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                                 /*try {
 265                                 RNA nRNA = new RNA(generateDefaultName());
 266                                 nRNA.setRNA(_seq.getText(), _str.getText());
 267                                 nRNA.drawRNARadiate(vp.getConfig());
 268                                 _rnaList.add(new VARNAConfig(),nRNA,true);
 269                                 } catch (ExceptionUnmatchedClosingParentheses e1) {
 270                                         JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
 271                                 } catch (ExceptionFileFormatOrSyntax e1) {
 272                                         JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
 273                                 }*/
 274                         }
 275                 });
 276
 277                 //_seqPanel.setLayout(new BorderLayout());
 278                 //_seqPanel.add(_seqLabel, BorderLayout.WEST);
 279                 //_seqPanel.add(_seq, BorderLayout.CENTER);
 280
 281                 _strLabel.setPreferredSize(new Dimension(marginTools, 15));
 282                 _strLabel.setHorizontalTextPosition(JLabel.LEFT);
 283                 _str.setFont(textFieldsFont);
 284                 _strPanel.setLayout(new BorderLayout());
 285                 _strPanel.add(_strLabel, BorderLayout.WEST);
 286                 _strPanel.add(_str, BorderLayout.CENTER);
 287
 288                 _input.setLayout(new GridLayout(1, 0));
 289                 //_input.add(_seqPanel);
 290                 _input.add(_strPanel);
 291
 292                 JPanel goPanel = new JPanel();
 293                 goPanel.setLayout(new BorderLayout());
 294
 295                 _tools.setLayout(new BorderLayout());
 296                 _tools.add(_input, BorderLayout.CENTER);
 297                 //_tools.add(_info, BorderLayout.SOUTH);
 298                 _tools.add(goPanel, BorderLayout.EAST);
 299
 300                 /*_deleteButton.addActionListener(new ActionListener() {
 301                         public void actionPerformed(ActionEvent e) {
 302                                 _rnaList.removeSelected();
 303                         }
 304                 });
 305                 _duplicateButton.addActionListener(new ActionListener() {
 306                         public void actionPerformed(ActionEvent e) {
 307                                         _rnaList.add((VARNAConfig)vp.getConfig().clone(),vp.getRNA().clone(),vp.getRNA().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new Date()),true);
 308                         }});
 309                 */
 310                 goPanel.add(_updateButton, BorderLayout.CENTER);
 311
 312
 313                 JPanel ops = new JPanel();
 314                 ops.setLayout(new GridLayout(1,2));
 315                 ops.add(_deleteButton);
 316                 ops.add(_duplicateButton);
 317
 318                 JLabel j = new JLabel("Structures Manager",JLabel.CENTER);
 319                 _listPanel.setLayout(new BorderLayout());
 320
 321                 _listPanel.add(ops,BorderLayout.SOUTH);
 322                 _listPanel.add(j,BorderLayout.NORTH);
 323                 _listPanel.add(listScroller,BorderLayout.CENTER);
 324
 325
 326
 327                 //JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,vp);
 328                 /**TODO
 329                 getContentPane().setLayout(new BorderLayout());
 330                 getContentPane().add(split, BorderLayout.CENTER);
 331                 getContentPane().add(_tools, BorderLayout.NORTH);
 332                  */
 333
 334                 //TODO setVisible(true);
 335                 DropTarget dt = new DropTarget(vp, this);
 336
 337                 vp.addVARNAListener(this);
 338         }
 339
 340         public JPanel getTools(){
 341                 return _tools;
 342         }
 343
 344         public JPanel getListPanel(){
 345                 return _listPanel;
 346         }
 347
 348         /*
 349         private void RNAPanelDemoInit()
 350         {
 351             DefaultListModel dlm = new DefaultListModel();
 352
 353
 354                 int marginTools = 40;
 355
 356             DefaultListSelectionModel m = new DefaultListSelectionModel();
 357             m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 358             m.setLeadAnchorNotificationEnabled(false);
 359
 360
 361                 _sideList = new ReorderableJList();
 362                 _sideList.setModel(dlm);
 363                 _sideList.addMouseListener(this);
 364             _sideList.setSelectionModel(m);
 365             _sideList.setPreferredSize(new Dimension(100, 0));
 366             _sideList.addListSelectionListener( new ListSelectionListener(){
 367                         public void valueChanged(ListSelectionEvent arg0) {
 368                                 //System.out.println(arg0);
 369                                 if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
 370                                 {
 371                                         FullBackup  sel = (FullBackup) _sideList.getSelectedValue();
