src/jalview/gui/AlignFrame.java

   1 /********************\r
   2  * 2004 Jalview Reengineered\r
   3  * Barton Group\r
   4  * Dundee University\r
   5  *\r
   6  * AM Waterhouse\r
   7  *******************/\r
   8 \r
   9 \r
  10 \r
  11 \r
  12 package jalview.gui;\r
  13 \r
  14 import jalview.jbgui.GAlignFrame;\r
  15 import jalview.schemes.*;\r
  16 import jalview.datamodel.*;\r
  17 import jalview.analysis.*;\r
  18 import jalview.io.*;\r
  19 import jalview.ws.*;\r
  20 import java.awt.*;\r
  21 import java.awt.event.*;\r
  22 import java.awt.print.*;\r
  23 import javax.swing.*;\r
  24 import javax.swing.event.*;\r
  25 import java.util.*;\r
  26 import  java.awt.datatransfer.*;\r
  27 \r
  28 \r
  29 public class AlignFrame extends GAlignFrame\r
  30 {\r
  31   final AlignmentPanel alignPanel;\r
  32   final AlignViewport viewport;\r
  33   public AlignFrame(AlignmentI al)\r
  34   {\r
  35     super();\r
  36     viewport = new AlignViewport(al,true,true,true,false);\r
  37     alignPanel = new AlignmentPanel(this, viewport);\r
  38     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
  39     fontNameMenuItem.setText(viewport.getFont().getName());\r
  40     fontSizeMenuItem.setText(viewport.getFont().getSize()+"");\r
  41 \r
  42     addInternalFrameListener(new InternalFrameAdapter()\r
  43    {\r
  44      public void internalFrameActivated(InternalFrameEvent evt)\r
  45      {\r
  46           javax.swing.SwingUtilities.invokeLater(new Runnable()\r
  47           {\r
  48             public void run()\r
  49             {      alignPanel.requestFocus();    }\r
  50           });\r
  51 \r
  52      }\r
  53    });\r
  54 \r
  55    AlignmentUtil.fetchSequenceFeatures(al, alignPanel);\r
  56   }\r
  57 \r
  58   protected void saveAs_actionPerformed(ActionEvent e)\r
  59   {\r
  60     JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
  61     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
  62     chooser.setToolTipText("Save");\r
  63     int value = chooser.showSaveDialog(this);\r
  64     if(value == JFileChooser.APPROVE_OPTION)\r
  65     {\r
  66       String choice =  chooser.getSelectedFile().getPath();\r
  67       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
  68       String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
  69       try{\r
  70         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
  71         out.println(output);\r
  72         out.close();\r
  73       }\r
  74       catch(Exception ex){}\r
  75     }\r
  76 \r
  77   }\r
  78 \r
  79   protected void outputText_actionPerformed(ActionEvent e)\r
  80   {\r
  81      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
  82      JInternalFrame frame = new JInternalFrame();\r
  83      cap.formatForOutput();\r
  84      frame.setContentPane(cap);\r
  85      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
  86      cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
  87   }\r
  88 \r
  89   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
  90   {\r
  91     HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
  92     htmlOutput = null;\r
  93   }\r
  94 \r
  95   protected void createJPG_actionPerformed(ActionEvent e)\r
  96   {\r
  97 \r
  98     int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;\r
  99     int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();\r
 100 \r
 101 \r
 102     if(!viewport.getWrapAlignment())\r
 103     {\r
 104       height = viewport.alignment.getHeight() * viewport.charHeight;\r
 105       width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;\r
 106     }\r
 107 \r
 108     alignPanel.makeJPG( width, height);\r
 109   }\r
 110 \r
 111 \r
 112   public void printMenuItem_actionPerformed(ActionEvent e)\r
 113   {\r
 114     //Putting in a thread avoids Swing painting problems\r
 115     PrintThread thread = new PrintThread();\r
 116     thread.start();\r
 117   }\r
 118 \r
 119   class PrintThread extends Thread\r
 120   {\r
 121     public void run()\r
 122     {\r
 123       PrinterJob printJob = PrinterJob.getPrinterJob();\r
 124       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
 125       printJob.setPrintable(alignPanel, pf);\r
 126       if (printJob.printDialog())\r
 127       {\r
 128         try\r
 129         {\r
 130           printJob.print();\r
 131         }\r
 132         catch (Exception PrintException)\r
