srcjar/fr/orsay/lri/varna/applications/VARNAEditor.java

   1 /*
   2  VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases.
   3  Copyright (C) 2008  Kevin Darty, Alain Denise and Yann Ponty.
   4  electronic mail : Yann.Ponty@lri.fr
   5  paper mail : LRI, bat 490 Université Paris-Sud 91405 Orsay Cedex France
   6
   7  This file is part of VARNA version 3.1.
   8  VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License
   9  as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10
  11  VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
  12  without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
  13  See the GNU General Public License for more details.
  14
  15  You should have received a copy of the GNU General Public License along with VARNA version 3.1.
  16  If not, see http://www.gnu.org/licenses.
  17  */
  18 package fr.orsay.lri.varna.applications;
  19
  20 import java.awt.BorderLayout;
  21 import java.awt.Color;
  22 import java.awt.Component;
  23 import java.awt.Dimension;
  24 import java.awt.Font;
  25 import java.awt.GridLayout;
  26 import java.awt.datatransfer.DataFlavor;
  27 import java.awt.datatransfer.Transferable;
  28 import java.awt.dnd.DnDConstants;
  29 import java.awt.dnd.DropTarget;
  30 import java.awt.dnd.DropTargetDragEvent;
  31 import java.awt.dnd.DropTargetDropEvent;
  32 import java.awt.dnd.DropTargetEvent;
  33 import java.awt.dnd.DropTargetListener;
  34 import java.awt.event.ActionEvent;
  35 import java.awt.event.ActionListener;
  36 import java.awt.event.MouseEvent;
  37 import java.awt.event.MouseListener;
  38 import java.awt.geom.Point2D.Double;
  39 import java.io.File;
  40 import java.text.DateFormat;
  41 import java.util.ArrayList;
  42 import java.util.Collection;
  43 import java.util.Date;
  44 import java.util.Hashtable;
  45 import java.util.List;
  46 import java.util.Set;
  47
  48 import javax.swing.DefaultListModel;
  49 import javax.swing.DefaultListSelectionModel;
  50 import javax.swing.Icon;
  51 import javax.swing.JButton;
  52 import javax.swing.JFrame;
  53 import javax.swing.JLabel;
  54 import javax.swing.JList;
  55 import javax.swing.JOptionPane;
  56 import javax.swing.JPanel;
  57 import javax.swing.JScrollPane;
  58 import javax.swing.JSplitPane;
  59 import javax.swing.JTextField;
  60 import javax.swing.ListModel;
  61 import javax.swing.ListSelectionModel;
  62 import javax.swing.UIManager;
  63 import javax.swing.UnsupportedLookAndFeelException;
  64 import javax.swing.event.ListSelectionEvent;
  65 import javax.swing.event.ListSelectionListener;
  66 import javax.swing.text.BadLocationException;
  67 import javax.swing.text.DefaultHighlighter;
  68
  69 import fr.orsay.lri.varna.VARNAPanel;
  70 import fr.orsay.lri.varna.components.ReorderableJList;
  71 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
  72 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
  73 import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
  74 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
  75 import fr.orsay.lri.varna.factories.RNAFactory;
  76 import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
  77 import fr.orsay.lri.varna.interfaces.InterfaceVARNARNAListener;
  78 import fr.orsay.lri.varna.interfaces.InterfaceVARNASelectionListener;
  79 import fr.orsay.lri.varna.models.BaseList;
  80 import fr.orsay.lri.varna.models.FullBackup;
  81 import fr.orsay.lri.varna.models.VARNAConfig;
  82 import fr.orsay.lri.varna.models.rna.Mapping;
  83 import fr.orsay.lri.varna.models.rna.ModeleBP;
  84 import fr.orsay.lri.varna.models.rna.ModeleBase;
  85 import fr.orsay.lri.varna.models.rna.RNA;
  86
  87 public class VARNAEditor extends JFrame implements DropTargetListener, InterfaceVARNAListener, MouseListener {
  88
  89         /**
  90          *
  91          */
  92 //      private static final_long serialVersionUID = -790155708306987257L;
  93
  94         private static final String DEFAULT_SEQUENCE = "CAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIA";
  95
  96         private static final String DEFAULT_STRUCTURE1 = "..(((((...(((((...(((((...(((((.....)))))...))))).....(((((...(((((.....)))))...))))).....)))))...)))))..";
  97         private static final String DEFAULT_STRUCTURE2 = "..(((((...(((((...(((((........(((((...(((((.....)))))...)))))..................))))).....)))))...)))))..";
  98         // private static final String DEFAULT_STRUCTURE1 = "((((....))))";
  99         // private static final String DEFAULT_STRUCTURE2 =
 100         // "((((..(((....)))..))))";
 101
 102         private VARNAPanel _vp;
