From 1c7cc70f56c2cef85aa483eff11a5ea778974340 Mon Sep 17 00:00:00 2001
From: Iain Milne <imilne@users.noreply.github.com>
Date: Tue, 3 Sep 2019 13:39:57 +0100
Subject: [PATCH] - BUG: JRE11 had stopped supporting the osxadapter code. This
 meant About/Prefs/etc options on macOS were no longer working.

---
 build.xml                  |   1 -
 installer/Tablet.install4j |   6 ++--
 lib/osxadapter.jar         | Bin 3723 -> 0 bytes
 src/tablet/gui/Tablet.java |  68 +++++++++++++++++--------------------
 4 files changed, 33 insertions(+), 42 deletions(-)
 delete mode 100644 lib/osxadapter.jar

diff --git a/build.xml b/build.xml
index fb833181..d8447be2 100644
--- a/build.xml
+++ b/build.xml
@@ -73,7 +73,6 @@
 				<attribute name="Main-Class" value="tablet.gui.Tablet"/>
 				<attribute name="Class-Path"
 					value="flamingo.jar
-						osxadapter.jar
 						scri-commons.jar
 						htsjdk-2.11.0.jar
 						samtools-all.jar
diff --git a/installer/Tablet.install4j b/installer/Tablet.install4j
index b281d1cd..a7a1f89c 100644
--- a/installer/Tablet.install4j
+++ b/installer/Tablet.install4j
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<install4j version="7.0.11" transformSequenceNumber="7">
+<install4j version="7.0.12" transformSequenceNumber="7">
   <directoryPresets config="../keys/icsmacbookpro-application-id.p12" />
   <application name="Tablet" distributionSourceDir="" applicationId="9483-2571-4596-9336" mediaDir="." mediaFilePattern="${compiler:sys.shortName}_${compiler:sys.platform}_${compiler:sys.version}" compression="6" lzmaCompression="false" pack200Compression="false" excludeSignedFromPacking="true" commonExternalFiles="false" createMd5Sums="true" shrinkRuntime="false" shortName="tablet" publisher="The James Hutton Institute" publisherWeb="https://www.hutton.ac.uk" version="x.xx.xx.xx" allPathsRelative="true" backupOnSave="false" autoSave="false" convertDotsToUnderscores="true" macSignature="????" macVolumeId="c8bcb8b04df17304" javaMinVersion="1.11" javaMaxVersion="" allowBetaVM="false" jdkMode="runtimeJre" jdkName="">
     <languages skipLanguageSelection="false" languageSelectionInPrincipalLanguage="false">
@@ -33,9 +33,7 @@
     <entries>
       <dirEntry mountPoint="19" file="../lib" overwriteMode="4" shared="false" fileMode="644" uninstallMode="0" overrideFileMode="false" overrideOverwriteMode="false" overrideUninstallMode="false" entryMode="direct" subDirectory="lib" excludeSuffixes="*.txt" dirMode="755" overrideDirMode="false">
         <exclude>
-          <entry location="i4jruntime.jar" fileType="regular" />
           <entry location="samtools-all.jar" fileType="regular" />
-          <entry location="sqlite-jdbc-3.6.19.jar" fileType="regular" />
         </exclude>
       </dirEntry>
       <dirEntry mountPoint="342" file="./licence" overwriteMode="4" shared="false" fileMode="644" uninstallMode="0" overrideFileMode="false" overrideOverwriteMode="false" overrideUninstallMode="false" entryMode="direct" subDirectory="" excludeSuffixes="" dirMode="755" overrideDirMode="false">
@@ -2562,7 +2560,7 @@ context.goForward(1, true, true);
       </autoUpdate>
       <topLevelFiles />
     </macos>
-    <unixInstaller name="Linux x64" id="433" customizedId="" mediaFileName="${compiler:sys.shortName}_linux_x64_${compiler:sys.version}" installDir="Tablet" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="linux-x86-11.0.3" manualJREEntry="false" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="" contentFilesType="1">
+    <unixInstaller name="Linux x64" id="433" customizedId="" mediaFileName="${compiler:sys.shortName}_linux_x64_${compiler:sys.version}" installDir="Tablet" overridePrincipalLanguage="false" jreBitType="all" runPostProcessor="false" postProcessor="" failOnPostProcessorError="false" useLegacyMediaFileIds="false" legacyMediaFileIds="" downloadURL="" includeAllDownloadableComponents="false" includedJRE="linux-amd64-11.0.3" manualJREEntry="false" bundleType="1" jreURL="" jreShared="false" directDownload="false" installOnlyIfNecessary="false" customInstallBaseDir="" contentFilesType="1">
       <excludedComponents />
       <includedDownloadableComponents />
       <excludedLaunchers />
diff --git a/lib/osxadapter.jar b/lib/osxadapter.jar
deleted file mode 100644
index 2001cf0b603fe813eb25d732aad0ec9b4a028e18..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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diff --git a/src/tablet/gui/Tablet.java b/src/tablet/gui/Tablet.java
index 4310a7f2..ffb2d05d 100644
--- a/src/tablet/gui/Tablet.java
+++ b/src/tablet/gui/Tablet.java
@@ -4,6 +4,7 @@
 package tablet.gui;
 