 133         {\r
 134           PrintException.printStackTrace();\r
 135         }\r
 136       }\r
 137     }\r
 138 \r
 139   }\r
 140 \r
 141 \r
 142 \r
 143 \r
 144   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 145   {\r
 146     try{\r
 147       this.setClosed(true);\r
 148     }catch(Exception ex){}\r
 149   }\r
 150 \r
 151   ArrayList  historyList = new ArrayList();\r
 152   ArrayList redoList = new ArrayList();\r
 153 \r
 154   void updateEditMenuBar()\r
 155   {\r
 156     if(historyList.size()>0)\r
 157      {\r
 158        undoMenuItem.setEnabled(true);\r
 159        Object [] history = (Object[])historyList.get(0);\r
 160        undoMenuItem.setText("Undo "+history[0]);\r
 161      }\r
 162     else\r
 163     {\r
 164       undoMenuItem.setEnabled(false);\r
 165       undoMenuItem.setText("Undo");\r
 166     }\r
 167 \r
 168     if(redoList.size()>0)\r
 169      {\r
 170        redoMenuItem.setEnabled(true);\r
 171        Object [] history = (Object[])redoList.get(0);\r
 172        redoMenuItem.setText("Redo "+history[0]);\r
 173      }\r
 174     else\r
 175     {\r
 176       redoMenuItem.setEnabled(false);\r
 177       redoMenuItem.setText("Redo");\r
 178     }\r
 179   }\r
 180 \r
 181   public void addHistoryItem(String type)\r
 182   {\r
 183     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 184     redoList.clear();\r
 185     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 186     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 187     {\r
 188       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 189                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 190     }\r
 191 \r
 192     historyList.add(0, new Object[]{type,  seq} );\r
 193     updateEditMenuBar();\r
 194   }\r
 195 \r
 196   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 197   {\r
 198     Object [] history = (Object[])historyList.remove(0);\r
 199     // add the redo state before continuing!!\r
 200     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 201     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 202     {\r
 203       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 204                             viewport.getAlignment().getSequenceAt(i).\r
 205                             getSequence());\r
 206     }\r
 207     /////////\r
 208 \r
 209     redoList.add(0, new Object[] {history[0], seq});\r
 210 \r
 211       seq = (SequenceI[]) history[1];\r
 212       viewport.setAlignment( new Alignment(seq) );\r
 213       updateEditMenuBar();\r
 214       alignPanel.RefreshPanels();\r
 215   }\r
 216 \r
 217   public void moveSelectedSequences(boolean up)\r
 218   {\r
 219     SequenceGroup sg = viewport.getRubberbandGroup();\r
 220     if (sg == null)\r
 221       return;\r
 222 \r
 223     if (up)\r
 224     {\r
 225       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 226       {\r
 227         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 228         if (!sg.sequences.contains(seq))\r
 229           continue;\r
 230 \r
 231         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 232         if (sg.sequences.contains(temp))\r
 233           continue;\r
 234 \r
 235         viewport.alignment.getSequences().setElementAt(temp, i);\r
 236         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 237       }\r
 238     }\r
 239     else\r
 240     {\r
 241       for (int i = viewport.alignment.getHeight() - 2; i > -1; 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 \r
 256     alignPanel.RefreshPanels();\r
 257   }\r
 258 \r
 259 \r
 260 \r
 261   protected void copy_actionPerformed(ActionEvent e)\r
 262   {\r
 263    if(viewport.getRubberbandGroup()==null)\r
 264      return;\r
 265 \r
 266    SequenceGroup sg = viewport.getRubberbandGroup();\r
 267 \r
 268      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 269      StringBuffer buffer= new StringBuffer();\r
 270 \r
 271        for(int i=0; i<sg.getSize(); i++)\r
 272        {\r
 273          SequenceI seq = sg.getSequenceAt(i);\r
 274          buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
 275                         +seq.findPosition( sg.getEndRes() )+ "\t"\r
 276                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
 277        }\r
 278      c.setContents( new StringSelection( buffer.toString()) , null ) ;\r
 279 \r
 280   }\r
 281 \r
 282 \r
