srcjar/fr/orsay/lri/varna/applications/VARNAGUI.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.Image;
  27 import java.awt.Point;
  28 import java.awt.Rectangle;
  29 import java.awt.Toolkit;
  30 import java.awt.datatransfer.DataFlavor;
  31 import java.awt.datatransfer.Transferable;
  32 import java.awt.dnd.DnDConstants;
  33 import java.awt.dnd.DropTarget;
  34 import java.awt.dnd.DropTargetDragEvent;
  35 import java.awt.dnd.DropTargetDropEvent;
  36 import java.awt.dnd.DropTargetEvent;
  37 import java.awt.dnd.DropTargetListener;
  38 import java.awt.event.ActionEvent;
  39 import java.awt.event.ActionListener;
  40 import java.awt.event.AdjustmentEvent;
  41 import java.awt.event.AdjustmentListener;
  42 import java.awt.event.MouseEvent;
  43 import java.awt.event.MouseListener;
  44 import java.awt.geom.Point2D.Double;
  45 import java.io.File;
  46 import java.text.DateFormat;
  47 import java.util.ArrayList;
  48 import java.util.Collection;
  49 import java.util.Date;
  50 import java.util.Hashtable;
  51 import java.util.List;
  52 import java.util.Set;
  53
  54 import javax.swing.DefaultListModel;
  55 import javax.swing.DefaultListSelectionModel;
  56 import javax.swing.Icon;
  57 import javax.swing.JButton;
  58 import javax.swing.JFrame;
  59 import javax.swing.JLabel;
  60 import javax.swing.JList;
  61 import javax.swing.JOptionPane;
  62 import javax.swing.JPanel;
  63 import javax.swing.JScrollBar;
  64 import javax.swing.JScrollPane;
  65 import javax.swing.JSplitPane;
  66 import javax.swing.JTextField;
  67 import javax.swing.ListModel;
  68 import javax.swing.ListSelectionModel;
  69 import javax.swing.UIManager;
  70 import javax.swing.UnsupportedLookAndFeelException;
  71 import javax.swing.event.ListSelectionEvent;
  72 import javax.swing.event.ListSelectionListener;
  73 import javax.swing.text.BadLocationException;
  74 import javax.swing.text.DefaultHighlighter;
  75
  76 import fr.orsay.lri.varna.VARNAPanel;
  77 import fr.orsay.lri.varna.components.ReorderableJList;
  78 import fr.orsay.lri.varna.components.ZoomWindow;
  79 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
  80 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
  81 import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
  82 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
  83 import fr.orsay.lri.varna.factories.RNAFactory;
  84 import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
  85 import fr.orsay.lri.varna.interfaces.InterfaceVARNARNAListener;
  86 import fr.orsay.lri.varna.interfaces.InterfaceVARNASelectionListener;
  87 import fr.orsay.lri.varna.models.BaseList;
  88 import fr.orsay.lri.varna.models.FullBackup;
  89 import fr.orsay.lri.varna.models.VARNAConfig;
  90 import fr.orsay.lri.varna.models.rna.Mapping;
  91 import fr.orsay.lri.varna.models.rna.ModeleBP;
  92 import fr.orsay.lri.varna.models.rna.ModeleBase;
  93 import fr.orsay.lri.varna.models.rna.RNA;
  94
  95 public class VARNAGUI extends JFrame implements DropTargetListener, InterfaceVARNAListener, MouseListener, AdjustmentListener {
  96
  97         /**
  98          *
  99          */
 100         private static final long serialVersionUID = -790155708306987257L;
 101
 102         private static final String DEFAULT_SEQUENCE = "CAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIA";
 103
 104         private static final String DEFAULT_STRUCTURE1 = "..(((((...(((((...(((((...(((((.....)))))...))))).....(((((...(((((.....)))))...))))).....)))))...)))))..";
 105         private static final String DEFAULT_STRUCTURE2 = "..(((((...(((((...(((((........(((((...(((((.....)))))...)))))..................))))).....)))))...)))))..";
 106         // private static final String DEFAULT_STRUCTURE1 = "((((....))))";
 107         // private static final String DEFAULT_STRUCTURE2 =
 108         // "((((..(((....)))..))))";
 109
 110         private VARNAPanel _vp;
 111
 112         private JPanel _tools = new JPanel();
 113         private JPanel _input = new JPanel();
 114
 115         private JPanel _seqPanel = new JPanel();
 116         private JPanel _strPanel = new JPanel();
 117         private JLabel _info = new JLabel();
 118
 119         private JTextField _str = new JTextField(DEFAULT_STRUCTURE1);
 120         Object _hoverHighlightStr = null;
 121         ArrayList<Object> _selectionHighlightStr = new ArrayList<Object>();
 122
 123         private JTextField _seq = new JTextField(DEFAULT_SEQUENCE);
 124         Object _hoverHighlightSeq = null;
