srcjar/fr/orsay/lri/varna/applications/templateEditor/TemplateEditor.java

   1 package fr.orsay.lri.varna.applications.templateEditor;
   2 import java.awt.BorderLayout;
   3 import java.awt.Color;
   4 import java.awt.Component;
   5 import java.awt.ComponentOrientation;
   6 import java.awt.Dimension;
   7 import java.awt.FlowLayout;
   8 import java.awt.GridLayout;
   9 import java.awt.datatransfer.DataFlavor;
  10 import java.awt.datatransfer.Transferable;
  11 import java.awt.dnd.DnDConstants;
  12 import java.awt.dnd.DropTarget;
  13 import java.awt.dnd.DropTargetDragEvent;
  14 import java.awt.dnd.DropTargetDropEvent;
  15 import java.awt.dnd.DropTargetEvent;
  16 import java.awt.dnd.DropTargetListener;
  17 import java.awt.event.ActionEvent;
  18 import java.awt.event.ActionListener;
  19 import java.awt.event.KeyEvent;
  20 import java.awt.event.KeyListener;
  21 import java.io.BufferedReader;
  22 import java.io.File;
  23 import java.io.IOException;
  24 import java.io.InputStream;
  25 import java.io.InputStreamReader;
  26 import java.io.Reader;
  27 import java.net.MalformedURLException;
  28 import java.net.URL;
  29 import java.net.URLConnection;
  30 import java.util.ArrayList;
  31 import java.util.List;
  32
  33 import javax.swing.BoxLayout;
  34 import javax.swing.ButtonGroup;
  35 import javax.swing.Icon;
  36 import javax.swing.JButton;
  37 import javax.swing.JComboBox;
  38 import javax.swing.JDialog;
  39 import javax.swing.JFileChooser;
  40 import javax.swing.JFrame;
  41 import javax.swing.JLabel;
  42 import javax.swing.JList;
  43 import javax.swing.JOptionPane;
  44 import javax.swing.JPanel;
  45 import javax.swing.JRadioButton;
  46 import javax.swing.JScrollPane;
  47 import javax.swing.JToggleButton;
  48 import javax.swing.JToolBar;
  49 import javax.swing.UIManager;
  50 import javax.swing.UIManager.LookAndFeelInfo;
  51 import javax.swing.filechooser.FileFilter;
  52 import javax.swing.undo.UndoManager;
  53
  54 import fr.orsay.lri.varna.VARNAPanel;
  55 import fr.orsay.lri.varna.applications.FileNameExtensionFilter;
  56 import fr.orsay.lri.varna.exceptions.ExceptionInvalidRNATemplate;
  57 import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
  58 import fr.orsay.lri.varna.exceptions.ExceptionXMLGeneration;
  59 import fr.orsay.lri.varna.models.templates.Benchmark;
  60 import fr.orsay.lri.varna.models.templates.DrawRNATemplateCurveMethod;
  61 import fr.orsay.lri.varna.models.templates.DrawRNATemplateMethod;
  62 import fr.orsay.lri.varna.models.templates.RNATemplate;
  63 import fr.orsay.lri.varna.models.templates.RNATemplateDrawingAlgorithmException;
  64 import fr.orsay.lri.varna.models.templates.RNATemplateMapping;
  65 import fr.orsay.lri.varna.models.templates.RNATemplate.RNATemplateElement;
  66
  67
  68
  69
  70 public class TemplateEditor extends JFrame implements KeyListener, ActionListener,DropTargetListener {
  71
  72         private TemplatePanel _sk;
  73         private VARNAPanel _vp;
  74         private File currentFilePath = null;
  75         private JButton saveButton;
  76         private JScrollPane jp;
  77         private UndoManager manager;
  78         private JButton flipButton;
  79         private JComboBox ellipseMethodList;
  80         private JComboBox applyMethodList;
  81         /*private JRadioButton ellipseButtons[];
  82         private JRadioButton methodButtons[];
  83         */
  84
  85
  86         public TemplateEditor()
  87         {
  88                 init();
  89                 clearCurrentFilePath();
  90         }
  91
  92         public JScrollPane getJp() {
  93                 return jp;
  94         }
  95
  96         private void init()
  97         {
  98                 try {
  99                         _vp = new VARNAPanel(" ",".");
 100                 } catch (ExceptionNonEqualLength e) {
 101                         e.printStackTrace();
 102                 }
 103                 _vp.setNumPeriod(0);
 104                 JPanel p = new JPanel();
 105                 p.setLayout(new GridLayout(1,2));
 106
 107                 JToolBar systemBar = new JToolBar();
 108                 JToolBar optionsBar = new JToolBar();
 109                 JButton newButton = new JButton("New",UIManager.getIcon("FileView.fileIcon"));
 110                 newButton.setActionCommand("new");
 111                 newButton.addActionListener(this);
