X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarnaBinding.java;h=9ba1d3d901cc308303d9b5e565736282c26baadf;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=105dd39ffa8a0b0ba75ec1cc787847cc0c81855e;hpb=722f0bee96b96ceeb8ef69b3ccd1aeff13786b2b;p=jalview.git

diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index 105dd39..9ba1d3d 100644
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -1,230 +1,978 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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;
 
-import java.awt.Container;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GridLayout;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTarget;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 import java.awt.event.ComponentEvent;
-import java.awt.event.ComponentListener;
-import java.awt.event.ContainerEvent;
-import java.awt.event.ContainerListener;
-import java.util.BitSet;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
 
+import javax.swing.DefaultListModel;
+import javax.swing.DefaultListSelectionModel;
+import javax.swing.JButton;
+import javax.swing.JLabel;
+import javax.swing.JList;
 import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextField;
+import javax.swing.ListModel;
+import javax.swing.ListSelectionModel;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
 
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.structure.StructureSelectionManager;
-
-import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.api.JmolViewer;
-import org.jmol.popup.JmolPopup;
-import org.openscience.jmol.app.jmolpanel.AppConsole;
+import fr.orsay.lri.varna.VARNAPanel;
+import fr.orsay.lri.varna.components.ReorderableJList;
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
+import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
+import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
+import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
+import fr.orsay.lri.varna.models.FullBackup;
+import fr.orsay.lri.varna.models.VARNAConfig;
+import fr.orsay.lri.varna.models.rna.Mapping;
+import fr.orsay.lri.varna.models.rna.RNA;
 
-public class AppVarnaBinding extends jalview.ext.jmol.JalviewJmolBinding
+public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
+        implements DropTargetListener, InterfaceVARNAListener,
+        MouseListener
 {
 
   /**
+	 * 
+	 */
+  // private static final long serialVersionUID = -790155708306987257L;
+
+  private String DEFAULT_SEQUENCE = "CAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIA";
+
+  private String DEFAULT_STRUCTURE1 = "..(((((...(((((...(((((...(((((.....)))))...))))).....(((((...(((((.....)))))...))))).....)))))...)))))..";
+
+  private String DEFAULT_STRUCTURE2 = "..(((((...(((((...(((((........(((((...(((((.....)))))...)))))..................))))).....)))))...)))))..";
+
+  public VARNAPanel vp;
+
+  protected JPanel _tools = new JPanel();
+
+  private JPanel _input = new JPanel();
+
+  private JPanel _seqPanel = new JPanel();
+
+  private JPanel _strPanel = new JPanel();
+
+  private JLabel _info = new JLabel();
+
+  private JTextField _str = new JTextField();
+
+  private JTextField _seq = new JTextField();
+
+  private JLabel _strLabel = new JLabel(
+          MessageManager.getString("label.str"));
+
+  private JLabel _seqLabel = new JLabel(
+          MessageManager.getString("label.seq"));
+
+  private JButton _createButton = new JButton(
+          MessageManager.getString("action.create"));
+
+  private JButton _updateButton = new JButton(
+          MessageManager.getString("action.update"));
+
+  private JButton _deleteButton = new JButton(
+          MessageManager.getString("action.delete"));
+
+  private JButton _duplicateButton = new JButton(
+          MessageManager.getString("action.snapshot"));
+
+  protected JPanel _listPanel = new JPanel();
+
+  private ReorderableJList _sideList = null;
+
+  private static String errorOpt = "error";
+
+  @SuppressWarnings("unused")
+  private boolean _error;
+
+  private Color _backgroundColor = Color.white;
+
+  private static int _nextID = 1;
+
+  @SuppressWarnings("unused")
+  private int _algoCode;
+
+  private BackupHolder _rnaList;
+
+  /*
+   * public AppVarnaBinding() { //super("VARNA in Jalview");
+   * //this.set_seq("ATGC"); //this.set_str(".()."); //RNAPanelDemoInit();
    * 
+   * //initVarna("ATGCATGATATATATATAT","....((((...))))....");
+   * initVarna(this.DEFAULT_SEQUENCE,this.DEFAULT_STRUCTURE1); }
    */
-  private AppJmol appJmolWindow;
 
