srcjar/fr/orsay/lri/varna/applications/fragseq/FragSeqGUI.java

   1 /*
   2  VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases.
   3  Copyright (C) 2008  Kevin Darty, Alain Denise and Yann Ponty.
   4  electronic mail : Yann.Ponty@lri.fr
   5  paper mail : LRI, bat 490 Université Paris-Sud 91405 Orsay Cedex France
   6
   7  This file is part of VARNA version 3.1.
   8  VARNA version 3.1 is free software: you can redistribute it and/or 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  VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
  12  without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
  13  See the GNU General Public License for more details.
  14
  15  You should have received a copy of the GNU General Public License along with VARNA version 3.1.
  16  If not, see http://www.gnu.org/licenses.
  17  */
  18 package fr.orsay.lri.varna.applications.fragseq;
  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.GridLayout;
  25 import java.awt.datatransfer.DataFlavor;
  26 import java.awt.datatransfer.Transferable;
  27 import java.awt.datatransfer.UnsupportedFlavorException;
  28 import java.awt.dnd.DropTarget;
  29 import java.awt.dnd.DropTargetDragEvent;
  30 import java.awt.dnd.DropTargetDropEvent;
  31 import java.awt.dnd.DropTargetEvent;
  32 import java.awt.dnd.DropTargetListener;
  33 import java.awt.event.ActionEvent;
  34 import java.awt.event.ActionListener;
  35 import java.awt.event.ComponentEvent;
  36 import java.awt.event.ComponentListener;
  37 import java.awt.event.FocusEvent;
  38 import java.awt.event.FocusListener;
  39 import java.awt.event.MouseEvent;
  40 import java.awt.event.MouseListener;
  41 import java.awt.event.WindowEvent;
  42 import java.awt.event.WindowListener;
  43 import java.io.IOException;
  44 import java.util.ArrayList;
  45
  46 import javax.swing.BorderFactory;
  47 import javax.swing.ButtonGroup;
  48 import javax.swing.DefaultListSelectionModel;
  49 import javax.swing.JButton;
  50 import javax.swing.JComboBox;
  51 import javax.swing.JComponent;
  52 import javax.swing.JFileChooser;
  53 import javax.swing.JFrame;
  54 import javax.swing.JLabel;
  55 import javax.swing.JList;
  56 import javax.swing.JOptionPane;
  57 import javax.swing.JPanel;
  58 import javax.swing.JRadioButton;
  59 import javax.swing.JScrollPane;
  60 import javax.swing.JSplitPane;
  61 import javax.swing.JTextPane;
  62 import javax.swing.JToolBar;
  63 import javax.swing.JTree;
  64 import javax.swing.ListSelectionModel;
  65 import javax.swing.LookAndFeel;
  66 import javax.swing.SwingUtilities;
  67 import javax.swing.TransferHandler;
  68 import javax.swing.UIManager;
  69 import javax.swing.UIManager.LookAndFeelInfo;
  70 import javax.swing.UnsupportedLookAndFeelException;
  71 import javax.swing.event.TreeModelEvent;
  72 import javax.swing.event.TreeModelListener;
  73 import javax.swing.event.TreeSelectionEvent;
  74 import javax.swing.event.TreeSelectionListener;
  75 import javax.swing.tree.DefaultMutableTreeNode;
  76 import javax.swing.tree.ExpandVetoException;
  77 import javax.swing.tree.TreePath;
  78 import javax.swing.tree.TreeSelectionModel;
  79
  80 import fr.orsay.lri.varna.VARNAPanel;
  81 import fr.orsay.lri.varna.applications.BasicINI;
  82 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
  83 import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
  84 import fr.orsay.lri.varna.models.FullBackup;
  85
  86
  87 public class FragSeqGUI extends JFrame implements TreeModelListener, MouseListener,DropTargetListener, WindowListener, ComponentListener, ActionListener, TreeSelectionListener {
  88
  89         private enum Commands
  90         {
  91                 NEW_FOLDER,
  92                 ADD_PANEL_UP,
  93                 ADD_PANEL_DOWN,
  94                 REMOVE_PANEL_UP,
  95                 REMOVE_PANEL_DOWN,
  96                 SORT_ID,
  97                 SORT_FILENAME,
  98                 REFRESH_ALL,
  99                 CHANGE_LNF,
 100                 TEST_XML,
 101         };
 102
 103
 104         /**
 105          *
 106          */
 107         private static final long serialVersionUID = -790155708306987257L;
 108
 109
 110
 111         private String _INIFilename = "FragSeqUI.ini";
 112         private boolean redrawOnSlide = false;
 113         private int dividerWidth = 5;
 114
 115         private JPanel _varnaUpperPanels = new JPanel();
 116         private JPanel _varnaLowerPanels = new JPanel();
 117
 118         private JPanel _listPanel = new JPanel();
 119         private JPanel _infoPanel = new JPanel();
 120         private FragSeqTree _sideList = null;
 121
 122
 123         private FragSeqTreeModel _treeModel;
 124         private JToolBar _toolbar = new JToolBar();
 125         private JFileChooser _choice = new JFileChooser();
 126
 127         private JScrollPane _listScroller;
 128
 129         private JList _selectedElems;
 130         private JSplitPane _splitLeft;
 131         private JSplitPane _splitRight;
 132         private JSplitPane _splitVARNA;
 133
 134         private JComboBox _lnf;