 112                 newButton.addKeyListener(this);
 113                 JButton loadButton = new JButton("Open...",UIManager.getIcon("FileView.directoryIcon"));
 114                 loadButton.setActionCommand("open");
 115                 loadButton.addActionListener(this);
 116                 loadButton.addKeyListener(this);
 117                 saveButton = new JButton("Save",UIManager.getIcon("FileView.floppyDriveIcon"));
 118                 saveButton.setActionCommand("save");
 119                 saveButton.addActionListener(this);
 120                 saveButton.addKeyListener(this);
 121                 saveButton.setEnabled(false);
 122                 JButton saveAsButton = new JButton("Save As...",UIManager.getIcon("FileView.floppyDriveIcon"));
 123                 saveAsButton.setActionCommand("save as");
 124                 saveAsButton.addActionListener(this);
 125                 saveAsButton.addKeyListener(this);
 126                 JButton undoButton = new JButton("Undo");
 127                 undoButton.setActionCommand("undo");
 128                 undoButton.addActionListener(this);
 129                 undoButton.addKeyListener(this);
 130                 JButton redoButton = new JButton("Redo");
 131                 redoButton.setActionCommand("redo");
 132                 redoButton.addActionListener(this);
 133                 redoButton.addKeyListener(this);
 134
 135                 JButton benchmarkButton = new JButton("Benchmark");
 136                 benchmarkButton.setActionCommand("benchmark");
 137                 benchmarkButton.addActionListener(this);
 138                 benchmarkButton.addKeyListener(this);
 139
 140                 DrawRNATemplateMethod applyMethods[] = DrawRNATemplateMethod.values();
 141                 applyMethodList = new JComboBox(applyMethods);
 142                 applyMethodList.setSelectedItem(DrawRNATemplateMethod.getDefault());
 143
 144                 DrawRNATemplateCurveMethod ellipseMethods[] = DrawRNATemplateCurveMethod.values();
 145                 ellipseMethodList = new JComboBox(ellipseMethods);
 146                 ellipseMethodList.setSelectedItem(DrawRNATemplateCurveMethod.getDefault());
 147
 148                 JButton applyButton = new JButton("Apply");
 149                 applyButton.setActionCommand("apply");
 150                 applyButton.addActionListener(this);
 151                 applyButton.addKeyListener(this);
 152
 153                 JButton retrieveButton = new JButton("Retrieve Templates");
 154                 retrieveButton.setActionCommand("retrieve");
 155                 retrieveButton.addActionListener(this);
 156
 157
 158                 flipButton = new JButton("Flip helix");
 159                 flipButton.setActionCommand("flip");
 160                 flipButton.addActionListener(this);
 161                 flipButton.addKeyListener(this);
 162                 flipButton.setEnabled(false);
 163
 164
 165                 systemBar.add(newButton);
 166                 systemBar.add(loadButton);
 167                 systemBar.add(saveButton);
 168                 systemBar.add(saveAsButton);
 169                 systemBar.addSeparator();
 170
 171                 systemBar.addSeparator();
 172                 systemBar.addSeparator();
 173                 systemBar.add(benchmarkButton);
 174                 systemBar.addKeyListener(this);
 175
 176                 optionsBar.setLayout(new FlowLayout(FlowLayout.LEFT));
 177                 optionsBar.add(new JLabel("Single-Stranded "));
 178                 optionsBar.add(this.ellipseMethodList);
 179                 optionsBar.addSeparator();
 180                 optionsBar.add(new JLabel("Layout "));
 181                 optionsBar.add(this.applyMethodList);
 182                 optionsBar.addSeparator();
 183                 optionsBar.add(applyButton);
 184                 optionsBar.addSeparator();
 185                 optionsBar.add(retrieveButton);
 186                 optionsBar.doLayout();
 187
 188                 /*optionsBar.add(new JLabel("Curves:"));
 189                 for (int i=0; i<ellipseButtons.length; i++)
 190                         optionsBar.add(ellipseButtons[i]);
 191                 optionsBar.addSeparator();
 192                 optionsBar.add(new JLabel("Helix positions:"));
