src/jalview/gui/AppVarnaBinding.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
   3  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * 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  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.gui;
  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.ComponentEvent;
  37 import java.awt.event.MouseEvent;
  38 import java.awt.event.MouseListener;
  39 import java.io.File;
  40 import java.text.DateFormat;
  41 import java.util.ArrayList;
  42 import java.util.Date;
  43 import java.util.List;
  44
  45 import javax.swing.DefaultListModel;
  46 import javax.swing.DefaultListSelectionModel;
  47 import javax.swing.Icon;
  48 import javax.swing.JButton;
  49 import javax.swing.JFrame;
  50 import javax.swing.JLabel;
  51 import javax.swing.JList;
  52 import javax.swing.JOptionPane;
  53 import javax.swing.JPanel;
  54 import javax.swing.JScrollPane;
  55 import javax.swing.JSplitPane;
  56 import javax.swing.JTextField;
  57 import javax.swing.ListModel;
  58 import javax.swing.ListSelectionModel;
  59 import javax.swing.UIManager;
  60 import javax.swing.UnsupportedLookAndFeelException;
  61 import javax.swing.event.ListSelectionEvent;
  62 import javax.swing.event.ListSelectionListener;
  63
  64 import fr.orsay.lri.varna.VARNAPanel;
  65 import fr.orsay.lri.varna.components.ReorderableJList;
  66 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
  67 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
  68 import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
  69 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
  70 import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
  71 import fr.orsay.lri.varna.models.FullBackup;
  72 import fr.orsay.lri.varna.models.VARNAConfig;
  73 import fr.orsay.lri.varna.models.rna.Mapping;
  74 import fr.orsay.lri.varna.models.rna.RNA;
  75
  76 public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding implements DropTargetListener, InterfaceVARNAListener, MouseListener {
  77
  78         /**
  79          *
  80          */
  81         //private static final long serialVersionUID = -790155708306987257L;
  82
  83         private String DEFAULT_SEQUENCE = "CAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIACAGCACGACACUAGCAGUCAGUGUCAGACUGCAIA";
  84         private String DEFAULT_STRUCTURE1 = "..(((((...(((((...(((((...(((((.....)))))...))))).....(((((...(((((.....)))))...))))).....)))))...)))))..";
  85         private String DEFAULT_STRUCTURE2 = "..(((((...(((((...(((((........(((((...(((((.....)))))...)))))..................))))).....)))))...)))))..";
  86         public VARNAPanel vp;
  87
  88         protected JPanel _tools = new JPanel();
  89         private JPanel _input = new JPanel();
  90
  91         private JPanel _seqPanel = new JPanel();
  92         private JPanel _strPanel = new JPanel();
  93         private JLabel _info = new JLabel();
  94         private JTextField _str = new JTextField();
  95         private JTextField _seq = new JTextField();
  96         private JLabel _strLabel = new JLabel(" Str:");
  97         private JLabel _seqLabel = new JLabel(" Seq:");
  98         private JButton _createButton = new JButton("Create");
  99         private JButton _updateButton = new JButton("Update");
 100         private JButton _deleteButton = new JButton("Delete");
 101         private JButton _duplicateButton = new JButton("Snapshot");
 102
 103         protected JPanel _listPanel = new JPanel();
 104         private ReorderableJList _sideList = null;
 105
 106
 107         private static String errorOpt = "error";
 108         @SuppressWarnings("unused")
 109         private boolean _error;
 110
 111         private Color _backgroundColor = Color.white;
 112
 113         private static int _nextID = 1;
 114         @SuppressWarnings("unused")
 115         private int _algoCode;
 116
 117         private BackupHolder _rnaList;
 118
 119
 120         /*public AppVarnaBinding() {
 121                 //super("VARNA in Jalview");
 122                 //this.set_seq("ATGC");
 123                 //this.set_str(".().");
 124                 //RNAPanelDemoInit();
 125
 126                 //initVarna("ATGCATGATATATATATAT","....((((...))))....");
 127                 initVarna(this.DEFAULT_SEQUENCE,this.DEFAULT_STRUCTURE1);
 128         }*/
 129
 130         public AppVarnaBinding(String seq,String struc){
 131                 //super("VARNA in Jalview");
 132                 initVarna(seq,struc);
 133         }
 134