 135
 136
 137         public FragSeqGUI() {
 138                 super("VARNA Explorer");
 139                 RNAPanelDemoInit();
 140         }
 141
 142
 143         private void RNAPanelDemoInit()
 144         {
 145                 JFrame.setDefaultLookAndFeelDecorated(true);
 146                 this.addWindowListener(this);
 147
 148                 _selectedElems = new JList();
 149
 150                 _lnf = new JComboBox(UIManager.getInstalledLookAndFeels());
 151
 152                 // Initializing Custom Tree Model
 153                 _treeModel = new FragSeqTreeModel();
 154                 _treeModel.addTreeModelListener(this);
 155
 156                 _sideList = new FragSeqTree(_treeModel);
 157                 _sideList.addMouseListener(this);
 158                 _sideList.setLargeModel(true);
 159                 _sideList.setEditable(true);
 160                 _sideList.addTreeWillExpandListener(_treeModel);
 161                 FragSeqCellRenderer renderer = new FragSeqCellRenderer(_sideList,_treeModel);
 162                 //_sideList.setUI(new CustomTreeUI());
 163                 _sideList.setCellRenderer(renderer);
 164                 _sideList.setCellEditor(new FragSeqCellEditor(_sideList,renderer,_treeModel));
 165                 TreeSelectionModel m = _sideList.getSelectionModel();
 166                 m.setSelectionMode(TreeSelectionModel.SINGLE_TREE_SELECTION);
 167                 _sideList.setSelectionModel(m);
 168                 m.addTreeSelectionListener(this);
 169                 _sideList.setShowsRootHandles(true);
 170                 _sideList.setDragEnabled(true);
 171                 _sideList.setRootVisible(false);
 172                 _sideList.setTransferHandler(new TransferHandler(null)
 173                 {
 174                         public int getSourceActions(JComponent c) {
 175                                 return COPY_OR_MOVE;
 176                         }
 177                         protected Transferable createTransferable(JComponent c) {
 178                                 JTree tree = (JTree) c;
 179                                 TreePath tp =tree.getSelectionPath();
 180                                 if (tp!=null)
 181                                 {
 182                                         DefaultMutableTreeNode node = (DefaultMutableTreeNode) tp.getLastPathComponent();
 183                                         if (node.getUserObject() instanceof FragSeqRNASecStrModel) {
 184                                                 return new Transferable(){
 185                                                         public DataFlavor[] getTransferDataFlavors() {
 186                                                                 DataFlavor[] dt = {FragSeqRNASecStrModel.Flavor};
 187                                                                 return dt;
 188                                                         }
 189                                                         public Object getTransferData(DataFlavor df)
 190                                                         throws UnsupportedFlavorException, IOException {
 191                                                                 if (!isDataFlavorSupported(df))
 192                                                                         throw new UnsupportedFlavorException(df);
 193                                                                 DefaultMutableTreeNode node = (DefaultMutableTreeNode) _sideList.getSelectionPath().getLastPathComponent();
 194                                                                 return node.getUserObject();
 195                                                         }
 196                                                         public boolean isDataFlavorSupported(DataFlavor df) {
 197                                                                 return FragSeqRNASecStrModel.Flavor.equals(df);
 198                                                         }
 199                                                 };
 200                                         } else  if (node.getUserObject() instanceof FragSeqAnnotationDataModel) {
 201                                                         return new Transferable(){
 202                                                                 public DataFlavor[] getTransferDataFlavors() {
 203                                                                         DataFlavor[] dt = { FragSeqAnnotationDataModel.Flavor};
 204                                                                         return dt;
 205                                                                 }
 206                                                                 public Object getTransferData(DataFlavor df)
 207                                                                 throws UnsupportedFlavorException, IOException {
 208                                                                         if (!isDataFlavorSupported(df))