 103
 104         private JPanel _tools = new JPanel();
 105         private JPanel _input = new JPanel();
 106
 107         private JPanel _seqPanel = new JPanel();
 108         private JPanel _strPanel = new JPanel();
 109         private JLabel _info = new JLabel();
 110
 111         private JTextField _str = new JTextField(DEFAULT_STRUCTURE1);
 112         Object _hoverHighlightStr = null;
 113         ArrayList<Object> _selectionHighlightStr = new ArrayList<Object>();
 114
 115         private JTextField _seq = new JTextField(DEFAULT_SEQUENCE);
 116         Object _hoverHighlightSeq = null;
 117         ArrayList<Object> _selectionHighlightSeq = new ArrayList<Object>();
 118
 119
 120         private JLabel _strLabel = new JLabel(" Str:");
 121         private JLabel _seqLabel = new JLabel(" Seq:");
 122         private JButton _deleteButton = new JButton("Delete");
 123         private JButton _duplicateButton = new JButton("Duplicate");
 124
 125         private JPanel _listPanel = new JPanel();
 126         private ReorderableJList _sideList = null;
 127
 128
 129
 130         private static String errorOpt = "error";
 131         @SuppressWarnings("unused")
 132         private boolean _error;
 133
 134         private Color _backgroundColor = Color.white;
 135
 136         private static int _nextID = 1;
 137         @SuppressWarnings("unused")
 138         private int _algoCode;
 139
 140         private BackupHolder _rnaList;
 141
 142
 143         public VARNAEditor() {
 144                 super("VARNA Editor");
 145                 RNAPanelDemoInit();
 146         }
 147
 148         private void RNAPanelDemoInit()
 149         {
 150             DefaultListModel dlm = new DefaultListModel();
 151
 152
 153                 int marginTools = 40;
 154
 155             DefaultListSelectionModel m = new DefaultListSelectionModel();
 156             m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 157             m.setLeadAnchorNotificationEnabled(false);
 158
 159
 160                 _sideList = new ReorderableJList();
 161                 _sideList.setModel(dlm);
 162                 _sideList.addMouseListener(this);
 163             _sideList.setSelectionModel(m);
 164             _sideList.setPreferredSize(new Dimension(100, 0));
 165             _sideList.addListSelectionListener( new ListSelectionListener(){
 166                         public void valueChanged(ListSelectionEvent arg0) {
 167                                 //System.out.println(arg0);
 168                                 if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
 169                                 {
 170                                         FullBackup  sel = (FullBackup) _sideList.getSelectedValue();
 171                                         Mapping map = Mapping.DefaultOutermostMapping(_vp.getRNA().getSize(), sel.rna.getSize());
 172                                         _vp.showRNAInterpolated(sel.rna,sel.config,map);
 173                                         _seq.setText(sel.rna.getSeq());
 174                                         _str.setText(sel.rna.getStructDBN(true));
 175                                 }
 176                         }
 177             });
 178
 179             _rnaList = new BackupHolder(dlm,_sideList);
 180                 RNA _RNA1 = new RNA("User defined 1");
 181                 RNA _RNA2 = new RNA("User defined 2");
 182                 try {
 183                         _vp = new VARNAPanel("0",".");
 184                         _RNA1.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE1);
 185                         _RNA1.drawRNARadiate(_vp.getConfig());
 186                         _RNA2.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE2);
 187                         _RNA2.drawRNARadiate(_vp.getConfig());
 188                 } catch (ExceptionNonEqualLength e) {
 189                         _vp.errorDialog(e);
 190                 } catch (ExceptionUnmatchedClosingParentheses e2) {
 191                 e2.printStackTrace();
 192                 } catch (ExceptionFileFormatOrSyntax e3) {
 193                 e3.printStackTrace();
 194                 }
 195                 _vp.setPreferredSize(new Dimension(400, 400));
 196                 //
 197
 198                  // BH 2018 this will NOT be a clone in SwingJS
 199             _rnaList.add(_vp.getConfig().clone(),_RNA2,generateDefaultName());
 200             _rnaList.add(_vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
 201
 202             JScrollPane listScroller = new JScrollPane(_sideList);
