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,false);\r
  37 \r
  38     String fontName = jalview.bin.Cache.getProperty("FONT_NAME");\r
  39     String fontStyle= jalview.bin.Cache.getProperty("FONT_STYLE");\r
  40     String fontSize = jalview.bin.Cache.getProperty("FONT_SIZE");\r
  41     if(fontName!=null && fontStyle!=null && fontSize!=null)\r
  42       viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );\r
  43 \r
  44 \r
  45 \r
  46     alignPanel = new AlignmentPanel(this, viewport);\r
  47     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
  48 \r
  49     addInternalFrameListener(new InternalFrameAdapter()\r
  50    {\r
  51      public void internalFrameActivated(InternalFrameEvent evt)\r
  52      {\r
  53           javax.swing.SwingUtilities.invokeLater(new Runnable()\r
  54           {\r
  55             public void run()\r
  56             {      alignPanel.requestFocus();    }\r
  57           });\r
  58 \r
  59      }\r
  60    });\r
  61 \r
  62   }\r
  63 \r
  64   protected void saveAs_actionPerformed(ActionEvent e)\r
  65   {\r
  66     String suffix = "";\r
  67     if(e.getActionCommand().equals("FASTA"))\r
  68       suffix = "fa";\r
  69     else if(e.getActionCommand().equals("MSF"))\r
  70       suffix = "msf";\r
  71     else if(e.getActionCommand().equals("CLUSTAL"))\r
  72       suffix = "aln";\r
  73     else if(e.getActionCommand().equals("BLC"))\r
  74       suffix = "blc";\r
  75     else if(e.getActionCommand().equals("PIR"))\r
  76       suffix = "pir";\r
  77     else if(e.getActionCommand().equals("PFAM"))\r
  78       suffix = "pfam";\r
  79 \r
  80     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")\r
  81         , new String[]{suffix}, e.getActionCommand()+" file");\r
  82     chooser.setFileView(new JalviewFileView());\r
  83     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
  84     chooser.setToolTipText("Save");\r
  85     int value = chooser.showSaveDialog(this);\r
  86     if(value == JalviewFileChooser.APPROVE_OPTION)\r
  87     {\r
  88       String choice =  chooser.getSelectedFile().getPath();\r
  89       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
  90       String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
  91       try{\r
  92         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
  93         out.println(output);\r
  94         out.close();\r
  95       }\r
  96       catch(Exception ex){}\r
  97     }\r
  98 \r
  99   }\r
 100 \r
 101   protected void outputText_actionPerformed(ActionEvent e)\r
 102   {\r
 103      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
 104      JInternalFrame frame = new JInternalFrame();\r
 105      cap.formatForOutput();\r
 106      frame.setContentPane(cap);\r
 107      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
 108      cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
 109   }\r
 110 \r
 111   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 112   {\r
 113     HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
 114     htmlOutput = null;\r
 115   }\r
 116 \r
 117   protected void createPNG_actionPerformed(ActionEvent e)\r
 118   {\r
 119     int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;\r
 120     int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();\r
 121 \r
 122     if(!viewport.getWrapAlignment())\r
 123     {\r
 124       height = viewport.alignment.getHeight() * viewport.charHeight;\r
 125       width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;\r
 126     }\r
 127 \r
 128     alignPanel.makePNG( width, height);\r
 129   }\r
 130 \r
 131   protected void epsFile_actionPerformed(ActionEvent e)\r
 132   {\r
 133     int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;\r
 134     int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();\r
 135 \r
 136     if(!viewport.getWrapAlignment())\r
 137     {\r
 138       height = viewport.alignment.getHeight() * viewport.charHeight;\r
 139       width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;\r
 140     }\r
 141 \r
 142     alignPanel.makeEPS( width, height);\r
 143 \r
 144   }\r
 145 \r
 146 \r
 147   public void printMenuItem_actionPerformed(ActionEvent e)\r
 148   {\r
 149     //Putting in a thread avoids Swing painting problems\r
 150     PrintThread thread = new PrintThread();\r
 151     thread.start();\r
 152   }\r
 153 \r
 154   class PrintThread extends Thread\r
 155   {\r
