src/jalview/gui/AppVarnaBinding.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   3  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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             _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),rnaInList.get(i).getName());
 238                         }else{
 239                                 _rnaList.add(vp.getConfig().clone(),rnaInList.get(i),rnaInList.get(i).getName(),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                 _updateButton.addActionListener(new ActionListener() {
 260                         public void actionPerformed(ActionEvent e) {
 261                                 FullBackup  sel = (FullBackup) _sideList.getSelectedValue();
 262                                 sel.rna.setSequence("A");
 263                                 }
 264                 });
 265
 266                 //_seqPanel.setLayout(new BorderLayout());
 267                 //_seqPanel.add(_seqLabel, BorderLayout.WEST);
 268                 //_seqPanel.add(_seq, BorderLayout.CENTER);
 269
 270                 _strLabel.setPreferredSize(new Dimension(marginTools, 15));
 271                 _strLabel.setHorizontalTextPosition(JLabel.LEFT);
 272                 _str.setFont(textFieldsFont);
 273                 _strPanel.setLayout(new BorderLayout());
 274                 _strPanel.add(_strLabel, BorderLayout.WEST);
 275                 _strPanel.add(_str, BorderLayout.CENTER);
 276
 277                 _input.setLayout(new GridLayout(1, 0));
 278                 //_input.add(_seqPanel);
 279                 _input.add(_strPanel);
 280
 281                 JPanel goPanel = new JPanel();
 282                 goPanel.setLayout(new BorderLayout());
 283
 284                 _tools.setLayout(new BorderLayout());
 285                 _tools.add(_input, BorderLayout.CENTER);
 286                 //_tools.add(_info, BorderLayout.SOUTH);
 287                 _tools.add(goPanel, BorderLayout.EAST);
 288
 289                 /*_deleteButton.addActionListener(new ActionListener() {
 290                         public void actionPerformed(ActionEvent e) {
 291                                 _rnaList.removeSelected();
 292                         }
 293                 });
 294                 _duplicateButton.addActionListener(new ActionListener() {
 295                         public void actionPerformed(ActionEvent e) {
 296                                         _rnaList.add((VARNAConfig)vp.getConfig().clone(),vp.getRNA().clone(),vp.getRNA().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new Date()),true);
 297                         }});
 298                 */
 299                 goPanel.add(_updateButton, BorderLayout.CENTER);
 300
 301
 302                 JPanel ops = new JPanel();
 303                 ops.setLayout(new GridLayout(1,2));
 304                 ops.add(_deleteButton);
 305                 ops.add(_duplicateButton);
 306
 307                 JLabel j = new JLabel("Structures Manager",JLabel.CENTER);
 308                 _listPanel.setLayout(new BorderLayout());
 309
 310                 _listPanel.add(ops,BorderLayout.SOUTH);
 311                 _listPanel.add(j,BorderLayout.NORTH);
 312                 _listPanel.add(listScroller,BorderLayout.CENTER);
 313
 314
 315
 316                 //JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,vp);
 317                 /**TODO
 318                 getContentPane().setLayout(new BorderLayout());
 319                 getContentPane().add(split, BorderLayout.CENTER);
 320                 getContentPane().add(_tools, BorderLayout.NORTH);
 321                  */
 322
 323                 //TODO setVisible(true);
 324                 DropTarget dt = new DropTarget(vp, this);
 325
 326                 vp.addVARNAListener(this);
 327         }
 328
 329         public JPanel getTools(){
 330                 return _tools;
 331         }
 332
 333         public JPanel getListPanel(){
 334                 return _listPanel;
 335         }
 336
 337         /**
 338          * TODO: Is it effective to transfer the whole RNA?
