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     alignPanel = new AlignmentPanel(this, viewport);\r
  46     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
  47 \r
  48     addInternalFrameListener(new InternalFrameAdapter()\r
  49    {\r
  50      public void internalFrameActivated(InternalFrameEvent evt)\r
  51      {\r
  52           javax.swing.SwingUtilities.invokeLater(new Runnable()\r
  53           {\r
  54             public void run()\r
  55             {      alignPanel.requestFocus();    }\r
  56           });\r
  57 \r
  58      }\r
  59    });\r
  60 \r
  61   }\r
  62 \r
  63   protected void saveAs_actionPerformed(ActionEvent e)\r
  64   {\r
  65     String suffix [] = null;\r
  66     if(e.getActionCommand().equals("FASTA"))\r
  67       suffix = new String[]{"fa", "fasta"};\r
  68     else if(e.getActionCommand().equals("MSF"))\r
  69       suffix = new String[]{"msf"};\r
  70     else if(e.getActionCommand().equals("CLUSTAL"))\r
  71       suffix = new String[]{"aln"};\r
  72     else if(e.getActionCommand().equals("BLC"))\r
  73       suffix = new String[]{"blc"};\r
  74     else if(e.getActionCommand().equals("PIR"))\r
  75       suffix = new String[]{"pir"};\r
  76     else if(e.getActionCommand().equals("PFAM"))\r
  77       suffix = new String[]{"pfam"};\r
  78 \r
  79     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")\r
  80         , suffix, e.getActionCommand()+" file");\r
  81     chooser.setFileView(new JalviewFileView());\r
  82     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
  83     chooser.setToolTipText("Save");\r
  84     int value = chooser.showSaveDialog(this);\r
  85     if(value == JalviewFileChooser.APPROVE_OPTION)\r
  86     {\r
  87       String choice =  chooser.getSelectedFile().getPath();\r
  88       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
  89       String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
  90       try{\r
  91         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
  92         out.println(output);\r
  93         out.close();\r
  94       }\r
  95       catch(Exception ex){}\r
  96     }\r
  97 \r
  98   }\r
  99 \r
 100   protected void outputText_actionPerformed(ActionEvent e)\r
 101   {\r
 102      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
 103      JInternalFrame frame = new JInternalFrame();\r
 104      cap.formatForOutput();\r
 105      frame.setContentPane(cap);\r
 106      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
 107      cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
 108   }\r
 109 \r
 110   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 111   {\r
 112     HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
 113     htmlOutput = null;\r
 114   }\r
 115 \r
 116   protected void createPNG_actionPerformed(ActionEvent e)\r
 117   {\r
 118     alignPanel.makePNG();\r
 119   }\r
 120 \r
 121   protected void epsFile_actionPerformed(ActionEvent e)\r
 122   {\r
 123     alignPanel.makeEPS();\r
 124   }\r
 125 \r
 126 \r
 127   public void printMenuItem_actionPerformed(ActionEvent e)\r
 128   {\r
 129     //Putting in a thread avoids Swing painting problems\r
 130     PrintThread thread = new PrintThread();\r
 131     thread.start();\r
 132   }\r
 133 \r
 134   class PrintThread extends Thread\r
 135   {\r
 136     public void run()\r
 137     {\r
 138       PrinterJob printJob = PrinterJob.getPrinterJob();\r
 139       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
 140       printJob.setPrintable(alignPanel, pf);\r
 141       if (printJob.printDialog())\r
 142       {\r
 143         try\r
 144         {\r
 145           printJob.print();\r
 146         }\r
 147         catch (Exception PrintException)\r
 148         {\r
 149           PrintException.printStackTrace();\r
 150         }\r
 151       }\r
 152     }\r
 153 \r
 154   }\r
 155 \r
 156 \r
 157 \r
 158 \r
 159   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 160   {\r
 161     try{\r
 162       this.setClosed(true);\r
 163     }catch(Exception ex){}\r
 164   }\r
 165 \r
 166   Stack historyList = new Stack();\r
 167   Stack redoList = new Stack();\r
 168   JMenuBar jMenuBar1 = new JMenuBar();\r
 169 \r
 170   void updateEditMenuBar()\r
 171   {\r
 172     if(historyList.size()>0)\r
 173      {\r
 174        undoMenuItem.setEnabled(true);\r
 175        Object [] history = (Object[])historyList.get(0);\r
 176        undoMenuItem.setText("Undo "+history[0]);\r
 177      }\r
 178     else\r
 179     {\r
 180       undoMenuItem.setEnabled(false);\r
 181       undoMenuItem.setText("Undo");\r
 182     }\r
 183 \r
 184     if(redoList.size()>0)\r
 185      {\r