 209                                                                                 throw new UnsupportedFlavorException(df);
 210                                                                         DefaultMutableTreeNode node = (DefaultMutableTreeNode) _sideList.getSelectionPath().getLastPathComponent();
 211                                                                         return node.getUserObject();
 212                                                                 }
 213                                                                 public boolean isDataFlavorSupported(DataFlavor df) {
 214                                                                         return FragSeqAnnotationDataModel.Flavor.equals(df);
 215                                                                 }
 216                                                         };
 217                                                 } else {
 218                                                 return null;
 219                                         }
 220                                 }
 221                                 return null;
 222                         }
 223                 });
 224
 225                 // Various buttons
 226                 JButton refreshAllFoldersButton = new JButton("Refresh All");
 227                 refreshAllFoldersButton.setActionCommand(""+Commands.REFRESH_ALL);
 228                 refreshAllFoldersButton.addActionListener(this);
 229
 230                 JButton watchFolderButton = new JButton("Add folder");
 231                 watchFolderButton.setActionCommand("" +Commands.NEW_FOLDER);
 232                 watchFolderButton.addActionListener(this);
 233
 234                 JButton addUpperButton = new JButton("+Up");
 235                 addUpperButton.setActionCommand(""+Commands.ADD_PANEL_UP);
 236                 addUpperButton.addActionListener(this);
 237
 238                 JButton removeUpperButton = new JButton("-Up");
 239                 removeUpperButton.setActionCommand(""+Commands.REMOVE_PANEL_UP);
 240                 removeUpperButton.addActionListener(this);
 241
 242                 JButton addLowerButton = new JButton("+Down");
 243                 addLowerButton.setActionCommand(""+Commands.ADD_PANEL_DOWN);
 244                 addLowerButton.addActionListener(this);
 245
 246                 JButton removeLowerButton = new JButton("-Down");
 247                 removeLowerButton.setActionCommand(""+Commands.REMOVE_PANEL_DOWN);
 248                 removeLowerButton.addActionListener(this);
 249
 250                 JButton changeLNFButton = new JButton("Change");
 251                 changeLNFButton.setActionCommand(""+Commands.CHANGE_LNF);
 252                 changeLNFButton.addActionListener(this);
 253
 254                 JButton XMLButton = new JButton("Test XML");
 255                 XMLButton.setActionCommand(""+Commands.TEST_XML);
 256                 XMLButton.addActionListener(this);
 257
 258                 _toolbar.setFloatable(false);
 259                 _toolbar.add(refreshAllFoldersButton);
 260                 _toolbar.addSeparator();
 261                 _toolbar.add(addUpperButton);
 262                 _toolbar.add(removeUpperButton);
 263                 _toolbar.add(addLowerButton);
 264                 _toolbar.add(removeLowerButton);
 265                 _toolbar.addSeparator();
 266                 _toolbar.add(XMLButton);
 267                 _toolbar.addSeparator();
 268                 _toolbar.add(_lnf);
 269                 _toolbar.add(changeLNFButton);
 270
 271                 // Scroller for File tree
 272             _listScroller = new JScrollPane(_sideList,JScrollPane.VERTICAL_SCROLLBAR_ALWAYS,JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
 273             _listScroller.setPreferredSize(new Dimension(300, 200));
 274             _listScroller.addComponentListener(this);
 275
 276
 277                 _listPanel.setLayout(new BorderLayout());
 278
 279                 _listPanel.add(_listScroller,BorderLayout.CENTER);
 280                 _listPanel.add(_selectedElems,BorderLayout.SOUTH);
 281                 _listPanel.setBorder(BorderFactory.createTitledBorder("Structures"));
 282                 _listPanel.setPreferredSize(new Dimension(300, 0));
 283
 284                 _varnaUpperPanels.setLayout(new GridLayout());
 285                 _varnaUpperPanels.setPreferredSize(new Dimension(800, 600));
 286
 287                 _varnaLowerPanels.setLayout(new GridLayout());
 288                 _varnaLowerPanels.setPreferredSize(new Dimension(800, 000));
 289
 290             JRadioButton sortFileName = new JRadioButton("Directory");
 291             sortFileName.setActionCommand("sortfilename");
 292             sortFileName.setSelected(true);
 293             sortFileName.setOpaque(false);
 294             sortFileName.setActionCommand(""+Commands.SORT_FILENAME);
 295             sortFileName.addActionListener(this);
 296             JRadioButton sortID = new JRadioButton("ID");
 297             sortID.setActionCommand("sortid");
 298             sortID.setOpaque(false);