 339          * @return Currently selected RNA
 340          */
 341         public RNA getSelectedRNA(){
 342                 return _rnaList.getElementAt(_sideList.getSelectedIndex()).rna;
 343         }
 344
 345         /**
 346          * Substitute currently selected RNA with the edited one
 347          * @param rnaEdit
 348          */
 349         public void updateSelectedRNA(RNA rnaEdit){
 350                 vp.repaint();
 351                 vp.showRNA(rnaEdit);
 352         }
 353
 354         /*
 355         private void RNAPanelDemoInit()
 356         {
 357             DefaultListModel dlm = new DefaultListModel();
 358
 359
 360                 int marginTools = 40;
 361
 362             DefaultListSelectionModel m = new DefaultListSelectionModel();
 363             m.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 364             m.setLeadAnchorNotificationEnabled(false);
 365
 366
 367                 _sideList = new ReorderableJList();
 368                 _sideList.setModel(dlm);
 369                 _sideList.addMouseListener(this);
 370             _sideList.setSelectionModel(m);
 371             _sideList.setPreferredSize(new Dimension(100, 0));
 372             _sideList.addListSelectionListener( new ListSelectionListener(){
 373                         public void valueChanged(ListSelectionEvent arg0) {
 374                                 //System.out.println(arg0);
 375                                 if (!_sideList.isSelectionEmpty() && !arg0.getValueIsAdjusting())
 376                                 {
 377                                         FullBackup  sel = (FullBackup) _sideList.getSelectedValue();
 378                                         Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA().getSize(), sel.rna.getSize());
 379                                         vp.showRNAInterpolated(sel.rna,sel.config,map);
 380                                         _seq.setText(sel.rna.getSeq());
 381                                         _str.setText(sel.rna.getStructDBN());
 382                                 }
 383                         }
 384             });
 385
 386             _rnaList = new BackupHolder(dlm,_sideList);
 387                 RNA _RNA1 = new RNA("User defined 1");
 388                 RNA _RNA2 = new RNA("User defined 2");
 389                 try {
 390                         vp = new VARNAPanel("0",".");
 391                         _RNA1.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE1);
 392                         _RNA1.drawRNARadiate(vp.getConfig());
 393                         _RNA2.setRNA(DEFAULT_SEQUENCE, DEFAULT_STRUCTURE2);
 394                         _RNA2.drawRNARadiate(vp.getConfig());
 395                 } catch (ExceptionNonEqualLength e) {
 396                         vp.errorDialog(e);
 397                 } catch (ExceptionUnmatchedClosingParentheses e2) {
 398                 e2.printStackTrace();
 399                 } catch (ExceptionFileFormatOrSyntax e3) {
 400                 e3.printStackTrace();
 401                 }
 402                 vp.setPreferredSize(new Dimension(400, 400));
 403             _rnaList.add(vp.getConfig().clone(),_RNA2,generateDefaultName());
 404             _rnaList.add(vp.getConfig().clone(),_RNA1,generateDefaultName(),true);
 405
 406             JScrollPane listScroller = new JScrollPane(_sideList);
 407             listScroller.setPreferredSize(new Dimension(150, 0));
 408
 409                 setBackground(_backgroundColor);
 410                 vp.setBackground(_backgroundColor);
 411
 412
 413                 Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
 414
 415                 _seqLabel.setHorizontalTextPosition(JLabel.LEFT);
 416                 _seqLabel.setPreferredSize(new Dimension(marginTools, 15));
 417                 _seq.setFont(textFieldsFont);
 418                 _seq.setText(DEFAULT_SEQUENCE);
 419
 420                 _createButton.addActionListener(new ActionListener() {
 421                         public void actionPerformed(ActionEvent e) {
 422                                 try {
 423                                 RNA nRNA = new RNA(generateDefaultName());
 424                                 nRNA.setRNA(_seq.getText(), _str.getText());
 425                                 nRNA.drawRNARadiate(vp.getConfig());
 426                                 _rnaList.add(new VARNAConfig(),nRNA,true);
 427                                 } catch (ExceptionUnmatchedClosingParentheses e1) {
 428                                         JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
 429                                 } catch (ExceptionFileFormatOrSyntax e1) {
 430                                         JOptionPane.showMessageDialog(vp, e1.getMessage(),"Error", JOptionPane.ERROR_MESSAGE);
 431                                 }
 432                         }
 433                 });
 434
 435
 436                 _seqPanel.setLayout(new BorderLayout());
 437                 _seqPanel.add(_seqLabel, BorderLayout.WEST);
 438                 _seqPanel.add(_seq, BorderLayout.CENTER);
 439
 440                 _strLabel.setPreferredSize(new Dimension(marginTools, 15));
 441                 _strLabel.setHorizontalTextPosition(JLabel.LEFT);
 442                 _str.setFont(textFieldsFont);
 443                 _strPanel.setLayout(new BorderLayout());
 444                 _strPanel.add(_strLabel, BorderLayout.WEST);
 445                 _strPanel.add(_str, BorderLayout.CENTER);
 446
 447                 _input.setLayout(new GridLayout(2, 0));
 448                 _input.add(_seqPanel);
 449                 _input.add(_strPanel);