 186        redoMenuItem.setEnabled(true);\r
 187        Object [] history = (Object[])redoList.get(0);\r
 188        redoMenuItem.setText("Redo "+history[0]);\r
 189      }\r
 190     else\r
 191     {\r
 192       redoMenuItem.setEnabled(false);\r
 193       redoMenuItem.setText("Redo");\r
 194     }\r
 195   }\r
 196 \r
 197   public void addHistoryItem(String type)\r
 198   {\r
 199     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 200     redoList.clear();\r
 201     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 202     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 203     {\r
 204       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 205                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 206     }\r
 207 \r
 208     historyList.add(0, new Object[]{type,  seq} );\r
 209     updateEditMenuBar();\r
 210   }\r
 211 \r
 212   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 213   {\r
 214     Object [] history = (Object[])historyList.remove(0);\r
 215     // add the redo state before continuing!!\r
 216     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 217     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 218     {\r
 219       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 220                             viewport.getAlignment().getSequenceAt(i).\r
 221                             getSequence());\r
 222     }\r
 223     /////////\r
 224 \r
 225     redoList.add(0, new Object[] {history[0], seq});\r
 226 \r
 227       seq = (SequenceI[]) history[1];\r
 228       viewport.setAlignment( new Alignment(seq) );\r
 229       updateEditMenuBar();\r
 230       alignPanel.RefreshPanels();\r
 231   }\r
 232 \r
 233   public void moveSelectedSequences(boolean up)\r
 234   {\r
 235     SequenceGroup sg = viewport.getSelectionGroup();\r
 236     if (sg == null)\r
 237       return;\r
 238 \r
 239     if (up)\r
 240     {\r
 241       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 242       {\r
 243         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 244         if (!sg.sequences.contains(seq))\r
 245           continue;\r
 246 \r
 247         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 248         if (sg.sequences.contains(temp))\r
 249           continue;\r
 250 \r
 251         viewport.alignment.getSequences().setElementAt(temp, i);\r
 252         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 253       }\r
 254     }\r
 255     else\r
 256     {\r
 257       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 258       {\r
 259         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 260         if (!sg.sequences.contains(seq))\r
 261           continue;\r
 262 \r
 263         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 264         if (sg.sequences.contains(temp))\r
 265           continue;\r
 266 \r
 267         viewport.alignment.getSequences().setElementAt(temp, i);\r
 268         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 269       }\r
 270     }\r
 271 \r
 272     alignPanel.RefreshPanels();\r
 273   }\r
 274 \r
 275 \r
 276 \r
 277   protected void copy_actionPerformed(ActionEvent e)\r
 278   {\r
 279    if(viewport.getSelectionGroup()==null)\r
 280      return;\r
 281 \r
 282    SequenceGroup sg = viewport.getSelectionGroup();\r
 283 \r
 284      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 285      StringBuffer buffer= new StringBuffer();\r
 286 \r
 287        for(int i=0; i<sg.getSize(); i++)\r
 288        {\r
 289          SequenceI seq = sg.getSequenceAt(i);\r
 290          buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
 291                         +seq.findPosition( sg.getEndRes() )+ "\t"\r
 292                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
 293        }\r
 294      c.setContents( new StringSelection( buffer.toString()) , null ) ;\r
 295 \r
 296   }\r
 297 \r
 298 \r
 299   protected void pasteNew_actionPerformed(ActionEvent e)\r
 300   {\r
 301     paste(true);\r
 302   }\r
 303 \r
 304   protected void pasteThis_actionPerformed(ActionEvent e)\r
 305   {\r
 306     addHistoryItem("Paste");\r
 307     paste(false);\r
 308   }\r
 309 \r
 310   void paste(boolean newAlignment)\r
 311   {\r
 312     try{\r
 313       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 314       Transferable contents = c.getContents(this);\r
 315       if (contents == null)\r
 316         return;\r
 317 \r
 318       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
 319       StringTokenizer st = new StringTokenizer(str);\r
 320       ArrayList seqs = new ArrayList();\r
 321       while (st.hasMoreElements())\r
 322       {\r
 323         String name = st.nextToken();\r
