X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=4dcb5d764faecb18057d79cc13c70fa50db52df4;hb=b28bddf12e2791a019fba9c233d46407deb65976;hp=3f2a76906728b1705cdb47c448711634be4221a5;hpb=2f4f1d8fb6878271b64f327bc58c895f458137af;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 3f2a769..4dcb5d7 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -1,38 +1,71 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 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"));
@@ -45,35 +78,47 @@ public class AppletJmol extends EmbmenuFrame implements
 
   Menu helpMenu = new Menu(MessageManager.getString("action.help"));
 
-  MenuItem mappingMenuItem = new MenuItem(MessageManager.getString("label.view_mapping"));
+  MenuItem mappingMenuItem = new MenuItem(
+          MessageManager.getString("label.view_mapping"));
 
-  CheckboxMenuItem seqColour = new CheckboxMenuItem(MessageManager.getString("action.by_sequence"), true);
+  CheckboxMenuItem seqColour = new CheckboxMenuItem(
+          MessageManager.getString("action.by_sequence"), true);
 
-  CheckboxMenuItem jmolColour = new CheckboxMenuItem(MessageManager.getString("action.using_jmol"), false);
+  CheckboxMenuItem jmolColour = new CheckboxMenuItem(
+          MessageManager.getString("action.using_jmol"), false);
 
   MenuItem chain = new MenuItem(MessageManager.getString("action.by_chain"));
 
-  MenuItem charge = new MenuItem(MessageManager.getString("label.charge_cysteine"));
+  MenuItem charge = new MenuItem(
+          MessageManager.getString("label.charge_cysteine"));
 
   MenuItem zappo = new MenuItem(MessageManager.getString("label.zappo"));
 
   MenuItem taylor = new MenuItem(MessageManager.getString("label.taylor"));
 
-  MenuItem hydro = new MenuItem(MessageManager.getString("label.hydrophobicity"));
+  MenuItem hydro = new MenuItem(
+          MessageManager.getString("label.hydrophobicity"));
 
-  MenuItem helix = new MenuItem(MessageManager.getString("label.helix_propensity"));
+  MenuItem helix = new MenuItem(
+          MessageManager.getString("label.helix_propensity"));
 
-  MenuItem strand = new MenuItem(MessageManager.getString("label.strand_propensity"));
+  MenuItem strand = new MenuItem(
+          MessageManager.getString("label.strand_propensity"));
 
-  MenuItem turn = new MenuItem(MessageManager.getString("label.turn_propensity"));
+  MenuItem turn = new MenuItem(
+          MessageManager.getString("label.turn_propensity"));
 
-  MenuItem buried = new MenuItem(MessageManager.getString("label.buried_index"));
+  MenuItem buried = new MenuItem(
+          MessageManager.getString("label.buried_index"));
 
-  MenuItem purinepyrimidine = new MenuItem(MessageManager.getString("label.purine_pyrimidine"));
+  MenuItem purinepyrimidine = new MenuItem(
+          MessageManager.getString("label.purine_pyrimidine"));
 
-  MenuItem user = new MenuItem(MessageManager.getString("label.user_defined_colours"));
+  MenuItem user = new MenuItem(
+          MessageManager.getString("label.user_defined_colours"));
 
-  MenuItem jmolHelp = new MenuItem(MessageManager.getString("label.jmol_help"));
+  MenuItem jmolHelp = new MenuItem(
+          MessageManager.getString("label.jmol_help"));
 
   Panel scriptWindow;
 
@@ -125,7 +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,
@@ -301,8 +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);
@@ -385,9 +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());
@@ -398,8 +442,9 @@ public class AppletJmol extends EmbmenuFrame implements
                 .println("Out of memory when trying to create dialog box with sequence-structure mapping.");
         return;
       }
-      jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.pdb_sequence_mapping"),
-              550, 600);
+      jalview.bin.JalviewLite.addFrame(frame,
+              MessageManager.getString("label.pdb_sequence_mapping"), 550,
+              600);
     }
     else if (evt.getSource() == charge)
     {
@@ -474,7 +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();
@@ -505,10 +552,12 @@ 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)
@@ -533,7 +582,7 @@ 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()
@@ -544,7 +593,7 @@ 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());
   }
@@ -617,7 +666,8 @@ public class AppletJmol extends EmbmenuFrame implements
         g.fillRect(0, 0, currentSize.width, currentSize.height);
         g.setColor(Color.white);
         g.setFont(new Font("Verdana", Font.BOLD, 14));
-        g.drawString(MessageManager.getString("label.retrieving_pdb_data"), 20, currentSize.height / 2);
+        g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
+                20, currentSize.height / 2);
       }
       else
       {