src/jalview/gui/AlignFrame.java

   1 /********************\r
   2  * 2004 Jalview Reengineered\r
   3  * Barton Group\r
   4  * Dundee University\r
   5  *\r
   6  * AM Waterhouse\r
   7  *******************/\r
   8 \r
   9 \r
  10 \r
  11 \r
  12 package jalview.gui;\r
  13 \r
  14 import jalview.jbgui.GAlignFrame;\r
  15 import jalview.schemes.*;\r
  16 import jalview.datamodel.*;\r
  17 import jalview.analysis.*;\r
  18 import jalview.io.*;\r
  19 import jalview.ws.*;\r
  20 import java.awt.*;\r
  21 import java.awt.event.*;\r
  22 import java.awt.print.*;\r
  23 import javax.swing.*;\r
  24 import javax.swing.event.*;\r
  25 import java.util.*;\r
  26 import  java.awt.datatransfer.*;\r
  27 \r
  28 \r
  29 public class AlignFrame extends GAlignFrame\r
  30 {\r
  31   final AlignmentPanel alignPanel;\r
  32   final AlignViewport viewport;\r
  33   public AlignFrame(AlignmentI al)\r
  34   {\r
  35     super();\r
  36     viewport = new AlignViewport(al,true,true,true,false);\r
  37     alignPanel = new AlignmentPanel(this, viewport);\r
  38     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
  39 \r
  40     addInternalFrameListener(new InternalFrameAdapter()\r
  41    {\r
  42      public void internalFrameActivated(InternalFrameEvent evt)\r
  43      {\r
  44           javax.swing.SwingUtilities.invokeLater(new Runnable()\r
  45           {\r
  46             public void run()\r
  47             {      alignPanel.requestFocus();    }\r
  48           });\r
  49 \r
  50      }\r
  51    });\r
  52 \r
  53   }\r
  54 \r
  55   protected void saveAs_actionPerformed(ActionEvent e)\r
  56   {\r
  57     JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
  58     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
  59     chooser.setToolTipText("Save");\r
  60     int value = chooser.showSaveDialog(this);\r
  61     if(value == JFileChooser.APPROVE_OPTION)\r
  62     {\r
  63       String choice =  chooser.getSelectedFile().getPath();\r
  64       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
  65       String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
  66       try{\r
  67         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
  68         out.println(output);\r
  69         out.close();\r
  70       }\r
  71       catch(Exception ex){}\r
  72     }\r
  73 \r
  74   }\r
  75 \r
  76   protected void outputText_actionPerformed(ActionEvent e)\r
  77   {\r
  78      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
  79      JInternalFrame frame = new JInternalFrame();\r
  80      cap.formatForOutput();\r
  81      frame.setContentPane(cap);\r
  82      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
  83      cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
  84   }\r
  85 \r
  86   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
  87   {\r
  88     HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
  89     htmlOutput = null;\r
  90   }\r
  91 \r
  92   protected void createJPG_actionPerformed(ActionEvent e)\r
  93   {\r
  94 \r
  95     int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;\r
  96     int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();\r
  97 \r
  98 \r
  99     if(!viewport.getWrapAlignment())\r
 100     {\r
 101       height = viewport.alignment.getHeight() * viewport.charHeight;\r
 102       width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;\r
 103     }\r
 104 \r
 105     alignPanel.makeJPG( width, height);\r
 106   }\r
 107 \r
 108 \r
 109   public void printMenuItem_actionPerformed(ActionEvent e)\r
 110   {\r
 111     //Putting in a thread avoids Swing painting problems\r
 112     PrintThread thread = new PrintThread();\r
 113     thread.start();\r
 114   }\r
 115 \r
 116   class PrintThread extends Thread\r
 117   {\r
 118     public void run()\r
 119     {\r
 120       PrinterJob printJob = PrinterJob.getPrinterJob();\r
 121       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
 122       printJob.setPrintable(alignPanel, pf);\r
 123       if (printJob.printDialog())\r
 124       {\r
 125         try\r
 126         {\r
 127           printJob.print();\r
 128         }\r
 129         catch (Exception PrintException)\r
 130         {\r
 131           PrintException.printStackTrace();\r
 132         }\r
 133       }\r
 134     }\r
 135 \r
 136   }\r
 137 \r
 138 \r
 139 \r
