src/jalview/gui/TreePanel.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.gui;\r
  20 \r
  21 import jalview.analysis.*;\r
  22 \r
  23 import jalview.datamodel.*;\r
  24 \r
  25 import jalview.io.*;\r
  26 \r
  27 import jalview.jbgui.*;\r
  28 \r
  29 import org.jibble.epsgraphics.*;\r
  30 \r
  31 import java.awt.*;\r
  32 import java.awt.event.*;\r
  33 import java.awt.image.*;\r
  34 \r
  35 import java.io.*;\r
  36 \r
  37 import java.util.*;\r
  38 \r
  39 import javax.imageio.*;\r
  40 \r
  41 import java.beans.PropertyChangeEvent;\r
  42 \r
  43 \r
  44 /**\r
  45  * DOCUMENT ME!\r
  46  *\r
  47  * @author $author$\r
  48  * @version $Revision$\r
  49  */\r
  50 public class TreePanel extends GTreePanel\r
  51 {\r
  52     String type;\r
  53     String pwtype;\r
  54     TreeCanvas treeCanvas;\r
  55     NJTree tree;\r
  56     AlignViewport av;\r
  57 \r
  58     /**\r
  59      * Creates a new TreePanel object.\r
  60      *\r
  61      * @param av DOCUMENT ME!\r
  62      * @param seqVector DOCUMENT ME!\r
  63      * @param type DOCUMENT ME!\r
  64      * @param pwtype DOCUMENT ME!\r
  65      * @param s DOCUMENT ME!\r
  66      * @param e DOCUMENT ME!\r
  67      */\r
  68     public TreePanel(AlignViewport av, String type, String pwtype)\r
  69     {\r
  70       super();\r
  71       initTreePanel(av, type, pwtype, null);\r
  72 \r
  73       // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default\r
  74       showDistances(true);\r
  75     }\r
  76 \r
  77     /**\r
  78      * Creates a new TreePanel object.\r
  79      *\r
  80      * @param av DOCUMENT ME!\r
  81      * @param seqVector DOCUMENT ME!\r
  82      * @param newtree DOCUMENT ME!\r
  83      * @param type DOCUMENT ME!\r
  84      * @param pwtype DOCUMENT ME!\r
  85      */\r
  86     public TreePanel(AlignViewport av,\r
  87                      String type,\r
  88                      String pwtype,\r
  89                      NewickFile newtree)\r
  90     {\r
  91       super();\r
  92       initTreePanel(av, type, pwtype, newtree);\r
  93     }\r
  94 \r
  95     public AlignmentI getAlignment()\r
  96     {\r
  97       return treeCanvas.av.getAlignment();\r
  98     }\r
  99 \r
 100 \r
 101     void initTreePanel(AlignViewport av, String type,  String pwtype,\r
 102                        NewickFile newTree)\r
 103     {\r
 104 \r
 105       this.type = type;\r
 106       this.pwtype = pwtype;\r
 107 \r
 108       treeCanvas = new TreeCanvas(av, scrollPane);\r
 109       scrollPane.setViewportView(treeCanvas);\r
 110 \r
 111       av.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
 112       {\r
 113         public void propertyChange(PropertyChangeEvent evt)\r
 114         {\r
 115           if (evt.getPropertyName().equals("alignment"))\r
 116           {\r
 117             if(tree==null)\r
 118               System.out.println("tree is null");\r
 119             if(evt.getNewValue()==null)\r
 120               System.out.println("new value is null");\r
 121 \r
 122             tree.UpdatePlaceHolders( (Vector) evt.getNewValue());\r
 123 \r
 124             repaint();\r
 125           }\r
 126         }\r
 127       });\r
 128 \r
 129       this.av = av;\r
 130 \r
 131 \r
 132       TreeLoader tl = new TreeLoader(newTree);\r
 133       tl.start();\r
 134 \r
 135     }\r
 136 \r
 137     class TreeLoader extends Thread\r
 138     {\r
 139       NewickFile newtree;\r
 140 \r
 141       public TreeLoader(NewickFile newtree)\r
 142       {\r
 143         this.newtree = newtree;\r
 144         if (newtree != null)\r
 145         {\r
 146           // Must be outside run(), as Jalview2XML tries to\r
 147           // update distance/bootstrap visibility at the same time\r
 148           showBootstrap(newtree.HasBootstrap());\r
