X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarnaBinding.java;h=ad91c207213825ce4191a9da2a503a7f037c5334;hb=0e2054d29bc49351f000d478659dc3c4371b251c;hp=02696ea6dbddc3ab8c845c0c81c9aaf2a52d7898;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git

diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index 02696ea..ad91c20 100644
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -1,22 +1,25 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * 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.
- * 
+ *  
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
+import jalview.util.MessageManager;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Component;
@@ -37,28 +40,20 @@ import java.awt.event.ComponentEvent;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.io.File;
-import java.text.DateFormat;
 import java.util.ArrayList;
 import java.util.Collection;
-import java.util.Date;
 import java.util.List;
 
 import javax.swing.DefaultListModel;
 import javax.swing.DefaultListSelectionModel;
-import javax.swing.Icon;
 import javax.swing.JButton;
-import javax.swing.JFrame;
 import javax.swing.JLabel;
 import javax.swing.JList;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
-import javax.swing.JSplitPane;
 import javax.swing.JTextField;
 import javax.swing.ListModel;
 import javax.swing.ListSelectionModel;
-import javax.swing.UIManager;
-import javax.swing.UnsupportedLookAndFeelException;
 import javax.swing.event.ListSelectionEvent;
 import javax.swing.event.ListSelectionListener;
 
@@ -106,17 +101,17 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
 
   private JTextField _seq = new JTextField();
 
-  private JLabel _strLabel = new JLabel(" Str:");
+  private JLabel _strLabel = new JLabel(MessageManager.getString("label.str"));
 
-  private JLabel _seqLabel = new JLabel(" Seq:");
+  private JLabel _seqLabel = new JLabel(MessageManager.getString("label.seq"));
 
-  private JButton _createButton = new JButton("Create");
+  private JButton _createButton = new JButton(MessageManager.getString("action.create"));
 
-  private JButton _updateButton = new JButton("Update");
+  private JButton _updateButton = new JButton(MessageManager.getString("action.update"));
 
-  private JButton _deleteButton = new JButton("Delete");
+  private JButton _deleteButton = new JButton(MessageManager.getString("action.delete"));
 
-  private JButton _duplicateButton = new JButton("Snapshot");
+  private JButton _duplicateButton = new JButton(MessageManager.getString("action.snapshot"));
 
   protected JPanel _listPanel = new JPanel();
 
@@ -148,16 +143,19 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
   {
     // super("VARNA in Jalview");
     initVarna(seq, struc);
+   
   }
 
   public AppVarnaBinding(ArrayList<RNA> rnaList)
   {
+
     // super("VARNA in Jalview");
     initVarnaEdit(rnaList);
   }
 
   private void initVarna(String seq, String str)
   {
+	  
     DefaultListModel dlm = new DefaultListModel();
 
     DefaultListSelectionModel m = new DefaultListSelectionModel();
@@ -190,6 +188,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
 
     try
     {
+    
       vp = new VARNAPanel("0", ".");
       _RNA1.setRNA(seq, str);
       _RNA1.drawRNARadiate(vp.getConfig());
@@ -218,6 +217,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
 
   private void initVarnaEdit(ArrayList<RNA> rnaInList)
   {
+	
     DefaultListModel dlm = new DefaultListModel();
 
     int marginTools = 40;
@@ -241,7 +241,8 @@ 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());
         }
@@ -251,10 +252,12 @@ 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)
     {
@@ -341,7 +344,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
     ops.add(_deleteButton);
     ops.add(_duplicateButton);
 
-    JLabel j = new JLabel("Structures Manager", JLabel.CENTER);
+    JLabel j = new JLabel(MessageManager.getString("label.structures_manager"), JLabel.CENTER);
     _listPanel.setLayout(new BorderLayout());
 
     // _listPanel.add(ops, BorderLayout.SOUTH);
@@ -803,7 +806,12 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
 
   public void onUINewStructure(VARNAConfig v, RNA r)
   {
-    _rnaList.add(v, r, "", true);
+    // patch to fix infinite loop
+    // 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.
+    
+    // _rnaList.add(v, r, "", true);
   }
 
   public void onWarningEmitted(String s)
@@ -933,6 +941,20 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
     // TODO Auto-generated method stub
 
   }
+
+  @Override
+  public void onZoomLevelChanged()
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  @Override
+  public void onTranslationChanged()
+  {
+    // TODO Auto-generated method stub
+    
+  }
 }
 
 /*
@@ -942,4 +964,4 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
  * AppVarnaBinding vab = new AppVarnaBinding(); vab.varnagui.set_seq(str);
  * vab.varnagui.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
  * vab.varnagui.pack(); vab.varnagui.setVisible(true); } }
- */
\ No newline at end of file
+ */