From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Wed, 16 Sep 2015 17:38:51 +0000 (+0100)
Subject: merge
X-Git-Tag: Release_2_10_0~400
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=68405aa972a7fc07ff21b35c7b2272d1d4ecb1b7;hp=b61d853baef9db35859efb45d331becfdd11e61d;p=jalview.git

merge
---

diff --git a/examples/applets.html b/examples/applets.html
index 3dfa83a..d811e94 100644
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -195,7 +195,7 @@ Try out JalviewLite by pressing one of the buttons below.<br/>
       <td valign="center">Displays a split window view showing aligned protein
         and a reconstructed cDNA alignment.<br />Proteins were aligned with <a
         href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31,
-        via the Jalvew Desktop).<br />Data retrieved from Uniprot and
+        via the Jalview Desktop).<br />Data retrieved from Uniprot and
         ENA, after Thornton, Need and Crews, <a
         href="http://dx.doi.org/10.1126/science.1086185">Science 19
           September 2003: 301 (5640), 1714-1717</a>
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index ee46581..4ea90e8 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -417,7 +417,7 @@ public class Cache
             System.out.println("# INFO: Setting default net timeout to "
                     + orgtimeout + " seconds.");
           }
-          String jnlpVersion = null;
+          String remoteVersion = null;
           try
           {
             System.setProperty("sun.net.client.defaultConnectTimeout",
@@ -437,20 +437,20 @@ public class Cache
 
               line = line.substring(line.indexOf("value=") + 7);
               line = line.substring(0, line.lastIndexOf("\""));
-              jnlpVersion = line;
+              remoteVersion = line;
               break;
             }
           } catch (Exception ex)
           {
             System.out
-                    .println("Non-fatal exceptions when checking version at www.jalview.org :");
+                    .println("Non-fatal exception when checking version at www.jalview.org :");
             System.out.println(ex);
-            jnlpVersion = getProperty("VERSION");
+            remoteVersion = getProperty("VERSION");
           }
           System.setProperty("sun.net.client.defaultConnectTimeout",
                   orgtimeout);
 
-          setProperty("LATEST_VERSION", jnlpVersion);
+          setProperty("LATEST_VERSION", remoteVersion);
         }
       }
 
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index f87fbe5..a448d19 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -3250,8 +3250,8 @@ public class Jalview2XML
      * indicate that annotation colours are applied across all groups (pre
      * Jalview 2.8.1 behaviour)
      */
-    boolean doGroupAnnColour = isVersionStringLaterThan("2.8.1",
-            object.getVersion());
+    boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan(
+            "2.8.1", object.getVersion());
 
     AlignmentPanel ap = null;
     boolean isnewview = true;
@@ -4037,7 +4037,7 @@ public class Jalview2XML
    * @return true if version is development/null or evaluates to the same or
    *         later X.Y.Z (where X,Y,Z are like [0-9]+b?[0-9]*)
    */
-  protected boolean isVersionStringLaterThan(String supported,
+  public static boolean isVersionStringLaterThan(String supported,
           String version)
   {
     if (version == null || version.equalsIgnoreCase("DEVELOPMENT BUILD")
@@ -4060,11 +4060,18 @@ public class Jalview2XML
         String fileT = fileV.nextToken().toLowerCase().replace('b', '.');
         try
         {
-          if (Float.valueOf(curT) > Float.valueOf(fileT))
+          float supportedVersionToken = Float.parseFloat(curT);
+          float myVersiontoken = Float.parseFloat(fileT);
+          if (supportedVersionToken > myVersiontoken)
           {
             // current version is newer than the version that wrote the file
             return false;
           }
+          if (supportedVersionToken < myVersiontoken)
+          {
+            // current version is older than the version that wrote the file
+            return true;
+          }
         } catch (NumberFormatException nfe)
         {
           System.err
diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index 3c634fd..b58a8a6 100644
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -20,6 +20,7 @@
  */
 package jalview.io;
 
+import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.api.AlignmentViewPanel;
@@ -412,4 +413,56 @@ public class Jalview2xmlTests
             Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
   }
 
+  @Test(groups = { "Functional" })
+  public void testIsVersionStringLaterThan()
+  {
+    /*
+     * No version / development / test / autobuild is leniently assumed to be
+     * compatible
+     */
+    assertTrue(Jalview2XML.isVersionStringLaterThan(null, null));
+    assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", null));
+    assertTrue(Jalview2XML.isVersionStringLaterThan(null,
+            "Development Build"));
+    assertTrue(Jalview2XML.isVersionStringLaterThan(null,
+            "DEVELOPMENT BUILD"));
