src/jalview/gui/TreePanel.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.gui;
  20
  21 import jalview.analysis.*;
  22
  23 import jalview.datamodel.*;
  24
  25 import jalview.io.*;
  26
  27 import jalview.jbgui.*;
  28
  29 import org.jibble.epsgraphics.*;
  30
  31 import java.awt.*;
  32 import java.awt.event.*;
  33 import java.awt.image.*;
  34
  35 import java.io.*;
  36
  37 import java.util.*;
  38
  39 import javax.swing.*;
  40 import javax.imageio.*;
  41
  42 import java.beans.PropertyChangeEvent;
  43
  44
  45 /**
  46  * DOCUMENT ME!
  47  *
  48  * @author $author$
  49  * @version $Revision$
  50  */
  51 public class TreePanel extends GTreePanel
  52 {
  53     String type;
  54     String pwtype;
  55     TreeCanvas treeCanvas;
  56     NJTree tree;
  57     AlignViewport av;
  58
  59     /**
  60      * Creates a new TreePanel object.
  61      *
  62      * @param av DOCUMENT ME!
  63      * @param seqVector DOCUMENT ME!
  64      * @param type DOCUMENT ME!
  65      * @param pwtype DOCUMENT ME!
  66      * @param s DOCUMENT ME!
  67      * @param e DOCUMENT ME!
  68      */
  69     public TreePanel(AlignmentPanel ap, String type, String pwtype)
  70     {
  71       super();
  72       initTreePanel(ap, type, pwtype, null, null);
  73
  74       // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
  75       // showDistances(true);
  76     }
  77
  78     /**
  79      * Creates a new TreePanel object.
  80      *
  81      * @param av DOCUMENT ME!
  82      * @param seqVector DOCUMENT ME!
  83      * @param newtree DOCUMENT ME!
  84      * @param type DOCUMENT ME!
  85      * @param pwtype DOCUMENT ME!
  86      */
  87     public TreePanel(AlignmentPanel ap,
  88                      String type,
  89                      String pwtype,
  90                      NewickFile newtree)
  91     {
  92       super();
  93       initTreePanel(ap, type, pwtype, newtree, null);
  94     }
  95
  96     public TreePanel(AlignmentPanel av,
  97         String type,
  98         String pwtype,
  99         NewickFile newtree, AlignmentView inputData) {
 100      super();
 101      initTreePanel(av,type,pwtype,newtree,inputData);
 102     }
 103
 104     public AlignmentI getAlignment()
 105     {
 106       return treeCanvas.av.getAlignment();
 107     }
 108     public AlignViewport getViewPort() {
 109       return treeCanvas.av;
 110     }
 111
 112     void initTreePanel(AlignmentPanel ap, String type,  String pwtype,
 113                        NewickFile newTree, AlignmentView inputData)
 114     {
 115
 116       av = ap.av;
 117       this.type = type;
 118       this.pwtype = pwtype;
 119
 120       treeCanvas = new TreeCanvas(this, ap, scrollPane);
 121       scrollPane.setViewportView(treeCanvas);
 122
 123       buildAssociatedViewMenu();
 124
 125       av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
 126       {
 127         public void propertyChange(PropertyChangeEvent evt)
 128         {
 129           if (evt.getPropertyName().equals("alignment"))
 130           {
 131             if(tree==null)
 132               System.out.println("tree is null");
 133             if(evt.getNewValue()==null)
 134               System.out.println("new alignment sequences vector value is null");
 135
 136             tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
 137             treeCanvas.nameHash.clear(); // reset the mapping between canvas rectangles and leafnodes
 138             repaint();
 139           }
 140         }
 141       });
 142
 143       TreeLoader tl = new TreeLoader(newTree);
 144       if (inputData!=null) {
 145         tl.odata=inputData;
 146       }
 147       tl.start();
 148
 149     }
 150
 151     public void viewMenu_menuSelected()
 152     {
 153       buildAssociatedViewMenu();
 154     }
 155
 156
 157     void buildAssociatedViewMenu()
 158     {
 159       AlignmentPanel [] aps = PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
 160       if(aps.length==1 && treeCanvas.ap==aps[0])
 161       {
 162         associateLeavesMenu.setVisible(false);
 163         return;
 164       }
 165
 166       associateLeavesMenu.setVisible(true);
 167
 168       if( (viewMenu.getItem(viewMenu.getItemCount()-2) instanceof JMenuItem))
 169       {
 170         viewMenu.insertSeparator(viewMenu.getItemCount()-1);
 171       }
 172
