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 _deleteButton = new JButton("Delete");
 100         private JButton _duplicateButton = new JButton("Snapshot");
 101
 102         protected 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
 226                 try {
 227                         vp = new VARNAPanel("0",".");
 228                         for(int i=0;i<rnaInList.size();i++){
 229                                 rnaInList.get(i).drawRNARadiate(vp.getConfig());
 230                         }
 231                 } catch (ExceptionNonEqualLength e) {
 232                         vp.errorDialog(e);
 233                 }
 234                 vp.setPreferredSize(new Dimension(400, 400));
 235                 for(int i=0;i<rnaInList.size();i++){
 236                         if(i<rnaInList.size()-1){
 237                                 _rnaList.add(vp.getConfig().clone(),rnaInList.get(i),generateDefaultName());
 238                         }else{
 239                                 _rnaList.add(vp.getConfig().clone(),rnaInList.get(i),generateDefaultName(),true);
 240                         }
 241                 }
 242
 243             /*_rnaList.add(vp.getConfig().clone(),_RNA2,generateDefaultName());
 244             _rnaList.add(vp.getConfig().clone(),_RNA1,generateDefaultName(),true);*/
 245
 246             JScrollPane listScroller = new JScrollPane(_sideList);
 247             listScroller.setPreferredSize(new Dimension(150, 0));
 248
 249                 vp.setBackground(_backgroundColor);
 250
 251                 /*
 252                 Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
 253
 254                 _seqLabel.setHorizontalTextPosition(JLabel.LEFT);
 255                 _seqLabel.setPreferredSize(new Dimension(marginTools, 15));
 256                 _seq.setFont(textFieldsFont);
 257                 _seq.setText(rnaInList.get(0).getSeq());
 258
 259                 _createButton.addActionListener(new ActionListener() {
 260                         public void actionPerformed(ActionEvent e) {
 261                                 try {
 262                                 RNA nRNA = new RNA(generateDefaultName());
 263                                 nRNA.setRNA(_seq.getText(), _str.getText());
 264                                 nRNA.drawRNARadiate(vp.getConfig());
 265                                 _rnaList.add(new VARNAConfig(),nRNA,true);
 266                                 } catch (ExceptionUnmatchedClosingParentheses e1) {
 267                                         JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
 268                                 } catch (ExceptionFileFormatOrSyntax e1) {
 269                                         JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
 270                                 }
 271                         }
 272                 });
 273
 274                 _seqPanel.setLayout(new BorderLayout());
 275                 _seqPanel.add(_seqLabel, BorderLayout.WEST);
 276                 _seqPanel.add(_seq, BorderLayout.CENTER);
 277
 278                 _strLabel.setPreferredSize(new Dimension(marginTools, 15));
 279                 _strLabel.setHorizontalTextPosition(JLabel.LEFT);
 280                 _str.setFont(textFieldsFont);
 281                 _strPanel.setLayout(new BorderLayout());
 282                 _strPanel.add(_strLabel, BorderLayout.WEST);
 283                 _strPanel.add(_str, BorderLayout.CENTER);
 284
 285                 _input.setLayout(new GridLayout(2, 0));
 286                 _input.add(_seqPanel);
 287                 _input.add(_strPanel);
 288
 289                 JPanel goPanel = new JPanel();
 290                 goPanel.setLayout(new BorderLayout());
 291
 292                 _tools.setLayout(new BorderLayout());
 293                 _tools.add(_input, BorderLayout.CENTER);
 294                 _tools.add(_info, BorderLayout.SOUTH);
 295                 _tools.add(goPanel, BorderLayout.EAST);
 296
 297                 _deleteButton.addActionListener(new ActionListener() {
 298                         public void actionPerformed(ActionEvent e) {
 299                                 _rnaList.removeSelected();
 300                         }
 301                 });
 302                 _duplicateButton.addActionListener(new ActionListener() {
 303                         public void actionPerformed(ActionEvent e) {
 304                                         _rnaList.add((VARNAConfig)vp.getConfig().clone(),vp.getRNA().clone(),vp.getRNA().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new Date()),true);
 305                         }});
 306                 goPanel.add(_createButton, BorderLayout.CENTER);
 307                 */
