JAL-3032 Jalview (as JS) parse query params to main arguments

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 018adb1..e528dec 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -41,6 +41,8 @@ import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.jws2.Jws2Discoverer;
 
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -60,8 +62,12 @@ import java.security.Policy;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Vector;
+import java.util.logging.ConsoleHandler;
+import java.util.logging.Level;
+import java.util.logging.Logger;
 
 import javax.swing.LookAndFeel;
+import javax.swing.Timer;
 import javax.swing.UIManager;
 
 import groovy.lang.Binding;
@@ -70,15 +76,31 @@ import groovy.util.GroovyScriptEngine;
 /**
  * Main class for Jalview Application <br>
  * <br>
- * start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
+ * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
+ * jalview.bin.Jalview
+ * 
+ * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
+ * jalview.bin.Jalview jalview.bin.Jalview
+ * 
+ * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
+ * embellish '*' to e.g. '*.jar')
  * 
  * @author $author$
  * @version $Revision$
  */
 public class Jalview
 {
-
-  // BH 6/19/2018 starting to work on JS version - just discovering issues
+       /**
+        * @j2sNative
+        * 
+        *  // set space-delimited query parameters as arguments to Jalview main
+        *      hr = decodeURI(document.location.href);
+        *  pos = hr.indexOf("?");
+        *  if (pos > 0)
+        *  {
+        *     thisApplet.__Info.args = hr.substring(pos+1).split(" ");
+        *  }
+        */
 
   /*
    * singleton instance of this class
@@ -89,13 +111,22 @@ public class Jalview
 
   public static AlignFrame currentAlignFrame;
 
-  public static boolean isJS = /** @j2sNative true || */ // BH 2018
-          false;
+//BH 2019.01.25 moved to Platform
+///**
+// * Answers true if Jalview is running as Javascript, else false. The value is
+// * set at compile time.
+// * 
+// * @return
+// */
+//public static boolean isJS()
+//{
+//  return /** @j2sNative true || */
+//  false;
+//}
 
   static
   {
-
-    if (!isJS)
+    if (!Platform.isJS())
     { // BH 2018
     // grab all the rights we can the JVM
     Policy.setPolicy(new Policy()
@@ -189,17 +220,47 @@ public class Jalview
    */
   public static void main(String[] args)
   {
+//     setLogging(); // BH - for event debugging in JavaScript
     instance = new Jalview();
     instance.doMain(args);
+}
+
+  private static void logClass(String name) 
+  {    
+         // BH - for event debugging in JavaScript
+      ConsoleHandler consoleHandler = new ConsoleHandler();
+      consoleHandler.setLevel(Level.ALL);
+      Logger logger = Logger.getLogger(name);
+      logger.setLevel(Level.ALL);
+      logger.addHandler(consoleHandler);
   }
 
+  @SuppressWarnings("unused")
+  private static void setLogging() 
+  {
+         // BH - for event debugging in JavaScript (Java mode only)
+       if (!(/** @j2sNative true ||*/false)) 
+       {
+               Logger.getLogger("").setLevel(Level.ALL);
+        logClass("java.awt.EventDispatchThread");
+        logClass("java.awt.EventQueue");
+        logClass("java.awt.Component");
+        logClass("java.awt.focus.Component");
+        logClass("java.awt.focus.DefaultKeyboardFocusManager"); 
+       }       
+
+  }
+  
+
+  
+
   /**
    * @param args
    */
   void doMain(String[] args)
   {
 
-    if (!isJS)
+    if (!Platform.isJS())
     {
       System.setSecurityManager(null);
     }
@@ -287,7 +348,7 @@ public class Jalview
     {
       error.printStackTrace();
       System.out.println("\nEssential logging libraries not found."
-              + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
+              + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
       System.exit(0);
     }
 
@@ -301,7 +362,7 @@ public class Jalview
       System.err.println("Unexpected Look and Feel Exception");
       ex.printStackTrace();
     }
-    if (Platform.isAMac())
+    if (Platform.isAMacAndNotJS())
     {
 
       LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
@@ -349,7 +410,16 @@ public class Jalview
 
     if (!headless)
     {
-      desktop = new Desktop();
+      desktop = new Desktop() 
+//      {
+// // BH testing
+//       @Override
+//       protected void processEvent(AWTEvent e) {
+//               System.out.println("Jalview.java " + e);
+//               super.processEvent(e);
+//       }
+//       }
+      ;
       desktop.setInBatchMode(true); // indicate we are starting up
       desktop.setVisible(true);
 
@@ -530,7 +600,7 @@ public class Jalview
       }
       System.out.println("CMD [-open " + file + "] executed successfully!");
 
-      if (!isJS && !file.startsWith("http://"))
+      if (!Platform.isJS() && !file.startsWith("http://"))
       {
         if (!(new File(file)).exists())
         {
@@ -749,7 +819,8 @@ public class Jalview
             continue;
           }
 
-          if (af.saveAlignment(file, format))
+          af.saveAlignment(file, format);
+          if (af.isSaveAlignmentSuccessful())
           {
             System.out.println("Written alignment in " + format
                     + " format to " + file);