 193                 for (int i=0; i<methodButtons.length; i++)
 194                         optionsBar.add(methodButtons[i]);
 195                 optionsBar.addKeyListener(this);
 196                 */
 197
 198                 JToolBar toolBar = new JToolBar();
 199                 ButtonGroup bg = new ButtonGroup();
 200                 toolBar.setOrientation(JToolBar.VERTICAL);
 201                 //toolBar.setLayout(new BoxLayout(toolBar, BoxLayout.PAGE_AXIS));
 202                 JToggleButton selectButton = new JToggleButton("Select");
 203                 selectButton.setActionCommand("select");
 204                 selectButton.addActionListener(this);
 205                 selectButton.addKeyListener(this);
 206                 JToggleButton helixButton = new JToggleButton("Helix");
 207                 helixButton.setActionCommand("helix");
 208                 helixButton.addActionListener(this);
 209                 helixButton.addKeyListener(this);
 210                 helixButton.setSelected(true);
 211                 JToggleButton unpairedButton = new JToggleButton("Unpaired");
 212                 unpairedButton.setActionCommand("unpaired");
 213                 unpairedButton.addActionListener(this);
 214                 unpairedButton.addKeyListener(this);
 215
 216                 bg.add(selectButton);
 217                 bg.add(helixButton);
 218                 bg.add(unpairedButton);
 219
 220                 toolBar.add(undoButton);
 221                 toolBar.add(redoButton);
 222                 toolBar.addSeparator();
 223                 toolBar.add(new JLabel("Tools:"));
 224                 toolBar.add(selectButton);
 225                 toolBar.add(helixButton);
 226                 toolBar.add(unpairedButton);
 227                 toolBar.addSeparator();
 228                 toolBar.add(flipButton);
 229                 systemBar.addKeyListener(this);
 230
 231
 232                 this.setLayout(new BorderLayout());
 233                 _sk = new TemplatePanel(this);
 234                 _sk.setPreferredSize(new Dimension(800,600));
 235                 manager = new UndoManager();
 236                 manager.setLimit(2000);
 237            _sk.addUndoableEditListener(manager);
 238            _sk.addKeyListener(this);
 239
 240                 jp = new JScrollPane(_sk,JScrollPane.VERTICAL_SCROLLBAR_ALWAYS,JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
 241                 p.add(jp);
 242                 p.add(_vp);
 243                 JPanel bars = new JPanel();
 244                 BoxLayout barsLayout = new BoxLayout(bars, BoxLayout.Y_AXIS);
 245                 bars.setLayout(barsLayout);
 246                 systemBar.setAlignmentX(0);
 247                 bars.add(systemBar);
 248                 optionsBar.setAlignmentX(0);
 249                 bars.add(optionsBar);
 250                 getContentPane().add(bars,BorderLayout.PAGE_START);
 251                 getContentPane().add(toolBar,BorderLayout.WEST);
 252                 getContentPane().add(p,BorderLayout.CENTER);
 253                 this.addKeyListener(this);
 254
 255             new DropTarget(_vp, this);
 256             new DropTarget(_sk, this);
 257             this.pack();
 258
 259                 _sk.requestFocusInWindow();
 260         }
 261
 262
 263         private File getCurrentFilePath() {
 264                 return currentFilePath;
 265         }
 266
 267         private void setCurrentFilePath(File currentFilePath) {
 268                 this.currentFilePath = currentFilePath;
 269                 saveButton.setEnabled(true);
 270                 setTitle("VARNA Template Editor: " + currentFilePath);
 271         }
 272
 273         private void clearCurrentFilePath() {
 274                 currentFilePath = null;
 275                 saveButton.setEnabled(false);
 276                 setTitle("VARNA Template Editor: New file");
 277         }
 278
 279
 280         /**
 281          *
 282          */
 283         private static final long serialVersionUID = -5942729520783690050L;
 284
 285         public static void main(String[] argv)
 286         {
 287                 try {
 288                         LookAndFeelInfo[] lfs = UIManager.getInstalledLookAndFeels();
 289                         int i = 1;
 290                     LookAndFeelInfo info = lfs[i % lfs.length];
 291             UIManager.setLookAndFeel(info.getClassName());
