From: Jim Procter <jprocter@dundee.ac.uk>
Date: Tue, 2 Dec 2014 13:22:20 +0000 (+0000)
Subject: Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch
X-Git-Tag: Release_2_8_2~1^2~6
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=da03c490b1cb9576a40430a477d093fbbecc8378;hp=6d69275a18e2773d73d84b9fe4291e7313abfda4;p=jalview.git

Merge branch 'JAL-1517_release282' into Release_2_8_2_Branch
---

diff --git a/utils/InstallAnywhere/Jalview.iap_xml b/utils/InstallAnywhere/Jalview.iap_xml
index c938a0b..99e5db8 100755
--- a/utils/InstallAnywhere/Jalview.iap_xml
+++ b/utils/InstallAnywhere/Jalview.iap_xml
@@ -1,18 +1,18 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!-- This script was automatically generated using InstallAnywhere 2013 Professional, Build 4538
+<!-- This script was automatically generated using InstallAnywhere 2014 Professional, Build 4783
      STATUS: Fully Functional LICENSED Edition
-     DATE:   Fri Nov 01 13:57:32 GMT 2013 -->
-<InstallAnywhere_Deployment_Project increments="5103">
+     DATE:   Mon Dec 01 23:27:13 GMT 2014 -->
+<InstallAnywhere_Deployment_Project increments="5258">
 	<!-- ** DO NOT EDIT ** Essential authorization and configuration data ** DO NOT EDIT ** -->
 	<essentialScriptInfo>
-		<versionID major="15" minor="0" revision="0"/>
-		<editionID>49,53,46,48,32,80,114,111,102,101,115,115,105,111,110,97,108,32,66,117,105,108,100,32,52,53,51,56</editionID>
+		<versionID major="16" minor="0" revision="0"/>
+		<editionID>49,54,46,48,32,80,114,111,102,101,115,115,105,111,110,97,108,32,66,117,105,108,100,32,52,55,56,51</editionID>
 		<scriptID>12,42,11,85,78,76,73,67,69,78,83,69,68</scriptID>
-		<buildID>3,13,71,76,105,110,117,120,44,32,50,46,54,46,51,50,45,50,55,57,46,50,50,46,49,46,101,108,54,46,120,56,54,95,54,52,44,32,97,109,100,54,52,59,32,74,97,118,97,32,49,46,55,46,48,95,50,53,44,32,79,114,97,99,108,101,32,67,111,114,112,111,114,97,116,105,111,110,44,32,104,116,116,112,58,47,47,106,97,118,97,46,111,114,97,99,108,101,46,99,111,109,47,59,32,101,110,44,32,85,110,107,110,111,119,110,59,32,73,83,79,45,56,56,53,57,45,49</buildID>
+		<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>1,0,0,64,29,-4,96,96,80,127,118,101,93,105,116,96,121,48,48,49,56,52,67,98,113,112,112,37,82,101,96,63,55,-11,2,0,1,84,19,2,1,0,0</authorizationID>
+		<authorizationID>1,0,0,64,13,34,-32,-128,80,127,118,101,93,105,116,96,121,48,48,49,56,52,67,98,113,112,112,37,82,101,96,63,55,-11,2,6,5,109,24,10,1,0,0</authorizationID>
 	</essentialScriptInfo>
-	<installationObjects uniqueObjects="217">
+	<installationObjects uniqueObjects="224">
 		<object class="com.zerog.ia.installer.Installer" objectID="fe7d63eda660">
 			<property name="belongsToUninstallPhase">
 				<boolean>false</boolean>
@@ -223,28 +223,28 @@ it will search for ones in this list]]></string>
 								</object>
 							</method>
 							<method name="addElement">
-								<object class="com.zerog.ia.installer.util.LAXPropertyData" objectID="bbb5f73fa453">
+								<object class="com.zerog.ia.installer.util.LAXPropertyData" objectID="97f991ffa6f7">
 									<property name="propertyValue">
-										<string><![CDATA[jalview.bin.Jalview]]></string>
+										<string><![CDATA[33554432]]></string>
 									</property>
 									<property name="propertyName">
-										<string><![CDATA[lax.main.class]]></string>
+										<string><![CDATA[lax.nl.java.option.java.heap.size.initial]]></string>
 									</property>
 									<property name="propertyComment">
-										<string><![CDATA[the class that contains the main method for the application]]></string>
+										<string><![CDATA[Initial heap size for Jalview]]></string>
 									</property>
 								</object>
 							</method>
 							<method name="addElement">
-								<object class="com.zerog.ia.installer.util.LAXPropertyData" objectID="97f991ffa6f7">
+								<object class="com.zerog.ia.installer.util.LAXPropertyData" objectID="bbb5f73fa453">
 									<property name="propertyValue">
-										<string><![CDATA[33554432]]></string>
+										<string><![CDATA[jalview.bin.Jalview]]></string>
 									</property>
 									<property name="propertyName">
-										<string><![CDATA[lax.nl.java.option.java.heap.size.initial]]></string>