-  public AppVarnaBinding(AppJmol appJmol, StructureSelectionManager sSm, PDBEntry[] pdbentry,
-          SequenceI[][] sequenceIs, String[][] chains, String protocol)
+  public AppVarnaBinding(String seq, String struc)
   {
-    super(sSm, pdbentry, sequenceIs, chains, protocol);
-    appJmolWindow = appJmol;
+    // super("VARNA in Jalview");
+    initVarna(seq, struc);
+
   }
 
-  FeatureRenderer fr = null;
+  public AppVarnaBinding(ArrayList<RNA> rnaList)
+  {
 
-  @Override
-  public jalview.api.FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+    // super("VARNA in Jalview");
+    initVarnaEdit(rnaList);
+  }
+
+  private void initVarna(String seq, String str)
   {
-    AlignmentPanel ap = (alignment==null) ? appJmolWindow.ap : (AlignmentPanel) alignment;
-    if (ap.av.showSequenceFeatures)
+
+    DefaultListModel dlm = new DefaultListModel();
+
+    DefaultListSelectionModel m = new DefaultListSelectionModel();
+    m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+    m.setLeadAnchorNotificationEnabled(false);
+
+    _sideList = new ReorderableJList();
+    _sideList.setModel(dlm);
+    _sideList.addMouseListener(this);
+    _sideList.setSelectionModel(m);
+    _sideList.setPreferredSize(new Dimension(100, 0));
+    _sideList.addListSelectionListener(new ListSelectionListener()
     {
-      if (fr == null)
+      public void valueChanged(ListSelectionEvent arg0)
       {
-        fr = new FeatureRenderer(ap);
+        if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
+        {
+          FullBackup sel = (FullBackup) _sideList.getSelectedValue();
+          Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA()
+                  .getSize(), sel.rna.getSize());
+          vp.showRNAInterpolated(sel.rna, sel.config, map);
+          _seq.setText(sel.rna.getSeq());
+          _str.setText(sel.rna.getStructDBN());
+        }
       }
+    });
+
+    _rnaList = new BackupHolder(dlm, _sideList);
+    RNA _RNA1 = new RNA("User defined 1");
+
+    try
+    {
 
-      fr.transferSettings(ap.
-              seqPanel.seqCanvas.getFeatureRenderer());
+      vp = new VARNAPanel("0", ".");
+      _RNA1.setRNA(seq, str);
+      _RNA1.drawRNARadiate(vp.getConfig());
+    } catch (ExceptionNonEqualLength e)
+    {
+      vp.errorDialog(e);
+    } catch (ExceptionUnmatchedClosingParentheses e2)
+    {
+      e2.printStackTrace();
+    } catch (ExceptionFileFormatOrSyntax e3)
+    {
+      e3.printStackTrace();
     }
+    vp.setPreferredSize(new Dimension(400, 400));
+    _rnaList.add(vp.getConfig().clone(), _RNA1, generateDefaultName(), true);
 
-    return fr;
-  }
+    // TODO setBackground(_backgroundColor);
+    vp.setBackground(_backgroundColor);
 
-  @Override
-  public jalview.api.SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
-  {
-    return new SequenceRenderer(((AlignmentPanel)alignment).av);
+    // TODO getContentPane().setLayout(new BorderLayout());
+    // TODO getContentPane().add(vp, BorderLayout.CENTER);
+
+    // setVisible(true);
+    vp.addVARNAListener(this);
   }
 