 372                                         Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA().getSize(), sel.rna.getSize());
 373                                         vp.showRNAInterpolated(sel.rna,sel.config,map);
 374                                         _seq.setText(sel.rna.getSeq());
 375                                         _str.setText(sel.rna.getStructDBN());
 376                                 }
 377                         }
 378             });
 379
 380             _rnaList = new BackupHolder(dlm,_sideList);
 381                 RNA _RNA1 = new RNA("User defined 1");
 382                 RNA _RNA2 = new RNA("User defined 2");
 383                 try {
 384                         vp = new VARNAPanel("0",".");
 385                         _RNA1.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE1);
 386                         _RNA1.drawRNARadiate(vp.getConfig());
 387                         _RNA2.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE2);
 388                         _RNA2.drawRNARadiate(vp.getConfig());
 389                 } catch (ExceptionNonEqualLength e) {
 390                         vp.errorDialog(e);
 391                 } catch (ExceptionUnmatchedClosingParentheses e2) {
 392                 e2.printStackTrace();
 393                 } catch (ExceptionFileFormatOrSyntax e3) {
 394                 e3.printStackTrace();
 395                 }
 396                 vp.setPreferredSize(new Dimension(400, 400));
 397             _rnaList.add(vp.getConfig().clone(),_RNA2,generateDefaultName());
 398             _rnaList.add(vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
 399
 400             JScrollPane listScroller = new JScrollPane(_sideList);
 401             listScroller.setPreferredSize(new Dimension(150, 0));
 402
 403                 setBackground(_backgroundColor);
 404                 vp.setBackground(_backgroundColor);
 405
 406
 407                 Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
 408
 409                 _seqLabel.setHorizontalTextPosition(JLabel.LEFT);
 410                 _seqLabel.setPreferredSize(new Dimension(marginTools, 15));
 411                 _seq.setFont(textFieldsFont);
 412                 _seq.setText(DEFAULT_SEQUENCE);
 413
 414                 _createButton.addActionListener(new ActionListener() {
 415                         public void actionPerformed(ActionEvent e) {
 416                                 try {
 417                                 RNA nRNA = new RNA(generateDefaultName());
 418                                 nRNA.setRNA(_seq.getText(), _str.getText());
 419                                 nRNA.drawRNARadiate(vp.getConfig());
 420                                 _rnaList.add(new VARNAConfig(),nRNA,true);
 421                                 } catch (ExceptionUnmatchedClosingParentheses e1) {
 422                                         JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
 423                                 } catch (ExceptionFileFormatOrSyntax e1) {
 424                                         JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
 425                                 }
 426                         }
 427                 });
 428
 429
 430                 _seqPanel.setLayout(new BorderLayout());
 431                 _seqPanel.add(_seqLabel, BorderLayout.WEST);
 432                 _seqPanel.add(_seq, BorderLayout.CENTER);
 433
 434                 _strLabel.setPreferredSize(new Dimension(marginTools, 15));
 435                 _strLabel.setHorizontalTextPosition(JLabel.LEFT);
 436                 _str.setFont(textFieldsFont);
 437                 _strPanel.setLayout(new BorderLayout());
 438                 _strPanel.add(_strLabel, BorderLayout.WEST);
 439                 _strPanel.add(_str, BorderLayout.CENTER);
 440
 441                 _input.setLayout(new GridLayout(2, 0));
 442                 _input.add(_seqPanel);
 443                 _input.add(_strPanel);
 444
 445                 JPanel goPanel = new JPanel();
 446                 goPanel.setLayout(new BorderLayout());
 447
 448                 _tools.setLayout(new BorderLayout());
 449                 _tools.add(_input, BorderLayout.CENTER);
 450                 _tools.add(_info, BorderLayout.SOUTH);
 451                 _tools.add(goPanel, BorderLayout.EAST);
 452
 453                 _deleteButton.addActionListener(new ActionListener() {
 454                         public void actionPerformed(ActionEvent e) {
 455                                 _rnaList.removeSelected();
 456                         }
 457                 });
 458                 _duplicateButton.addActionListener(new ActionListener() {
 459                         public void actionPerformed(ActionEvent e) {
 460                                         _rnaList.add((VARNAConfig)vp.getConfig().clone(),vp.getRNA().clone(),vp.getRNA().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new Date()),true);
 461                         }});
 462
 463                 JPanel ops = new JPanel();
 464                 ops.setLayout(new GridLayout(1,2));
 465                 ops.add(_deleteButton);
 466                 ops.add(_duplicateButton);
 467
