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       PaintRefresher.Register(this, ap.av.getSequenceSetId());
 124
 125       buildAssociatedViewMenu();
 126
 127       av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
 128       {
 129         public void propertyChange(PropertyChangeEvent evt)
 130         {
 131           if (evt.getPropertyName().equals("alignment"))
 132           {
 133             if(tree==null)
 134               System.out.println("tree is null");
 135             if(evt.getNewValue()==null)
 136               System.out.println("new alignment sequences vector value is null");
 137
 138             tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
 139             treeCanvas.nameHash.clear(); // reset the mapping between canvas rectangles and leafnodes
 140             repaint();
 141           }
 142         }
 143       });
 144
 145       TreeLoader tl = new TreeLoader(newTree);
 146       if (inputData!=null) {
 147         tl.odata=inputData;
 148       }
 149       tl.start();
 150
 151     }
 152
 153     public void viewMenu_menuSelected()
 154     {
 155       buildAssociatedViewMenu();
 156     }
 157
 158
 159     void buildAssociatedViewMenu()
 160     {
 161       AlignmentPanel [] aps = PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
 162       if(aps.length==1 && treeCanvas.ap==aps[0])
 163       {
 164         associateLeavesMenu.setVisible(false);
 165         return;
 166       }
 167
 168       associateLeavesMenu.setVisible(true);
 169
 170       if( (viewMenu.getItem(viewMenu.getItemCount()-2) instanceof JMenuItem))
 171       {
 172         viewMenu.insertSeparator(viewMenu.getItemCount()-1);
 173       }
 174
 175       associateLeavesMenu.removeAll();
 176
 177
 178       JRadioButtonMenuItem item;
 179       ButtonGroup buttonGroup = new ButtonGroup();
 180       int i, iSize = aps.length;
 181       final TreePanel thisTreePanel = this;
 182       for(i=0; i<iSize; i++)
 183       {
 184           final AlignmentPanel ap = aps[i];
 185           item = new JRadioButtonMenuItem(ap.av.viewName, ap==treeCanvas.ap );
 186           buttonGroup.add(item);
 187           item.addActionListener(new ActionListener()
 188               {
 189                 public void actionPerformed(ActionEvent evt)
 190                 {
 191                   treeCanvas.applyToAllViews = false;
 192                   treeCanvas.ap = ap;
 193                   treeCanvas.av = ap.av;
 194                   PaintRefresher.Register(thisTreePanel, ap.av.getSequenceSetId());
 195                 }
 196               });
 197
 198           associateLeavesMenu.add(item);
 199       }
 200
 201       final JRadioButtonMenuItem itemf =
 202           new JRadioButtonMenuItem("All Views", treeCanvas.applyToAllViews);
 203       buttonGroup.add(itemf);
 204       itemf.addActionListener(new ActionListener()
 205       {
 206         public void actionPerformed(ActionEvent evt)
 207         {
 208           treeCanvas.applyToAllViews = itemf.isSelected();
 209         }
 210       });
 211       associateLeavesMenu.add(itemf);
 212
 213     }
 214
 215     class TreeLoader extends Thread
 216     {
 217       NewickFile newtree;
 218       jalview.datamodel.AlignmentView odata=null;
 219       public TreeLoader(NewickFile newtree)
 220       {
 221         this.newtree = newtree;
 222         if (newtree != null)
 223         {
 224           // Must be outside run(), as Jalview2XML tries to
 225           // update distance/bootstrap visibility at the same time
 226           showBootstrap(newtree.HasBootstrap());
 227           showDistances(newtree.HasDistances());
 228         }
 229       }
 230
 231       public void run()
 232       {
 233
 234         if(newtree!=null)
 235         {
 236           if (odata==null) {
 237             tree = new NJTree(av.alignment.getSequencesArray(),
 238                               newtree);
 239           } else {
 240             tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
 241           }
 242           if (!tree.hasOriginalSequenceData())
 243             allowOriginalSeqData(false);
 244         }
 245         else
 246         {
 247           int start, end;
 248           SequenceI [] seqs;
 249           AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);
 250           if(av.getSelectionGroup()==null)
 251           {
 252             start = 0;
 253             end = av.alignment.getWidth();
 254             seqs = av.alignment.getSequencesArray();
 255           }
 256           else
 257           {
 258             start = av.getSelectionGroup().getStartRes();
 259             end = av.getSelectionGroup().getEndRes()+1;
 260             seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
 261           }
 262
 263           tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
 264           showDistances(true);
 265         }
 266
 267
 268         tree.reCount(tree.getTopNode());
 269         tree.findHeight(tree.getTopNode());
 270         treeCanvas.setTree(tree);
 271         treeCanvas.repaint();
 272         av.setCurrentTree(tree);
 273
 274       }
 275     }
 276
 277     public void showDistances(boolean b)
 278     {
 279       treeCanvas.setShowDistances(b);
 280       distanceMenu.setSelected(b);
 281     }
 282
 283     public void showBootstrap(boolean b)
 284     {
 285       treeCanvas.setShowBootstrap(b);
 286       bootstrapMenu.setSelected(b);
 287     }
 288
 289     public void showPlaceholders(boolean b)
 290     {
 291       placeholdersMenu.setState(b);
 292       treeCanvas.setMarkPlaceholders(b);
 293     }
 294
 295     private void allowOriginalSeqData(boolean b) {
 296       originalSeqData.setVisible(b);
 297     }
 298
 299
 300
 301     /**
 302      * DOCUMENT ME!