-  public void sendConsoleEcho(String strEcho)
+  private void initVarnaEdit(ArrayList<RNA> rnaInList)
   {
-    if (console != null)
+
+    DefaultListModel dlm = new DefaultListModel();
+
+    int marginTools = 40;
+
+    DefaultListSelectionModel m = new DefaultListSelectionModel();
+    m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+    m.setLeadAnchorNotificationEnabled(false);
+
+    _sideList = new ReorderableJList();
+    _sideList.setModel(dlm);
+    _sideList.addMouseListener(this);
+    _sideList.setSelectionModel(m);
+    _sideList.setPreferredSize(new Dimension(100, 0));
+    _sideList.addListSelectionListener(new ListSelectionListener()
+    {
+      public void valueChanged(ListSelectionEvent arg0)
+      {
+        // System.out.println(arg0);
+        if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
+        {
+          FullBackup sel = (FullBackup) _sideList.getSelectedValue();
+          Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA()
+                  .getSize(), sel.rna.getSize());
+          // vp.showRNAInterpolated(sel.rna, sel.config, map);
+          vp.showRNA(sel.rna, sel.config);
+          // _seq.setText(sel.rna.getSeq());
+          _str.setText(sel.rna.getStructDBN());
+        }
+      }
+    });
+    _rnaList = new BackupHolder(dlm, _sideList);
+
+    try
+    {
+
+      vp = new VARNAPanel("0", ".");
+      for (int i = 0; i < rnaInList.size(); i++)
+      {
+        rnaInList.get(i).drawRNARadiate(vp.getConfig());
+
+      }
+    } catch (ExceptionNonEqualLength e)
     {
-      console.sendConsoleEcho(strEcho);
+      vp.errorDialog(e);
     }
+    vp.setPreferredSize(new Dimension(400, 400));
+    for (int i = 0; i < rnaInList.size(); i++)
+    {
+      if (i < rnaInList.size() - 1)
+      {
+        _rnaList.add(vp.getConfig().clone(), rnaInList.get(i), rnaInList
+                .get(i).getName());
+      }
+      else
+      {
+        _rnaList.add(vp.getConfig().clone(), rnaInList.get(i), rnaInList
+                .get(i).getName(), true);
+      }
+    }
+
+    /*
+     * _rnaList.add(vp.getConfig().clone(),_RNA2,generateDefaultName());
+     * _rnaList.add(vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
+     */
+
+    JScrollPane listScroller = new JScrollPane(_sideList);
+    listScroller.setPreferredSize(new Dimension(150, 0));
+
+    vp.setBackground(_backgroundColor);
+
+    Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
+
+    // _seqLabel.setHorizontalTextPosition(JLabel.LEFT);
+    // _seqLabel.setPreferredSize(new Dimension(marginTools, 15));
+    _seq.setFont(textFieldsFont);
+    _seq.setText(rnaInList.get(0).getSeq());
+
+    _updateButton.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        FullBackup sel = (FullBackup) _sideList.getSelectedValue();
+        sel.rna.setSequence("A");
+      }
+    });
+
+    // _seqPanel.setLayout(new BorderLayout());
+    // _seqPanel.add(_seqLabel, BorderLayout.WEST);
+    // _seqPanel.add(_seq, BorderLayout.CENTER);
+
+    _strLabel.setPreferredSize(new Dimension(marginTools, 15));
+    _strLabel.setHorizontalTextPosition(JLabel.LEFT);
+    _str.setFont(textFieldsFont);
+    _strPanel.setLayout(new BorderLayout());
+    _strPanel.add(_strLabel, BorderLayout.WEST);
+    _strPanel.add(_str, BorderLayout.CENTER);
+
+    _input.setLayout(new GridLayout(1, 0));
+    // _input.add(_seqPanel);
+    _input.add(_strPanel);
+
+    JPanel goPanel = new JPanel();
+    goPanel.setLayout(new BorderLayout());
+
+    _tools.setLayout(new BorderLayout());
+    _tools.add(_input, BorderLayout.CENTER);
+    // _tools.add(_info, BorderLayout.SOUTH);
+    _tools.add(goPanel, BorderLayout.EAST);
+
+    /*
+     * _deleteButton.addActionListener(new ActionListener() { public void
+     * actionPerformed(ActionEvent e) { _rnaList.removeSelected(); } });
+     * _duplicateButton.addActionListener(new ActionListener() { public void
+     * actionPerformed(ActionEvent e) {
+     * _rnaList.add((VARNAConfig)vp.getConfig().
+     * clone(),vp.getRNA().clone(),vp.getRNA
+     * ().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new
+     * Date()),true); }});
+     */
+    goPanel.add(_updateButton, BorderLayout.CENTER);
+
+    JPanel ops = new JPanel();
+    ops.setLayout(new GridLayout(1, 2));
+    ops.add(_deleteButton);
+    ops.add(_duplicateButton);
+
+    JLabel j = new JLabel(
+            MessageManager.getString("label.structures_manager"),
+            JLabel.CENTER);
+    _listPanel.setLayout(new BorderLayout());
+
+    // _listPanel.add(ops, BorderLayout.SOUTH);
+    _listPanel.add(j, BorderLayout.NORTH);
+    _listPanel.add(listScroller, BorderLayout.CENTER);
+
+    // JSplitPane split = new
+    // JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,vp);
+    /**
+     * TODO getContentPane().setLayout(new BorderLayout());
+     * getContentPane().add(split, BorderLayout.CENTER);
+     * getContentPane().add(_tools, BorderLayout.NORTH);
+     */
+
+    // TODO setVisible(true);
+    DropTarget dt = new DropTarget(vp, this);
+
+    vp.addVARNAListener(this);
+  }
+
+  public JPanel getTools()
+  {
+    return _tools;
   }
 
