JAL-1620 version bump and release notes

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

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 3f2a769..4b014d1 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * 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;
@@ -32,7 +34,7 @@ import jalview.util.MessageManager;
 
 public class AppletJmol extends EmbmenuFrame implements
 // StructureListener,
-        KeyListener, ActionListener, ItemListener, SequenceStructureBinding
+        KeyListener, ActionListener, ItemListener
 
 {
   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
@@ -45,35 +47,47 @@ 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 +139,7 @@ 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 +315,7 @@ 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);
@@ -398,8 +411,9 @@ 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)
     {
@@ -617,7 +631,8 @@ 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
       {