Merge branch 'develop' into Jalview-JS/develop

Conflicts:
	.classpath

diff --cc .classpath
index c1e931c,7b2b32a..004d432
--- 1/.classpath
--- 2/.classpath
+++ b/.classpath
@@@ -67,8 -67,6 +67,8 @@@
        <classpathentry kind="lib" path="lib/htsjdk-2.12.0.jar"/>
        <classpathentry kind="lib" path="lib/groovy-all-2.4.12-indy.jar"/>
        <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
 +      <classpathentry exported="true" kind="con" path="GROOVY_DSL_SUPPORT"/>
 +      <classpathentry kind="lib" path="lib/Jmol-14.29.17.jar"/>
-       <classpathentry kind="lib" path="lib/intervalstore-v0.4.jar"/>
+       <classpathentry kind="lib" path="lib/intervalstore-v1.0.jar"/>
        <classpathentry kind="output" path="classes"/>
  </classpath>

diff --cc .classpath.js
index 84f3371,0000000..1a6df64
mode 100644,000000..100644
--- 1/.classpath.js
--- /dev/null
+++ b/.classpath.js
@@@ -1,74 -1,0 +1,74 @@@
 +<?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-v0.4.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"/>
 +</classpath>

diff --cc build.xml
Simple merge