 135         public AppVarnaBinding(ArrayList<RNA> rnaList){
 136                 //super("VARNA in Jalview");
 137                 initVarnaEdit(rnaList);
 138         }
 139
 140
 141
 142         private void initVarna(String seq, String str){
 143                 DefaultListModel dlm = new DefaultListModel();
 144
 145                 DefaultListSelectionModel m = new DefaultListSelectionModel();
 146             m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 147             m.setLeadAnchorNotificationEnabled(false);
 148
 149             _sideList = new ReorderableJList();
 150                 _sideList.setModel(dlm);
 151                 _sideList.addMouseListener(this);
 152             _sideList.setSelectionModel(m);
 153             _sideList.setPreferredSize(new Dimension(100, 0));
 154             _sideList.addListSelectionListener( new ListSelectionListener(){
 155                         public void valueChanged(ListSelectionEvent arg0) {
 156                                 if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
 157                                 {
 158                                         FullBackup  sel = (FullBackup) _sideList.getSelectedValue();
 159                                         Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA().getSize(), sel.rna.getSize());
 160                                         vp.showRNAInterpolated(sel.rna,sel.config,map);
 161                                         _seq.setText(sel.rna.getSeq());
 162                                         _str.setText(sel.rna.getStructDBN());
 163                                 }
 164                         }
 165             });
 166
 167             _rnaList = new BackupHolder(dlm,_sideList);
 168                 RNA _RNA1 = new RNA("User defined 1");
 169
 170                 try {
 171                         vp = new VARNAPanel("0",".");
 172                         _RNA1.setRNA(seq, str);
 173                         _RNA1.drawRNARadiate(vp.getConfig());
 174                 } catch (ExceptionNonEqualLength e) {
 175                         vp.errorDialog(e);
 176                 } catch (ExceptionUnmatchedClosingParentheses e2) {
 177                 e2.printStackTrace();
 178                 } catch (ExceptionFileFormatOrSyntax e3) {
 179                 e3.printStackTrace();
 180                 }
 181                 vp.setPreferredSize(new Dimension(400, 400));
 182                 _rnaList.add(vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
 183
 184                 //TODO setBackground(_backgroundColor);
 185                 vp.setBackground(_backgroundColor);
 186
 187                 //TODO getContentPane().setLayout(new BorderLayout());
 188                 //TODO getContentPane().add(vp, BorderLayout.CENTER);
 189
 190                 //setVisible(true);
 191                 vp.addVARNAListener(this);
 192         }
 193
 194         private void initVarnaEdit(ArrayList<RNA> rnaInList)
 195         {
 196             DefaultListModel dlm = new DefaultListModel();
 197
 198
 199                 int marginTools = 40;
 200
 201             DefaultListSelectionModel m = new DefaultListSelectionModel();
 202             m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 203             m.setLeadAnchorNotificationEnabled(false);
 204
 205
 206                 _sideList = new ReorderableJList();
 207                 _sideList.setModel(dlm);
 208                 _sideList.addMouseListener(this);
 209             _sideList.setSelectionModel(m);
 210             _sideList.setPreferredSize(new Dimension(100, 0));
 211             _sideList.addListSelectionListener( new ListSelectionListener(){
 212                         public void valueChanged(ListSelectionEvent arg0) {
 213                                 //System.out.println(arg0);
 214                                 if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
 215                                 {
 216                                         FullBackup  sel = (FullBackup) _sideList.getSelectedValue();
 217                                         Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA().getSize(), sel.rna.getSize());
 218                                         vp.showRNAInterpolated(sel.rna,sel.config,map);
 219                                         //_seq.setText(sel.rna.getSeq());
 220                                         _str.setText(sel.rna.getStructDBN());
 221                                 }
 222                         }
 223             });
 224
