From: Ben Soares <bsoares@dundee.ac.uk>
Date: Mon, 27 May 2019 15:06:02 +0000 (+0100)
Subject: Merge branch 'task/JAL-3247_JAL-3246_JAL-3254_JAL-3236_merge' into task/JAL-3141_JAL... 
X-Git-Tag: Release_2_11_1_0~53^2~11
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=54360f0110522c5832ebabff8a8498ed4a087261;hp=b8683aaaf600239e94d658bdf99012f5e684d9a8;p=jalview.git

Merge branch 'task/JAL-3247_JAL-3246_JAL-3254_JAL-3236_merge' into task/JAL-3141_JAL-3247_merge

merge attempt
---

diff --git a/build.gradle b/build.gradle
index 07a4095..fb311a4 100644
--- a/build.gradle
+++ b/build.gradle
@@ -846,15 +846,26 @@ task copyInstall4jTemplate(type: Copy) {
   outputs.files(install4jConf)
 
   doLast {
+    // include file associations in installer
     def installerFileAssociationsXml = file("$install4jDir/$install4jInstallerFileAssociations").text
     ant.replaceregexp(
       byline: false,
       flags: "s",
       match: '<action name="EXTENSIONS_REPLACED_BY_GRADLE".*?</action>',
-      //match: '<action.*?EXTENSIONS_REPLACED_BY_GRADLE.*?</action>',
       replace: installerFileAssociationsXml,
       file: install4jConf
     )
+    /*
+    // include uninstaller applescript app files in dmg
+    def installerDMGUninstallerXml = file("$install4jDir/$install4jDMGUninstallerAppFiles").text
+    ant.replaceregexp(
+      byline: false,
+      flags: "s",
+      match: '<file name="UNINSTALL_OLD_JALVIEW_APP_REPLACED_IN_GRADLE" file=.*?>',
+      replace: installerDMGUninstallerXml,
+      file: install4jConf
+    )
+    */
   }
 }
 
diff --git a/getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar b/getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar
index 7230883..c09d3e4 100644
Binary files a/getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar and b/getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar differ
diff --git a/getdown/lib/getdown-launcher.jar b/getdown/lib/getdown-launcher.jar
index cb5f670..321b5ce 100644
Binary files a/getdown/lib/getdown-launcher.jar and b/getdown/lib/getdown-launcher.jar differ
diff --git a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java
index 25cd109..0de5c8a 100644
--- a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java
+++ b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java
@@ -26,6 +26,7 @@ import java.util.zip.GZIPInputStream;
 import com.sun.management.OperatingSystemMXBean;
 import java.lang.management.ManagementFactory;
 
+import jalview.bin.MemorySetting;
 
 import com.threerings.getdown.util.*;
 // avoid ambiguity with java.util.Base64 which we can't use as it's 1.8+
@@ -753,28 +754,34 @@ public class Application
             jvmmempc = config.getInt(appPrefix + "jvmmempc", jvmmempc);
         }
         if (0 <= jvmmempc && jvmmempc <= 100) {
-            final Object o = ManagementFactory.getOperatingSystemMXBean();
-
-            try {
-                if (o instanceof OperatingSystemMXBean) {
-                    final OperatingSystemMXBean osb = (OperatingSystemMXBean) o;
-                    long physicalMem = osb.getTotalPhysicalMemorySize();
-                    long requestedMem = physicalMem*jvmmempc/100;
-                    String[] maxMemHeapArg = new String[]{"-Xmx"+Long.toString(requestedMem)};
-                    // remove other max heap size arg
-                    ARG: for (int i = 0; i < _jvmargs.size(); i++) {
-                           if (_jvmargs.get(i) instanceof java.lang.String && _jvmargs.get(i).startsWith("-Xmx")) {
-                                _jvmargs.remove(i);
-                           }
-                    }
-                    addAll(maxMemHeapArg, _jvmargs);
+          
+          long maxMemLong = -1;
+
+          try
+          {
+            maxMemLong = MemorySetting.memPercent(jvmmempc);
+          } catch (Exception e)
+          {
+            e.printStackTrace();
+          } catch (Throwable t)
+          {
+            t.printStackTrace();
+          }
 
-                }
-            }
-            catch (NoClassDefFoundError e) {
-                // com.sun.management.OperatingSystemMXBean doesn't exist in this JVM
-                System.out.println("No com.sun.management.OperatingSystemMXBean. Cannot use 'jvmmempc'.");
+          if (maxMemLong > 0)
+          {
+            
+            String[] maxMemHeapArg = new String[]{"-Xmx"+Long.toString(maxMemLong)};
+            // remove other max heap size arg
+            ARG: for (int i = 0; i < _jvmargs.size(); i++) {
+              if (_jvmargs.get(i) instanceof java.lang.String && _jvmargs.get(i).startsWith("-Xmx")) {
+                _jvmargs.remove(i);
+              }
             }
+            addAll(maxMemHeapArg, _jvmargs);
+            
+          }
+
         } else if (jvmmempc != -1) {
           System.out.println("'jvmmempc' value must be in range 0 to 100 (read as '"+Integer.toString(jvmmempc)+"')");
         }
diff --git a/getdown/src/getdown/core/src/main/java/jalview/bin/MemorySetting.java b/getdown/src/getdown/core/src/main/java/jalview/bin/MemorySetting.java
new file mode 100644
index 0000000..b3bae2d
--- /dev/null
+++ b/getdown/src/getdown/core/src/main/java/jalview/bin/MemorySetting.java
@@ -0,0 +1,51 @@
+package jalview.bin;
+
+import java.lang.management.ManagementFactory;
+import java.lang.management.OperatingSystemMXBean;
+
+public class MemorySetting
+{
+  public static final long leaveFreeMinMemory = 536870912; // 0.5 GB
+
+  public static final long applicationMinMemory = 536870912; // 0.5 GB
+
+  protected static long getPhysicalMemory()
+  {
+    final OperatingSystemMXBean o = ManagementFactory
+            .getOperatingSystemMXBean();
+
+    try
+    {
+      if (o instanceof com.sun.management.OperatingSystemMXBean)
+      {
+        final com.sun.management.OperatingSystemMXBean osb = (com.sun.management.OperatingSystemMXBean) o;
+        return osb.getTotalPhysicalMemorySize();
+      }
+    } catch (NoClassDefFoundError e)
+    {
+      // com.sun.management.OperatingSystemMXBean doesn't exist in this JVM
+      System.out.println("No com.sun.management.OperatingSystemMXBean");
+    }
+
+    // We didn't get a com.sun.management.OperatingSystemMXBean.
+    return -1;
+  }
+
+  public static long memPercent(int percent)
+  {
+    long memPercent = -1;
+
+    long physicalMem = getPhysicalMemory();
+    if (physicalMem > applicationMinMemory)
+    {
+      // try and set at least applicationMinMemory and thereafter ensure
+      // leaveFreeMinMemory is left for the OS
+      memPercent = Math.max(applicationMinMemory,
+              physicalMem - Math.max(physicalMem * (100 - percent) / 100,
+                      leaveFreeMinMemory));
+    }
+
+    return memPercent;
+  }
+
+}
diff --git a/gradle.properties b/gradle.properties
index e49c3ab..57119cb 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -59,7 +59,7 @@ getdown_txt_title = Jalview
 getdown_channel_base = http://www.jalview.org/getdown/jalview
 getdown_channel_name = TEST
 getdown_txt_allow_offline = true
-getdown_txt_jvmmempc = 95
+getdown_txt_jalview.jvmmempc = 90
 getdown_txt_multi_jvmarg = -Dgetdownappdir="%APPDIR%"
 getdown_txt_strict_comments = true
 getdown_txt_title = Jalview
@@ -100,8 +100,8 @@ install4jResourceDir = utils/install4j
 install4jTemplate = install4j_template.install4j
 install4jInfoPlistFileAssociations = file_associations_auto-Info_plist.xml
 install4jInstallerFileAssociations = file_associations_auto-install4j.xml
+install4jDMGUninstallerAppFiles = uninstall_old_jalview_files.xml
 install4jBuildDir = build/install4j
-install4jMediaTypes = windows,macosArchive,linuxRPM,linuxDeb,unixArchive
 install4jMediaTypes = windows,macosArchive,linuxRPM,linuxDeb,unixArchive,unixInstaller
 install4jFaster = false
 
