From 053d128eb450f8a7c6300eb38633f14b58fc7ca4 Mon Sep 17 00:00:00 2001
From: Ben Soares <bsoares@dundee.ac.uk>
Date: Thu, 8 Aug 2019 13:47:55 +0100
Subject: [PATCH] JAL-3210 ben testing

---
 .classpath                           |  122 ++++++++----------
 .classpath.js                        |  232 +++++++++++++++++++++++-----------
 .settings/org.eclipse.jdt.core.prefs |    8 +-
 gradle.properties                    |    4 +-
 4 files changed, 220 insertions(+), 146 deletions(-)

diff --git a/.classpath b/.classpath
index 462a76f..038fd0d 100644
--- a/.classpath
+++ b/.classpath
@@ -14,79 +14,63 @@
 			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11/"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8/"/>
 	<classpathentry kind="con" path="org.eclipse.buildship.core.gradleclasspathcontainer"/>
 	<classpathentry kind="output" path="bin/main"/>
 	<classpathentry kind="lib" path="help"/>
 	<classpathentry kind="lib" path="resources"/>
-	<classpathentry kind="lib" path="j11lib/jsoup-1.8.1.jar"/>
-	<classpathentry kind="lib" path="j11lib/jswingreader-0.3.jar"/>
-	<classpathentry kind="lib" path="j11lib/mail-MODULE.jar"/>
-	<classpathentry kind="lib" path="j11lib/javax.servlet-api-MODULE.jar"/>
-	<classpathentry kind="lib" path="j11lib/httpclient-4.0.3.jar"/>
-	<classpathentry kind="lib" path="j11lib/regex.jar"/>
-	<classpathentry kind="lib" path="j11lib/getdown-core.jar"/>
-	<classpathentry kind="lib" path="j11lib/policy.jar"/>
-	<classpathentry kind="lib" path="j11lib/jaxb-api-java9.jar"/>
-	<classpathentry kind="lib" path="j11lib/JGoogleAnalytics_0.3.jar"/>
-	<classpathentry kind="lib" path="j11lib/jetty-http-9.2.10.v20150310.jar"/>
-	<classpathentry kind="lib" path="j11lib/javax.activation-MODULE.jar"/>
-	<classpathentry kind="lib" path="j11lib/commons-logging-1.1.1.jar"/>
-	<classpathentry kind="lib" path="j11lib/slf4j-log4j12-1.7.7.jar"/>
-	<classpathentry kind="lib" path="j11lib/i4jruntime.jar"/>
-	<classpathentry kind="lib" path="j11lib/miglayout-4.0-swing.jar"/>
-	<classpathentry kind="lib" path="j11lib/txw2.jar"/>
-	<classpathentry kind="lib" path="j11lib/jersey-json-1.19.1.jar"/>
-	<classpathentry kind="lib" path="j11lib/quaqua-filechooser-only-8.0.jar"/>
-	<classpathentry kind="lib" path="j11lib/VARNAv3-93.jar"/>
-	<classpathentry kind="lib" path="j11lib/groovy-2.5.6.jar"/>
-	<classpathentry kind="lib" path="j11lib/Jmol-14.29.17-no_netscape.jar"/>
-	<classpathentry kind="lib" path="j11lib/jaxb-runtime.jar"/>
-	<classpathentry kind="lib" path="j11lib/commons-discovery.jar"/>
-	<classpathentry kind="lib" path="j11lib/slf4j-api-1.7.7.jar"/>
-	<classpathentry kind="lib" path="j11lib/VAqua5-patch.jar"/>
-	<classpathentry kind="lib" path="j11lib/jaxws-api.jar"/>
-	<classpathentry kind="lib" path="j11lib/javax.xml.soap-api.jar"/>
-	<classpathentry kind="lib" path="j11lib/jsr311-api-1.1.1.jar"/>
-	<classpathentry kind="lib" path="j11lib/libquaqua-8.0.jnilib.jar"/>
-	<classpathentry kind="lib" path="j11lib/istack-commons-runtime.jar"/>
-	<classpathentry kind="lib" path="j11lib/stax-ex.jar"/>
-	<classpathentry kind="lib" path="j11lib/httpmime-4.0.3.jar"/>
-	<classpathentry kind="lib" path="j11lib/biojava-core-4.1.0.jar"/>