 225             _rnaList = new BackupHolder(dlm,_sideList);
 226
 227                 try {
 228                         vp = new VARNAPanel("0",".");
 229                         for(int i=0;i<rnaInList.size();i++){
 230                                 rnaInList.get(i).drawRNARadiate(vp.getConfig());
 231                         }
 232                 } catch (ExceptionNonEqualLength e) {
 233                         vp.errorDialog(e);
 234                 }
 235                 vp.setPreferredSize(new Dimension(400, 400));
 236                 for(int i=0;i<rnaInList.size();i++){
 237                         if(i<rnaInList.size()-1){
 238                                 _rnaList.add(vp.getConfig().clone(),rnaInList.get(i),rnaInList.get(i).getName());
 239                         }else{
 240                                 _rnaList.add(vp.getConfig().clone(),rnaInList.get(i),rnaInList.get(i).getName(),true);
 241                         }
 242                 }
 243
 244             /*_rnaList.add(vp.getConfig().clone(),_RNA2,generateDefaultName());
 245             _rnaList.add(vp.getConfig().clone(),_RNA1,generateDefaultName(),true);*/
 246
 247             JScrollPane listScroller = new JScrollPane(_sideList);
 248             listScroller.setPreferredSize(new Dimension(150, 0));
 249
 250                 vp.setBackground(_backgroundColor);
 251
 252
 253                 Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
 254
 255                 //_seqLabel.setHorizontalTextPosition(JLabel.LEFT);
 256                 //_seqLabel.setPreferredSize(new Dimension(marginTools, 15));
 257                 _seq.setFont(textFieldsFont);
 258                 _seq.setText(rnaInList.get(0).getSeq());
 259
 260                 _updateButton.addActionListener(new ActionListener() {
 261                         public void actionPerformed(ActionEvent e) {
 262                                 FullBackup  sel = (FullBackup) _sideList.getSelectedValue();
 263                                 sel.rna.setSequence("A");
 264                                 }
 265                 });
 266
 267                 //_seqPanel.setLayout(new BorderLayout());
 268                 //_seqPanel.add(_seqLabel, BorderLayout.WEST);
 269                 //_seqPanel.add(_seq, BorderLayout.CENTER);
 270
 271                 _strLabel.setPreferredSize(new Dimension(marginTools, 15));
 272                 _strLabel.setHorizontalTextPosition(JLabel.LEFT);
 273                 _str.setFont(textFieldsFont);
 274                 _strPanel.setLayout(new BorderLayout());
 275                 _strPanel.add(_strLabel, BorderLayout.WEST);
 276                 _strPanel.add(_str, BorderLayout.CENTER);
 277
 278                 _input.setLayout(new GridLayout(1, 0));
 279                 //_input.add(_seqPanel);
 280                 _input.add(_strPanel);
 281
 282                 JPanel goPanel = new JPanel();
 283                 goPanel.setLayout(new BorderLayout());
 284
 285                 _tools.setLayout(new BorderLayout());
 286                 _tools.add(_input, BorderLayout.CENTER);
 287                 //_tools.add(_info, BorderLayout.SOUTH);
 288                 _tools.add(goPanel, BorderLayout.EAST);
 289
 290                 /*_deleteButton.addActionListener(new ActionListener() {
 291                         public void actionPerformed(ActionEvent e) {
 292                                 _rnaList.removeSelected();
 293                         }
 294                 });
 295                 _duplicateButton.addActionListener(new ActionListener() {
 296                         public void actionPerformed(ActionEvent e) {
 297                                         _rnaList.add((VARNAConfig)vp.getConfig().clone(),vp.getRNA().clone(),vp.getRNA().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new Date()),true);
 298                         }});
 299                 */
 300                 goPanel.add(_updateButton, BorderLayout.CENTER);
 301
 302
 303                 JPanel ops = new JPanel();
 304                 ops.setLayout(new GridLayout(1,2));
 305                 ops.add(_deleteButton);
 306                 ops.add(_duplicateButton);
 307
 308                 JLabel j = new JLabel("Structures Manager",JLabel.CENTER);
 309                 _listPanel.setLayout(new BorderLayout());
 310
 311                 _listPanel.add(ops,BorderLayout.SOUTH);
 312                 _listPanel.add(j,BorderLayout.NORTH);
 313                 _listPanel.add(listScroller,BorderLayout.CENTER);
 314
 315
 316
