X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FJalviewJS.java;h=84a17a47be50a6217b0fce3a276a04fd41ffbc25;hb=c945c9641de88cad01b09b3db19e45667dfe751e;hp=18be43b13a27c215e70f7ff94baa029b94c83e1c;hpb=abb67d70ddbcaf52374cc4d611959317d18e012e;p=jalview.git

diff --git a/src/jalview/bin/JalviewJS.java b/src/jalview/bin/JalviewJS.java
index 18be43b..84a17a4 100644
--- a/src/jalview/bin/JalviewJS.java
+++ b/src/jalview/bin/JalviewJS.java
@@ -4,7 +4,6 @@ import jalview.analysis.AlignmentUtils;
 import jalview.datamodel.AlignmentI;
 import jalview.gui.AlignFrame;
 import jalview.gui.SplitFrame;
-import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormatException;
 import jalview.io.FileFormatI;
@@ -34,6 +33,20 @@ import javax.swing.JInternalFrame;
 // TODO or format as file=/examples/uniref50.fa (etc)?
 public class JalviewJS
 {
+
+  static
+  {
+    /**
+     * @j2sNative
+     * 
+     *            thisApplet.__Info.args =
+     *            ["file","examples/uniref50.fa","features",
+     *            "examples/exampleFeatures.txt",
+     *            "props","/Users/gmcarstairs/.jalview_properties"];
+     */
+
+  }
+
   private static final String PARAM_FILE = "file";
 
   private static final String PARAM_FILE2 = "file2";
@@ -54,15 +67,9 @@ public class JalviewJS
 
   private List<String> pdbFileParams;
 
-  public static void main(String[] args)
+  public static void main(String[] args) throws Exception
   {
-    try
-    {
-      new JalviewJS().doMain(args);
-    } catch (Throwable e)
-    {
-      e.printStackTrace();
-    }
+    new JalviewJS().doMain(args);
   }
 
   /**
@@ -280,7 +287,7 @@ public class JalviewJS
       // todo extract helper for protocol resolution from JalviewLite
       DataSourceType sourceType = featureFile.startsWith("http")
               ? DataSourceType.URL
-              : DataSourceType.FILE;
+              : DataSourceType.RELATIVE_URL;
       alignFrame.parseFeaturesFile(featureFile, sourceType);
     }
   }
@@ -300,7 +307,9 @@ public class JalviewJS
     String file = getParameter(fileParam);
     if (file != null)
     {
-      DataSourceType protocol = AppletFormatAdapter.checkProtocol(file);
+      DataSourceType protocol = file.startsWith("http") ? DataSourceType.URL
+              : DataSourceType.RELATIVE_URL;
+      // DataSourceType protocol = AppletFormatAdapter.checkProtocol(file);
       FileFormatI format = new IdentifyFile().identify(file, protocol);
       FileLoader fileLoader = new FileLoader(false);
       af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);