X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=f54717d8393be239f94a2fecf57a1cae09ecfe5a;hb=ecdc53f0d45b7533878cef236fff851ea64ef9a9;hp=4b014d1868ff644863e1ce70116d8099b9ad6514;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 4b014d1..f54717d 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 2.8.2b1)
- * 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.
  * 
@@ -20,16 +20,47 @@
  */
 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 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;
+
+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;
 
 public class AppletJmol extends EmbmenuFrame implements
@@ -398,12 +429,7 @@ public class AppletJmol extends EmbmenuFrame implements
       StringBuffer sb = new StringBuffer();
       try
       {
-        for (int s = 0; s < jmb.pdbentry.length; s++)
-        {
-          sb.append(jmb.printMapping(jmb.pdbentry[s].getFile()));
-          sb.append("\n");
-        }
-        cap.setText(sb.toString());
+        cap.setText(jmb.printMappings());
       } catch (OutOfMemoryError ex)
       {
         frame.dispose();
@@ -488,7 +514,9 @@ 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();
@@ -519,10 +547,12 @@ public class AppletJmol extends EmbmenuFrame implements
     else if (evt.getSource() == seqColour)
     {
       setEnabled(seqColour);
-      jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+      jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
     }
     else if (!allChainsSelected)
+    {
       centerViewer();
+    }
   }
 
   public void keyPressed(KeyEvent evt)
@@ -547,7 +577,7 @@ public class AppletJmol extends EmbmenuFrame implements
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
-    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+    jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
   }
 
   public void updateTitleAndMenus()
@@ -558,7 +588,7 @@ public class AppletJmol extends EmbmenuFrame implements
       return;
     }
     setChainMenuItems(jmb.chainNames);
-    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+    jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
 
     setTitle(jmb.getViewerTitle());
   }