 149           showDistances(newtree.HasDistances());\r
 150         }\r
 151       }\r
 152 \r
 153       public void run()\r
 154       {\r
 155 \r
 156         if(newtree!=null)\r
 157           tree = new NJTree(av.alignment.getSequencesArray(),\r
 158                             newtree);\r
 159         else\r
 160         {\r
 161           int start, end;\r
 162           SequenceI [] seqs;\r
 163           String [] seqStrings = null;\r
 164           if (av.hasHiddenColumns)\r
 165           {\r
 166             seqStrings = av.getViewAsString(true);\r
 167           }\r
 168 \r
 169           if(av.getSelectionGroup()==null)\r
 170           {\r
 171             start = 0;\r
 172             end = av.alignment.getWidth();\r
 173             seqs = av.alignment.getSequencesArray();\r
 174           }\r
 175           else\r
 176           {\r
 177             start = av.getSelectionGroup().getStartRes();\r
 178             end = av.getSelectionGroup().getEndRes()+1;\r
 179             seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
 180           }\r
 181 \r
 182           tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);\r
 183         }\r
 184 \r
 185 \r
 186         tree.reCount(tree.getTopNode());\r
 187         tree.findHeight(tree.getTopNode());\r
 188         treeCanvas.setTree(tree);\r
 189 \r
 190         treeCanvas.repaint();\r
 191 \r
 192         av.setCurrentTree(tree);\r
 193 \r
 194       }\r
 195     }\r
 196 \r
 197     public void showDistances(boolean b)\r
 198     {\r
 199       treeCanvas.setShowDistances(b);\r
 200       distanceMenu.setSelected(b);\r
 201     }\r
 202 \r
 203     public void showBootstrap(boolean b)\r
 204     {\r
 205       treeCanvas.setShowBootstrap(b);\r
 206       bootstrapMenu.setSelected(b);\r
 207     }\r
 208 \r
 209     public void showPlaceholders(boolean b)\r
 210     {\r
 211       placeholdersMenu.setState(b);\r
 212       treeCanvas.setMarkPlaceholders(b);\r
 213     }\r
 214 \r
 215 \r
 216 \r
 217 \r
 218     /**\r
 219      * DOCUMENT ME!\r
 220      *\r
 221      * @return DOCUMENT ME!\r
 222      */\r
 223     public NJTree getTree()\r
 224     {\r
 225         return tree;\r
 226     }\r
 227 \r
 228 \r
 229     /**\r
 230      * DOCUMENT ME!\r
 231      *\r
 232      * @param e DOCUMENT ME!\r
 233      */\r
 234     public void textbox_actionPerformed(ActionEvent e)\r
 235     {\r
 236         CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 237 \r
 238         StringBuffer buffer = new StringBuffer();\r
 239 \r
 240         if (type.equals("AV"))\r
 241         {\r
 242             buffer.append("Average distance tree using ");\r
 243         }\r
 244         else\r
 245         {\r
 246             buffer.append("Neighbour joining tree using ");\r
 247         }\r
 248 \r
 249         if (pwtype.equals("BL"))\r
 250         {\r
 251             buffer.append("BLOSUM62");\r
 252         }\r
 253         else\r
 254         {\r
 255             buffer.append("PID");\r
 256         }\r
 257 \r
 258         Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);\r
 259 \r
 260         jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
 261         cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));\r
 262     }\r
 263 \r
 264     /**\r
 265      * DOCUMENT ME!\r
 266      *\r
 267      * @param e DOCUMENT ME!\r
 268      */\r
 269     public void saveAsNewick_actionPerformed(ActionEvent e)\r
 270     {\r
 271         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 272                     "LAST_DIRECTORY"));\r
 273         chooser.setFileView(new JalviewFileView());\r
 274         chooser.setDialogTitle("Save tree as newick file");\r
 275         chooser.setToolTipText("Save");\r
 276 \r
 277         int value = chooser.showSaveDialog(null);\r
 278 \r