-	<classpathentry kind="lib" path="j11lib/libquaqua64-8.0.jnilib.jar"/>
-	<classpathentry kind="lib" path="j11lib/jabaws-min-client-2.2.0.jar"/>
-	<classpathentry kind="lib" path="j11lib/jersey-client-1.19.1.jar"/>
-	<classpathentry kind="lib" path="j11lib/jetty-io-9.2.10.v20150310.jar"/>
-	<classpathentry kind="lib" path="j11lib/intervalstore-v1.0.jar"/>
-	<classpathentry kind="lib" path="j11lib/htsjdk-2.12.0.jar"/>
-	<classpathentry kind="lib" path="j11lib/groovy-console-2.5.6.jar"/>
-	<classpathentry kind="lib" path="j11lib/commons-codec-1.3.jar"/>
-	<classpathentry kind="lib" path="j11lib/jaxws-rt-java9.jar"/>
-	<classpathentry kind="lib" path="j11lib/vamsas-client.jar"/>
-	<classpathentry kind="lib" path="j11lib/saaj-impl.jar"/>
-	<classpathentry kind="lib" path="j11lib/jersey-core-1.19.1.jar"/>
-	<classpathentry kind="lib" path="j11lib/jetty-server-9.2.10.v20150310.jar"/>
-	<classpathentry kind="lib" path="j11lib/jetty-util-9.2.10.v20150310.jar"/>
-	<classpathentry kind="lib" path="j11lib/xercesImpl.jar"/>
-	<classpathentry kind="lib" path="j11lib/FastInfoset.jar"/>
-	<classpathentry kind="lib" path="j11lib/commons-compress-1.18.jar"/>
-	<classpathentry kind="lib" path="j11lib/biojava-ontology-4.1.0.jar"/>
-	<classpathentry kind="lib" path="j11lib/log4j-to-slf4j-2.0-rc2.jar"/>
-	<classpathentry kind="lib" path="j11lib/wsdl4j-MODULE.jar"/>
-	<classpathentry kind="lib" path="j11lib/httpcore-4.0.1.jar"/>
-	<classpathentry kind="lib" path="j11lib/jhall.jar"/>
-	<classpathentry kind="lib" path="j11lib/stax2-api-MODULE.jar"/>
-	<classpathentry kind="lib" path="j11lib/gmbal-api-only-MODULE.jar"/>
-	<classpathentry kind="lib" path="j11lib/javax.jws-api-1.1.jar"/>
-	<classpathentry kind="lib" path="j11lib/axis.jar"/>
-	<classpathentry kind="lib" path="j11lib/javax.xml.rpc-api-1.1.2.jar"/>
-	<classpathentry kind="lib" path="j11lib/javax.annotation-api-MODULE.jar"/>
-	<classpathentry kind="lib" path="j11lib/java-json.jar"/>
-	<classpathentry kind="lib" path="j11lib/mimepull.jar"/>
-	<classpathentry kind="lib" path="j11lib/jfreesvg-2.1.jar"/>
-	<classpathentry kind="lib" path="j11lib/streambuffer.jar"/>
-	<classpathentry kind="lib" path="j11lib/apache-mime4j-0.6.jar"/>
-	<classpathentry kind="lib" path="j11lib/json_simple-1.1.jar"/>
+	<classpathentry kind="lib" path="j8lib/jsoup-1.8.1.jar"/>
+	<classpathentry kind="lib" path="j8lib/jswingreader-0.3.jar"/>
+	<classpathentry kind="lib" path="j8lib/mail.jar"/>
+	<classpathentry kind="lib" path="j8lib/httpclient-4.0.3.jar"/>
+	<classpathentry kind="lib" path="j8lib/regex.jar"/>
+	<classpathentry kind="lib" path="j8lib/getdown-core.jar"/>
+	<classpathentry kind="lib" path="j8lib/JGoogleAnalytics_0.3.jar"/>
+	<classpathentry kind="lib" path="j8lib/jetty-http-9.2.10.v20150310.jar"/>
+	<classpathentry kind="lib" path="j8lib/commons-logging-1.1.1.jar"/>
+	<classpathentry kind="lib" path="j8lib/slf4j-log4j12-1.7.7.jar"/>
+	<classpathentry kind="lib" path="j8lib/servlet-api-3.1.jar"/>
+	<classpathentry kind="lib" path="j8lib/i4jruntime.jar"/>
+	<classpathentry kind="lib" path="j8lib/miglayout-4.0-swing.jar"/>
+	<classpathentry kind="lib" path="j8lib/activation.jar"/>
