JAL-2089 Merge branch releases/Release_2_10_Branch to master

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

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index c9f275b..4e173ef 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
  * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -25,6 +25,7 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FileParse;
+import jalview.io.StructureFile;
 import jalview.schemes.BuriedColourScheme;
 import jalview.schemes.HelixColourScheme;
 import jalview.schemes.HydrophobicColourScheme;
@@ -63,6 +64,8 @@ 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
@@ -204,7 +207,7 @@ public class AppletJmol extends EmbmenuFrame implements
     String alreadyMapped = StructureSelectionManager
             .getStructureSelectionManager(ap.av.applet)
             .alreadyMappedToFile(pdbentry.getId());
-    MCview.PDBfile reader = null;
+    StructureFile reader = null;
     if (alreadyMapped != null)
     {
       reader = StructureSelectionManager.getStructureSelectionManager(
@@ -268,6 +271,7 @@ 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
@@ -283,6 +287,7 @@ public class AppletJmol extends EmbmenuFrame implements
 
     this.addWindowListener(new WindowAdapter()
     {
+      @Override
       public void windowClosing(WindowEvent evt)
       {
         closeViewer();
@@ -415,6 +420,7 @@ public class AppletJmol extends EmbmenuFrame implements
     this.setVisible(false);
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == mappingMenuItem)
@@ -535,6 +541,7 @@ public class AppletJmol extends EmbmenuFrame implements
     jmb.setColourBySequence(itm == seqColour);
   }
 
+  @Override
   public void itemStateChanged(ItemEvent evt)
   {
     if (evt.getSource() == jmolColour)
@@ -553,6 +560,7 @@ public class AppletJmol extends EmbmenuFrame implements
     }
   }
 
+  @Override
   public void keyPressed(KeyEvent evt)
   {
     if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
@@ -564,10 +572,12 @@ public class AppletJmol extends EmbmenuFrame implements
 
   }
 
+  @Override
   public void keyTyped(KeyEvent evt)
   {
   }
 
+  @Override
   public void keyReleased(KeyEvent evt)
   {
   }
@@ -641,11 +651,13 @@ public class AppletJmol extends EmbmenuFrame implements
   {
     Dimension currentSize = new Dimension();
 
+    @Override
     public void update(Graphics g)
     {
       paint(g);
     }
 
+    @Override
     public void paint(Graphics g)
     {
       currentSize = this.getSize();