Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 18e7d1a..9d4779c 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -61,7 +61,6 @@ import java.awt.event.KeyListener;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
 import java.util.ArrayList;
-import java.util.Hashtable;
 import java.util.List;
 import java.util.Vector;
 
@@ -182,7 +181,7 @@ public class AppletJmol extends EmbmenuFrame implements
     this.ap = ap;
     jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
             new PDBEntry[] { pdbentry }, new SequenceI[][] { seq },
-            new String[][] { chains }, protocol);
+            protocol);
     jmb.setColourBySequence(true);
     if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
     {
@@ -291,12 +290,9 @@ public class AppletJmol extends EmbmenuFrame implements
         closeViewer();
       }
     });
-    if (pdbentry.getProperty() == null)
-    {
-      pdbentry.setProperty(new Hashtable<String, String>());
-      pdbentry.getProperty().put("protocol", protocol.toString());
-    }
+    pdbentry.setProperty("protocol", protocol);
     if (pdbentry.getFile() != null)
+    
     {
       // import structure data from pdbentry.getFile based on given protocol
       if (protocol == DataSourceType.PASTE)
@@ -374,7 +370,7 @@ public class AppletJmol extends EmbmenuFrame implements
     jmb.loadInline(string);
   }
 
-  void setChainMenuItems(Vector<String> chains)
+  void setChainMenuItems(List<String> chains)
   {
     chainMenu.removeAll();
 
@@ -593,7 +589,7 @@ public class AppletJmol extends EmbmenuFrame implements
       repaint();
       return;
     }
-    setChainMenuItems(jmb.chainNames);
+    setChainMenuItems(jmb.getChainNames());
     jmb.colourBySequence(ap);
 
     setTitle(jmb.getViewerTitle());