diff --git a/j11lib/getdown-core.jar b/j11lib/getdown-core.jar
index 7230883..c09d3e4 100644
Binary files a/j11lib/getdown-core.jar and b/j11lib/getdown-core.jar differ
diff --git a/j8lib/getdown-core.jar b/j8lib/getdown-core.jar
index 7230883..c09d3e4 100644
Binary files a/j8lib/getdown-core.jar and b/j8lib/getdown-core.jar differ
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index c66e63e..449c1fb 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -360,10 +360,12 @@ public class Jalview
         JalviewTaskbar.setTaskbar(this);
       } catch (Exception e)
       {
-        e.printStackTrace();
+        System.out.println("Cannot set Taskbar");
+        // e.printStackTrace();
       } catch (Throwable t)
       {
-        t.printStackTrace();
+        System.out.println("Cannot set Taskbar");
+        // t.printStackTrace();
       }
 
       desktop.setVisible(true);
diff --git a/src/jalview/bin/JalviewTaskbar.java b/src/jalview/bin/JalviewTaskbar.java
index 5747263..7dd0382 100644
--- a/src/jalview/bin/JalviewTaskbar.java
+++ b/src/jalview/bin/JalviewTaskbar.java
@@ -29,7 +29,7 @@ public class JalviewTaskbar
           }
         } catch (Exception e)
         {
-          e.printStackTrace();
+          System.out.println("Unable to setIconImage()");
         }
       }
     }
diff --git a/src/jalview/bin/Launcher.java b/src/jalview/bin/Launcher.java
index aec3acd..412f119 100644
--- a/src/jalview/bin/Launcher.java
+++ b/src/jalview/bin/Launcher.java
@@ -1,8 +1,8 @@
 package jalview.bin;
 
 import java.io.File;
+import java.io.IOException;
 import java.lang.management.ManagementFactory;
-import java.lang.management.OperatingSystemMXBean;
 import java.util.ArrayList;
 
 public class Launcher
@@ -10,7 +10,9 @@ public class Launcher
 
   private final static String startClass = "jalview.bin.Jalview";
 
-  private final static int maxHeapSizePerCent = 95;
+  private final static int maxHeapSizePerCent = 90;
+
+  private final static String maxHeapSizePerCentProperty = "jvmmempc";
 
   private final static String dockIconPath = "JalviewLogo_Huge.png";
 
@@ -22,6 +24,8 @@ public class Launcher
     ArrayList<String> command = new ArrayList<>();
     command.add(javaBin);
 
+    String memSetting = null;
+
     boolean isAMac = System.getProperty("os.name").indexOf("Mac") > -1;
 
     for (String jvmArg : ManagementFactory.getRuntimeMXBean()
@@ -40,39 +44,81 @@ public class Launcher
     // add memory setting if not specified
     boolean memSet = false;
     boolean dockIcon = false;
+    boolean dockName = false;
     ARG: for (int i = 0; i < command.size(); i++)
     {
       String arg = command.get(i);
       if (arg.startsWith("-Xmx"))
       {
+        memSetting = arg;
         memSet = true;
       }
       else if (arg.startsWith("-Xdock:icon"))
       {
         dockIcon = true;
       }
+      else if (arg.startsWith("-Xdock:name"))
+      {
+        dockName = true;
+      }
     }
 
     if (!memSet)
     {
       long maxMemLong = -1;
-      long physicalMem = getPhysicalMemory();
-      if (physicalMem > 0)
+      int percent = maxHeapSizePerCent;
+      String jvmmempc = System.getProperty(maxHeapSizePerCentProperty);
+      try
+      {
+        if (jvmmempc != null)
+        {
+          int trypercent = Integer.parseInt(jvmmempc);
+          if (0 < trypercent && trypercent <= 100)
+          {
+            percent = trypercent;
+          }
+          else
+          {
+            System.out.println("Property '" + maxHeapSizePerCentProperty
+                    + "' should be in range 1..100");
+          }
+        }
+      } catch (Exception e)
+      {
+        System.out.println("Error parsing " + maxHeapSizePerCentProperty
+                + " '" + jvmmempc + "'");
+      }
+
+      try
       {
-        maxMemLong = physicalMem * maxHeapSizePerCent / 100;
+        maxMemLong = MemorySetting.memPercent(percent);
+      } catch (Exception e)
+      {
+        e.printStackTrace();
+      } catch (Throwable t)
+      {
+        t.printStackTrace();
       }
+
       if (maxMemLong > 0)
       {
-        command.add("-Xmx" + Long.toString(maxMemLong));
+        memSetting = "-Xmx" + Long.toString(maxMemLong);
+        command.add(memSetting);
       }
     }
 