 308                 JPanel ops = new JPanel();
 309                 ops.setLayout(new GridLayout(1,2));
 310                 ops.add(_deleteButton);
 311                 ops.add(_duplicateButton);
 312
 313                 JLabel j = new JLabel("Structures Manager",JLabel.CENTER);
 314                 _listPanel.setLayout(new BorderLayout());
 315
 316                 _listPanel.add(ops,BorderLayout.SOUTH);
 317                 _listPanel.add(j,BorderLayout.NORTH);
 318                 _listPanel.add(listScroller,BorderLayout.CENTER);
 319
 320
 321
 322                 //JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,vp);
 323                 /**TODO
 324                 getContentPane().setLayout(new BorderLayout());
 325                 getContentPane().add(split, BorderLayout.CENTER);
 326                 getContentPane().add(_tools, BorderLayout.NORTH);
 327                  */
 328
 329                 //TODO setVisible(true);
 330                 DropTarget dt = new DropTarget(vp, this);
 331
 332                 vp.addVARNAListener(this);
 333         }
 334
 335         public JPanel getTools(){
 336                 return _tools;
 337         }
 338
 339         public JPanel getListPanel(){
 340                 return _listPanel;
 341         }
 342
 343         /*
 344         private void RNAPanelDemoInit()
 345         {
 346             DefaultListModel dlm = new DefaultListModel();
 347
 348
 349                 int marginTools = 40;
 350
 351             DefaultListSelectionModel m = new DefaultListSelectionModel();
 352             m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 353             m.setLeadAnchorNotificationEnabled(false);
 354
 355
 356                 _sideList = new ReorderableJList();
 357                 _sideList.setModel(dlm);
 358                 _sideList.addMouseListener(this);
 359             _sideList.setSelectionModel(m);
 360             _sideList.setPreferredSize(new Dimension(100, 0));
 361             _sideList.addListSelectionListener( new ListSelectionListener(){
 362                         public void valueChanged(ListSelectionEvent arg0) {
 363                                 //System.out.println(arg0);
 364                                 if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
 365                                 {
 366                                         FullBackup  sel = (FullBackup) _sideList.getSelectedValue();
 367                                         Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA().getSize(), sel.rna.getSize());
 368                                         vp.showRNAInterpolated(sel.rna,sel.config,map);
 369                                         _seq.setText(sel.rna.getSeq());
 370                                         _str.setText(sel.rna.getStructDBN());
 371                                 }
 372                         }
 373             });
 374
 375             _rnaList = new BackupHolder(dlm,_sideList);
 376                 RNA _RNA1 = new RNA("User defined 1");
 377                 RNA _RNA2 = new RNA("User defined 2");
 378                 try {
 379                         vp = new VARNAPanel("0",".");
 380                         _RNA1.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE1);
 381                         _RNA1.drawRNARadiate(vp.getConfig());
 382                         _RNA2.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE2);
 383                         _RNA2.drawRNARadiate(vp.getConfig());
 384                 } catch (ExceptionNonEqualLength e) {
 385                         vp.errorDialog(e);
 386                 } catch (ExceptionUnmatchedClosingParentheses e2) {
 387                 e2.printStackTrace();
 388                 } catch (ExceptionFileFormatOrSyntax e3) {
 389                 e3.printStackTrace();
 390                 }
 391                 vp.setPreferredSize(new Dimension(400, 400));
 392             _rnaList.add(vp.getConfig().clone(),_RNA2,generateDefaultName());
 393             _rnaList.add(vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
 394
 395             JScrollPane listScroller = new JScrollPane(_sideList);
 396             listScroller.setPreferredSize(new Dimension(150, 0));
 397
 398                 setBackground(_backgroundColor);
 399                 vp.setBackground(_backgroundColor);
 400
 401
 402                 Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
 403
 404                 _seqLabel.setHorizontalTextPosition(JLabel.LEFT);
 405                 _seqLabel.setPreferredSize(new Dimension(marginTools, 15));
 406                 _seq.setFont(textFieldsFont);
 407                 _seq.setText(DEFAULT_SEQUENCE);
 408
 409                 _createButton.addActionListener(new ActionListener() {