 468                 JLabel j = new JLabel("Structures Manager",JLabel.CENTER);
 469                 _listPanel.setLayout(new BorderLayout());
 470
 471                 _listPanel.add(ops,BorderLayout.SOUTH);
 472                 _listPanel.add(j,BorderLayout.NORTH);
 473                 _listPanel.add(listScroller,BorderLayout.CENTER);
 474
 475                 goPanel.add(_createButton, BorderLayout.CENTER);
 476
 477                 JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,vp);
 478                 getContentPane().setLayout(new BorderLayout());
 479                 getContentPane().add(split, BorderLayout.CENTER);
 480                 getContentPane().add(_tools, BorderLayout.NORTH);
 481
 482                 setVisible(true);
 483                 DropTarget dt = new DropTarget(vp, this);
 484
 485                 vp.addVARNAListener(this);
 486         }
 487         */
 488         public static String generateDefaultName()
 489         {
 490                 return "User file #"+_nextID++;
 491         }
 492
 493         public RNA getRNA() {
 494                 return (RNA)_sideList.getSelectedValue();
 495         }
 496
 497
 498
 499         public String[][] getParameterInfo() {
 500                 String[][] info = {
 501                                 // Parameter Name Kind of Value Description,
 502                                 { "sequenceDBN", "String", "A raw RNA sequence" },
 503                                 { "structureDBN", "String",
 504                                                 "An RNA structure in dot bracket notation (DBN)" },
 505                                 { errorOpt, "boolean", "To show errors" }, };
 506                 return info;
 507         }
 508
 509         public void init() {
 510                 vp.setBackground(_backgroundColor);
 511                 _error = true;
 512         }
 513
 514         @SuppressWarnings("unused")
 515         private Color getSafeColor(String col, Color def) {
 516                 Color result;
 517                 try {
 518                         result = Color.decode(col);
 519                 } catch (Exception e) {
 520                         try {
 521                                 result = Color.getColor(col, def);
 522                         } catch (Exception e2) {
 523                                 return def;
 524                         }
 525                 }
 526                 return result;
 527         }
 528
 529         public VARNAPanel get_varnaPanel() {
 530                 return vp;
 531         }
 532
 533         public void set_varnaPanel(VARNAPanel surface) {
 534                 vp = surface;
 535         }
 536
 537
 538         public String get_seq() {
 539                 return _seq.getText();
 540         }
 541
 542         public void set_seq(String _seq) {
 543                 this._seq.setText(_seq);
 544         }
 545
 546         public String get_str(){
 547                 return _str.getText();
 548         }
 549
 550         public void set_str(String _str){
 551                 this._str.setText(_str);
 552         }
 553
 554         public JLabel get_info() {
 555                 return _info;
 556         }
 557
 558         public void set_info(JLabel _info) {
 559                 this._info = _info;
 560         }
 561
 562         /*public static void main(String[] args) {
 563                 AppVarnaBinding d = new AppVarnaBinding();
 564                 d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
 565                 d.pack();
 566                 d.setVisible(true);
 567         }*/
 568
 569
 570         public void dragEnter(DropTargetDragEvent arg0) {
 571                 // TODO Auto-generated method stub
 572
 573         }
 574
 575         public void dragExit(DropTargetEvent arg0) {
 576                 // TODO Auto-generated method stub
 577
 578         }
 579
 580         public void dragOver(DropTargetDragEvent arg0) {
 581                 // TODO Auto-generated method stub
 582
 583         }
 584
 585         public void drop(DropTargetDropEvent dtde) {
 586             try {
 587                 Transferable tr = dtde.getTransferable();
 588                 DataFlavor[] flavors = tr.getTransferDataFlavors();
 589                 for (int i = 0; i < flavors.length; i++) {
 590             if (flavors[i].isFlavorJavaFileListType()) {
 591               dtde.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
 592               Object ob = tr.getTransferData(flavors[i]);
 593               if (ob instanceof List)
 594               {
 595                   List list = (List) ob;
 596                   for (int j = 0; j < list.size(); j++) {
 597                   Object o = list.get(j);
 598
 599                   if (dtde.getSource() instanceof DropTarget)
 600                   {
 601                           DropTarget dt = (DropTarget) dtde.getSource();
 602                           Component c = dt.getComponent();
 603                           if (c instanceof VARNAPanel)
 604                           {
 605                                           String path = o.toString();
 606                                   VARNAPanel vp = (VARNAPanel) c;