 299             sortID.setActionCommand(""+Commands.SORT_ID);
 300             sortID.addActionListener(this);
 301
 302             ButtonGroup group = new ButtonGroup();
 303             group.add(sortFileName);
 304             group.add(sortID);
 305
 306                 JToolBar listTools = new JToolBar();
 307                 listTools.setFloatable(false);
 308                 listTools.add(watchFolderButton);
 309                 listTools.addSeparator();
 310             listTools.add(new JLabel("Sort by"));
 311                 listTools.add(sortFileName);
 312                 listTools.add(sortID);
 313
 314                 JPanel sidePanel = new JPanel();
 315                 sidePanel.setLayout(new BorderLayout());
 316                 sidePanel.add(listTools,BorderLayout.NORTH);
 317                 sidePanel.add(_listPanel,BorderLayout.CENTER);
 318
 319
 320                 JPanel mainVARNAPanel = new JPanel();
 321                 mainVARNAPanel.setLayout(new BorderLayout());
 322                 _splitVARNA = new JSplitPane(JSplitPane.VERTICAL_SPLIT,redrawOnSlide,_varnaUpperPanels,_varnaLowerPanels);
 323                 _splitVARNA.setDividerSize(dividerWidth);
 324                 _splitVARNA.setResizeWeight(1.0);
 325                 _splitLeft = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,redrawOnSlide,sidePanel,_splitVARNA);
 326                 _splitLeft.setResizeWeight(0.1);
 327                 _splitLeft.setDividerSize(dividerWidth);
 328                 _splitRight = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,redrawOnSlide,_splitLeft,_infoPanel);
 329                 _splitRight.setResizeWeight(0.85);
 330                 _splitRight.setDividerSize(dividerWidth);
 331
 332                 _infoPanel.setLayout(new GridLayout(0,1));
 333
 334                 this.restoreConfig();
 335                 this.getContentPane().setLayout(new BorderLayout());
 336                 this.getContentPane().add(_splitRight, BorderLayout.CENTER);
 337                 this.getContentPane().add(_toolbar, BorderLayout.NORTH);
 338                 addUpperPanel();
 339                 addUpperPanel();
 340                 this.setVisible(true);
 341         }
 342
 343         public FragSeqGUI getSelf()
 344         {
 345                 return this;
 346         }
 347
 348         public VARNAHolder createIntegratedPanel(int height)
 349         {
 350                 VARNAHolder vh = new VARNAHolder(this);
 351                 _varnaPanels.add(vh);
 352                 return vh;
 353         }
 354
 355
 356         public void removeUpperPanel()
 357         {
 358                 if (_varnaUpperPanels.getComponentCount()>1)
 359                 {
 360                         VARNAHolder vh = (VARNAHolder) _varnaUpperPanels.getComponent(_varnaUpperPanels.getComponentCount()-1);
 361                         _infoPanel.remove(vh.getInfoPane());
 362                         _varnaUpperPanels.remove(vh);
 363                         _splitLeft.validate();
 364                         _splitRight.validate();
 365                 }
 366         }
 367
 368         public void addUpperPanel()
 369         {
 370                 VARNAHolder vh = createIntegratedPanel(100);
 371                 _varnaUpperPanels.add(vh);
 372                 _infoPanel.add(vh.getInfoPane());
 373                 _splitRight.validate();
 374                 _splitLeft.validate();
 375         }
 376
 377
 378         public void removeLowerPanel()
 379         {
 380                 if (_varnaLowerPanels.getComponentCount()>0)
 381                 {
 382                         _varnaLowerPanels.remove(_varnaLowerPanels.getComponentCount()-1);
 383                         if (_varnaLowerPanels.getComponentCount()==0)
 384                         {
 385                                 _splitVARNA.setDividerLocation(1.0);
 386                                 _splitVARNA.validate();
 387                                 _splitVARNA.repaint();
 388                         }
 389                         _splitLeft.validate();
 390                 }
 391         }
 392
 393         public void addLowerPanel()
 394         {
 395                 if (_varnaLowerPanels.getComponentCount()==0)
 396                 {
 397                         _splitVARNA.setDividerLocation(0.7);
 398                         _splitVARNA.validate();
 399                 }
 400                 _varnaLowerPanels.add(createIntegratedPanel(400));
 401                 _splitLeft.validate();
 402         }
 403
 404
 405         public void treeNodesChanged(TreeModelEvent e) {
 406                DefaultMutableTreeNode node;
 407                 node = (DefaultMutableTreeNode)
 408                          (e.getTreePath().getLastPathComponent());
 409
 410                 /*
 411                  * If the event lists children, then the changed
 412                  * node is the child of the node we have already
 413                  * gotten.  Otherwise, the changed node and the
 414                  * specified node are the same.
