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JAL-3594 added BG logo. Changed some named Jalviews to app_name property. Added test-release and default channels.

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    ./channels/default/channel_gradle.properties
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    ./channels/default/images/barton_group-512.png
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    ./channels/default/images/barton_group-62.png
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    ./channels/default/images/barton_group-white-512.png
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    ./channels/default/images/barton_group-white.svg
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    ./channels/default/images/barton_group.svg
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    ./channels/default/images/jalview_default_dmg_DS_Store
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    ./channels/default/images/jalview_default_dmg_background.png
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    ./channels/default/images/jalview_default_dmg_background.svg
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    ./channels/default/images/jalview_getdown_background.png
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    ./channels/default/images/jalview_getdown_background.xcf
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    ./channels/default/images/jalview_getdown_background_error.png
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    ./channels/default/images/jalview_getdown_background_initialising.png
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    ./channels/default/images/jalview_getdown_progress_bar.png
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JAL-3594 Default values for channel properties defined in code as fallback

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JAL-3594 Added rotating logo png

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    ./channels/develop/resources/images/jalview_develop_logo-38.png
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    ./channels/release/resources/images/jalview_logo-38.png
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    ./install4j/README_convert_PNG_to_ICNS_and_ICO
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JAL-3594 New jalview.util.ChannelProperties to get/cache values and images used in the application. Starting to tidy images in resources/images.

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    ./channels/release/images/jalview_getdown_background_initialising.png
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JAL-3594 Generating GIMP XCF files for getdown and new release getdown images

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    ./channels/develop/images/jalview_develop_getdown_background.xcf
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    ./channels/release/images/jalview_getdown_background.xcf
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    ./channels/release/images/jalview_getdown_background_initialising.png
JAL-3594 Release images and channel properties

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    ./channels/develop/resources/images/UoD_banner.png
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    ./channels/develop/resources/images/jalview_develop_banner.png
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    ./channels/release/channel_gradle.properties
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    ./channels/release/channel_properties
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JAL-3594 New way for build.gradle to override properties with channel based properties files. Starting to tidy up some old image files

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    ./channels/develop/channel_gradle.properties
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    ./channels/develop/getdown/resource/jalview_develop_getdown_background_initialising.png
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    ./channels/develop/getdown/resource/jalview_develop_logo.png
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    ./channels/develop/images/jalview_develop_getdown_background.png
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    ./channels/develop/images/jalview_develop_getdown_background_error.png
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    ./channels/develop/images/jalview_develop_getdown_background_initialising.png
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    ./channels/develop/images/jalview_develop_getdown_progress_bar.png
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    ./channels/develop/images/jalview_develop_logo.icns
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    ./channels/develop/images/jalview_develop_logo.ico
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    ./channels/develop/images/jalview_develop_logo.png
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    ./channels/develop/install4j/jalview_develop_logo.icns
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    ./channels/develop/install4j/jalview_develop_logo.ico
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JAL-3594 new logos, icons and cosmetics for getdown and install4j

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    ./getdown/develop/jalview_logo_background_blur-640x480.xcf
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    ./getdown/develop/jalview_logo_background_getdown-640x480.png
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    ./getdown/develop/jalview_logo_background_getdown_error-640x480.png
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    ./getdown/develop/jalview_logo_background_getdown_instant-640x480.png
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    ./install4j/develop/Jalview-Logo.png
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    ./install4j/develop/README_convert_PNG_to_ICNS_and_ICO
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    ./install4j/develop/jalview_develop/JalviewDevelopLogo.svg
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    ./install4j/develop/jalview_develop/jalview_logos_16x16x32.png
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    ./install4j/develop/jalview_develop/jalview_logos_32x32x32.png
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    ./install4j/develop/jalview_develop/jalview_logos_48x48x32.png
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JAL-3775 Adding Mockito jars for tests. Needed for HiDPISettingTest1

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    ./testnglibs/byte-buddy-1.10.15.jar
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    ./testnglibs/byte-buddy-agent-1.10.15.jar
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    ./testnglibs/mockito-core-3.6.0.jar
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    ./testnglibs/objenesis-3.1.jar
JAL-3594 Different icon/getdown styling when launching jalview built with -PCHANNEL=DEVELOP