 283   protected void pasteNew_actionPerformed(ActionEvent e)\r
 284   {\r
 285     paste(true);\r
 286   }\r
 287 \r
 288   protected void pasteThis_actionPerformed(ActionEvent e)\r
 289   {\r
 290     paste(false);\r
 291   }\r
 292 \r
 293   void paste(boolean newAlignment)\r
 294   {\r
 295     try{\r
 296       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 297       Transferable contents = c.getContents(this);\r
 298       if (contents == null)\r
 299         return;\r
 300 \r
 301       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
 302       StringTokenizer st = new StringTokenizer(str);\r
 303       ArrayList seqs = new ArrayList();\r
 304       while (st.hasMoreElements())\r
 305       {\r
 306         String name = st.nextToken();\r
 307         int start = Integer.parseInt(st.nextToken());\r
 308         int end = Integer.parseInt(st.nextToken());\r
 309         Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
 310 \r
 311         if(!newAlignment)\r
 312           viewport.alignment.addSequence(sequence);\r
 313         else\r
 314           seqs.add(sequence);\r
 315       }\r
 316 \r
 317       if(newAlignment)\r
 318       {\r
 319         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 320         seqs.toArray(newSeqs);\r
 321         AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
 322         int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;\r
 323         if (newHeight > 500)\r
 324           newHeight = 500;\r
 325         Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
 326       }\r
 327       else\r
 328       {\r
 329         viewport.setEndSeq(viewport.alignment.getHeight());\r
 330         viewport.alignment.getWidth();\r
 331         alignPanel.RefreshPanels();\r
 332       }\r
 333 \r
 334     }catch(Exception ex){}// could be anything being pasted in here\r
 335 \r
 336   }\r
 337 \r
 338 \r
 339   protected void cut_actionPerformed(ActionEvent e)\r
 340   {\r
 341     copy_actionPerformed(null);\r
 342     delete_actionPerformed(null);\r
 343   }\r
 344 \r
 345   protected void delete_actionPerformed(ActionEvent e)\r
 346   {\r
 347     if (viewport.getRubberbandGroup() == null)\r
 348       return;\r
 349 \r
 350      SequenceGroup sg = viewport.getRubberbandGroup();\r
 351      for (int i=0;i < sg.sequences.size(); i++)\r
 352              viewport.getAlignment().deleteSequence(sg.getSequenceAt(i));\r
 353 \r
 354      viewport.alignment.deleteGroup(sg);\r
 355      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
 356      if(viewport.getAlignment().getHeight()<1)\r
 357      try\r
 358      {\r
 359        this.setClosed(true);\r
 360      }catch(Exception ex){}\r
 361      alignPanel.RefreshPanels();\r
 362 \r
 363   }\r
 364 \r
 365 \r
 366 \r
 367   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 368   {\r
 369      Object [] history = (Object[])redoList.remove(0);\r
 370      SequenceI[] seq = (SequenceI[]) history[1];\r
 371      viewport.setAlignment( new Alignment(seq) );\r
 372      updateEditMenuBar();\r
 373      alignPanel.RefreshPanels();\r
 374   }\r
 375 \r
 376 \r
 377   public void groupsMenuItem_actionPerformed(ActionEvent e)\r
 378   {\r
 379     GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
 380     JInternalFrame frame = new JInternalFrame();\r
 381     frame.setContentPane(geditor);\r
 382     Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
 383     frame.setResizable(false);\r
 384   }\r
 385 \r
 386   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 387   {\r
 388     viewport.alignment.deleteAllGroups();\r
 389     viewport.getSelection().clear();\r
 390 \r
 391     alignPanel.RefreshPanels();\r
 392   }\r
 393 \r
 394 \r
 395 \r
 396   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 397   {\r
 398     Selection sel = viewport.getSelection();\r
 399     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 400       sel.addElement( viewport.getAlignment().getSequenceAt(i));\r
 401     PaintRefresher.Refresh(null);\r
 402   }\r
 403 \r
 404   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 405   {\r
 406     viewport.setRubberbandGroup(null);\r
 407     viewport.getSelection().clear();\r
 408     PaintRefresher.Refresh(null);\r
 409   }\r
 410 \r
 411   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 412   {\r
 413     Selection sel = viewport.getSelection();\r