 324         int start = Integer.parseInt(st.nextToken());\r
 325         int end = Integer.parseInt(st.nextToken());\r
 326         Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
 327 \r
 328         if(!newAlignment)\r
 329           viewport.alignment.addSequence(sequence);\r
 330         else\r
 331           seqs.add(sequence);\r
 332       }\r
 333 \r
 334       if(newAlignment)\r
 335       {\r
 336         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 337         seqs.toArray(newSeqs);\r
 338         AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
 339         int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;\r
 340         if (newHeight > 500)\r
 341           newHeight = 500;\r
 342         Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
 343       }\r
 344       else\r
 345       {\r
 346         viewport.setEndSeq(viewport.alignment.getHeight());\r
 347         viewport.alignment.getWidth();\r
 348         alignPanel.RefreshPanels();\r
 349       }\r
 350 \r
 351     }catch(Exception ex){}// could be anything being pasted in here\r
 352 \r
 353   }\r
 354 \r
 355 \r
 356   protected void cut_actionPerformed(ActionEvent e)\r
 357   {\r
 358     copy_actionPerformed(null);\r
 359     delete_actionPerformed(null);\r
 360   }\r
 361 \r
 362   protected void delete_actionPerformed(ActionEvent e)\r
 363   {\r
 364     addHistoryItem("Delete");\r
 365     if (viewport.getSelectionGroup() == null)\r
 366       return;\r
 367 \r
 368      SequenceGroup sg = viewport.getSelectionGroup();\r
 369      for (int i=0;i < sg.sequences.size(); i++)\r
 370      {\r
 371        SequenceI seq = sg.getSequenceAt(i);\r
 372        int index = viewport.getAlignment().findIndex(seq);\r
 373        seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);\r
 374 \r
 375        if(seq.getSequence().length()<1)\r
 376           viewport.getAlignment().deleteSequence(seq);\r
 377       else\r
 378           viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 379      }\r
 380 \r
 381      viewport.setSelectionGroup(null);\r
 382      viewport.alignment.deleteGroup(sg);\r
 383      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
 384      if(viewport.getAlignment().getHeight()<1)\r
 385      try\r
 386      {\r
 387        this.setClosed(true);\r
 388      }catch(Exception ex){}\r
 389      alignPanel.RefreshPanels();\r
 390 \r
 391   }\r
 392 \r
 393 \r
 394 \r
 395   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 396   {\r
 397      Object [] history = (Object[])redoList.remove(0);\r
 398      SequenceI[] seq = (SequenceI[]) history[1];\r
 399      viewport.setAlignment( new Alignment(seq) );\r
 400      updateEditMenuBar();\r
 401      alignPanel.RefreshPanels();\r
 402   }\r
 403 \r
 404 \r
 405   public void groupsMenuItem_actionPerformed(ActionEvent e)\r
 406   {\r
 407     GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
 408     JInternalFrame frame = new JInternalFrame();\r
 409     frame.setContentPane(geditor);\r
 410     Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
 411     frame.setResizable(false);\r
 412   }\r
 413 \r
 414   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 415   {\r
 416     viewport.alignment.deleteAllGroups();\r
 417     viewport.setSelectionGroup(null);\r
 418 \r
 419     alignPanel.RefreshPanels();\r
 420   }\r
 421 \r
 422 \r
 423 \r
 424   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 425   {\r
 426     SequenceGroup sg = new SequenceGroup();\r
 427     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 428       sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
 429     sg.setEndRes(viewport.alignment.getWidth());\r
 430     viewport.setSelectionGroup(sg);\r
 431     PaintRefresher.Refresh(null);\r
 432   }\r
 433 \r
 434   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 435   {\r
 436     viewport.setSelectionGroup(null);\r
 437     PaintRefresher.Refresh(null);\r
 438   }\r
 439 \r
 440   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 441   {\r
 442     SequenceGroup sg = viewport.getSelectionGroup();\r
 443     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 444       sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
 445 \r
 446     PaintRefresher.Refresh(null);\r
 447   }\r
 448 \r
 449 \r
 450   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 451   {\r
 452     viewport.getColumnSelection().clear();\r
 453     repaint();\r
 454   }\r
 455 \r
 456   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 457   {\r
 458     addHistoryItem("delete columns");\r
 459     ColumnSelection colSel = viewport.getColumnSelection();\r
 460     if (colSel.size() > 0)\r