-  public void sendConsoleMessage(String strStatus)
+  public JPanel getListPanel()
+  {
+    return _listPanel;
+  }
+
+  /**
+   * TODO: Is it effective to transfer the whole RNA?
+   * 
+   * @return Currently selected RNA
+   */
+  public RNA getSelectedRNA()
+  {
+    return _rnaList.getElementAt(_sideList.getSelectedIndex()).rna;
+  }
+
+  /**
+   * Substitute currently selected RNA with the edited one
+   * 
+   * @param rnaEdit
+   */
+  public void updateSelectedRNA(RNA rnaEdit)
   {
-    if (console != null && strStatus != null)
-    // && !strStatus.equals("Script completed"))
-    // should we squash the script completed string ?
+    vp.repaint();
+    vp.showRNA(rnaEdit);
+  }
+
+  /*
+   * private void RNAPanelDemoInit() { DefaultListModel dlm = new
+   * DefaultListModel();
+   * 
+   * 
+   * int marginTools = 40;
+   * 
+   * DefaultListSelectionModel m = new DefaultListSelectionModel();
+   * m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+   * m.setLeadAnchorNotificationEnabled(false);
+   * 
+   * 
+   * _sideList = new ReorderableJList(); _sideList.setModel(dlm);
+   * _sideList.addMouseListener(this); _sideList.setSelectionModel(m);
+   * _sideList.setPreferredSize(new Dimension(100, 0));
+   * _sideList.addListSelectionListener( new ListSelectionListener(){ public
+   * void valueChanged(ListSelectionEvent arg0) { //System.out.println(arg0); if
+   * (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting()) { FullBackup
+   * sel = (FullBackup) _sideList.getSelectedValue(); Mapping map =
+   * Mapping.DefaultOutermostMapping(vp.getRNA().getSize(), sel.rna.getSize());
+   * vp.showRNAInterpolated(sel.rna,sel.config,map);
+   * _seq.setText(sel.rna.getSeq()); _str.setText(sel.rna.getStructDBN()); } }
+   * });
+   * 
+   * _rnaList = new BackupHolder(dlm,_sideList); RNA _RNA1 = new
+   * RNA("User defined 1"); RNA _RNA2 = new RNA("User defined 2"); try { vp =
+   * new VARNAPanel("0","."); _RNA1.setRNA(DEFAULT_SEQUENCE,
+   * DEFAULT_STRUCTURE1); _RNA1.drawRNARadiate(vp.getConfig());
+   * _RNA2.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE2);
+   * _RNA2.drawRNARadiate(vp.getConfig()); } catch (ExceptionNonEqualLength e) {
+   * vp.errorDialog(e); } catch (ExceptionUnmatchedClosingParentheses e2) {
+   * e2.printStackTrace(); } catch (ExceptionFileFormatOrSyntax e3) {
+   * e3.printStackTrace(); } vp.setPreferredSize(new Dimension(400, 400));
+   * _rnaList.add(vp.getConfig().clone(),_RNA2,generateDefaultName());
+   * _rnaList.add(vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
+   * 
+   * JScrollPane listScroller = new JScrollPane(_sideList);
+   * listScroller.setPreferredSize(new Dimension(150, 0));
+   * 
+   * setBackground(_backgroundColor); vp.setBackground(_backgroundColor);
+   * 
+   * 
+   * Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
+   * 
+   * _seqLabel.setHorizontalTextPosition(JLabel.LEFT);
+   * _seqLabel.setPreferredSize(new Dimension(marginTools, 15));
+   * _seq.setFont(textFieldsFont); _seq.setText(DEFAULT_SEQUENCE);
+   * 
+   * _createButton.addActionListener(new ActionListener() { public void
+   * actionPerformed(ActionEvent e) { try { RNA nRNA = new
