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       buildAssociatedViewMenu();
 121
 122       treeCanvas = new TreeCanvas(ap, scrollPane);
 123       scrollPane.setViewportView(treeCanvas);
 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     void buildAssociatedViewMenu()
 152     {
 153       AlignmentPanel [] aps = PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
 154       if(aps.length<2)
 155       {
 156         associateLeavesMenu.setVisible(false);
 157         return;
 158       }
 159       associateLeavesMenu.addSeparator();
 160
 161       JRadioButtonMenuItem item;
 162       ButtonGroup buttonGroup = new ButtonGroup();
 163       int i, iSize = aps.length;
 164       for(i=0; i<iSize; i++)
 165       {
 166           final AlignmentPanel ap = aps[i];
 167           item = new JRadioButtonMenuItem(ap.av.viewName, ap.av==av );
 168           buttonGroup.add(item);
 169           item.addActionListener(new ActionListener()
 170               {
 171                 public void actionPerformed(ActionEvent evt)
 172                 {
 173                   treeCanvas.applyToAllViews = false;
 174                   treeCanvas.ap = ap;
 175                   treeCanvas.av = ap.av;
 176                   PaintRefresher.RemoveComponent(treeCanvas);
 177                   PaintRefresher.Register(treeCanvas, ap.av.getSequenceSetId());
 178                 }
 179               });
 180
 181           associateLeavesMenu.add(item);
 182       }
 183
 184       final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
 185       buttonGroup.add(itemf);
 186       itemf.addActionListener(new ActionListener()
 187       {
 188         public void actionPerformed(ActionEvent evt)
 189         {
 190           treeCanvas.applyToAllViews = itemf.isSelected();
 191         }
 192       });
 193       associateLeavesMenu.add(itemf);
 194
 195     }
 196
 197     class TreeLoader extends Thread
 198     {
 199       NewickFile newtree;
 200       jalview.datamodel.AlignmentView odata=null;
 201       public TreeLoader(NewickFile newtree)
 202       {
 203         this.newtree = newtree;
 204         if (newtree != null)
 205         {
 206           // Must be outside run(), as Jalview2XML tries to
 207           // update distance/bootstrap visibility at the same time
 208           showBootstrap(newtree.HasBootstrap());
 209           showDistances(newtree.HasDistances());
 210         }
 211       }
 212
 213       public void run()
 214       {
 215
 216         if(newtree!=null)
 217         {
 218           if (odata==null) {
 219             tree = new NJTree(av.alignment.getSequencesArray(),
 220                               newtree);
 221           } else {
 222             tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
 223           }
 224           if (!tree.hasOriginalSequenceData())
 225             allowOriginalSeqData(false);
 226         }
 227         else
 228         {
 229           int start, end;
 230           SequenceI [] seqs;
 231           AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);
 232           if(av.getSelectionGroup()==null)
 233           {
 234             start = 0;
 235             end = av.alignment.getWidth();
 236             seqs = av.alignment.getSequencesArray();
 237           }
 238           else
 239           {
 240             start = av.getSelectionGroup().getStartRes();
 241             end = av.getSelectionGroup().getEndRes()+1;
 242             seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
 243           }
 244
 245           tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
 246           showDistances(true);
 247         }
 248
 249
 250         tree.reCount(tree.getTopNode());
 251         tree.findHeight(tree.getTopNode());
 252         treeCanvas.setTree(tree);
 253         treeCanvas.repaint();
 254         av.setCurrentTree(tree);
 255
 256       }
 257     }
 258
 259     public void showDistances(boolean b)
 260     {
 261       treeCanvas.setShowDistances(b);
 262       distanceMenu.setSelected(b);
 263     }
 264
 265     public void showBootstrap(boolean b)
 266     {
 267       treeCanvas.setShowBootstrap(b);
 268       bootstrapMenu.setSelected(b);
 269     }
 270
 271     public void showPlaceholders(boolean b)
 272     {
 273       placeholdersMenu.setState(b);
 274       treeCanvas.setMarkPlaceholders(b);
 275     }
 276
 277     private void allowOriginalSeqData(boolean b) {
 278       originalSeqData.setVisible(b);
 279     }
 280
 281
 282
 283     /**
 284      * DOCUMENT ME!
 285      *
 286      * @return DOCUMENT ME!
 287      */
 288     public NJTree getTree()
 289     {
 290         return tree;
 291     }
 292
 293
 294     /**
 295      * DOCUMENT ME!
