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.imageio.*;
  40
  41 import java.beans.PropertyChangeEvent;
  42
  43
  44 /**
  45  * DOCUMENT ME!
  46  *
  47  * @author $author$
  48  * @version $Revision$
  49  */
  50 public class TreePanel extends GTreePanel
  51 {
  52     String type;
  53     String pwtype;
  54     TreeCanvas treeCanvas;
  55     NJTree tree;
  56     AlignViewport av;
  57
  58     /**
  59      * Creates a new TreePanel object.
  60      *
  61      * @param av DOCUMENT ME!
  62      * @param seqVector DOCUMENT ME!
  63      * @param type DOCUMENT ME!
  64      * @param pwtype DOCUMENT ME!
  65      * @param s DOCUMENT ME!
  66      * @param e DOCUMENT ME!
  67      */
  68     public TreePanel(AlignmentPanel ap, String type, String pwtype)
  69     {
  70       super();
  71       initTreePanel(ap, type, pwtype, null, null);
  72
  73       // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
  74       // showDistances(true);
  75     }
  76
  77     /**
  78      * Creates a new TreePanel object.
  79      *
  80      * @param av DOCUMENT ME!
  81      * @param seqVector DOCUMENT ME!
  82      * @param newtree DOCUMENT ME!
  83      * @param type DOCUMENT ME!
  84      * @param pwtype DOCUMENT ME!
  85      */
  86     public TreePanel(AlignmentPanel ap,
  87                      String type,
  88                      String pwtype,
  89                      NewickFile newtree)
  90     {
  91       super();
  92       initTreePanel(ap, type, pwtype, newtree, null);
  93     }
  94
  95     public TreePanel(AlignmentPanel av,
  96         String type,
  97         String pwtype,
  98         NewickFile newtree, AlignmentView inputData) {
  99      super();
 100      initTreePanel(av,type,pwtype,newtree,inputData);
 101     }
 102
 103     public AlignmentI getAlignment()
 104     {
 105       return treeCanvas.av.getAlignment();
 106     }
 107     public AlignViewport getViewPort() {
 108       return treeCanvas.av;
 109     }
 110
 111     void initTreePanel(AlignmentPanel ap, String type,  String pwtype,
 112                        NewickFile newTree, AlignmentView inputData)
 113     {
 114
 115       av = ap.av;
 116       this.type = type;
 117       this.pwtype = pwtype;
 118
 119       treeCanvas = new TreeCanvas(ap, scrollPane);
 120       scrollPane.setViewportView(treeCanvas);
 121
 122       av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
 123       {
 124         public void propertyChange(PropertyChangeEvent evt)
 125         {
 126           if (evt.getPropertyName().equals("alignment"))
 127           {
 128             if(tree==null)
 129               System.out.println("tree is null");
 130             if(evt.getNewValue()==null)
 131               System.out.println("new alignment sequences vector value is null");
 132
 133             tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
 134             treeCanvas.nameHash.clear(); // reset the mapping between canvas rectangles and leafnodes
 135             repaint();
 136           }
 137         }
 138       });
 139
 140       TreeLoader tl = new TreeLoader(newTree);
 141       if (inputData!=null) {
 142         tl.odata=inputData;
 143       }
 144       tl.start();
 145
 146     }
 147
 148     class TreeLoader extends Thread
 149     {
 150       NewickFile newtree;
 151       jalview.datamodel.AlignmentView odata=null;
 152       public TreeLoader(NewickFile newtree)
 153       {
 154         this.newtree = newtree;
 155         if (newtree != null)
 156         {
 157           // Must be outside run(), as Jalview2XML tries to
 158           // update distance/bootstrap visibility at the same time
 159           showBootstrap(newtree.HasBootstrap());
 160           showDistances(newtree.HasDistances());
 161         }
 162       }
 163
 164       public void run()
 165       {
 166
 167         if(newtree!=null)
 168         {
 169           if (odata==null) {
 170             tree = new NJTree(av.alignment.getSequencesArray(),
 171                               newtree);
 172           } else {
 173             tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
 174           }
 175           if (!tree.hasOriginalSequenceData())
 176             allowOriginalSeqData(false);
 177         }
 178         else
 179         {
 180           int start, end;
 181           SequenceI [] seqs;
 182           AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup()!=null);
 183           if(av.getSelectionGroup()==null)
 184           {
 185             start = 0;
 186             end = av.alignment.getWidth();
 187             seqs = av.alignment.getSequencesArray();
 188           }
 189           else
 190           {
 191             start = av.getSelectionGroup().getStartRes();
 192             end = av.getSelectionGroup().getEndRes()+1;
 193             seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
 194           }
 195
 196           tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
 197           showDistances(true);
 198         }
 199
 200
 201         tree.reCount(tree.getTopNode());
 202         tree.findHeight(tree.getTopNode());
 203         treeCanvas.setTree(tree);
 204         treeCanvas.repaint();
 205         av.setCurrentTree(tree);
 206
 207       }
 208     }
 209
 210     public void showDistances(boolean b)
 211     {
 212       treeCanvas.setShowDistances(b);
 213       distanceMenu.setSelected(b);
 214     }
 215
 216     public void showBootstrap(boolean b)
 217     {
 218       treeCanvas.setShowBootstrap(b);
 219       bootstrapMenu.setSelected(b);
 220     }
 221
 222     public void showPlaceholders(boolean b)
 223     {
 224       placeholdersMenu.setState(b);
 225       treeCanvas.setMarkPlaceholders(b);
 226     }
 227
 228     private void allowOriginalSeqData(boolean b) {
 229       originalSeqData.setVisible(b);
 230     }
 231
 232
 233
 234     /**
 235      * DOCUMENT ME!
