tasks for cloverInstr and cloverReport. Rationalised compileClasspaths for main, clover and test.

    • binary
    ./clover/lib/clover-ant-4.4.1.jar
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JAL-3541 JavaExec tasks for cloverInstr and cloverReport. Rationalised compileClasspaths for main, clover and test.

    • binary
    ./clover/lib/clover-ant-4.4.1.jar
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JAL-3609 Fixed typo

JAL-3609 Tested as POSIX compliant

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    ./install4j/set_hidpi_in_linux_test.sh
JAL-3609 Add to the unix/linux launch script to detect HiDPI and set GDK_SCALE

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    ./install4j/install4j8_template.install4j
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    ./install4j/set_hidpi_in_linux.sh
JAL-3611 added quotation marks for appdir argument install4j uses to invoke getdown-launcher.jar

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    ./install4j/install4j8_template.install4j
JAL-3611 added quotation marks for appdir argument install4j uses to invoke getdown-launcher.jar

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    ./install4j/install4j8_template.install4j
JAL-3225 save auto formatting settings in org.eclipse.jdt.ui.prefs. Not yet put into place, but these settings should be used

JAL-3577 Added newer install dirs to the deletion list in the uninstaller and tidied the list

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    ./install4j/install4j8_template.install4j
JAL-3289 New getdown splashscreens to be used with different getdown channels

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    ./getdown/jalview_logo_background_fade-640x480.xcf
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    ./getdown/jalview_logo_background_getdown-ARCHIVE-640x480.png
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    ./getdown/jalview_logo_background_getdown-BUILD-640x480.png
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    ./getdown/jalview_logo_background_getdown-DEVELOP-640x480.png
    • binary
    ./getdown/jalview_logo_background_getdown-LOCAL-640x480.png
    • binary
    ./getdown/jalview_logo_background_getdown-NON-RELEASE-640x480.png

changeset discussion

  1. Jim Procter: Hi Ben Soares - maybe nicer to have these generated by the getdown launcher in the future ? Worth an issue perhaps ?
  2. Ben Soares: Would be nicer. Currently the getdown-launcher is agnostic of which CHANNEL the Jalview version it's in was created w...
JAL-3588 Auto insert of Examples folder into DMG and an attempt to style both the Volume icon and the Examples folder icon (icons not working)

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    ./install4j/DMG.VolumeIcon.icns
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    ./install4j/examples_folder.png
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    ./install4j/install4j8_template.install4j
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    ./install4j/jalview_macos_examples_folder_icon
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JAL-3577 improvement to non-release DMG background and source SVG. Updated docs on image specification/creation.

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    ./install4j/DMG_background_image_creation_README.md
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    ./install4j/jalview_dmg_background-NON-RELEASE.png
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    ./install4j/jalview_dmg_background-NON-RELEASE.svg
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    ./install4j/jalview_dmg_background_blur_layers-NON-RELEASE.svg
JAL-3577 Added DEVELOP DMG styling. Improved TEST-RELEASE and NON-RELEASE styling

    • binary
    ./install4j/DS_Store-DEVELOP
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    ./install4j/install4j8_template.install4j
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    ./install4j/jalview_dmg_background-DEVELOP.png
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    ./install4j/jalview_dmg_background-NON-RELEASE.png
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    ./install4j/jalview_dmg_background-TEST.png
  1. … 1 more file in changeset.
JAL-3577 Fixed Jalview Programme Group in Windows menu. Added examples folder for RELEASE channel only and Examples folder in Jalview Programme Group in Windows.

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    ./install4j/install4j8_template.install4j
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JAL-3577 Moved application Categories for freedesktop menus into correct place in install4j

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    ./install4j/install4j8_template.install4j
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JAL-3577 Added existing and new Application IDs for Windows. Fixed Desktop shortcut and Menu entry.

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    ./install4j/install4j8_template.install4j
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JAL-3577 Changed shortName to INTERNAL_ID

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    ./install4j/install4j8_template.install4j
JAL-3577 Changed Windows internal ID to a new value which is backward compatible with the 2.11.0 installation. i.e. release versions will have internal ID 'Jalview'

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    ./install4j/install4j8_template.install4j
  1. … 2 more files in changeset.
JAL-3577 Added DS_Store for Test release to look like proper installer

    • binary
    ./install4j/DS_Store-TEST-RELEASE
  1. … 1 more file in changeset.
JAL-3577 Added a jalviewt scheme ONLY to TEST-RELEASE and TEST-LOCAL channels so that a test jvl can be made to ONLY open in the Test installation

    • -0
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    ./install4j/install4j8_template.install4j
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JAL-3577 cleaned up old DMG files. Added NON-RELEASE DMG files. Changed how Jalview name propogates through install4j -- now dynamically created depending on the CHANNEL

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    ./install4j/DMG_background_image_creation_README.md
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    ./install4j/DMG_creation_README.md
    • binary
    ./install4j/DS_Store-NON-RELEASE
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    ./install4j/install4j8_template.install4j
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    ./install4j/jalview_dmg_background-NON-RELEASE.png
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    ./install4j/jalview_dmg_background-NON-RELEASE.svg
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    ./install4j/jalview_dmg_background_blur.png
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    ./install4j/jalview_dmg_background_blur_72dpi.png
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    ./install4j/jalview_dmg_background_large.png
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    ./install4j/jalview_dmg_background_layers.pdf
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    ./install4j/jalview_dmg_background_layers.svg
  1. … 4 more files in changeset.
JAL-3577 First attempt at new folder names

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    ./install4j/install4j8_template.install4j
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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

    • binary
    ./eclipse/eclipse_startup_files.zip
    • binary
    ./jalviewjs/eclipse/eclipse_files.zip