 140 \r
 141   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 142   {\r
 143     try{\r
 144       this.setClosed(true);\r
 145     }catch(Exception ex){}\r
 146   }\r
 147 \r
 148   Stack historyList = new Stack();\r
 149   Stack redoList = new Stack();\r
 150 \r
 151   void updateEditMenuBar()\r
 152   {\r
 153     if(historyList.size()>0)\r
 154      {\r
 155        undoMenuItem.setEnabled(true);\r
 156        Object [] history = (Object[])historyList.get(0);\r
 157        undoMenuItem.setText("Undo "+history[0]);\r
 158      }\r
 159     else\r
 160     {\r
 161       undoMenuItem.setEnabled(false);\r
 162       undoMenuItem.setText("Undo");\r
 163     }\r
 164 \r
 165     if(redoList.size()>0)\r
 166      {\r
 167        redoMenuItem.setEnabled(true);\r
 168        Object [] history = (Object[])redoList.get(0);\r
 169        redoMenuItem.setText("Redo "+history[0]);\r
 170      }\r
 171     else\r
 172     {\r
 173       redoMenuItem.setEnabled(false);\r
 174       redoMenuItem.setText("Redo");\r
 175     }\r
 176   }\r
 177 \r
 178   public void addHistoryItem(String type)\r
 179   {\r
 180     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 181     redoList.clear();\r
 182     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 183     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 184     {\r
 185       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 186                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 187     }\r
 188 \r
 189     historyList.add(0, new Object[]{type,  seq} );\r
 190     updateEditMenuBar();\r
 191   }\r
 192 \r
 193   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 194   {\r
 195     Object [] history = (Object[])historyList.remove(0);\r
 196     // add the redo state before continuing!!\r
 197     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 198     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 199     {\r
 200       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 201                             viewport.getAlignment().getSequenceAt(i).\r
 202                             getSequence());\r
 203     }\r
 204     /////////\r
 205 \r
 206     redoList.add(0, new Object[] {history[0], seq});\r
 207 \r
 208       seq = (SequenceI[]) history[1];\r
 209       viewport.setAlignment( new Alignment(seq) );\r
 210       updateEditMenuBar();\r
 211       alignPanel.RefreshPanels();\r
 212   }\r
 213 \r
 214   public void moveSelectedSequences(boolean up)\r
 215   {\r
 216     SequenceGroup sg = viewport.getRubberbandGroup();\r
 217     if (sg == null)\r
 218       return;\r
 219 \r
 220     if (up)\r
 221     {\r
 222       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 223       {\r
 224         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 225         if (!sg.sequences.contains(seq))\r
 226           continue;\r
 227 \r
 228         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 229         if (sg.sequences.contains(temp))\r
 230           continue;\r
 231 \r
 232         viewport.alignment.getSequences().setElementAt(temp, i);\r
 233         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 234       }\r
 235     }\r
 236     else\r
 237     {\r
 238       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 239       {\r
 240         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 241         if (!sg.sequences.contains(seq))\r
 242           continue;\r
 243 \r
 244         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 245         if (sg.sequences.contains(temp))\r
 246           continue;\r
 247 \r
 248         viewport.alignment.getSequences().setElementAt(temp, i);\r
 249         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 250       }\r
 251     }\r
 252 \r
 253     alignPanel.RefreshPanels();\r
 254   }\r
 255 \r
 256 \r
 257 \r
 258   protected void copy_actionPerformed(ActionEvent e)\r
 259   {\r
 260    if(viewport.getRubberbandGroup()==null)\r
 261      return;\r
 262 \r
 263    SequenceGroup sg = viewport.getRubberbandGroup();\r
 264 \r
 265      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 266      StringBuffer buffer= new StringBuffer();\r
 267 \r
 268        for(int i=0; i<sg.getSize(); i++)\r
 269        {\r
 270          SequenceI seq = sg.getSequenceAt(i);\r
 271          buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