 410                         public void actionPerformed(ActionEvent e) {
 411                                 try {
 412                                 RNA nRNA = new RNA(generateDefaultName());
 413                                 nRNA.setRNA(_seq.getText(), _str.getText());
 414                                 nRNA.drawRNARadiate(vp.getConfig());
 415                                 _rnaList.add(new VARNAConfig(),nRNA,true);
 416                                 } catch (ExceptionUnmatchedClosingParentheses e1) {
 417                                         JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
 418                                 } catch (ExceptionFileFormatOrSyntax e1) {
 419                                         JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
 420                                 }
 421                         }
 422                 });
 423
 424
 425                 _seqPanel.setLayout(new BorderLayout());
 426                 _seqPanel.add(_seqLabel, BorderLayout.WEST);
 427                 _seqPanel.add(_seq, BorderLayout.CENTER);
 428
 429                 _strLabel.setPreferredSize(new Dimension(marginTools, 15));
 430                 _strLabel.setHorizontalTextPosition(JLabel.LEFT);
 431                 _str.setFont(textFieldsFont);
 432                 _strPanel.setLayout(new BorderLayout());
 433                 _strPanel.add(_strLabel, BorderLayout.WEST);
 434                 _strPanel.add(_str, BorderLayout.CENTER);
 435
 436                 _input.setLayout(new GridLayout(2, 0));
 437                 _input.add(_seqPanel);
 438                 _input.add(_strPanel);
 439
 440                 JPanel goPanel = new JPanel();
 441                 goPanel.setLayout(new BorderLayout());
 442
 443                 _tools.setLayout(new BorderLayout());
 444                 _tools.add(_input, BorderLayout.CENTER);
 445                 _tools.add(_info, BorderLayout.SOUTH);
 446                 _tools.add(goPanel, BorderLayout.EAST);
 447
 448                 _deleteButton.addActionListener(new ActionListener() {
 449                         public void actionPerformed(ActionEvent e) {
 450                                 _rnaList.removeSelected();
 451                         }
 452                 });
 453                 _duplicateButton.addActionListener(new ActionListener() {
 454                         public void actionPerformed(ActionEvent e) {
 455                                         _rnaList.add((VARNAConfig)vp.getConfig().clone(),vp.getRNA().clone(),vp.getRNA().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new Date()),true);
 456                         }});
 457
 458                 JPanel ops = new JPanel();
 459                 ops.setLayout(new GridLayout(1,2));
 460                 ops.add(_deleteButton);
 461                 ops.add(_duplicateButton);
 462
 463                 JLabel j = new JLabel("Structures Manager",JLabel.CENTER);
 464                 _listPanel.setLayout(new BorderLayout());
 465
 466                 _listPanel.add(ops,BorderLayout.SOUTH);
 467                 _listPanel.add(j,BorderLayout.NORTH);
 468                 _listPanel.add(listScroller,BorderLayout.CENTER);
 469
 470                 goPanel.add(_createButton, BorderLayout.CENTER);
 471
 472                 JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,vp);
 473                 getContentPane().setLayout(new BorderLayout());
 474                 getContentPane().add(split, BorderLayout.CENTER);
 475                 getContentPane().add(_tools, BorderLayout.NORTH);
 476
 477                 setVisible(true);
 478                 DropTarget dt = new DropTarget(vp, this);
 479
 480                 vp.addVARNAListener(this);
 481         }
 482         */
 483         public static String generateDefaultName()
 484         {
 485                 return "User file #"+_nextID++;
 486         }
 487
 488         public RNA getRNA() {
 489                 return (RNA)_sideList.getSelectedValue();
 490         }
 491
 492
 493
 494         public String[][] getParameterInfo() {
 495                 String[][] info = {
 496                                 // Parameter Name Kind of Value Description,
 497                                 { "sequenceDBN", "String", "A raw RNA sequence" },
 498                                 { "structureDBN", "String",
 499                                                 "An RNA structure in dot bracket notation (DBN)" },
 500                                 { errorOpt, "boolean", "To show errors" }, };
 501                 return info;
 502         }
 503
 504         public void init() {
 505                 vp.setBackground(_backgroundColor);