+										<string><![CDATA[lax.main.class]]></string>
 									</property>
 									<property name="propertyComment">
-										<string><![CDATA[Initial heap size for Jalview]]></string>
+										<string><![CDATA[the class that contains the main method for the application]]></string>
 									</property>
 								</object>
 							</method>
@@ -1042,110 +1042,110 @@ 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="244ffffaa672">
-              <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[log4j-to-slf4j-2.0-rc2.jar]]></string>
-              </property>
-              <property name="overrideUnixPermissions">
-                <boolean>false</boolean>
-              </property>
-              <property name="sourcePath">
-                <string><![CDATA[/home/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[log4j-to-slf4j-2.0-rc2.jar]]></string>
-              </property>
-              <property name="fileSize">
-                <long>348699</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="244f00faa672">
-              <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[slf4j-log4j12-1.7.7.jar]]></string>
-              </property>
-              <property name="overrideUnixPermissions">
-                <boolean>false</boolean>
-              </property>
-              <property name="sourcePath">
-                <string><![CDATA[/home/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[slf4j-log4j12-1.7.7.jar]]></string>
-              </property>
-              <property name="fileSize">
-                <long>348699</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="244ffffaa672">
+							<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[log4j-to-slf4j-2.0-rc2.jar]]></string>
+							</property>
+							<property name="overrideUnixPermissions">
+								<boolean>false</boolean>
+							</property>
+							<property name="sourcePath">
+								<string><![CDATA[/home/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[log4j-to-slf4j-2.0-rc2.jar]]></string>
+							</property>
+							<property name="fileSize">
+								<long>348699</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="244f00faa672">
+							<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[slf4j-log4j12-1.7.7.jar]]></string>
+							</property>
+							<property name="overrideUnixPermissions">
+								<boolean>false</boolean>
+							</property>
+							<property name="sourcePath">
+								<string><![CDATA[/home/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[slf4j-log4j12-1.7.7.jar]]></string>
+							</property>
+							<property name="fileSize">
+								<long>348699</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="88d4aff3b0c6">
 							<property name="belongsToUninstallPhase">
@@ -2069,7 +2069,59 @@ and any path to a file to save to the file]]></string>
 								<string><![CDATA[jfreesvg-2.1.jar]]></string>
 							</property>
 							<property name="fileSize">
-								<long>382442</long>
+								<long>49768</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="1f46efeefab93">
+							<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[json_simple-1.1.jar]]></string>
+							</property>
+							<property name="overrideUnixPermissions">
+								<boolean>false</boolean>
+							</property>
+							<property name="sourcePath">
+								<string><![CDATA[/home/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[json_simple-1.1.jar]]></string>
+							</property>
+							<property name="fileSize">
+								<long>16046</long>
 							</property>
 							<property name="macBinary">
 								<boolean>false</boolean>
@@ -2897,7 +2949,7 @@ Press "Done" to quit the installer.]]></string>
 												<boolean>false</boolean>
 											</property>
 											<property name="withoutVmSearchOption">
-												<short>13</short>
+												<short>10</short>
 											</property>
 											<property name="withVMSearchOption">
 												<short>21</short>
@@ -3150,7 +3202,7 @@ Press "Done" to quit the installer.]]></string>
 												<boolean>true</boolean>
 											</property>
 											<property name="bundledVM">
-												<string><![CDATA[SunJRE160_02LinuxINTEL.vm]]></string>
