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JAL-3874 - replace Jmol with custom build of 14.31.53 from Jmol-SwingJS GitHub repo

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JAL-3871 replaced Jmol with zip -F version fo Jmol and added excludeDuplicates flags to build.gradle

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    ./Jmol-14.31.53.jar
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JAL-3829 Fixed Jmol jar -- duplicates of other classes were causing problem with shadow jar

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    ./Jmol-14.31.53-dedup.jar
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JAL-3829 upgrade Jmol to 14.31.53, SwingJS-JSMol to 14.31.54 and SwingJS to 3.3.1

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    ./Jmol-14.31.53.jar
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Merge branch 'improvement/JAL-3848_slivka_0.8' into alpha/JAL-3066_Jalview_212_slivka-integration

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JAL-3848 add latest slivka-client fixes.

WIP
WIP
JAL-3848 Update slivka client library.

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WIP

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JAL-3633 new getdown jars

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JAL-3633 new getdown jars

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JAL-3503 New getdown version and jar files

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JAL-3523 Advanced the getdown version number

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JAL-3523 Remove getdown setting the working directory to appdir

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JAL-3690 Fix typo in enum name in slivka client.

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JAL-3690 Fix typo in enum name in slivka client.

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JAL-3416 Added FlatLightLaf, use with -Dlaf=flat property

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JAL-3790 New getdown version and jar files

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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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    ./groovy-all-2.4.12-indy.jar
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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.

I think there are lots of things that could be tidied up (particularly the overloading and additional logging functions via Cache which don't really reduce code at point of use, but are certainly u...

I think there are lots of things that could be tidied up (particularly the overloading and additional logging functions via Cache which don't really reduce code at point of use, but are certainly useful in spirit), but now is most definitely not the time to optimise and beautify code.

Ben Soares as far as I can see the only thing missing after this branch is merged to develop is this logic. I just did a quick test and it appears 'Platform.isAMac()' returns false under JalviewJS,...

Ben Soares as far as I can see the only thing missing after this branch is merged to develop is this logic. I just did a quick test and it appears 'Platform.isAMac()' returns false under JalviewJS, so probably not a dealbreaker. Do you agree ?

JAL-3608 cherry pick of 92cb745e7
JAL-3608 cherry pick of 92cb745e7
JAL-3609 JAL-3775 Updated getdown with re-factored HiDPISetting and ScreenInfo. No real functionality change.

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JAL-3775 Re-compiled Getdown jars

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JAL-3718 Fixed getdown auto-update. This commit Getdown jars and version files.

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JAL-3718 fixed getdown auto-update for future updates. Getdown Jars and version files.

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JAL-3718 force re-initialise of getdown.txt file when new getdown.txt downloaded from appbase. getdown jar and version files

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