 415                  */
 416                 try {
 417                     int index = e.getChildIndices()[0];
 418                     node = (DefaultMutableTreeNode)
 419                            (node.getChildAt(index));
 420                 } catch (NullPointerException exc) {}
 421
 422         }
 423
 424
 425
 426
 427         public void addFolder(String path) {
 428                 addFolder( path, true);
 429         }
 430
 431     public void addFolder(String path,
 432             boolean shouldBeVisible)
 433     {
 434         DefaultMutableTreeNode childNode = _treeModel.addFolder(path);
 435
 436                 if ((childNode!=null) && shouldBeVisible ) {
 437                           System.out.println("  Expanding: "+childNode.getUserObject());
 438                           TreePath tp = new TreePath(childNode.getPath());
 439                         _sideList.scrollPathToVisible(tp);
 440                         _sideList.expandRow(_sideList.getRowForPath(tp));
 441                         _sideList.updateUI();
 442                         _sideList.validate();
 443                 }
 444     }
 445
 446         public void treeNodesInserted(TreeModelEvent e) {
 447                 System.out.println(e);
 448
 449         }
 450
 451         public void treeNodesRemoved(TreeModelEvent e) {
 452                 // TODO Auto-generated method stub
 453
 454         }
 455
 456         public void treeStructureChanged(TreeModelEvent e) {
 457                 // TODO Auto-generated method stub
 458
 459         }
 460
 461         public void mouseClicked(MouseEvent e) {
 462                 // TODO Auto-generated method stub
 463
 464         }
 465
 466         public void mousePressed(MouseEvent e) {
 467
 468         }
 469
 470         int index = 0;
 471
 472         public void mouseReleased(MouseEvent e) {
 473                 // TODO Auto-generated method stub
 474                 if (e.getSource() == this._sideList)
 475                 {
 476                         if (e.getClickCount() == 1)
 477                         {
 478                                 /*TreePath t = _sideList.getSelectionPath();
 479                                 if (t!=null)
 480                                 {
 481                                 DefaultMutableTreeNode node = (DefaultMutableTreeNode) t.getLastPathComponent();
 482                                 if (node.getUserObject() instanceof FragSeqFileModel)
 483                                 {
 484                                         int row = _sideList.getRowForPath(t);
 485                                         System.out.println("[A]"+row);
 486                                         if (!_sideList.isExpanded(row))
 487                                         {
 488                                                 try {
 489                                                         _sideList.fireTreeWillExpand(t);
 490                                                         _sideList.expandPath(t);
 491                                                 } catch (ExpandVetoException e1) {
 492                                                         // TODO Auto-generated catch block
 493                                                         e1.printStackTrace();
 494                                                 }
 495                                         }
 496                                         else
 497                                         {
 498                                                 try {
 499                                                         _sideList.fireTreeWillCollapse(t);
 500                                                         _sideList.collapsePath(t);
 501                                                 } catch (ExpandVetoException e1) {
 502                                                         // TODO Auto-generated catch block
 503                                                         e1.printStackTrace();
 504                                                 }
 505                                         }
 506                                 }
 507                                 }*/
 508                         }
 509                         else if (e.getClickCount() == 2)
 510                         {
 511                                 TreePath t = _sideList.getSelectionPath();
 512                                 if (t!= null)
 513                                 {
 514                                         DefaultMutableTreeNode node = (DefaultMutableTreeNode) t.getLastPathComponent();
 515                                         if (node.getUserObject() instanceof FragSeqFileModel)
 516                                         {
 517                                                 if (!_sideList.isExpanded(t))
 518                                                 {
 519                                                         try {
 520                                                                 _sideList.fireTreeWillExpand(t);
 521                                                                 _sideList.expandPath(t);
 522                                                         } catch (ExpandVetoException e1) {
 523                                                                 e1.printStackTrace();
 524                                                         }
 525                                                 }
 526                                                 else
 527                                                 {
 528                                                         try {
 529                                                                 _sideList.fireTreeWillCollapse(t);
 530                                                                 _sideList.collapsePath(t);
 531                                                         } catch (ExpandVetoException e1) {
 532                                                                 e1.printStackTrace();
 533                                                         }
 534                                                 }
 535                                         }
 536                                         else if (node.getUserObject() instanceof FragSeqModel)
 537                                         {
 538                                                 FragSeqModel model = (FragSeqModel) node.getUserObject();
 539
 540                                                 // Figuring out which panel to add object to...
