Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into Jalview-BH/JAL-3026

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index ea2f1d6..018adb1 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -77,6 +77,9 @@ import groovy.util.GroovyScriptEngine;
  */
 public class Jalview
 {
+
+  // BH 6/19/2018 starting to work on JS version - just discovering issues
+
   /*
    * singleton instance of this class
    */
@@ -86,8 +89,14 @@ public class Jalview
 
   public static AlignFrame currentAlignFrame;
 
+  public static boolean isJS = /** @j2sNative true || */ // BH 2018
+          false;
+
   static
   {
+
+    if (!isJS)
+    { // BH 2018
     // grab all the rights we can the JVM
     Policy.setPolicy(new Policy()
     {
@@ -104,6 +113,8 @@ public class Jalview
       {
       }
     });
+
+    }
   }
 
   /**
@@ -187,7 +198,12 @@ public class Jalview
    */
   void doMain(String[] args)
   {
-    System.setSecurityManager(null);
+
+    if (!isJS)
+    {
+      System.setSecurityManager(null);
+    }
+
     System.out
             .println("Java version: " + System.getProperty("java.version"));
     System.out.println(System.getProperty("os.arch") + " "
@@ -197,17 +213,6 @@ public class Jalview
     ArgsParser aparser = new ArgsParser(args);
     boolean headless = false;
 
-    if (aparser.contains("help") || aparser.contains("h"))
-    {
-      showUsage();
-      System.exit(0);
-    }
-    if (aparser.contains("nodisplay") || aparser.contains("nogui")
-            || aparser.contains("headless"))
-    {
-      System.setProperty("java.awt.headless", "true");
-      headless = true;
-    }
     String usrPropsFile = aparser.getValue("props");
     Cache.loadProperties(usrPropsFile); // must do this before
     if (usrPropsFile != null)
@@ -216,23 +221,41 @@ public class Jalview
               "CMD [-props " + usrPropsFile + "] executed successfully!");
     }
 
-    // anything else!
-
-    final String jabawsUrl = aparser.getValue("jabaws");
-    if (jabawsUrl != null)
+    /**
+     * BH 2018 ignoring this section for JS
+     * 
+     * @j2sNative
+     */
     {
-      try
+      if (aparser.contains("help") || aparser.contains("h"))
       {
-        Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
-        System.out.println(
-                "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
-      } catch (MalformedURLException e)
+        showUsage();
+        System.exit(0);
+      }
+      if (aparser.contains("nodisplay") || aparser.contains("nogui")
+              || aparser.contains("headless"))
       {
-        System.err.println(
-                "Invalid jabaws parameter: " + jabawsUrl + " ignored");
+        System.setProperty("java.awt.headless", "true");
+        headless = true;
+      }
+      // anything else!
+
+      final String jabawsUrl = aparser.getValue("jabaws");
+      if (jabawsUrl != null)
+      {
+        try
+        {
+          Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+          System.out.println(
+                  "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
+        } catch (MalformedURLException e)
+        {
+          System.err.println(
+                  "Invalid jabaws parameter: " + jabawsUrl + " ignored");
+        }
       }
-    }
 
+    }
     String defs = aparser.getValue("setprop");
     while (defs != null)
     {
@@ -329,55 +352,65 @@ public class Jalview
       desktop = new Desktop();
       desktop.setInBatchMode(true); // indicate we are starting up
       desktop.setVisible(true);
-      desktop.startServiceDiscovery();
-      if (!aparser.contains("nousagestats"))
-      {
-        startUsageStats(desktop);
-      }
-      else
-      {
-        System.err.println("CMD [-nousagestats] executed successfully!");
-      }
 
-      if (!aparser.contains("noquestionnaire"))
+      /**
+       * BH 2018 JS bypass this section
+       * 
+       * @j2sNative
+       * 
+       */
       {
-        String url = aparser.getValue("questionnaire");
-        if (url != null)
+        desktop.startServiceDiscovery();
+        if (!aparser.contains("nousagestats"))
         {
-          // Start the desktop questionnaire prompter with the specified
-          // questionnaire
-          Cache.log.debug("Starting questionnaire url at " + url);
-          desktop.checkForQuestionnaire(url);
-          System.out.println(
-                  "CMD questionnaire[-" + url + "] executed successfully!");
+          startUsageStats(desktop);
         }
         else
         {
-          if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+          System.err.println("CMD [-nousagestats] executed successfully!");
+        }
+
+        if (!aparser.contains("noquestionnaire"))
+        {
+          String url = aparser.getValue("questionnaire");
+          if (url != null)
           {
             // Start the desktop questionnaire prompter with the specified
             // questionnaire
-            // String defurl =
-            // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
-            // //
-            String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
-            Cache.log.debug(
-                    "Starting questionnaire with default url: " + defurl);
-            desktop.checkForQuestionnaire(defurl);
+            Cache.log.debug("Starting questionnaire url at " + url);
+            desktop.checkForQuestionnaire(url);
+            System.out.println("CMD questionnaire[-" + url
+                    + "] executed successfully!");
+          }
+          else
+          {
+            if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+            {
+              // Start the desktop questionnaire prompter with the specified
+              // questionnaire
+              // String defurl =
+              // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
+              // //
+              String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
+              Cache.log.debug(
+                      "Starting questionnaire with default url: " + defurl);
+              desktop.checkForQuestionnaire(defurl);
+            }
           }
         }
-      }
-      else
-      {
-        System.err.println("CMD [-noquestionnaire] executed successfully!");
-      }
+        else
+        {
+          System.err
+                  .println("CMD [-noquestionnaire] executed successfully!");
+        }
 
-      if (!aparser.contains("nonews"))
-      {
-        desktop.checkForNews();
-      }
+        if (!aparser.contains("nonews"))
+        {
+          desktop.checkForNews();
+        }
 
-      BioJsHTMLOutput.updateBioJS();
+        BioJsHTMLOutput.updateBioJS();
+      }
     }
 
     String file = null, data = null;
@@ -497,7 +530,7 @@ public class Jalview
       }
       System.out.println("CMD [-open " + file + "] executed successfully!");
 
-      if (!file.startsWith("http://"))
+      if (!isJS && !file.startsWith("http://"))
       {
         if (!(new File(file)).exists())
         {
@@ -509,7 +542,7 @@ public class Jalview
         }
       }
 
-      protocol = AppletFormatAdapter.checkProtocol(file);
+        protocol = AppletFormatAdapter.checkProtocol(file);
 
       try
       {
@@ -740,7 +773,8 @@ public class Jalview
     // And the user
     // ////////////////////
 
-    if (!headless && file == null && vamsasImport == null
+    if (/** @j2sNative false && */ // BH 2018
+    !headless && file == null && vamsasImport == null
             && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
     {
       file = jalview.bin.Cache.getDefault("STARTUP_FILE",