 317                 //JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,vp);
 318                 /**TODO
 319                 getContentPane().setLayout(new BorderLayout());
 320                 getContentPane().add(split, BorderLayout.CENTER);
 321                 getContentPane().add(_tools, BorderLayout.NORTH);
 322                  */
 323
 324                 //TODO setVisible(true);
 325                 DropTarget dt = new DropTarget(vp, this);
 326
 327                 vp.addVARNAListener(this);
 328         }
 329
 330         public JPanel getTools(){
 331                 return _tools;
 332         }
 333
 334         public JPanel getListPanel(){
 335                 return _listPanel;
 336         }
 337
 338         /*
 339         private void RNAPanelDemoInit()
 340         {
 341             DefaultListModel dlm = new DefaultListModel();
 342
 343
 344                 int marginTools = 40;
 345
 346             DefaultListSelectionModel m = new DefaultListSelectionModel();
 347             m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 348             m.setLeadAnchorNotificationEnabled(false);
 349
 350
 351                 _sideList = new ReorderableJList();
 352                 _sideList.setModel(dlm);
 353                 _sideList.addMouseListener(this);
 354             _sideList.setSelectionModel(m);
 355             _sideList.setPreferredSize(new Dimension(100, 0));
 356             _sideList.addListSelectionListener( new ListSelectionListener(){
 357                         public void valueChanged(ListSelectionEvent arg0) {
 358                                 //System.out.println(arg0);
 359                                 if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
 360                                 {
 361                                         FullBackup  sel = (FullBackup) _sideList.getSelectedValue();
 362                                         Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA().getSize(), sel.rna.getSize());
 363                                         vp.showRNAInterpolated(sel.rna,sel.config,map);
 364                                         _seq.setText(sel.rna.getSeq());
 365                                         _str.setText(sel.rna.getStructDBN());
 366                                 }
 367                         }
 368             });
 369
 370             _rnaList = new BackupHolder(dlm,_sideList);
 371                 RNA _RNA1 = new RNA("User defined 1");
 372                 RNA _RNA2 = new RNA("User defined 2");
 373                 try {
 374                         vp = new VARNAPanel("0",".");
 375                         _RNA1.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE1);
 376                         _RNA1.drawRNARadiate(vp.getConfig());
 377                         _RNA2.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE2);
 378                         _RNA2.drawRNARadiate(vp.getConfig());
 379                 } catch (ExceptionNonEqualLength e) {
 380                         vp.errorDialog(e);
 381                 } catch (ExceptionUnmatchedClosingParentheses e2) {
 382                 e2.printStackTrace();
 383                 } catch (ExceptionFileFormatOrSyntax e3) {
 384                 e3.printStackTrace();
 385                 }
 386                 vp.setPreferredSize(new Dimension(400, 400));
 387             _rnaList.add(vp.getConfig().clone(),_RNA2,generateDefaultName());
 388             _rnaList.add(vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
 389
 390             JScrollPane listScroller = new JScrollPane(_sideList);
 391             listScroller.setPreferredSize(new Dimension(150, 0));
 392
 393                 setBackground(_backgroundColor);
 394                 vp.setBackground(_backgroundColor);
 395
 396
 397                 Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
 398
 399                 _seqLabel.setHorizontalTextPosition(JLabel.LEFT);
 400                 _seqLabel.setPreferredSize(new Dimension(marginTools, 15));
 401                 _seq.setFont(textFieldsFont);
 402                 _seq.setText(DEFAULT_SEQUENCE);
 403
 404                 _createButton.addActionListener(new ActionListener() {
 405                         public void actionPerformed(ActionEvent e) {
 406                                 try {
 407                                 RNA nRNA = new RNA(generateDefaultName());
 408                                 nRNA.setRNA(_seq.getText(), _str.getText());
 409                                 nRNA.drawRNARadiate(vp.getConfig());