 156     public void run()\r
 157     {\r
 158       PrinterJob printJob = PrinterJob.getPrinterJob();\r
 159       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
 160       printJob.setPrintable(alignPanel, pf);\r
 161       if (printJob.printDialog())\r
 162       {\r
 163         try\r
 164         {\r
 165           printJob.print();\r
 166         }\r
 167         catch (Exception PrintException)\r
 168         {\r
 169           PrintException.printStackTrace();\r
 170         }\r
 171       }\r
 172     }\r
 173 \r
 174   }\r
 175 \r
 176 \r
 177 \r
 178 \r
 179   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 180   {\r
 181     try{\r
 182       this.setClosed(true);\r
 183     }catch(Exception ex){}\r
 184   }\r
 185 \r
 186   Stack historyList = new Stack();\r
 187   Stack redoList = new Stack();\r
 188 \r
 189   void updateEditMenuBar()\r
 190   {\r
 191     if(historyList.size()>0)\r
 192      {\r
 193        undoMenuItem.setEnabled(true);\r
 194        Object [] history = (Object[])historyList.get(0);\r
 195        undoMenuItem.setText("Undo "+history[0]);\r
 196      }\r
 197     else\r
 198     {\r
 199       undoMenuItem.setEnabled(false);\r
 200       undoMenuItem.setText("Undo");\r
 201     }\r
 202 \r
 203     if(redoList.size()>0)\r
 204      {\r
 205        redoMenuItem.setEnabled(true);\r
 206        Object [] history = (Object[])redoList.get(0);\r
 207        redoMenuItem.setText("Redo "+history[0]);\r
 208      }\r
 209     else\r
 210     {\r
 211       redoMenuItem.setEnabled(false);\r
 212       redoMenuItem.setText("Redo");\r
 213     }\r
 214   }\r
 215 \r
 216   public void addHistoryItem(String type)\r
 217   {\r
 218     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 219     redoList.clear();\r
 220     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 221     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 222     {\r
 223       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 224                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 225     }\r
 226 \r
 227     historyList.add(0, new Object[]{type,  seq} );\r
 228     updateEditMenuBar();\r
 229   }\r
 230 \r
 231   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 232   {\r
 233     Object [] history = (Object[])historyList.remove(0);\r
 234     // add the redo state before continuing!!\r
 235     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 236     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 237     {\r
 238       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 239                             viewport.getAlignment().getSequenceAt(i).\r
 240                             getSequence());\r
 241     }\r
 242     /////////\r
 243 \r
 244     redoList.add(0, new Object[] {history[0], seq});\r
 245 \r
 246       seq = (SequenceI[]) history[1];\r
 247       viewport.setAlignment( new Alignment(seq) );\r
 248       updateEditMenuBar();\r
 249       alignPanel.RefreshPanels();\r
 250   }\r
 251 \r
 252   public void moveSelectedSequences(boolean up)\r
 253   {\r
 254     SequenceGroup sg = viewport.getSelectionGroup();\r
 255     if (sg == null)\r
 256       return;\r
 257 \r
 258     if (up)\r
 259     {\r
 260       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 261       {\r
 262         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 263         if (!sg.sequences.contains(seq))\r
 264           continue;\r
 265 \r
 266         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 267         if (sg.sequences.contains(temp))\r
 268           continue;\r
 269 \r
 270         viewport.alignment.getSequences().setElementAt(temp, i);\r
 271         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 272       }\r
 273     }\r
 274     else\r
 275     {\r
 276       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 277       {\r
 278         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 279         if (!sg.sequences.contains(seq))\r
 280           continue;\r
 281 \r
 282         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 283         if (sg.sequences.contains(temp))\r
 284           continue;\r
 285 \r
 286         viewport.alignment.getSequences().setElementAt(temp, i);\r
 287         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 288       }\r
 289     }\r
 290 \r
 291     alignPanel.RefreshPanels();\r
 292   }\r
 293 \r
 294 \r
 295 \r
