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       alignPanel.RefreshPanels();\r
 466     }\r
 467   }\r
 468 \r
 469   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 470   {\r
 471     addHistoryItem("delete columns");\r
 472     ColumnSelection colSel = viewport.getColumnSelection();\r
 473     if (colSel.size() > 0)\r
 474     {\r
 475       int max = colSel.getMax();\r
 476       if(max>1)\r
 477         viewport.getAlignment().trimRight(max);\r
 478 \r
 479       alignPanel.RefreshPanels();\r
 480     }\r
 481 \r
 482   }\r
 483 \r
 484   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 485   {\r
 486     addHistoryItem("delete gapped columns");\r
 487     viewport.getAlignment().removeGaps();\r
 488     alignPanel.RefreshPanels();\r
 489   }\r
 490 \r
 491   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 492   {\r
 493     addHistoryItem("delete all gaps");\r
 494     SequenceI current;\r
 495     int jSize;\r
 496     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 497     {\r
 498       current = viewport.getAlignment().getSequenceAt(i);\r
 499       jSize = current.getLength();\r
 500       for (int j=0; j < jSize; j++)\r
 501         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 502         {\r
 503           current.deleteCharAt(j);\r
 504           j--;\r
 505           jSize--;\r
 506         }\r
 507     }\r
 508 \r
 509     alignPanel.RefreshPanels();\r
 510   }\r
 511 \r
 512   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 513   {\r
 514     char thisChar = '-';\r
 515     char nextChar = '.';\r
 516     if(viewport.getGapCharacter()=='-')\r
 517     {\r
 518       thisChar = '.';\r
 519       nextChar = '-';\r
 520     }\r
 521     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 522     viewport.setGapCharacter(thisChar);\r
 523     alignPanel.RefreshPanels();\r
 524   }\r
 525 \r
 526   public void findMenuItem_actionPerformed(ActionEvent e)\r
 527   {\r
 528       JInternalFrame frame = new JInternalFrame();\r
 529       Finder finder = new Finder(viewport, alignPanel, frame);\r
 530       frame.setContentPane(finder);\r
 531      Desktop.addInternalFrame(frame, "Find", 340,110);\r
 532 \r
 533   }\r
 534 \r
 535 \r
 536   public void font_actionPerformed(ActionEvent e)\r
 537   {\r
 538    // JOptionPane op = new JOptionPane();\r
 539     JInternalFrame frame = new JInternalFrame();\r
 540     FontChooser fc = new FontChooser( alignPanel, frame );\r
 541     frame.setContentPane(fc);\r
 542     Desktop.addInternalFrame(frame, "Change Font", 480,100);\r
 543   }\r
 544 \r
 545   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 546   {\r
 547     viewport.setShowFullId( fullSeqId.isSelected() );\r
 548 \r
 549     alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );\r
 550     alignPanel.RefreshPanels();\r
 551   }\r
 552 \r
 553   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 554   {\r
 555       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 556       alignPanel.RefreshPanels();\r
 557   }\r
 558 \r
 559   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 560   {\r
 561     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 562     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
 563   }\r
 564 \r
 565 \r
 566   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 567   {\r
 568     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 569     alignPanel.RefreshPanels();\r
 570   }\r
 571 \r
 572   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 573   {\r
 574     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 575     alignPanel.RefreshPanels();\r
 576   }\r
 577 \r
 578 \r
 579   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 580   {\r
 581     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 582     alignPanel.RefreshPanels();\r
 583   }\r
 584 \r
 585   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 586   {\r
 587     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 588     if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
 589     {\r
 590          AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);\r
 591          ((Alignment)viewport.alignment).featuresAdded = true;\r
 592     }\r
 593     alignPanel.RefreshPanels();\r
 594   }\r
 595 \r
 596   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 597   {\r
 598     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
 599   }\r
 600 \r
 601   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 602   {\r
