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       jalview.datamodel.CigarArray odata=null;\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 \r
 158           if (odata==null) {\r
 159             tree = new NJTree(av.alignment.getSequencesArray(),\r
 160                               newtree);\r
 161           } else {\r
 162             tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);\r
 163           }\r
 164           if (!tree.hasOriginalSequenceData())\r
 165             allowOriginalSeqData(false);\r
 166         }\r
 167         else\r
 168         {\r
 169           int start, end;\r
 170           SequenceI [] seqs;\r
 171           CigarArray seqStrings = av.getViewAsCigars(av.getSelectionGroup()!=null);\r
 172           if(av.getSelectionGroup()==null)\r
 173           {\r
 174             start = 0;\r
 175             end = av.alignment.getWidth();\r
 176             seqs = av.alignment.getSequencesArray();\r
 177           }\r
 178           else\r
 179           {\r
 180             start = av.getSelectionGroup().getStartRes();\r
 181             end = av.getSelectionGroup().getEndRes()+1;\r
 182             seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
 183           }\r
 184 \r
 185           tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);\r
 186           showDistances(true);\r
 187         }\r
 188 \r
 189 \r
 190         tree.reCount(tree.getTopNode());\r
 191         tree.findHeight(tree.getTopNode());\r
 192         treeCanvas.setTree(tree);\r
 193         treeCanvas.repaint();\r
 194         av.setCurrentTree(tree);\r
 195 \r
 196       }\r
 197     }\r
 198 \r
 199     public void showDistances(boolean b)\r
 200     {\r
 201       treeCanvas.setShowDistances(b);\r
 202       distanceMenu.setSelected(b);\r
 203     }\r
 204 \r
 205     public void showBootstrap(boolean b)\r
 206     {\r
 207       treeCanvas.setShowBootstrap(b);\r
 208       bootstrapMenu.setSelected(b);\r
 209     }\r
 210 \r
 211     public void showPlaceholders(boolean b)\r
 212     {\r
 213       placeholdersMenu.setState(b);\r
 214       treeCanvas.setMarkPlaceholders(b);\r
 215     }\r
 216     private void allowOriginalSeqData(boolean b) {\r
 217       originalSeqData.setVisible(b);\r
 218     }\r
 219 \r
 220 \r
 221 \r
 222     /**\r
 223      * DOCUMENT ME!\r
 224      *\r
 225      * @return DOCUMENT ME!\r
 226      */\r
 227     public NJTree getTree()\r
 228     {\r
 229         return tree;\r
 230     }\r
 231 \r
 232 \r
 233     /**\r
 234      * DOCUMENT ME!\r
 235      *\r
 236      * @param e DOCUMENT ME!\r
 237      */\r
 238     public void textbox_actionPerformed(ActionEvent e)\r
 239     {\r
 240         CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 241 \r
 242         StringBuffer buffer = new StringBuffer();\r
 243 \r
 244         if (type.equals("AV"))\r
 245         {\r
 246             buffer.append("Average distance tree using ");\r
 247         }\r
 248         else\r
 249         {\r
 250             buffer.append("Neighbour joining tree using ");\r
 251         }\r
 252 \r
 253         if (pwtype.equals("BL"))\r
 254         {\r
 255             buffer.append("BLOSUM62");\r
 256         }\r
 257         else\r
 258         {\r
 259             buffer.append("PID");\r
 260         }\r
 261 \r
 262         Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);\r
 263 \r
 264         jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
 265         cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));\r
 266     }\r
 267 \r
 268     /**\r
 269      * DOCUMENT ME!\r
 270      *\r
 271      * @param e DOCUMENT ME!\r
 272      */\r
 273     public void saveAsNewick_actionPerformed(ActionEvent e)\r
 274     {\r
 275         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 276                     "LAST_DIRECTORY"));\r
 277         chooser.setFileView(new JalviewFileView());\r
 278         chooser.setDialogTitle("Save tree as newick file");\r
 279         chooser.setToolTipText("Save");\r
 280 \r
 281         int value = chooser.showSaveDialog(null);\r
 282 \r
 283         if (value == JalviewFileChooser.APPROVE_OPTION)\r
 284         {\r
 285             String choice = chooser.getSelectedFile().getPath();\r
 286             jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
 287                 chooser.getSelectedFile().getParent());\r
 288 \r
 289             try\r
 290             {\r
 291                 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
 292                 String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());\r
 293                 java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(\r
 294                             choice));\r
 295                 out.println(output);\r
 296                 out.close();\r
 297             }\r
 298             catch (Exception ex)\r
 299             {\r
 300                 ex.printStackTrace();\r
 301             }\r
 302         }\r
 303     }\r
 304 \r
 305     /**\r
 306      * DOCUMENT ME!\r
 307      *\r
 308      * @param e DOCUMENT ME!\r
 309      */\r
 310     public void printMenu_actionPerformed(ActionEvent e)\r
 311     {\r
 312         //Putting in a thread avoids Swing painting problems\r
 313         treeCanvas.startPrinting();\r
 314     }\r
 315 \r
 316 \r
 317     public void originalSeqData_actionPerformed(ActionEvent e)\r
 318     {\r
 319       String originalData = tree.printOriginalSequenceData(av.getGapCharacter());\r
 320       if (originalData!=null) {\r
 321         CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 322         cap.setText(originalData);\r
 323         Desktop.addInternalFrame(cap, "Original Data",\r
 324                                  400, 400);\r
 325       } else {\r
 326         System.err.println("IMPLEMENTATION BUG! originalSeqData is not available.");\r
 327       }\r
 328 \r
 329     }\r
 330 \r