 296   protected void copy_actionPerformed(ActionEvent e)\r
 297   {\r
 298    if(viewport.getSelectionGroup()==null)\r
 299      return;\r
 300 \r
 301    SequenceGroup sg = viewport.getSelectionGroup();\r
 302 \r
 303      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 304      StringBuffer buffer= new StringBuffer();\r
 305 \r
 306        for(int i=0; i<sg.getSize(); i++)\r
 307        {\r
 308          SequenceI seq = sg.getSequenceAt(i);\r
 309          buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
 310                         +seq.findPosition( sg.getEndRes() )+ "\t"\r
 311                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
 312        }\r
 313      c.setContents( new StringSelection( buffer.toString()) , null ) ;\r
 314 \r
 315   }\r
 316 \r
 317 \r
 318   protected void pasteNew_actionPerformed(ActionEvent e)\r
 319   {\r
 320     paste(true);\r
 321   }\r
 322 \r
 323   protected void pasteThis_actionPerformed(ActionEvent e)\r
 324   {\r
 325     addHistoryItem("Paste");\r
 326     paste(false);\r
 327   }\r
 328 \r
 329   void paste(boolean newAlignment)\r
 330   {\r
 331     try{\r
 332       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 333       Transferable contents = c.getContents(this);\r
 334       if (contents == null)\r
 335         return;\r
 336 \r
 337       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
 338       StringTokenizer st = new StringTokenizer(str);\r
 339       ArrayList seqs = new ArrayList();\r
 340       while (st.hasMoreElements())\r
 341       {\r
 342         String name = st.nextToken();\r
 343         int start = Integer.parseInt(st.nextToken());\r
 344         int end = Integer.parseInt(st.nextToken());\r
 345         Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
 346 \r
 347         if(!newAlignment)\r
 348           viewport.alignment.addSequence(sequence);\r
 349         else\r
 350           seqs.add(sequence);\r
 351       }\r
 352 \r
 353       if(newAlignment)\r
 354       {\r
 355         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 356         seqs.toArray(newSeqs);\r
 357         AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
 358         int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;\r
 359         if (newHeight > 500)\r
 360           newHeight = 500;\r
 361         Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
 362       }\r
 363       else\r
 364       {\r
 365         viewport.setEndSeq(viewport.alignment.getHeight());\r
 366         viewport.alignment.getWidth();\r
 367         alignPanel.RefreshPanels();\r
 368       }\r
 369 \r
 370     }catch(Exception ex){}// could be anything being pasted in here\r
 371 \r
 372   }\r
 373 \r
 374 \r
 375   protected void cut_actionPerformed(ActionEvent e)\r
 376   {\r
 377     copy_actionPerformed(null);\r
 378     delete_actionPerformed(null);\r
 379   }\r
 380 \r
 381   protected void delete_actionPerformed(ActionEvent e)\r
 382   {\r
 383     addHistoryItem("Delete");\r
 384     if (viewport.getSelectionGroup() == null)\r
 385       return;\r
 386 \r
 387      SequenceGroup sg = viewport.getSelectionGroup();\r
 388      for (int i=0;i < sg.sequences.size(); i++)\r
 389      {\r
 390        SequenceI seq = sg.getSequenceAt(i);\r
 391        int index = viewport.getAlignment().findIndex(seq);\r
 392        seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);\r
 393 \r
 394        if(seq.getSequence().length()<1)\r
 395           viewport.getAlignment().deleteSequence(seq);\r
 396       else\r
 397           viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 398      }\r
 399 \r
 400      viewport.setSelectionGroup(null);\r
 401      viewport.alignment.deleteGroup(sg);\r
 402      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
 403      if(viewport.getAlignment().getHeight()<1)\r
 404      try\r
 405      {\r
 406        this.setClosed(true);\r
 407      }catch(Exception ex){}\r
 408      alignPanel.RefreshPanels();\r
 409 \r
 410   }\r
 411 \r
 412 \r
 413 \r
 414   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 415   {\r
 416      Object [] history = (Object[])redoList.remove(0);\r
 417      SequenceI[] seq = (SequenceI[]) history[1];\r
 418      viewport.setAlignment( new Alignment(seq) );\r
 419      updateEditMenuBar();\r
 420      alignPanel.RefreshPanels();\r
 421   }\r
 422 \r
 423 \r
 424   public void groupsMenuItem_actionPerformed(ActionEvent e)\r
 425   {\r
