From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 29 Mar 2019 11:15:31 +0000 (+0000)
Subject: Merge branch 'develop' into Jalview-JS/develop
X-Git-Tag: Develop-2_11_2_0-d20201215~24^2~68^2~200
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=136df5f299843e2b21dcc3d37a1d7523a322e0e0;hp=b8196b19d8f419759df704d0f016de59b0c6ead0;p=jalview.git

Merge branch 'develop' into Jalview-JS/develop

Conflicts:
	.classpath
---

diff --git a/.classpath b/.classpath
index c1e931c..004d432 100644
--- a/.classpath
+++ b/.classpath
@@ -69,6 +69,6 @@
 	<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 --git a/.classpath.js b/.classpath.js
index 84f3371..1a6df64 100644
--- a/.classpath.js
+++ b/.classpath.js
@@ -67,7 +67,7 @@
 	<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"/>
diff --git a/build.xml b/build.xml
index dd90373..5a8fbc6 100755
--- a/build.xml
+++ b/build.xml
@@ -982,8 +982,9 @@
 </target>
 
 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
+<target name="pubapplet" description="Dummy target to keep legacy Jalview build system happy. We don't actually publish the applet anymore."/>
 
-<target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
+<target name="_pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
 
   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
diff --git a/lib/intervalstore-src-v0.4.jar b/lib/intervalstore-src-v0.4.jar
deleted file mode 100644
index 3feafbb..0000000
Binary files a/lib/intervalstore-src-v0.4.jar and /dev/null differ
diff --git a/lib/intervalstore-v0.4.jar b/lib/intervalstore-v1.0.jar
similarity index 100%
rename from lib/intervalstore-v0.4.jar
rename to lib/intervalstore-v1.0.jar
diff --git a/test/jalview/util/PlatformTest.java b/test/jalview/util/PlatformTest.java
index 307f450..5052894 100644
--- a/test/jalview/util/PlatformTest.java
+++ b/test/jalview/util/PlatformTest.java
@@ -27,6 +27,7 @@ import jalview.gui.JvOptionPane;
 
 import java.awt.Button;
 import java.awt.Event;
+import java.awt.Toolkit;
 import java.awt.event.MouseEvent;
 
 import org.testng.annotations.BeforeClass;
@@ -51,6 +52,16 @@ public class PlatformTest
   @Test(groups = "Functional")
   public void testIsControlDown_mac()
   {
+    String toolkit = Toolkit.getDefaultToolkit().getClass().getName();
+    if ("sun.awt.X11.XToolkit".equals(toolkit))
+    {
+      /*
+       * this toolkit on the build server fails these tests,
+       * because it returns 2, not 4, for getMenuShortcutKeyMask
+       */
+      return;
+    }
+
     int clickCount = 1;
     boolean isPopupTrigger = false;
     int buttonNo = MouseEvent.BUTTON1;
diff --git a/utils/InstallAnywhere/Jalview.iap_xml b/utils/InstallAnywhere/Jalview.iap_xml
index c69d554..3afa211 100755
--- a/utils/InstallAnywhere/Jalview.iap_xml
+++ b/utils/InstallAnywhere/Jalview.iap_xml
@@ -1280,7 +1280,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="b1a16838a449">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="b1a16839a449">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -1297,7 +1297,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[castor-1.1-cycle-xml.jar]]></string>
+								<string><![CDATA[vamsas-client.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -1315,10 +1315,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[castor-1.1-cycle-xml.jar]]></string>
+								<string><![CDATA[vamsas-client.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>1035998</long>
+								<long>682375</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -1332,7 +1332,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="b1a16839a449">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="495aeddb8b3d">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -1349,7 +1349,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[vamsas-client.jar]]></string>
+								<string><![CDATA[JGoogleAnalytics_0.3.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -1367,10 +1367,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[vamsas-client.jar]]></string>
+								<string><![CDATA[JGoogleAnalytics_0.3.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>682375</long>
+								<long>8300</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -1384,7 +1384,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="495aeddb8b3d">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="4996716cba8e">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -1401,7 +1401,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[JGoogleAnalytics_0.3.jar]]></string>
+								<string><![CDATA[jabaws-min-client-2.2.0.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -1419,10 +1419,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[JGoogleAnalytics_0.3.jar]]></string>
+								<string><![CDATA[jabaws-min-client-2.2.0.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>8300</long>
+								<long>601804</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -1436,7 +1436,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="4996716cba8e">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="8fbb17529b9c">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -1453,7 +1453,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[jabaws-min-client-2.2.0.jar]]></string>
+								<string><![CDATA[httpcore-4.0.1.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -1471,10 +1471,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[min-jabaws-client-2.2.0.jar]]></string>
+								<string><![CDATA[httpcore-4.0.1.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>601804</long>
+								<long>172888</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -1488,7 +1488,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="8fbb17529b9c">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="8fbb17519b9c">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -1505,7 +1505,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[httpcore-4.0.1.jar]]></string>
+								<string><![CDATA[httpclient-4.0.3.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -1523,10 +1523,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[httpcore-4.0.1.jar]]></string>
+								<string><![CDATA[httpclient-4.0.3.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>172888</long>
+								<long>292893</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -1540,7 +1540,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="8fbb17519b9c">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="8fbb17539b9c">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -1557,7 +1557,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[httpclient-4.0.3.jar]]></string>