 461     {\r
 462       int min = colSel.getMin();\r
 463       viewport.getAlignment().trimLeft(min);\r
 464       colSel.compensateForEdit(0,min);\r
 465 \r
 466       if(viewport.getSelectionGroup()!=null)\r
 467         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 468 \r
 469       Vector groups = viewport.alignment.getGroups();\r
 470       for(int i=0; i<groups.size(); i++)\r
 471       {\r
 472         SequenceGroup sg = (SequenceGroup) groups.get(i);\r
 473         if(!sg.adjustForRemoveLeft(min))\r
 474           viewport.alignment.deleteGroup(sg);\r
 475       }\r
 476 \r
 477       alignPanel.RefreshPanels();\r
 478     }\r
 479   }\r
 480 \r
 481   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 482   {\r
 483     addHistoryItem("delete columns");\r
 484     ColumnSelection colSel = viewport.getColumnSelection();\r
 485     if (colSel.size() > 0)\r
 486     {\r
 487       int max = colSel.getMax();\r
 488       viewport.getAlignment().trimRight(max);\r
 489       if(viewport.getSelectionGroup()!=null)\r
 490         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 491 \r
 492       Vector groups = viewport.alignment.getGroups();\r
 493       for(int i=0; i<groups.size(); i++)\r
 494       {\r
 495         SequenceGroup sg = (SequenceGroup) groups.get(i);\r
 496         if(!sg.adjustForRemoveRight(max))\r
 497           viewport.alignment.deleteGroup(sg);\r
 498       }\r
 499 \r
 500 \r
 501 \r
 502       alignPanel.RefreshPanels();\r
 503     }\r
 504 \r
 505   }\r
 506 \r
 507   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 508   {\r
 509     addHistoryItem("delete gapped columns");\r
 510     viewport.getAlignment().removeGaps();\r
 511     alignPanel.RefreshPanels();\r
 512   }\r
 513 \r
 514   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 515   {\r
 516     addHistoryItem("delete all gaps");\r
 517     SequenceI current;\r
 518     int jSize;\r
 519     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 520     {\r
 521       current = viewport.getAlignment().getSequenceAt(i);\r
 522       jSize = current.getLength();\r
 523       for (int j=0; j < jSize; j++)\r
 524         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 525         {\r
 526           current.deleteCharAt(j);\r
 527           j--;\r
 528           jSize--;\r
 529         }\r
 530     }\r
 531 \r
 532     alignPanel.RefreshPanels();\r
 533   }\r
 534 \r
 535   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 536   {\r
 537     char thisChar = '-';\r
 538     char nextChar = '.';\r
 539     if(viewport.getGapCharacter()=='-')\r
 540     {\r
 541       thisChar = '.';\r
 542       nextChar = '-';\r
 543     }\r
 544     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 545     viewport.setGapCharacter(thisChar);\r
 546     alignPanel.RefreshPanels();\r
 547   }\r
 548 \r
 549   public void findMenuItem_actionPerformed(ActionEvent e)\r
 550   {\r
 551       JInternalFrame frame = new JInternalFrame();\r
 552       Finder finder = new Finder(viewport, alignPanel, frame);\r
 553       frame.setContentPane(finder);\r
 554      Desktop.addInternalFrame(frame, "Find", 340,110);\r
 555 \r
 556   }\r
 557 \r
 558 \r
 559   public void font_actionPerformed(ActionEvent e)\r
 560   {\r
 561    // JOptionPane op = new JOptionPane();\r
 562     JInternalFrame frame = new JInternalFrame();\r
 563     FontChooser fc = new FontChooser( alignPanel, frame );\r
 564     frame.setContentPane(fc);\r
 565     Desktop.addInternalFrame(frame, "Change Font", 480,100);\r
 566   }\r
 567 \r
 568   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 569   {\r
 570     viewport.setShowFullId( fullSeqId.isSelected() );\r
 571 \r
 572     alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );\r
 573     alignPanel.RefreshPanels();\r
 574   }\r
 575 \r
 576   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 577   {\r
 578       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 579       alignPanel.RefreshPanels();\r
 580   }\r
 581 \r
 582   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 583   {\r
 584     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 585     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
 586   }\r
 587 \r
 588 \r
 589   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 590   {\r
 591     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 592     alignPanel.RefreshPanels();\r
 593   }\r
 594 \r
 595   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 596   {\r
 597     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 598     alignPanel.RefreshPanels();\r
 599   }\r
 600 \r
 601 \r