 272                         +seq.findPosition( sg.getEndRes() )+ "\t"\r
 273                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
 274        }\r
 275      c.setContents( new StringSelection( buffer.toString()) , null ) ;\r
 276 \r
 277   }\r
 278 \r
 279 \r
 280   protected void pasteNew_actionPerformed(ActionEvent e)\r
 281   {\r
 282     paste(true);\r
 283   }\r
 284 \r
 285   protected void pasteThis_actionPerformed(ActionEvent e)\r
 286   {\r
 287     addHistoryItem("Paste");\r
 288     paste(false);\r
 289   }\r
 290 \r
 291   void paste(boolean newAlignment)\r
 292   {\r
 293     try{\r
 294       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 295       Transferable contents = c.getContents(this);\r
 296       if (contents == null)\r
 297         return;\r
 298 \r
 299       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
 300       StringTokenizer st = new StringTokenizer(str);\r
 301       ArrayList seqs = new ArrayList();\r
 302       while (st.hasMoreElements())\r
 303       {\r
 304         String name = st.nextToken();\r
 305         int start = Integer.parseInt(st.nextToken());\r
 306         int end = Integer.parseInt(st.nextToken());\r
 307         Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
 308 \r
 309         if(!newAlignment)\r
 310           viewport.alignment.addSequence(sequence);\r
 311         else\r
 312           seqs.add(sequence);\r
 313       }\r
 314 \r
 315       if(newAlignment)\r
 316       {\r
 317         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 318         seqs.toArray(newSeqs);\r
 319         AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
 320         int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;\r
 321         if (newHeight > 500)\r
 322           newHeight = 500;\r
 323         Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
 324       }\r
 325       else\r
 326       {\r
 327         viewport.setEndSeq(viewport.alignment.getHeight());\r
 328         viewport.alignment.getWidth();\r
 329         alignPanel.RefreshPanels();\r
 330       }\r
 331 \r
 332     }catch(Exception ex){}// could be anything being pasted in here\r
 333 \r
 334   }\r
 335 \r
 336 \r
 337   protected void cut_actionPerformed(ActionEvent e)\r
 338   {\r
 339     copy_actionPerformed(null);\r
 340     delete_actionPerformed(null);\r
 341   }\r
 342 \r
 343   protected void delete_actionPerformed(ActionEvent e)\r
 344   {\r
 345     addHistoryItem("Delete");\r
 346     if (viewport.getRubberbandGroup() == null)\r
 347       return;\r
 348 \r
 349      SequenceGroup sg = viewport.getRubberbandGroup();\r
 350      for (int i=0;i < sg.sequences.size(); i++)\r
 351      {\r
 352        SequenceI seq = sg.getSequenceAt(i);\r
 353        int index = viewport.getAlignment().findIndex(seq);\r
 354        seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);\r
 355 \r
 356        if(seq.getSequence().length()<1)\r
 357           viewport.getAlignment().deleteSequence(seq);\r
 358       else\r
 359           viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 360      }\r
 361 \r
 362      viewport.setRubberbandGroup(null);\r
 363      viewport.alignment.deleteGroup(sg);\r
 364      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
 365      if(viewport.getAlignment().getHeight()<1)\r
 366      try\r
 367      {\r
 368        this.setClosed(true);\r
 369      }catch(Exception ex){}\r
 370      alignPanel.RefreshPanels();\r
 371 \r
 372   }\r
 373 \r
 374 \r
 375 \r
 376   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 377   {\r
 378      Object [] history = (Object[])redoList.remove(0);\r
 379      SequenceI[] seq = (SequenceI[]) history[1];\r
 380      viewport.setAlignment( new Alignment(seq) );\r
 381      updateEditMenuBar();\r
 382      alignPanel.RefreshPanels();\r
 383   }\r
 384 \r
 385 \r
 386   public void groupsMenuItem_actionPerformed(ActionEvent e)\r
 387   {\r
 388     GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
 389     JInternalFrame frame = new JInternalFrame();\r
 390     frame.setContentPane(geditor);\r
 391     Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
 392     frame.setResizable(false);\r
 393   }\r
 394 \r
 395   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 396   {\r
 397     viewport.alignment.deleteAllGroups();\r