 506                 _error = true;
 507         }
 508
 509         @SuppressWarnings("unused")
 510         private Color getSafeColor(String col, Color def) {
 511                 Color result;
 512                 try {
 513                         result = Color.decode(col);
 514                 } catch (Exception e) {
 515                         try {
 516                                 result = Color.getColor(col, def);
 517                         } catch (Exception e2) {
 518                                 return def;
 519                         }
 520                 }
 521                 return result;
 522         }
 523
 524         public VARNAPanel get_varnaPanel() {
 525                 return vp;
 526         }
 527
 528         public void set_varnaPanel(VARNAPanel surface) {
 529                 vp = surface;
 530         }
 531
 532
 533         public String get_seq() {
 534                 return _seq.getText();
 535         }
 536
 537         public void set_seq(String _seq) {
 538                 this._seq.setText(_seq);
 539         }
 540
 541         public String get_str(){
 542                 return _str.getText();
 543         }
 544
 545         public void set_str(String _str){
 546                 this._str.setText(_str);
 547         }
 548
 549         public JLabel get_info() {
 550                 return _info;
 551         }
 552
 553         public void set_info(JLabel _info) {
 554                 this._info = _info;
 555         }
 556
 557         /*public static void main(String[] args) {
 558                 AppVarnaBinding d = new AppVarnaBinding();
 559                 d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
 560                 d.pack();
 561                 d.setVisible(true);
 562         }*/
 563
 564
 565         public void dragEnter(DropTargetDragEvent arg0) {
 566                 // TODO Auto-generated method stub
 567
 568         }
 569
 570         public void dragExit(DropTargetEvent arg0) {
 571                 // TODO Auto-generated method stub
 572
 573         }
 574
 575         public void dragOver(DropTargetDragEvent arg0) {
 576                 // TODO Auto-generated method stub
 577
 578         }
 579
 580         public void drop(DropTargetDropEvent dtde) {
 581             try {
 582                 Transferable tr = dtde.getTransferable();
 583                 DataFlavor[] flavors = tr.getTransferDataFlavors();
 584                 for (int i = 0; i < flavors.length; i++) {
 585             if (flavors[i].isFlavorJavaFileListType()) {
 586               dtde.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
 587               Object ob = tr.getTransferData(flavors[i]);
 588               if (ob instanceof List)
 589               {
 590                   List list = (List) ob;
 591                   for (int j = 0; j < list.size(); j++) {
 592                   Object o = list.get(j);
 593
 594                   if (dtde.getSource() instanceof DropTarget)
 595                   {
 596                           DropTarget dt = (DropTarget) dtde.getSource();
 597                           Component c = dt.getComponent();
 598                           if (c instanceof VARNAPanel)
 599                           {
 600                                           String path = o.toString();
 601                                   VARNAPanel vp = (VARNAPanel) c;
 602                                           try{
 603                                   FullBackup bck =  VARNAPanel.importSession(path);
 604                                   _rnaList.add(bck.config, bck.rna,bck.name,true);
 605                                           }
 606                                           catch (ExceptionLoadingFailed e3)
 607                                           {
 608                                                   RNA r = new RNA();
 609                                                   r.loadSecStr(path);
 610                                                   r.drawRNA(vp.getConfig());
 611                                                   String name =r.getName();
 612                                                   if (name.equals(""))
 613                                                   {
 614                                                           name = path.substring(path.lastIndexOf(File.separatorChar)+1);
 615                                                   }
 616                                                   _rnaList.add(vp.getConfig().clone(),r,name,true);
 617                                           }
 618                           }
 619                   }
 620                   }
 621               }
 622               // If we made it this far, everything worked.