 410                                 _rnaList.add(new VARNAConfig(),nRNA,true);
 411                                 } catch (ExceptionUnmatchedClosingParentheses e1) {
 412                                         JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
 413                                 } catch (ExceptionFileFormatOrSyntax e1) {
 414                                         JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
 415                                 }
 416                         }
 417                 });
 418
 419
 420                 _seqPanel.setLayout(new BorderLayout());
 421                 _seqPanel.add(_seqLabel, BorderLayout.WEST);
 422                 _seqPanel.add(_seq, BorderLayout.CENTER);
 423
 424                 _strLabel.setPreferredSize(new Dimension(marginTools, 15));
 425                 _strLabel.setHorizontalTextPosition(JLabel.LEFT);
 426                 _str.setFont(textFieldsFont);
 427                 _strPanel.setLayout(new BorderLayout());
 428                 _strPanel.add(_strLabel, BorderLayout.WEST);
 429                 _strPanel.add(_str, BorderLayout.CENTER);
 430
 431                 _input.setLayout(new GridLayout(2, 0));
 432                 _input.add(_seqPanel);
 433                 _input.add(_strPanel);
 434
 435                 JPanel goPanel = new JPanel();
 436                 goPanel.setLayout(new BorderLayout());
 437
 438                 _tools.setLayout(new BorderLayout());
 439                 _tools.add(_input, BorderLayout.CENTER);
 440                 _tools.add(_info, BorderLayout.SOUTH);
 441                 _tools.add(goPanel, BorderLayout.EAST);
 442
 443                 _deleteButton.addActionListener(new ActionListener() {
 444                         public void actionPerformed(ActionEvent e) {
 445                                 _rnaList.removeSelected();
 446                         }
 447                 });
 448                 _duplicateButton.addActionListener(new ActionListener() {
 449                         public void actionPerformed(ActionEvent e) {
 450                                         _rnaList.add((VARNAConfig)vp.getConfig().clone(),vp.getRNA().clone(),vp.getRNA().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new Date()),true);
 451                         }});
 452
 453                 JPanel ops = new JPanel();
 454                 ops.setLayout(new GridLayout(1,2));
 455                 ops.add(_deleteButton);
 456                 ops.add(_duplicateButton);
 457
 458                 JLabel j = new JLabel("Structures Manager",JLabel.CENTER);
 459                 _listPanel.setLayout(new BorderLayout());
 460
 461                 _listPanel.add(ops,BorderLayout.SOUTH);
 462                 _listPanel.add(j,BorderLayout.NORTH);
 463                 _listPanel.add(listScroller,BorderLayout.CENTER);
 464
 465                 goPanel.add(_createButton, BorderLayout.CENTER);
 466
 467                 JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,vp);
 468                 getContentPane().setLayout(new BorderLayout());
 469                 getContentPane().add(split, BorderLayout.CENTER);
 470                 getContentPane().add(_tools, BorderLayout.NORTH);
 471
 472                 setVisible(true);
 473                 DropTarget dt = new DropTarget(vp, this);
 474
 475                 vp.addVARNAListener(this);
 476         }
 477         */
 478         public static String generateDefaultName()
 479         {
 480                 return "User file #"+_nextID++;
 481         }
 482
 483         public RNA getRNA() {
 484                 return (RNA)_sideList.getSelectedValue();
 485         }
 486
 487
 488
 489         public String[][] getParameterInfo() {
 490                 String[][] info = {
 491                                 // Parameter Name Kind of Value Description,
 492                                 { "sequenceDBN", "String", "A raw RNA sequence" },
 493                                 { "structureDBN", "String",
 494                                                 "An RNA structure in dot bracket notation (DBN)" },
 495                                 { errorOpt, "boolean", "To show errors" }, };
 496                 return info;
 497         }
 498
 499         public void init() {
 500                 vp.setBackground(_backgroundColor);
 501                 _error = true;
 502         }
 503
 504         @SuppressWarnings("unused")
 505         private Color getSafeColor(String col, Color def) {
 506                 Color result;