 296      *
 297      * @param e DOCUMENT ME!
 298      */
 299     public void textbox_actionPerformed(ActionEvent e)
 300     {
 301         CutAndPasteTransfer cap = new CutAndPasteTransfer();
 302
 303         StringBuffer buffer = new StringBuffer();
 304
 305         if (type.equals("AV"))
 306         {
 307             buffer.append("Average distance tree using ");
 308         }
 309         else
 310         {
 311             buffer.append("Neighbour joining tree using ");
 312         }
 313
 314         if (pwtype.equals("BL"))
 315         {
 316             buffer.append("BLOSUM62");
 317         }
 318         else
 319         {
 320             buffer.append("PID");
 321         }
 322
 323         Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
 324
 325         jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
 326         cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));
 327     }
 328
 329     /**
 330      * DOCUMENT ME!
 331      *
 332      * @param e DOCUMENT ME!
 333      */
 334     public void saveAsNewick_actionPerformed(ActionEvent e)
 335     {
 336         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
 337                     "LAST_DIRECTORY"));
 338         chooser.setFileView(new JalviewFileView());
 339         chooser.setDialogTitle("Save tree as newick file");
 340         chooser.setToolTipText("Save");
 341
 342         int value = chooser.showSaveDialog(null);
 343
 344         if (value == JalviewFileChooser.APPROVE_OPTION)
 345         {
 346             String choice = chooser.getSelectedFile().getPath();
 347             jalview.bin.Cache.setProperty("LAST_DIRECTORY",
 348                 chooser.getSelectedFile().getParent());
 349
 350             try
 351             {
 352                 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
 353                 String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());
 354                 java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
 355                             choice));
 356                 out.println(output);
 357                 out.close();
 358             }
 359             catch (Exception ex)
 360             {
 361                 ex.printStackTrace();
 362             }
 363         }
 364     }
 365
 366     /**
 367      * DOCUMENT ME!
 368      *
 369      * @param e DOCUMENT ME!
 370      */
 371     public void printMenu_actionPerformed(ActionEvent e)
 372     {
 373         //Putting in a thread avoids Swing painting problems
 374         treeCanvas.startPrinting();
 375     }
 376
 377
 378     public void originalSeqData_actionPerformed(ActionEvent e)
 379     {
 380       if (!tree.hasOriginalSequenceData())
 381       {
 382         jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
 383         return;
 384       }
 385       // decide if av alignment is sufficiently different to original data to warrant a new window to be created
 386       // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
 387       // or create a selection box around columns in alignment view
 388       // test Alignment(SeqCigar[])
 389       Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
 390           getGapCharacter());
 391
 392
 393       if (alAndColsel != null && alAndColsel[0]!=null)
 394        {
 395          // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
 396
 397          Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
 398          Alignment dataset = av.getAlignment().getDataset();
 399          if (dataset != null)
 400          {
 401            al.setDataset(dataset);
 402          }
 403
 404          if (true)
 405          {
 406            // make a new frame!
 407            AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],
 408                                            AlignFrame.DEFAULT_WIDTH,
 409                                            AlignFrame.DEFAULT_HEIGHT
 410 );
 411
 412            //>>>This is a fix for the moment, until a better solution is found!!<<<
 413            // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
 414
 415        //           af.addSortByOrderMenuItem(ServiceName + " Ordering",
 416        //                                     msaorder);
 417
 418            Desktop.addInternalFrame(af, "Original Data for " + this.title,
 419                                     AlignFrame.DEFAULT_WIDTH,
 420                                     AlignFrame.DEFAULT_HEIGHT);
 421          }
 422        }
 423     }
 424
 425
 426     /**
 427      * DOCUMENT ME!
 428      *
 429      * @param e DOCUMENT ME!
 430      */
 431     public void fitToWindow_actionPerformed(ActionEvent e)
 432     {
 433         treeCanvas.fitToWindow = fitToWindow.isSelected();
 434         repaint();
 435     }
 436
 437     /**
 438      * DOCUMENT ME!
 439      *
 440      * @param e DOCUMENT ME!
 441      */
 442     public void font_actionPerformed(ActionEvent e)
 443     {
 444         if (treeCanvas == null)
 445         {
 446             return;
 447         }
 448
 449         new FontChooser(this);
 450     }
 451
 452     public Font getTreeFont()
 453     {
 454         return treeCanvas.font;
 455     }
 456
 457     public void setTreeFont(Font font)
 458     {
 459       if(treeCanvas!=null)
 460       treeCanvas.setFont(font);
 461     }
 462
 463     /**
 464      * DOCUMENT ME!