 450
 451                 JPanel goPanel = new JPanel();
 452                 goPanel.setLayout(new BorderLayout());
 453
 454                 _tools.setLayout(new BorderLayout());
 455                 _tools.add(_input, BorderLayout.CENTER);
 456                 _tools.add(_info, BorderLayout.SOUTH);
 457                 _tools.add(goPanel, BorderLayout.EAST);
 458
 459                 _deleteButton.addActionListener(new ActionListener() {
 460                         public void actionPerformed(ActionEvent e) {
 461                                 _rnaList.removeSelected();
 462                         }
 463                 });
 464                 _duplicateButton.addActionListener(new ActionListener() {
 465                         public void actionPerformed(ActionEvent e) {
 466                                         _rnaList.add((VARNAConfig)vp.getConfig().clone(),vp.getRNA().clone(),vp.getRNA().getName()+"-"+DateFormat.getTimeInstance(DateFormat.LONG).format(new Date()),true);
 467                         }});
 468
 469                 JPanel ops = new JPanel();
 470                 ops.setLayout(new GridLayout(1,2));
 471                 ops.add(_deleteButton);
 472                 ops.add(_duplicateButton);
 473
 474                 JLabel j = new JLabel("Structures Manager",JLabel.CENTER);
 475                 _listPanel.setLayout(new BorderLayout());
 476
 477                 _listPanel.add(ops,BorderLayout.SOUTH);
 478                 _listPanel.add(j,BorderLayout.NORTH);
 479                 _listPanel.add(listScroller,BorderLayout.CENTER);
 480
 481                 goPanel.add(_createButton, BorderLayout.CENTER);
 482
 483                 JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,_listPanel,vp);
 484                 getContentPane().setLayout(new BorderLayout());
 485                 getContentPane().add(split, BorderLayout.CENTER);
 486                 getContentPane().add(_tools, BorderLayout.NORTH);
 487
 488                 setVisible(true);
 489                 DropTarget dt = new DropTarget(vp, this);
 490
 491                 vp.addVARNAListener(this);
 492         }
 493         */
 494         public static String generateDefaultName()
 495         {
 496                 return "User file #"+_nextID++;
 497         }
 498
 499         public RNA getRNA() {
 500                 return (RNA)_sideList.getSelectedValue();
 501         }
 502
 503
 504
 505         public String[][] getParameterInfo() {
 506                 String[][] info = {
 507                                 // Parameter Name Kind of Value Description,
 508                                 { "sequenceDBN", "String", "A raw RNA sequence" },
 509                                 { "structureDBN", "String",
 510                                                 "An RNA structure in dot bracket notation (DBN)" },
 511                                 { errorOpt, "boolean", "To show errors" }, };
 512                 return info;
 513         }
 514
 515         public void init() {
 516                 vp.setBackground(_backgroundColor);
 517                 _error = true;
 518         }
 519
 520         @SuppressWarnings("unused")
 521         private Color getSafeColor(String col, Color def) {
 522                 Color result;
 523                 try {
 524                         result = Color.decode(col);
 525                 } catch (Exception e) {
 526                         try {
 527                                 result = Color.getColor(col, def);
 528                         } catch (Exception e2) {
 529                                 return def;
 530                         }
 531                 }
 532                 return result;
 533         }
 534
 535         public VARNAPanel get_varnaPanel() {
 536                 return vp;
 537         }
 538
 539         public void set_varnaPanel(VARNAPanel surface) {
 540                 vp = surface;
 541         }
 542
 543
 544         public String get_seq() {
 545                 return _seq.getText();
 546         }
 547
 548         public void set_seq(String _seq) {
 549                 this._seq.setText(_seq);
 550         }
 551
 552         public String get_str(){
 553                 return _str.getText();
 554         }
 555
 556         public void set_str(String _str){
 557                 this._str.setText(_str);
 558         }
 559
 560         public JLabel get_info() {
 561                 return _info;
 562         }
 563
 564         public void set_info(JLabel _info) {
 565                 this._info = _info;
 566         }
 567
 568         /*public static void main(String[] args) {
 569                 AppVarnaBinding d = new AppVarnaBinding();
 570                 d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
 571                 d.pack();
 572                 d.setVisible(true);
 573         }*/
 574
 575
 576         public void dragEnter(DropTargetDragEvent arg0) {
 577                 // TODO Auto-generated method stub
 578
 579         }
 580
 581         public void dragExit(DropTargetEvent arg0) {
 582                 // TODO Auto-generated method stub
 583
 584         }
 585
 586         public void dragOver(DropTargetDragEvent arg0) {
 587                 // TODO Auto-generated method stub
 588
 589         }
 590
 591         public void drop(DropTargetDropEvent dtde) {
 592             try {
 593                 Transferable tr = dtde.getTransferable();
 594                 DataFlavor[] flavors = tr.getTransferDataFlavors();
 595                 for (int i = 0; i < flavors.length; i++) {
 596             if (flavors[i].isFlavorJavaFileListType()) {