 292                 } catch (Exception e) {
 293                     // If Nimbus is not available, you can set the GUI to another look and feel.
 294                 }
 295                 TemplateEditor frame = new TemplateEditor();
 296                 frame.pack();
 297                 frame.setVisible(true);
 298                 frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
 299         }
 300
 301         public void keyPressed(KeyEvent e) {
 302                 System.out.println(e);
 303                 switch (e.getKeyCode())
 304                 {
 305                   case (KeyEvent.VK_DELETE):
 306                   {
 307                           GraphicalTemplateElement h = _sk.getSelected();
 308                           _sk.Unselect();
 309                           _sk.getTemplateUI().removeElementUI(h);
 310                           _sk.repaint();
 311                   }
 312                   break;
 313                   case (KeyEvent.VK_Z):
 314                   {
 315                           if (e.isControlDown())
 316                           {
 317                                   undo();
 318                           }
 319                   }
 320                   break;
 321                   case (KeyEvent.VK_Y):
 322                   {
 323                           if (e.isControlDown())
 324                           {
 325                                   redo();
 326                           }
 327                   }
 328                   break;
 329                 }
 330         }
 331
 332         public void undo()
 333         {
 334                 if (manager.canUndo())
 335                 {
 336                         //System.out.println("Undo: "+manager.getUndoPresentationName());
 337                         manager.undo();
 338                 }
 339         }
 340
 341         public void redo()
 342         {
 343                   if (manager.canRedo())
 344                   {
 345                           //System.out.println("Redo: "+manager.getRedoPresentationName());
 346                       manager.redo();
 347                   }
 348         }
 349
 350         public void clearTemplate() {
 351                 _sk.clearTemplate();
 352                 clearCurrentFilePath();
 353
 354                 // Empty the cancel history
 355                 manager.discardAllEdits();
 356         }
 357
 358         public void loadTemplate(File templatePath) {
 359                 _sk.loadFromXmlFile(templatePath);
 360                 setCurrentFilePath(templatePath);
 361
 362                 // Empty the cancel history
 363                 manager.discardAllEdits();
 364         }
 365
 366         public void keyReleased(KeyEvent e) {
 367                 System.out.println(e);
 368         }
 369
 370         public void keyTyped(KeyEvent e) {
 371                 System.out.println(e);
 372         }
 373
 374         public void actionPerformed(ActionEvent e) {
 375                 if (e.getActionCommand().equals("undo"))
 376                 {
 377                         undo();
 378                 }
 379                 else if (e.getActionCommand().equals("redo"))
 380                 {
 381                         redo();
 382                 }
 383                 else if (e.getActionCommand().equals("flip"))
 384                 {
 385                         GraphicalTemplateElement gr = _sk.getSelected();
 386                         if (gr != null)
 387                         {
 388                                 if (gr instanceof Helix)
 389                                 {
 390                                         _sk.getTemplateUI().flipHelixUI((Helix)gr);
 391                                 }
 392                         }
 393                 }
 394                 else if (e.getActionCommand().equals("select")) {
 395                         _sk.getTemplateUI().setSelectedTool(TemplateEditorPanelUI.Tool.SELECT);
 396                 }
 397                 else if (e.getActionCommand().equals("helix")) {
 398                         _sk.getTemplateUI().setSelectedTool(TemplateEditorPanelUI.Tool.CREATE_HELIX);
 399                 }
 400                 else if (e.getActionCommand().equals("retrieve")) {
 401                         retrieveTemplates();
 402                 }