 465      *
 466      * @param e DOCUMENT ME!
 467      */
 468     public void distanceMenu_actionPerformed(ActionEvent e)
 469     {
 470         treeCanvas.setShowDistances(distanceMenu.isSelected());
 471     }
 472
 473     /**
 474      * DOCUMENT ME!
 475      *
 476      * @param e DOCUMENT ME!
 477      */
 478     public void bootstrapMenu_actionPerformed(ActionEvent e)
 479     {
 480         treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
 481     }
 482
 483     /**
 484      * DOCUMENT ME!
 485      *
 486      * @param e DOCUMENT ME!
 487      */
 488     public void placeholdersMenu_actionPerformed(ActionEvent e)
 489     {
 490         treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
 491     }
 492
 493     /**
 494      * DOCUMENT ME!
 495      *
 496      * @param e DOCUMENT ME!
 497      */
 498     public void epsTree_actionPerformed(ActionEvent e)
 499     {
 500       boolean accurateText = true;
 501
 502       String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
 503           "Prompt each time");
 504
 505     // If we need to prompt, and if the GUI is visible then
 506     // Prompt for EPS rendering style
 507       if (renderStyle.equalsIgnoreCase("Prompt each time")
 508           && !
 509           (System.getProperty("java.awt.headless") != null
 510            && System.getProperty("java.awt.headless").equals("true")))
 511       {
 512         EPSOptions eps = new EPSOptions();
 513         renderStyle = eps.getValue();
 514
 515         if (renderStyle==null || eps.cancelled)
 516           return;
 517
 518
 519       }
 520
 521       if (renderStyle.equalsIgnoreCase("text"))
 522       {
 523         accurateText = false;
 524       }
 525
 526         int width = treeCanvas.getWidth();
 527         int height = treeCanvas.getHeight();
 528
 529         try
 530         {
 531             jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
 532                         "LAST_DIRECTORY"), new String[] { "eps" },
 533                     new String[] { "Encapsulated Postscript" },
 534                     "Encapsulated Postscript");
 535             chooser.setFileView(new jalview.io.JalviewFileView());
 536             chooser.setDialogTitle("Create EPS file from tree");
 537             chooser.setToolTipText("Save");
 538
 539             int value = chooser.showSaveDialog(this);
 540
 541             if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
 542             {
 543                 return;
 544             }
 545
 546             jalview.bin.Cache.setProperty("LAST_DIRECTORY",
 547                                           chooser.getSelectedFile().getParent());
 548
 549             FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
 550             EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
 551                                                  height);
 552
 553             pg.setAccurateTextMode(accurateText);
 554
 555             treeCanvas.draw(pg, width, height);
 556
 557             pg.flush();
 558             pg.close();
 559         }
 560         catch (Exception ex)
 561         {
 562             ex.printStackTrace();
 563         }
 564     }
 565
 566     /**
 567      * DOCUMENT ME!
 568      *
 569      * @param e DOCUMENT ME!
 570      */
 571     public void pngTree_actionPerformed(ActionEvent e)
 572     {
 573         int width = treeCanvas.getWidth();
 574         int height = treeCanvas.getHeight();
 575
 576         try
 577         {
 578             jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
 579                         "LAST_DIRECTORY"), new String[] { "png" },
 580                     new String[] { "Portable network graphics" },
 581                     "Portable network graphics");
 582
 583             chooser.setFileView(new jalview.io.JalviewFileView());
 584             chooser.setDialogTitle("Create PNG image from tree");
 585             chooser.setToolTipText("Save");
 586
 587             int value = chooser.showSaveDialog(this);
 588
 589             if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
 590             {
 591                 return;
 592             }
 593
 594             jalview.bin.Cache.setProperty("LAST_DIRECTORY",
 595                 chooser.getSelectedFile().getParent());
 596
 597             FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
 598
 599             BufferedImage bi = new BufferedImage(width, height,
 600                     BufferedImage.TYPE_INT_RGB);
 601             Graphics png = bi.getGraphics();
 602
 603             treeCanvas.draw(png, width, height);
 604
 605             ImageIO.write(bi, "png", out);
 606             out.close();
 607         }
 608         catch (Exception ex)
 609         {
 610             ex.printStackTrace();
 611         }
 612     }
 613 }