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