 173       associateLeavesMenu.removeAll();
 174
 175
 176       JRadioButtonMenuItem item;
 177       ButtonGroup buttonGroup = new ButtonGroup();
 178       int i, iSize = aps.length;
 179       final TreePanel thisTreePanel = this;
 180       for(i=0; i<iSize; i++)
 181       {
 182           final AlignmentPanel ap = aps[i];
 183           item = new JRadioButtonMenuItem(ap.av.viewName, ap==treeCanvas.ap );
 184           buttonGroup.add(item);
 185           item.addActionListener(new ActionListener()
 186               {
 187                 public void actionPerformed(ActionEvent evt)
 188                 {
 189                   treeCanvas.applyToAllViews = false;
 190                   treeCanvas.ap = ap;
 191                   treeCanvas.av = ap.av;
 192                   PaintRefresher.RemoveComponent(thisTreePanel);
 193                   PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
 194                 }
 195               });
 196
 197           associateLeavesMenu.add(item);
 198       }
 199
 200       final JRadioButtonMenuItem itemf =
 201           new JRadioButtonMenuItem("All Views", treeCanvas.applyToAllViews);
 202       buttonGroup.add(itemf);
 203       itemf.addActionListener(new ActionListener()
 204       {
 205         public void actionPerformed(ActionEvent evt)
 206         {
 207           treeCanvas.applyToAllViews = itemf.isSelected();
 208         }
 209       });
 210       associateLeavesMenu.add(itemf);
 211
 212     }
 213
 214     class TreeLoader extends Thread
 215     {
 216       NewickFile newtree;
 217       jalview.datamodel.AlignmentView odata=null;
 218       public TreeLoader(NewickFile newtree)
 219       {
 220         this.newtree = newtree;
 221         if (newtree != null)
 222         {
 223           // Must be outside run(), as Jalview2XML tries to
 224           // update distance/bootstrap visibility at the same time
 225           showBootstrap(newtree.HasBootstrap());
 226           showDistances(newtree.HasDistances());
 227         }
 228       }
 229
 230       public void run()
 231       {
 232
 233         if(newtree!=null)
 234         {
 235           if (odata==null) {
 236             tree = new NJTree(av.alignment.getSequencesArray(),
 237                               newtree);
 238           } else {
 239             tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
 240           }
 241           if (!tree.hasOriginalSequenceData())
 242             allowOriginalSeqData(false);
 243         }
 244         else
 245         {
 246           int start, end;
 247           SequenceI [] seqs;
 248           AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);
 249           if(av.getSelectionGroup()==null)
 250           {
 251             start = 0;
 252             end = av.alignment.getWidth();
 253             seqs = av.alignment.getSequencesArray();
 254           }
 255           else
 256           {
 257             start = av.getSelectionGroup().getStartRes();
 258             end = av.getSelectionGroup().getEndRes()+1;
 259             seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
 260           }
 261
 262           tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
 263           showDistances(true);
 264         }
 265
 266
 267         tree.reCount(tree.getTopNode());
 268         tree.findHeight(tree.getTopNode());
 269         treeCanvas.setTree(tree);
 270         treeCanvas.repaint();
 271         av.setCurrentTree(tree);
 272
 273       }
 274     }
 275
 276     public void showDistances(boolean b)
 277     {
 278       treeCanvas.setShowDistances(b);
 279       distanceMenu.setSelected(b);
 280     }
 281
 282     public void showBootstrap(boolean b)
 283     {
 284       treeCanvas.setShowBootstrap(b);
 285       bootstrapMenu.setSelected(b);
 286     }
 287
 288     public void showPlaceholders(boolean b)
 289     {
 290       placeholdersMenu.setState(b);
 291       treeCanvas.setMarkPlaceholders(b);
 292     }
 293
 294     private void allowOriginalSeqData(boolean b) {
 295       originalSeqData.setVisible(b);
 296     }
 297
 298
 299
 300     /**
 301      * DOCUMENT ME!
 302      *
 303      * @return DOCUMENT ME!
 304      */
 305     public NJTree getTree()
 306     {
 307         return tree;
 308     }
 309
 310
 311     /**
 312      * DOCUMENT ME!
 313      *
 314      * @param e DOCUMENT ME!