 597               dtde.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
 598               Object ob = tr.getTransferData(flavors[i]);
 599               if (ob instanceof List)
 600               {
 601                   List list = (List) ob;
 602                   for (int j = 0; j < list.size(); j++) {
 603                   Object o = list.get(j);
 604
 605                   if (dtde.getSource() instanceof DropTarget)
 606                   {
 607                           DropTarget dt = (DropTarget) dtde.getSource();
 608                           Component c = dt.getComponent();
 609                           if (c instanceof VARNAPanel)
 610                           {
 611                                           String path = o.toString();
 612                                   VARNAPanel vp = (VARNAPanel) c;
 613                                           try{
 614                                   FullBackup bck =  VARNAPanel.importSession(path);
 615                                   _rnaList.add(bck.config, bck.rna,bck.name,true);
 616                                           }
 617                                           catch (ExceptionLoadingFailed e3)
 618                                           {
 619                                                   RNA r = new RNA();
 620                                                   r.loadSecStr(path);
 621                                                   r.drawRNA(vp.getConfig());
 622                                                   String name =r.getName();
 623                                                   if (name.equals(""))
 624                                                   {
 625                                                           name = path.substring(path.lastIndexOf(File.separatorChar)+1);
 626                                                   }
 627                                                   _rnaList.add(vp.getConfig().clone(),r,name,true);
 628                                           }
 629                           }
 630                   }
 631                   }
 632               }
 633               // If we made it this far, everything worked.
 634               dtde.dropComplete(true);
 635               return;
 636             }
 637                 }
 638                 // Hmm, the user must not have dropped a file list
 639                 dtde.rejectDrop();
 640               } catch (Exception e) {
 641                 e.printStackTrace();
 642                 dtde.rejectDrop();
 643               }
 644
 645         }
 646
 647         public void dropActionChanged(DropTargetDragEvent arg0) {
 648         }
 649
 650         private class BackupHolder{
 651                 private DefaultListModel _rnaList;
 652                 private ArrayList<RNA> _rnas = new ArrayList<RNA>();
 653                 JList _l;
 654
 655                 public BackupHolder(DefaultListModel rnaList, JList l)
 656                 {
 657                         _rnaList = rnaList;
 658                         _l = l;
 659                 }
 660
 661                 public void add(VARNAConfig c, RNA r)
 662                 {
 663                         add(c, r, r.getName(),false);
 664                 }
 665
 666                 public void add(VARNAConfig c, RNA r,boolean select)
 667                 {
 668                         add(c, r, r.getName(),select);
 669                 }
 670
 671                 public void add(VARNAConfig c, RNA r, String name)
 672                 {
 673                         add(c, r, name,false);
 674                 }
 675                 public void add(VARNAConfig c, RNA r, String name, boolean select)
 676                 {
 677                         if (select){
 678                                 _l.removeSelectionInterval(0, _rnaList.size());
 679                         }
 680                         if (name.equals(""))
 681                         {
 682                                 name = generateDefaultName();
 683                         }
 684                         FullBackup bck = new FullBackup(c,r,name);
 685                         _rnas.add(0, r);
 686                         _rnaList.add(0,bck);
 687                         if (select){
 688                           _l.setSelectedIndex(0);
 689                         }
 690                 }
 691
 692                 public void remove(int i)
 693                 {
 694                         _rnas.remove(i);
 695                         _rnaList.remove(i);
 696
 697                 }
 698                 public DefaultListModel getModel()
 699                 {
 700                         return _rnaList;
 701                 }
 702                 public boolean contains(RNA r)
 703                 {
 704                         return _rnas.contains(r);
 705                 }
 706                 /*public int getSize()
 707                 {
 708                         return _rnaList.getSize();
 709                 }*/
 710                 public FullBackup getElementAt(int i)
 711                 {
 712                         return (FullBackup) _rnaList.getElementAt(i);
 713                 }
 714
 715                 public void removeSelected()
 716                 {
 717                         int i = _l.getSelectedIndex();
 718                         if (i!=-1)
 719                         {
 720                           if (_rnaList.getSize()==1)
 721                           {
 722                                   RNA r = new RNA();
 723                                   try {
 724                                         r.setRNA(" ", ".");