 303      *
 304      * @return DOCUMENT ME!
 305      */
 306     public NJTree getTree()
 307     {
 308         return tree;
 309     }
 310
 311
 312     /**
 313      * DOCUMENT ME!
 314      *
 315      * @param e DOCUMENT ME!
 316      */
 317     public void textbox_actionPerformed(ActionEvent e)
 318     {
 319         CutAndPasteTransfer cap = new CutAndPasteTransfer();
 320
 321         StringBuffer buffer = new StringBuffer();
 322
 323         if (type.equals("AV"))
 324         {
 325             buffer.append("Average distance tree using ");
 326         }
 327         else
 328         {
 329             buffer.append("Neighbour joining tree using ");
 330         }
 331
 332         if (pwtype.equals("BL"))
 333         {
 334             buffer.append("BLOSUM62");
 335         }
 336         else
 337         {
 338             buffer.append("PID");
 339         }
 340
 341         Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
 342
 343         jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
 344         cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));
 345     }
 346
 347     /**
 348      * DOCUMENT ME!
 349      *
 350      * @param e DOCUMENT ME!
 351      */
 352     public void saveAsNewick_actionPerformed(ActionEvent e)
 353     {
 354         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
 355                     "LAST_DIRECTORY"));
 356         chooser.setFileView(new JalviewFileView());
 357         chooser.setDialogTitle("Save tree as newick file");
 358         chooser.setToolTipText("Save");
 359
 360         int value = chooser.showSaveDialog(null);
 361
 362         if (value == JalviewFileChooser.APPROVE_OPTION)
 363         {
 364             String choice = chooser.getSelectedFile().getPath();
 365             jalview.bin.Cache.setProperty("LAST_DIRECTORY",
 366                 chooser.getSelectedFile().getParent());
 367
 368             try
 369             {
 370                 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
 371                 String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());
 372                 java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
 373                             choice));
 374                 out.println(output);
 375                 out.close();
 376             }
 377             catch (Exception ex)
 378             {
 379                 ex.printStackTrace();
 380             }
 381         }
 382     }
 383
 384     /**
 385      * DOCUMENT ME!
 386      *
 387      * @param e DOCUMENT ME!
 388      */
 389     public void printMenu_actionPerformed(ActionEvent e)
 390     {
 391         //Putting in a thread avoids Swing painting problems
 392         treeCanvas.startPrinting();
 393     }
 394
 395
 396     public void originalSeqData_actionPerformed(ActionEvent e)
 397     {
 398       if (!tree.hasOriginalSequenceData())
 399       {
 400         jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
 401         return;
 402       }
 403       // decide if av alignment is sufficiently different to original data to warrant a new window to be created
 404       // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
 405       // or create a selection box around columns in alignment view
 406       // test Alignment(SeqCigar[])
 407       Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
 408           getGapCharacter());
 409
 410
 411       if (alAndColsel != null && alAndColsel[0]!=null)
 412        {
 413          // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
 414
 415          Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
 416          Alignment dataset = av.getAlignment().getDataset();
 417          if (dataset != null)
 418          {
 419            al.setDataset(dataset);
 420          }
 421
 422          if (true)
 423          {
 424            // make a new frame!
 425            AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],
 426                                            AlignFrame.DEFAULT_WIDTH,
 427                                            AlignFrame.DEFAULT_HEIGHT
 428 );
 429
 430            //>>>This is a fix for the moment, until a better solution is found!!<<<
 431            // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
 432
 433        //           af.addSortByOrderMenuItem(ServiceName + " Ordering",
 434        //                                     msaorder);
 435
 436            Desktop.addInternalFrame(af, "Original Data for " + this.title,
 437                                     AlignFrame.DEFAULT_WIDTH,
 438                                     AlignFrame.DEFAULT_HEIGHT);
 439          }
 440        }
 441     }
 442
 443
 444     /**
 445      * DOCUMENT ME!
 446      *
 447      * @param e DOCUMENT ME!
 448      */
 449     public void fitToWindow_actionPerformed(ActionEvent e)
 450     {
 451         treeCanvas.fitToWindow = fitToWindow.isSelected();
 452         repaint();
 453     }
 454
 455     /**
 456      * DOCUMENT ME!
