X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=32465c1e8cb6cf325d54e4dff54415699883ac3f;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=0f317aee297ea4b4d8289107e6d73c2af4e59de8;hpb=648f0d7f48b5865bd43b5edbe71f5e483f0cc455;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 0f317ae..32465c1 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,21 +20,52 @@
  */
 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, SequenceStructureBinding
+        KeyListener, ActionListener, ItemListener
 
 {
   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
@@ -139,7 +170,7 @@ public class AppletJmol extends EmbmenuFrame implements
           String[][] boundchains, boolean align, AlignmentPanel ap,
           String protocol)
   {
-    throw new Error("Not yet implemented.");
+    throw new Error(MessageManager.getString("error.not_yet_implemented"));
   }
 
   public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
@@ -315,8 +346,7 @@ public class AppletJmol extends EmbmenuFrame implements
           }
           if (freader == null)
           {
-            throw new Exception(
-                    "Invalid datasource. Could not obtain Reader.");
+            throw new Exception(MessageManager.getString("exception.invalid_datasource_couldnt_obtain_reader"));
           }
           jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
                   freader);
@@ -399,9 +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());
@@ -489,7 +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();
@@ -523,7 +555,9 @@ public class AppletJmol extends EmbmenuFrame implements
       jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
     }
     else if (!allChainsSelected)
+    {
       centerViewer();
+    }
   }
 
   public void keyPressed(KeyEvent evt)