X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=2b935ed9590fdd1c9e19724337a8d1b3864c0e3b;hb=52e125bdf62f520d88a7aff8e6d9afe007dee15c;hp=e7fc917226043235f067edde85f121bc635a90ab;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index e7fc917..2b935ed 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -81,8 +81,9 @@ public class Jalview
             + System.getProperty("os.version"));
     if (new Platform().isAMac())
     {
-    	System.setProperty("com.apple.mrj.application.apple.menu.about.name", "Jalview");
-    	System.setProperty("apple.laf.useScreenMenuBar", "true");
+      System.setProperty("com.apple.mrj.application.apple.menu.about.name",
+              "Jalview");
+      System.setProperty("apple.laf.useScreenMenuBar", "true");
     }
 
     ArgsParser aparser = new ArgsParser(args);
@@ -247,7 +248,7 @@ public class Jalview
       {
         try
         {
-          String viprotocol = Jalview.checkProtocol(vamsasImport);
+          String viprotocol = jalview.io.AppletFormatAdapter.checkProtocol(vamsasImport);
           if (viprotocol == jalview.io.FormatAdapter.FILE)
           {
             inSession = desktop.vamsasImport(new File(vamsasImport));
@@ -332,7 +333,7 @@ public class Jalview
         }
       }
 
-      protocol = checkProtocol(file);
+      protocol = jalview.io.AppletFormatAdapter.checkProtocol(file);
 
       format = new jalview.io.IdentifyFile().Identify(file, protocol);
 
@@ -368,20 +369,20 @@ public class Jalview
       data = aparser.getValue("groups", true);
       if (data != null)
       {
-        af.parseFeaturesFile(data, checkProtocol(data));
+        af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data));
         System.out.println("Added " + data);
       }
       data = aparser.getValue("features", true);
       if (data != null)
       {
-        af.parseFeaturesFile(data, checkProtocol(data));
+        af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data));
         System.out.println("Added " + data);
       }
 
       data = aparser.getValue("annotations", true);
       if (data != null)
       {
-        af.loadJalviewDataFile(data);
+        af.loadJalviewDataFile(data, null, null, null);
         System.out.println("Added " + data);
       }
       // set or clear the sortbytree flag.
@@ -399,7 +400,7 @@ public class Jalview
         jalview.io.NewickFile fin = null;
         try
         {
-          fin = new jalview.io.NewickFile(data, checkProtocol(data));
+          fin = new jalview.io.NewickFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data));
           if (fin != null)
           {
             af.getViewport().setCurrentTree(
@@ -553,7 +554,7 @@ public class Jalview
       }
     }
     // and finally, turn off batch mode indicator - if the desktop still exists
-    if (desktop!=null)
+    if (desktop != null)
     {
       desktop.setInBatchMode(false);
     }
@@ -790,17 +791,6 @@ public class Jalview
     }
     return ff;
   }
-
-  private static String checkProtocol(String file)
-  {
-    String protocol = jalview.io.FormatAdapter.FILE;
-
-    if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
-    {
-      protocol = jalview.io.FormatAdapter.URL;
-    }
-    return protocol;
-  }
 }
 
 /**