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