 203             listScroller.setPreferredSize(new Dimension(150, 0));
 204
 205                 setBackground(_backgroundColor);
 206                 _vp.setBackground(_backgroundColor);
 207
 208
 209                 Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
 210
 211                 _seqLabel.setHorizontalTextPosition(JLabel.LEFT);
 212                 _seqLabel.setPreferredSize(new Dimension(marginTools, 15));
 213                 _seq.setFont(textFieldsFont);
 214                 _seq.setText(DEFAULT_SEQUENCE);
 215                 _seq.setEditable(false);
 216
 217
 218                 _seqPanel.setLayout(new BorderLayout());
 219                 _seqPanel.add(_seqLabel, BorderLayout.WEST);
 220                 _seqPanel.add(_seq, BorderLayout.CENTER);
 221
 222                 _strLabel.setPreferredSize(new Dimension(marginTools, 15));
 223                 _strLabel.setHorizontalTextPosition(JLabel.LEFT);
 224                 _str.setFont(textFieldsFont);
 225                 _str.setEditable(false);
 226                 _strPanel.setLayout(new BorderLayout());
 227                 _strPanel.add(_strLabel, BorderLayout.WEST);
 228                 _strPanel.add(_str, BorderLayout.CENTER);
 229
 230                 _input.setLayout(new GridLayout(2, 0));
 231                 _input.add(_seqPanel);
 232                 _input.add(_strPanel);
 233
 234
 235                 _tools.setLayout(new BorderLayout());
 236                 _tools.add(_input, BorderLayout.CENTER);
 237                 _tools.add(_info, BorderLayout.SOUTH);
 238
 239                 _deleteButton.addActionListener(new ActionListener() {
 240                         public void actionPerformed(ActionEvent e) {
 241                                 _rnaList.removeSelected();
 242                         }
 243                 });
 244 //              _duplicateButton.addActionListener(new ActionListener() {
 245 //                      public void actionPerformed(ActionEvent e) {
 246 //                                      _rnaList.add((VARNAConfig)_vp.getConfig().clone(),_vp.getRNA().clone(),_vp.getRNA().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new Date()),true);
 247 //                      }});
 248
 249                 JPanel ops = new JPanel();
 250                 ops.setLayout(new GridLayout(1,2));
 251                 ops.add(_deleteButton);
 252                 ops.add(_duplicateButton);
 253
 254                 JLabel j = new JLabel("Structures",JLabel.CENTER);
 255                 _listPanel.setLayout(new BorderLayout());
 256
 257                 _listPanel.add(ops,BorderLayout.SOUTH);
 258                 _listPanel.add(j,BorderLayout.NORTH);
 259                 _listPanel.add(listScroller,BorderLayout.CENTER);
 260
 261
 262                 JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,_vp);
 263                 getContentPane().setLayout(new BorderLayout());
 264                 getContentPane().add(split, BorderLayout.CENTER);
 265                 getContentPane().add(_tools, BorderLayout.NORTH);
 266
 267                 setVisible(true);
 268                 DropTarget dt = new DropTarget(_vp, this);
 269
 270                 _vp.addRNAListener(new InterfaceVARNARNAListener(){
 271                         public void onSequenceModified(int index, String oldseq, String newseq) {
 272                                 _seq.setText(_vp.getRNA().getSeq());
 273                         }
 274
 275                         public void onStructureModified(Set<ModeleBP> current,
 276                                         Set<ModeleBP> addedBasePairs, Set<ModeleBP> removedBasePairs) {
 277                                 _str.setText(_vp.getRNA().getStructDBN(true));
 278                         }
 279
 280                         public void onRNALayoutChanged(Hashtable<Integer, Double> previousPositions) {
 281                         }
 282
 283                 });
 284
 285                 _vp.addSelectionListener(new InterfaceVARNASelectionListener(){
 286
 287                         public void onHoverChanged(ModeleBase oldbase, ModeleBase newBase) {
 288                                 if (_hoverHighlightSeq!=null)
 289                                 {
 290                                         _seq.getHighlighter().removeHighlight(_hoverHighlightSeq);
 291                                         _hoverHighlightSeq = null;
 292                                 }
 293                                 if (_hoverHighlightStr!=null)
 294                                 {