 602   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 603   {\r
 604     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 605     alignPanel.RefreshPanels();\r
 606   }\r
 607 \r
 608   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 609   {\r
 610     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 611     if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
 612     {\r
 613          AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);\r
 614          ((Alignment)viewport.alignment).featuresAdded = true;\r
 615     }\r
 616     alignPanel.RefreshPanels();\r
 617   }\r
 618 \r
 619   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 620   {\r
 621     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
 622   }\r
 623 \r
 624   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 625   {\r
 626     if (alignPanel.overviewPanel != null)\r
 627       return;\r
 628 \r
 629     JInternalFrame frame = new JInternalFrame();\r
 630     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 631    try{\r
 632      overview = new OverviewPanel(alignPanel, viewport);\r
 633      frame.setContentPane(overview);\r
 634     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 635                              frame.getWidth(), frame.getHeight());\r
 636     frame.pack();\r
 637     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 638     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 639       {\r
 640             alignPanel.setOverviewPanel(null);\r
 641       };\r
 642     });\r
 643     alignPanel.setOverviewPanel( overview );\r
 644 \r
 645   }catch(java.lang.OutOfMemoryError ex)\r
 646    {\r
 647      JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 648                                    +"\nTry reducing the font size.",\r
 649                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 650    }\r
 651 \r
 652 \r
 653   }\r
 654 \r
 655   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 656   {\r
 657     changeColour( null );\r
 658   }\r
 659 \r
 660 \r
 661   public void clustalColour_actionPerformed(ActionEvent e)\r
 662   {\r
 663     abovePIDThreshold.setSelected(false);\r
 664     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 665   }\r
 666 \r
 667   public void zappoColour_actionPerformed(ActionEvent e)\r
 668   {\r
 669     changeColour(new ZappoColourScheme());\r
 670   }\r
 671 \r
 672   public void taylorColour_actionPerformed(ActionEvent e)\r
 673   {\r
 674     changeColour(new TaylorColourScheme());\r
 675   }\r
 676 \r
 677 \r
 678   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 679   {\r
 680     changeColour( new HydrophobicColourScheme() );\r
 681   }\r
 682 \r
 683   public void helixColour_actionPerformed(ActionEvent e)\r
 684   {\r
 685     changeColour(new HelixColourScheme() );\r
 686   }\r
 687 \r
 688 \r
 689   public void strandColour_actionPerformed(ActionEvent e)\r
 690   {\r
 691     changeColour(new StrandColourScheme());\r
 692   }\r
 693 \r
 694 \r
 695   public void turnColour_actionPerformed(ActionEvent e)\r
 696   {\r
 697     changeColour(new TurnColourScheme());\r
 698   }\r
 699 \r
 700 \r
 701   public void buriedColour_actionPerformed(ActionEvent e)\r
 702   {\r
 703     changeColour(new BuriedColourScheme() );\r
 704   }\r
 705 \r
 706   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 707   {\r
 708     changeColour(new NucleotideColourScheme());\r
 709   }\r
 710 \r
 711 \r
 712   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 713   {\r
 714     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
 715   }\r
 716 \r
 717 \r
 718 \r
 719   void changeColour(ColourSchemeI cs)\r
 720   {\r
 721 \r
 722     if(viewport.getColourAppliesToAllGroups())\r
 723     {\r
 724       Vector groups = viewport.alignment.getGroups();\r
 725       for(int i=0; i<groups.size(); i++)\r
 726       {\r
 727         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 728         sg.cs = cs;\r
 729 \r
 730         if(abovePIDThreshold.isSelected())\r
 731           abovePIDThreshold_actionPerformed(null);\r
 732         else if( viewport.getConservationSelected() )\r
 733         {\r
 734           Conservation c = new Conservation("Group",\r
 735                                             ResidueProperties.propHash, 3,\r
 736                                             sg.sequences, sg.getStartRes(),\r
 737                                             sg.getEndRes());\r
 738           c.calculate();\r
 739           c.verdict(false, 100);\r
 740           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 741 \r
 742           sg.cs = ccs;\r
 743         }\r
 744 \r
 745       }\r
 746     }\r
 747 \r
 748 \r
