reverted dodgy test code

[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 0aefe9b..14606b7 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -24,7 +24,10 @@ import java.util.*;
 import java.awt.*;
 import java.awt.event.*;
 
+import org.jmol.api.JmolViewer;
+
 import jalview.analysis.*;
+import jalview.api.SequenceStructureBinding;
 import jalview.bin.JalviewLite;
 import jalview.commands.*;
 import jalview.datamodel.*;
@@ -2577,8 +2580,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         {
           System.out.println("Show url: " + url);
         }
-        viewport.applet.getAppletContext().showDocument(
+        if (url.indexOf("javascript:")==0)
+        {
+          // no target for the javascript context
+          viewport.applet.getAppletContext().showDocument(new java.net.URL(url));
+        } else{
+          viewport.applet.getAppletContext().showDocument(
                 new java.net.URL(url), target);
+        }
       } catch (Exception ex)
       {
         ex.printStackTrace();
@@ -3180,4 +3189,22 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
               DEFAULT_HEIGHT);
     }
   }
+
+  public SequenceStructureBinding addJmolInstance(JmolViewer viewer, String[] sequenceIds)
+  {
+    SequenceI[] seqs=null;
+    if (sequenceIds==null || sequenceIds.length==0)
+    {
+      seqs = viewport.getAlignment().getSequencesArray();
+    } else {
+      // resolve seqs for sequenceIds.
+    }
+    if (// viewer is not mapped)
+            true){
+      AppletJmol jmv = new AppletJmol(viewer, alignPanel, seqs);
+      return jmv;
+    }
+    return null;
+    
+  }
 }