 414     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 415     {\r
 416       if (sel.contains(viewport.getAlignment().getSequenceAt(i)))\r
 417         sel.removeElement(viewport.getAlignment().getSequenceAt(i));\r
 418       else\r
 419         sel.addElement(viewport.getAlignment().getSequenceAt(i));\r
 420     }\r
 421     PaintRefresher.Refresh(null);\r
 422   }\r
 423 \r
 424 \r
 425   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 426   {\r
 427     viewport.getColumnSelection().clear();\r
 428     repaint();\r
 429   }\r
 430 \r
 431   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 432   {\r
 433     addHistoryItem("delete columns");\r
 434     ColumnSelection colSel = viewport.getColumnSelection();\r
 435     if (colSel.size() > 0)\r
 436     {\r
 437       int min = colSel.getMin();\r
 438       viewport.getAlignment().trimLeft(min);\r
 439       colSel.compensateForEdit(0,min);\r
 440       alignPanel.RefreshPanels();\r
 441     }\r
 442   }\r
 443 \r
 444   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 445   {\r
 446     addHistoryItem("delete columns");\r
 447     ColumnSelection colSel = viewport.getColumnSelection();\r
 448     if (colSel.size() > 0)\r
 449     {\r
 450       int max = colSel.getMax();\r
 451       if(max>1)\r
 452         viewport.getAlignment().trimRight(max);\r
 453 \r
 454       alignPanel.RefreshPanels();\r
 455     }\r
 456 \r
 457   }\r
 458 \r
 459   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 460   {\r
 461     addHistoryItem("delete gapped columns");\r
 462     viewport.getAlignment().removeGaps();\r
 463     alignPanel.RefreshPanels();\r
 464   }\r
 465 \r
 466   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 467   {\r
 468     addHistoryItem("delete all gaps");\r
 469     SequenceI current;\r
 470     int jSize;\r
 471     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 472     {\r
 473       current = viewport.getAlignment().getSequenceAt(i);\r
 474       jSize = current.getLength();\r
 475       for (int j=0; j < jSize; j++)\r
 476         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 477         {\r
 478           current.deleteCharAt(j);\r
 479           j--;\r
 480           jSize--;\r
 481         }\r
 482     }\r
 483 \r
 484     alignPanel.RefreshPanels();\r
 485   }\r
 486 \r
 487   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 488   {\r
 489     char thisChar = '-';\r
 490     char nextChar = '.';\r
 491     if(viewport.getGapCharacter()=='-')\r
 492     {\r
 493       thisChar = '.';\r
 494       nextChar = '-';\r
 495     }\r
 496     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 497     viewport.setGapCharacter(thisChar);\r
 498     alignPanel.RefreshPanels();\r
 499   }\r
 500 \r
 501   public void findMenuItem_actionPerformed(ActionEvent e)\r
 502   {\r
 503     JOptionPane op = new JOptionPane();\r
 504     JInternalFrame frame =  op.createInternalFrame(this, "Find");\r
 505     Finder finder = new Finder(viewport, alignPanel, frame);\r
 506     frame.setClosable(true);\r
 507     frame.setContentPane(finder);\r
 508     frame.setSize(340,110);\r
 509     frame.setVisible(true);\r
 510   }\r
 511 \r
 512 \r
 513 \r
 514   public void fontNameMenuItem_actionPerformed(ActionEvent e)\r
 515   {\r
 516     String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
 517 \r
 518 \r
 519     String selection = JOptionPane.showInternalInputDialog(this,\r
 520                                 "Select font",\r
 521                                 "Font selection",\r
 522                                 JOptionPane.QUESTION_MESSAGE,\r
 523                                 null,fonts\r
 524                                 ,fontNameMenuItem.getText()).toString();\r
 525     if(selection!=null)\r
 526     {\r
 527        fontNameMenuItem.setText(selection);\r
 528        SetFont();\r
 529      }\r
 530 \r
 531   }\r
 532 \r
 533   public void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
 534   {\r
 535     String selection = JOptionPane.showInternalInputDialog(this,\r
 536                                 "Select font size",\r
 537                                 "Font size",\r
 538                                 JOptionPane.QUESTION_MESSAGE,\r
 539                                 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
 540                                 ,fontSizeMenuItem.getText()).toString();\r
 541     if(selection!=null)\r