+								<string><![CDATA[httpmime-4.0.3.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -1575,10 +1575,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[httpclient-4.0.3.jar]]></string>
+								<string><![CDATA[httpmime-4.0.3.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>292893</long>
+								<long>25447</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -1592,7 +1592,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="8fbb17539b9c">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="8fbb17529b9d">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -1609,7 +1609,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[httpmime-4.0.3.jar]]></string>
+								<string><![CDATA[apache-mime4j-0.6.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -1627,10 +1627,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[httpmime-4.0.3.jar]]></string>
+								<string><![CDATA[apache-mime4j-0.6.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>25447</long>
+								<long>345048</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -1644,7 +1644,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="8fbb17529b9d">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="aa3a521fb6bc">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -1661,7 +1661,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[apache-mime4j-0.6.jar]]></string>
+								<string><![CDATA[miglayout-4.0-swing.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -1679,10 +1679,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[apache-mime4j-0.6.jar]]></string>
+								<string><![CDATA[miglayout-4.0-swing.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>345048</long>
+								<long>77291</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -1696,7 +1696,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="aa3a521fb6bc">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="aa3a5220b6bc1">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -1713,7 +1713,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[miglayout-4.0-swing.jar]]></string>
+								<string><![CDATA[commons-codec-1.3.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -1731,10 +1731,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[miglayout-4.0-swing.jar]]></string>
+								<string><![CDATA[commons-codec-1.3.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>77291</long>
+								<long>46725</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -1748,7 +1748,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="aa3a5220b6bc1">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="aa3a5220b6bc">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -1765,7 +1765,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[commons-codec-1.3.jar]]></string>
+								<string><![CDATA[jswingreader-0.3.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -1783,10 +1783,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[commons-codec-1.3.jar]]></string>
+								<string><![CDATA[jswingreader-0.3.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>46725</long>
+								<long>86618</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -1800,7 +1800,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="aa3a5220b6bc">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="df3a5220b6bc">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -1817,7 +1817,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[jswingreader-0.3.jar]]></string>
+								<string><![CDATA[VARNAv3-93.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -1835,10 +1835,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[jswingreader-0.3.jar]]></string>
+								<string><![CDATA[VARNAv3-93.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>86618</long>
+								<long>695802</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -1852,7 +1852,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="df3a5220b6bc">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="f44ca393ab9f">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -1869,7 +1869,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[VARNAv3-93.jar]]></string>
+								<string><![CDATA[groovy-all-2.4.12-indy.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -1887,10 +1887,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[VARNAv3-93.jar]]></string>
+								<string><![CDATA[groovy-all-2.4.12-indy.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>695802</long>
+								<long>6149494</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -1904,7 +1904,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="f44ca391ab9f">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1f46cffffab93">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -1921,7 +1921,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[spring-web-3.0.5.RELEASE.jar]]></string>
+								<string><![CDATA[jfreesvg-2.1.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -1939,10 +1939,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[spring-web-3.0.5.RELEASE.jar]]></string>
+								<string><![CDATA[jfreesvg-2.1.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>395587</long>
+								<long>49768</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -1956,7 +1956,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="f44ca392ab9f">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1f46efeefab93">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -1973,7 +1973,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[jdas-1.0.4.jar]]></string>
+								<string><![CDATA[json_simple-1.1.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -1991,10 +1991,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[jdas-1.0.4.jar]]></string>
+								<string><![CDATA[json_simple-1.1.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>249906</long>
+								<long>16046</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -2008,7 +2008,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="f44ca393ab9f">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="841f46efeefab93">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -2025,7 +2025,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[groovy-all-2.4.12-indy.jar]]></string>
+								<string><![CDATA[libquaqua64-8.0.jnilib.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -2043,10 +2043,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[groovy-all-2.4.12-indy.jar]]></string>
+								<string><![CDATA[libquaqua64-8.0.jnilib.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>6149494</long>
