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