 295                                         _str.getHighlighter().removeHighlight(_hoverHighlightStr);
 296                                         _hoverHighlightStr = null;
 297                                 }
 298                                 if (newBase!=null)
 299                                 {
 300                                         try {
 301                                                 _hoverHighlightSeq = _seq.getHighlighter().addHighlight(newBase.getIndex(), newBase.getIndex()+1, new DefaultHighlighter.DefaultHighlightPainter(Color.green) );
 302                                                 _hoverHighlightStr = _str.getHighlighter().addHighlight(newBase.getIndex(), newBase.getIndex()+1, new DefaultHighlighter.DefaultHighlightPainter(Color.green) );
 303                                         } catch (BadLocationException e) {
 304                                                 e.printStackTrace();
 305                                         }
 306                                 }
 307                         }
 308
 309                         public void onSelectionChanged(BaseList selection,
 310                                         BaseList addedBases, BaseList removedBases) {
 311                                 for(Object tag: _selectionHighlightSeq)
 312                                 {
 313                                         _seq.getHighlighter().removeHighlight(tag);
 314                                 }
 315                                 _selectionHighlightSeq.clear();
 316                                 for(Object tag: _selectionHighlightStr)
 317                                 {
 318                                         _str.getHighlighter().removeHighlight(tag);
 319                                 }
 320                                 _selectionHighlightStr.clear();
 321                                 for (ModeleBase m: selection.getBases())
 322                                 {
 323                                         try {
 324                                                 _selectionHighlightSeq.add(_seq.getHighlighter().addHighlight(m.getIndex(), m.getIndex()+1, new DefaultHighlighter.DefaultHighlightPainter(Color.orange) ));
 325                                                 _selectionHighlightStr.add(_str.getHighlighter().addHighlight(m.getIndex(), m.getIndex()+1, new DefaultHighlighter.DefaultHighlightPainter(Color.orange) ));
 326                                         } catch (BadLocationException e) {
 327                                                 e.printStackTrace();
 328                                         }
 329                                 }
 330                         }
 331
 332                 });
 333
 334                 _vp.addVARNAListener(this);
 335         }
 336
 337         public static String generateDefaultName()
 338         {
 339                 return "User file #"+_nextID++;
 340         }
 341
 342         public RNA getRNA() {
 343                 return (RNA)_sideList.getSelectedValue();
 344         }
 345
 346
 347
 348         public String[][] getParameterInfo() {
 349                 String[][] info = {
 350                                 // Parameter Name Kind of Value Description,
 351                                 { "sequenceDBN", "String", "A raw RNA sequence" },
 352                                 { "structureDBN", "String",
 353                                                 "An RNA structure in dot bracket notation (DBN)" },
 354                                 { errorOpt, "boolean", "To show errors" }, };
 355                 return info;
 356         }
 357
 358         public void init() {
 359                 _vp.setBackground(_backgroundColor);
 360                 _error = true;
 361         }
 362
 363         @SuppressWarnings("unused")
 364         private Color getSafeColor(String col, Color def) {
 365                 Color result;
 366                 try {
 367                         result = Color.decode(col);
 368                 } catch (Exception e) {
 369                         try {
 370                                 result = Color.getColor(col, def);
 371                         } catch (Exception e2) {
 372                                 return def;
 373                         }
 374                 }
 375                 return result;
 376         }
 377
 378         public VARNAPanel get_varnaPanel() {
 379                 return _vp;
 380         }
 381
 382         public void set_varnaPanel(VARNAPanel surface) {
 383                 _vp = surface;
 384         }
 385
 386