+   * RNA(generateDefaultName()); nRNA.setRNA(_seq.getText(), _str.getText());
+   * nRNA.drawRNARadiate(vp.getConfig()); _rnaList.add(new
+   * VARNAConfig(),nRNA,true); } catch (ExceptionUnmatchedClosingParentheses e1)
+   * { JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error",
+   * JOptionPane.ERROR_MESSAGE); } catch (ExceptionFileFormatOrSyntax e1) {
+   * JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error",
+   * JOptionPane.ERROR_MESSAGE); } } });
+   * 
+   * 
+   * _seqPanel.setLayout(new BorderLayout()); _seqPanel.add(_seqLabel,
+   * BorderLayout.WEST); _seqPanel.add(_seq, BorderLayout.CENTER);
+   * 
+   * _strLabel.setPreferredSize(new Dimension(marginTools, 15));
+   * _strLabel.setHorizontalTextPosition(JLabel.LEFT);
+   * _str.setFont(textFieldsFont); _strPanel.setLayout(new BorderLayout());
+   * _strPanel.add(_strLabel, BorderLayout.WEST); _strPanel.add(_str,
+   * BorderLayout.CENTER);
+   * 
+   * _input.setLayout(new GridLayout(2, 0)); _input.add(_seqPanel);
+   * _input.add(_strPanel);
+   * 
+   * JPanel goPanel = new JPanel(); goPanel.setLayout(new BorderLayout());
+   * 
+   * _tools.setLayout(new BorderLayout()); _tools.add(_input,
+   * BorderLayout.CENTER); _tools.add(_info, BorderLayout.SOUTH);
+   * _tools.add(goPanel, BorderLayout.EAST);
+   * 
+   * _deleteButton.addActionListener(new ActionListener() { public void
+   * actionPerformed(ActionEvent e) { _rnaList.removeSelected(); } });
+   * _duplicateButton.addActionListener(new ActionListener() { public void
+   * actionPerformed(ActionEvent e) {
+   * _rnaList.add((VARNAConfig)vp.getConfig().clone
+   * (),vp.getRNA().clone(),vp.getRNA
+   * ().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new
+   * Date()),true); }});
+   * 
+   * JPanel ops = new JPanel(); ops.setLayout(new GridLayout(1,2));
+   * ops.add(_deleteButton); ops.add(_duplicateButton);
+   * 
+   * JLabel j = new JLabel("Structures Manager",JLabel.CENTER);
+   * _listPanel.setLayout(new BorderLayout());
+   * 
+   * _listPanel.add(ops,BorderLayout.SOUTH);
+   * _listPanel.add(j,BorderLayout.NORTH);
+   * _listPanel.add(listScroller,BorderLayout.CENTER);
+   * 
+   * goPanel.add(_createButton, BorderLayout.CENTER);
+   * 
+   * JSplitPane split = new
+   * JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,vp);
+   * getContentPane().setLayout(new BorderLayout()); getContentPane().add(split,
+   * BorderLayout.CENTER); getContentPane().add(_tools, BorderLayout.NORTH);
+   * 
+   * setVisible(true); DropTarget dt = new DropTarget(vp, this);
+   * 
+   * vp.addVARNAListener(this); }
+   */
+  public static String generateDefaultName()
+  {
+    return "User file #" + _nextID++;
+  }
+
+  public RNA getRNA()
+  {
+    return (RNA) _sideList.getSelectedValue();
+  }
+
+  public String[][] getParameterInfo()
+  {
+    String[][] info =
     {
-      console.sendConsoleMessage(strStatus);
-    }
+        // Parameter Name Kind of Value Description,
+        { "sequenceDBN", "String", "A raw RNA sequence" },
+        { "structureDBN", "String",
+            "An RNA structure in dot bracket notation (DBN)" },
+        { errorOpt, "boolean", "To show errors" }, };
+    return info;
   }
 
