From: Ben Soares <bsoares@dundee.ac.uk>
Date: Fri, 31 May 2019 14:44:07 +0000 (+0100)
Subject: JAL-3247 Adjusted Uninstall Old Jalview.app to just run the old uninstaller if it... 
X-Git-Tag: Release_2_11_1_0~53^2~1
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=1413ed295402b90cccddc8ee814cb5be0d1fc75e

JAL-3247 Adjusted Uninstall Old Jalview.app to just run the old uninstaller if it finds it, aded '(optional)' to the link name in the DMG. It will need re-signing. Edited VCFReader to allow java 1.8 compiling.
---

diff --git a/src/jalview/ext/htsjdk/VCFReader.java b/src/jalview/ext/htsjdk/VCFReader.java
index 3e7fbc2..2859e0f 100644
--- a/src/jalview/ext/htsjdk/VCFReader.java
+++ b/src/jalview/ext/htsjdk/VCFReader.java
@@ -135,7 +135,7 @@ public class VCFReader implements Closeable, Iterable<VariantContext>
   {
     final CloseableIterator<VariantContext> it = reader.iterator();
     
-    return new CloseableIterator<>()
+    return new CloseableIterator<VariantContext>()
     {
       boolean atEnd = false;
 
diff --git a/utils/install4j/DS_Store b/utils/install4j/DS_Store
index 2eafdbc..21fc79e 100644
Binary files a/utils/install4j/DS_Store and b/utils/install4j/DS_Store differ
diff --git a/utils/install4j/DS_Store_3 b/utils/install4j/DS_Store_3
new file mode 100644
index 0000000..21fc79e
Binary files /dev/null and b/utils/install4j/DS_Store_3 differ
diff --git a/utils/install4j/Uninstall Old Jalview.app/Contents/Info.plist b/utils/install4j/Uninstall Old Jalview.app/Contents/Info.plist
index c10a834..06399cf 100644
--- a/utils/install4j/Uninstall Old Jalview.app/Contents/Info.plist	
+++ b/utils/install4j/Uninstall Old Jalview.app/Contents/Info.plist	
@@ -11,11 +11,11 @@
 	<key>CFBundleIconFile</key>
 	<string>applet</string>
 	<key>CFBundleIdentifier</key>
-	<string>com.apple.ScriptEditor.id.Uninstall-Old-Jalview</string>
+	<string>com.apple.ScriptEditor.id.Uninstall-Old-Jalview--optional</string>
 	<key>CFBundleInfoDictionaryVersion</key>
 	<string>6.0</string>
 	<key>CFBundleName</key>
-	<string>Uninstall Old Jalview</string>
+	<string>Uninstall Old Jalview (optional)</string>
 	<key>CFBundlePackageType</key>
 	<string>APPL</string>
 	<key>CFBundleShortVersionString</key>
@@ -42,9 +42,9 @@
 		<key>name</key>
 		<string>ScriptWindowState</string>
 		<key>positionOfDivider</key>
-		<real>223</real>
+		<real>421</real>
 		<key>savedFrame</key>
-		<string>329 957 700 672 0 0 3360 1867 </string>
+		<string>20 1180 700 672 0 0 3360 1867 </string>
 		<key>selectedTab</key>
 		<string>description</string>
 	</dict>
diff --git a/utils/install4j/Uninstall Old Jalview.app/Contents/MacOS/applet b/utils/install4j/Uninstall Old Jalview.app/Contents/MacOS/applet
index f11986e..171d0cc 100755
Binary files a/utils/install4j/Uninstall Old Jalview.app/Contents/MacOS/applet and b/utils/install4j/Uninstall Old Jalview.app/Contents/MacOS/applet differ
diff --git a/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/Scripts/main.scpt b/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/Scripts/main.scpt
index 1dce96c..7afbebc 100644
Binary files a/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/Scripts/main.scpt and b/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/Scripts/main.scpt differ
diff --git a/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/applet.rsrc b/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/applet.rsrc
index c41bb4e..cf9920e 100644
Binary files a/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/applet.rsrc and b/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/applet.rsrc differ
diff --git a/utils/install4j/Uninstall Old Jalview.scpt b/utils/install4j/Uninstall Old Jalview.scpt
index 1692009..7afbebc 100644
Binary files a/utils/install4j/Uninstall Old Jalview.scpt and b/utils/install4j/Uninstall Old Jalview.scpt differ
diff --git a/utils/install4j/install4j_template.install4j b/utils/install4j/install4j_template.install4j
index 2f65f51..bec9829 100644
--- a/utils/install4j/install4j_template.install4j
+++ b/utils/install4j/install4j_template.install4j
@@ -1910,7 +1910,7 @@ return console.askYesNo(message, true);
         <symlink name="Jalview.app/Contents/Resources/app/${compiler:JRE_DIR}/Contents/MacOS/libjli.dylib" target="../Home/lib/jli/libjli.dylib" />
         <file name="Jalview.app/Contents/Resources/Jalview-File.icns" file="./Jalview-File.icns" />
         <file name="Jalview.app/Contents/Resources/Jalview-Version-Locator.icns" file="Jalview-Version-Locator.icns" />
-        <symlink name="Uninstall Old Jalview.app" target="Jalview.app/Contents/Resources/app/Uninstall Old Jalview.app" />
+        <symlink name="Uninstall Old Jalview (optional).app" target="Jalview.app/Contents/Resources/app/Uninstall Old Jalview.app" />
       </topLevelFiles>
     </macosArchive>
     <macosArchive name="Network macOS Disk Image" id="1274" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${compiler:sys.platform}-app_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false" archiveType="dmg" volumeName="${compiler:sys.shortName} Installer" launcherId="1402">
@@ -1939,7 +1939,7 @@ return console.askYesNo(message, true);
         <symlink name="Jalview.app/Contents/Resources/app/${compiler:JRE_DIR}/Contents/MacOS/libjli.dylib" target="../Home/lib/jli/libjli.dylib" />
         <file name="Jalview.app/Contents/Resources/Jalview-Version-Locator.icns" file="Jalview-Version-Locator.icns" />
         <file name="Jalview.app/Contents/Resources/Jalview-File.icns" file="Jalview-File.icns" />
-        <symlink name="Uninstall Old Jalview.app" target="Jalview.app/Contents/Resources/app/Uninstall Old Jalview.app" />
+        <symlink name="Uninstall Old Jalview (optional).app" target="Jalview.app/Contents/Resources/app/Uninstall Old Jalview.app" />
       </topLevelFiles>
     </macosArchive>
     <unixInstaller name="Offline Unix Shell Installer" id="1595" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}_installer_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="" manualJREEntry="false" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="~/opt/" contentFilesType="1">