-    if (!dockIcon && isAMac)
+    if (isAMac)
     {
-      command.add("-Xdock:icon=" + dockIconPath);
-      // -Xdock:name=... doesn't actually work :(
-      // Leaving it in in case it gets fixed
-      command.add("-Xdock:name=" + "Jalview");
+      if (!dockIcon)
+      {
+        command.add("-Xdock:icon=" + dockIconPath);
+      }
+      if (!dockName)
+      {
+        // -Xdock:name=... doesn't actually work :(
+        // Leaving it in in case it gets fixed
+        command.add("-Xdock:name=" + "Jalview");
+      }
     }
 
     command.add(startClass);
@@ -80,41 +126,53 @@ public class Launcher
 
     final ProcessBuilder builder = new ProcessBuilder(command);
 
-    System.out.println("COMMAND: " + String.join(" ", builder.command()));
+    // System.out.println("COMMAND: " + String.join(" ", builder.command()));
+    System.out.println("Running " + startClass + " with "
+            + (memSetting == null ? "no memSetting" : memSetting));
 
     try
     {
       builder.inheritIO();
       Process process = builder.start();
       process.waitFor();
-    } catch (Exception e)
+    } catch (IOException e)
     {
-      e.printStackTrace();
-    }
-    // System.exit(0);
-
-  }
-
-  public static long getPhysicalMemory()
-  {
-    final OperatingSystemMXBean o = ManagementFactory
-            .getOperatingSystemMXBean();
-
-    try
-    {
-      if (o instanceof com.sun.management.OperatingSystemMXBean)
+      if (e.getMessage().toLowerCase().contains("memory"))
+      {
+        System.out.println("Caught a memory exception: " + e.getMessage());
+        // Probably the "Cannot allocate memory" error, try without the memory setting
+        ArrayList<String> commandNoMem = new ArrayList<>();
+        for (int i = 0; i < command.size(); i++)
+        {
+          if (!command.get(i).startsWith("-Xmx"))
+          {
+            commandNoMem.add(command.get(i));
+          }
+        }
+        final ProcessBuilder builderNoMem = new ProcessBuilder(
+                commandNoMem);
+        System.out.println("NO MEM COMMAND: "
+                + String.join(" ", builderNoMem.command()));
+        try
+        {
+          builderNoMem.inheritIO();
+          Process processNoMem = builderNoMem.start();
+          processNoMem.waitFor();
+        } catch (Exception ex)
+        {
+          ex.printStackTrace();
+        }
+      }
+      else
       {
-        final com.sun.management.OperatingSystemMXBean osb = (com.sun.management.OperatingSystemMXBean) o;
-        return osb.getTotalPhysicalMemorySize();
+        e.printStackTrace();
       }
-    } catch (NoClassDefFoundError e)
+    } catch (Exception e)
     {
-      // com.sun.management.OperatingSystemMXBean doesn't exist in this JVM
-      System.out.println("No com.sun.management.OperatingSystemMXBean");
+      e.printStackTrace();
     }
+    // System.exit(0);
 
-    // We didn't get a com.sun.management.OperatingSystemMXBean.
-    return -1;
   }
 
 }
diff --git a/src/jalview/bin/MemorySetting.java b/src/jalview/bin/MemorySetting.java
new file mode 100644
index 0000000..b3bae2d
--- /dev/null
+++ b/src/jalview/bin/MemorySetting.java
@@ -0,0 +1,51 @@
+package jalview.bin;
+
+import java.lang.management.ManagementFactory;
+import java.lang.management.OperatingSystemMXBean;
+
+public class MemorySetting
+{
+  public static final long leaveFreeMinMemory = 536870912; // 0.5 GB
+
+  public static final long applicationMinMemory = 536870912; // 0.5 GB
+
+  protected static long getPhysicalMemory()
+  {
+    final OperatingSystemMXBean o = ManagementFactory
+            .getOperatingSystemMXBean();
+
+    try
+    {
+      if (o instanceof com.sun.management.OperatingSystemMXBean)
+      {
+        final com.sun.management.OperatingSystemMXBean osb = (com.sun.management.OperatingSystemMXBean) o;
+        return osb.getTotalPhysicalMemorySize();
+      }
+    } catch (NoClassDefFoundError e)
+    {
+      // com.sun.management.OperatingSystemMXBean doesn't exist in this JVM
+      System.out.println("No com.sun.management.OperatingSystemMXBean");
+    }
+
+    // We didn't get a com.sun.management.OperatingSystemMXBean.
+    return -1;
+  }
+
+  public static long memPercent(int percent)
+  {
+    long memPercent = -1;
+
+    long physicalMem = getPhysicalMemory();
+    if (physicalMem > applicationMinMemory)
+    {
+      // try and set at least applicationMinMemory and thereafter ensure
+      // leaveFreeMinMemory is left for the OS
+      memPercent = Math.max(applicationMinMemory,
+              physicalMem - Math.max(physicalMem * (100 - percent) / 100,
+                      leaveFreeMinMemory));
+    }
+
+    return memPercent;
+  }
+
+}
diff --git a/src/jalview/gui/APQHandlers.java b/src/jalview/gui/APQHandlers.java
index 5f6651c..05f5e08 100644
--- a/src/jalview/gui/APQHandlers.java
+++ b/src/jalview/gui/APQHandlers.java
@@ -135,12 +135,12 @@ public class APQHandlers
       {
         System.out.println(
                 "Exception when looking for About, Preferences, Quit Handlers");
-        e.printStackTrace();
+        // e.printStackTrace();
       } catch (Throwable t)
       {
         System.out.println(
                 "Throwable when looking for About, Preferences, Quit Handlers");
-        t.printStackTrace();
+        // t.printStackTrace();
       }
 