+    assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
+            "Development Build"));
+    assertTrue(Jalview2XML.isVersionStringLaterThan(null, "Test"));
+    assertTrue(Jalview2XML.isVersionStringLaterThan(null, "TEST"));
+    assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Test"));
+    assertTrue(Jalview2XML
+            .isVersionStringLaterThan(null, "Automated Build"));
+    assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
+            "Automated Build"));
+    assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3",
+            "AUTOMATED BUILD"));
+
+    /*
+     * same version returns true i.e. compatible
+     */
+    assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8"));
+    assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3"));
+    assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3b1"));
+    assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3B1", "2.8.3b1"));
+    assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3B1"));
+
+    /*
+     * later version returns true
+     */
+    assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.4"));
+    assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9"));
+    assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9.2"));
+    assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8.3"));
+    assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3b1"));
+
+    /*
+     * earlier version returns false
+     */
+    assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8"));
+    assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.4", "2.8.3"));
+    assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3"));
+    assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1"));
+    assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1"));
+  }
 }
diff --git a/utils/InstallAnywhere/Jalview.iap_xml b/utils/InstallAnywhere/Jalview.iap_xml
index 18c7e75..cd9987c 100755
--- a/utils/InstallAnywhere/Jalview.iap_xml
+++ b/utils/InstallAnywhere/Jalview.iap_xml
@@ -1,8 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!-- This script was automatically generated using InstallAnywhere 2014 Professional, Build 4783
      STATUS: Fully Functional LICENSED Edition
-     DATE:   Tue Dec 02 16:16:02 GMT 2014 -->
-<!--
  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
  * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
@@ -19,8 +17,8 @@
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
-<InstallAnywhere_Deployment_Project increments="5299">
+     DATE:   Wed Sep 16 18:09:53 BST 2015 -->
+<InstallAnywhere_Deployment_Project increments="5904">
 	<!-- ** DO NOT EDIT ** Essential authorization and configuration data ** DO NOT EDIT ** -->
 	<essentialScriptInfo>
 		<versionID major="16" minor="0" revision="0"/>
@@ -28,9 +26,9 @@
 		<scriptID>12,42,11,85,78,76,73,67,69,78,83,69,68</scriptID>
 		<buildID>3,13,71,76,105,110,117,120,44,32,50,46,54,46,51,50,45,51,53,56,46,54,46,50,46,101,108,54,46,120,56,54,95,54,52,44,32,97,109,100,54,52,59,32,74,97,118,97,32,49,46,55,46,48,95,54,48,44,32,79,114,97,99,108,101,32,67,111,114,112,111,114,97,116,105,111,110,44,32,104,116,116,112,58,47,47,106,97,118,97,46,111,114,97,99,108,101,46,99,111,109,47,59,32,101,110,44,32,85,110,107,110,111,119,110,59,32,73,83,79,45,56,56,53,57,45,49</buildID>
 		<!-- The authorizationID may change between project saves and builds.  This does not effect the integrity of the project, nor do changes in this value represent changes in the actual InstallAnywhere project. -->
-		<authorizationID>1,0,0,64,13,-64,-128,0,80,127,118,101,93,105,116,96,121,48,48,49,56,52,67,98,113,112,112,37,82,101,96,63,55,-11,2,9,1,105,27,10,1,0,0</authorizationID>
+		<authorizationID>1,0,0,64,-35,32,64,-48,80,127,118,101,93,105,116,96,121,48,48,49,56,52,67,98,113,112,112,37,82,101,96,63,55,-11,2,9,13,114,23,15,1,0,0</authorizationID>
 	</essentialScriptInfo>
-	<installationObjects uniqueObjects="225">
+	<installationObjects uniqueObjects="243">
 		<object class="com.zerog.ia.installer.Installer" objectID="fe7d63eda660">
 			<property name="belongsToUninstallPhase">
 				<boolean>false</boolean>
@@ -280,6 +278,19 @@ and any path to a file to save to the file]]></string>
 									</property>
 								</object>
 							</method>
+							<method name="addElement">
+								<object class="com.zerog.ia.installer.util.LAXPropertyData" objectID="e9482ad387eb">
+									<property name="propertyValue">
+										<string><![CDATA[$PLATFORM_JVM_OPTS$]]></string>
+									</property>
+									<property name="propertyName">
+										<string><![CDATA[lax.nl.java.option.additional]]></string>
+									</property>
+									<property name="propertyComment">
+										<string><![CDATA[specific launch options for the platform]]></string>
+									</property>
+								</object>
+							</method>
 						</object>
 					</property>
 					<property name="shouldUninstall">
@@ -371,7 +382,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[jalview.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>4232225</long>
+								<long>5584573</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -475,7 +486,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[xercesImpl.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>1010204</long>