 603     if (alignPanel.overviewPanel != null)\r
 604       return;\r
 605 \r
 606     JInternalFrame frame = new JInternalFrame();\r
 607     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 608    try{\r
 609      overview = new OverviewPanel(alignPanel, viewport);\r
 610      frame.setContentPane(overview);\r
 611     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 612                              frame.getWidth(), frame.getHeight());\r
 613     frame.pack();\r
 614     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 615     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 616       {\r
 617             alignPanel.setOverviewPanel(null);\r
 618       };\r
 619     });\r
 620     alignPanel.setOverviewPanel( overview );\r
 621 \r
 622   }catch(java.lang.OutOfMemoryError ex)\r
 623    {\r
 624      JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 625                                    +"\nTry reducing the font size.",\r
 626                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 627    }\r
 628 \r
 629 \r
 630   }\r
 631 \r
 632   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 633   {\r
 634     changeColour( null );\r
 635   }\r
 636 \r
 637 \r
 638   public void clustalColour_actionPerformed(ActionEvent e)\r
 639   {\r
 640     abovePIDThreshold.setSelected(false);\r
 641     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 642   }\r
 643 \r
 644   public void zappoColour_actionPerformed(ActionEvent e)\r
 645   {\r
 646     changeColour(new ZappoColourScheme());\r
 647   }\r
 648 \r
 649   public void taylorColour_actionPerformed(ActionEvent e)\r
 650   {\r
 651     changeColour(new TaylorColourScheme());\r
 652   }\r
 653 \r
 654 \r
 655   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 656   {\r
 657     changeColour( new HydrophobicColourScheme() );\r
 658   }\r
 659 \r
 660   public void helixColour_actionPerformed(ActionEvent e)\r
 661   {\r
 662     changeColour(new HelixColourScheme() );\r
 663   }\r
 664 \r
 665 \r
 666   public void strandColour_actionPerformed(ActionEvent e)\r
 667   {\r
 668     changeColour(new StrandColourScheme());\r
 669   }\r
 670 \r
 671 \r
 672   public void turnColour_actionPerformed(ActionEvent e)\r
 673   {\r
 674     changeColour(new TurnColourScheme());\r
 675   }\r
 676 \r
 677 \r
 678   public void buriedColour_actionPerformed(ActionEvent e)\r
 679   {\r
 680     changeColour(new BuriedColourScheme() );\r
 681   }\r
 682 \r
 683   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 684   {\r
 685     changeColour(new NucleotideColourScheme());\r
 686   }\r
 687 \r
 688 \r
 689   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 690   {\r
 691     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
 692   }\r
 693 \r
 694 \r
 695 \r
 696   void changeColour(ColourSchemeI cs)\r
 697   {\r
 698 \r
 699     if(viewport.getColourAppliesToAllGroups())\r
 700     {\r
 701       Vector groups = viewport.alignment.getGroups();\r
 702       for(int i=0; i<groups.size(); i++)\r
 703       {\r
 704         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 705         sg.cs = cs;\r
 706 \r
 707         if(abovePIDThreshold.isSelected())\r
 708           abovePIDThreshold_actionPerformed(null);\r
 709         else if( viewport.getConservationSelected() )\r
 710         {\r
 711           Conservation c = new Conservation("Group",\r
 712                                             ResidueProperties.propHash, 3,\r
 713                                             sg.sequences, sg.getStartRes(),\r
 714                                             sg.getEndRes());\r
 715           c.calculate();\r
 716           c.verdict(false, 100);\r
 717           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 718 \r
 719           sg.cs = ccs;\r
 720         }\r
 721 \r
 722       }\r
 723     }\r
 724 \r
 725 \r
 726     if ( viewport.getAbovePIDThreshold())\r
 727     {\r
 728       int threshold = 0;\r
 729       threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");\r
 730       Desktop.hideConservationSlider();\r
 731 \r
 732       if (cs instanceof ResidueColourScheme)\r
 733         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 734       else if (cs instanceof ScoreColourScheme)\r
 735         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 736 \r
 737       viewport.setGlobalColourScheme(cs);\r
 738 \r
 739     }\r
 740     else\r
 741     if (cs instanceof ResidueColourScheme)\r