+								<long>16046</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -2060,7 +2060,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="f46c2f42ab93">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="9a1f46efeefab93">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -2077,7 +2077,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[spring-core-3.0.5.RELEASE.jar]]></string>
+								<string><![CDATA[libquaqua-8.0.jnilib.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -2095,10 +2095,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[spring-core-3.0.5.RELEASE.jar]]></string>
+								<string><![CDATA[libquaqua-8.0.jnilib.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>382442</long>
+								<long>16046</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -2111,8 +2111,61 @@ and any path to a file to save to the file]]></string>
 							</property>
 						</object>
 					</method>
+
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1f46cffffab93">
+            <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="9a1f46efeef911a">
+              <property name="belongsToUninstallPhase">
+                <boolean>false</boolean>
+              </property>
+              <property name="rollbackEnabledCancel">
+                <boolean>true</boolean>
+              </property>
+              <property name="rollbackEnabledError">
+                <boolean>true</boolean>
+              </property>
+              <property name="ruleExpression">
+                <string><![CDATA[]]></string>
+              </property>
+              <property name="unixPermissions">
+                <string><![CDATA[664]]></string>
+              </property>
+              <property name="sourceName">
+                <string><![CDATA[VAqua5-patch.jar]]></string>
+              </property>
+              <property name="overrideUnixPermissions">
+                <boolean>false</boolean>
+              </property>
+              <property name="sourcePath">
+                <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
+              </property>
+              <property name="shouldUninstall">
+                <boolean>true</boolean>
+              </property>
+              <property name="rollbackEnabledCancel">
+                <boolean>true</boolean>
+              </property>
+              <property name="rollbackEnabledError">
+                <boolean>true</boolean>
+              </property>
+              <property name="destinationName">
+                <string><![CDATA[VAqua5-patch.jar]]></string>
+              </property>
+              <property name="fileSize">
+                <long>1370564</long>
+              </property>
+              <property name="macBinary">
+                <boolean>false</boolean>
+              </property>
+              <property name="targetCheckKind">
+                <int>0</int>
+              </property>
+              <property name="ruleExpression">
+                <string><![CDATA[]]></string>
+              </property>
+            </object>
+          </method>
+          <method name="addElement">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1936efeefab93">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -2129,7 +2182,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[jfreesvg-2.1.jar]]></string>
+								<string><![CDATA[quaqua-filechooser-only-8.0.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -2147,10 +2200,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[jfreesvg-2.1.jar]]></string>
+								<string><![CDATA[quaqua-filechooser-only-8.0.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>49768</long>
+								<long>660179</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -2164,7 +2217,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1f46efeefab93">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="10936efeefab93">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -2181,7 +2234,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[json_simple-1.1.jar]]></string>
+								<string><![CDATA[jersey-client-1.19.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -2199,10 +2252,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[json_simple-1.1.jar]]></string>
+								<string><![CDATA[jersey-client-1.19.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>16046</long>
+								<long>134021</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -2216,7 +2269,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="841f46efeefab93">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="11936efeefab93">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -2233,7 +2286,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[libqaqua64.jnilib]]></string>
+								<string><![CDATA[jersey-core-1.19.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -2251,10 +2304,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[libqaqua64.jnilib]]></string>
+								<string><![CDATA[jersey-core-1.19.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>16046</long>
+								<long>436689</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -2268,7 +2321,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="9a1f46efeefab93">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="12936efeefab93">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -2285,7 +2338,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[libquaqua.jnilib]]></string>
+								<string><![CDATA[jersey-json-1.19.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -2303,10 +2356,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[libquaqua.jnilib]]></string>
+								<string><![CDATA[jersey-json-1.19.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>16046</long>
+								<long>165345</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -2320,59 +2373,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-            <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="9a1f46efeef911a">
-              <property name="belongsToUninstallPhase">
-                <boolean>false</boolean>
-              </property>
-              <property name="rollbackEnabledCancel">
-                <boolean>true</boolean>
-              </property>
-              <property name="rollbackEnabledError">
-                <boolean>true</boolean>
-              </property>
-              <property name="ruleExpression">
-                <string><![CDATA[]]></string>
-              </property>
-              <property name="unixPermissions">
-                <string><![CDATA[664]]></string>
-              </property>
-              <property name="sourceName">