 507                 try {
 508                         result = Color.decode(col);
 509                 } catch (Exception e) {
 510                         try {
 511                                 result = Color.getColor(col, def);
 512                         } catch (Exception e2) {
 513                                 return def;
 514                         }
 515                 }
 516                 return result;
 517         }
 518
 519         public VARNAPanel get_varnaPanel() {
 520                 return vp;
 521         }
 522
 523         public void set_varnaPanel(VARNAPanel surface) {
 524                 vp = surface;
 525         }
 526
 527
 528         public String get_seq() {
 529                 return _seq.getText();
 530         }
 531
 532         public void set_seq(String _seq) {
 533                 this._seq.setText(_seq);
 534         }
 535
 536         public String get_str(){
 537                 return _str.getText();
 538         }
 539
 540         public void set_str(String _str){
 541                 this._str.setText(_str);
 542         }
 543
 544         public JLabel get_info() {
 545                 return _info;
 546         }
 547
 548         public void set_info(JLabel _info) {
 549                 this._info = _info;
 550         }
 551
 552         /*public static void main(String[] args) {
 553                 AppVarnaBinding d = new AppVarnaBinding();
 554                 d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
 555                 d.pack();
 556                 d.setVisible(true);
 557         }*/
 558
 559
 560         public void dragEnter(DropTargetDragEvent arg0) {
 561                 // TODO Auto-generated method stub
 562
 563         }
 564
 565         public void dragExit(DropTargetEvent arg0) {
 566                 // TODO Auto-generated method stub
 567
 568         }
 569
 570         public void dragOver(DropTargetDragEvent arg0) {
 571                 // TODO Auto-generated method stub
 572
 573         }
 574
 575         public void drop(DropTargetDropEvent dtde) {
 576             try {
 577                 Transferable tr = dtde.getTransferable();
 578                 DataFlavor[] flavors = tr.getTransferDataFlavors();
 579                 for (int i = 0; i < flavors.length; i++) {
 580             if (flavors[i].isFlavorJavaFileListType()) {
 581               dtde.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
 582               Object ob = tr.getTransferData(flavors[i]);
 583               if (ob instanceof List)
 584               {
 585                   List list = (List) ob;
 586                   for (int j = 0; j < list.size(); j++) {
 587                   Object o = list.get(j);
 588
 589                   if (dtde.getSource() instanceof DropTarget)
 590                   {
 591                           DropTarget dt = (DropTarget) dtde.getSource();
 592                           Component c = dt.getComponent();
 593                           if (c instanceof VARNAPanel)
 594                           {
 595                                           String path = o.toString();
 596                                   VARNAPanel vp = (VARNAPanel) c;
 597                                           try{
 598                                   FullBackup bck =  VARNAPanel.importSession(path);
 599                                   _rnaList.add(bck.config, bck.rna,bck.name,true);
 600                                           }
 601                                           catch (ExceptionLoadingFailed e3)
 602                                           {
 603                                                   RNA r = new RNA();
 604                                                   r.loadSecStr(path);
 605                                                   r.drawRNA(vp.getConfig());
 606                                                   String name =r.getName();
 607                                                   if (name.equals(""))
 608                                                   {
 609                                                           name = path.substring(path.lastIndexOf(File.separatorChar)+1);
 610                                                   }
 611                                                   _rnaList.add(vp.getConfig().clone(),r,name,true);
 612                                           }
 613                           }
 614                   }
 615                   }
 616               }
 617               // If we made it this far, everything worked.