     }
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index ac5ed6d..0523d41 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -366,12 +366,12 @@ public class Desktop extends jalview.jbgui.GDesktop
       APQHandlers.setAPQHandlers(this);
     } catch (Exception e)
     {
-      System.out.println("Exception when trying to set APQHandlers");
-      e.printStackTrace();
+      System.out.println("Cannot set APQHandlers");
+      // e.printStackTrace();
     } catch (Throwable t)
     {
-      System.out.println("Throwable when trying to set APQHandlers");
-      t.printStackTrace();
+      System.out.println("Cannot set APQHandlers");
+      // t.printStackTrace();
     }
 
 
diff --git a/utils/install4j/DS_Store b/utils/install4j/DS_Store
index 374da46..2eafdbc 100644
Binary files a/utils/install4j/DS_Store and b/utils/install4j/DS_Store differ
diff --git a/utils/install4j/DS_Store_1 b/utils/install4j/DS_Store_1
new file mode 100644
index 0000000..374da46
Binary files /dev/null and b/utils/install4j/DS_Store_1 differ
diff --git a/utils/install4j/DS_Store_2 b/utils/install4j/DS_Store_2
new file mode 100644
index 0000000..2eafdbc
Binary files /dev/null and b/utils/install4j/DS_Store_2 differ
diff --git a/utils/install4j/Uninstall Old Jalview.app/Contents/Info.plist b/utils/install4j/Uninstall Old Jalview.app/Contents/Info.plist
new file mode 100644
index 0000000..c10a834
--- /dev/null
+++ b/utils/install4j/Uninstall Old Jalview.app/Contents/Info.plist	
@@ -0,0 +1,52 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+	<key>CFBundleAllowMixedLocalizations</key>
+	<true/>
+	<key>CFBundleDevelopmentRegion</key>
+	<string>English</string>
+	<key>CFBundleExecutable</key>
+	<string>applet</string>
+	<key>CFBundleIconFile</key>
+	<string>applet</string>
+	<key>CFBundleIdentifier</key>
+	<string>com.apple.ScriptEditor.id.Uninstall-Old-Jalview</string>
+	<key>CFBundleInfoDictionaryVersion</key>
+	<string>6.0</string>
+	<key>CFBundleName</key>
+	<string>Uninstall Old Jalview</string>
+	<key>CFBundlePackageType</key>
+	<string>APPL</string>
+	<key>CFBundleShortVersionString</key>
+	<string>1.0</string>
+	<key>CFBundleSignature</key>
+	<string>aplt</string>
+	<key>LSMinimumSystemVersionByArchitecture</key>
+	<dict>
+		<key>x86_64</key>
+		<string>10.6</string>
+	</dict>
+	<key>LSRequiresCarbon</key>
+	<true/>
+	<key>WindowState</key>
+	<dict>
+		<key>bundleDividerCollapsed</key>
+		<true/>
+		<key>bundlePositionOfDivider</key>
+		<real>0.0</real>
+		<key>dividerCollapsed</key>
+		<false/>
+		<key>eventLogLevel</key>
+		<integer>2</integer>
+		<key>name</key>
+		<string>ScriptWindowState</string>
+		<key>positionOfDivider</key>
+		<real>223</real>
+		<key>savedFrame</key>
+		<string>329 957 700 672 0 0 3360 1867 </string>
+		<key>selectedTab</key>
+		<string>description</string>
+	</dict>
+</dict>
+</plist>
diff --git a/utils/install4j/Uninstall Old Jalview.app/Contents/MacOS/applet b/utils/install4j/Uninstall Old Jalview.app/Contents/MacOS/applet
new file mode 100755
index 0000000..171d0cc
Binary files /dev/null and b/utils/install4j/Uninstall Old Jalview.app/Contents/MacOS/applet differ
diff --git a/utils/install4j/Uninstall Old Jalview.app/Contents/PkgInfo b/utils/install4j/Uninstall Old Jalview.app/Contents/PkgInfo
new file mode 100644
index 0000000..3253614
--- /dev/null
+++ b/utils/install4j/Uninstall Old Jalview.app/Contents/PkgInfo	
@@ -0,0 +1 @@
+APPLaplt
\ No newline at end of file
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
new file mode 100644
index 0000000..1dce96c
Binary files /dev/null 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.icns b/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/applet.icns
new file mode 100644
index 0000000..67a2cbd
Binary files /dev/null and b/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/applet.icns 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
new file mode 100644
index 0000000..c41bb4e
Binary files /dev/null and b/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/applet.rsrc differ
diff --git a/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/description.rtfd/TXT.rtf b/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/description.rtfd/TXT.rtf
new file mode 100644
index 0000000..76ac711
--- /dev/null
+++ b/utils/install4j/Uninstall Old Jalview.app/Contents/Resources/description.rtfd/TXT.rtf	
@@ -0,0 +1,5 @@
+{\rtf1\ansi\ansicpg1252\cocoartf1561\cocoasubrtf600
+{\fonttbl}
+{\colortbl;\red255\green255\blue255;}
+{\*\expandedcolortbl;;}
+}
\ No newline at end of file
diff --git a/utils/install4j/Uninstall Old Jalview.scpt b/utils/install4j/Uninstall Old Jalview.scpt
new file mode 100644
index 0000000..1692009
Binary files /dev/null and b/utils/install4j/Uninstall Old Jalview.scpt differ
diff --git a/utils/install4j/install4j_template.install4j b/utils/install4j/install4j_template.install4j
index 7a924e2..2f65f51 100644
--- a/utils/install4j/install4j_template.install4j
+++ b/utils/install4j/install4j_template.install4j
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <install4j version="7.0.9" transformSequenceNumber="7">
-  <directoryPresets config="../../../../../buildtools/jre/openjdk-java_vm/macos-jdk8u202-b08-jre" />
+  <directoryPresets config="." />
   <application name="Jalview" distributionSourceDir="" applicationId="6595-2347-1923-0725" mediaDir="../../build/install4j" mediaFilePattern="${compiler:sys.shortName}_${compiler:sys.platform}_${compiler:sys.version}" compression="6" lzmaCompression="true" pack200Compression="false" excludeSignedFromPacking="true" commonExternalFiles="false" createMd5Sums="true" shrinkRuntime="true" shortName="Jalview" publisher="University of Dundee" publisherWeb="http://www.jalview.org/" version="$$VERSION$$" allPathsRelative="true" backupOnSave="false" autoSave="false" convertDotsToUnderscores="true" macSignature="????" macVolumeId="5aac4968c304f65" javaMinVersion="9999999999" javaMaxVersion="" allowBetaVM="true" jdkMode="jdk" jdkName="JDK 11.0">
     <languages skipLanguageSelection="false" languageSelectionInPrincipalLanguage="false">
       <principalLanguage id="en" customLocalizationFile="" />
@@ -8,6 +8,8 @@
     </languages>
     <searchSequence>
       <directory location="${compiler:JRE_DIR}" />
+      <registry />
+      <envVar name="JAVA_HOME" />
     </searchSequence>
     <variables>
       <variable name="OSX_KEYSTORE" value="" description="" category="" />
@@ -25,17 +27,23 @@
       <fileset name="Full file set" id="734" customizedId="" />
       <fileset name="Mac OS X JRE" id="880" customizedId="" />
       <fileset name="Windows JRE" id="882" customizedId="" />
+      <fileset name="Jalview application" id="1873" customizedId="" />
+      <fileset name="MacOS Old Jalview Uninstaller" id="2105" customizedId="" />