 398     viewport.getSelection().clear();\r
 399 \r
 400     alignPanel.RefreshPanels();\r
 401   }\r
 402 \r
 403 \r
 404 \r
 405   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 406   {\r
 407     Selection sel = viewport.getSelection();\r
 408     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 409       sel.addElement( viewport.getAlignment().getSequenceAt(i));\r
 410     PaintRefresher.Refresh(null);\r
 411   }\r
 412 \r
 413   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 414   {\r
 415     viewport.setRubberbandGroup(null);\r
 416     viewport.getSelection().clear();\r
 417     PaintRefresher.Refresh(null);\r
 418   }\r
 419 \r
 420   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 421   {\r
 422     Selection sel = viewport.getSelection();\r
 423     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 424     {\r
 425       if (sel.contains(viewport.getAlignment().getSequenceAt(i)))\r
 426         sel.removeElement(viewport.getAlignment().getSequenceAt(i));\r
 427       else\r
 428         sel.addElement(viewport.getAlignment().getSequenceAt(i));\r
 429     }\r
 430     PaintRefresher.Refresh(null);\r
 431   }\r
 432 \r
 433 \r
 434   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 435   {\r
 436     viewport.getColumnSelection().clear();\r
 437     repaint();\r
 438   }\r
 439 \r
 440   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 441   {\r
 442     addHistoryItem("delete columns");\r
 443     ColumnSelection colSel = viewport.getColumnSelection();\r
 444     if (colSel.size() > 0)\r
 445     {\r
 446       int min = colSel.getMin();\r
 447       viewport.getAlignment().trimLeft(min);\r
 448       colSel.compensateForEdit(0,min);\r
 449       alignPanel.RefreshPanels();\r
 450     }\r
 451   }\r
 452 \r
 453   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 454   {\r
 455     addHistoryItem("delete columns");\r
 456     ColumnSelection colSel = viewport.getColumnSelection();\r
 457     if (colSel.size() > 0)\r
 458     {\r
 459       int max = colSel.getMax();\r
 460       if(max>1)\r
 461         viewport.getAlignment().trimRight(max);\r
 462 \r
 463       alignPanel.RefreshPanels();\r
 464     }\r
 465 \r
 466   }\r
 467 \r
 468   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 469   {\r
 470     addHistoryItem("delete gapped columns");\r
 471     viewport.getAlignment().removeGaps();\r
 472     alignPanel.RefreshPanels();\r
 473   }\r
 474 \r
 475   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 476   {\r
 477     addHistoryItem("delete all gaps");\r
 478     SequenceI current;\r
 479     int jSize;\r
 480     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 481     {\r
 482       current = viewport.getAlignment().getSequenceAt(i);\r
 483       jSize = current.getLength();\r
 484       for (int j=0; j < jSize; j++)\r
 485         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 486         {\r
 487           current.deleteCharAt(j);\r
 488           j--;\r
 489           jSize--;\r
 490         }\r
 491     }\r
 492 \r
 493     alignPanel.RefreshPanels();\r
 494   }\r
 495 \r
 496   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 497   {\r
 498     char thisChar = '-';\r
 499     char nextChar = '.';\r
 500     if(viewport.getGapCharacter()=='-')\r
 501     {\r
 502       thisChar = '.';\r
 503       nextChar = '-';\r
 504     }\r
 505     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 506     viewport.setGapCharacter(thisChar);\r
 507     alignPanel.RefreshPanels();\r
 508   }\r
 509 \r
 510   public void findMenuItem_actionPerformed(ActionEvent e)\r
 511   {\r
 512     JOptionPane op = new JOptionPane();\r
 513     JInternalFrame frame =  op.createInternalFrame(this, "Find");\r
 514     Finder finder = new Finder(viewport, alignPanel, frame);\r
 515     frame.setClosable(true);\r
 516     frame.setContentPane(finder);\r
 517     frame.setSize(340,110);\r
 518     frame.setVisible(true);\r
 519   }\r
 520 \r
 521 \r
 522   public void font_actionPerformed(ActionEvent e)\r
 523   {\r
 524     JOptionPane op = new JOptionPane();\r
 525     JInternalFrame frame = op.createInternalFrame(this, "Change Font");\r
 526     FontChooser fc = new FontChooser( alignPanel );\r
 527     frame.setClosable(true);\r
 528     frame.setContentPane(fc);\r
 529     frame.setSize(480, 100);\r