 618               dtde.dropComplete(true);
 619               return;
 620             }
 621                 }
 622                 // Hmm, the user must not have dropped a file list
 623                 dtde.rejectDrop();
 624               } catch (Exception e) {
 625                 e.printStackTrace();
 626                 dtde.rejectDrop();
 627               }
 628
 629         }
 630
 631         public void dropActionChanged(DropTargetDragEvent arg0) {
 632         }
 633
 634         private class BackupHolder{
 635                 private DefaultListModel _rnaList;
 636                 private ArrayList<RNA> _rnas = new ArrayList<RNA>();
 637                 JList _l;
 638
 639                 public BackupHolder(DefaultListModel rnaList, JList l)
 640                 {
 641                         _rnaList = rnaList;
 642                         _l = l;
 643                 }
 644
 645                 public void add(VARNAConfig c, RNA r)
 646                 {
 647                         add(c, r, r.getName(),false);
 648                 }
 649
 650                 public void add(VARNAConfig c, RNA r,boolean select)
 651                 {
 652                         add(c, r, r.getName(),select);
 653                 }
 654
 655                 public void add(VARNAConfig c, RNA r, String name)
 656                 {
 657                         add(c, r, name,false);
 658                 }
 659                 public void add(VARNAConfig c, RNA r, String name, boolean select)
 660                 {
 661                         if (select){
 662                                 _l.removeSelectionInterval(0, _rnaList.size());
 663                         }
 664                         if (name.equals(""))
 665                         {
 666                                 name = generateDefaultName();
 667                         }
 668                         FullBackup bck = new FullBackup(c,r,name);
 669                         _rnas.add(0, r);
 670                         _rnaList.add(0,bck);
 671                         if (select){
 672                           _l.setSelectedIndex(0);
 673                         }
 674                 }
 675
 676                 public void remove(int i)
 677                 {
 678                         _rnas.remove(i);
 679                         _rnaList.remove(i);
 680
 681                 }
 682                 public DefaultListModel getModel()
 683                 {
 684                         return _rnaList;
 685                 }
 686                 public boolean contains(RNA r)
 687                 {
 688                         return _rnas.contains(r);
 689                 }
 690                 /*public int getSize()
 691                 {
 692                         return _rnaList.getSize();
 693                 }*/
 694                 public FullBackup getElementAt(int i)
 695                 {
 696                         return (FullBackup) _rnaList.getElementAt(i);
 697                 }
 698
 699                 public void removeSelected()
 700                 {
 701                         int i = _l.getSelectedIndex();
 702                         if (i!=-1)
 703                         {
 704                           if (_rnaList.getSize()==1)
 705                           {
 706                                   RNA r = new RNA();
 707                                   try {
 708                                         r.setRNA(" ", ".");
 709                                   } catch (ExceptionUnmatchedClosingParentheses e1) {
 710                                   } catch (ExceptionFileFormatOrSyntax e1) {
 711                                   }
 712                                   vp.showRNA(r);
 713                                   vp.repaint();
 714                           }
 715                           else
 716                           {
 717                                  int newi = i+1;
 718                                  if (newi==_rnaList.getSize())
 719                                  {
 720                                          newi = _rnaList.getSize()-2;
 721                                  }
 722                                  FullBackup bck = (FullBackup) _rnaList.getElementAt(newi);
 723                                  _l.setSelectedValue(bck,true);
 724                           }
 725                           _rnaList.remove(i);
 726                         }
 727
 728                 }
 729         }
 730