-  @Override
-  public void showUrl(String url, String target)
+  public void init()
   {
+    vp.setBackground(_backgroundColor);
+    _error = true;
+  }
+
+  @SuppressWarnings("unused")
+  private Color getSafeColor(String col, Color def)
+  {
+    Color result;
     try
     {
-      jalview.util.BrowserLauncher.openURL(url);
+      result = Color.decode(col);
     } catch (Exception e)
     {
-      Cache.log.error("Failed to launch Jmol-associated url " + url, e);
-      // TODO: 2.6 : warn user if browser was not configured.
+      try
+      {
+        result = Color.getColor(col, def);
+      } catch (Exception e2)
+      {
+        return def;
+      }
     }
+    return result;
   }
 
-  @Override
-  public void refreshGUI()
+  public VARNAPanel get_varnaPanel()
   {
-    // appJmolWindow.repaint();
-    javax.swing.SwingUtilities.invokeLater(new Runnable()
-    {
-      public void run()
-      {
-        appJmolWindow.updateTitleAndMenus();
-        appJmolWindow.revalidate();
-      }
-    });
+    return vp;
   }
 
-  public void updateColours(Object source)
+  public void set_varnaPanel(VARNAPanel surface)
   {
-    AlignmentPanel ap = (AlignmentPanel) source,topap;
-    // ignore events from unrelated or non-user interactive frames
-    if ((topap=appJmolWindow.getAlignmentPanelFor(ap.av.getAlignment()))==null || topap.alignFrame.getCurrentView() != ap.av || !appJmolWindow.isUsedforcolourby(ap))
-      return;
-    if (!isLoadingFromArchive()) {
-      colourBySequence(ap.av.getShowSequenceFeatures(), ap);
-    }
+    vp = surface;
+  }
+
+  public String get_seq()
+  {
+    return _seq.getText();
   }
 
-  public void notifyScriptTermination(String strStatus, int msWalltime)
+  public void set_seq(String _seq)
   {
-    // todo - script termination doesn't happen ?
-    // if (console != null)
-    // console.notifyScriptTermination(strStatus,
-    // msWalltime);
+    this._seq.setText(_seq);
   }
 
-  public void showUrl(String url)
+  public String get_str()
   {
-    showUrl(url, "jmol");
+    return _str.getText();
   }
 
-  public void newJmolPopup(boolean translateLocale, String menuName,
-          boolean asPopup)
+  public void set_str(String _str)
   {
+    this._str.setText(_str);
+  }
 
-    jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
-            asPopup);
+  public JLabel get_info()
+  {
+    return _info;
   }
 
-  public void selectionChanged(BitSet arg0)
+  public void set_info(JLabel _info)
+  {
+    this._info = _info;
+  }
+
+  /*
+   * public static void main(String[] args) { AppVarnaBinding d = new
+   * AppVarnaBinding(); d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+   * d.pack(); d.setVisible(true); }
+   */
+
+  public void dragEnter(DropTargetDragEvent arg0)
   {
     // TODO Auto-generated method stub
 
   }
 
-  public void refreshPdbEntries()
+  public void dragExit(DropTargetEvent arg0)
   {
     // TODO Auto-generated method stub
 