 125         ArrayList<Object> _selectionHighlightSeq = new ArrayList<Object>();
 126
 127
 128         private ZoomWindow _zoomWindow;
 129         private JLabel _strLabel = new JLabel(" Str:");
 130         private JLabel _seqLabel = new JLabel(" Seq:");
 131         private JButton _createButton = new JButton("Create");
 132         private JButton _deleteButton = new JButton("Delete");
 133         private JButton _duplicateButton = new JButton("Snapshot");
 134
 135         private JPanel _listPanel = new JPanel();
 136         private ReorderableJList _sideList = null;
 137
 138
 139         private static String errorOpt = "error";
 140         @SuppressWarnings("unused")
 141         private boolean _error;
 142
 143         private Color _backgroundColor = Color.white;
 144
 145         private JScrollBar _vert = new JScrollBar(JScrollBar.VERTICAL);
 146         private JScrollBar _horiz = new JScrollBar(JScrollBar.HORIZONTAL);
 147
 148         private static int _nextID = 1;
 149         @SuppressWarnings("unused")
 150         private int _algoCode;
 151
 152         private BackupHolder _rnaList;
 153
 154
 155         public VARNAGUI() {
 156                 super("VARNA GUI");
 157                 RNAPanelDemoInit();
 158         }
 159
 160         private void RNAPanelDemoInit()
 161         {
 162             DefaultListModel dlm = new DefaultListModel();
 163
 164
 165                 int marginTools = 40;
 166
 167             DefaultListSelectionModel m = new DefaultListSelectionModel();
 168             m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 169             m.setLeadAnchorNotificationEnabled(false);
 170
 171
 172                 _sideList = new ReorderableJList();
 173                 _sideList.setModel(dlm);
 174                 _sideList.addMouseListener(this);
 175             _sideList.setSelectionModel(m);
 176             _sideList.setPreferredSize(null);
 177
 178             _sideList.addListSelectionListener( new ListSelectionListener(){
 179                         public void valueChanged(ListSelectionEvent arg0) {
 180                                 //System.out.println(arg0);
 181                                 if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
 182                                 {
 183                                         FullBackup  sel = (FullBackup) _sideList.getSelectedValue();
 184                                         _vp.setConfig(sel.config);
 185                                         showRNA(sel.rna);
 186                                         _seq.setText(sel.rna.getSeq());
 187                                         _str.setText(sel.rna.getStructDBN(true));
 188                                 }
 189                         }
 190             });
 191
 192             _rnaList = new BackupHolder(dlm,_sideList);
 193                 RNA _RNA1 = new RNA("User defined 1");
 194                 RNA _RNA2 = new RNA("User defined 2");
 195                 try {
 196                         _vp = new VARNAPanel("0",".");
 197                         _zoomWindow = new ZoomWindow(_vp);
 198                         _RNA1.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE1);
 199                         _RNA1.drawRNARadiate(_vp.getConfig());
 200                         _RNA2.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE2);
 201                         _RNA2.drawRNARadiate(_vp.getConfig());
 202                 } catch (ExceptionNonEqualLength e) {
 203                         _vp.errorDialog(e);
 204                 } catch (ExceptionUnmatchedClosingParentheses e2) {
 205                 e2.printStackTrace();
 206                 } catch (ExceptionFileFormatOrSyntax e3) {
 207                 e3.printStackTrace();
 208                 }
 209                 _vp.setPreferredSize(new Dimension(400, 400));
 210             _rnaList.add(_vp.getConfig().clone(),_RNA2,generateDefaultName());
 211             _rnaList.add(_vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
 212
 213
 214             JScrollPane listScroller = new JScrollPane(_sideList);//,JScrollPane.VERTICAL_SCROLLBAR_ALWAYS,JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
 215             listScroller.setPreferredSize(new Dimension(150, 0));
 216
 217                 setBackground(_backgroundColor);
 218                 _vp.setBackground(_backgroundColor);
 219
 220
 221                 Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