 403                 else if (e.getActionCommand().equals("unpaired")) {
 404                         _sk.getTemplateUI().setSelectedTool(TemplateEditorPanelUI.Tool.CREATE_UNPAIRED);
 405                 }
 406                 else if (e.getActionCommand().equals("apply"))
 407                 {
 408                         try {
 409                                 DrawRNATemplateMethod method = (DrawRNATemplateMethod)applyMethodList.getSelectedItem();
 410                                 DrawRNATemplateCurveMethod curveMethod = (DrawRNATemplateCurveMethod)ellipseMethodList.getSelectedItem();
 411                                 RNATemplateMapping map =  _vp.getRNA().drawRNATemplate(_sk.getTemplate(),_vp.getConfig(), method, curveMethod, getStraightBulges());
 412                                 for(int i: map.getSourceElemsAsSet())
 413                                 {
 414                                         RNATemplateElement t = map.getPartner(i);
 415                                         Color c = _sk.getElement(t).getDominantColor();
 416                                         _vp.getRNA().getBaseAt(i).getStyleBase().setBaseInnerColor(c);
 417                                 }
 418                                 _vp.repaint();
 419                         } catch (RNATemplateDrawingAlgorithmException e1) {
 420                                 e1.printStackTrace();
 421                                 JOptionPane.showMessageDialog(this, e1.getMessage(), "Template-based RNA drawing error", JOptionPane.ERROR_MESSAGE);
 422                         }
 423                 }
 424                 else if (e.getActionCommand().equals("save"))
 425                 {
 426                         try {
 427                                 _sk.getTemplate().toXMLFile(getCurrentFilePath());
 428                                 System.out.println("Template saved in " + getCurrentFilePath().toString());
 429                         } catch (ExceptionXMLGeneration e1) {
 430                                 e1.printStackTrace();
 431                         } catch (ExceptionInvalidRNATemplate e1) {
 432                                 e1.printStackTrace();
 433                         }
 434                 }
 435                 else if (e.getActionCommand().equals("save as"))
 436                 {
 437                         JFileChooser chooser = new JFileChooser();
 438                         FileFilter filter = new FileNameExtensionFilter("VARNA RNA template (.xml)", "xml");
 439                     chooser.setFileFilter(filter);
 440                         if (chooser.showSaveDialog(_sk) == JFileChooser.APPROVE_OPTION) {
 441                                 String path = chooser.getSelectedFile().getAbsolutePath();
 442                                 if (!path.toLowerCase().endsWith(".xml")) {
 443                                         path = path + ".xml";
 444                                 }
 445                                 try {
 446                                         _sk.getTemplate().toXMLFile(new File(path));
 447                                         System.out.println("Template saved in " + path);
 448                                         setCurrentFilePath(new File(path));
 449                                 } catch (ExceptionXMLGeneration e1) {
 450                                         e1.printStackTrace();
 451                                 } catch (ExceptionInvalidRNATemplate e1) {
 452                                         e1.printStackTrace();
 453                                 }
 454                         }
 455                 }
 456                 else if (e.getActionCommand().equals("new"))
 457                 {
 458                         clearTemplate();
 459                 }
 460                 else if (e.getActionCommand().equals("open"))
 461                 {
 462                         JFileChooser chooser = new JFileChooser();
 463                     FileFilter filter = new FileNameExtensionFilter("VARNA RNA template (.xml)", "xml");
 464                     chooser.setFileFilter(filter);
 465                         if (chooser.showOpenDialog(_sk) == JFileChooser.APPROVE_OPTION) {
 466                                 File templatePath = chooser.getSelectedFile();
 467                                 loadTemplate(templatePath);
 468                         }
 469                 }