-                <string><![CDATA[VAqua5-patch.jar]]></string>
-              </property>
-              <property name="overrideUnixPermissions">
-                <boolean>false</boolean>
-              </property>
-              <property name="sourcePath">
-                <string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
-              </property>
-              <property name="shouldUninstall">
-                <boolean>true</boolean>
-              </property>
-              <property name="rollbackEnabledCancel">
-                <boolean>true</boolean>
-              </property>
-              <property name="rollbackEnabledError">
-                <boolean>true</boolean>
-              </property>
-              <property name="destinationName">
-                <string><![CDATA[VAqua5-patch.jar]]></string>
-              </property>
-              <property name="fileSize">
-                <long>1370564</long>
-              </property>
-              <property name="macBinary">
-                <boolean>false</boolean>
-              </property>
-              <property name="targetCheckKind">
-                <int>0</int>
-              </property>
-              <property name="ruleExpression">
-                <string><![CDATA[]]></string>
-              </property>
-            </object>
-          </method>
-          <method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1936efeefab93">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="13936efeefab93">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -2389,7 +2390,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[quaqua-filechooser-only-8.0.jar]]></string>
+								<string><![CDATA[java-json.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -2407,10 +2408,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[quaqua-filechooser-only-8.0.jar]]></string>
+								<string><![CDATA[java-json.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>660179</long>
+								<long>84697</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -2424,7 +2425,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="10936efeefab93">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="14936efeefab93">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -2441,7 +2442,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[jersey-client-1.19.jar]]></string>
+								<string><![CDATA[jsr311-api-1.1.1.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -2459,10 +2460,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[jersey-client-1.19.jar]]></string>
+								<string><![CDATA[jsr311-api-1.1.1.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>134021</long>
+								<long>46367</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -2476,7 +2477,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="11936efeefab93">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="15936efeefab93">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -2493,7 +2494,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[jersey-core-1.19.jar]]></string>
+								<string><![CDATA[jetty-http-9.2.10.v20150310.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -2511,10 +2512,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[jersey-core-1.19.jar]]></string>
+								<string><![CDATA[jetty-http-9.2.10.v20150310.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>436689</long>
+								<long>105748</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -2528,7 +2529,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="12936efeefab93">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="16936efeefab93">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -2545,7 +2546,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[jersey-json-1.19.jar]]></string>
+								<string><![CDATA[jetty-io-9.2.10.v20150310.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -2563,10 +2564,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[jersey-json-1.19.jar]]></string>
+								<string><![CDATA[jetty-io-9.2.10.v20150310.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>165345</long>
+								<long>108132</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -2580,7 +2581,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="13936efeefab93">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="17936efeefab93">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -2597,7 +2598,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[java-json.jar]]></string>
+								<string><![CDATA[jetty-server-9.2.10.v20150310.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -2615,10 +2616,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[java-json.jar]]></string>
+								<string><![CDATA[jetty-server-9.2.10.v20150310.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>84697</long>
+								<long>418917</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -2632,7 +2633,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="14936efeefab93">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="18936efeefab93">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -2649,7 +2650,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[jsr311-api-1.1.1.jar]]></string>
+								<string><![CDATA[jetty-util-9.2.10.v20150310.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -2667,10 +2668,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[jsr311-api-1.1.1.jar]]></string>
+								<string><![CDATA[jetty-util-9.2.10.v20150310.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>46367</long>
+								<long>356253</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -2684,7 +2685,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="15936efeefab93">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1899e36efeefab93">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -2701,7 +2702,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[jetty-http-9.2.10.v20150310.jar]]></string>
+								<string><![CDATA[jetty-servlet-9.2.10.v20150310.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -2719,10 +2720,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[jetty-http-9.2.10.v20150310.jar]]></string>
+								<string><![CDATA[jetty-servlet-9.2.10.v20150310.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>105748</long>
+								<long>356253</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -2736,7 +2737,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="16936efeefab93">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1899d6efeefab93">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -2753,7 +2754,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[jetty-io-9.2.10.v20150310.jar]]></string>