 222
 223                 _seqLabel.setHorizontalTextPosition(JLabel.LEFT);
 224                 _seqLabel.setPreferredSize(new Dimension(marginTools, 15));
 225                 _seq.setFont(textFieldsFont);
 226                 _seq.setText(DEFAULT_SEQUENCE);
 227
 228                 _createButton.addActionListener(new ActionListener() {
 229                         public void actionPerformed(ActionEvent e) {
 230                                 try {
 231                                 RNA nRNA = new RNA(generateDefaultName());
 232                                 nRNA.setRNA(_seq.getText(), _str.getText());
 233                                 nRNA.drawRNARadiate(_vp.getConfig());
 234                                 _rnaList.add(new VARNAConfig(),nRNA,true);
 235                                 } catch (ExceptionUnmatchedClosingParentheses e1) {
 236                                         JOptionPane.showMessageDialog(_vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
 237                                 } catch (ExceptionFileFormatOrSyntax e1) {
 238                                         JOptionPane.showMessageDialog(_vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
 239                                 }
 240                         }
 241                 });
 242
 243
 244                 _seqPanel.setLayout(new BorderLayout());
 245                 _seqPanel.add(_seqLabel, BorderLayout.WEST);
 246                 _seqPanel.add(_seq, BorderLayout.CENTER);
 247
 248                 _strLabel.setPreferredSize(new Dimension(marginTools, 15));
 249                 _strLabel.setHorizontalTextPosition(JLabel.LEFT);
 250                 _str.setFont(textFieldsFont);
 251                 _strPanel.setLayout(new BorderLayout());
 252                 _strPanel.add(_strLabel, BorderLayout.WEST);
 253                 _strPanel.add(_str, BorderLayout.CENTER);
 254
 255                 _input.setLayout(new GridLayout(2, 0));
 256                 _input.add(_seqPanel);
 257                 _input.add(_strPanel);
 258
 259                 JPanel goPanel = new JPanel();
 260                 goPanel.setLayout(new BorderLayout());
 261
 262                 _tools.setLayout(new BorderLayout());
 263                 _tools.add(_input, BorderLayout.CENTER);
 264                 _tools.add(_info, BorderLayout.SOUTH);
 265                 _tools.add(goPanel, BorderLayout.EAST);
 266
 267                 _deleteButton.addActionListener(new ActionListener() {
 268                         public void actionPerformed(ActionEvent e) {
 269                                 _rnaList.removeSelected();
 270                         }
 271                 });
 272                 // BH 2018 SwingJS can't clone, as it does not implement serialization
 273                 if (/** @j2sNative false && */ true)
 274                 _duplicateButton.addActionListener(new ActionListener() {
 275                         public void actionPerformed(ActionEvent e) {
 276                                         _rnaList.add((VARNAConfig)_vp.getConfig().clone(),_vp.getRNA().clone(),_vp.getRNA().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new Date()),true);
 277                         }});
 278
 279                 JPanel ops = new JPanel();
 280                 ops.setLayout(new GridLayout(1,2));
 281                 ops.add(_deleteButton);
 282                 ops.add(_duplicateButton);
 283
 284                 JPanel opspanel = new JPanel(new BorderLayout());
 285                 opspanel.add(ops,BorderLayout.NORTH);
 286                 opspanel.add(_zoomWindow,BorderLayout.SOUTH);
 287
 288                 _zoomWindow.setPreferredSize(new Dimension(-1,200));
 289
 290
 291                 JLabel j = new JLabel("Structure Manager",JLabel.CENTER);
 292                 _listPanel.setLayout(new BorderLayout());
 293
 294                 _listPanel.add(opspanel,BorderLayout.SOUTH);
 295                 _listPanel.add(j,BorderLayout.NORTH);
 296                 _listPanel.add(listScroller,BorderLayout.CENTER);
 297
 298                 goPanel.add(_createButton, BorderLayout.CENTER);
 299
 300                 JPanel vpScroll = new JPanel();
 301                 vpScroll.setLayout(new BorderLayout());
 302                 _horiz.setVisible(false);
 303                 _horiz.addAdjustmentListener(this);
 304                 _vert.setVisible(false);
 305                 _vert.addAdjustmentListener(this);
 306                 vpScroll.add(_horiz,BorderLayout.SOUTH);