+												<string><![CDATA[ORACLEJRE7u60_linux32.vm]]></string>
 											</property>
 											<property name="withoutVmSearchOption">
 												<short>10</short>
@@ -4193,7 +4245,7 @@ Press "Done" to quit the installer.]]></string>
 								<boolean>true</boolean>
 							</property>
 							<property name="credentialInformation">
-								<object class="com.flexera.ia.vapp.datastructures.VMWareCredentialInformationImpl" objectID="27759feba050">
+								<object class="com.flexera.ia.vapp.datastructures.VMWareCredentialInformationImpl" objectID="1baf22668814">
 									<property name="hostName">
 										<string><![CDATA[]]></string>
 									</property>
@@ -4315,7 +4367,7 @@ Press "Done" to quit the installer.]]></string>
 					</method>
 					<method name="put">
 						<string><![CDATA[com.zerog.ia.installer.options.valid.vm.list]]></string>
-						<string><![CDATA[1.6,1.7,1.8+]]></string>
+						<string><![CDATA[1.7+]]></string>
 					</method>
 					<method name="put">
 						<string><![CDATA[com.zerog.ia.project.build.last.date]]></string>
@@ -4387,7 +4439,7 @@ Press "Done" to quit the installer.]]></string>
 					</method>
 					<method name="put">
 						<string><![CDATA[com.zerog.ia.project.save.last.date]]></string>
-						<string><![CDATA[01 November 2013 13:57:31 o'clock GMT]]></string>
+						<string><![CDATA[01 December 2014 23:27:12 o'clock GMT]]></string>
 					</method>
 					<method name="put">
 						<string><![CDATA[com.zerog.ia.build.options.optimization.platform.cdrom]]></string>
@@ -4411,7 +4463,7 @@ Press "Done" to quit the installer.]]></string>
 					</method>
 					<method name="put">
 						<string><![CDATA[com.zerog.ia.installer.options.platform.macosx.vm.version]]></string>
-						<string><![CDATA[1.6+]]></string>
+						<string><![CDATA[1.7+]]></string>
 					</method>
 					<method name="put">
 						<string><![CDATA[com.zerog.ia.build.platform.java.novm]]></string>
@@ -4668,13 +4720,20 @@ Press "Done" to quit the installer.]]></string>
 								<int>8</int>
 							</property>
 							<property name="revision">
-								<int>0</int>
+								<int>2</int>
 							</property>
 							<property name="subRevision">
 								<int>0</int>
 							</property>
 						</object>
 					</property>
+					<property name="upgradeCode">
+						<object class="com.zerog.registry.UUID">
+							<method name="update">
+								<string><![CDATA[fe7d6410-1ed5-11b2-a662-f4777f28dbfc]]></string>
+							</method>
+						</object>
+					</property>
 					<property name="supportURL">
 						<string><![CDATA[http://www.jalview.org/faq]]></string>
 					</property>
@@ -4695,7 +4754,7 @@ Press "Done" to quit the installer.]]></string>
 						<string><![CDATA[jalview-discuss@jalview.org]]></string>
 					</property>
 					<property name="copyright">
-						<string><![CDATA[2013]]></string>
+						<string><![CDATA[2014]]></string>
 					</property>
 					<property name="license">
 						<string><![CDATA[Commercial]]></string>
@@ -5688,6 +5747,80 @@ This will remove features installed by InstallAnywhere.  It will not remove file
 			<property name="oldStyleInstallersEnabled">
 				<boolean>false</boolean>
 			</property>
+			<property name="upgradeSettings">
+				<object class="com.zerog.ia.installer.UpgradeSettings" objectID="1b941ce786e7">
+					<property name="enableUpgrade">
+						<boolean>false</boolean>
+					</property>
+					<property name="upgradeConfigurationsList">
+						<object class="java.util.ArrayList" list="true">
+							<method name="add">
+								<object class="com.zerog.ia.installer.UpgradeConfiguration" objectID="1b941ce886e7">
+									<property name="detectionBasedOn">
+										<string><![CDATA[PRODUCT_CODE]]></string>
+									</property>
+									<property name="requireValidationForPreviousProductCode">
+										<boolean>false</boolean>
+									</property>
+									<property name="maxVersion">
+										<object class="com.zerog.ia.installer.util.Version" objectID="1b941cea86e7">
+											<property name="major">
+												<int>1</int>
+											</property>
+											<property name="minor">
+												<int>0</int>
+											</property>