 315      */
 316     public void textbox_actionPerformed(ActionEvent e)
 317     {
 318         CutAndPasteTransfer cap = new CutAndPasteTransfer();
 319
 320         StringBuffer buffer = new StringBuffer();
 321
 322         if (type.equals("AV"))
 323         {
 324             buffer.append("Average distance tree using ");
 325         }
 326         else
 327         {
 328             buffer.append("Neighbour joining tree using ");
 329         }
 330
 331         if (pwtype.equals("BL"))
 332         {
 333             buffer.append("BLOSUM62");
 334         }
 335         else
 336         {
 337             buffer.append("PID");
 338         }
 339
 340         Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
 341
 342         jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
 343         cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));
 344     }
 345
 346     /**
 347      * DOCUMENT ME!
 348      *
 349      * @param e DOCUMENT ME!
 350      */
 351     public void saveAsNewick_actionPerformed(ActionEvent e)
 352     {
 353         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
 354                     "LAST_DIRECTORY"));
 355         chooser.setFileView(new JalviewFileView());
 356         chooser.setDialogTitle("Save tree as newick file");
 357         chooser.setToolTipText("Save");
 358
 359         int value = chooser.showSaveDialog(null);
 360
 361         if (value == JalviewFileChooser.APPROVE_OPTION)
 362         {
 363             String choice = chooser.getSelectedFile().getPath();
 364             jalview.bin.Cache.setProperty("LAST_DIRECTORY",
 365                 chooser.getSelectedFile().getParent());
 366
 367             try
 368             {
 369                 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
 370                 String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());
 371                 java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
 372                             choice));
 373                 out.println(output);
 374                 out.close();
 375             }
 376             catch (Exception ex)
 377             {
 378                 ex.printStackTrace();
 379             }
 380         }
 381     }
 382
 383     /**
 384      * DOCUMENT ME!
 385      *
 386      * @param e DOCUMENT ME!
 387      */
 388     public void printMenu_actionPerformed(ActionEvent e)
 389     {
 390         //Putting in a thread avoids Swing painting problems
 391         treeCanvas.startPrinting();
 392     }
 393
 394
 395     public void originalSeqData_actionPerformed(ActionEvent e)
 396     {
 397       if (!tree.hasOriginalSequenceData())
 398       {
 399         jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
 400         return;
 401       }
 402       // decide if av alignment is sufficiently different to original data to warrant a new window to be created
 403       // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
 404       // or create a selection box around columns in alignment view
 405       // test Alignment(SeqCigar[])
 406       Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
 407           getGapCharacter());
 408
 409
 410       if (alAndColsel != null && alAndColsel[0]!=null)
 411        {
 412          // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
 413
 414          Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
 415          Alignment dataset = av.getAlignment().getDataset();
 416          if (dataset != null)
 417          {
 418            al.setDataset(dataset);
 419          }
 420
 421          if (true)
 422          {
 423            // make a new frame!
 424            AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],
 425                                            AlignFrame.DEFAULT_WIDTH,
 426                                            AlignFrame.DEFAULT_HEIGHT
 427 );
 428
 429            //>>>This is a fix for the moment, until a better solution is found!!<<<
 430            // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
 431
 432        //           af.addSortByOrderMenuItem(ServiceName + " Ordering",
 433        //                                     msaorder);
 434
 435            Desktop.addInternalFrame(af, "Original Data for " + this.title,
 436                                     AlignFrame.DEFAULT_WIDTH,
 437                                     AlignFrame.DEFAULT_HEIGHT);
 438          }
 439        }
 440     }
 441
 442
 443     /**
 444      * DOCUMENT ME!
 445      *
 446      * @param e DOCUMENT ME!
 447      */
 448     public void fitToWindow_actionPerformed(ActionEvent e)
 449     {
 450         treeCanvas.fitToWindow = fitToWindow.isSelected();
 451         repaint();
 452     }
 453
 454     /**
 455      * DOCUMENT ME!
 456      *
 457      * @param e DOCUMENT ME!
 458      */
 459     public void font_actionPerformed(ActionEvent e)
 460     {
 461         if (treeCanvas == null)
 462         {
 463             return;
 464         }
 465
 466         new FontChooser(this);
 467     }
 468
 469     public Font getTreeFont()
 470     {
 471         return treeCanvas.font;
 472     }
 473
 474     public void setTreeFont(Font font)
 475     {
 476       if(treeCanvas!=null)
 477       treeCanvas.setFont(font);
 478     }
 479
 480     /**
 481      * DOCUMENT ME!