 307                 vpScroll.add(_vert,BorderLayout.EAST);
 308                 vpScroll.add(_vp,BorderLayout.CENTER);
 309                 JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,vpScroll);
 310                 getContentPane().setLayout(new BorderLayout());
 311                 getContentPane().add(split, BorderLayout.CENTER);
 312                 getContentPane().add(_tools, BorderLayout.NORTH);
 313
 314
 315                 setVisible(true);
 316                 DropTarget dt = new DropTarget(_vp, this);
 317
 318                 _vp.addRNAListener(new InterfaceVARNARNAListener(){
 319                         public void onSequenceModified(int index, String oldseq, String newseq) {
 320                                 //System.out.println("Sequence changed: Index:"+index+" ["+oldseq+"]=>["+newseq+"]");
 321                         }
 322
 323                         public void onStructureModified(Set<ModeleBP> current,
 324                                         Set<ModeleBP> addedBasePairs, Set<ModeleBP> removedBasePairs) {
 325                                 String result = "";
 326                                 //System.out.println("Structure changed: ");
 327                                 for (ModeleBP s:addedBasePairs)
 328                                 {  result +=s;  }
 329                                 //System.out.println("     Added: "+result);
 330                                 result = "";
 331                                 for (ModeleBP s:removedBasePairs)
 332                                 {  result +=s;  }
 333                                 //System.out.println("   Removed: "+result);
 334                         }
 335
 336                         public void onRNALayoutChanged(Hashtable<Integer, Double> previousPositions) {
 337                                 //System.out.print("Layout changed, bases#: ");
 338                                 String result = "";
 339                                 for (Integer s:previousPositions.keySet())
 340                                 {  result +=s+" ";  }
 341                                 //System.out.println(result);
 342                         }
 343
 344                 });
 345
 346                 _vp.addSelectionListener(new InterfaceVARNASelectionListener(){
 347
 348                         public void onHoverChanged(ModeleBase oldbase, ModeleBase newBase) {
 349                                 if (_hoverHighlightSeq!=null)
 350                                 {
 351                                         _seq.getHighlighter().removeHighlight(_hoverHighlightSeq);
 352                                         _hoverHighlightSeq = null;
 353                                 }
 354                                 if (_hoverHighlightStr!=null)
 355                                 {
 356                                         _str.getHighlighter().removeHighlight(_hoverHighlightStr);
 357                                         _hoverHighlightStr = null;
 358                                 }
 359                                 if (newBase!=null)
 360                                 {
 361                                         try {
 362                                                 int i = newBase.getIndex();
 363                                                 int[] shifts = _vp.getRNA().getStrandShifts();
 364                                                 _hoverHighlightSeq = _seq.getHighlighter().addHighlight(i+shifts[i], i+shifts[i]+1, new DefaultHighlighter.DefaultHighlightPainter(Color.green) );
 365                                                 _hoverHighlightStr = _str.getHighlighter().addHighlight(i+shifts[i], i+shifts[i]+1, new DefaultHighlighter.DefaultHighlightPainter(Color.green) );
 366                                         } catch (BadLocationException e) {
 367                                                 e.printStackTrace();
 368                                         }
 369                                 }
 370                         }
 371
 372                         public void onSelectionChanged(BaseList selection,
 373                                         BaseList addedBases, BaseList removedBases) {
 374                                 for(Object tag: _selectionHighlightSeq)
 375                                 {
 376                                         _seq.getHighlighter().removeHighlight(tag);
 377                                 }