 749     if ( viewport.getAbovePIDThreshold())\r
 750     {\r
 751       int threshold = 0;\r
 752       threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");\r
 753       Desktop.hideConservationSlider();\r
 754 \r
 755       if (cs instanceof ResidueColourScheme)\r
 756         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 757       else if (cs instanceof ScoreColourScheme)\r
 758         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 759 \r
 760       viewport.setGlobalColourScheme(cs);\r
 761 \r
 762     }\r
 763     else\r
 764     if (cs instanceof ResidueColourScheme)\r
 765       ( (ResidueColourScheme) cs).setThreshold(0);\r
 766     else if (cs instanceof ScoreColourScheme)\r
 767       ( (ScoreColourScheme) cs).setThreshold(0);\r
 768 \r
 769 \r
 770 \r
 771 \r
 772 if ( viewport.getConservationSelected() )\r
 773  {\r
 774    ConservationColourScheme ccs = null;\r
 775 \r
 776    Alignment al = (Alignment) viewport.alignment;\r
 777    Conservation c = new Conservation("All",\r
 778                                      ResidueProperties.propHash, 3,\r
 779                                      al.getSequences(), 0,\r
 780                                      al.getWidth());\r
 781 \r
 782    c.calculate();\r
 783    c.verdict(false, 100);\r
 784 \r
 785    ccs = new ConservationColourScheme(c, cs);\r
 786 \r
 787    int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,\r
 788        "Background");\r
 789 \r
 790    ccs.inc = threshold;\r
 791 \r
 792    viewport.setGlobalColourScheme(ccs);\r
 793 \r
 794   }\r
 795   else\r
 796        viewport.setGlobalColourScheme( cs );\r
 797 \r
 798     alignPanel.RefreshPanels();\r
 799   }\r
 800 \r
 801 \r
 802   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 803   {\r
 804     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 805     if(coloursChanging)\r
 806       return;\r
 807 \r
 808     coloursChanging = true;\r
 809 \r
 810     viewport.setAbovePIDThreshold(false);\r
 811     abovePIDThreshold.setSelected(false);\r
 812     Desktop.hidePIDSlider();\r
 813     if(!viewport.getConservationSelected())\r
 814       Desktop.hideConservationSlider();\r
 815 \r
 816    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 817    if(cs instanceof ConservationColourScheme )\r
 818      changeColour( ((ConservationColourScheme)cs).cs );\r
 819     else\r
 820       changeColour( cs );\r
 821 \r
 822     coloursChanging = false;\r
 823   }\r
 824 \r
 825   boolean coloursChanging = false;\r
 826   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 827   {\r
 828     if(coloursChanging)\r
 829       return;\r
 830 \r
 831     coloursChanging = true;\r
 832     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
 833 \r
 834     conservationMenuItem.setSelected(false);\r
 835     viewport.setConservationSelected(false);\r
 836     Desktop.hideConservationSlider();\r
 837 \r
 838     if(!viewport.getAbovePIDThreshold())\r
 839       Desktop.hidePIDSlider();\r
 840 \r
 841 \r
 842     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 843     if(cs instanceof ConservationColourScheme )\r
 844         changeColour( ((ConservationColourScheme)cs).cs );\r
 845     else\r
 846         changeColour( cs );\r
 847 \r
 848     coloursChanging = false;\r
 849   }\r
 850 \r
 851 \r
 852 \r
 853   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 854   {\r
 855     JInternalFrame frame = new JInternalFrame();\r
 856     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 857     frame.setContentPane(chooser);\r
 858     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 859     frame.setResizable(false);\r
 860     frame.setIconifiable(false);\r
 861     frame.setMaximizable(false);\r
 862   }\r
 863 \r
 864   public void PIDColour_actionPerformed(ActionEvent e)\r
 865   {\r
 866     changeColour( new PIDColourScheme() );\r
 867   }\r
 868 \r
 869 \r
 870   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 871   {\r
 872     changeColour(new Blosum62ColourScheme(viewport) );\r
 873   }\r
 874 \r
 875 \r
 876 \r
 877   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 878   {\r
 879     addHistoryItem("sort");\r
 880     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 881     alignPanel.RefreshPanels();\r
 882   }\r
 883 \r
 884   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 885   {\r
 886     addHistoryItem("sort");\r
 887     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 888     alignPanel.RefreshPanels();\r
 889   }\r
 890 \r
 891   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 892   {\r
 893     addHistoryItem("sort");\r
