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