X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=133cc9475cc7348c869a97b5ce1b0d6698e95a54;hb=d3cabbfdd38d554bb8a8b17d3e2c4b113c102545;hp=c39204f5eca8c66e5196a50a40eca92d464fd62b;hpb=e838644df5d5a10a16cf0ad7fb23d24dd7d2729a;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index c39204f..133cc94 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -63,8 +63,6 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.Vector;
 
-import org.jmol.util.Logger;
-
 public class AppletJmol extends EmbmenuFrame implements
 // StructureListener,
         KeyListener, ActionListener, ItemListener
@@ -182,7 +180,7 @@ 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)
     {
@@ -270,7 +268,6 @@ public class AppletJmol extends EmbmenuFrame implements
       jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()
               + "_jmol_", ap.av.applet.getDocumentBase(),
               ap.av.applet.getCodeBase(), "-applet", scriptWindow, null);
-      Logger.setLogLevel(Logger.LEVEL_WARN);
     } catch (Exception e)
     {
       System.err
@@ -372,7 +369,7 @@ public class AppletJmol extends EmbmenuFrame implements
     jmb.loadInline(string);
   }
 
-  void setChainMenuItems(Vector<String> chains)
+  void setChainMenuItems(List<String> chains)
   {
     chainMenu.removeAll();
 
@@ -591,7 +588,7 @@ public class AppletJmol extends EmbmenuFrame implements
       repaint();
       return;
     }
-    setChainMenuItems(jmb.chainNames);
+    setChainMenuItems(jmb.getChainNames());
     jmb.colourBySequence(ap);
 
     setTitle(jmb.getViewerTitle());