+	<classpathentry kind="lib" path="j8lib/quaqua-filechooser-only-8.0.jar"/>
+	<classpathentry kind="lib" path="j8lib/VARNAv3-93.jar"/>
+	<classpathentry kind="lib" path="j8lib/jersey-client-1.19.jar"/>
+	<classpathentry kind="lib" path="j8lib/wsdl4j.jar"/>
+	<classpathentry kind="lib" path="j8lib/commons-discovery.jar"/>
+	<classpathentry kind="lib" path="j8lib/slf4j-api-1.7.7.jar"/>
+	<classpathentry kind="lib" path="j8lib/VAqua5-patch.jar"/>
+	<classpathentry kind="lib" path="j8lib/jsr311-api-1.1.1.jar"/>
+	<classpathentry kind="lib" path="j8lib/libquaqua-8.0.jnilib.jar"/>
+	<classpathentry kind="lib" path="j8lib/Jmol-14.29.17.jar"/>
+	<classpathentry kind="lib" path="j8lib/jersey-json-1.19.jar"/>
+	<classpathentry kind="lib" path="j8lib/httpmime-4.0.3.jar"/>
+	<classpathentry kind="lib" path="j8lib/groovy-all-2.4.12-indy.jar"/>
+	<classpathentry kind="lib" path="j8lib/biojava-core-4.1.0.jar"/>
+	<classpathentry kind="lib" path="j8lib/libquaqua64-8.0.jnilib.jar"/>
+	<classpathentry kind="lib" path="j8lib/jabaws-min-client-2.2.0.jar"/>
+	<classpathentry kind="lib" path="j8lib/jetty-io-9.2.10.v20150310.jar"/>
+	<classpathentry kind="lib" path="j8lib/intervalstore-v1.0.jar"/>
+	<classpathentry kind="lib" path="j8lib/htsjdk-2.12.0.jar"/>
+	<classpathentry kind="lib" path="j8lib/commons-codec-1.3.jar"/>
+	<classpathentry kind="lib" path="j8lib/vamsas-client.jar"/>
+	<classpathentry kind="lib" path="j8lib/xml-apis.jar"/>
+	<classpathentry kind="lib" path="j8lib/jetty-server-9.2.10.v20150310.jar"/>
+	<classpathentry kind="lib" path="j8lib/jetty-util-9.2.10.v20150310.jar"/>
+	<classpathentry kind="lib" path="j8lib/xercesImpl.jar"/>
+	<classpathentry kind="lib" path="j8lib/commons-compress-1.18.jar"/>
+	<classpathentry kind="lib" path="j8lib/biojava-ontology-4.1.0.jar"/>
+	<classpathentry kind="lib" path="j8lib/log4j-to-slf4j-2.0-rc2.jar"/>
+	<classpathentry kind="lib" path="j8lib/jersey-core-1.19.jar"/>
+	<classpathentry kind="lib" path="j8lib/httpcore-4.0.1.jar"/>
+	<classpathentry kind="lib" path="j8lib/jhall.jar"/>
+	<classpathentry kind="lib" path="j8lib/axis.jar"/>
+	<classpathentry kind="lib" path="j8lib/jaxrpc.jar"/>
+	<classpathentry kind="lib" path="j8lib/java-json.jar"/>
+	<classpathentry kind="lib" path="j8lib/jfreesvg-2.1.jar"/>
+	<classpathentry kind="lib" path="j8lib/apache-mime4j-0.6.jar"/>
+	<classpathentry kind="lib" path="j8lib/saaj.jar"/>
+	<classpathentry kind="lib" path="j8lib/json_simple-1.1.jar"/>
 	<classpathentry kind="lib" path="utils/proguard_5.3.3.jar">
 		<attributes>
 			<attribute name="test" value="true"/>
diff --git a/.classpath.js b/.classpath.js
index 1a6df64..038fd0d 100644
--- a/.classpath.js
+++ b/.classpath.js
@@ -1,74 +1,164 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path="src"/>
-	<!-- Not needed for java2script build
-        <classpathentry kind="src" path="utils"/>
-	<classpathentry kind="src" path="test"/>
-	-->
-        <classpathentry kind="lib" path="lib/activation.jar"/>
-	<classpathentry kind="lib" path="lib/axis.jar" sourcepath="D:/axis-1_2RC2-src/axis-1_2RC2"/>
-	<classpathentry kind="lib" path="lib/commons-discovery.jar"/>