 426     GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
 427     JInternalFrame frame = new JInternalFrame();\r
 428     frame.setContentPane(geditor);\r
 429     Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
 430     frame.setResizable(false);\r
 431   }\r
 432 \r
 433   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 434   {\r
 435     viewport.alignment.deleteAllGroups();\r
 436     viewport.setSelectionGroup(null);\r
 437 \r
 438     alignPanel.RefreshPanels();\r
 439   }\r
 440 \r
 441 \r
 442 \r
 443   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 444   {\r
 445     SequenceGroup sg = new SequenceGroup();\r
 446     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 447       sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
 448     sg.setEndRes(viewport.alignment.getWidth());\r
 449     viewport.setSelectionGroup(sg);\r
 450     PaintRefresher.Refresh(null);\r
 451   }\r
 452 \r
 453   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 454   {\r
 455     viewport.setSelectionGroup(null);\r
 456     PaintRefresher.Refresh(null);\r
 457   }\r
 458 \r
 459   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 460   {\r
 461     SequenceGroup sg = viewport.getSelectionGroup();\r
 462     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 463       sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
 464 \r
 465     PaintRefresher.Refresh(null);\r
 466   }\r
 467 \r
 468 \r
 469   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 470   {\r
 471     viewport.getColumnSelection().clear();\r
 472     repaint();\r
 473   }\r
 474 \r
 475   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 476   {\r
 477     addHistoryItem("delete columns");\r
 478     ColumnSelection colSel = viewport.getColumnSelection();\r
 479     if (colSel.size() > 0)\r
 480     {\r
 481       int min = colSel.getMin();\r
 482       viewport.getAlignment().trimLeft(min);\r
 483       colSel.compensateForEdit(0,min);\r
 484       alignPanel.RefreshPanels();\r
 485     }\r
 486   }\r
 487 \r
 488   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 489   {\r
 490     addHistoryItem("delete columns");\r
 491     ColumnSelection colSel = viewport.getColumnSelection();\r
 492     if (colSel.size() > 0)\r
 493     {\r
 494       int max = colSel.getMax();\r
 495       if(max>1)\r
 496         viewport.getAlignment().trimRight(max);\r
 497 \r
 498       alignPanel.RefreshPanels();\r
 499     }\r
 500 \r
 501   }\r
 502 \r
 503   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 504   {\r
 505     addHistoryItem("delete gapped columns");\r
 506     viewport.getAlignment().removeGaps();\r
 507     alignPanel.RefreshPanels();\r
 508   }\r
 509 \r
 510   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 511   {\r
 512     addHistoryItem("delete all gaps");\r
 513     SequenceI current;\r
 514     int jSize;\r
 515     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 516     {\r
 517       current = viewport.getAlignment().getSequenceAt(i);\r
 518       jSize = current.getLength();\r
 519       for (int j=0; j < jSize; j++)\r
 520         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 521         {\r
 522           current.deleteCharAt(j);\r
 523           j--;\r
 524           jSize--;\r
 525         }\r
 526     }\r
 527 \r
 528     alignPanel.RefreshPanels();\r
 529   }\r
 530 \r
 531   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 532   {\r
 533     char thisChar = '-';\r
 534     char nextChar = '.';\r
 535     if(viewport.getGapCharacter()=='-')\r
 536     {\r
 537       thisChar = '.';\r
 538       nextChar = '-';\r
 539     }\r
 540     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 541     viewport.setGapCharacter(thisChar);\r
 542     alignPanel.RefreshPanels();\r
 543   }\r
 544 \r
 545   public void findMenuItem_actionPerformed(ActionEvent e)\r
 546   {\r
 547       JInternalFrame frame = new JInternalFrame();\r
 548       Finder finder = new Finder(viewport, alignPanel, frame);\r
 549       frame.setContentPane(finder);\r
 550      Desktop.addInternalFrame(frame, "Find", 340,110);\r
 551 \r
 552   }\r
 553 \r
 554 \r
 555   public void font_actionPerformed(ActionEvent e)\r
 556   {\r
 557    // JOptionPane op = new JOptionPane();\r
 558     JInternalFrame frame = new JInternalFrame();\r
 559     FontChooser fc = new FontChooser( alignPanel, frame );\r
 560     frame.setContentPane(fc);\r