     </filesets>
     <roots>
       <root id="735" fileset="734" location="" />
       <root id="881" fileset="880" location="" />
       <root id="883" fileset="882" location="" />
+      <root id="1874" fileset="1873" location="" />
+      <root id="2106" fileset="2105" location="" />
     </roots>
     <mountPoints>
       <mountPoint id="454" root="" location="" mode="755" />
       <mountPoint id="736" root="735" location="" mode="755" />
       <mountPoint id="884" root="881" location="" mode="755" />
       <mountPoint id="885" root="883" location="" mode="755" />
+      <mountPoint id="1875" root="1874" location="" mode="755" />
+      <mountPoint id="2107" root="2106" location="" mode="755" />
     </mountPoints>
     <entries>
       <dirEntry mountPoint="454" file="../../getdown/files/$$JAVA_VERSION$$" overwriteMode="4" shared="false" fileMode="644" uninstallMode="2" overrideFileMode="false" overrideOverwriteMode="true" overrideUninstallMode="true" entryMode="direct" subDirectory="files" excludeSuffixes="" dirMode="755" overrideDirMode="false">
@@ -50,6 +58,12 @@
       <dirEntry mountPoint="885" file="$$WINDOWS_JAVA_VM_DIR$$" overwriteMode="4" shared="false" fileMode="755" uninstallMode="0" overrideFileMode="true" overrideOverwriteMode="false" overrideUninstallMode="true" entryMode="subdir" subDirectory="${compiler:JRE_DIR}" excludeSuffixes="" dirMode="755" overrideDirMode="false">
         <exclude />
       </dirEntry>
+      <dirEntry mountPoint="1875" file="../../getdown/website/$$JAVA_VERSION$$/dist" overwriteMode="1" shared="false" fileMode="644" uninstallMode="2" overrideFileMode="true" overrideOverwriteMode="true" overrideUninstallMode="true" entryMode="subdir" subDirectory="dist" excludeSuffixes="" dirMode="755" overrideDirMode="true">
+        <exclude />
+      </dirEntry>
+      <dirEntry mountPoint="2107" file="Uninstall Old Jalview.app" overwriteMode="4" shared="false" fileMode="755" uninstallMode="0" overrideFileMode="true" overrideOverwriteMode="false" overrideUninstallMode="false" entryMode="subdir" subDirectory="Uninstall Old Jalview.app" excludeSuffixes="" dirMode="755" overrideDirMode="true">
+        <exclude />
+      </dirEntry>
     </entries>
     <components>
       <component name="jalview_getdown" id="1031" customizedId="" displayDescription="false" hideHelpButton="false" selected="true" changeable="true" downloadable="false" hidden="false">
@@ -80,6 +94,20 @@
         </include>
         <dependencies />
       </component>
+      <component name="jalview" id="1881" customizedId="" displayDescription="false" hideHelpButton="false" selected="true" changeable="true" downloadable="false" hidden="false">
+        <description />
+        <include all="false">
+          <entry location=".i4j_fileset_1873" fileType="regular" />
+        </include>
+        <dependencies />
+      </component>
+      <component name="macos_old_jalview_uninstaller" id="2110" customizedId="" displayDescription="false" hideHelpButton="false" selected="true" changeable="true" downloadable="false" hidden="false">
+        <description />
+        <include all="false">
+          <entry location=".i4j_fileset_2105" fileType="regular" />
+        </include>
+        <dependencies />
+      </component>
     </components>
   </files>
   <launchers>
@@ -149,6 +177,39 @@
         <file path="../../resources/images/JalviewLogo_Huge.png" />
       </iconImageFiles>
     </launcher>
+    <launcher name="Jalview package" id="1876" customizedId="" external="false" excludeFromMenu="false" unixMode="755" unixAutoStart="true" menuName="${compiler:sys.shortName} $$VERSION$$" icnsFile="" customMacBundleIdentifier="false" macBundleIdentifier="" swtApp="false" fileset="1873" macBundleBinary="JavaApplicationStub" addMacEntitlements="false" macEntitlementsFile="" useCustomMacosExecutableName="false" customMacosExecutableName="" useJavaMinVersionOverride="false" javaMinVersionOverride="" useJavaMaxVersionOverride="false" javaMaxVersionOverride="" checkUpdater="false" updateExecutionMode="unattendedProgress" unattendedUpdateTitle="${i18n:updater.WindowTitle(&quot;${compiler:sys.fullName}&quot;)}">
+      <executable name="${compiler:sys.shortName}" type="1" iconSet="true" iconFile="" executableDir="" redirectStderr="false" stderrFile="error.log" stderrMode="overwrite" redirectStdout="false" stdoutFile="output.log" stdoutMode="overwrite" failOnStderrOutput="false" executableMode="1" changeWorkingDirectory="false" workingDirectory="." singleInstance="true" serviceStartType="2" serviceDependencies="" serviceDescription="" jreLocation="" executionLevel="asInvoker" checkConsoleParameter="false" globalSingleInstance="false" singleInstanceActivate="true" dpiAware="java9+">
+        <versionInfo include="false" fileVersion="" fileDescription="" legalCopyright="" internalName="" productName="" />
+      </executable>
+      <splashScreen show="false" width="0" height="0" bitmapFile="" textOverlay="false">
+        <text>
+          <statusLine x="20" y="20" text="" fontSize="8" fontColor="0,0,0" bold="false" />
+          <versionLine x="20" y="40" text="version ${compiler:sys.version}" fontSize="8" fontColor="0,0,0" bold="false" />
+        </text>
+      </splashScreen>
+      <java mainClass="jalview.bin.Launcher" mainMode="1" vmParameters="" arguments="" allowVMPassthroughParameters="true" preferredVM="" bundleRuntime="true">
+        <classPath>
+          <scanDirectory location="dist" failOnError="false" />
+        </classPath>
+        <modulePath />
+        <nativeLibraryDirectories />
+        <vmOptions />
+      </java>
+      <includedFiles />
+      <unextractableFiles />
+      <vmOptionsFile mode="template" overwriteMode="0" fileMode="644">
+        <content />
+      </vmOptionsFile>
+      <customScript mode="1" file="">
+        <content />
+      </customScript>
+      <infoPlist mode="1" file="">
+        <content />
+      </infoPlist>
+      <iconImageFiles>
+        <file path="../../resources/images/JalviewLogo_Huge.png" />
+      </iconImageFiles>
+    </launcher>
   </launchers>
   <installerGui installerType="1" addOnAppId="" suggestPreviousLocations="true" autoUpdateDescriptorUrl="https://www.jalview.org/install4j/updates.xml" useAutoUpdateBaseUrl="false" autoUpdateBaseUrl="">
     <staticMembers script="" />
@@ -700,6 +761,36 @@ return console.askOkCancel(message, true);
             <preActivation />
             <postActivation />
             <actions>
+              <action name="" id="2012" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateStartMenuEntryAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="">
+                <serializedBean>
+                  <java class="java.beans.XMLDecoder">