 236      *
 237      * @return DOCUMENT ME!
 238      */
 239     public NJTree getTree()
 240     {
 241         return tree;
 242     }
 243
 244
 245     /**
 246      * DOCUMENT ME!
 247      *
 248      * @param e DOCUMENT ME!
 249      */
 250     public void textbox_actionPerformed(ActionEvent e)
 251     {
 252         CutAndPasteTransfer cap = new CutAndPasteTransfer();
 253
 254         StringBuffer buffer = new StringBuffer();
 255
 256         if (type.equals("AV"))
 257         {
 258             buffer.append("Average distance tree using ");
 259         }
 260         else
 261         {
 262             buffer.append("Neighbour joining tree using ");
 263         }
 264
 265         if (pwtype.equals("BL"))
 266         {
 267             buffer.append("BLOSUM62");
 268         }
 269         else
 270         {
 271             buffer.append("PID");
 272         }
 273
 274         Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
 275
 276         jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
 277         cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));
 278     }
 279
 280     /**
 281      * DOCUMENT ME!
 282      *
 283      * @param e DOCUMENT ME!
 284      */
 285     public void saveAsNewick_actionPerformed(ActionEvent e)
 286     {
 287         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
 288                     "LAST_DIRECTORY"));
 289         chooser.setFileView(new JalviewFileView());
 290         chooser.setDialogTitle("Save tree as newick file");
 291         chooser.setToolTipText("Save");
 292
 293         int value = chooser.showSaveDialog(null);
 294
 295         if (value == JalviewFileChooser.APPROVE_OPTION)
 296         {
 297             String choice = chooser.getSelectedFile().getPath();
 298             jalview.bin.Cache.setProperty("LAST_DIRECTORY",
 299                 chooser.getSelectedFile().getParent());
 300
 301             try
 302             {
 303                 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
 304                 String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());
 305                 java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
 306                             choice));
 307                 out.println(output);
 308                 out.close();
 309             }
 310             catch (Exception ex)
 311             {
 312                 ex.printStackTrace();
 313             }
 314         }
 315     }
 316
 317     /**
 318      * DOCUMENT ME!
 319      *
 320      * @param e DOCUMENT ME!
 321      */
 322     public void printMenu_actionPerformed(ActionEvent e)
 323     {
 324         //Putting in a thread avoids Swing painting problems
 325         treeCanvas.startPrinting();
 326     }
 327
 328
 329     public void originalSeqData_actionPerformed(ActionEvent e)
 330     {
 331       if (!tree.hasOriginalSequenceData())
 332       {
 333         jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
 334         return;
 335       }
 336       // decide if av alignment is sufficiently different to original data to warrant a new window to be created
 337       // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
 338       // or create a selection box around columns in alignment view
 339       // test Alignment(SeqCigar[])
 340       Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
 341           getGapCharacter());
 342
 343
 344       if (alAndColsel != null && alAndColsel[0]!=null)
 345        {
 346          // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
 347
 348          Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
 349          Alignment dataset = av.getAlignment().getDataset();
 350          if (dataset != null)
 351          {
 352            al.setDataset(dataset);
 353          }
 354
 355          if (true)
 356          {
 357            // make a new frame!
 358            AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],
 359                                            AlignFrame.DEFAULT_WIDTH,
 360                                            AlignFrame.DEFAULT_HEIGHT
 361 );
 362
 363            //>>>This is a fix for the moment, until a better solution is found!!<<<
 364            // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
 365
 366        //           af.addSortByOrderMenuItem(ServiceName + " Ordering",
 367        //                                     msaorder);
 368
 369            Desktop.addInternalFrame(af, "Original Data for " + this.title,
 370                                     AlignFrame.DEFAULT_WIDTH,
 371                                     AlignFrame.DEFAULT_HEIGHT);
 372          }
 373        }
 374     }
 375
 376
 377     /**
 378      * DOCUMENT ME!
 379      *
 380      * @param e DOCUMENT ME!
 381      */
 382     public void fitToWindow_actionPerformed(ActionEvent e)
 383     {
 384         treeCanvas.fitToWindow = fitToWindow.isSelected();
 385         repaint();
 386     }
 387
 388     /**
 389      * DOCUMENT ME!