+								<long>1367760</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -631,7 +642,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[xml-apis.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>124344</long>
+								<long>220536</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -1047,7 +1058,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[slf4j-api-1.7.7.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>348699</long>
+								<long>29257</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -1058,8 +1069,8 @@ and any path to a file to save to the file]]></string>
 							<property name="ruleExpression">
 								<string><![CDATA[]]></string>
 							</property>
-						</object>				
-					</method>		
+						</object>
+					</method>
 					<method name="addElement">
 						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="244fff00ffff">
 							<property name="belongsToUninstallPhase">
@@ -1099,7 +1110,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[jsoup-1.8.1.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>348699</long>
+								<long>300844</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -1151,7 +1162,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[log4j-to-slf4j-2.0-rc2.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>348699</long>
+								<long>15996</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -1203,7 +1214,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[slf4j-log4j12-1.7.7.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>348699</long>
+								<long>8870</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -1255,7 +1266,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[Jmol-14.2.14_2015.06.11.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>4938027</long>
+								<long>5417196</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -1463,7 +1474,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[min-jabaws-client-2.1.0.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>133065</long>
+								<long>601804</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -1879,7 +1890,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[VARNAv3-93.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>663408</long>
+								<long>695802</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -2347,7 +2358,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[quaqua-filechooser-only-8.0.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>16046</long>
+								<long>660179</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -2515,7 +2526,7 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[]]></string>
 							</property>
 						</object>
-					</method>					
+					</method>
 					<method name="addElement">
 						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="13936efeefab93">
 							<property name="belongsToUninstallPhase">
@@ -3171,6 +3182,94 @@ You may cancel this installation at any time by clicking the 'Cancel' button.]]>
 						</object>
 					</method>
 					<method name="addElement">
+						<object class="com.zerog.ia.installer.actions.EditVariableTable" objectID="ea739b658d07">
+							<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[CP904]]></string>
+							</property>
+							<property name="name">
+								<string><![CDATA[PLATFORM_JVM_OPTS]]></string>
+							</property>
+							<property name="value">
+								<string><![CDATA[-Xdock:name=Jalview -Xdock:icon=$USER_INSTALL_DIR$/Jalview.app/Contents/Resources/LaunchAnywhere.icns]]></string>
+							</property>
+							<property name="passByValue">
+								<boolean>true</boolean>
+							</property>
+							<property name="substituteUnknownVariable">
+								<boolean>false</boolean>
+							</property>
+							<rules logicalOperation="AND">
+								<object class="com.zerog.ia.installer.rules.PlatformChk" objectID="ea74fe6b8d07">
+									<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="installOnPlatformList">
+										<object class="java.util.Vector">
+											<method name="addElement">
+												<string><![CDATA[Mac OS X]]></string>
+											</method>
+										</object>
+									</property>
+									<property name="doNotInstallOnPlatformList">
+										<object class="java.util.Vector">
+											<method name="addElement">
+												<string><![CDATA[^Windows.*]]></string>
+											</method>
+											<method name="addElement">
+												<string><![CDATA[Solaris]]></string>
+											</method>
+											<method name="addElement">
+												<string><![CDATA[SunOS]]></string>
+											</method>
+											<method name="addElement">
+												<string><![CDATA[HP-UX]]></string>
+											</method>
+											<method name="addElement">
+												<string><![CDATA[Linux]]></string>
+											</method>
+											<method name="addElement">
+												<string><![CDATA[AIX]]></string>
+											</method>
+											<method name="addElement">
+												<string><![CDATA[FreeBSD]]></string>
+											</method>
+											<method name="addElement">
