static debug flag controlling output of excessive info. showfeaturegroups and hidefea...

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 4d1c216..c9977fd 100755 (executable)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -198,12 +198,18 @@ public class JalviewLite
   boolean embedded = false;
 
   public boolean jmolAvailable = false;
+  public static boolean debug;
 
   /**
    * init method for Jalview Applet
    */
   public void init()
   {
+    String dbg = getParameter("debug");
+    if (dbg!=null)
+    {
+      debug = dbg.toLowerCase().equals("true");
+    }
     int r = 255;
     int g = 255;
     int b = 255;
@@ -323,7 +329,10 @@ public class JalviewLite
         if (frame instanceof AlignFrame)
         {
           currentAlignFrame = (AlignFrame) frame;
-          System.err.println("Activated window "+frame);
+          if (debug)
+          {
+            System.err.println("Activated window "+frame);
+          }
         }
       }
 
@@ -390,6 +399,10 @@ public class JalviewLite
     public LoadingThread(String _file,
                          JalviewLite _applet)
     {
+      if (applet.debug)
+      {
+        System.err.println("Loading thread started with:\n>>file\n"+_file+">>endfile");
+      }
       file = _file;
       if (file.startsWith("PASTE"))
       {
@@ -405,7 +418,15 @@ public class JalviewLite
         file = addProtocol(file);
         protocol = AppletFormatAdapter.URL;
       }
+      if (applet.debug)
+      {
+        System.err.println("Protocol identified as '"+protocol+"'");
+      }
       format = new jalview.io.IdentifyFile().Identify(file, protocol);
+      if (applet.debug)
+      {
+        System.err.println("File identified as '"+format+"'");
+      }
       applet = _applet;
     }
 
@@ -651,7 +672,22 @@ public class JalviewLite
           pdbFileCount++;
         }
         while(pdbFileCount < 10);
-
+        
+        /////////////////////////////
+        // modify display of features
+        //
+        // hide specific groups
+        param = getParameter("hidefeaturegroups");
+        if (param != null)
+        {
+          applet.setFeatureGroupState(param, false);
+        }
+        // show specific groups
+        param = getParameter("showfeaturegroups");
+        if (param != null)
+        {
+          applet.setFeatureGroupState(param, true);
+        }
       }
       else
       {
@@ -711,10 +747,16 @@ public class JalviewLite
     { String[] v = new String[jv.size()];
       jv.copyInto(v);
       jv.removeAllElements();
-      System.err.println("Array from Tabbed List:\n"+v.length+"\n"+v.toString());
+      if (debug)
+      {
+        System.err.println("Array from Tabbed List:\n"+v.length+"\n"+v.toString());
+      }
       return v;
     }
-    System.err.println("Empty Array from Tabbed List");
+    if (debug)
+    {
+      System.err.println("Empty Array from Tabbed List");
+    }
     return null;
   }
 
@@ -734,10 +776,16 @@ public class JalviewLite
       if (list[list.length-1]!=null)
       { v.append(list[list.length-1]);
       }
-      System.err.println("Tabbed List:\n"+v.toString());
+      if (debug)
+      {
+        System.err.println("Tabbed List:\n"+v.toString());
+      }
       return v.toString();
     }
-    System.err.println("Empty Tabbed List\n");
+    if (debug)
+    {
+      System.err.println("Empty Tabbed List\n");
+    }
     return "";
   }
   /**