-	<classpathentry kind="lib" path="lib/jaxrpc.jar"/>
-	<classpathentry kind="lib" path="lib/jhall.jar"/>
-	<classpathentry kind="lib" path="lib/mail.jar"/>
-	<classpathentry kind="lib" path="lib/regex.jar"/>
-	<classpathentry kind="lib" path="lib/saaj.jar"/>
-	<classpathentry kind="lib" path="lib/wsdl4j.jar"/>
-	<classpathentry kind="lib" path="lib/xercesImpl.jar"/>
-	<classpathentry kind="lib" path="lib/JGoogleAnalytics_0.3.jar" sourcepath="/JGoogleAnalytics/src/main/java"/>
-	<classpathentry kind="lib" path="lib/vamsas-client.jar"/>
-	<classpathentry kind="lib" path="lib/commons-logging-1.1.1.jar"/>
-	<classpathentry kind="lib" path="lib/apache-mime4j-0.6.jar" sourcepath="G:/InstallsDir/Sources for Development/apache-mime4j-0.6-src.zip"/>
-	<classpathentry kind="lib" path="lib/httpclient-4.0.3.jar">
-		<attributes>
-			<attribute name="javadoc_location" value="file:/D:/InstallsDir/Sources for Development/httpconnect/httpcomponents-client-4.0.3/javadoc/"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="lib" path="lib/httpcore-4.0.1.jar">
-		<attributes>
-			<attribute name="javadoc_location" value="file:/D:/InstallsDir/Sources for Development/httpconnect/httpcomponents-client-4.0.3/javadoc/"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="lib" path="lib/httpmime-4.0.3.jar">
-		<attributes>
-			<attribute name="javadoc_location" value="file:/D:/InstallsDir/Sources for Development/httpconnect/httpcomponents-client-4.0.3/javadoc/"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="lib" path="lib/miglayout-4.0-swing.jar"/>
-	<classpathentry kind="lib" path="lib/jswingreader-0.3.jar" sourcepath="/jswingreader"/>
-	<classpathentry kind="lib" path="lib/commons-codec-1.3.jar"/>
-	<classpathentry kind="lib" path="lib/jabaws-min-client-2.2.0.jar" sourcepath="/clustengine"/>
-	<classpathentry kind="lib" path="lib/json_simple-1.1.jar" sourcepath="/Users/jimp/Downloads/json_simple-1.1-all.zip"/>
-	<classpathentry kind="lib" path="lib/slf4j-api-1.7.7.jar"/>
-	<classpathentry kind="lib" path="lib/jsoup-1.8.1.jar"/>
-	<classpathentry kind="lib" path="lib/log4j-to-slf4j-2.0-rc2.jar"/>
-	<classpathentry kind="lib" path="lib/slf4j-log4j12-1.7.7.jar"/>
-	<classpathentry kind="lib" path="lib/VARNAv3-93.jar"/>
-	<classpathentry kind="lib" path="lib/jfreesvg-2.1.jar"/>
-	<classpathentry kind="lib" path="lib/quaqua-filechooser-only-8.0.jar"/>
-	<classpathentry kind="lib" path="lib/VAqua5-patch.jar"/>
-	<classpathentry kind="lib" path="utils/classgraph-4.1.6.jar"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin"/>
-	<classpathentry kind="lib" path="lib/xml-apis.jar"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Plugin.jar"/>
-	<classpathentry kind="lib" path="lib/jersey-client-1.19.jar"/>
-	<classpathentry kind="lib" path="lib/jersey-core-1.19.jar"/>
-	<classpathentry kind="lib" path="lib/jsr311-api-1.1.1.jar"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
-	<classpathentry kind="lib" path="lib/jetty-server-9.2.10.v20150310.jar"/>
-	<classpathentry kind="lib" path="lib/servlet-api-3.1.jar"/>
-	<classpathentry kind="lib" path="lib/jetty-util-9.2.10.v20150310.jar"/>