 482      *
 483      * @param e DOCUMENT ME!
 484      */
 485     public void distanceMenu_actionPerformed(ActionEvent e)
 486     {
 487         treeCanvas.setShowDistances(distanceMenu.isSelected());
 488     }
 489
 490     /**
 491      * DOCUMENT ME!
 492      *
 493      * @param e DOCUMENT ME!
 494      */
 495     public void bootstrapMenu_actionPerformed(ActionEvent e)
 496     {
 497         treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
 498     }
 499
 500     /**
 501      * DOCUMENT ME!
 502      *
 503      * @param e DOCUMENT ME!
 504      */
 505     public void placeholdersMenu_actionPerformed(ActionEvent e)
 506     {
 507         treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
 508     }
 509
 510     /**
 511      * DOCUMENT ME!
 512      *
 513      * @param e DOCUMENT ME!
 514      */
 515     public void epsTree_actionPerformed(ActionEvent e)
 516     {
 517       boolean accurateText = true;
 518
 519       String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
 520           "Prompt each time");
 521
 522     // If we need to prompt, and if the GUI is visible then
 523     // Prompt for EPS rendering style
 524       if (renderStyle.equalsIgnoreCase("Prompt each time")
 525           && !
 526           (System.getProperty("java.awt.headless") != null
 527            && System.getProperty("java.awt.headless").equals("true")))
 528       {
 529         EPSOptions eps = new EPSOptions();
 530         renderStyle = eps.getValue();
 531
 532         if (renderStyle==null || eps.cancelled)
 533           return;
 534
 535
 536       }
 537
 538       if (renderStyle.equalsIgnoreCase("text"))
 539       {
 540         accurateText = false;
 541       }
 542
 543         int width = treeCanvas.getWidth();
 544         int height = treeCanvas.getHeight();
 545
 546         try
 547         {
 548             jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
 549                         "LAST_DIRECTORY"), new String[] { "eps" },
 550                     new String[] { "Encapsulated Postscript" },
 551                     "Encapsulated Postscript");
 552             chooser.setFileView(new jalview.io.JalviewFileView());
 553             chooser.setDialogTitle("Create EPS file from tree");
 554             chooser.setToolTipText("Save");
 555
 556             int value = chooser.showSaveDialog(this);
 557
 558             if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
 559             {
 560                 return;
 561             }
 562
 563             jalview.bin.Cache.setProperty("LAST_DIRECTORY",
 564                                           chooser.getSelectedFile().getParent());
 565
 566             FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
 567             EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
 568                                                  height);
 569
 570             pg.setAccurateTextMode(accurateText);
 571
 572             treeCanvas.draw(pg, width, height);
 573
 574             pg.flush();
 575             pg.close();
 576         }
 577         catch (Exception ex)
 578         {
 579             ex.printStackTrace();
 580         }
 581     }
 582
 583     /**
 584      * DOCUMENT ME!
 585      *
 586      * @param e DOCUMENT ME!
 587      */
 588     public void pngTree_actionPerformed(ActionEvent e)
 589     {
 590         int width = treeCanvas.getWidth();
 591         int height = treeCanvas.getHeight();
 592
 593         try
 594         {
 595             jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
 596                         "LAST_DIRECTORY"), new String[] { "png" },
 597                     new String[] { "Portable network graphics" },
 598                     "Portable network graphics");
 599
 600             chooser.setFileView(new jalview.io.JalviewFileView());
 601             chooser.setDialogTitle("Create PNG image from tree");
 602             chooser.setToolTipText("Save");
 603
 604             int value = chooser.showSaveDialog(this);
 605
 606             if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
 607             {
 608                 return;
 609             }
 610
 611             jalview.bin.Cache.setProperty("LAST_DIRECTORY",
 612                 chooser.getSelectedFile().getParent());
 613
 614             FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
 615
 616             BufferedImage bi = new BufferedImage(width, height,
 617                     BufferedImage.TYPE_INT_RGB);
 618             Graphics png = bi.getGraphics();
 619
 620             treeCanvas.draw(png, width, height);
 621
 622             ImageIO.write(bi, "png", out);
 623             out.close();
 624         }
 625         catch (Exception ex)
 626         {
 627             ex.printStackTrace();
 628         }
 629     }
 630 }