 731         public void onLayoutChanged() {
 732                 // TODO Auto-generated method stub
 733
 734         }
 735
 736         public void onUINewStructure(VARNAConfig v, RNA r) {
 737                 _rnaList.add(v, r,"",true);
 738         }
 739
 740         public void onWarningEmitted(String s) {
 741                 // TODO Auto-generated method stub
 742
 743         }
 744
 745         public void mouseClicked(MouseEvent e) {
 746                            if(e.getClickCount() == 2){
 747                              int index = _sideList.locationToIndex(e.getPoint());
 748                              ListModel dlm = _sideList.getModel();
 749                              FullBackup item = (FullBackup) dlm.getElementAt(index);;
 750                              _sideList.ensureIndexIsVisible(index);
 751                              /*TODO Object newName = JOptionPane.showInputDialog(
 752                                             this,
 753                                             "Specify a new name for this RNA",
 754                                             "Rename RNA",
 755                                             JOptionPane.QUESTION_MESSAGE,
 756                                             (Icon)null,
 757                                             null,
 758                                             item.toString());
 759                              if (newName!=null)
 760                              {
 761                                  item.name = newName.toString();
 762                                  this._sideList.repaint();
 763                              }*/
 764                              }
 765         }
 766
 767         public void mouseEntered(MouseEvent arg0) {
 768                 // TODO Auto-generated method stub
 769
 770         }
 771
 772         public void mouseExited(MouseEvent arg0) {
 773                 // TODO Auto-generated method stub
 774
 775         }
 776
 777         public void mousePressed(MouseEvent arg0) {
 778                 // TODO Auto-generated method stub
 779
 780         }
 781
 782         public void mouseReleased(MouseEvent arg0) {
 783                 // TODO Auto-generated method stub
 784
 785         }
 786
 787         @Override
 788         public Color getColour(int atomIndex, int pdbResNum, String chain,
 789                         String pdbId) {
 790                 // TODO Auto-generated method stub
 791                 return null;
 792         }
 793
 794         @Override
 795         public String[] getPdbFile() {
 796                 // TODO Auto-generated method stub
 797                 return null;
 798         }
 799
 800         @Override
 801         public void highlightAtom(int atomIndex, int pdbResNum, String chain,
 802                         String pdbId) {
 803                 // TODO Auto-generated method stub
 804
 805         }
 806
 807         @Override
 808         public void mouseOverStructure(int atomIndex, String strInfo) {
 809                 // TODO Auto-generated method stub
 810
 811         }
 812
 813         @Override
 814         public void releaseReferences(Object svl) {
 815                 // TODO Auto-generated method stub
 816
 817         }
 818
 819         @Override
 820         public void updateColours(Object source) {
 821                 // TODO Auto-generated method stub
 822
 823         }
 824
 825         @Override
 826         public void componentHidden(ComponentEvent e) {
 827                 // TODO Auto-generated method stub
 828
 829         }
 830
 831         @Override
 832         public void componentMoved(ComponentEvent e) {
 833                 // TODO Auto-generated method stub
 834
 835         }
 836
 837         @Override
 838         public void componentResized(ComponentEvent e) {
 839                 // TODO Auto-generated method stub
 840
 841         }
 842
 843         @Override
 844         public void componentShown(ComponentEvent e) {
 845                 // TODO Auto-generated method stub
 846
 847         }
 848 }
 849
 850
 851 /*
 852         public static void main(String[] args)
 853         {
 854                 JTextField str = new JTextField("ATGC");
 855
 856                 AppVarnaBinding vab = new AppVarnaBinding();
 857                 vab.varnagui.set_seq(str);
 858                 vab.varnagui.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
 859                 vab.varnagui.pack();
 860                 vab.varnagui.setVisible(true);
 861         }
 862 }
 863 */