 542      {\r
 543        fontSizeMenuItem.setText(selection);\r
 544        SetFont();\r
 545      }\r
 546   }\r
 547 \r
 548   public void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
 549   {\r
 550     String selection = JOptionPane.showInternalInputDialog(this,\r
 551                                 "Select font style",\r
 552                                 "Font style",\r
 553                                 JOptionPane.QUESTION_MESSAGE,\r
 554                                 null, new String[]{"plain", "bold", "italic"}\r
 555                                 ,fontStyleMenuItem.getText()).toString();\r
 556     if(selection!=null)\r
 557     {\r
 558       fontStyleMenuItem.setText(selection);\r
 559       SetFont();\r
 560     }\r
 561 \r
 562   }\r
 563 \r
 564   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 565   {\r
 566       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 567       alignPanel.RefreshPanels();\r
 568   }\r
 569 \r
 570   void SetFont()\r
 571   {\r
 572       int style = java.awt.Font.PLAIN;\r
 573       if(fontStyleMenuItem.getText().equals("bold"))\r
 574         style = java.awt.Font.BOLD;\r
 575       else if(fontStyleMenuItem.getText().equals("italic"))\r
 576         style = java.awt.Font.ITALIC;\r
 577 \r
 578       viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),\r
 579                                            style,\r
 580                                            Integer.parseInt(fontSizeMenuItem.getText())));\r
 581       alignPanel.RefreshPanels();\r
 582 \r
 583   }\r
 584 \r
 585   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 586   {\r
 587     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 588     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
 589   }\r
 590 \r
 591 \r
 592   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 593   {\r
 594     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 595     alignPanel.RefreshPanels();\r
 596   }\r
 597 \r
 598   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 599   {\r
 600     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 601     alignPanel.RefreshPanels();\r
 602   }\r
 603 \r
 604 \r
 605   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 606   {\r
 607     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 608     alignPanel.RefreshPanels();\r
 609   }\r
 610 \r
 611   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 612   {\r
 613     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 614     alignPanel.RefreshPanels();\r
 615   }\r
 616 \r
 617   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 618   {\r
 619     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
 620   }\r
 621 \r
 622   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 623   {\r
 624     if (alignPanel.overviewPanel != null)\r
 625       return;\r
 626 \r
 627     JInternalFrame frame = new JInternalFrame();\r
 628     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 629    try{\r
 630      overview = new OverviewPanel(alignPanel, viewport);\r
 631      frame.setContentPane(overview);\r
 632     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 633                              frame.getWidth(), frame.getHeight());\r
 634     frame.pack();\r
 635     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 636     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 637       {\r
 638             alignPanel.setOverviewPanel(null);\r
 639       };\r
 640     });\r
 641     alignPanel.setOverviewPanel( overview );\r
 642 \r
 643   }catch(java.lang.OutOfMemoryError ex)\r
 644    {\r
 645      JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 646                                    +"\nTry reducing the font size.",\r
 647                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 648    }\r
 649 \r
 650 \r
 651   }\r
 652 \r
 653   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 654   {\r
 655     changeColour( null );\r
 656   }\r
 657 \r
 658 \r
 659   public void clustalColour_actionPerformed(ActionEvent e)\r
 660   {\r
 661     abovePIDThreshold.setSelected(false);\r
 662     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 663   }\r
 664 \r
 665   public void zappoColour_actionPerformed(ActionEvent e)\r
 666   {\r
 667     changeColour(new ZappoColourScheme());\r
 668   }\r
 669 \r
 670   public void taylorColour_actionPerformed(ActionEvent e)\r