 378                                 _selectionHighlightSeq.clear();
 379                                 for(Object tag: _selectionHighlightStr)
 380                                 {
 381                                         _str.getHighlighter().removeHighlight(tag);
 382                                 }
 383                                 _selectionHighlightStr.clear();
 384                                 int[] shifts = _vp.getRNA().getStrandShifts();
 385                                 for (ModeleBase m: selection.getBases())
 386                                 {
 387                                         try {
 388                                                 int i = m.getIndex();
 389                                                 _selectionHighlightSeq.add(_seq.getHighlighter().addHighlight(i+shifts[i], i+shifts[i]+1, new DefaultHighlighter.DefaultHighlightPainter(Color.orange) ));
 390                                                 _selectionHighlightStr.add(_str.getHighlighter().addHighlight(i+shifts[i], i+shifts[i]+1, new DefaultHighlighter.DefaultHighlightPainter(Color.orange) ));
 391                                         } catch (BadLocationException e) {
 392                                                 e.printStackTrace();
 393                                         }
 394                                 }
 395                         }
 396
 397                 });
 398
 399                 _vp.addVARNAListener(this);
 400
 401                 new Thread(_zoomWindow).start();
 402         }
 403
 404         protected void showRNA(RNA rna) {
 405                 _vp.showRNAInterpolated(rna);
 406                 _zoomWindow.repaint();
 407         }
 408
 409
 410         public void addRNA(RNA r, VARNAConfig cfg)
 411         {
 412                 _rnaList.add(cfg,r);
 413         }
 414
 415         public static String generateDefaultName()
 416         {
 417                 return "User file #"+_nextID++;
 418         }
 419
 420         public RNA getRNA() {
 421                 return (RNA)_sideList.getSelectedValue();
 422         }
 423
 424
 425
 426         public String[][] getParameterInfo() {
 427                 String[][] info = {
 428                                 // Parameter Name Kind of Value Description,
 429                                 { "sequenceDBN", "String", "A raw RNA sequence" },
 430                                 { "structureDBN", "String",
 431                                                 "An RNA structure in dot bracket notation (DBN)" },
 432                                 { errorOpt, "boolean", "To show errors" }, };
 433                 return info;
 434         }
 435
 436         public void init() {
 437                 _vp.setBackground(_backgroundColor);
 438                 _error = true;
 439         }
 440
 441         @SuppressWarnings("unused")
 442         private Color getSafeColor(String col, Color def) {
 443                 Color result;
 444                 try {
 445                         result = Color.decode(col);
 446                 } catch (Exception e) {
 447                         try {
 448                                 result = Color.getColor(col, def);
 449                         } catch (Exception e2) {
 450                                 return def;
 451                         }
 452                 }
 453                 return result;
 454         }
 455
 456         public VARNAPanel get_varnaPanel() {
 457                 return _vp;
 458         }
 459
 460         public void set_varnaPanel(VARNAPanel surface) {
 461                 _vp = surface;
 462         }
 463
 464
 465         public JTextField get_seq() {
 466                 return _seq;
 467         }
 468
 469         public void set_seq(JTextField _seq) {
 470                 this._seq = _seq;
 471         }
 472
 473         public JLabel get_info() {
 474                 return _info;
 475         }
 476
 477         public void set_info(JLabel _info) {
 478                 this._info = _info;
 479         }
 480
 481         public static void main(String[] args) {
 482                 List<Image> icons = new ArrayList<Image>();
 483                 //JOptionPane.showMessageDialog(null, ""+Toolkit.getDefaultToolkit().getImage("./VARNA16x16.png"), "Check", JOptionPane.INFORMATION_MESSAGE);
 484                 icons.add(Toolkit.getDefaultToolkit().getImage("./VARNA16x16.png"));
 485                 icons.add(Toolkit.getDefaultToolkit().getImage("./VARNA32x32.png"));