+                    <object class="com.install4j.runtime.beans.actions.desktop.CreateStartMenuEntryAction">
+                      <void property="allUsers">
+                        <boolean>false</boolean>
+                      </void>
+                      <void property="entryName">
+                        <string>${compiler:sys.shortName}</string>
+                      </void>
+                      <void property="file">
+                        <object class="java.io.File">
+                          <string>${compiler:sys.shortName}</string>
+                        </object>
+                      </void>
+                      <void property="icon">
+                        <object class="com.install4j.api.beans.ExternalFile">
+                          <string>../../resources/images/jalview_logos.ico</string>
+                        </object>
+                      </void>
+                      <void property="unixIconFile">
+                        <object class="com.install4j.api.beans.ExternalFile">
+                          <string>../../resources/images/JalviewLogo_Huge.png</string>
+                        </object>
+                      </void>
+                    </object>
+                  </java>
+                </serializedBean>
+                <condition>!context.getBooleanVariable("sys.programGroupDisabled")</condition>
+              </action>
               <action name="" id="573" customizedId="" beanClass="com.install4j.runtime.beans.actions.desktop.CreateDesktopLinkAction" enabled="true" commentSet="false" comment="" actionElevationType="elevated" rollbackBarrier="false" rollbackBarrierExitCode="0" multiExec="false" failureStrategy="1" errorMessage="Could not make desktop link">
                 <serializedBean>
                   <java class="java.beans.XMLDecoder">
@@ -1666,20 +1757,24 @@ return console.askYesNo(message, true);
     </styles>
   </installerGui>
   <mediaSets>
-    <linuxDeb name="Linux Deb Archive" id="153" customizedId="" mediaFileName="" installDir="/opt/${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false" overwriteNeverAsConfigFiles="false" dependencies="" bzip="true" description="Jalview Desktop" maintainerEmail="help@jalview.org" architectureSet="false" architecture="">
+    <linuxDeb name="Jalview .deb Package" id="153" customizedId="" mediaFileName="jalview-$$VERSION$$" installDir="/opt/${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false" overwriteNeverAsConfigFiles="false" dependencies="openjdk-8-jre" bzip="true" description="Jalview Desktop" maintainerEmail="help@jalview.org" architectureSet="false" architecture="">
       <excludedComponents>
+        <component id="1031" />
         <component id="1155" />
         <component id="1156" />
         <component id="1276" />
+        <component id="2110" />
       </excludedComponents>
       <includedDownloadableComponents />
       <excludedLaunchers>
+        <launcher id="737" />
         <launcher id="1402" />
       </excludedLaunchers>
       <excludedBeans />
       <overriddenPrincipalLanguage id="en" customLocalizationFile="" />
       <exclude>
         <entry location=".i4j_fileset_" fileType="regular" />
+        <entry location=".i4j_fileset_734" fileType="regular" />
         <entry location=".i4j_fileset_880" fileType="regular" />
         <entry location=".i4j_fileset_882" fileType="regular" />
       </exclude>
@@ -1701,20 +1796,24 @@ return console.askYesNo(message, true);
         <content />
       </postUninstallScript>
     </linuxDeb>
-    <linuxRPM name="Linux RPM" id="570" customizedId="" mediaFileName="" installDir="/opt/${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false" overwriteNeverAsConfigFiles="false" dependencies="" os="linux" arch="i386">
+    <linuxRPM name="Jalview RPM Package" id="570" customizedId="" mediaFileName="jalview-$$VERSION$$" installDir="/opt/${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false" overwriteNeverAsConfigFiles="false" dependencies="java-1.8.0-openjdk" os="linux" arch="noarch">
       <excludedComponents>
+        <component id="1031" />
         <component id="1155" />
         <component id="1156" />
         <component id="1276" />
+        <component id="2110" />
       </excludedComponents>
       <includedDownloadableComponents />
       <excludedLaunchers>
+        <launcher id="737" />
         <launcher id="1402" />
       </excludedLaunchers>
       <excludedBeans />
       <overriddenPrincipalLanguage id="en" customLocalizationFile="" />
       <exclude>
         <entry location=".i4j_fileset_" fileType="regular" />
+        <entry location=".i4j_fileset_734" fileType="regular" />
         <entry location=".i4j_fileset_880" fileType="regular" />
         <entry location=".i4j_fileset_882" fileType="regular" />
       </exclude>
@@ -1736,11 +1835,13 @@ return console.askYesNo(message, true);
         <content />
       </postUninstallScript>
     </linuxRPM>
-    <windows name="Offline Windows" id="743" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="64" runPostProcessor="true" postProcessor="${compiler:JSIGN_SH} $EXECUTABLE" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="$$WINDOWS_JAVA_VM_TGZ$$" manualJREEntry="true" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="~/AppData/Local" contentFilesType="1" verifyIntegrity="true">
+    <windows name="Offline Windows x64 Installer" id="743" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="64" runPostProcessor="true" postProcessor="${compiler:JSIGN_SH} $EXECUTABLE" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="$$WINDOWS_JAVA_VM_TGZ$$" manualJREEntry="true" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="~/AppData/Local" contentFilesType="1" verifyIntegrity="true">
       <excludedComponents>
         <component id="1155" />
         <component id="1156" />
         <component id="1276" />
+        <component id="1881" />
+        <component id="2110" />
       </excludedComponents>
       <includedDownloadableComponents />
       <excludedLaunchers>
@@ -1751,6 +1852,31 @@ return console.askYesNo(message, true);
       <exclude>
         <entry location=".i4j_fileset_" fileType="regular" />
         <entry location=".i4j_fileset_880" fileType="regular" />
+        <entry location=".i4j_fileset_882" fileType="regular" />
+        <entry location=".i4j_fileset_1873" fileType="regular" />
+      </exclude>
+      <variables />
+      <autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
+        <commentFiles />
+        <customAttributes />
+      </autoUpdate>
+    </windows>