 561     Desktop.addInternalFrame(frame, "Change Font", 480,100);\r
 562   }\r
 563 \r
 564   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 565   {\r
 566     viewport.setShowFullId( fullSeqId.isSelected() );\r
 567 \r
 568     alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );\r
 569     alignPanel.RefreshPanels();\r
 570   }\r
 571 \r
 572   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 573   {\r
 574       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 575       alignPanel.RefreshPanels();\r
 576   }\r
 577 \r
 578   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 579   {\r
 580     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 581     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
 582   }\r
 583 \r
 584 \r
 585   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 586   {\r
 587     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 588     alignPanel.RefreshPanels();\r
 589   }\r
 590 \r
 591   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 592   {\r
 593     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 594     alignPanel.RefreshPanels();\r
 595   }\r
 596 \r
 597 \r
 598   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 599   {\r
 600     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 601     alignPanel.RefreshPanels();\r
 602   }\r
 603 \r
 604   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 605   {\r
 606     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 607     if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
 608     {\r
 609          AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);\r
 610          ((Alignment)viewport.alignment).featuresAdded = true;\r
 611     }\r
 612     alignPanel.RefreshPanels();\r
 613   }\r
 614 \r
 615   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 616   {\r
 617     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
 618   }\r
 619 \r
 620   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 621   {\r
 622     if (alignPanel.overviewPanel != null)\r
 623       return;\r
 624 \r
 625     JInternalFrame frame = new JInternalFrame();\r
 626     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 627    try{\r
 628      overview = new OverviewPanel(alignPanel, viewport);\r
 629      frame.setContentPane(overview);\r
 630     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 631                              frame.getWidth(), frame.getHeight());\r
 632     frame.pack();\r
 633     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 634     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 635       {\r
 636             alignPanel.setOverviewPanel(null);\r
 637       };\r
 638     });\r
 639     alignPanel.setOverviewPanel( overview );\r
 640 \r
 641   }catch(java.lang.OutOfMemoryError ex)\r
 642    {\r
 643      JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 644                                    +"\nTry reducing the font size.",\r
 645                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 646    }\r
 647 \r
 648 \r
 649   }\r
 650 \r
 651   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 652   {\r
 653     changeColour( null );\r
 654   }\r
 655 \r
 656 \r
 657   public void clustalColour_actionPerformed(ActionEvent e)\r
 658   {\r
 659     abovePIDThreshold.setSelected(false);\r
 660     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 661   }\r
 662 \r
 663   public void zappoColour_actionPerformed(ActionEvent e)\r
 664   {\r
 665     changeColour(new ZappoColourScheme());\r
 666   }\r
 667 \r
 668   public void taylorColour_actionPerformed(ActionEvent e)\r
 669   {\r
 670     changeColour(new TaylorColourScheme());\r
 671   }\r
 672 \r
 673 \r
 674   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 675   {\r
 676     changeColour( new HydrophobicColourScheme() );\r
 677   }\r
 678 \r
 679   public void helixColour_actionPerformed(ActionEvent e)\r
 680   {\r
 681     changeColour(new HelixColourScheme() );\r
 682   }\r
 683 \r
 684 \r
 685   public void strandColour_actionPerformed(ActionEvent e)\r
 686   {\r
 687     changeColour(new StrandColourScheme());\r
 688   }\r
 689 \r
 690 \r
 691   public void turnColour_actionPerformed(ActionEvent e)\r
 692   {\r
 693     changeColour(new TurnColourScheme());\r
 694   }\r
 695 \r
 696 \r
 697   public void buriedColour_actionPerformed(ActionEvent e)\r
 698   {\r
 699     changeColour(new BuriedColourScheme() );\r