+												<string><![CDATA[NetWare]]></string>
+											</method>
+											<method name="addElement">
+												<string><![CDATA[OS/400]]></string>
+											</method>
+											<method name="addElement">
+												<string><![CDATA[Unlisted Platforms]]></string>
+											</method>
+										</object>
+									</property>
+									<property name="ruleId">
+										<string><![CDATA[CP904]]></string>
+									</property>
+								</object>
+							</rules>
+						</object>
+					</method>
+					<method name="addElement">
 						<object class="com.zerog.ia.installer.actions.InstallSummary" objectID="fe7d64bfa66c">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
@@ -4039,7 +4138,7 @@ Press "Done" to quit the installer.]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="buildOutputLocation">
-								<string><![CDATA[/home/cruisecontrol/checkout/release-jalview/utils/InstallAnywhere/Jalview_Build_Output]]></string>
+								<string><![CDATA[/opt/homes/cruisecontrol/live/cruisecontrol/checkout/next-release-jalview/utils/InstallAnywhere/Jalview_Build_Output]]></string>
 							</property>
 							<property name="relatedProjectSettings">
 								<object class="com.zerog.ia.installer.RelatedProjectSettings" objectID="97f2363da6ac">
@@ -4945,7 +5044,7 @@ Press "Done" to quit the installer.]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="credentialInformation">
-								<object class="com.flexera.ia.vapp.datastructures.VMWareCredentialInformationImpl" objectID="1f4abcab8706">
+								<object class="com.flexera.ia.vapp.datastructures.VMWareCredentialInformationImpl" objectID="eaa38cb2933b">
 									<property name="hostName">
 										<string><![CDATA[]]></string>
 									</property>
@@ -5071,7 +5170,7 @@ Press "Done" to quit the installer.]]></string>
 					</method>
 					<method name="put">
 						<string><![CDATA[com.zerog.ia.project.build.last.date]]></string>
-						<string><![CDATA[21 October 2013 14:27:40 o'clock BST]]></string>
+						<string><![CDATA[16 September 2015 18:09:53 o'clock BST]]></string>
 					</method>
 					<method name="put">
 						<string><![CDATA[com.zerog.ia.build.platform.windows.vm]]></string>
@@ -5139,7 +5238,7 @@ Press "Done" to quit the installer.]]></string>
 					</method>
 					<method name="put">
 						<string><![CDATA[com.zerog.ia.project.save.last.date]]></string>
-						<string><![CDATA[02 December 2014 16:16:01 o'clock GMT]]></string>
+						<string><![CDATA[16 September 2015 18:09:53 o'clock BST]]></string>
 					</method>
 					<method name="put">
 						<string><![CDATA[com.zerog.ia.build.options.optimization.platform.cdrom]]></string>
@@ -5417,13 +5516,13 @@ Press "Done" to quit the installer.]]></string>
 								<int>2</int>
 							</property>
 							<property name="minor">
-								<int>8</int>
+								<int>9</int>
 							</property>
 							<property name="revision">
-								<int>2</int>
+								<int>0</int>
 							</property>
 							<property name="subRevision">
-								<int>0</int>
+								<int>1</int>
 							</property>
 						</object>
 					</property>
@@ -5454,7 +5553,7 @@ Press "Done" to quit the installer.]]></string>
 						<string><![CDATA[jalview-discuss@jalview.org]]></string>
 					</property>
 					<property name="copyright">
-						<string><![CDATA[2014]]></string>
+						<string><![CDATA[2015]]></string>
 					</property>
 					<property name="license">
 						<string><![CDATA[Commercial]]></string>
@@ -7018,11 +7117,9 @@ and any path to a file to read from that file]]></string>
 										<object refID="24485f8aa671"/>
 										<object refID="24485f89a672"/>
 										<object refID="24485f8aa672"/>
-
 										<object refID="244fff00ffff"/>
-					                    <object refID="244ffffaa672"/>
-					                    <object refID="244f00faa672"/>
-
+										<object refID="244ffffaa672"/>
+										<object refID="244f00faa672"/>
 										<object refID="24485f8ba672"/>
 										<object refID="24485f8aa673"/>
 										<object refID="24485f8ba673"/>
@@ -7181,7 +7278,7 @@ and any path to a file to read from that file]]></string>
 												<string><![CDATA[building.html]]></string>
 											</property>
 											<property name="fileSize">
-												<long>4444</long>
+												<long>4447</long>
 											</property>
 											<property name="macBinary">
 												<boolean>false</boolean>
@@ -7209,8 +7306,6 @@ and any path to a file to read from that file]]></string>
 										<object refID="f46c2f42ab93"/>
 										<object refID="1f46cffffab93"/>
 										<object refID="1f46efeefab93"/>
-										<object refID="841f46efeefab93"/>
-										<object refID="9a1f46efeefab93"/>
 										<object refID="1936efeefab93"/>
 										<object refID="10936efeefab93"/>
 										<object refID="11936efeefab93"/>
@@ -7423,7 +7518,7 @@ and any path to a file to read from that file]]></string>
 												<string><![CDATA[exampleFile_2_7.jar]]></string>
 											</property>
 											<property name="fileSize">
-												<long>107135</long>
+												<long>107635</long>
 											</property>
 											<property name="macBinary">
 												<boolean>false</boolean>