+    <windows name="Network Windows x64 Installer" id="1862" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${compiler:sys.platform}_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="64" runPostProcessor="true" postProcessor="${compiler:JSIGN_SH} $EXECUTABLE" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="$$WINDOWS_JAVA_VM_TGZ$$" manualJREEntry="true" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="~/AppData/Local" contentFilesType="1" verifyIntegrity="true">
+      <excludedComponents>
+        <component id="1031" />
+        <component id="1155" />
+        <component id="1156" />
+        <component id="1881" />
+        <component id="2110" />
+      </excludedComponents>
+      <includedDownloadableComponents />
+      <excludedLaunchers />
+      <excludedBeans />
+      <overriddenPrincipalLanguage id="en" customLocalizationFile="" />
+      <exclude>
+        <entry location=".i4j_fileset_734" fileType="regular" />
+        <entry location=".i4j_fileset_880" fileType="regular" />
+        <entry location=".i4j_fileset_1873" fileType="regular" />
       </exclude>
       <variables />
       <autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
@@ -1758,10 +1884,11 @@ return console.askYesNo(message, true);
         <customAttributes />
       </autoUpdate>
     </windows>
-    <macosArchive name="Offline macOS Single Bundle Archive" id="878" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${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="737">
+    <macosArchive name="Offline macOS Disk Image" id="878" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${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="737">
       <excludedComponents>
         <component id="1156" />
         <component id="1276" />
+        <component id="1881" />
       </excludedComponents>
       <includedDownloadableComponents />
       <excludedBeans />
@@ -1769,6 +1896,7 @@ return console.askYesNo(message, true);
       <exclude>
         <entry location=".i4j_fileset_" fileType="regular" />
         <entry location=".i4j_fileset_882" fileType="regular" />
+        <entry location=".i4j_fileset_1873" fileType="regular" />
       </exclude>
       <variables />
       <autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
@@ -1782,12 +1910,14 @@ return console.askYesNo(message, true);
         <symlink name="Jalview.app/Contents/Resources/app/${compiler:JRE_DIR}/Contents/MacOS/libjli.dylib" target="../Home/lib/jli/libjli.dylib" />
         <file name="Jalview.app/Contents/Resources/Jalview-File.icns" file="./Jalview-File.icns" />
         <file name="Jalview.app/Contents/Resources/Jalview-Version-Locator.icns" file="Jalview-Version-Locator.icns" />
+        <symlink name="Uninstall Old Jalview.app" target="Jalview.app/Contents/Resources/app/Uninstall Old Jalview.app" />
       </topLevelFiles>
     </macosArchive>
-    <macosArchive name="Network macOS Single Bundle Archive" id="1274" customizedId="" mediaFileName="${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">
+    <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">
       <excludedComponents>
         <component id="1031" />
         <component id="1156" />
+        <component id="1881" />
       </excludedComponents>
       <includedDownloadableComponents />
       <excludedBeans />
@@ -1795,6 +1925,7 @@ return console.askYesNo(message, true);
       <exclude>
         <entry location=".i4j_fileset_734" fileType="regular" />
         <entry location=".i4j_fileset_882" fileType="regular" />
+        <entry location=".i4j_fileset_1873" fileType="regular" />
       </exclude>
       <variables />
       <autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
@@ -1808,10 +1939,17 @@ return console.askYesNo(message, true);
         <symlink name="Jalview.app/Contents/Resources/app/${compiler:JRE_DIR}/Contents/MacOS/libjli.dylib" target="../Home/lib/jli/libjli.dylib" />
         <file name="Jalview.app/Contents/Resources/Jalview-Version-Locator.icns" file="Jalview-Version-Locator.icns" />
         <file name="Jalview.app/Contents/Resources/Jalview-File.icns" file="Jalview-File.icns" />
+        <symlink name="Uninstall Old Jalview.app" target="Jalview.app/Contents/Resources/app/Uninstall Old Jalview.app" />
       </topLevelFiles>
     </macosArchive>
-    <unixInstaller name="Unix Installer" id="1595" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}_installer_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="" manualJREEntry="false" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="" contentFilesType="1">
-      <excludedComponents />
+    <unixInstaller name="Offline Unix Shell Installer" id="1595" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}_installer_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="" manualJREEntry="false" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="~/opt/" contentFilesType="1">
+      <excludedComponents>
+        <component id="1155" />
+        <component id="1156" />
+        <component id="1276" />
+        <component id="1881" />
+        <component id="2110" />
+      </excludedComponents>
       <includedDownloadableComponents />
       <excludedLaunchers>
         <launcher id="1402" />
@@ -1819,9 +1957,10 @@ return console.askYesNo(message, true);
       <excludedBeans />
       <overriddenPrincipalLanguage id="en" customLocalizationFile="" />
       <exclude>
-        <entry location=".i4j_fileset_734" fileType="regular" />
+        <entry location=".i4j_fileset_" fileType="regular" />
         <entry location=".i4j_fileset_880" fileType="regular" />
         <entry location=".i4j_fileset_882" fileType="regular" />
+        <entry location=".i4j_fileset_1873" fileType="regular" />
       </exclude>
       <variables />
       <autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
@@ -1832,11 +1971,40 @@ return console.askYesNo(message, true);
         <content />
       </installerScript>
     </unixInstaller>
-    <unixArchive name="Unix Archive" id="1596" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}_archive_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false">
+    <unixInstaller name="Network Unix Shell Installer" id="1867" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${compiler:sys.platform}_installer_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="" manualJREEntry="false" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="~/opt/" contentFilesType="1">
       <excludedComponents>
         <component id="1031" />
         <component id="1155" />
         <component id="1156" />
+        <component id="1881" />
+        <component id="2110" />
+      </excludedComponents>
+      <includedDownloadableComponents />
+      <excludedLaunchers />
+      <excludedBeans />
+      <overriddenPrincipalLanguage id="en" customLocalizationFile="" />
+      <exclude>