 486                 icons.add(Toolkit.getDefaultToolkit().getImage("./VARNA64x64.png"));
 487                 VARNAGUI d = new VARNAGUI();
 488                 d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
 489                 d.pack();
 490                 d.setIconImages(icons);
 491                 d.setVisible(true);
 492         }
 493
 494
 495         public void dragEnter(DropTargetDragEvent arg0) {
 496                 // TODO Auto-generated method stub
 497
 498         }
 499
 500         public void dragExit(DropTargetEvent arg0) {
 501                 // TODO Auto-generated method stub
 502
 503         }
 504
 505         public void dragOver(DropTargetDragEvent arg0) {
 506                 // TODO Auto-generated method stub
 507
 508         }
 509
 510         public void drop(DropTargetDropEvent dtde) {
 511             try {
 512                 Transferable tr = dtde.getTransferable();
 513                 DataFlavor[] flavors = tr.getTransferDataFlavors();
 514                 for (int i = 0; i < flavors.length; i++) {
 515             if (flavors[i].isFlavorJavaFileListType()) {
 516               dtde.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
 517               Object ob = tr.getTransferData(flavors[i]);
 518               if (ob instanceof List)
 519               {
 520                   List list = (List) ob;
 521                   for (int j = 0; j < list.size(); j++) {
 522                   Object o = list.get(j);
 523
 524                   if (dtde.getSource() instanceof DropTarget)
 525                   {
 526                           DropTarget dt = (DropTarget) dtde.getSource();
 527                           Component c = dt.getComponent();
 528                           if (c instanceof VARNAPanel)
 529                           {
 530                                           String path = o.toString();
 531                                   VARNAPanel vp = (VARNAPanel) c;
 532                                           try{
 533                                   FullBackup bck =  VARNAPanel.importSession((File) o);  // BH SwingJS
 534                                   _rnaList.add(bck.config, bck.rna,bck.name,true);
 535                                           }
 536                                           catch (ExceptionLoadingFailed e3)
 537                                           {
 538                                                   ArrayList<RNA> rnas = RNAFactory.loadSecStr((File) o); // BH SwingJS
 539                                                   if (rnas.isEmpty())
 540                                                   {
 541                                                           throw new ExceptionFileFormatOrSyntax("No RNA could be parsed from that source.");
 542                                                   }
 543
 544                                               dtde.dropComplete(true);
 545                                                   _vp.getVARNAUI().UIChooseRNAs(rnas);
 546                                               return;
 547                                                   /*
 548                                                   for(RNA r: rnas)
 549                                                   {
 550                                                           r.drawRNA(vp.getConfig());
 551                                                           String name = r.getName();
 552                                                           if (name.equals(""))
 553                                                           {
 554                                                                   name = path.substring(path.lastIndexOf(File.separatorChar)+1);
 555                                                           }
 556                                                           if (rnas.size()>1)
 557                                                           {
 558                                                                   name += " - Molecule# "+id++;
 559                                                           }
 560                                                           _rnaList.add(vp.getConfig().clone(),r,name,true);
 561                                                   }*/
 562                                           }
 563                           }
 564                   }
 565                   }
 566               }
 567               // If we made it this far, everything worked.