-	<classpathentry kind="lib" path="lib/jetty-http-9.2.10.v20150310.jar"/>
-	<classpathentry kind="lib" path="lib/jetty-io-9.2.10.v20150310.jar"/>
-	<classpathentry kind="lib" path="lib/java-json.jar"/>
-	<classpathentry kind="con" path="org.testng.TESTNG_CONTAINER"/>
-	<classpathentry kind="lib" path="lib/biojava-core-4.1.0.jar"/>
-	<classpathentry kind="lib" path="lib/biojava-ontology-4.1.0.jar"/>
-	<classpathentry kind="lib" path="lib/htsjdk-2.12.0.jar"/>
-	<classpathentry kind="lib" path="lib/groovy-all-2.4.12-indy.jar"/>
-	<classpathentry kind="lib" path="lib/intervalstore-v1.0.jar"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
-        <classpathentry kind="lib" path="lib/Jmol-14.29.17.jar"/>
-	<classpathentry kind="output" path="classes"/>
+	<classpathentry kind="output" path="bin/default"/>
+	<classpathentry output="bin/main" kind="src" path="src">
+		<attributes>
+			<attribute name="gradle_scope" value="main"/>
+			<attribute name="gradle_used_by_scope" value=""/>
+		</attributes>
+	</classpathentry>
+	<classpathentry output="bin/test" kind="src" path="test">
+		<attributes>
+			<attribute name="gradle_scope" value="test"/>
+			<attribute name="gradle_used_by_scope" value=""/>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8/"/>
+	<classpathentry kind="con" path="org.eclipse.buildship.core.gradleclasspathcontainer"/>
+	<classpathentry kind="output" path="bin/main"/>
+	<classpathentry kind="lib" path="help"/>
+	<classpathentry kind="lib" path="resources"/>
+	<classpathentry kind="lib" path="j8lib/jsoup-1.8.1.jar"/>
+	<classpathentry kind="lib" path="j8lib/jswingreader-0.3.jar"/>
+	<classpathentry kind="lib" path="j8lib/mail.jar"/>
+	<classpathentry kind="lib" path="j8lib/httpclient-4.0.3.jar"/>
+	<classpathentry kind="lib" path="j8lib/regex.jar"/>
+	<classpathentry kind="lib" path="j8lib/getdown-core.jar"/>
+	<classpathentry kind="lib" path="j8lib/JGoogleAnalytics_0.3.jar"/>
+	<classpathentry kind="lib" path="j8lib/jetty-http-9.2.10.v20150310.jar"/>
+	<classpathentry kind="lib" path="j8lib/commons-logging-1.1.1.jar"/>
+	<classpathentry kind="lib" path="j8lib/slf4j-log4j12-1.7.7.jar"/>
+	<classpathentry kind="lib" path="j8lib/servlet-api-3.1.jar"/>
+	<classpathentry kind="lib" path="j8lib/i4jruntime.jar"/>
+	<classpathentry kind="lib" path="j8lib/miglayout-4.0-swing.jar"/>
+	<classpathentry kind="lib" path="j8lib/activation.jar"/>
+	<classpathentry kind="lib" path="j8lib/quaqua-filechooser-only-8.0.jar"/>
+	<classpathentry kind="lib" path="j8lib/VARNAv3-93.jar"/>
+	<classpathentry kind="lib" path="j8lib/jersey-client-1.19.jar"/>
+	<classpathentry kind="lib" path="j8lib/wsdl4j.jar"/>
+	<classpathentry kind="lib" path="j8lib/commons-discovery.jar"/>
+	<classpathentry kind="lib" path="j8lib/slf4j-api-1.7.7.jar"/>
+	<classpathentry kind="lib" path="j8lib/VAqua5-patch.jar"/>
+	<classpathentry kind="lib" path="j8lib/jsr311-api-1.1.1.jar"/>
+	<classpathentry kind="lib" path="j8lib/libquaqua-8.0.jnilib.jar"/>
+	<classpathentry kind="lib" path="j8lib/Jmol-14.29.17.jar"/>
+	<classpathentry kind="lib" path="j8lib/jersey-json-1.19.jar"/>
+	<classpathentry kind="lib" path="j8lib/httpmime-4.0.3.jar"/>