+        <entry location=".i4j_fileset_734" fileType="regular" />
+        <entry location=".i4j_fileset_880" fileType="regular" />
+        <entry location=".i4j_fileset_882" fileType="regular" />
+        <entry location=".i4j_fileset_1873" fileType="regular" />
+      </exclude>
+      <variables />
+      <autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
+        <commentFiles />
+        <customAttributes />
+      </autoUpdate>
+      <installerScript mode="1" file="">
+        <content />
+      </installerScript>
+    </unixInstaller>
+    <unixArchive name="Offline Unix .tar.gz Archive" id="1596" customizedId="" mediaFileName="${compiler:sys.shortName}-OFFLINE_${compiler:sys.platform}_archive_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false">
+      <excludedComponents>
+        <component id="1155" />
+        <component id="1156" />
+        <component id="1276" />
+        <component id="1881" />
+        <component id="2110" />
       </excludedComponents>
       <includedDownloadableComponents />
       <excludedLaunchers>
@@ -1844,18 +2012,25 @@ return console.askYesNo(message, true);
       </excludedLaunchers>
       <excludedBeans />
       <overriddenPrincipalLanguage id="en" customLocalizationFile="" />
-      <exclude />
+      <exclude>
+        <entry location=".i4j_fileset_" fileType="regular" />
+        <entry location=".i4j_fileset_880" fileType="regular" />
+        <entry location=".i4j_fileset_882" fileType="regular" />
+        <entry location=".i4j_fileset_1873" fileType="regular" />
+      </exclude>
       <variables />
       <autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
         <commentFiles />
         <customAttributes />
       </autoUpdate>
     </unixArchive>
-    <windows name="Network Windows" id="1862" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${compiler:sys.platform}_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="64" runPostProcessor="true" postProcessor="${compiler:JSIGN_SH} $EXECUTABLE" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="$$WINDOWS_JAVA_VM_TGZ$$" manualJREEntry="true" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="~/AppData/Local" contentFilesType="1" verifyIntegrity="true">
+    <unixArchive name="Network Unix .tar.gz Archive" id="1871" customizedId="" mediaFileName="${compiler:sys.shortName}-NETWORK_${compiler:sys.platform}_archive_${compiler:sys.version}-j$$JAVA_INTEGER_VERSION$$" installDir="${compiler:sys.shortName}" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="true" includedJRE="" manualJREEntry="false">
       <excludedComponents>
         <component id="1031" />
         <component id="1155" />
         <component id="1156" />
+        <component id="1881" />
+        <component id="2110" />
       </excludedComponents>
       <includedDownloadableComponents />
       <excludedLaunchers />
@@ -1864,13 +2039,15 @@ return console.askYesNo(message, true);
       <exclude>
         <entry location=".i4j_fileset_734" fileType="regular" />
         <entry location=".i4j_fileset_880" fileType="regular" />
+        <entry location=".i4j_fileset_882" fileType="regular" />
+        <entry location=".i4j_fileset_1873" fileType="regular" />
       </exclude>
       <variables />
       <autoUpdate useMinUpdatableVersion="false" minUpdatableVersion="" useMaxUpdatableVersion="false" maxUpdatableVersion="">
         <commentFiles />
         <customAttributes />
       </autoUpdate>
-    </windows>
+    </unixArchive>
   </mediaSets>
   <buildIds buildAll="true">
     <mediaSet refId="153" />
@@ -1881,6 +2058,8 @@ return console.askYesNo(message, true);
     <mediaSet refId="1595" />
     <mediaSet refId="1596" />
     <mediaSet refId="1862" />
+    <mediaSet refId="1867" />
+    <mediaSet refId="1871" />
   </buildIds>
   <buildOptions verbose="false" faster="false" disableSigning="false" disableJreBundling="false" debug="false" />
 </install4j>
diff --git a/utils/install4j/uninstall_app_dmg_file_inclusions.sh b/utils/install4j/uninstall_app_dmg_file_inclusions.sh
new file mode 100644
index 0000000..f5bed50
--- /dev/null
+++ b/utils/install4j/uninstall_app_dmg_file_inclusions.sh
@@ -0,0 +1,7 @@
+#!/usr/bin/env bash
+
+find Uninstall\ Old\ Jalview.app | perl -p -e 'chomp;$_=qq(            <file name=").$_.qq(" file="./).$_.qq(" />\n);' > uninstall_old_jalview_files.xml
+
+# makes the file used to replace the line
+# <file name="UNINSTALL_OLD_JALVIEW_APP_REPLACED_IN_GRADLE" file="./Uninstall Old Jalview.app" />
+# (replacement happens in gradle)
diff --git a/utils/install4j/uninstall_old_jalview.icns b/utils/install4j/uninstall_old_jalview.icns
new file mode 100644
index 0000000..67a2cbd
Binary files /dev/null and b/utils/install4j/uninstall_old_jalview.icns differ
diff --git a/utils/install4j/uninstall_old_jalview_files.xml b/utils/install4j/uninstall_old_jalview_files.xml
new file mode 100644
index 0000000..342fd90
--- /dev/null
+++ b/utils/install4j/uninstall_old_jalview_files.xml
@@ -0,0 +1,13 @@
+            <file name="Uninstall Old Jalview.app" file="./Uninstall Old Jalview.app" />
+            <file name="Uninstall Old Jalview.app/Contents" file="./Uninstall Old Jalview.app/Contents" />
+            <file name="Uninstall Old Jalview.app/Contents/MacOS" file="./Uninstall Old Jalview.app/Contents/MacOS" />
+            <file name="Uninstall Old Jalview.app/Contents/MacOS/applet" file="./Uninstall Old Jalview.app/Contents/MacOS/applet" />
+            <file name="Uninstall Old Jalview.app/Contents/Resources" file="./Uninstall Old Jalview.app/Contents/Resources" />
+            <file name="Uninstall Old Jalview.app/Contents/Resources/applet.rsrc" file="./Uninstall Old Jalview.app/Contents/Resources/applet.rsrc" />
+            <file name="Uninstall Old Jalview.app/Contents/Resources/description.rtfd" file="./Uninstall Old Jalview.app/Contents/Resources/description.rtfd" />
+            <file name="Uninstall Old Jalview.app/Contents/Resources/description.rtfd/TXT.rtf" file="./Uninstall Old Jalview.app/Contents/Resources/description.rtfd/TXT.rtf" />
+            <file name="Uninstall Old Jalview.app/Contents/Resources/Scripts" file="./Uninstall Old Jalview.app/Contents/Resources/Scripts" />
+            <file name="Uninstall Old Jalview.app/Contents/Resources/Scripts/main.scpt" file="./Uninstall Old Jalview.app/Contents/Resources/Scripts/main.scpt" />
+            <file name="Uninstall Old Jalview.app/Contents/Resources/applet.icns" file="./Uninstall Old Jalview.app/Contents/Resources/applet.icns" />
+            <file name="Uninstall Old Jalview.app/Contents/Info.plist" file="./Uninstall Old Jalview.app/Contents/Info.plist" />
+            <file name="Uninstall Old Jalview.app/Contents/PkgInfo" file="./Uninstall Old Jalview.app/Contents/PkgInfo" />