 742       ( (ResidueColourScheme) cs).setThreshold(0);\r
 743     else if (cs instanceof ScoreColourScheme)\r
 744       ( (ScoreColourScheme) cs).setThreshold(0);\r
 745 \r
 746 \r
 747 \r
 748 \r
 749 if ( viewport.getConservationSelected() )\r
 750  {\r
 751    ConservationColourScheme ccs = null;\r
 752 \r
 753    Alignment al = (Alignment) viewport.alignment;\r
 754    Conservation c = new Conservation("All",\r
 755                                      ResidueProperties.propHash, 3,\r
 756                                      al.getSequences(), 0,\r
 757                                      al.getWidth());\r
 758 \r
 759    c.calculate();\r
 760    c.verdict(false, 100);\r
 761 \r
 762    ccs = new ConservationColourScheme(c, cs);\r
 763 \r
 764    int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,\r
 765        "Background");\r
 766 \r
 767    ccs.inc = threshold;\r
 768 \r
 769    viewport.setGlobalColourScheme(ccs);\r
 770 \r
 771   }\r
 772   else\r
 773        viewport.setGlobalColourScheme( cs );\r
 774 \r
 775     alignPanel.RefreshPanels();\r
 776   }\r
 777 \r
 778 \r
 779   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 780   {\r
 781     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 782     if(coloursChanging)\r
 783       return;\r
 784 \r
 785     coloursChanging = true;\r
 786 \r
 787     viewport.setAbovePIDThreshold(false);\r
 788     abovePIDThreshold.setSelected(false);\r
 789     Desktop.hidePIDSlider();\r
 790     if(!viewport.getConservationSelected())\r
 791       Desktop.hideConservationSlider();\r
 792 \r
 793    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 794    if(cs instanceof ConservationColourScheme )\r
 795      changeColour( ((ConservationColourScheme)cs).cs );\r
 796     else\r
 797       changeColour( cs );\r
 798 \r
 799     coloursChanging = false;\r
 800   }\r
 801 \r
 802   boolean coloursChanging = false;\r
 803   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 804   {\r
 805     if(coloursChanging)\r
 806       return;\r
 807 \r
 808     coloursChanging = true;\r
 809     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
 810 \r
 811     conservationMenuItem.setSelected(false);\r
 812     viewport.setConservationSelected(false);\r
 813     Desktop.hideConservationSlider();\r
 814 \r
 815     if(!viewport.getAbovePIDThreshold())\r
 816       Desktop.hidePIDSlider();\r
 817 \r
 818 \r
 819     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 820     if(cs instanceof ConservationColourScheme )\r
 821         changeColour( ((ConservationColourScheme)cs).cs );\r
 822     else\r
 823         changeColour( cs );\r
 824 \r
 825     coloursChanging = false;\r
 826   }\r
 827 \r
 828 \r
 829 \r
 830   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 831   {\r
 832     JInternalFrame frame = new JInternalFrame();\r
 833     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 834     frame.setContentPane(chooser);\r
 835     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 836     frame.setResizable(false);\r
 837     frame.setIconifiable(false);\r
 838     frame.setMaximizable(false);\r
 839   }\r
 840 \r
 841   public void PIDColour_actionPerformed(ActionEvent e)\r
 842   {\r
 843     changeColour( new PIDColourScheme() );\r
 844   }\r
 845 \r
 846 \r
 847   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 848   {\r
 849     changeColour(new Blosum62ColourScheme(viewport) );\r
 850   }\r
 851 \r
 852 \r
 853 \r
 854   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 855   {\r
 856     addHistoryItem("sort");\r
 857     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 858     alignPanel.RefreshPanels();\r
 859   }\r
 860 \r
 861   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 862   {\r
 863     addHistoryItem("sort");\r
 864     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 865     alignPanel.RefreshPanels();\r
 866   }\r
 867 \r
 868   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 869   {\r
 870     addHistoryItem("sort");\r
 871     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 872     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 873     alignPanel.RefreshPanels();\r
 874   }\r
 875 \r
 876   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 877   {\r
 878     addHistoryItem("sort");\r
 879     if(viewport.getCurrentTree()==null)\r
 880       return;\r
 881 \r
 882     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 883     alignPanel.RefreshPanels();\r