 700   }\r
 701 \r
 702   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 703   {\r
 704     changeColour(new NucleotideColourScheme());\r
 705   }\r
 706 \r
 707 \r
 708   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 709   {\r
 710     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
 711   }\r
 712 \r
 713 \r
 714 \r
 715   void changeColour(ColourSchemeI cs)\r
 716   {\r
 717 \r
 718     if(viewport.getColourAppliesToAllGroups())\r
 719     {\r
 720       Vector groups = viewport.alignment.getGroups();\r
 721       for(int i=0; i<groups.size(); i++)\r
 722       {\r
 723         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 724         sg.cs = cs;\r
 725 \r
 726         if(abovePIDThreshold.isSelected())\r
 727           abovePIDThreshold_actionPerformed(null);\r
 728         else if( viewport.getConservationSelected() )\r
 729         {\r
 730           Conservation c = new Conservation("Group",\r
 731                                             ResidueProperties.propHash, 3,\r
 732                                             sg.sequences, sg.getStartRes(),\r
 733                                             sg.getEndRes());\r
 734           c.calculate();\r
 735           c.verdict(false, 100);\r
 736           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 737 \r
 738           sg.cs = ccs;\r
 739         }\r
 740 \r
 741       }\r
 742     }\r
 743 \r
 744 \r
 745     if ( viewport.getAbovePIDThreshold())\r
 746     {\r
 747       int threshold = 0;\r
 748       threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");\r
 749       Desktop.hideConservationSlider();\r
 750 \r
 751       if (cs instanceof ResidueColourScheme)\r
 752         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 753       else if (cs instanceof ScoreColourScheme)\r
 754         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 755 \r
 756       viewport.setGlobalColourScheme(cs);\r
 757 \r
 758     }\r
 759     else\r
 760     if (cs instanceof ResidueColourScheme)\r
 761       ( (ResidueColourScheme) cs).setThreshold(0);\r
 762     else if (cs instanceof ScoreColourScheme)\r
 763       ( (ScoreColourScheme) cs).setThreshold(0);\r
 764 \r
 765 \r
 766 \r
 767 \r
 768 if ( viewport.getConservationSelected() )\r
 769  {\r
 770    ConservationColourScheme ccs = null;\r
 771 \r
 772    Alignment al = (Alignment) viewport.alignment;\r
 773    Conservation c = new Conservation("All",\r
 774                                      ResidueProperties.propHash, 3,\r
 775                                      al.getSequences(), 0,\r
 776                                      al.getWidth());\r
 777 \r
 778    c.calculate();\r
 779    c.verdict(false, 100);\r
 780 \r
 781    ccs = new ConservationColourScheme(c, cs);\r
 782 \r
 783    int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,\r
 784        "Background");\r
 785 \r
 786    ccs.inc = threshold;\r
 787 \r
 788    viewport.setGlobalColourScheme(ccs);\r
 789 \r
 790   }\r
 791   else\r
 792        viewport.setGlobalColourScheme( cs );\r
 793 \r
 794     alignPanel.RefreshPanels();\r
 795   }\r
 796 \r
 797 \r
 798   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 799   {\r
 800     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 801 \r
 802     viewport.setAbovePIDThreshold(false);\r
 803     abovePIDThreshold.setSelected(false);\r
 804     Desktop.hidePIDSlider();\r
 805     if(!viewport.getConservationSelected())\r
 806       Desktop.hideConservationSlider();\r
 807 \r
 808    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 809    if(cs instanceof ConservationColourScheme )\r
 810      changeColour( ((ConservationColourScheme)cs).cs );\r
 811     else\r
 812       changeColour( cs );\r
 813   }\r
 814 \r
 815 \r
 816   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 817   {\r
 818     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
 819 \r
 820     conservationMenuItem.setSelected(false);\r
 821     viewport.setConservationSelected(false);\r
 822     Desktop.hideConservationSlider();\r
 823 \r
 824     if(!viewport.getAbovePIDThreshold())\r
 825       Desktop.hidePIDSlider();\r
 826 \r
 827 \r
 828     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 829     if(cs instanceof ConservationColourScheme )\r
 830         changeColour( ((ConservationColourScheme)cs).cs );\r
 831     else\r
 832         changeColour( cs );\r
 833 \r
 834   }\r
 835 \r
 836 \r