 390      *
 391      * @param e DOCUMENT ME!
 392      */
 393     public void font_actionPerformed(ActionEvent e)
 394     {
 395         if (treeCanvas == null)
 396         {
 397             return;
 398         }
 399
 400         new FontChooser(this);
 401     }
 402
 403     public Font getTreeFont()
 404     {
 405         return treeCanvas.font;
 406     }
 407
 408     public void setTreeFont(Font font)
 409     {
 410       if(treeCanvas!=null)
 411       treeCanvas.setFont(font);
 412     }
 413
 414     /**
 415      * DOCUMENT ME!
 416      *
 417      * @param e DOCUMENT ME!
 418      */
 419     public void distanceMenu_actionPerformed(ActionEvent e)
 420     {
 421         treeCanvas.setShowDistances(distanceMenu.isSelected());
 422     }
 423
 424     /**
 425      * DOCUMENT ME!
 426      *
 427      * @param e DOCUMENT ME!
 428      */
 429     public void bootstrapMenu_actionPerformed(ActionEvent e)
 430     {
 431         treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
 432     }
 433
 434     /**
 435      * DOCUMENT ME!
 436      *
 437      * @param e DOCUMENT ME!
 438      */
 439     public void placeholdersMenu_actionPerformed(ActionEvent e)
 440     {
 441         treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
 442     }
 443
 444     /**
 445      * DOCUMENT ME!
 446      *
 447      * @param e DOCUMENT ME!
 448      */
 449     public void epsTree_actionPerformed(ActionEvent e)
 450     {
 451       boolean accurateText = true;
 452
 453       String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
 454           "Prompt each time");
 455
 456     // If we need to prompt, and if the GUI is visible then
 457     // Prompt for EPS rendering style
 458       if (renderStyle.equalsIgnoreCase("Prompt each time")
 459           && !
 460           (System.getProperty("java.awt.headless") != null
 461            && System.getProperty("java.awt.headless").equals("true")))
 462       {
 463         EPSOptions eps = new EPSOptions();
 464         renderStyle = eps.getValue();
 465
 466         if (renderStyle==null || eps.cancelled)
 467           return;
 468
 469
 470       }
 471
 472       if (renderStyle.equalsIgnoreCase("text"))
 473       {
 474         accurateText = false;
 475       }
 476
 477         int width = treeCanvas.getWidth();
 478         int height = treeCanvas.getHeight();
 479
 480         try
 481         {
 482             jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
 483                         "LAST_DIRECTORY"), new String[] { "eps" },
 484                     new String[] { "Encapsulated Postscript" },
 485                     "Encapsulated Postscript");
 486             chooser.setFileView(new jalview.io.JalviewFileView());
 487             chooser.setDialogTitle("Create EPS file from tree");
 488             chooser.setToolTipText("Save");
 489
 490             int value = chooser.showSaveDialog(this);
 491
 492             if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
 493             {
 494                 return;
 495             }
 496
 497             jalview.bin.Cache.setProperty("LAST_DIRECTORY",
 498                                           chooser.getSelectedFile().getParent());
 499
 500             FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
 501             EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
 502                                                  height);
 503
 504             pg.setAccurateTextMode(accurateText);
 505
 506             treeCanvas.draw(pg, width, height);
 507
 508             pg.flush();
 509             pg.close();
 510         }
 511         catch (Exception ex)
 512         {
 513             ex.printStackTrace();
 514         }
 515     }
 516
 517     /**
 518      * DOCUMENT ME!
 519      *
 520      * @param e DOCUMENT ME!
 521      */
 522     public void pngTree_actionPerformed(ActionEvent e)
 523     {
 524         int width = treeCanvas.getWidth();
 525         int height = treeCanvas.getHeight();
 526
 527         try
 528         {
 529             jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
 530                         "LAST_DIRECTORY"), new String[] { "png" },
 531                     new String[] { "Portable network graphics" },
 532                     "Portable network graphics");
 533
 534             chooser.setFileView(new jalview.io.JalviewFileView());
 535             chooser.setDialogTitle("Create PNG image from tree");
 536             chooser.setToolTipText("Save");
 537
 538             int value = chooser.showSaveDialog(this);
 539
 540             if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
 541             {
 542                 return;
 543             }
 544
 545             jalview.bin.Cache.setProperty("LAST_DIRECTORY",
 546                 chooser.getSelectedFile().getParent());
 547
 548             FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
 549
 550             BufferedImage bi = new BufferedImage(width, height,
 551                     BufferedImage.TYPE_INT_RGB);
 552             Graphics png = bi.getGraphics();
 553
 554             treeCanvas.draw(png, width, height);
 555
 556             ImageIO.write(bi, "png", out);
 557             out.close();
 558         }
 559         catch (Exception ex)
 560         {
 561             ex.printStackTrace();
 562         }
 563     }
 564 }