 884   }\r
 885 \r
 886   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 887   {\r
 888     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 889     JInternalFrame frame = new JInternalFrame();\r
 890     frame.setContentPane(sp);\r
 891     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
 892     frame.setMaximizable(false);\r
 893     frame.setResizable(false);\r
 894 \r
 895   }\r
 896 \r
 897   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 898   {\r
 899     if(viewport.getSelectionGroup().getSize()<2)\r
 900       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 901     else\r
 902     {\r
 903       JInternalFrame frame = new JInternalFrame();\r
 904       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 905       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 906     }\r
 907   }\r
 908 \r
 909   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 910   {\r
 911 \r
 912     if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
 913        || viewport.getAlignment().getHeight()<4)\r
 914     {\r
 915       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 916                                     +"at least 4 input sequences.",\r
 917                                     "Sequence selection insufficient",\r
 918                                     JOptionPane.WARNING_MESSAGE);\r
 919       return;\r
 920     }\r
 921 \r
 922     try{\r
 923       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 924       JInternalFrame frame = new JInternalFrame();\r
 925       frame.setContentPane(pcaPanel);\r
 926       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 927    }catch(java.lang.OutOfMemoryError ex)\r
 928    {\r
 929      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 930                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 931    }\r
 932 \r
 933 \r
 934   }\r
 935 \r
 936   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 937   {\r
 938     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 939   }\r
 940 \r
 941   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 942   {\r
 943     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 944   }\r
 945 \r
 946 \r
 947   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 948   {\r
 949     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 950   }\r
 951 \r
 952   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 953   {\r
 954     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 955   }\r
 956 \r
 957   void NewTreePanel(String type, String pwType, String title)\r
 958   {\r
 959     //are the sequences aligned?\r
 960     if(!viewport.alignment.isAligned())\r
 961     {\r
 962       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
 963                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
 964       return;\r
 965     }\r
 966 \r
 967     TreePanel tp=null;\r
 968    if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)\r
 969    {\r
 970      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,\r
 971                          0, viewport.alignment.getWidth());\r
 972    }\r
 973    else\r
 974    {\r
 975      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 976                          type, pwType,  0, viewport.alignment.getWidth());\r
 977    }\r
 978 \r
 979    Desktop.addInternalFrame(tp, title, 600, 500);\r
 980   }\r
 981 \r
 982 \r
 983 \r
 984 \r
 985   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 986   {\r
 987     JInternalFrame frame = new JInternalFrame();\r
 988     ClustalThread ct = new ClustalThread(frame);\r
 989     Thread t = new Thread(ct);\r
 990     t.start();\r
 991     frame.setContentPane(ct);\r
 992      Desktop.addInternalFrame(frame, title, 300, 80);\r
 993 \r
 994   }\r
 995 \r
 996   class ClustalThread extends JPanel implements Runnable\r
 997   {\r
 998     Image [] image;\r
 999     int imageIndex = 0;\r
1000     boolean webServiceRunning = false;\r
1001     JInternalFrame frame;\r
1002     public ClustalThread(JInternalFrame frame)\r
1003     {\r
1004       this.frame = frame;\r
1005       image = new Image[9];\r
1006       for(int i=0; i<9; i++)\r
1007       {\r
1008         java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");\r
1009         if (url != null)\r
1010         {\r
1011           image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
1012           MediaTracker mt = new MediaTracker(this);\r
1013           mt.addImage(image[i], i);\r