   }
 
-  public void showConsole(boolean b)
+  public void dragOver(DropTargetDragEvent arg0)
   {
-    appJmolWindow.showConsole(b);
+    // TODO Auto-generated method stub
+
   }
 
-  /**
-   * add the given sequences to the mapping scope for the given pdb file handle
-   * 
-   * @param pdbFile
-   *          - pdbFile identifier
-   * @param seq
-   *          - set of sequences it can be mapped to
-   */
-  public void addSequenceForStructFile(String pdbFile, SequenceI[] seq)
+  public void drop(DropTargetDropEvent dtde)
   {
-    for (int pe = 0; pe < pdbentry.length; pe++)
+    try
     {
-      if (pdbentry[pe].getFile().equals(pdbFile))
+      Transferable tr = dtde.getTransferable();
+      DataFlavor[] flavors = tr.getTransferDataFlavors();
+      for (int i = 0; i < flavors.length; i++)
       {
-        addSequence(pe, seq);
+        if (flavors[i].isFlavorJavaFileListType())
+        {
+          dtde.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+          Object ob = tr.getTransferData(flavors[i]);
+          if (ob instanceof List)
+          {
+            List list = (List) ob;
+            for (int j = 0; j < list.size(); j++)
+            {
+              Object o = list.get(j);
+
+              if (dtde.getSource() instanceof DropTarget)
+              {
+                DropTarget dt = (DropTarget) dtde.getSource();
+                Component c = dt.getComponent();
+                if (c instanceof VARNAPanel)
+                {
+                  String path = o.toString();
+                  VARNAPanel vp = (VARNAPanel) c;
+                  try
+                  {
+                    FullBackup bck = VARNAPanel.importSession(path);
+                    _rnaList.add(bck.config, bck.rna, bck.name, true);
+                  } catch (ExceptionLoadingFailed e3)
+                  {
+                    int mn = 1;
+                    Collection<RNA> mdls = fr.orsay.lri.varna.factories.RNAFactory
+                            .loadSecStr(path);
+                    for (RNA r : mdls)
+                    {
+                      r.drawRNA(vp.getConfig());
+                      String name = r.getName();
+                      if (name.equals(""))
+                      {
+                        name = path.substring(path
+                                .lastIndexOf(File.separatorChar) + 1);
+                      }
+                      if (mdls.size() > 1)
+                      {
+                        name += " (Model " + mn++ + ")";
+                      }
+                      _rnaList.add(vp.getConfig().clone(), r, name, true);
+                    }
+                  }
+                }
+              }
+            }
+          }
+          // If we made it this far, everything worked.
+          dtde.dropComplete(true);
+          return;
+        }
       }
+      // Hmm, the user must not have dropped a file list
+      dtde.rejectDrop();
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+      dtde.rejectDrop();
     }
+
   }
 
-  @Override
-  protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
-          Container consolePanel, String buttonsToShow)
+  public void dropActionChanged(DropTargetDragEvent arg0)
   {
-    return new AppConsole(viewer, consolePanel, buttonsToShow);
   }
 