 837 \r
 838   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 839   {\r
 840     JInternalFrame frame = new JInternalFrame();\r
 841     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 842     frame.setContentPane(chooser);\r
 843     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 844     frame.setResizable(false);\r
 845     frame.setIconifiable(false);\r
 846     frame.setMaximizable(false);\r
 847   }\r
 848 \r
 849   public void PIDColour_actionPerformed(ActionEvent e)\r
 850   {\r
 851     changeColour( new PIDColourScheme() );\r
 852   }\r
 853 \r
 854 \r
 855   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 856   {\r
 857     changeColour(new Blosum62ColourScheme(viewport) );\r
 858   }\r
 859 \r
 860 \r
 861 \r
 862   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 863   {\r
 864     addHistoryItem("sort");\r
 865     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 866     alignPanel.RefreshPanels();\r
 867   }\r
 868 \r
 869   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 870   {\r
 871     addHistoryItem("sort");\r
 872     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 873     alignPanel.RefreshPanels();\r
 874   }\r
 875 \r
 876   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 877   {\r
 878     addHistoryItem("sort");\r
 879     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 880     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 881     alignPanel.RefreshPanels();\r
 882   }\r
 883 \r
 884   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 885   {\r
 886     addHistoryItem("sort");\r
 887     if(viewport.getCurrentTree()==null)\r
 888       return;\r
 889 \r
 890     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 891     alignPanel.RefreshPanels();\r
 892   }\r
 893 \r
 894   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 895   {\r
 896     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 897     JInternalFrame frame = new JInternalFrame();\r
 898     frame.setContentPane(sp);\r
 899     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
 900     frame.setMaximizable(false);\r
 901     frame.setResizable(false);\r
 902 \r
 903   }\r
 904 \r
 905   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 906   {\r
 907     if(viewport.getSelectionGroup().getSize()<2)\r
 908       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 909     else\r
 910     {\r
 911       JInternalFrame frame = new JInternalFrame();\r
 912       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 913       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 914     }\r
 915   }\r
 916 \r
 917   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 918   {\r
 919 \r
 920     if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
 921        || viewport.getAlignment().getHeight()<4)\r
 922     {\r
 923       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 924                                     +"at least 4 input sequences.",\r
 925                                     "Sequence selection insufficient",\r
 926                                     JOptionPane.WARNING_MESSAGE);\r
 927       return;\r
 928     }\r
 929 \r
 930     try{\r
 931       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 932       JInternalFrame frame = new JInternalFrame();\r
 933       frame.setContentPane(pcaPanel);\r
 934       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 935    }catch(java.lang.OutOfMemoryError ex)\r
 936    {\r
 937      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 938                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 939    }\r
 940 \r
 941 \r
 942   }\r
 943 \r
 944   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 945   {\r
 946     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 947   }\r
 948 \r
 949   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 950   {\r
 951     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 952   }\r
 953 \r
 954 \r
 955   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 956   {\r
 957     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 958   }\r
 959 \r
 960   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 961   {\r
 962     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 963   }\r
 964 \r
 965   void NewTreePanel(String type, String pwType, String title)\r
 966   {\r
 967     //are the sequences aligned?\r
 968     if(!viewport.alignment.isAligned())\r