 607                                           try{
 608                                   FullBackup bck =  VARNAPanel.importSession(path);
 609                                   _rnaList.add(bck.config, bck.rna,bck.name,true);
 610                                           }
 611                                           catch (ExceptionLoadingFailed e3)
 612                                           {
 613                                                   RNA r = new RNA();
 614                                                   r.loadSecStr(path);
 615                                                   r.drawRNA(vp.getConfig());
 616                                                   String name =r.getName();
 617                                                   if (name.equals(""))
 618                                                   {
 619                                                           name = path.substring(path.lastIndexOf(File.separatorChar)+1);
 620                                                   }
 621                                                   _rnaList.add(vp.getConfig().clone(),r,name,true);
 622                                           }
 623                           }
 624                   }
 625                   }
 626               }
 627               // If we made it this far, everything worked.
 628               dtde.dropComplete(true);
 629               return;
 630             }
 631                 }
 632                 // Hmm, the user must not have dropped a file list
 633                 dtde.rejectDrop();
 634               } catch (Exception e) {
 635                 e.printStackTrace();
 636                 dtde.rejectDrop();
 637               }
 638
 639         }
 640
 641         public void dropActionChanged(DropTargetDragEvent arg0) {
 642         }
 643
 644         private class BackupHolder{
 645                 private DefaultListModel _rnaList;
 646                 private ArrayList<RNA> _rnas = new ArrayList<RNA>();
 647                 JList _l;
 648
 649                 public BackupHolder(DefaultListModel rnaList, JList l)
 650                 {
 651                         _rnaList = rnaList;
 652                         _l = l;
 653                 }
 654
 655                 public void add(VARNAConfig c, RNA r)
 656                 {
 657                         add(c, r, r.getName(),false);
 658                 }
 659
 660                 public void add(VARNAConfig c, RNA r,boolean select)
 661                 {
 662                         add(c, r, r.getName(),select);
 663                 }
 664
 665                 public void add(VARNAConfig c, RNA r, String name)
 666                 {
 667                         add(c, r, name,false);
 668                 }
 669                 public void add(VARNAConfig c, RNA r, String name, boolean select)
 670                 {
 671                         if (select){
 672                                 _l.removeSelectionInterval(0, _rnaList.size());
 673                         }
 674                         if (name.equals(""))
 675                         {
 676                                 name = generateDefaultName();
 677                         }
 678                         FullBackup bck = new FullBackup(c,r,name);
 679                         _rnas.add(0, r);
 680                         _rnaList.add(0,bck);
 681                         if (select){
 682                           _l.setSelectedIndex(0);
 683                         }
 684                 }
 685
 686                 public void remove(int i)
 687                 {
 688                         _rnas.remove(i);
 689                         _rnaList.remove(i);
 690
 691                 }
 692                 public DefaultListModel getModel()
 693                 {
 694                         return _rnaList;
 695                 }
 696                 public boolean contains(RNA r)
 697                 {
 698                         return _rnas.contains(r);
 699                 }
 700                 /*public int getSize()
 701                 {
 702                         return _rnaList.getSize();
 703                 }*/
 704                 public FullBackup getElementAt(int i)
 705                 {
 706                         return (FullBackup) _rnaList.getElementAt(i);
 707                 }
 708
 709                 public void removeSelected()
 710                 {
 711                         int i = _l.getSelectedIndex();
 712                         if (i!=-1)
 713                         {
 714                           if (_rnaList.getSize()==1)
 715                           {
 716                                   RNA r = new RNA();
 717                                   try {
 718                                         r.setRNA(" ", ".");
 719                                   } catch (ExceptionUnmatchedClosingParentheses e1) {
 720                                   } catch (ExceptionFileFormatOrSyntax e1) {
 721                                   }
 722                                   vp.showRNA(r);
 723                                   vp.repaint();
 724                           }
