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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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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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    ./Jmol-14.29.17-no_netscape.jar
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    ./commons-compress-1.18.jar
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    ./gmbal-api-only-MODULE.jar
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    ./intervalstore-v1.0.jar
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    ./istack-commons-runtime.jar
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    ./javax.activation-api-1.2.0.jar
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    ./javax.annotation-api-1.3.2.jar
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    ./javax.jws-api-1.1.jar
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    ./javax.servlet-api-4.0.1.jar
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    ./javax.xml.rpc-api-1.1.2.jar
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    ./javax.xml.soap-api-1.4.0.jar
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    ./jaxb-api-2.3.1.jar
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JAL-3140 update intervalstore jar to v1-1 tagged version

JAL-3397 impl.IntervalStore and nonc.IntervalStore unified api

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    ./intervalstore-v1.1.jar
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JAL-3210 Barebones gradle/buildship/eclipse. See README

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JAL-3337 remove the old lib directory !

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    ./Jmol-14.6.4_2016.10.26-no_netscape.jar
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JAL-3210 updated Jmol library in j11lib, j8lib

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    ./Jmol-14.6.4_2016.10.26-no_netscape.jar
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Can remove class Jalview$FeatureFetcher.

Can remove class Jalview$FeatureFetcher.

JAL-3224 JAL-3225 Some fixes in install4j template and build.gradle, and a correction of the Policy code in Jalview.java that I messed up earlier

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JAL-3224 JAL-3225 To be compatible with install4j bundled JRE on windows, have changed all the java_vm folder references to jre in getdown jars too. Install4j Windows media now bundles a JRE (into this location) so it can launch install4j installer too. Java 11 installers working on Windows, but Java 1.8 complaining about com.sun.xml.ws.policy.Policy not found.

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JAL-3224 JAL-3225 Added lines to check for updates to getdown-launcher.jar into Jalview. Put getdown-core into Jalview libs instead of getdown-launcher (enables update of getdown-launcher). Adjusted Eclipse to not error on use of com.sun.management.OperatingSystemMXBean.

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    ./getdown-core-1.8.3-SNAPSHOT.jar
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Merge branch 'task/JAL-3225_Integration_Gradle_building_into_Eclipse' into bug/JAL-3224_getdown_changed_to_unpack_tgz_resources

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    ./Jmol-14.6.4_2016.10.26-no_netscape.jar
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    ./groovy-console-2.5.6.jar
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JAL-3225 I THINK I HAVE WON\! Run 'gradle cleanEclipse eclipse' to get a new set of eclipse .project, .classpath, .settings/\* files that should work. You might need to have a Java 11 linked to 'org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11/' in your Installed JREs and Java compliance.

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    ./Jmol-14.6.4_2016.10.26-no_netscape.jar
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    ./groovy-console-2.5.6.jar
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JAL-3130 moved jar needed for getdown to libs (not a module)

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    ./commons-compress-1.18.jar
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JAL-3140 intervalstore now v1.0 (public release)

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    ./intervalstore-v1.0.jar
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JAL-3035 removed spring libraries as only used for jdas

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Were added 2012 commit 3d37b44 "jdas runtime dependencies". All classes in jars are org.springframework.*, no longer referenced in any source code in Jalview. I will remove from classpath and THIRD...

Were added 2012 commit 3d37b44 "jdas runtime dependencies".
All classes in jars are org.springframework.*, no longer referenced in any source code in Jalview.
I will remove from classpath and THIRDPARTYLIBS.

yeah. probably.

yeah. probably.

I tried removing these (Spring jars) and Jalview seemed to function ok. Can they go?

I tried removing these (Spring jars) and Jalview seemed to function ok. Can they go?

JAL-3140 reduced coupling to intervalstore.jar

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    ./intervalstore-src-v0.4.jar
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    ./intervalstore-v0.4.jar
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JAL-3140 updated to latest intervalstore.jar

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    ./intervalstore-v0.3.jar
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JAL-3063 removed all core castor dependent code from Jalview

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JAL-3130 Some re-reorganisation for build process

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    ./gmbal-api-only-MODULE.jar
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    ./jaxws-rt-java9.jar
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JAL-3130 incorporating feature/JAL-3063jaxbNoCastor and new script utils/jdeps_jlink_all.sh which works out module dependencies (not as straightforward as it should be) and makes a java 11 JRE

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JAL-3063 Castor removed from codebase

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JAL-3140 updated IntervalStore jar

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    ./intervalstore-v0.2.jar
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JAL-3140 named tagged version of intervalstore.jar

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    ./intervalstore-v1.0-beta.jar
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JAL-1988 JAVA 11 enabled version with Quit, Preferences and About handlers enabled for Mac. Run with openjdk-11 and 'java -classpath "classes:lib/*:j11lib/*" jalview.bin.Jalview'

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massacre manifest for classgraph and add illegal-access=warn for java 9/10 relaunch

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promote classgraph to desktop dependency

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    ./classgraph-4.1.6.jar
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