 623               dtde.dropComplete(true);
 624               return;
 625             }
 626                 }
 627                 // Hmm, the user must not have dropped a file list
 628                 dtde.rejectDrop();
 629               } catch (Exception e) {
 630                 e.printStackTrace();
 631                 dtde.rejectDrop();
 632               }
 633
 634         }
 635
 636         public void dropActionChanged(DropTargetDragEvent arg0) {
 637         }
 638
 639         private class BackupHolder{
 640                 private DefaultListModel _rnaList;
 641                 private ArrayList<RNA> _rnas = new ArrayList<RNA>();
 642                 JList _l;
 643
 644                 public BackupHolder(DefaultListModel rnaList, JList l)
 645                 {
 646                         _rnaList = rnaList;
 647                         _l = l;
 648                 }
 649
 650                 public void add(VARNAConfig c, RNA r)
 651                 {
 652                         add(c, r, r.getName(),false);
 653                 }
 654
 655                 public void add(VARNAConfig c, RNA r,boolean select)
 656                 {
 657                         add(c, r, r.getName(),select);
 658                 }
 659
 660                 public void add(VARNAConfig c, RNA r, String name)
 661                 {
 662                         add(c, r, name,false);
 663                 }
 664                 public void add(VARNAConfig c, RNA r, String name, boolean select)
 665                 {
 666                         if (select){
 667                                 _l.removeSelectionInterval(0, _rnaList.size());
 668                         }
 669                         if (name.equals(""))
 670                         {
 671                                 name = generateDefaultName();
 672                         }
 673                         FullBackup bck = new FullBackup(c,r,name);
 674                         _rnas.add(0, r);
 675                         _rnaList.add(0,bck);
 676                         if (select){
 677                           _l.setSelectedIndex(0);
 678                         }
 679                 }
 680
 681                 public void remove(int i)
 682                 {
 683                         _rnas.remove(i);
 684                         _rnaList.remove(i);
 685
 686                 }
 687                 public DefaultListModel getModel()
 688                 {
 689                         return _rnaList;
 690                 }
 691                 public boolean contains(RNA r)
 692                 {
 693                         return _rnas.contains(r);
 694                 }
 695                 /*public int getSize()
 696                 {
 697                         return _rnaList.getSize();
 698                 }*/
 699                 public FullBackup getElementAt(int i)
 700                 {
 701                         return (FullBackup) _rnaList.getElementAt(i);
 702                 }
 703
 704                 public void removeSelected()
 705                 {
 706                         int i = _l.getSelectedIndex();
 707                         if (i!=-1)
 708                         {
 709                           if (_rnaList.getSize()==1)
 710                           {
 711                                   RNA r = new RNA();
 712                                   try {
 713                                         r.setRNA(" ", ".");
 714                                   } catch (ExceptionUnmatchedClosingParentheses e1) {
 715                                   } catch (ExceptionFileFormatOrSyntax e1) {
 716                                   }
 717                                   vp.showRNA(r);
 718                                   vp.repaint();
 719                           }
 720                           else
 721                           {
 722                                  int newi = i+1;
 723                                  if (newi==_rnaList.getSize())
 724                                  {
 725                                          newi = _rnaList.getSize()-2;
 726                                  }
 727                                  FullBackup bck = (FullBackup) _rnaList.getElementAt(newi);
 728                                  _l.setSelectedValue(bck,true);
 729                           }
 730                           _rnaList.remove(i);
 731                         }
 732
 733                 }
 734         }
 735