 541                                                 int res;
 542                                                 if (model instanceof FragSeqRNASecStrModel)
 543                                                 {
 544                                                         res = index % (_varnaUpperPanels.getComponentCount()+_varnaLowerPanels.getComponentCount());
 545                                                 }
 546                                                 else
 547                                                 {
 548                                                         res = (index+_varnaUpperPanels.getComponentCount()+_varnaLowerPanels.getComponentCount()-1) % (_varnaUpperPanels.getComponentCount()+_varnaLowerPanels.getComponentCount());
 549                                                 }
 550                                                 Component c = null;
 551                                                 if (res<_varnaUpperPanels.getComponentCount())
 552                                                 {
 553                                                         c = (VARNAHolder)_varnaUpperPanels.getComponent(res);
 554                                                 }
 555                                                 else
 556                                                 {
 557                                                         res -= _varnaUpperPanels.getComponentCount();
 558                                                         c = (VARNAHolder)_varnaLowerPanels.getComponent(res);
 559                                                 }
 560
 561                                                 if (c instanceof VARNAHolder)
 562                                                 {
 563                                                         VARNAHolder h = (VARNAHolder) c;
 564                                                         if (model instanceof FragSeqRNASecStrModel)
 565                                                         {
 566                                                                 h.setSecStrModel((FragSeqRNASecStrModel)model);
 567                                                                 index ++;
 568                                                         }
 569                                                         else if (model instanceof FragSeqAnnotationDataModel)
 570                                                         {
 571                                                                 h.setDataModel((FragSeqAnnotationDataModel)model);
 572                                                         }
 573                                                 }
 574                                         }
 575                                 }
 576                         }
 577                 }
 578         }
 579
 580
 581
 582
 583         class VARNAHolder extends JPanel
 584         {
 585                 VARNAPanel vp;
 586                 FragSeqRNASecStrModel _m;
 587                 FragSeqAnnotationDataModel _data;
 588                 JPanel _infoPanel;
 589                 JTextPane _infoTxt;
 590
 591
 592                 public VARNAHolder(DropTargetListener f)
 593                 {
 594                         super();
 595                         vp = new VARNAPanel();
 596                         vp.addFocusListener(new FocusListener(){
 597                                 public void focusGained(FocusEvent e) {
 598                                         //focus(_m);
 599                                 }
 600                                 public void focusLost(FocusEvent e) {
 601                                 }});
 602                         vp.setPreferredSize(new Dimension(800, 400));
 603
 604                         _infoTxt = new JTextPane();
 605                         _infoTxt.setPreferredSize(new Dimension(200,0));
 606                         _infoTxt.setContentType("text/html");
 607
 608                         JScrollPane scroll = new JScrollPane(_infoTxt,JScrollPane.VERTICAL_SCROLLBAR_ALWAYS,JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
 609
 610                         _infoPanel = new JPanel();
 611                         _infoPanel.setLayout(new BorderLayout());
 612                         _infoPanel.setPreferredSize(new Dimension(200,0));
 613                         _infoPanel.setBorder(BorderFactory.createTitledBorder("Info"));
 614                         _infoPanel.add(scroll,BorderLayout.CENTER);
 615                         _infoPanel.validate();
 616
 617                         this.setLayout(new BorderLayout());
 618                         this.setPreferredSize(new Dimension(300,600));
 619                         this.setBorder(BorderFactory.createTitledBorder("None"));
 620                         this.add(vp, BorderLayout.CENTER);
 621
 622                         DropTarget dt = new DropTarget(vp, f);
 623                 }
 624
 625                 VARNAPanel getVARNAPanel()
 626                 {
 627                         return vp;
 628                 }
 629                 void setSecStrModel(FragSeqRNASecStrModel m)
 630                 {
 631                         _m = m;
 632                         vp.showRNAInterpolated(m.getRNA());
 633                         setBorder(BorderFactory.createTitledBorder(m.toString()));
 634                         _infoTxt.setText(m.getRNA().getHTMLDescription());
 635                         _infoPanel.setBorder(BorderFactory.createTitledBorder("Info ("+_m+")"));
 636                         vp.requestFocus();
 637                 }
 638                 void setDataModel(FragSeqAnnotationDataModel data)
 639                 {
 640                         _data = data;
 641                         data.applyTo(vp.getRNA());
 642                         vp.repaint();
 643                         vp.requestFocus();
 644                 }
 645                 FragSeqModel getModel()
 646                 {
 647                         setBorder(BorderFactory.createTitledBorder(_m.toString()));
 648                         return _m;
 649                 }
 650                 public void setInfoTxt(String s)
 651                 {
 652                         _infoTxt.setText(vp.getRNA().getHTMLDescription());
 653                         _infoTxt.validate();