 470                 else if (e.getActionCommand().equals("benchmark")) {
 471                         new Benchmark(_vp.getRNA()).printAll();
 472                 }
 473
 474         }
 475
 476
 477         private boolean getStraightBulges() {
 478                 return false;
 479         }
 480
 481         public void dragEnter(DropTargetDragEvent arg0) {
 482         }
 483
 484         public void dragExit(DropTargetEvent arg0) {
 485         }
 486
 487         public void dragOver(DropTargetDragEvent arg0) {
 488         }
 489
 490         public void drop(DropTargetDropEvent dtde)
 491         {
 492           try
 493           {
 494             Transferable tr = dtde.getTransferable();
 495             DataFlavor[] flavors = tr.getTransferDataFlavors();
 496             for (int i = 0; i < flavors.length; i++)
 497             {
 498               if (flavors[i].isFlavorJavaFileListType())
 499               {
 500                   dtde.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
 501                   List list = (List) tr.getTransferData(flavors[i]);
 502                   for (int j = 0; j < list.size(); j++)
 503                   {
 504                           Object o = list.get(j);
 505                           if (dtde.getSource() instanceof DropTarget)
 506                           {
 507                                   DropTarget dt = (DropTarget) dtde.getSource();
 508                                   Component c = dt.getComponent();
 509                                   if (c instanceof VARNAPanel)
 510                                   {
 511                                           VARNAPanel vp = (VARNAPanel) c;
 512                                           //String path = o.toString();
 513                                           vp.loadFile((File) o, true); // BH SwingJS
 514                                           vp.repaint();
 515                                   }
 516                                   else if (c instanceof TemplatePanel)
 517                                   {
 518                                           TemplatePanel sk = (TemplatePanel) c;
 519                                           //String path = o.toString();
 520                                           sk.loadFromXmlFile((File) o); // BH SwingJS
 521                                           sk.repaint();
 522                                   }
 523                           }
 524                   }
 525                   dtde.dropComplete(true);
 526                   return;
 527               }
 528             }
 529         dtde.rejectDrop();
 530          }
 531          catch (Exception e)
 532          {
 533                  e.printStackTrace();
 534              dtde.rejectDrop();
 535           }
 536         }
 537
 538         public void dropActionChanged(DropTargetDragEvent arg0) {
 539         }
 540
 541         public VARNAPanel getVarnaPanel() {
 542                 return _vp;
 543         }
 544
 545         public void flipButtonEnable() {
 546                 flipButton.setEnabled(true);
 547         }
 548
 549         public void flipButtonDisable() {
 550                 flipButton.setEnabled(false);
 551         }
 552
 553         public void retrieveTemplates()
 554         {
 555                 URL u;
 556
 557                 try {
 558                         u = new URL("http://127.0.0.1/VARNA/templateShare/actions.php?action=retrieve&nbHelices=3&nbMultiLoops=1&length=50");
 559                 URLConnection uc = u.openConnection();
 560                 InputStreamReader  isr = new InputStreamReader(uc.getInputStream());
 561                 BufferedReader b = new BufferedReader(isr);
 562                 ArrayList<String> res = new ArrayList<String>();
 563                 String s = b.readLine();
 564                 while(s!=null)
 565                 {
 566                         res.add(s);
 567                         s = b.readLine();
 568                 }
 569                 } catch (MalformedURLException e) {
 570                         // TODO Auto-generated catch block
 571                         e.printStackTrace();
 572                 } catch (IOException e) {
 573                         // TODO Auto-generated catch block
 574                         e.printStackTrace();
 575                 }
 576         }
 577 }