 736         public void onLayoutChanged() {
 737                 // TODO Auto-generated method stub
 738
 739         }
 740
 741         public void onUINewStructure(VARNAConfig v, RNA r) {
 742                 _rnaList.add(v, r,"",true);
 743         }
 744
 745         public void onWarningEmitted(String s) {
 746                 // TODO Auto-generated method stub
 747
 748         }
 749
 750         public void mouseClicked(MouseEvent e) {
 751                            if(e.getClickCount() == 2){
 752                              int index = _sideList.locationToIndex(e.getPoint());
 753                              ListModel dlm = _sideList.getModel();
 754                              FullBackup item = (FullBackup) dlm.getElementAt(index);;
 755                              _sideList.ensureIndexIsVisible(index);
 756                              /*TODO Object newName = JOptionPane.showInputDialog(
 757                                             this,
 758                                             "Specify a new name for this RNA",
 759                                             "Rename RNA",
 760                                             JOptionPane.QUESTION_MESSAGE,
 761                                             (Icon)null,
 762                                             null,
 763                                             item.toString());
 764                              if (newName!=null)
 765                              {
 766                                  item.name = newName.toString();
 767                                  this._sideList.repaint();
 768                              }*/
 769                              }
 770         }
 771
 772         public void mouseEntered(MouseEvent arg0) {
 773                 // TODO Auto-generated method stub
 774
 775         }
 776
 777         public void mouseExited(MouseEvent arg0) {
 778                 // TODO Auto-generated method stub
 779
 780         }
 781
 782         public void mousePressed(MouseEvent arg0) {
 783                 // TODO Auto-generated method stub
 784
 785         }
 786
 787         public void mouseReleased(MouseEvent arg0) {
 788                 // TODO Auto-generated method stub
 789
 790         }
 791
 792         @Override
 793         public Color getColour(int atomIndex, int pdbResNum, String chain,
 794                         String pdbId) {
 795                 // TODO Auto-generated method stub
 796                 return null;
 797         }
 798
 799         @Override
 800         public String[] getPdbFile() {
 801                 // TODO Auto-generated method stub
 802                 return null;
 803         }
 804
 805         @Override
 806         public void highlightAtom(int atomIndex, int pdbResNum, String chain,
 807                         String pdbId) {
 808                 // TODO Auto-generated method stub
 809
 810         }
 811
 812         @Override
 813         public void mouseOverStructure(int atomIndex, String strInfo) {
 814                 // TODO Auto-generated method stub
 815
 816         }
 817
 818         @Override
 819         public void releaseReferences(Object svl) {
 820                 // TODO Auto-generated method stub
 821
 822         }
 823
 824         @Override
 825         public void updateColours(Object source) {
 826                 // TODO Auto-generated method stub
 827
 828         }
 829
 830         @Override
 831         public void componentHidden(ComponentEvent e) {
 832                 // TODO Auto-generated method stub
 833
 834         }
 835
 836         @Override
 837         public void componentMoved(ComponentEvent e) {
 838                 // TODO Auto-generated method stub
 839
 840         }
 841
 842         @Override
 843         public void componentResized(ComponentEvent e) {
 844                 // TODO Auto-generated method stub
 845
 846         }
 847
 848         @Override
 849         public void componentShown(ComponentEvent e) {
 850                 // TODO Auto-generated method stub
 851
 852         }
 853 }
 854
 855
 856 /*
 857         public static void main(String[] args)
 858         {
 859                 JTextField str = new JTextField("ATGC");
 860
 861                 AppVarnaBinding vab = new AppVarnaBinding();
 862                 vab.varnagui.set_seq(str);
 863                 vab.varnagui.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
 864                 vab.varnagui.pack();
 865                 vab.varnagui.setVisible(true);
 866         }
 867 }
 868 */