 530     frame.setVisible(true);\r
 531   }\r
 532 \r
 533   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 534   {\r
 535       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 536       alignPanel.RefreshPanels();\r
 537   }\r
 538 \r
 539   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 540   {\r
 541     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 542     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
 543   }\r
 544 \r
 545 \r
 546   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 547   {\r
 548     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 549     alignPanel.RefreshPanels();\r
 550   }\r
 551 \r
 552   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 553   {\r
 554     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 555     alignPanel.RefreshPanels();\r
 556   }\r
 557 \r
 558 \r
 559   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 560   {\r
 561     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 562     alignPanel.RefreshPanels();\r
 563   }\r
 564 \r
 565   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 566   {\r
 567     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 568     if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
 569     {\r
 570          AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);\r
 571          ((Alignment)viewport.alignment).featuresAdded = true;\r
 572     }\r
 573     alignPanel.RefreshPanels();\r
 574   }\r
 575 \r
 576   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 577   {\r
 578     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
 579   }\r
 580 \r
 581   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 582   {\r
 583     if (alignPanel.overviewPanel != null)\r
 584       return;\r
 585 \r
 586     JInternalFrame frame = new JInternalFrame();\r
 587     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 588    try{\r
 589      overview = new OverviewPanel(alignPanel, viewport);\r
 590      frame.setContentPane(overview);\r
 591     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 592                              frame.getWidth(), frame.getHeight());\r
 593     frame.pack();\r
 594     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 595     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 596       {\r
 597             alignPanel.setOverviewPanel(null);\r
 598       };\r
 599     });\r
 600     alignPanel.setOverviewPanel( overview );\r
 601 \r
 602   }catch(java.lang.OutOfMemoryError ex)\r
 603    {\r
 604      JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 605                                    +"\nTry reducing the font size.",\r
 606                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 607    }\r
 608 \r
 609 \r
 610   }\r
 611 \r
 612   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 613   {\r
 614     changeColour( null );\r
 615   }\r
 616 \r
 617 \r
 618   public void clustalColour_actionPerformed(ActionEvent e)\r
 619   {\r
 620     abovePIDThreshold.setSelected(false);\r
 621     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 622   }\r
 623 \r
 624   public void zappoColour_actionPerformed(ActionEvent e)\r
 625   {\r
 626     changeColour(new ZappoColourScheme());\r
 627   }\r
 628 \r
 629   public void taylorColour_actionPerformed(ActionEvent e)\r
 630   {\r
 631     changeColour(new TaylorColourScheme());\r
 632   }\r
 633 \r
 634 \r
 635   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 636   {\r
 637     changeColour( new HydrophobicColourScheme() );\r
 638   }\r
 639 \r
 640   public void helixColour_actionPerformed(ActionEvent e)\r
 641   {\r
 642     changeColour(new HelixColourScheme() );\r
 643   }\r
 644 \r
 645 \r
 646   public void strandColour_actionPerformed(ActionEvent e)\r
 647   {\r
 648     changeColour(new StrandColourScheme());\r
 649   }\r
 650 \r
 651 \r
 652   public void turnColour_actionPerformed(ActionEvent e)\r
 653   {\r
 654     changeColour(new TurnColourScheme());\r
 655   }\r
 656 \r
 657 \r
 658   public void buriedColour_actionPerformed(ActionEvent e)\r
 659   {\r
 660     changeColour(new BuriedColourScheme() );\r
 661   }\r
 662 \r
 663   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 664   {\r
 665     changeColour(new NucleotideColourScheme());\r
 666   }\r
 667 \r
 668 \r
 669   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 670   {\r