+	<classpathentry kind="lib" path="j8lib/groovy-all-2.4.12-indy.jar"/>
+	<classpathentry kind="lib" path="j8lib/biojava-core-4.1.0.jar"/>
+	<classpathentry kind="lib" path="j8lib/libquaqua64-8.0.jnilib.jar"/>
+	<classpathentry kind="lib" path="j8lib/jabaws-min-client-2.2.0.jar"/>
+	<classpathentry kind="lib" path="j8lib/jetty-io-9.2.10.v20150310.jar"/>
+	<classpathentry kind="lib" path="j8lib/intervalstore-v1.0.jar"/>
+	<classpathentry kind="lib" path="j8lib/htsjdk-2.12.0.jar"/>
+	<classpathentry kind="lib" path="j8lib/commons-codec-1.3.jar"/>
+	<classpathentry kind="lib" path="j8lib/vamsas-client.jar"/>
+	<classpathentry kind="lib" path="j8lib/xml-apis.jar"/>
+	<classpathentry kind="lib" path="j8lib/jetty-server-9.2.10.v20150310.jar"/>
+	<classpathentry kind="lib" path="j8lib/jetty-util-9.2.10.v20150310.jar"/>
+	<classpathentry kind="lib" path="j8lib/xercesImpl.jar"/>
+	<classpathentry kind="lib" path="j8lib/commons-compress-1.18.jar"/>
+	<classpathentry kind="lib" path="j8lib/biojava-ontology-4.1.0.jar"/>
+	<classpathentry kind="lib" path="j8lib/log4j-to-slf4j-2.0-rc2.jar"/>
+	<classpathentry kind="lib" path="j8lib/jersey-core-1.19.jar"/>
+	<classpathentry kind="lib" path="j8lib/httpcore-4.0.1.jar"/>
+	<classpathentry kind="lib" path="j8lib/jhall.jar"/>
+	<classpathentry kind="lib" path="j8lib/axis.jar"/>
+	<classpathentry kind="lib" path="j8lib/jaxrpc.jar"/>
+	<classpathentry kind="lib" path="j8lib/java-json.jar"/>
+	<classpathentry kind="lib" path="j8lib/jfreesvg-2.1.jar"/>
+	<classpathentry kind="lib" path="j8lib/apache-mime4j-0.6.jar"/>
+	<classpathentry kind="lib" path="j8lib/saaj.jar"/>
+	<classpathentry kind="lib" path="j8lib/json_simple-1.1.jar"/>
+	<classpathentry kind="lib" path="utils/proguard_5.3.3.jar">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="lib" path="utils/junit-4.12.jar">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="lib" path="utils/wsdl4j.jar">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="lib" path="utils/axis-ant.jar">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="lib" path="utils/classgraph-4.1.6.jar">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="lib" path="utils/testnglibs/testng-sources.jar">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="lib" path="utils/testnglibs/jcommander.jar">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="lib" path="utils/testnglibs/snakeyaml.jar">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="lib" path="utils/testnglibs/junit-4.12.jar">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="lib" path="utils/testnglibs/bsh-2.0b4.jar">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="lib" path="utils/testnglibs/testng.jar">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="lib" path="utils/testnglibs/guava-collections-r03.jar">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="lib" path="utils/testnglibs/guava-base-r03.jar">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="lib" path="utils/jhindexer.jar">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="lib" path="utils/ant-contrib-1.0b3.jar">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="lib" path="utils/hamcrest-core-1.3.jar">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="lib" path="utils/roxes-ant-tasks-1.2-2004-01-30.jar">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="lib" path="utils/jhall.jar">