@@ -7467,7 +7562,7 @@ and any path to a file to read from that file]]></string>
 												<string><![CDATA[1gaq.txt]]></string>
 											</property>
 											<property name="fileSize">
-												<long>56649</long>
+												<long>55958</long>
 											</property>
 											<property name="macBinary">
 												<boolean>false</boolean>
@@ -7508,7 +7603,7 @@ and any path to a file to read from that file]]></string>
 												<string><![CDATA[uniref50.fa]]></string>
 											</property>
 											<property name="fileSize">
-												<long>3039</long>
+												<long>2979</long>
 											</property>
 											<property name="macBinary">
 												<boolean>false</boolean>
@@ -7590,7 +7685,7 @@ and any path to a file to read from that file]]></string>
 												<string><![CDATA[exampleFeatures.txt]]></string>
 											</property>
 											<property name="fileSize">
-												<long>31397</long>
+												<long>31399</long>
 											</property>
 											<property name="macBinary">
 												<boolean>false</boolean>
@@ -7672,7 +7767,7 @@ and any path to a file to read from that file]]></string>
 												<string><![CDATA[ferredoxin.nw]]></string>
 											</property>
 											<property name="fileSize">
-												<long>392</long>
+												<long>391</long>
 											</property>
 											<property name="macBinary">
 												<boolean>false</boolean>
@@ -7772,8 +7867,8 @@ and any path to a file to read from that file]]></string>
 												<object refID="24485f89a672"/>
 												<object refID="24485f8aa672"/>
 												<object refID="244fff00ffff"/>
-						                        <object refID="244ffffaa672"/>
-						                        <object refID="244f00faa672"/>
+												<object refID="244ffffaa672"/>
+												<object refID="244f00faa672"/>
 												<object refID="24485f8ba672"/>
 												<object refID="24485f8aa673"/>
 												<object refID="24485f8ba673"/>
@@ -7845,7 +7940,7 @@ and any path to a file to read from that file]]></string>
 												<boolean>false</boolean>
 											</property>
 											<property name="totalSize">
-												<long>1</long>
+												<long>30621</long>
 											</property>
 											<property name="macBinary">
 												<boolean>false</boolean>
@@ -7907,6 +8002,88 @@ and any path to a file to read from that file]]></string>
 												<object refID="f44fc68baba3"/>
 											</visualChildren>
 										</object>
+										<object class="com.zerog.ia.installer.actions.InstallFile" objectID="ea43799f8a5c">
+											<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[THIRDPARTYLIBS]]></string>
+											</property>
+											<property name="overrideUnixPermissions">
+												<boolean>false</boolean>
+											</property>
+											<property name="sourcePath">
+												<string><![CDATA[/opt/homes/cruisecontrol/live/cruisecontrol/checkout/next-release-jalview/]]></string>
+											</property>
+											<property name="shouldUninstall">
+												<boolean>true</boolean>
+											</property>
+											<property name="destinationName">
+												<string><![CDATA[THIRDPARTYLIBS]]></string>
+											</property>
+											<property name="fileSize">
+												<long>2612</long>
+											</property>
+											<property name="macBinary">
+												<boolean>false</boolean>
+											</property>
+											<property name="targetCheckKind">
+												<int>0</int>
+											</property>
+										</object>
+										<object class="com.zerog.ia.installer.actions.InstallFile" objectID="ea4379a48a5c">
+											<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[AUTHORS]]></string>
+											</property>
+											<property name="overrideUnixPermissions">
+												<boolean>false</boolean>
+											</property>
+											<property name="sourcePath">
+												<string><![CDATA[/opt/homes/cruisecontrol/live/cruisecontrol/checkout/next-release-jalview/]]></string>
+											</property>
+											<property name="shouldUninstall">
+												<boolean>true</boolean>
+											</property>
+											<property name="destinationName">
+												<string><![CDATA[AUTHORS]]></string>
+											</property>
+											<property name="fileSize">
+												<long>809</long>
+											</property>
+											<property name="macBinary">
+												<boolean>false</boolean>
+											</property>
+											<property name="targetCheckKind">
+												<int>0</int>
+											</property>
+										</object>
 									</installChildren>
 								</object>
 								<object class="com.zerog.ia.installer.InstallComponent" objectID="fe7d6497a66b">
@@ -8322,6 +8499,8 @@ and any path to a file to read from that file]]></string>
 								<object refID="24485f85a670"/>
 								<object refID="f44fc598aba0"/>
 								<object refID="094ab0d49607"/>
+								<object refID="ea43799f8a5c"/>
+								<object refID="ea4379a48a5c"/>
 							</visualChildren>
 						</object>
 						<object class="com.zerog.ia.installer.GhostDirectory" objectID="3cd94e29a677">