 671   {\r
 672     changeColour(new TaylorColourScheme());\r
 673   }\r
 674 \r
 675 \r
 676   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 677   {\r
 678     changeColour( new HydrophobicColourScheme() );\r
 679   }\r
 680 \r
 681   public void helixColour_actionPerformed(ActionEvent e)\r
 682   {\r
 683     changeColour(new HelixColourScheme() );\r
 684   }\r
 685 \r
 686 \r
 687   public void strandColour_actionPerformed(ActionEvent e)\r
 688   {\r
 689     changeColour(new StrandColourScheme());\r
 690   }\r
 691 \r
 692 \r
 693   public void turnColour_actionPerformed(ActionEvent e)\r
 694   {\r
 695     changeColour(new TurnColourScheme());\r
 696   }\r
 697 \r
 698 \r
 699   public void buriedColour_actionPerformed(ActionEvent e)\r
 700   {\r
 701     changeColour(new BuriedColourScheme() );\r
 702   }\r
 703 \r
 704   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 705   {\r
 706     changeColour(new NucleotideColourScheme());\r
 707   }\r
 708 \r
 709 \r
 710   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 711   {\r
 712     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
 713   }\r
 714 \r
 715 \r
 716 \r
 717   void changeColour(ColourSchemeI cs)\r
 718   {\r
 719 \r
 720     if(viewport.getColourAppliesToAllGroups())\r
 721     {\r
 722       Vector groups = viewport.alignment.getGroups();\r
 723       for(int i=0; i<groups.size(); i++)\r
 724       {\r
 725         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 726         sg.cs = cs;\r
 727 \r
 728         if(abovePIDThreshold.isSelected())\r
 729           abovePIDThreshold_actionPerformed(null);\r
 730         else if( viewport.getConservationSelected() )\r
 731         {\r
 732           Conservation c = new Conservation("Group",\r
 733                                             ResidueProperties.propHash, 3,\r
 734                                             sg.sequences, sg.getStartRes(),\r
 735                                             sg.getEndRes());\r
 736           c.calculate();\r
 737           c.verdict(false, 100);\r
 738           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 739 \r
 740           sg.cs = ccs;\r
 741         }\r
 742 \r
 743       }\r
 744     }\r
 745 \r
 746 \r
 747     if ( viewport.getAbovePIDThreshold())\r
 748     {\r
 749       int threshold = 0;\r
 750       threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");\r
 751       Desktop.hideConservationSlider();\r
 752 \r
 753       if (cs instanceof ResidueColourScheme)\r
 754         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 755       else if (cs instanceof ScoreColourScheme)\r
 756         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 757 \r
 758       viewport.setGlobalColourScheme(cs);\r
 759 \r
 760     }\r
 761     else\r
 762     if (cs instanceof ResidueColourScheme)\r
 763       ( (ResidueColourScheme) cs).setThreshold(0);\r
 764     else if (cs instanceof ScoreColourScheme)\r
 765       ( (ScoreColourScheme) cs).setThreshold(0);\r
 766 \r
 767 \r
 768 \r
 769 \r
 770 if ( viewport.getConservationSelected() )\r
 771  {\r
 772    ConservationColourScheme ccs = null;\r
 773 \r
 774    Alignment al = (Alignment) viewport.alignment;\r
 775    Conservation c = new Conservation("All",\r
 776                                      ResidueProperties.propHash, 3,\r
 777                                      al.getSequences(), 0,\r
 778                                      al.getWidth());\r
 779 \r
 780    c.calculate();\r
 781    c.verdict(false, 100);\r
 782 \r
 783    ccs = new ConservationColourScheme(c, cs);\r
 784 \r
 785    int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,\r
 786        "Background");\r
 787 \r
 788    ccs.inc = threshold;\r
 789 \r
 790    viewport.setGlobalColourScheme(ccs);\r
 791 \r
 792   }\r
 793   else\r
 794        viewport.setGlobalColourScheme( cs );\r
 795 \r
 796     alignPanel.RefreshPanels();\r
 797   }\r
 798 \r
 799 \r
 800   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 801   {\r
 802     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 803 \r
 804     viewport.setAbovePIDThreshold(false);\r
 805     abovePIDThreshold.setSelected(false);\r
 806     Desktop.hidePIDSlider();\r
 807     if(!viewport.getConservationSelected())\r
 808       Desktop.hideConservationSlider();\r
 809 \r
