JAL-1588 refactoring prior to 'save Chimera project'

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

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 42fbd70..0db3e30 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -20,18 +20,49 @@
  */
 package jalview.appletgui;
 
-import java.util.*;
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.api.SequenceStructureBinding;
-import jalview.datamodel.*;
-import jalview.structure.*;
-import jalview.io.*;
-
-import jalview.schemes.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.FileParse;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.UserColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 
+import java.awt.BorderLayout;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.Rectangle;
+import java.awt.TextArea;
+import java.awt.TextField;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyEvent;
+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.Vector;
+
 public class AppletJmol extends EmbmenuFrame implements
 // StructureListener,
         KeyListener, ActionListener, ItemListener
@@ -398,9 +429,9 @@ public class AppletJmol extends EmbmenuFrame implements
       StringBuffer sb = new StringBuffer();
       try
       {
-        for (int s = 0; s < jmb.pdbentry.length; s++)
+        for (int s = 0; s < jmb.getPdbCount(); s++)
         {
-          sb.append(jmb.printMapping(jmb.pdbentry[s].getFile()));
+          sb.append(jmb.printMapping(jmb.getPdbEntry(s).getFile()));
           sb.append("\n");
         }
         cap.setText(sb.toString());
@@ -488,7 +519,9 @@ public class AppletJmol extends EmbmenuFrame implements
       for (int i = 0; i < chainMenu.getItemCount(); i++)
       {
         if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
+        {
           ((CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
+        }
       }
 
       centerViewer();
@@ -522,7 +555,9 @@ public class AppletJmol extends EmbmenuFrame implements
       jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
     }
     else if (!allChainsSelected)
+    {
       centerViewer();
+    }
   }
 
   public void keyPressed(KeyEvent evt)