-  @Override
-  protected void releaseUIResources()
+  private class BackupHolder
   {
-    appJmolWindow = null;
-    if (console != null)
+    private DefaultListModel _rnaList;
+
+    private ArrayList<RNA> _rnas = new ArrayList<RNA>();
+
+    JList _l;
+
+    public BackupHolder(DefaultListModel rnaList, JList l)
     {
-      try
+      _rnaList = rnaList;
+      _l = l;
+    }
+
+    public void add(VARNAConfig c, RNA r)
+    {
+      add(c, r, r.getName(), false);
+    }
+
+    public void add(VARNAConfig c, RNA r, boolean select)
+    {
+      add(c, r, r.getName(), select);
+    }
+
+    public void add(VARNAConfig c, RNA r, String name)
+    {
+      add(c, r, name, false);
+    }
+
+    public void add(VARNAConfig c, RNA r, String name, boolean select)
+    {
+      if (select)
       {
-        console.setVisible(false);
-      } catch (Error e)
+        _l.removeSelectionInterval(0, _rnaList.size());
+      }
+      if (name.equals(""))
       {
-      } catch (Exception x)
+        name = generateDefaultName();
+      }
+      FullBackup bck = new FullBackup(c, r, name);
+      _rnas.add(0, r);
+      _rnaList.add(0, bck);
+      if (select)
       {
+        _l.setSelectedIndex(0);
       }
+    }
+
+    public void remove(int i)
+    {
+      _rnas.remove(i);
+      _rnaList.remove(i);
+
+    }
+
+    public DefaultListModel getModel()
+    {
+      return _rnaList;
+    }
+
+    public boolean contains(RNA r)
+    {
+      return _rnas.contains(r);
+    }
+
+    /*
+     * public int getSize() { return _rnaList.getSize(); }
+     */
+    public FullBackup getElementAt(int i)
+    {
+      return (FullBackup) _rnaList.getElementAt(i);
+    }
+
+    public void removeSelected()
+    {
+      int i = _l.getSelectedIndex();
+      if (i != -1)
+      {
+        if (_rnaList.getSize() == 1)
+        {
+          RNA r = new RNA();
+          try
+          {
+            r.setRNA(" ", ".");
+          } catch (ExceptionUnmatchedClosingParentheses e1)
+          {
+          } catch (ExceptionFileFormatOrSyntax e1)
+          {
+          }
+          vp.showRNA(r);
+          vp.repaint();
+        }
+        else
+        {
+          int newi = i + 1;
+          if (newi == _rnaList.getSize())
+          {
+            newi = _rnaList.getSize() - 2;
+          }
+          FullBackup bck = (FullBackup) _rnaList.getElementAt(newi);
+          _l.setSelectedValue(bck, true);
+        }
+        _rnaList.remove(i);
+      }
+
+    }
+  }
+
+  public void onLayoutChanged()
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  public void onUINewStructure(VARNAConfig v, RNA r)
+  {
+    // 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)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  public void mouseClicked(MouseEvent e)
+  {
+    if (e.getClickCount() == 2)
+    {
+      int index = _sideList.locationToIndex(e.getPoint());
+      ListModel dlm = _sideList.getModel();
+      FullBackup item = (FullBackup) dlm.getElementAt(index);
       ;
-      console = null;
+      _sideList.ensureIndexIsVisible(index);
+      /*
+       * TODO Object newName = JOptionPane.showInputDialog( this,
+       * "Specify a new name for this RNA", "Rename RNA",
+       * JOptionPane.QUESTION_MESSAGE, (Icon)null, null, item.toString()); if
+       * (newName!=null) { item.name = newName.toString();
+       * this._sideList.repaint(); }
+       */
     }
+  }
+
+  public void mouseEntered(MouseEvent arg0)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  public void mouseExited(MouseEvent arg0)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  public void mousePressed(MouseEvent arg0)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  public void mouseReleased(MouseEvent arg0)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public Color getColour(int atomIndex, int pdbResNum, String chain,
+          String pdbId)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String[] getPdbFile()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
+          String pdbId)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void mouseOverStructure(int atomIndex, String strInfo)
+  {
+    // TODO Auto-generated method stub
 
   }
 
   @Override
   public void releaseReferences(Object svl)
   {
-    if (svl instanceof SeqPanel) {
-      appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
-      
-    };
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void updateColours(Object source)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void componentHidden(ComponentEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void componentMoved(ComponentEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void componentResized(ComponentEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void componentShown(ComponentEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void onStructureRedrawn()
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void onZoomLevelChanged()
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void onTranslationChanged()
+  {
+    // TODO Auto-generated method stub
+
   }
 }
+
+/*
+ * public static void main(String[] args) { JTextField str = new
+ * JTextField("ATGC");
+ * 
+ * AppVarnaBinding vab = new AppVarnaBinding(); vab.varnagui.set_seq(str);
+ * vab.varnagui.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+ * vab.varnagui.pack(); vab.varnagui.setVisible(true); } }
+ */