 568               dtde.dropComplete(true);
 569               return;
 570             }
 571                 }
 572                 // Hmm, the user must not have dropped a file list
 573                 dtde.rejectDrop();
 574               } catch (Exception e) {
 575                 e.printStackTrace();
 576                 dtde.rejectDrop();
 577               }
 578
 579         }
 580
 581         public void dropActionChanged(DropTargetDragEvent arg0) {
 582         }
 583
 584         private class BackupHolder{
 585                 private DefaultListModel _rnaList;
 586                 private ArrayList<RNA> _rnas = new ArrayList<RNA>();
 587                 JList _l;
 588
 589                 public BackupHolder(DefaultListModel rnaList, JList l)
 590                 {
 591                         _rnaList = rnaList;
 592                         _l = l;
 593                 }
 594
 595                 public void add(VARNAConfig c, RNA r)
 596                 {
 597                         add(c, r, r.getName(),false);
 598                 }
 599
 600                 public void add(VARNAConfig c, RNA r,boolean select)
 601                 {
 602                         add(c, r, r.getName(),select);
 603                 }
 604
 605                 public void add(VARNAConfig c, RNA r, String name)
 606                 {
 607                         add(c, r, name,false);
 608                 }
 609                 public void add(VARNAConfig c, RNA r, String name, boolean select)
 610                 {
 611                         if (!_rnas.contains(r))
 612                         {
 613                         if (select){
 614                                 _l.removeSelectionInterval(0, _rnaList.size());
 615                         }
 616                         if (name.equals(""))
 617                         {
 618                                 name = generateDefaultName();
 619                         }
 620                         FullBackup bck = new FullBackup(c,r,name);
 621                         _rnas.add(0, r);
 622                         _rnaList.add(0,bck);
 623                         _l.doLayout();
 624                         if (select){
 625                           _l.setSelectedIndex(0);
 626                         }
 627                         }
 628                 }
 629
 630                 public void remove(int i)
 631                 {
 632                         _rnas.remove(i);
 633                         _rnaList.remove(i);
 634
 635                 }
 636                 public DefaultListModel getModel()
 637                 {
 638                         return _rnaList;
 639                 }
 640                 public boolean contains(RNA r)
 641                 {
 642                         return _rnas.contains(r);
 643                 }
 644                 /*public int getSize()
 645                 {
 646                         return _rnaList.getSize();
 647                 }*/
 648                 public FullBackup getElementAt(int i)
 649                 {
 650                         return (FullBackup) _rnaList.getElementAt(i);
 651                 }
 652
 653                 public void removeSelected()
 654                 {
 655                         int i = _l.getSelectedIndex();
 656                         if (i!=-1)
 657                         {
 658                           if (_rnaList.getSize()==1)
 659                           {
 660                                   RNA r = new RNA();
 661                                   try {
 662                                         r.setRNA(" ", ".");
 663                                   } catch (ExceptionUnmatchedClosingParentheses e1) {
 664                                   } catch (ExceptionFileFormatOrSyntax e1) {
 665                                   }
 666                                   showRNA(r);
 667                           }
 668                           else
 669                           {
 670                                  int newi = i+1;
 671                                  if (newi==_rnaList.getSize())
 672                                  {
 673                                          newi = _rnaList.getSize()-2;
 674                                  }
 675                                  FullBackup bck = (FullBackup) _rnaList.getElementAt(newi);
 676                                  _l.setSelectedValue(bck,true);
 677                           }
 678                           _rnaList.remove(i);
 679                         }
 680
 681                 }
 682         }
 683
 684         public void onStructureRedrawn() {