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    ./channels/develop_properties
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    ./channels/release_properties
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    ./getdown/Jalview-Logo.png
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    ./getdown/develop/Jalview-Logo.png
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    ./getdown/develop/jalview_logo_background_blur-640x480.xcf
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    ./getdown/develop/jalview_logo_background_getdown-640x480.png
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    ./getdown/develop/jalview_logo_background_getdown-progress.png
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    ./getdown/develop/jalview_logo_background_getdown-progress3.xcf
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    ./getdown/develop/jalview_logo_background_getdown_error-640x480.png
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    ./getdown/develop/jalview_logo_background_getdown_instant-640x480.png
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    ./getdown/develop/jalview_logos.icns
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    ./getdown/jalview_logos.icns
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    ./install4j/Jalview-Logo.png
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    ./install4j/develop/Jalview-Logo.png
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    ./install4j/develop/cmds
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JAL-3594 Different icon/getdown styling when launching jalview built with -PCHANNEL=DEVELOP

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    ./channels/develop_properties
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    ./channels/release_properties
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    ./getdown/Jalview-Logo.png
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    ./getdown/develop/Jalview-Logo.png
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    ./getdown/develop/jalview_logo_background_blur-640x480.xcf
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    ./getdown/develop/jalview_logo_background_getdown-640x480.png
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    ./getdown/develop/jalview_logo_background_getdown-progress.png
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    ./getdown/develop/jalview_logo_background_getdown-progress3.xcf
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    ./getdown/develop/jalview_logo_background_getdown_error-640x480.png
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    ./getdown/develop/jalview_logo_background_getdown_instant-640x480.png
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    ./getdown/develop/jalview_logos.icns
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    ./getdown/jalview_logos.icns
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    ./install4j/Jalview-Logo.png
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    ./install4j/develop/Jalview-Logo.png
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    ./install4j/develop/cmds
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JAL-3728 Icon and setting icon for Java Console

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    ./images/JalviewConsole_Huge.xcf
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JAL-1424 streamlined message checker, corrected applet lookup keys

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JAL-1424 slight tidying of reporting

JAL-3658 Now only making cores from utils/jalviewjs/classlists/*.txt

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    ./jalviewjs/classlists/_jvjmol.txt
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    ./jalviewjs/classlists/jalview.txt
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    ./jalviewjs/classlists/jvexamplefile.txt
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    ./jalviewjs/classlists/jvjmol.txt
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    ./jalviewjs/classlists/stevesoft.txt
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JAL-3446 rearranged parameters for JalviewJS API methods

JAL-3446 reorganized JalviewJSApp (accidentally put that in jalview/api) and fixes for 2-applet example

- API.md

- follows commit 01717e2 (missing JAL-3446 tag)

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reorganized JalviewJSApp (accidentally put that in jalview/api) and fixes for 2-applet example

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    ./jalviewjs/site-resources/_jalview_bin_JalviewJS_core.html
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    ./jalviewjs/site-resources/_jalview_embedded_example1.html
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    ./jalviewjs/site-resources/_jalview_embedded_example2.html
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JAL-3446 adds Jmol viewer embedding.

JAL-3446 embedded file for proper name matching

web app name "Jalview"

div id="Jalview-desktop-div"

So whatever name you give the applet must match the div tags.

Previously, the div name was associated with a different name,

Info.j2sAppID, or something like that. This is much more sensible.

Just don't name it "jalview", because that is a package name!

JAL-3225 Removed dependency on command line pandoc to convert .md files to .html. Now all files in doc/*.md will get converted to doc/*.html using flexmark within gradle process.

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JAL-3225 Removed dependency on command line pandoc to convert .md files to .html. Now all files in doc/*.md will get converted to doc/*.html using flexmark within gradle process.

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adds link for __j2sflags.htm to template.html

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    ./jalviewjs/site-resources/___j2sflags.htm
_jvjmol.txt

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    ./jalviewjs/classlists/_jvjmol.txt
JAL-3664 support for user.home, user.dir, user

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    ./jalviewjs/classlists/_j2sclasslist_jmol.txt
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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.

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    ./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.

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    ./clover/lib/clover-ant-4.4.1.jar
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