 725                           else
 726                           {
 727                                  int newi = i+1;
 728                                  if (newi==_rnaList.getSize())
 729                                  {
 730                                          newi = _rnaList.getSize()-2;
 731                                  }
 732                                  FullBackup bck = (FullBackup) _rnaList.getElementAt(newi);
 733                                  _l.setSelectedValue(bck,true);
 734                           }
 735                           _rnaList.remove(i);
 736                         }
 737
 738                 }
 739         }
 740
 741         public void onLayoutChanged() {
 742                 // TODO Auto-generated method stub
 743
 744         }
 745
 746         public void onUINewStructure(VARNAConfig v, RNA r) {
 747                 _rnaList.add(v, r,"",true);
 748         }
 749
 750         public void onWarningEmitted(String s) {
 751                 // TODO Auto-generated method stub
 752
 753         }
 754
 755         public void mouseClicked(MouseEvent e) {
 756                            if(e.getClickCount() == 2){
 757                              int index = _sideList.locationToIndex(e.getPoint());
 758                              ListModel dlm = _sideList.getModel();
 759                              FullBackup item = (FullBackup) dlm.getElementAt(index);;
 760                              _sideList.ensureIndexIsVisible(index);
 761                              /*TODO Object newName = JOptionPane.showInputDialog(
 762                                             this,
 763                                             "Specify a new name for this RNA",
 764                                             "Rename RNA",
 765                                             JOptionPane.QUESTION_MESSAGE,
 766                                             (Icon)null,
 767                                             null,
 768                                             item.toString());
 769                              if (newName!=null)
 770                              {
 771                                  item.name = newName.toString();
 772                                  this._sideList.repaint();
 773                              }*/
 774                              }
 775         }
 776
 777         public void mouseEntered(MouseEvent arg0) {
 778                 // TODO Auto-generated method stub
 779
 780         }
 781
 782         public void mouseExited(MouseEvent arg0) {
 783                 // TODO Auto-generated method stub
 784
 785         }
 786
 787         public void mousePressed(MouseEvent arg0) {
 788                 // TODO Auto-generated method stub
 789
 790         }
 791
 792         public void mouseReleased(MouseEvent arg0) {
 793                 // TODO Auto-generated method stub
 794
 795         }
 796
 797         @Override
 798         public Color getColour(int atomIndex, int pdbResNum, String chain,
 799                         String pdbId) {
 800                 // TODO Auto-generated method stub
 801                 return null;
 802         }
 803
 804         @Override
 805         public String[] getPdbFile() {
 806                 // TODO Auto-generated method stub
 807                 return null;
 808         }
 809
 810         @Override
 811         public void highlightAtom(int atomIndex, int pdbResNum, String chain,
 812                         String pdbId) {
 813                 // TODO Auto-generated method stub
 814
 815         }
 816
 817         @Override
 818         public void mouseOverStructure(int atomIndex, String strInfo) {
 819                 // TODO Auto-generated method stub
 820
 821         }
 822
 823         @Override
 824         public void releaseReferences(Object svl) {
 825                 // TODO Auto-generated method stub
 826
 827         }
 828
 829         @Override
 830         public void updateColours(Object source) {
 831                 // TODO Auto-generated method stub
 832
 833         }
 834
 835         @Override
 836         public void componentHidden(ComponentEvent e) {
 837                 // TODO Auto-generated method stub
 838
 839         }
 840
 841         @Override
 842         public void componentMoved(ComponentEvent e) {
 843                 // TODO Auto-generated method stub
 844
 845         }
 846
 847         @Override
 848         public void componentResized(ComponentEvent e) {
 849                 // TODO Auto-generated method stub
 850
 851         }
 852
 853         @Override
 854         public void componentShown(ComponentEvent e) {
 855                 // TODO Auto-generated method stub
 856
 857         }
 858 }
 859
 860
 861 /*
 862         public static void main(String[] args)
 863         {
 864                 JTextField str = new JTextField("ATGC");
 865
 866                 AppVarnaBinding vab = new AppVarnaBinding();
 867                 vab.varnagui.set_seq(str);
 868                 vab.varnagui.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
 869                 vab.varnagui.pack();
 870                 vab.varnagui.setVisible(true);
 871         }
 872 }
 873 */