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JAL-3560 from JAL-3563. This commit is expected to be reverted. Just getting back to a branch that Bamboo is compiling.

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JAL-3563 adds Jalview.setSynchronous()

- avoids NullPointerExceptions in CommandLineOperations and

Jalview2xmlTests

- allows headless processes to avoid spawning threads and using

SwingUtilities.invokeLater.

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Java 11/Gradle 2.5 upgrade

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Java 11 integration;

-- compiler complaining about javax.xml module

Failed to resolve resource /.build_properties:

@swingjs/j2s/jalview/bin/Cache.js:164:24

transpiler was 3.2.9-v1 now 3.2.4.07 for net.miginfocom.swing.MigLayout

TypeError: C$.UNIT_MAP.put$TK$TV is not a function

-- some runtime errors involving resources

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JAL-3210 .j2s fix to exclude /utils directory

Revert "JAL-3210 Moving j2s components around"

This reverts commit ea88f37133ba49aca6cd7bf0cc4242c0594cebf1.

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JAL-3210 Moving j2s components around

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JAL-3210 Moving j2s components around

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JAL-3210 Barebones gradle/buildship/eclipse. See README

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Java2Script 3.2.2 upgrade

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JAL-3026 adds org.json.simple to srcjars and jsonsimple-site.zip

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Bob first commit JAL-3032

- jalview/bin/cache.java

propsAreReadable true for JS

authordetails, builddetails "xxx" for JS for now

- org.apache.log4j -> jalview.javascript.log4j (minimal)

- jalview/util/MessageManager switch to org.apache.log4j

JavaScript Status:

jalview.io.FileFormatException: Failed to read data from source: CANNOT

ACCESS DATA AT URL 'http://www.jalview.org/examples/uniref50.fa'

((intermediate value).toBIS$O is not a function

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JAL-1807 add j2s nature to project

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