 387         public JTextField get_seq() {
 388                 return _seq;
 389         }
 390
 391         public void set_seq(JTextField _seq) {
 392                 this._seq = _seq;
 393         }
 394
 395         public JLabel get_info() {
 396                 return _info;
 397         }
 398
 399         public void set_info(JLabel _info) {
 400                 this._info = _info;
 401         }
 402
 403         public static void main(String[] args) {
 404                 VARNAEditor d = new VARNAEditor();
 405                 d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
 406                 d.pack();
 407                 d.setVisible(true);
 408         }
 409
 410
 411         public void dragEnter(DropTargetDragEvent arg0) {
 412                 // TODO Auto-generated method stub
 413
 414         }
 415
 416         public void dragExit(DropTargetEvent arg0) {
 417                 // TODO Auto-generated method stub
 418
 419         }
 420
 421         public void dragOver(DropTargetDragEvent arg0) {
 422                 // TODO Auto-generated method stub
 423
 424         }
 425
 426         public void drop(DropTargetDropEvent dtde) {
 427             try {
 428                 Transferable tr = dtde.getTransferable();
 429                 DataFlavor[] flavors = tr.getTransferDataFlavors();
 430                 for (int i = 0; i < flavors.length; i++) {
 431             if (flavors[i].isFlavorJavaFileListType()) {
 432               dtde.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
 433               Object ob = tr.getTransferData(flavors[i]);
 434               if (ob instanceof List)
 435               {
 436                   List list = (List) ob;
 437                   for (int j = 0; j < list.size(); j++) {
 438                   Object o = list.get(j);
 439
 440                   if (dtde.getSource() instanceof DropTarget)
 441                   {
 442                           DropTarget dt = (DropTarget) dtde.getSource();
 443                           Component c = dt.getComponent();
 444                           if (c instanceof VARNAPanel)
 445                           {
 446                                           String path = o.toString();
 447                                   VARNAPanel vp = (VARNAPanel) c;
 448                                           try{
 449                                   FullBackup bck =  VARNAPanel.importSession((File) o); // BH SwingJS
 450                                   _rnaList.add(bck.config, bck.rna,bck.name,true);
 451                                           }
 452                                           catch (ExceptionLoadingFailed e3)
 453                                           {
 454                                                   Collection<RNA> rnas = RNAFactory.loadSecStr((File) o); // BH SwingJS
 455                                                   if (rnas.isEmpty())
 456                                                   {
 457                                                           throw new ExceptionFileFormatOrSyntax("No RNA could be parsed from that source.");
 458                                                   }
 459
 460                                                   int id = 1;
 461                                                   for(RNA r: rnas)
 462                                                   {
 463                                                           r.drawRNA(vp.getConfig());
 464                                                           String name = r.getName();
 465                                                           if (name.equals(""))
 466                                                           {
 467                                                                   name = path.substring(path.lastIndexOf(File.separatorChar)+1);
 468                                                           }
 469                                                           if (rnas.size()>1)
 470                                                           {
 471                                                                   name += " - Molecule# "+id++;
 472                                                           }
 473                                                           _rnaList.add(vp.getConfig().clone(),r,name,true);
 474                                                   }
 475                                           }
 476                           }
 477                   }
 478                   }
 479               }
 480               // If we made it this far, everything worked.
