JAL-1620 version bump and release notes

[jalview.git] / src / jalview / gui / AppVarnaBinding.java

diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index ad91c20..9ba1d3d 100644 (file)
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * 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.gui;
@@ -101,17 +103,23 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
 
   private JTextField _seq = new JTextField();
 
-  private JLabel _strLabel = new JLabel(MessageManager.getString("label.str"));
+  private JLabel _strLabel = new JLabel(
+          MessageManager.getString("label.str"));
 
-  private JLabel _seqLabel = new JLabel(MessageManager.getString("label.seq"));
+  private JLabel _seqLabel = new JLabel(
+          MessageManager.getString("label.seq"));
 
-  private JButton _createButton = new JButton(MessageManager.getString("action.create"));
+  private JButton _createButton = new JButton(
+          MessageManager.getString("action.create"));
 
-  private JButton _updateButton = new JButton(MessageManager.getString("action.update"));
+  private JButton _updateButton = new JButton(
+          MessageManager.getString("action.update"));
 
-  private JButton _deleteButton = new JButton(MessageManager.getString("action.delete"));
+  private JButton _deleteButton = new JButton(
+          MessageManager.getString("action.delete"));
 
-  private JButton _duplicateButton = new JButton(MessageManager.getString("action.snapshot"));
+  private JButton _duplicateButton = new JButton(
+          MessageManager.getString("action.snapshot"));
 
   protected JPanel _listPanel = new JPanel();
 
@@ -143,7 +151,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
   {
     // super("VARNA in Jalview");
     initVarna(seq, struc);
-   
+
   }
 
   public AppVarnaBinding(ArrayList<RNA> rnaList)
@@ -155,7 +163,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
 
   private void initVarna(String seq, String str)
   {
-         
+
     DefaultListModel dlm = new DefaultListModel();
 
     DefaultListSelectionModel m = new DefaultListSelectionModel();
@@ -188,7 +196,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
 
     try
     {
-    
+
       vp = new VARNAPanel("0", ".");
       _RNA1.setRNA(seq, str);
       _RNA1.drawRNARadiate(vp.getConfig());
@@ -217,7 +225,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
 
   private void initVarnaEdit(ArrayList<RNA> rnaInList)
   {
-       
+
     DefaultListModel dlm = new DefaultListModel();
 
     int marginTools = 40;
@@ -241,7 +249,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
           FullBackup sel = (FullBackup) _sideList.getSelectedValue();
           Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA()
                   .getSize(), sel.rna.getSize());
-          //vp.showRNAInterpolated(sel.rna, sel.config, map);
+          // vp.showRNAInterpolated(sel.rna, sel.config, map);
           vp.showRNA(sel.rna, sel.config);
           // _seq.setText(sel.rna.getSeq());
           _str.setText(sel.rna.getStructDBN());
@@ -252,12 +260,12 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
 
     try
     {
-       
+
       vp = new VARNAPanel("0", ".");
       for (int i = 0; i < rnaInList.size(); i++)
       {
         rnaInList.get(i).drawRNARadiate(vp.getConfig());
-       
+
       }
     } catch (ExceptionNonEqualLength e)
     {
@@ -344,7 +352,9 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
     ops.add(_deleteButton);
     ops.add(_duplicateButton);
 
-    JLabel j = new JLabel(MessageManager.getString("label.structures_manager"), JLabel.CENTER);
+    JLabel j = new JLabel(
+            MessageManager.getString("label.structures_manager"),
+            JLabel.CENTER);
     _listPanel.setLayout(new BorderLayout());
 
     // _listPanel.add(ops, BorderLayout.SOUTH);
@@ -807,10 +817,11 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
   public void onUINewStructure(VARNAConfig v, RNA r)
   {
     // patch to fix infinite loop
-    // The problem is that onUINewStructure is called when user clicks 
+    // The problem is that onUINewStructure is called when user clicks
     // check with Yann about whether Jalview should do anything with this event.
-    // e.g. if user has used VARNA's menu to import a structure .. Jalview may need to be told which structure is displayed.
-    
+    // e.g. if user has used VARNA's menu to import a structure .. Jalview may
+    // need to be told which structure is displayed.
+
     // _rnaList.add(v, r, "", true);
   }
 
@@ -946,14 +957,14 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
   public void onZoomLevelChanged()
   {
     // TODO Auto-generated method stub
-    
+
   }
 
   @Override
   public void onTranslationChanged()
   {
     // TODO Auto-generated method stub
-    
+
   }
 }