 654                 }
 655                 public JPanel getInfoPane()
 656                 {
 657                         return _infoPanel;
 658                 }
 659
 660         }
 661
 662
 663         private ArrayList<VARNAHolder> _varnaPanels = new ArrayList<VARNAHolder>();
 664
 665         private VARNAHolder getHolder(Component vp)
 666         {
 667                 if (vp instanceof VARNAHolder)
 668                 {
 669                         int i= _varnaPanels.indexOf(vp);
 670                         if (i!=-1)
 671                         {
 672                                 return _varnaPanels.get(i);
 673                         }
 674                 }
 675                 if (vp instanceof VARNAPanel)
 676                 {
 677                         for (VARNAHolder vh: _varnaPanels)
 678                         {
 679                                 if (vh.getVARNAPanel()==vp)
 680                                 return vh;
 681                         }
 682                 }
 683                 return null;
 684         }
 685
 686
 687
 688         public void mouseEntered(MouseEvent e) {
 689                 // TODO Auto-generated method stub
 690
 691         }
 692
 693         public void mouseExited(MouseEvent e) {
 694                 // TODO Auto-generated method stub
 695
 696         }
 697
 698         public void dragEnter(DropTargetDragEvent arg0) {
 699                 // TODO Auto-generated method stub
 700
 701         }
 702
 703         public void dragExit(DropTargetEvent arg0) {
 704                 // TODO Auto-generated method stub
 705
 706         }
 707
 708         public void dragOver(DropTargetDragEvent arg0) {
 709
 710         }
 711
 712         public void drop(DropTargetDropEvent arg0) {
 713                         try {
 714
 715                                 DropTarget o = (DropTarget)arg0.getSource();
 716                                 if (o.getComponent() instanceof VARNAPanel)
 717                                 {
 718                                         VARNAHolder h = getHolder(o.getComponent());
 719                                         if (h!=null)
 720                                         {
 721                                                 System.out.println("[X]");
 722                                                 Transferable t = arg0.getTransferable();
 723                                                 if (t.isDataFlavorSupported(FragSeqRNASecStrModel.Flavor))
 724                                                 {
 725                                                         Object data = t.getTransferData(FragSeqRNASecStrModel.Flavor);
 726                                                         if (data instanceof FragSeqRNASecStrModel)
 727                                                         {
 728                                                                 h.setSecStrModel((FragSeqRNASecStrModel) data);
 729                                                         }
 730                                                 }
 731                                                 else if (t.isDataFlavorSupported(FragSeqAnnotationDataModel.Flavor))
 732                                                 {
 733                                                         System.out.println("[Y]");
 734                                                         Object data = t.getTransferData(FragSeqAnnotationDataModel.Flavor);
 735                                                         if (data instanceof FragSeqAnnotationDataModel)
 736                                                         {
 737                                                                 FragSeqAnnotationDataModel d = (FragSeqAnnotationDataModel) data;
 738                                                                 h.setDataModel(d);
 739                                                         }
 740                                                 }
 741                                         }
 742                                 }
 743                         } catch (UnsupportedFlavorException e) {
 744                                 // TODO Auto-generated catch block
 745                                 e.printStackTrace();
 746                         } catch (IOException e) {
 747                                 // TODO Auto-generated catch block
 748                                 e.printStackTrace();
 749                         }
 750         }
 751
 752         public void dropActionChanged(DropTargetDragEvent arg0) {
 753                 // TODO Auto-generated method stub
 754
 755         }
 756
 757         public void windowOpened(WindowEvent e) {
 758                 // TODO Auto-generated method stub
 759
 760         }
 761
 762         public void windowClosing(WindowEvent e) {
 763                 saveConfig();
 764                 System.exit(0);
 765         }
 766
 767         public void windowClosed(WindowEvent e) {
 768                 // TODO Auto-generated method stub
 769
 770         }
 771
 772         public void windowIconified(WindowEvent e) {
 773                 // TODO Auto-generated method stub
 774
 775         }
 776
 777         public void windowDeiconified(WindowEvent e) {
 778                 // TODO Auto-generated method stub
 779
 780         }
 781
 782         public void windowActivated(WindowEvent e) {
 783                 // TODO Auto-generated method stub
 784
 785         }
 786
 787         public void windowDeactivated(WindowEvent e) {
 788                 // TODO Auto-generated method stub
 789
 790         }
 791
 792         private void restoreConfig()
 793         {
 794                 BasicINI config = BasicINI.loadINI(_INIFilename);
 795         ArrayList<String> vals = config.getItemList("folders");
 796                 System.out.print("[C]"+vals);
 797
 798             for(String path:vals)
 799                 {
 800                 System.out.println("Loading folder "+path);
 801                   addFolder(path);
 802                 }
 803             _sideList.validate();
 804             _listScroller.validate();
 805         }
 806
 807         private void saveConfig()
 808         {
 809                 BasicINI data = new BasicINI();
 810                 int i=0;
