Ben Soares

JAL-3594 Added rotating logo png

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    /src/jalview/gui/WebserviceInfo.java
JAL-3754 fixed a problem with jar task creating a stray dir when building

JAL-3775 added the Platform.isLinux() check for test HiDPISetting2

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    /test/jalview/bin/HiDPISettingTest2.java
Agreed. I seem to remember (this was a while ago now) that I found isAMacAndNotJS() and thought it might be an important distinction. Sounds like it's just redundant? Can tidy this another time then.

Agreed. I seem to remember (this was a while ago now) that I found isAMacAndNotJS() and thought it might be an important distinction. Sounds like it's just redundant? Can tidy this another time then.

Agree this is just touching on a much bigger task. However... The reason I /needed/ to do this rather than just /wanted/ to do this is that several of the classes I've been working on (e.g. jalview...

Agree this is just touching on a much bigger task.
However...
The reason I /needed/ to do this rather than just /wanted/ to do this is that several of the classes I've been working on (e.g. jalview.bin.Launcher, jalview.bin.HiDPISetting, jalview.bin.MemorySetting) run very early on (especially jalview.bin.Launcher!). This means Cache.log has perhaps not yet been initialised, so a Cache.log.debug doesn't log (unless you count reams of NullPointerExceptions as logging!).

In the case of HiDPISetting and MemorySetting that also get used in Getdown, where there is no jalview.bin.Cache, they currently have to use System.out and System.err [or maybe I could stub jalview.bin.Cache too]. I'd prefer them to use Cache.log when they can so this is an attempt at starting to decouple jalview.bin.Cache from other jalview things so it can be used standalone within Getdown. The main reason for wanting to do that is to have shared code to read the preferences between Jalview and Getdown.

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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    /resources/images/JalviewLogo_Huge.png
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    /resources/images/JalviewLogo_big.png
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    /resources/images/Jalview_Logo_small.png
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    /resources/images/jalview_logo_background_fade-640x480.png
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    /src/jalview/bin/JalviewTaskbar.java
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    /src/jalview/gui/SplashScreen.java
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    /src/jalview/util/ChannelProperties.java
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JAL-3594 Generating GIMP XCF files for getdown and new release getdown images

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    /utils/channels/release/images/jalview_getdown_background.xcf
JAL-3594 Release images and channel properties

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    /utils/channels/develop/resources/images/UoD_banner.png
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    /utils/channels/release/channel_gradle.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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    /resources/images/JalviewDevelopLogo_Huge.png
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    /utils/channels/develop/channel_gradle.properties
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    /utils/channels/develop/images/jalview_develop_getdown_background_initialising.png
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    /utils/channels/develop/images/jalview_develop_logo.icns
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    /utils/channels/develop/images/jalview_develop_logo.ico
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JAL-3594 new logos, icons and cosmetics for getdown and install4j

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    /utils/getdown/develop/Jalview-Logo.png
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    /utils/getdown/develop/jalview_logo_background_getdown_error-640x480.png
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    /utils/getdown/develop/jalview_logo_background_getdown_instant-640x480.png
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    /utils/install4j/develop/Jalview-Logo.png
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Merge branch 'develop' into merge/develop_and_rebase_squashed_merge_JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch

JAL-3609 JAL-3775 Updated getdown with re-factored HiDPISetting and ScreenInfo. No real functionality change.

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    /getdown/lib/getdown-launcher-local.jar
JAL-3609 JAL-3775 Tests for jalview.bin.HiDPISetting

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    /test/jalview/bin/HiDPISettingTest1.java
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    /test/jalview/bin/HiDPISettingTest2.java
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    /test/jalview/bin/hidpiTestProps.jvprops
JAL-3609 JAL-3775 Refactoring a bit of jalview.bin.HiDPISetting so screen display can be mocked in tests by Mockito

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    /src/jalview/bin/ScreenInfo.java
JAL-3775 Adding Mockito jars for tests. Needed for HiDPISettingTest1

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    /utils/testnglibs/byte-buddy-1.10.15.jar
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    /utils/testnglibs/byte-buddy-agent-1.10.15.jar
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    /utils/testnglibs/mockito-core-3.6.0.jar
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    /utils/testnglibs/objenesis-3.1.jar
JAL-3530 Added a -nowebservicediscovery command line argument.

JAL-3660 Fix for specified output format when using command line arg to convert a file

JAL-3660 Fix for specified output format when using command line arg to convert a file

JAL-3521 removed unnecessary parts of the ext project in build.gradle

JAL-3521 Minimal plugins and tasks needed to run tests and build jalview.jar

JAL-3775 Re-compiled Getdown jars

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    /getdown/lib/getdown-launcher-local.jar
JAL-3775 Eclipse re-formatting commit

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    /src/jalview/gui/Preferences.java
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    /src/jalview/jbgui/GPreferences.java
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    /src/jalview/project/Jalview2XML.java
JAL-3628 Error when saving alert box has been moved in develop for JS, adding Platform.isHeadless test to new isSaveAlignmentSuccessful method.

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    /src/jalview/gui/AlignFrame.java
JAL-3609 formatting save after cherry-picks

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    /src/jalview/bin/MemorySetting.java
JAL-3608 cherry pick of 92cb745e7

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    /src/jalview/bin/Jalview.java
JAL-3248 Added mention of version 'TEST' in shadow jar filename in building.md/html since develop branch currently uses this by default.

JAL-3248 Fixed path typos in building.md/html and corrected shadow jar filename

JAL-3248 Fixed path typos in building.md/html and corrected shadow jar filename

JAL-3248 Added step to create the eclipse files before project import. Noted non-fatal NPEs during build with gradle 6.6+

JAL-3248 Added step to create the eclipse files before project import. Noted non-fatal NPEs during build with gradle 6.6+

Cherry pick from release, generated new building.html as it's a different process. Also added in a "**/*.md" into build.gradle (wasn't finding anything with "*.md")