Merge branch 'releases/Release_2_10_4_Branch' into develop

diff --combined .classpath
index c85feaf,9a0a468..17523b9
--- 1/.classpath
--- 2/.classpath
+++ b/.classpath
@@@ -48,6 -48,7 +48,6 @@@
        <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/htsjdk-1.133.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"/>
@@@ -66,8 -67,7 +66,9 @@@
        <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="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
 +      <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 kind="output" path="classes"/>
  </classpath>

diff --combined build.xml
index d636a42,3ef3ed3..0088485
--- 1/build.xml
--- 2/build.xml
+++ b/build.xml
@@@ -38,7 -38,7 +38,7 @@@
      <echo message="testng - run jalview's tests via testNG. Default group is '${testng-groups}'" />
      <echo message="      you can specify particular test groups as a list via -Dtestng-groups=" />
      <echo message="See docs/building.html and the comments in build file for other targets." />
-     <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
+     <echo message="note: compile and makeApplet optionally compile/obfuscate applet against a different Java version by specifying -Djava118.home=<Path to JDK>/lib which is the lib directory in the JDK install that contains rt.jar " />
      <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
    </target>
  
@@@ -182,17 -182,14 +182,14 @@@
      </path>
      <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
      <!-- The Location of the java 1.1.8 jdk -->
-     <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
      <property name="java118.home" value="${java.home}" />
-     <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
-               -->
      <!-- jre for 1.4 version -->
-     <property name="applet.jre.tools" value="${java.home}/lib/rt.jar" />
+     <property name="applet.jre.tools" value="${java118.home}/lib/rt.jar" />
  
      <!-- the classpath for building the 1.1 applet -->
      <path id="jalviewlite.deps">
        <fileset dir="${java118.home}">
-         <include name="lib/classes.zip" />
+         <include name="lib/rt.jar" />
        </fileset>
        <fileset dir="${java.home}/lib">
          <include name="plugin.jar" />
@@@ -462,7 -459,8 +459,7 @@@
      <!-- add the add-modules j2se attribute for java 9 -->
      <replace file="${jnlpFile}" value="j2se version=&quot;1.8+&quot; initial-heap-size=&quot;${inih}&quot; max-heap-size=&quot;${maxh}&quot; java-vm-args=&quot;--add-modules=java.se.ee --illegal-access=warn&quot;">
            <replacetoken>j2se version="1.8+"</replacetoken>
 -           
 -        </replace>
 +    </replace>
    </target>
  
    <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">