 671     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
 672   }\r
 673 \r
 674 \r
 675 \r
 676   void changeColour(ColourSchemeI cs)\r
 677   {\r
 678 \r
 679     if(viewport.getColourAppliesToAllGroups())\r
 680     {\r
 681       Vector groups = viewport.alignment.getGroups();\r
 682       for(int i=0; i<groups.size(); i++)\r
 683       {\r
 684         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 685         sg.cs = cs;\r
 686 \r
 687         if(abovePIDThreshold.isSelected())\r
 688           abovePIDThreshold_actionPerformed(null);\r
 689         else if( viewport.getConservationSelected() )\r
 690         {\r
 691           Conservation c = new Conservation("Group",\r
 692                                             ResidueProperties.propHash, 3,\r
 693                                             sg.sequences, sg.getStartRes(),\r
 694                                             sg.getEndRes());\r
 695           c.calculate();\r
 696           c.verdict(false, 100);\r
 697           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 698 \r
 699           sg.cs = ccs;\r
 700         }\r
 701 \r
 702       }\r
 703     }\r
 704 \r
 705 \r
 706     if ( viewport.getAbovePIDThreshold())\r
 707     {\r
 708       int threshold = 0;\r
 709       threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");\r
 710       Desktop.hideConservationSlider();\r
 711 \r
 712       if (cs instanceof ResidueColourScheme)\r
 713         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 714       else if (cs instanceof ScoreColourScheme)\r
 715         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 716 \r
 717       viewport.setGlobalColourScheme(cs);\r
 718 \r
 719     }\r
 720     else\r
 721     if (cs instanceof ResidueColourScheme)\r
 722       ( (ResidueColourScheme) cs).setThreshold(0);\r
 723     else if (cs instanceof ScoreColourScheme)\r
 724       ( (ScoreColourScheme) cs).setThreshold(0);\r
 725 \r
 726 \r
 727 \r
 728 \r
 729 if ( viewport.getConservationSelected() )\r
 730  {\r
 731    ConservationColourScheme ccs = null;\r
 732 \r
 733    Alignment al = (Alignment) viewport.alignment;\r
 734    Conservation c = new Conservation("All",\r
 735                                      ResidueProperties.propHash, 3,\r
 736                                      al.getSequences(), 0,\r
 737                                      al.getWidth());\r
 738 \r
 739    c.calculate();\r
 740    c.verdict(false, 100);\r
 741 \r
 742    ccs = new ConservationColourScheme(c, cs);\r
 743 \r
 744    int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,\r
 745        "Background");\r
 746 \r
 747    ccs.inc = threshold;\r
 748 \r
 749    viewport.setGlobalColourScheme(ccs);\r
 750 \r
 751   }\r
 752   else\r
 753        viewport.setGlobalColourScheme( cs );\r
 754 \r
 755     alignPanel.RefreshPanels();\r
 756   }\r
 757 \r
 758 \r
 759   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 760   {\r
 761     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 762 \r
 763     viewport.setAbovePIDThreshold(false);\r
 764     abovePIDThreshold.setSelected(false);\r
 765     Desktop.hidePIDSlider();\r
 766     if(!viewport.getConservationSelected())\r
 767       Desktop.hideConservationSlider();\r
 768 \r
 769    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 770    if(cs instanceof ConservationColourScheme )\r
 771      changeColour( ((ConservationColourScheme)cs).cs );\r
 772     else\r
 773       changeColour( cs );\r
 774   }\r
 775 \r
 776 \r
 777   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 778   {\r
 779     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
 780 \r
 781     conservationMenuItem.setSelected(false);\r
 782     viewport.setConservationSelected(false);\r
 783     Desktop.hideConservationSlider();\r
 784 \r
 785     if(!viewport.getAbovePIDThreshold())\r
 786       Desktop.hidePIDSlider();\r
 787 \r
 788 \r
 789     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 790     if(cs instanceof ConservationColourScheme )\r
 791         changeColour( ((ConservationColourScheme)cs).cs );\r
 792     else\r
 793         changeColour( cs );\r
 794 \r
 795   }\r
 796 \r
 797 \r
 798 \r
 799   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 800   {\r
 801     JInternalFrame frame = new JInternalFrame();\r