+								<string><![CDATA[jetty-security-9.2.10.v20150310.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -2771,10 +2772,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[jetty-io-9.2.10.v20150310.jar]]></string>
+								<string><![CDATA[jetty-security-9.2.10.v20150310.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>108132</long>
+								<long>356253</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -2788,7 +2789,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="17936efeefab93">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1000ddddfab93">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -2805,7 +2806,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[jetty-server-9.2.10.v20150310.jar]]></string>
+								<string><![CDATA[htsjdk-2.12.0.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -2823,10 +2824,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[jetty-server-9.2.10.v20150310.jar]]></string>
+								<string><![CDATA[htsjdk-2.12.0.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>418917</long>
+								<long>16046</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -2840,7 +2841,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="18936efeefab93">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1000ddddfb93">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -2857,7 +2858,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[jetty-util-9.2.10.v20150310.jar]]></string>
+								<string><![CDATA[intervalstore-v1.0.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -2875,7 +2876,59 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[jetty-util-9.2.10.v20150310.jar]]></string>
+								<string><![CDATA[intervalstore-v1.0.jar]]></string>
+							</property>
+							<property name="fileSize">
+								<long>26303</long>
+							</property>
+							<property name="macBinary">
+								<boolean>false</boolean>
+							</property>
+							<property name="targetCheckKind">
+								<int>0</int>
+							</property>
+							<property name="ruleExpression">
+								<string><![CDATA[]]></string>
+							</property>
+						</object>
+					</method>
+					<method name="addElement">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="b10a3">
+							<property name="belongsToUninstallPhase">
+								<boolean>false</boolean>
+							</property>
+							<property name="rollbackEnabledCancel">
+								<boolean>true</boolean>
+							</property>
+							<property name="rollbackEnabledError">
+								<boolean>true</boolean>
+							</property>
+							<property name="ruleExpression">
+								<string><![CDATA[]]></string>
+							</property>
+							<property name="unixPermissions">
+								<string><![CDATA[664]]></string>
+							</property>
+							<property name="sourceName">
+								<string><![CDATA[biojava-core-4.1.0.jar]]></string>
+							</property>
+							<property name="overrideUnixPermissions">
+								<boolean>false</boolean>
+							</property>
+							<property name="sourcePath">
+								<string><![CDATA[/homes/cruisecontrol/jalview/lib/]]></string>
+							</property>
+							<property name="shouldUninstall">
+								<boolean>true</boolean>
+							</property>
+							<property name="rollbackEnabledCancel">
+								<boolean>true</boolean>
+							</property>
+							<property name="rollbackEnabledError">
+								<boolean>true</boolean>
+							</property>
+							<property name="destinationName">
+								<string><![CDATA[biojava-core-4.1.0.jar]]></string>
 							</property>
 							<property name="fileSize">
 								<long>356253</long>
@@ -2892,7 +2945,7 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
-						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1000ddddfab93">
+						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="b10a30">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
 							</property>
@@ -2909,7 +2962,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[664]]></string>
 							</property>
 							<property name="sourceName">
-								<string><![CDATA[htsjdk-1.133.jar]]></string>
+								<string><![CDATA[biojava-ontology-4.1.0.jar]]></string>
 							</property>
 							<property name="overrideUnixPermissions">
 								<boolean>false</boolean>
@@ -2927,10 +2980,10 @@ and any path to a file to save to the file]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="destinationName">
-								<string><![CDATA[htsjdk-1.133.jar]]></string>
+								<string><![CDATA[biojava-ontology-4.1.0.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>16046</long>
+								<long>356253</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -2943,6 +2996,7 @@ and any path to a file to save to the file]]></string>
 							</property>
 						</object>
 					</method>
+
 					<method name="addElement">
 						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1000ddddfab939">
 							<property name="belongsToUninstallPhase">
@@ -7445,7 +7499,6 @@ and any path to a file to read from that file]]></string>
 											</property>
 										</object>
 										<object refID="88d4aff3b0c6"/>
-										<object refID="b1a16838a449"/>
 										<object refID="b1a16839a449"/>
 										<object refID="495aeddb8b3d"/>
 										<object refID="4996716cba8e"/>
@@ -7457,14 +7510,14 @@ and any path to a file to read from that file]]></string>
 										<object refID="aa3a5220b6bc"/>
 										<object refID="df3a5220b6bc"/>
 										<object refID="aa3a5220b6bc1"/>
-										<object refID="f44ca391ab9f"/>
-										<object refID="f44ca392ab9f"/>
+
 										<object refID="f44ca393ab9f"/>
-										<object refID="f46c2f42ab93"/>
+
 										<object refID="1f46cffffab93"/>
 										<object refID="1f46efeefab93"/>
 										<object refID="1936efeefab93"/>
 										<object refID="1000ddddfab93"/>
+										<object refID="1000ddddfb93"/>
 										<object refID="1000ddddfab939"/>
 										<object refID="10936efeefab93"/>
 										<object refID="11936efeefab93"/>
@@ -7475,6 +7528,11 @@ and any path to a file to read from that file]]></string>
 										<object refID="16936efeefab93"/>
 										<object refID="17936efeefab93"/>
 										<object refID="18936efeefab93"/>
+										<object refID="b10a3"/>
+										<object refID="b10a30"/>
+										<object refID="1899e36efeefab93"/>
+										<object refID="1899d6efeefab93"/>
+
 										<object class="com.zerog.ia.installer.actions.InstallFile" objectID="f44fc5b2aba1">
 											<property name="belongsToUninstallPhase">
 												<boolean>false</boolean>