 import java.awt.*;
+import java.awt.desktop.*;
 import java.awt.event.*;
 import java.io.*;
 import java.util.*;
@@ -18,9 +19,7 @@
 import scri.commons.gui.*;
 import scri.commons.io.*;
 
-import apple.dts.samplecode.osxadapter.*;
-
-public class Tablet implements Thread.UncaughtExceptionHandler
+public class Tablet implements Thread.UncaughtExceptionHandler, OpenFilesHandler
 {
 	private static File prefsFile = getPrefsFile();
 	private static File mruFile;
@@ -41,8 +40,6 @@ public class Tablet implements Thread.UncaughtExceptionHandler
 	public static void main(String[] args)
 		throws Exception
 	{
-		// OS X: This has to be set before anything else
-		System.setProperty("com.apple.mrj.application.apple.menu.about.name", "Tablet");
 		// This disables the API preferences, which can cause problems on Linux
 		// - see: http://www.allaboutbalance.com/articles/disableprefs
 //		System.setProperty("java.util.prefs.PreferencesFactory", "scri.commons.gui.DisabledPreferencesFactory");
@@ -297,27 +294,32 @@ private static File getPrefsFile()
 		return file;
 	}
 
+	public static File getLogFile()
+	{
+		try
+		{
+			File root = new File(System.getProperty("user.home"));
+			File folder = new File(root, ".scri-bioinf");
+			File logFile = new File(folder, "tablet.log");
+
+			return logFile;
+		}
+		catch (Throwable e) { return new File(""); }
+	}
+
+
 	// --------------------------------------------------
 	// Methods required for better native support on OS X
 
 	private void handleOSXStupidities()
 	{
-		try
-		{
-			// Register handlers to deal with the System menu about/quit options
-			OSXAdapter.setPreferencesHandler(this,
-				getClass().getDeclaredMethod("osxPreferences", (Class[])null));
-			OSXAdapter.setAboutHandler(this,
-				getClass().getDeclaredMethod("osxAbout", (Class[])null));
-			OSXAdapter.setQuitHandler(this,
-				getClass().getDeclaredMethod("osxShutdown", (Class[])null));
-			OSXAdapter.setFileHandler(this,
-				getClass().getDeclaredMethod("osxOpen", new Class[] { String.class }));
-
-			// Dock the menu bar at the top of the screen
-			System.setProperty("apple.laf.useScreenMenuBar", "true");
-		}
-		catch (Exception e) {}
+		Desktop desktop = Desktop.getDesktop();
+
+		// Register handlers to deal with the System menu about/quit options
+        desktop.setAboutHandler(e -> osxAbout());
+        desktop.setPreferencesHandler(e -> osxPreferences());
+        desktop.setQuitHandler((e,r) -> osxShutdown());
+		desktop.setOpenFileHandler(this);
 	}
 
 	/** "Preferences" on the OS X system menu. */
@@ -342,14 +344,19 @@ public boolean osxShutdown()
 		return true;
 	}
 
-	public void osxOpen(String path)
+	/** Deal with desktop-double clicking of registered files */
+	public void openFiles(OpenFilesEvent e)
 	{
+		String[] paths = new String[e.getFiles().size()];
+		for (int i = 0; i < paths.length; i++)
+			paths[i] = e.getFiles().get(i).toString();
+
 		// If Tablet is already open, then open the file straight away
 		if (winMain != null && winMain.isVisible())
 		{
 			// TODO: If we have project modified checks, do them here too
 			TabletFile tabletFile =
-				TabletFileHandler.createFromFileList(new String[] { path });
+				TabletFileHandler.createFromFileList(paths);
 			winMain.getCommands().fileOpen(tabletFile);
 		}
 
@@ -357,20 +364,7 @@ public void osxOpen(String path)
 		else
 		{
 			initialFiles = new String[1];
-			initialFiles[0] = path;
+			initialFiles[0] = paths[0];
 		}
 	}
-
-	public static File getLogFile()
-	{
-		try
-		{
-			File root = new File(System.getProperty("user.home"));
-			File folder = new File(root, ".scri-bioinf");
-			File logFile = new File(folder, "tablet.log");
-
-			return logFile;
-		}
-		catch (Throwable e) { return new File(""); }
-	}
 }
\ No newline at end of file