 802     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 803     frame.setContentPane(chooser);\r
 804     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 805     frame.setResizable(false);\r
 806     frame.setIconifiable(false);\r
 807     frame.setMaximizable(false);\r
 808   }\r
 809 \r
 810   public void PIDColour_actionPerformed(ActionEvent e)\r
 811   {\r
 812     changeColour( new PIDColourScheme() );\r
 813   }\r
 814 \r
 815 \r
 816   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 817   {\r
 818     changeColour(new Blosum62ColourScheme(viewport) );\r
 819   }\r
 820 \r
 821 \r
 822 \r
 823   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 824   {\r
 825     addHistoryItem("sort");\r
 826     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 827     alignPanel.RefreshPanels();\r
 828   }\r
 829 \r
 830   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 831   {\r
 832     addHistoryItem("sort");\r
 833     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 834     alignPanel.RefreshPanels();\r
 835   }\r
 836 \r
 837   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 838   {\r
 839     addHistoryItem("sort");\r
 840     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 841     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 842     alignPanel.RefreshPanels();\r
 843   }\r
 844 \r
 845   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 846   {\r
 847     addHistoryItem("sort");\r
 848     if(viewport.getCurrentTree()==null)\r
 849       return;\r
 850 \r
 851     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 852     alignPanel.RefreshPanels();\r
 853   }\r
 854 \r
 855   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 856   {\r
 857     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 858     JInternalFrame frame = new JInternalFrame();\r
 859     frame.setContentPane(sp);\r
 860     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
 861     frame.setMaximizable(false);\r
 862     frame.setResizable(false);\r
 863 \r
 864   }\r
 865 \r
 866   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 867   {\r
 868     if(viewport.getSelection().size()<2)\r
 869       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 870     else\r
 871     {\r
 872       JInternalFrame frame = new JInternalFrame();\r
 873       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 874       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 875     }\r
 876   }\r
 877 \r
 878   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 879   {\r
 880     if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)\r
 881        || viewport.getAlignment().getHeight()<4)\r
 882     {\r
 883       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 884                                     +"at least 4 input sequences.",\r
 885                                     "Sequence selection insufficient",\r
 886                                     JOptionPane.WARNING_MESSAGE);\r
 887       return;\r
 888     }\r
 889 \r
 890     try{\r
 891       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 892       JInternalFrame frame = new JInternalFrame();\r
 893       frame.setContentPane(pcaPanel);\r
 894       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 895    }catch(java.lang.OutOfMemoryError ex)\r
 896    {\r
 897      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 898                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 899    }\r
 900 \r
 901 \r
 902   }\r
 903 \r
 904   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 905   {\r
 906     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 907   }\r
 908 \r
 909   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 910   {\r
 911     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 912   }\r
 913 \r
 914 \r
 915   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 916   {\r
 917     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 918   }\r
 919 \r
 920   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 921   {\r
 922     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 923   }\r
 924 \r
 925   void NewTreePanel(String type, String pwType, String title)\r
 926   {\r
 927     //are the sequences aligned?\r
 928     if(!viewport.alignment.isAligned())\r
 929     {\r
 930       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