 279         if (value == JalviewFileChooser.APPROVE_OPTION)\r
 280         {\r
 281             String choice = chooser.getSelectedFile().getPath();\r
 282             jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
 283                 chooser.getSelectedFile().getParent());\r
 284 \r
 285             try\r
 286             {\r
 287                 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
 288                 String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());\r
 289                 java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(\r
 290                             choice));\r
 291                 out.println(output);\r
 292                 out.close();\r
 293             }\r
 294             catch (Exception ex)\r
 295             {\r
 296                 ex.printStackTrace();\r
 297             }\r
 298         }\r
 299     }\r
 300 \r
 301     /**\r
 302      * DOCUMENT ME!\r
 303      *\r
 304      * @param e DOCUMENT ME!\r
 305      */\r
 306     public void printMenu_actionPerformed(ActionEvent e)\r
 307     {\r
 308         //Putting in a thread avoids Swing painting problems\r
 309         treeCanvas.startPrinting();\r
 310     }\r
 311 \r
 312 \r
 313     public void originalSeqData_actionPerformed(ActionEvent e)\r
 314     {\r
 315       CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 316       cap.setText(tree.printOriginalSequenceData());\r
 317       Desktop.addInternalFrame(cap, "Original Data",\r
 318           400, 400);\r
 319     }\r
 320 \r
 321 \r
 322     /**\r
 323      * DOCUMENT ME!\r
 324      *\r
 325      * @param e DOCUMENT ME!\r
 326      */\r
 327     public void fitToWindow_actionPerformed(ActionEvent e)\r
 328     {\r
 329         treeCanvas.fitToWindow = fitToWindow.isSelected();\r
 330         repaint();\r
 331     }\r
 332 \r
 333     /**\r
 334      * DOCUMENT ME!\r
 335      *\r
 336      * @param e DOCUMENT ME!\r
 337      */\r
 338     public void font_actionPerformed(ActionEvent e)\r
 339     {\r
 340         if (treeCanvas == null)\r
 341         {\r
 342             return;\r
 343         }\r
 344 \r
 345         new FontChooser(this);\r
 346     }\r
 347 \r
 348     public Font getTreeFont()\r
 349     {\r
 350         return treeCanvas.font;\r
 351     }\r
 352 \r
 353     public void setTreeFont(Font font)\r
 354     {\r
 355       if(treeCanvas!=null)\r
 356       treeCanvas.setFont(font);\r
 357     }\r
 358 \r
 359     /**\r
 360      * DOCUMENT ME!\r
 361      *\r
 362      * @param e DOCUMENT ME!\r
 363      */\r
 364     public void distanceMenu_actionPerformed(ActionEvent e)\r
 365     {\r
 366         treeCanvas.setShowDistances(distanceMenu.isSelected());\r
 367     }\r
 368 \r
 369     /**\r
 370      * DOCUMENT ME!\r
 371      *\r
 372      * @param e DOCUMENT ME!\r
 373      */\r
 374     public void bootstrapMenu_actionPerformed(ActionEvent e)\r
 375     {\r
 376         treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());\r
 377     }\r
 378 \r
 379     /**\r
 380      * DOCUMENT ME!\r
 381      *\r
 382      * @param e DOCUMENT ME!\r
 383      */\r
 384     public void placeholdersMenu_actionPerformed(ActionEvent e)\r
 385     {\r
 386         treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());\r
 387     }\r
 388 \r
 389     /**\r
 390      * DOCUMENT ME!\r
 391      *\r
 392      * @param e DOCUMENT ME!\r
 393      */\r
 394     public void epsTree_actionPerformed(ActionEvent e)\r
 395     {\r
 396       boolean accurateText = true;\r
 397 \r
 398       String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",\r
 399           "Prompt each time");\r
 400 \r
 401     // If we need to prompt, and if the GUI is visible then\r
 402     // Prompt for EPS rendering style\r
 403       if (renderStyle.equalsIgnoreCase("Prompt each time")\r
 404           && !\r