 894     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 895     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 896     alignPanel.RefreshPanels();\r
 897   }\r
 898 \r
 899   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 900   {\r
 901     addHistoryItem("sort");\r
 902     if(viewport.getCurrentTree()==null)\r
 903       return;\r
 904 \r
 905     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 906     alignPanel.RefreshPanels();\r
 907   }\r
 908 \r
 909   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 910   {\r
 911     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 912     JInternalFrame frame = new JInternalFrame();\r
 913     frame.setContentPane(sp);\r
 914     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
 915     frame.setMaximizable(false);\r
 916     frame.setResizable(false);\r
 917 \r
 918   }\r
 919 \r
 920   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 921   {\r
 922     if(viewport.getSelectionGroup().getSize()<2)\r
 923       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 924     else\r
 925     {\r
 926       JInternalFrame frame = new JInternalFrame();\r
 927       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 928       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 929     }\r
 930   }\r
 931 \r
 932   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 933   {\r
 934 \r
 935     if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
 936        || viewport.getAlignment().getHeight()<4)\r
 937     {\r
 938       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 939                                     +"at least 4 input sequences.",\r
 940                                     "Sequence selection insufficient",\r
 941                                     JOptionPane.WARNING_MESSAGE);\r
 942       return;\r
 943     }\r
 944 \r
 945     try{\r
 946       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 947       JInternalFrame frame = new JInternalFrame();\r
 948       frame.setContentPane(pcaPanel);\r
 949       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 950    }catch(java.lang.OutOfMemoryError ex)\r
 951    {\r
 952      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 953                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 954    }\r
 955 \r
 956 \r
 957   }\r
 958 \r
 959   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 960   {\r
 961     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 962   }\r
 963 \r
 964   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 965   {\r
 966     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 967   }\r
 968 \r
 969 \r
 970   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 971   {\r
 972     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 973   }\r
 974 \r
 975   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 976   {\r
 977     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 978   }\r
 979 \r
 980   void NewTreePanel(String type, String pwType, String title)\r
 981   {\r
 982     //are the sequences aligned?\r
 983     if(!viewport.alignment.isAligned())\r
 984     {\r
 985       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
 986                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
 987       return;\r
 988     }\r
 989 \r
 990     TreePanel tp=null;\r
 991    if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)\r
 992    {\r
 993      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,\r
 994                          0, viewport.alignment.getWidth());\r
 995    }\r
 996    else\r
 997    {\r
 998      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 999                          type, pwType,  0, viewport.alignment.getWidth());\r
1000    }\r
1001 \r
1002    Desktop.addInternalFrame(tp, title, 600, 500);\r
1003   }\r
1004 \r
1005 \r
1006 \r
1007 \r
1008   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
1009   {\r
1010     JInternalFrame frame = new JInternalFrame();\r
1011     ClustalThread ct = new ClustalThread(frame);\r
1012     Thread t = new Thread(ct);\r
1013     t.start();\r
1014     frame.setContentPane(ct);\r
1015      Desktop.addInternalFrame(frame, title, 300, 80);\r
1016 \r
1017   }\r
1018 \r
1019   class ClustalThread extends JPanel implements Runnable\r
1020   {\r
1021     Image [] image;\r
1022     int imageIndex = 0;\r
1023     boolean webServiceRunning = false;\r
1024     JInternalFrame frame;\r
1025     public ClustalThread(JInternalFrame frame)\r
1026     {\r
1027       this.frame = frame;\r
1028       image = new Image[9];\r
1029       for(int i=0; i<9; i++)\r
1030       {\r
1031         java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");\r
1032         if (url != null)\r