+											<property name="revision">
+												<int>0</int>
+											</property>
+											<property name="subRevision">
+												<int>0</int>
+											</property>
+										</object>
+									</property>
+									<property name="minVersion">
+										<object class="com.zerog.ia.installer.util.Version" objectID="1b941ce886e8">
+											<property name="major">
+												<int>1</int>
+											</property>
+											<property name="minor">
+												<int>0</int>
+											</property>
+											<property name="revision">
+												<int>0</int>
+											</property>
+											<property name="subRevision">
+												<int>0</int>
+											</property>
+										</object>
+									</property>
+									<property name="configurationName">
+										<string><![CDATA[Default Upgrade Configuration]]></string>
+									</property>
+								</object>
+							</method>
+						</object>
+					</property>
+					<property name="abortInstallationIfUninstallFails">
+						<boolean>true</boolean>
+					</property>
+					<property name="automaticallyRemoveAllExistingInstallations">
+						<boolean>true</boolean>
+					</property>
+					<property name="promptUserOnExistanceOfMultiplePreviousInstallations">
+						<boolean>false</boolean>
+					</property>
+					<property name="allowCustomizationOfUserInstallDirectory">
+						<boolean>false</boolean>
+					</property>
+					<property name="retainFeaturePreferences">
+						<boolean>false</boolean>
+					</property>
+				</object>
+			</property>
+			<property name="tomcatServerNamesList">
+				<object class="java.util.ArrayList" list="true"/>
+			</property>
 			<visualChildren>
 				<object class="com.zerog.ia.installer.InstallSet" objectID="fe7d6493a66a">
 					<property name="belongsToUninstallPhase">
@@ -6185,8 +6318,8 @@ and any path to a file to read from that file]]></string>
 										<object refID="24485f8aa671"/>
 										<object refID="24485f89a672"/>
 										<object refID="24485f8aa672"/>
-                    <object refID="244ffffaa672"/>
-                    <object refID="244f00faa672"/>
+										<object refID="244ffffaa672"/>
+										<object refID="244f00faa672"/>
 										<object refID="24485f8ba672"/>
 										<object refID="24485f8aa673"/>
 										<object refID="24485f8ba673"/>
@@ -6370,7 +6503,9 @@ and any path to a file to read from that file]]></string>
 										<object refID="f44ca391ab9f"/>
 										<object refID="f44ca392ab9f"/>
 										<object refID="f44ca393ab9f"/>
-										<object refID=""1f46cffffab93"/>
+										<object refID="f46c2f42ab93"/>
+										<object refID="1f46cffffab93"/>
+										<object refID="1f46efeefab93"/>
 										<object class="com.zerog.ia.installer.actions.InstallFile" objectID="f44fc5b2aba1">
 											<property name="belongsToUninstallPhase">
 												<boolean>false</boolean>
@@ -6872,7 +7007,6 @@ and any path to a file to read from that file]]></string>
 												<int>0</int>
 											</property>
 										</object>
-										<object refID="f46c2f42ab93"/>
 										<object class="com.zerog.ia.installer.actions.InstallDirectory" objectID="24485f85a670">
 											<property name="belongsToUninstallPhase">
 												<boolean>false</boolean>
@@ -6922,8 +7056,8 @@ and any path to a file to read from that file]]></string>
 												<object refID="24485f8aa671"/>
 												<object refID="24485f89a672"/>
 												<object refID="24485f8aa672"/>
-                        <object refID="244ffffaa672"/>
-                        <object refID="244f00faa672"/>
+												<object refID="244ffffaa672"/>
+												<object refID="244f00faa672"/>
 												<object refID="24485f8ba672"/>
 												<object refID="24485f8aa673"/>
 												<object refID="24485f8ba673"/>
@@ -6947,6 +7081,7 @@ and any path to a file to read from that file]]></string>
 												<object refID="f44ca393ab9f"/>
 												<object refID="f46c2f42ab93"/>
 												<object refID="1f46cffffab93"/>
+												<object refID="1f46efeefab93"/>
 											</visualChildren>
 										</object>
 										<object class="com.zerog.ia.installer.actions.InstallDirectory" objectID="f44fc5d5aba1">