 811                 for (String folderPath: _treeModel.getFolders())
 812                 {
 813                   data.addItem("folders", "val"+i, folderPath);
 814                   i++;
 815                 }
 816                 BasicINI.saveINI(data, _INIFilename);
 817         }
 818
 819
 820         public void componentResized(ComponentEvent e) {
 821                 _sideList.validate();
 822         }
 823
 824
 825         public void componentMoved(ComponentEvent e) {
 826                 // TODO Auto-generated method stub
 827
 828         }
 829
 830
 831         public void componentShown(ComponentEvent e) {
 832                 // TODO Auto-generated method stub
 833
 834         }
 835
 836
 837         public void componentHidden(ComponentEvent e) {
 838                 // TODO Auto-generated method stub
 839
 840         }
 841
 842
 843         public void actionPerformed(ActionEvent e) {
 844                 String cmd = e.getActionCommand();
 845                 System.out.println(cmd);
 846                 if (cmd.equals(""+Commands.NEW_FOLDER))
 847                 {
 848                         _choice.setDialogTitle("Watch new folder...");
 849                         _choice.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
 850                         _choice.setAcceptAllFileFilterUsed(false);
 851                         try {
 852                                 if (_choice.showOpenDialog(getSelf()) == JFileChooser.APPROVE_OPTION) {
 853                                         addFolder(_choice.getSelectedFile().getCanonicalPath());
 854                                 }
 855                                 else {
 856                                         System.out.println("No Selection ");
 857                                 }
 858                         } catch (IOException e1) {
 859                                 e1.printStackTrace();
 860                         }
 861                 }
 862                 else if (cmd.equals(""+Commands.ADD_PANEL_DOWN))
 863                 {
 864                         addLowerPanel();
 865                 }
 866                 else if (cmd.equals(""+Commands.ADD_PANEL_UP))
 867                 {
 868                         addUpperPanel();
 869                 }
 870                 else if (cmd.equals(""+Commands.REMOVE_PANEL_DOWN))
 871                 {
 872                         removeLowerPanel();
 873                 }
 874                 else if (cmd.equals(""+Commands.REMOVE_PANEL_UP))
 875                 {
 876                         removeUpperPanel();
 877                 }
 878                 else if (cmd.equals(""+Commands.SORT_FILENAME))
 879                 {
 880                         _sideList.switchToPath();
 881                 }
 882                 else if (cmd.equals(""+Commands.SORT_ID))
 883                 {
 884                         _sideList.switchToID();
 885                 }
 886                 else if (cmd.equals(""+Commands.TEST_XML))
 887                 {
 888                         String path = "temp.xml";
 889                         VARNAHolder vh = (VARNAHolder) _varnaUpperPanels.getComponent(0);
 890                         vh.vp.toXML(path);
 891                         try {
 892                                 FullBackup b = vh.vp.importSession(path);
 893                                 VARNAHolder vh2 = (VARNAHolder) _varnaUpperPanels.getComponent(1);
 894                                 vh2.vp.setConfig(b.config);
 895                                 vh2.vp.showRNAInterpolated(b.rna);
 896                                 vh2.vp.repaint();
 897                         } catch (ExceptionLoadingFailed e1) {
 898                                 e1.printStackTrace();
 899                         }
 900                 }
 901                 else if (cmd.equals(""+Commands.CHANGE_LNF))
 902                 {
 903                         try {
 904
 905                                 Object o  = _lnf.getModel().getSelectedItem();
 906                                 System.out.println(o);
 907                                 UIManager.setLookAndFeel(((LookAndFeelInfo)_lnf.getModel().getSelectedItem()).getClassName());
 908                                 SwingUtilities.updateComponentTreeUI(this);
 909                                 this.pack();
 910                         } catch (UnsupportedLookAndFeelException e1) {
 911                                 // TODO Auto-generated catch block
 912                                 e1.printStackTrace();
 913                         } catch (ClassNotFoundException e2) {
 914                                 // TODO Auto-generated catch block
 915                                 e2.printStackTrace();
 916                         } catch (InstantiationException e3) {
 917                                 // TODO Auto-generated catch block
 918                                 e3.printStackTrace();
 919                         } catch (IllegalAccessException e4) {
 920                                 // TODO Auto-generated catch block
 921                                 e4.printStackTrace();
 922                         }
 923                 }
 924                 else
 925                 {
 926                         JOptionPane.showMessageDialog(this, "Command '"+cmd+"' not implemented yet.");
 927                 }
 928         }
 929
 930
 931         public void valueChanged(TreeSelectionEvent e) {
 932                 int[] t = _sideList.getSelectionRows();
 933                 if (t==null)
 934                 {
 935                         System.out.print("null");
 936                 }
 937                 else
 938                 {
 939                         System.out.print("[");
 940                         for(int i=0;i<t.length;i++)
 941                         {
 942                                 System.out.print(t[i]+",");
 943                         }
 944                         System.out.println("]");
 945                 }
 946         }
 947
 948
 949         public static void main(String[] args) {
 950                 FragSeqGUI d = new FragSeqGUI();
 951                 d.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
 952                 d.pack();
 953                 d.setVisible(true);
 954         }
 955
 956
 957 }
 958