1033         {\r
1034           image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
1035           MediaTracker mt = new MediaTracker(this);\r
1036           mt.addImage(image[i], i);\r
1037           try{mt.waitForID(i);}\r
1038           catch(Exception ex){}\r
1039         }\r
1040       }\r
1041       DNATwirler twirler = new DNATwirler();\r
1042       twirler.start();\r
1043       webServiceRunning = true;\r
1044     }\r
1045 \r
1046     class DNATwirler extends Thread\r
1047     {\r
1048       public void run()\r
1049       {\r
1050         while(webServiceRunning)\r
1051         {\r
1052           try{\r
1053             Thread.sleep(100);\r
1054             imageIndex++;\r
1055             imageIndex %=9;\r
1056             repaint();\r
1057           }\r
1058           catch(Exception ex){}\r
1059         }\r
1060       }\r
1061     }\r
1062 \r
1063     // JBPNote\r
1064     // Should check to see if the server settings are valid\r
1065     // Need visual-delay indication here.\r
1066     public void run()\r
1067        {\r
1068          jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
1069          Vector sv = viewport.getAlignment().getSequences();\r
1070          SequenceI[] seqs = new SequenceI[sv.size()];\r
1071 \r
1072          int i = 0;\r
1073          do\r
1074          {\r
1075            seqs[i] = (SequenceI) sv.elementAt(i);\r
1076          }\r
1077          while (++i < sv.size());\r
1078 \r
1079          SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
1080 \r
1081          if (alignment != null)\r
1082          {\r
1083            AlignFrame af = new AlignFrame(new Alignment(alignment));\r
1084           af.clustalColour.setSelected(true);\r
1085           af.clustalColour_actionPerformed(null);\r
1086            Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
1087                                     700, 500); // JBPNote - is there a new window geom. property ?\r
1088          }\r
1089          else\r
1090            JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
1091                                          JOptionPane.WARNING_MESSAGE);\r
1092 \r
1093          webServiceRunning = false;\r
1094          try{\r
1095            frame.setClosed(true);\r
1096          }catch(Exception ex){}\r
1097        }\r
1098 \r
1099        public void paintComponent(Graphics g)\r
1100        {\r
1101          g.setColor(Color.white);\r
1102          g.fillRect(0,0,getWidth(), getHeight());\r
1103          if(image!=null)\r
1104          {\r
1105            g.drawImage(image[imageIndex],10,10,this);\r
1106          }\r
1107          g.setFont(new Font("Arial", Font.BOLD, 12));\r
1108          g.setColor(Color.black);\r
1109          g.drawString("Clustal Alignment Web Service running", 30,30);\r
1110        }\r
1111   }\r
1112   public void jpredMenuItem_actionPerformed(ActionEvent e)\r
1113     {\r
1114     //  JInternalFrame frame = new JInternalFrame();\r
1115 //      JPredClient ct = new JPredClient((SequenceI)\r
1116     ///                                   viewport.getAlignment().getSequences().elementAt(0));\r
1117     }\r
1118 \r
1119     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
1120     // Pick the tree file\r
1121     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
1122         getProperty("LAST_DIRECTORY"));\r
1123     chooser.setFileView(new JalviewFileView());\r
1124     chooser.setDialogTitle("Select a newick-like tree file");\r
1125     chooser.setToolTipText("Load a tree file");\r
1126     int value = chooser.showOpenDialog(null);\r
1127     if (value == JalviewFileChooser.APPROVE_OPTION)\r
1128     {\r
1129       String choice = chooser.getSelectedFile().getPath();\r
1130       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1131       TreePanel treepanel = null;\r
1132       try\r
1133       {\r
1134         jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");\r
1135         fin.parse();\r
1136 \r
1137         if (fin.getTree() != null)\r
1138         {\r
1139           TreePanel tp = null;\r
1140           tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1141                              fin, "FromFile", choice);\r
1142           Desktop.addInternalFrame(tp, title, 600, 500);\r
1143         }\r
1144       }\r
1145       catch (Exception ex)\r
1146       {\r
1147         JOptionPane.showMessageDialog(Desktop.desktop,\r
1148                                       "Problem reading tree file",\r
1149                                       ex.getMessage(),\r
1150                                       JOptionPane.WARNING_MESSAGE);\r
1151         ex.printStackTrace();\r
1152       }\r
1153     }\r
1154   }\r
1155 \r
1156 }\r