 481               dtde.dropComplete(true);
 482               return;
 483             }
 484                 }
 485                 // Hmm, the user must not have dropped a file list
 486                 dtde.rejectDrop();
 487               } catch (Exception e) {
 488                 e.printStackTrace();
 489                 dtde.rejectDrop();
 490               }
 491
 492         }
 493
 494         public void dropActionChanged(DropTargetDragEvent arg0) {
 495         }
 496
 497         private class BackupHolder{
 498                 private DefaultListModel _rnaList;
 499                 private ArrayList<RNA> _rnas = new ArrayList<RNA>();
 500                 JList _l;
 501
 502                 public BackupHolder(DefaultListModel rnaList, JList l)
 503                 {
 504                         _rnaList = rnaList;
 505                         _l = l;
 506                 }
 507
 508                 public void add(VARNAConfig c, RNA r)
 509                 {
 510                         add(c, r, r.getName(),false);
 511                 }
 512
 513                 public void add(VARNAConfig c, RNA r,boolean select)
 514                 {
 515                         add(c, r, r.getName(),select);
 516                 }
 517
 518                 public void add(VARNAConfig c, RNA r, String name)
 519                 {
 520                         add(c, r, name,false);
 521                 }
 522                 public void add(VARNAConfig c, RNA r, String name, boolean select)
 523                 {
 524                         if (select){
 525                                 _l.removeSelectionInterval(0, _rnaList.size());
 526                         }
 527                         if (name.equals(""))
 528                         {
 529                                 name = generateDefaultName();
 530                         }
 531                         FullBackup bck = new FullBackup(c,r,name);
 532                         _rnas.add(0, r);
 533                         _rnaList.add(0,bck);
 534                         if (select){
 535                           _l.setSelectedIndex(0);
 536                         }
 537                 }
 538
 539                 public void remove(int i)
 540                 {
 541                         _rnas.remove(i);
 542                         _rnaList.remove(i);
 543
 544                 }
 545                 public DefaultListModel getModel()
 546                 {
 547                         return _rnaList;
 548                 }
 549                 public boolean contains(RNA r)
 550                 {
 551                         return _rnas.contains(r);
 552                 }
 553                 /*public int getSize()
 554                 {
 555                         return _rnaList.getSize();
 556                 }*/
 557                 public FullBackup getElementAt(int i)
 558                 {
 559                         return (FullBackup) _rnaList.getElementAt(i);
 560                 }
 561
 562                 public void removeSelected()
 563                 {
 564                         int i = _l.getSelectedIndex();
 565                         if (i!=-1)
 566                         {
 567                           if (_rnaList.getSize()==1)
 568                           {
 569                                   RNA r = new RNA();
 570                                   try {
 571                                         r.setRNA(" ", ".");
 572                                   } catch (ExceptionUnmatchedClosingParentheses e1) {
 573                                   } catch (ExceptionFileFormatOrSyntax e1) {
 574                                   }
 575                                   _vp.showRNA(r);
 576                                   _vp.repaint();
 577                           }
 578                           else
 579                           {
 580                                  int newi = i+1;
 581                                  if (newi==_rnaList.getSize())
 582                                  {
 583                                          newi = _rnaList.getSize()-2;
 584                                  }
 585                                  FullBackup bck = (FullBackup) _rnaList.getElementAt(newi);
 586                                  _l.setSelectedValue(bck,true);
 587                           }
 588                           _rnaList.remove(i);
 589                         }
 590
 591                 }
 592         }
 593
 594         public void onStructureRedrawn() {
 595                 // TODO Auto-generated method stub
 596
 597         }
 598
 599         public void onUINewStructure(VARNAConfig v, RNA r) {
 600                 _rnaList.add(v, r,"",true);
 601         }
 602
 603         public void onWarningEmitted(String s) {
 604                 // TODO Auto-generated method stub
 605
 606         }
 607
 608         public void mouseClicked(MouseEvent e) {
 609                            if(e.getClickCount() == 2){
 610                              int index = _sideList.locationToIndex(e.getPoint());
 611                              ListModel dlm = _sideList.getModel();
 612                              FullBackup item = (FullBackup) dlm.getElementAt(index);;
 613                              _sideList.ensureIndexIsVisible(index);
 614                              Object newName = JOptionPane.showInputDialog(
 615                                             this,
 616                                             "Specify a new name for this RNA",
 617                                             "Rename RNA",
 618                                             JOptionPane.QUESTION_MESSAGE,
 619                                             (Icon)null,
 620                                             null,
 621                                             item.toString());
 622                              if (newName!=null)
 623                              {
 624                                  item.name = newName.toString();
 625                                  this._sideList.repaint();
 626                              }
 627                              }
 628         }
 629
 630         public void mouseEntered(MouseEvent arg0) {
 631                 // TODO Auto-generated method stub
 632
 633         }
 634
 635         public void mouseExited(MouseEvent arg0) {
 636                 // TODO Auto-generated method stub
 637
 638         }
 639
 640         public void mousePressed(MouseEvent arg0) {
 641                 // TODO Auto-generated method stub
 642
 643         }
 644
 645         public void mouseReleased(MouseEvent arg0) {
 646                 // TODO Auto-generated method stub
 647
 648         }
 649
 650         public void onZoomLevelChanged() {
 651                 // TODO Auto-generated method stub
 652
 653         }
 654
 655         public void onTranslationChanged() {
 656                 // TODO Auto-generated method stub
 657
 658         }
 659 }