 331 \r
 332     /**\r
 333      * DOCUMENT ME!\r
 334      *\r
 335      * @param e DOCUMENT ME!\r
 336      */\r
 337     public void fitToWindow_actionPerformed(ActionEvent e)\r
 338     {\r
 339         treeCanvas.fitToWindow = fitToWindow.isSelected();\r
 340         repaint();\r
 341     }\r
 342 \r
 343     /**\r
 344      * DOCUMENT ME!\r
 345      *\r
 346      * @param e DOCUMENT ME!\r
 347      */\r
 348     public void font_actionPerformed(ActionEvent e)\r
 349     {\r
 350         if (treeCanvas == null)\r
 351         {\r
 352             return;\r
 353         }\r
 354 \r
 355         new FontChooser(this);\r
 356     }\r
 357 \r
 358     public Font getTreeFont()\r
 359     {\r
 360         return treeCanvas.font;\r
 361     }\r
 362 \r
 363     public void setTreeFont(Font font)\r
 364     {\r
 365       if(treeCanvas!=null)\r
 366       treeCanvas.setFont(font);\r
 367     }\r
 368 \r
 369     /**\r
 370      * DOCUMENT ME!\r
 371      *\r
 372      * @param e DOCUMENT ME!\r
 373      */\r
 374     public void distanceMenu_actionPerformed(ActionEvent e)\r
 375     {\r
 376         treeCanvas.setShowDistances(distanceMenu.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 bootstrapMenu_actionPerformed(ActionEvent e)\r
 385     {\r
 386         treeCanvas.setShowBootstrap(bootstrapMenu.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 placeholdersMenu_actionPerformed(ActionEvent e)\r
 395     {\r
 396         treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());\r
 397     }\r
 398 \r
 399     /**\r
 400      * DOCUMENT ME!\r
 401      *\r
 402      * @param e DOCUMENT ME!\r
 403      */\r
 404     public void epsTree_actionPerformed(ActionEvent e)\r
 405     {\r
 406       boolean accurateText = true;\r
 407 \r
 408       String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",\r
 409           "Prompt each time");\r
 410 \r
 411     // If we need to prompt, and if the GUI is visible then\r
 412     // Prompt for EPS rendering style\r
 413       if (renderStyle.equalsIgnoreCase("Prompt each time")\r
 414           && !\r
 415           (System.getProperty("java.awt.headless") != null\r
 416            && System.getProperty("java.awt.headless").equals("true")))\r
 417       {\r
 418         EPSOptions eps = new EPSOptions();\r
 419         renderStyle = eps.getValue();\r
 420 \r
 421         if (renderStyle==null || eps.cancelled)\r
 422           return;\r
 423 \r
 424 \r
 425       }\r
 426 \r
 427       if (renderStyle.equalsIgnoreCase("text"))\r
 428       {\r
 429         accurateText = false;\r
 430       }\r
 431 \r
 432         int width = treeCanvas.getWidth();\r
 433         int height = treeCanvas.getHeight();\r
 434 \r
 435         try\r
 436         {\r
 437             jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 438                         "LAST_DIRECTORY"), new String[] { "eps" },\r
 439                     new String[] { "Encapsulated Postscript" },\r
 440                     "Encapsulated Postscript");\r
 441             chooser.setFileView(new jalview.io.JalviewFileView());\r
 442             chooser.setDialogTitle("Create EPS file from tree");\r
 443             chooser.setToolTipText("Save");\r
 444 \r
 445             int value = chooser.showSaveDialog(this);\r
 446 \r
 447             if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
 448             {\r
 449                 return;\r
 450             }\r
 451 \r
 452             jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
 453                                           chooser.getSelectedFile().getParent());\r
 454 \r
 455             FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
 456             EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,\r
 457                                                  height);\r
 458 \r
 459             pg.setAccurateTextMode(accurateText);\r
 460 \r
 461             treeCanvas.draw(pg, width, height);\r
 462 \r
 463             pg.flush();\r
 464             pg.close();\r
 465         }\r
 466         catch (Exception ex)\r
 467         {\r
 468             ex.printStackTrace();\r
 469         }\r
 470     }\r
 471 \r
 472     /**\r
 473      * DOCUMENT ME!\r
 474      *\r
 475      * @param e DOCUMENT ME!\r
 476      */\r
 477     public void pngTree_actionPerformed(ActionEvent e)\r
 478     {\r
 479         int width = treeCanvas.getWidth();\r
 480         int height = treeCanvas.getHeight();\r
 481 \r
 482         try\r
 483         {\r
 484             jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 485                         "LAST_DIRECTORY"), new String[] { "png" },\r
 486                     new String[] { "Portable network graphics" },\r
 487                     "Portable network graphics");\r
 488 \r
 489             chooser.setFileView(new jalview.io.JalviewFileView());\r
 490             chooser.setDialogTitle("Create PNG image from tree");\r
 491             chooser.setToolTipText("Save");\r
 492 \r
 493             int value = chooser.showSaveDialog(this);\r
 494 \r
 495             if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
 496             {\r
 497                 return;\r
 498             }\r
 499 \r
 500             jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
 501                 chooser.getSelectedFile().getParent());\r
 502 \r
 503             FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
 504 \r
 505             BufferedImage bi = new BufferedImage(width, height,\r
 506                     BufferedImage.TYPE_INT_RGB);\r
 507             Graphics png = bi.getGraphics();\r
 508 \r
 509             treeCanvas.draw(png, width, height);\r
 510 \r
 511             ImageIO.write(bi, "png", out);\r
 512             out.close();\r
 513         }\r
 514         catch (Exception ex)\r
 515         {\r
 516             ex.printStackTrace();\r
 517         }\r
 518     }\r
 519 }\r