X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=9d4779cd8db8eabaa541ef47f19c2025af3de5c2;hb=b2014a1ca8c4ceee99933578e6cece2c3028c4f3;hp=264ac14e1aa7018eaffd4cc288ccc81b48db1537;hpb=ab889432b2f2ebea75aca36e814efc42ab50b9ac;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 264ac14..9d4779c 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -20,11 +20,12 @@
  */
 package jalview.appletgui;
 
+import jalview.bin.JalviewLite;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
 import jalview.io.FileParse;
+import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
 import jalview.schemes.BuriedColourScheme;
 import jalview.schemes.HelixColourScheme;
@@ -60,12 +61,9 @@ 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;
 
-import org.jmol.util.Logger;
-
 public class AppletJmol extends EmbmenuFrame implements
 // StructureListener,
         KeyListener, ActionListener, ItemListener
@@ -178,16 +176,16 @@ public class AppletJmol extends EmbmenuFrame implements
   }
 
   public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
-          AlignmentPanel ap, String protocol)
+          AlignmentPanel ap, DataSourceType protocol)
   {
     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)
     {
-      if (protocol.equals(AppletFormatAdapter.PASTE))
+      if (protocol == DataSourceType.PASTE)
       {
         pdbentry.setId("PASTED PDB"
                 + (chains == null ? "_" : chains.toString()));
@@ -198,7 +196,7 @@ public class AppletJmol extends EmbmenuFrame implements
       }
     }
 
-    if (jalview.bin.JalviewLite.debug)
+    if (JalviewLite.debug)
     {
       System.err
               .println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'");
@@ -271,7 +269,6 @@ 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
@@ -293,22 +290,19 @@ public class AppletJmol extends EmbmenuFrame implements
         closeViewer();
       }
     });
-    if (pdbentry.getProperty() == null)
-    {
-      pdbentry.setProperty(new Hashtable());
-      pdbentry.getProperty().put("protocol", protocol);
-    }
+    pdbentry.setProperty("protocol", protocol);
     if (pdbentry.getFile() != null)
+    
     {
       // import structure data from pdbentry.getFile based on given protocol
-      if (protocol.equals(AppletFormatAdapter.PASTE))
+      if (protocol == DataSourceType.PASTE)
       {
         // TODO: JAL-623 : correctly record file contents for matching up later
         // pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode());
         loadInline(pdbentry.getFile());
       }
-      else if (protocol.equals(AppletFormatAdapter.FILE)
-              || protocol.equals(AppletFormatAdapter.URL))
+      else if (protocol == DataSourceType.FILE
+              || protocol == DataSourceType.URL)
       {
         jmb.viewer.openFile(pdbentry.getFile());
       }
@@ -376,7 +370,7 @@ public class AppletJmol extends EmbmenuFrame implements
     jmb.loadInline(string);
   }
 
-  void setChainMenuItems(Vector<String> chains)
+  void setChainMenuItems(List<String> chains)
   {
     chainMenu.removeAll();
 
@@ -595,7 +589,7 @@ public class AppletJmol extends EmbmenuFrame implements
       repaint();
       return;
     }
-    setChainMenuItems(jmb.chainNames);
+    setChainMenuItems(jmb.getChainNames());
     jmb.colourBySequence(ap);
 
     setTitle(jmb.getViewerTitle());