1014           try{mt.waitForID(i);}\r
1015           catch(Exception ex){}\r
1016         }\r
1017       }\r
1018       DNATwirler twirler = new DNATwirler();\r
1019       twirler.start();\r
1020       webServiceRunning = true;\r
1021     }\r
1022 \r
1023     class DNATwirler extends Thread\r
1024     {\r
1025       public void run()\r
1026       {\r
1027         while(webServiceRunning)\r
1028         {\r
1029           try{\r
1030             Thread.sleep(100);\r
1031             imageIndex++;\r
1032             imageIndex %=9;\r
1033             repaint();\r
1034           }\r
1035           catch(Exception ex){}\r
1036         }\r
1037       }\r
1038     }\r
1039 \r
1040     // JBPNote\r
1041     // Should check to see if the server settings are valid\r
1042     // Need visual-delay indication here.\r
1043     public void run()\r
1044        {\r
1045          jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
1046          Vector sv = viewport.getAlignment().getSequences();\r
1047          SequenceI[] seqs = new SequenceI[sv.size()];\r
1048 \r
1049          int i = 0;\r
1050          do\r
1051          {\r
1052            seqs[i] = (SequenceI) sv.elementAt(i);\r
1053          }\r
1054          while (++i < sv.size());\r
1055 \r
1056          SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
1057 \r
1058          if (alignment != null)\r
1059          {\r
1060            AlignFrame af = new AlignFrame(new Alignment(alignment));\r
1061           af.clustalColour.setSelected(true);\r
1062           af.clustalColour_actionPerformed(null);\r
1063            Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
1064                                     700, 500); // JBPNote - is there a new window geom. property ?\r
1065          }\r
1066          else\r
1067            JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
1068                                          JOptionPane.WARNING_MESSAGE);\r
1069 \r
1070          webServiceRunning = false;\r
1071          try{\r
1072            frame.setClosed(true);\r
1073          }catch(Exception ex){}\r
1074        }\r
1075 \r
1076        public void paintComponent(Graphics g)\r
1077        {\r
1078          g.setColor(Color.white);\r
1079          g.fillRect(0,0,getWidth(), getHeight());\r
1080          if(image!=null)\r
1081          {\r
1082            g.drawImage(image[imageIndex],10,10,this);\r
1083          }\r
1084          g.setFont(new Font("Arial", Font.BOLD, 12));\r
1085          g.setColor(Color.black);\r
1086          g.drawString("Clustal Alignment Web Service running", 30,30);\r
1087        }\r
1088   }\r
1089   public void jpredMenuItem_actionPerformed(ActionEvent e)\r
1090     {\r
1091     //  JInternalFrame frame = new JInternalFrame();\r
1092 //      JPredClient ct = new JPredClient((SequenceI)\r
1093     ///                                   viewport.getAlignment().getSequences().elementAt(0));\r
1094     }\r
1095 \r
1096     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
1097     // Pick the tree file\r
1098     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
1099         getProperty("LAST_DIRECTORY"));\r
1100     chooser.setFileView(new JalviewFileView());\r
1101     chooser.setDialogTitle("Select a newick-like tree file");\r
1102     chooser.setToolTipText("Load a tree file");\r
1103     int value = chooser.showOpenDialog(null);\r
1104     if (value == JalviewFileChooser.APPROVE_OPTION)\r
1105     {\r
1106       String choice = chooser.getSelectedFile().getPath();\r
1107       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1108       TreePanel treepanel = null;\r
1109       try\r
1110       {\r
1111         jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");\r
1112         fin.parse();\r
1113 \r
1114         if (fin.getTree() != null)\r
1115         {\r
1116           TreePanel tp = null;\r
1117           tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1118                              fin, "FromFile", choice);\r
1119           Desktop.addInternalFrame(tp, title, 600, 500);\r
1120         }\r
1121       }\r
1122       catch (Exception ex)\r
1123       {\r
1124         JOptionPane.showMessageDialog(Desktop.desktop,\r
1125                                       "Problem reading tree file",\r
1126                                       ex.getMessage(),\r
1127                                       JOptionPane.WARNING_MESSAGE);\r
1128         ex.printStackTrace();\r
1129       }\r
1130     }\r
1131   }\r
1132 \r
1133 }\r