 457      *
 458      * @param e DOCUMENT ME!
 459      */
 460     public void font_actionPerformed(ActionEvent e)
 461     {
 462         if (treeCanvas == null)
 463         {
 464             return;
 465         }
 466
 467         new FontChooser(this);
 468     }
 469
 470     public Font getTreeFont()
 471     {
 472         return treeCanvas.font;
 473     }
 474
 475     public void setTreeFont(Font font)
 476     {
 477       if(treeCanvas!=null)
 478       treeCanvas.setFont(font);
 479     }
 480
 481     /**
 482      * DOCUMENT ME!
 483      *
 484      * @param e DOCUMENT ME!
 485      */
 486     public void distanceMenu_actionPerformed(ActionEvent e)
 487     {
 488         treeCanvas.setShowDistances(distanceMenu.isSelected());
 489     }
 490
 491     /**
 492      * DOCUMENT ME!
 493      *
 494      * @param e DOCUMENT ME!
 495      */
 496     public void bootstrapMenu_actionPerformed(ActionEvent e)
 497     {
 498         treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
 499     }
 500
 501     /**
 502      * DOCUMENT ME!
 503      *
 504      * @param e DOCUMENT ME!
 505      */
 506     public void placeholdersMenu_actionPerformed(ActionEvent e)
 507     {
 508         treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
 509     }
 510
 511     /**
 512      * DOCUMENT ME!
 513      *
 514      * @param e DOCUMENT ME!
 515      */
 516     public void epsTree_actionPerformed(ActionEvent e)
 517     {
 518       boolean accurateText = true;
 519
 520       String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
 521           "Prompt each time");
 522
 523     // If we need to prompt, and if the GUI is visible then
 524     // Prompt for EPS rendering style
 525       if (renderStyle.equalsIgnoreCase("Prompt each time")
 526           && !
 527           (System.getProperty("java.awt.headless") != null
 528            && System.getProperty("java.awt.headless").equals("true")))
 529       {
 530         EPSOptions eps = new EPSOptions();
 531         renderStyle = eps.getValue();
 532
 533         if (renderStyle==null || eps.cancelled)
 534           return;
 535
 536
 537       }
 538
 539       if (renderStyle.equalsIgnoreCase("text"))
 540       {
 541         accurateText = false;
 542       }
 543
 544         int width = treeCanvas.getWidth();
 545         int height = treeCanvas.getHeight();
 546
 547         try
 548         {
 549             jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
 550                         "LAST_DIRECTORY"), new String[] { "eps" },
 551                     new String[] { "Encapsulated Postscript" },
 552                     "Encapsulated Postscript");
 553             chooser.setFileView(new jalview.io.JalviewFileView());
 554             chooser.setDialogTitle("Create EPS file from tree");
 555             chooser.setToolTipText("Save");
 556
 557             int value = chooser.showSaveDialog(this);
 558
 559             if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
 560             {
 561                 return;
 562             }
 563
 564             jalview.bin.Cache.setProperty("LAST_DIRECTORY",
 565                                           chooser.getSelectedFile().getParent());
 566
 567             FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
 568             EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
 569                                                  height);
 570
 571             pg.setAccurateTextMode(accurateText);
 572
 573             treeCanvas.draw(pg, width, height);
 574
 575             pg.flush();
 576             pg.close();
 577         }
 578         catch (Exception ex)
 579         {
 580             ex.printStackTrace();
 581         }
 582     }
 583
 584     /**
 585      * DOCUMENT ME!
 586      *
 587      * @param e DOCUMENT ME!
 588      */
 589     public void pngTree_actionPerformed(ActionEvent e)
 590     {
 591         int width = treeCanvas.getWidth();
 592         int height = treeCanvas.getHeight();
 593
 594         try
 595         {
 596             jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
 597                         "LAST_DIRECTORY"), new String[] { "png" },
 598                     new String[] { "Portable network graphics" },
 599                     "Portable network graphics");
 600
 601             chooser.setFileView(new jalview.io.JalviewFileView());
 602             chooser.setDialogTitle("Create PNG image from tree");
 603             chooser.setToolTipText("Save");
 604
 605             int value = chooser.showSaveDialog(this);
 606
 607             if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
 608             {
 609                 return;
 610             }
 611
 612             jalview.bin.Cache.setProperty("LAST_DIRECTORY",
 613                 chooser.getSelectedFile().getParent());
 614
 615             FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
 616
 617             BufferedImage bi = new BufferedImage(width, height,
 618                     BufferedImage.TYPE_INT_RGB);
 619             Graphics png = bi.getGraphics();
 620
 621             treeCanvas.draw(png, width, height);
 622
 623             ImageIO.write(bi, "png", out);
 624             out.close();
 625         }
 626         catch (Exception ex)
 627         {
 628             ex.printStackTrace();
 629         }
 630     }
 631 }