 405           (System.getProperty("java.awt.headless") != null\r
 406            && System.getProperty("java.awt.headless").equals("true")))\r
 407       {\r
 408         EPSOptions eps = new EPSOptions();\r
 409         renderStyle = eps.getValue();\r
 410 \r
 411         if (renderStyle==null || eps.cancelled)\r
 412           return;\r
 413 \r
 414 \r
 415       }\r
 416 \r
 417       if (renderStyle.equalsIgnoreCase("text"))\r
 418       {\r
 419         accurateText = false;\r
 420       }\r
 421 \r
 422         int width = treeCanvas.getWidth();\r
 423         int height = treeCanvas.getHeight();\r
 424 \r
 425         try\r
 426         {\r
 427             jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 428                         "LAST_DIRECTORY"), new String[] { "eps" },\r
 429                     new String[] { "Encapsulated Postscript" },\r
 430                     "Encapsulated Postscript");\r
 431             chooser.setFileView(new jalview.io.JalviewFileView());\r
 432             chooser.setDialogTitle("Create EPS file from tree");\r
 433             chooser.setToolTipText("Save");\r
 434 \r
 435             int value = chooser.showSaveDialog(this);\r
 436 \r
 437             if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
 438             {\r
 439                 return;\r
 440             }\r
 441 \r
 442             jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
 443                                           chooser.getSelectedFile().getParent());\r
 444 \r
 445             FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
 446             EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,\r
 447                                                  height);\r
 448 \r
 449             pg.setAccurateTextMode(accurateText);\r
 450 \r
 451             treeCanvas.draw(pg, width, height);\r
 452 \r
 453             pg.flush();\r
 454             pg.close();\r
 455         }\r
 456         catch (Exception ex)\r
 457         {\r
 458             ex.printStackTrace();\r
 459         }\r
 460     }\r
 461 \r
 462     /**\r
 463      * DOCUMENT ME!\r
 464      *\r
 465      * @param e DOCUMENT ME!\r
 466      */\r
 467     public void pngTree_actionPerformed(ActionEvent e)\r
 468     {\r
 469         int width = treeCanvas.getWidth();\r
 470         int height = treeCanvas.getHeight();\r
 471 \r
 472         try\r
 473         {\r
 474             jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 475                         "LAST_DIRECTORY"), new String[] { "png" },\r
 476                     new String[] { "Portable network graphics" },\r
 477                     "Portable network graphics");\r
 478 \r
 479             chooser.setFileView(new jalview.io.JalviewFileView());\r
 480             chooser.setDialogTitle("Create PNG image from tree");\r
 481             chooser.setToolTipText("Save");\r
 482 \r
 483             int value = chooser.showSaveDialog(this);\r
 484 \r
 485             if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
 486             {\r
 487                 return;\r
 488             }\r
 489 \r
 490             jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
 491                 chooser.getSelectedFile().getParent());\r
 492 \r
 493             FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
 494 \r
 495             BufferedImage bi = new BufferedImage(width, height,\r
 496                     BufferedImage.TYPE_INT_RGB);\r
 497             Graphics png = bi.getGraphics();\r
 498 \r
 499             treeCanvas.draw(png, width, height);\r
 500 \r
 501             ImageIO.write(bi, "png", out);\r
 502             out.close();\r
 503         }\r
 504         catch (Exception ex)\r
 505         {\r
 506             ex.printStackTrace();\r
 507         }\r
 508     }\r
 509 }\r