 725                                   } catch (ExceptionUnmatchedClosingParentheses e1) {
 726                                   } catch (ExceptionFileFormatOrSyntax e1) {
 727                                   }
 728                                   vp.showRNA(r);
 729                                   vp.repaint();
 730                           }
 731                           else
 732                           {
 733                                  int newi = i+1;
 734                                  if (newi==_rnaList.getSize())
 735                                  {
 736                                          newi = _rnaList.getSize()-2;
 737                                  }
 738                                  FullBackup bck = (FullBackup) _rnaList.getElementAt(newi);
 739                                  _l.setSelectedValue(bck,true);
 740                           }
 741                           _rnaList.remove(i);
 742                         }
 743
 744                 }
 745         }
 746
 747         public void onLayoutChanged() {
 748                 // TODO Auto-generated method stub
 749
 750         }
 751
 752         public void onUINewStructure(VARNAConfig v, RNA r) {
 753                 _rnaList.add(v, r,"",true);
 754         }
 755
 756         public void onWarningEmitted(String s) {
 757                 // TODO Auto-generated method stub
 758
 759         }
 760
 761         public void mouseClicked(MouseEvent e) {
 762                            if(e.getClickCount() == 2){
 763                              int index = _sideList.locationToIndex(e.getPoint());
 764                              ListModel dlm = _sideList.getModel();
 765                              FullBackup item = (FullBackup) dlm.getElementAt(index);;
 766                              _sideList.ensureIndexIsVisible(index);
 767                              /*TODO Object newName = JOptionPane.showInputDialog(
 768                                             this,
 769                                             "Specify a new name for this RNA",
 770                                             "Rename RNA",
 771                                             JOptionPane.QUESTION_MESSAGE,
 772                                             (Icon)null,
 773                                             null,
 774                                             item.toString());
 775                              if (newName!=null)
 776                              {
 777                                  item.name = newName.toString();
 778                                  this._sideList.repaint();
 779                              }*/
 780                              }
 781         }
 782
 783         public void mouseEntered(MouseEvent arg0) {
 784                 // TODO Auto-generated method stub
 785
 786         }
 787
 788         public void mouseExited(MouseEvent arg0) {
 789                 // TODO Auto-generated method stub
 790
 791         }
 792
 793         public void mousePressed(MouseEvent arg0) {
 794                 // TODO Auto-generated method stub
 795
 796         }
 797
 798         public void mouseReleased(MouseEvent arg0) {
 799                 // TODO Auto-generated method stub
 800
 801         }
 802
 803         @Override
 804         public Color getColour(int atomIndex, int pdbResNum, String chain,
 805                         String pdbId) {
 806                 // TODO Auto-generated method stub
 807                 return null;
 808         }
 809
 810         @Override
 811         public String[] getPdbFile() {
 812                 // TODO Auto-generated method stub
 813                 return null;
 814         }
 815
 816         @Override
 817         public void highlightAtom(int atomIndex, int pdbResNum, String chain,
 818                         String pdbId) {
 819                 // TODO Auto-generated method stub
 820
 821         }
 822
 823         @Override
 824         public void mouseOverStructure(int atomIndex, String strInfo) {
 825                 // TODO Auto-generated method stub
 826
 827         }
 828
 829         @Override
 830         public void releaseReferences(Object svl) {
 831                 // TODO Auto-generated method stub
 832
 833         }
 834
 835         @Override
 836         public void updateColours(Object source) {
 837                 // TODO Auto-generated method stub
 838
 839         }
 840
 841         @Override
 842         public void componentHidden(ComponentEvent e) {
 843                 // TODO Auto-generated method stub
 844
 845         }
 846
 847         @Override
 848         public void componentMoved(ComponentEvent e) {
 849                 // TODO Auto-generated method stub
 850
 851         }
 852
 853         @Override
 854         public void componentResized(ComponentEvent e) {
 855                 // TODO Auto-generated method stub
 856
 857         }
 858
 859         @Override
 860         public void componentShown(ComponentEvent e) {
 861                 // TODO Auto-generated method stub
 862
 863         }
 864
 865   @Override
 866   public void onStructureRedrawn()
 867   {
 868     // TODO Auto-generated method stub
 869
 870   }
 871 }
 872
 873
 874 /*
 875         public static void main(String[] args)
 876         {
 877                 JTextField str = new JTextField("ATGC");
 878
 879                 AppVarnaBinding vab = new AppVarnaBinding();
 880                 vab.varnagui.set_seq(str);
 881                 vab.varnagui.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
 882                 vab.varnagui.pack();
 883                 vab.varnagui.setVisible(true);
 884         }
 885 }
 886 */