+		<attributes>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
 </classpath>
diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs
index bc894d5..dd28862 100644
--- a/.settings/org.eclipse.jdt.core.prefs
+++ b/.settings/org.eclipse.jdt.core.prefs
@@ -1,5 +1,5 @@
 #
-#Thu Aug 08 12:00:23 BST 2019
+#Thu Aug 08 13:46:15 BST 2019
 org.eclipse.jdt.core.formatter.insert_space_after_ellipsis=insert
 org.eclipse.jdt.core.formatter.insert_space_after_comma_in_enum_declarations=insert
 org.eclipse.jdt.core.formatter.insert_new_line_in_empty_annotation_declaration=insert
@@ -165,7 +165,7 @@ org.eclipse.jdt.core.formatter.alignment_for_resources_in_try=80
 org.eclipse.jdt.core.formatter.use_tabs_only_for_leading_indentations=false
 org.eclipse.jdt.core.formatter.alignment_for_selector_in_method_invocation=16
 org.eclipse.jdt.core.formatter.never_indent_block_comments_on_first_column=false
-org.eclipse.jdt.core.compiler.source=11
+org.eclipse.jdt.core.compiler.source=1.8
 org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_synchronized=do not insert
 org.eclipse.jdt.core.formatter.insert_space_after_comma_in_constructor_declaration_throws=insert
 org.eclipse.jdt.core.formatter.tabulation.size=2
@@ -188,7 +188,7 @@ org.eclipse.jdt.core.formatter.alignment_for_superclass_in_type_declaration=16
 org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_enum_declaration=16
 org.eclipse.jdt.core.formatter.insert_space_before_parenthesized_expression_in_throw=insert
 org.eclipse.jdt.core.formatter.insert_space_before_colon_in_labeled_statement=do not insert
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=11
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
 org.eclipse.jdt.core.formatter.brace_position_for_switch=next_line
 org.eclipse.jdt.core.formatter.insert_space_before_comma_in_superinterfaces=do not insert
 org.eclipse.jdt.core.formatter.insert_space_after_comma_in_method_declaration_parameters=insert
@@ -258,7 +258,7 @@ org.eclipse.jdt.core.formatter.wrap_before_binary_operator=true
 org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_method_declaration=insert
 org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_parameters=insert
 org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_catch=do not insert
-org.eclipse.jdt.core.compiler.compliance=11
+org.eclipse.jdt.core.compiler.compliance=1.8
 org.eclipse.jdt.core.formatter.insert_space_before_closing_bracket_in_array_reference=do not insert
 org.eclipse.jdt.core.formatter.insert_space_after_comma_in_annotation=insert
 org.eclipse.jdt.core.formatter.insert_space_before_comma_in_enum_constant_arguments=do not insert
diff --git a/gradle.properties b/gradle.properties
index 16ff61d..eec61da 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -1,7 +1,7 @@
 jalviewDir = .
 
-#JAVA_VERSION = 1.8
-JAVA_VERSION = 11
+JAVA_VERSION = 1.8
+#JAVA_VERSION = 11
 JALVIEW_VERSION = DEVELOPMENT
 INSTALLATION = Source
 jalview_keystore = keys/.keystore
-- 
1.7.10.2