 969     {\r
 970       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
 971                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
 972       return;\r
 973     }\r
 974 \r
 975     TreePanel tp=null;\r
 976    if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)\r
 977    {\r
 978      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,\r
 979                          0, viewport.alignment.getWidth());\r
 980    }\r
 981    else\r
 982    {\r
 983      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 984                          type, pwType,  0, viewport.alignment.getWidth());\r
 985    }\r
 986 \r
 987    Desktop.addInternalFrame(tp, title, 600, 500);\r
 988   }\r
 989 \r
 990 \r
 991 \r
 992 \r
 993   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 994   {\r
 995     JInternalFrame frame = new JInternalFrame();\r
 996     ClustalThread ct = new ClustalThread(frame);\r
 997     Thread t = new Thread(ct);\r
 998     t.start();\r
 999     frame.setContentPane(ct);\r
1000      Desktop.addInternalFrame(frame, title, 300, 80);\r
1001 \r
1002   }\r
1003 \r
1004   class ClustalThread extends JPanel implements Runnable\r
1005   {\r
1006     Image [] image;\r
1007     int imageIndex = 0;\r
1008     boolean webServiceRunning = false;\r
1009     JInternalFrame frame;\r
1010     public ClustalThread(JInternalFrame frame)\r
1011     {\r
1012       this.frame = frame;\r
1013       image = new Image[9];\r
1014       for(int i=0; i<9; i++)\r
1015       {\r
1016         java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");\r
1017         if (url != null)\r
1018         {\r
1019           image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
1020           MediaTracker mt = new MediaTracker(this);\r
1021           mt.addImage(image[i], i);\r
1022           try{mt.waitForID(i);}\r
1023           catch(Exception ex){}\r
1024         }\r
1025       }\r
1026       DNATwirler twirler = new DNATwirler();\r
1027       twirler.start();\r
1028       webServiceRunning = true;\r
1029     }\r
1030 \r
1031     class DNATwirler extends Thread\r
1032     {\r
1033       public void run()\r
1034       {\r
1035         while(webServiceRunning)\r
1036         {\r
1037           try{\r
1038             Thread.sleep(100);\r
1039             imageIndex++;\r
1040             imageIndex %=9;\r
1041             repaint();\r
1042           }\r
1043           catch(Exception ex){}\r
1044         }\r
1045       }\r
1046     }\r
1047 \r
1048     // JBPNote\r
1049     // Should check to see if the server settings are valid\r
1050     // Need visual-delay indication here.\r
1051     public void run()\r
1052        {\r
1053          jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
1054          Vector sv = viewport.getAlignment().getSequences();\r
1055          SequenceI[] seqs = new SequenceI[sv.size()];\r
1056 \r
1057          int i = 0;\r
1058          do\r
1059          {\r
1060            seqs[i] = (SequenceI) sv.elementAt(i);\r
1061          }\r
1062          while (++i < sv.size());\r
1063 \r
1064          SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
1065 \r
1066          if (alignment != null)\r
1067          {\r
1068            AlignFrame af = new AlignFrame(new Alignment(alignment));\r
1069           af.clustalColour.setSelected(true);\r
1070           af.clustalColour_actionPerformed(null);\r
1071            Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
1072                                     700, 500); // JBPNote - is there a new window geom. property ?\r
1073          }\r
1074          else\r
1075            JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
1076                                          JOptionPane.WARNING_MESSAGE);\r
1077 \r
1078          webServiceRunning = false;\r
1079          try{\r
1080            frame.setClosed(true);\r
1081          }catch(Exception ex){}\r
1082        }\r
1083 \r
1084        public void paintComponent(Graphics g)\r
1085        {\r
1086          g.setColor(Color.white);\r
1087          g.fillRect(0,0,getWidth(), getHeight());\r
1088          if(image!=null)\r
1089          {\r
1090            g.drawImage(image[imageIndex],10,10,this);\r
1091          }\r
1092          g.setFont(new Font("Arial", Font.BOLD, 12));\r
1093          g.setColor(Color.black);\r
1094          g.drawString("Clustal Alignment Web Service running", 30,30);\r
1095        }\r
1096   }\r
1097 }\r