 685                 // TODO Auto-generated method stub
 686
 687         }
 688
 689         public void onUINewStructure(VARNAConfig v, RNA r) {
 690                 _rnaList.add(v, r,r.getName(),true);
 691                 onZoomLevelChanged();
 692         }
 693
 694         public void onWarningEmitted(String s) {
 695                 // TODO Auto-generated method stub
 696
 697         }
 698
 699         public void mouseClicked(MouseEvent e) {
 700                            if(e.getClickCount() == 2){
 701                              int index = _sideList.locationToIndex(e.getPoint());
 702                              ListModel dlm = _sideList.getModel();
 703                              FullBackup item = (FullBackup) dlm.getElementAt(index);;
 704                              _sideList.ensureIndexIsVisible(index);
 705                              Object newName = JOptionPane.showInputDialog(
 706                                             this,
 707                                             "Specify a new name for this RNA",
 708                                             "Rename RNA",
 709                                             JOptionPane.QUESTION_MESSAGE,
 710                                             (Icon)null,
 711                                             null,
 712                                             item.toString());
 713                              if (newName!=null)
 714                              {
 715                                  item.name = newName.toString();
 716                                  this._sideList.repaint();
 717                              }
 718                              }
 719         }
 720
 721         public void mouseEntered(MouseEvent arg0) {
 722                 // TODO Auto-generated method stub
 723
 724         }
 725
 726         public void mouseExited(MouseEvent arg0) {
 727                 // TODO Auto-generated method stub
 728
 729         }
 730
 731         public void mousePressed(MouseEvent arg0) {
 732                 // TODO Auto-generated method stub
 733
 734         }
 735
 736         public void mouseReleased(MouseEvent arg0) {
 737                 // TODO Auto-generated method stub
 738
 739         }
 740
 741         public void onZoomLevelChanged() {
 742                 if (_vp.getZoom()>1.02)
 743                 {
 744                   Rectangle r = _vp.getZoomedInTranslationBox();
 745                   _horiz.setMinimum(r.x);
 746                   _horiz.setMaximum(r.x+r.width+_vp.getWidth());
 747                   _horiz.getModel().setExtent(_vp.getWidth());
 748                   _horiz.getModel().setValue(_vp.getTranslation().x);
 749                   _horiz.doLayout();
 750                   _horiz.setVisible(true);
 751
 752                   _vert.setMinimum(r.y);
 753                   _vert.setMaximum(r.y+r.height+_vp.getHeight());
 754                   _vert.getModel().setExtent(_vp.getHeight());
 755                   _vert.getModel().setValue(_vp.getTranslation().y);
 756                   _vert.doLayout();
 757                   _vert.setVisible(true);
 758                 }
 759                 else
 760                 {
 761                   _horiz.setVisible(false);
 762                   _vert.setVisible(false);
 763                 }
 764         }
 765
 766         public void onTranslationChanged() {
 767                 if (_vp.getZoom()>1.02)
 768                 {
 769                         int nx = _horiz.getMaximum()-(_vp.getTranslation().x-_horiz.getMinimum())-_vp.getWidth();
 770                         int ny = _vert.getMaximum()-(_vp.getTranslation().y-_vert.getMinimum())-_vp.getHeight();
 771                         _horiz.getModel().setValue(nx);
 772                         _horiz.doLayout();
 773                         _vert.getModel().setValue(ny);
 774                         _vert.doLayout();
 775                 }
 776         }
 777
 778         public void adjustmentValueChanged(AdjustmentEvent arg0) {
 779                 if (arg0.getSource()==_horiz)
 780                 {
 781                         _vp.setTranslation(new Point(_horiz.getMaximum()-(arg0.getValue()-_horiz.getMinimum())-_vp.getWidth(),_vp.getTranslation().y));
 782                         _vp.repaint();
 783                 }
 784                 else if (arg0.getSource()==_vert)
 785                 {
 786                         _vp.setTranslation(new Point(_vp.getTranslation().x,_vert.getMaximum()-(arg0.getValue()-_vert.getMinimum())-_vp.getHeight()));
 787                         _vp.repaint();
 788                 }
 789         }
 790 }