 931                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
 932       return;\r
 933     }\r
 934 \r
 935     TreePanel tp=null;\r
 936    if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
 937    {\r
 938      tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,\r
 939                          0, viewport.alignment.getWidth());\r
 940    }\r
 941    else\r
 942    {\r
 943      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 944                          type, pwType,  0, viewport.alignment.getWidth());\r
 945    }\r
 946 \r
 947    Desktop.addInternalFrame(tp, title, 600, 500);\r
 948   }\r
 949 \r
 950 \r
 951 \r
 952 \r
 953   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 954   {\r
 955     JInternalFrame frame = new JInternalFrame();\r
 956     ClustalThread ct = new ClustalThread(frame);\r
 957     Thread t = new Thread(ct);\r
 958     t.start();\r
 959     frame.setContentPane(ct);\r
 960      Desktop.addInternalFrame(frame, title, 300, 80);\r
 961 \r
 962   }\r
 963 \r
 964   class ClustalThread extends JPanel implements Runnable\r
 965   {\r
 966     Image [] image;\r
 967     int imageIndex = 0;\r
 968     boolean webServiceRunning = false;\r
 969     JInternalFrame frame;\r
 970     public ClustalThread(JInternalFrame frame)\r
 971     {\r
 972       this.frame = frame;\r
 973       image = new Image[9];\r
 974       for(int i=0; i<9; i++)\r
 975       {\r
 976         java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");\r
 977         if (url != null)\r
 978         {\r
 979           image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
 980           MediaTracker mt = new MediaTracker(this);\r
 981           mt.addImage(image[i], i);\r
 982           try{mt.waitForID(i);}\r
 983           catch(Exception ex){}\r
 984         }\r
 985       }\r
 986       DNATwirler twirler = new DNATwirler();\r
 987       twirler.start();\r
 988       webServiceRunning = true;\r
 989     }\r
 990 \r
 991     class DNATwirler extends Thread\r
 992     {\r
 993       public void run()\r
 994       {\r
 995         while(webServiceRunning)\r
 996         {\r
 997           try{\r
 998             Thread.sleep(100);\r
 999             imageIndex++;\r
1000             imageIndex %=9;\r
1001             repaint();\r
1002           }\r
1003           catch(Exception ex){}\r
1004         }\r
1005       }\r
1006     }\r
1007 \r
1008     // JBPNote\r
1009     // Should check to see if the server settings are valid\r
1010     // Need visual-delay indication here.\r
1011     public void run()\r
1012        {\r
1013          jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
1014          Vector sv = viewport.getAlignment().getSequences();\r
1015          SequenceI[] seqs = new SequenceI[sv.size()];\r
1016 \r
1017          int i = 0;\r
1018          do\r
1019          {\r
1020            seqs[i] = (SequenceI) sv.elementAt(i);\r
1021          }\r
1022          while (++i < sv.size());\r
1023 \r
1024          SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
1025 \r
1026          if (alignment != null)\r
1027          {\r
1028            AlignFrame af = new AlignFrame(new Alignment(alignment));\r
1029           af.clustalColour.setSelected(true);\r
1030           af.clustalColour_actionPerformed(null);\r
1031            Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
1032                                     700, 500); // JBPNote - is there a new window geom. property ?\r
1033          }\r
1034          else\r
1035            JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
1036                                          JOptionPane.WARNING_MESSAGE);\r
1037 \r
1038          webServiceRunning = false;\r
1039          try{\r
1040            frame.setClosed(true);\r
1041          }catch(Exception ex){}\r
1042        }\r
1043 \r
1044        public void paintComponent(Graphics g)\r
1045        {\r
1046          g.setColor(Color.white);\r
1047          g.fillRect(0,0,getWidth(), getHeight());\r
1048          if(image!=null)\r
1049          {\r
1050            g.drawImage(image[imageIndex],10,10,this);\r
1051          }\r
1052          g.setFont(new Font("Arial", Font.BOLD, 12));\r
1053          g.setColor(Color.black);\r
1054          g.drawString("Clustal Alignment Web Service running", 30,30);\r
1055        }\r
1056   }\r
1057 }\r