 810    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 811    if(cs instanceof ConservationColourScheme )\r
 812      changeColour( ((ConservationColourScheme)cs).cs );\r
 813     else\r
 814       changeColour( cs );\r
 815   }\r
 816 \r
 817 \r
 818   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 819   {\r
 820     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
 821 \r
 822     conservationMenuItem.setSelected(false);\r
 823     viewport.setConservationSelected(false);\r
 824     Desktop.hideConservationSlider();\r
 825 \r
 826     if(!viewport.getAbovePIDThreshold())\r
 827       Desktop.hidePIDSlider();\r
 828 \r
 829 \r
 830     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 831     if(cs instanceof ConservationColourScheme )\r
 832         changeColour( ((ConservationColourScheme)cs).cs );\r
 833     else\r
 834         changeColour( cs );\r
 835 \r
 836   }\r
 837 \r
 838 \r
 839 \r
 840   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 841   {\r
 842     JInternalFrame frame = new JInternalFrame();\r
 843     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 844     frame.setContentPane(chooser);\r
 845     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 846     frame.setResizable(false);\r
 847     frame.setIconifiable(false);\r
 848     frame.setMaximizable(false);\r
 849   }\r
 850 \r
 851   public void PIDColour_actionPerformed(ActionEvent e)\r
 852   {\r
 853     changeColour( new PIDColourScheme() );\r
 854   }\r
 855 \r
 856 \r
 857   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 858   {\r
 859     changeColour(new Blosum62ColourScheme(viewport) );\r
 860   }\r
 861 \r
 862 \r
 863 \r
 864   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 865   {\r
 866     addHistoryItem("sort");\r
 867     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 868     alignPanel.RefreshPanels();\r
 869   }\r
 870 \r
 871   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 872   {\r
 873     addHistoryItem("sort");\r
 874     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 875     alignPanel.RefreshPanels();\r
 876   }\r
 877 \r
 878   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 879   {\r
 880     addHistoryItem("sort");\r
 881     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 882     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 883     alignPanel.RefreshPanels();\r
 884   }\r
 885 \r
 886   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 887   {\r
 888     addHistoryItem("sort");\r
 889     if(viewport.getCurrentTree()==null)\r
 890       return;\r
 891 \r
 892     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 893     alignPanel.RefreshPanels();\r
 894   }\r
 895 \r
 896   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 897   {\r
 898     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 899     JInternalFrame frame = new JInternalFrame();\r
 900     frame.setContentPane(sp);\r
 901     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
 902     frame.setMaximizable(false);\r
 903     frame.setResizable(false);\r
 904 \r
 905   }\r
 906 \r
 907   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 908   {\r
 909     if(viewport.getSelection().size()<2)\r
 910       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 911     else\r
 912     {\r
 913       JInternalFrame frame = new JInternalFrame();\r
 914       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 915       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 916     }\r
 917   }\r
 918 \r
 919   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 920   {\r
 921     if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>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     JInternalFrame frame = new javax.swing.JInternalFrame();\r
 977     TreePanel tp=null;\r
 978    if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
 979    {\r
 980      tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,\r
 981                          0, viewport.alignment.getWidth());\r
 982    }\r
 983    else\r
 984    {\r
 985      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 986                          type, pwType,  0, viewport.alignment.getWidth());\r
 987    }\r
 988 \r
 989    frame.setContentPane(tp);\r
 990    Desktop.addInternalFrame(frame, title, 600, 500);\r
 991   }\r
 992 \r
 993 \r
 994 \r
 995 \r
 996   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 997   {\r
 998     JInternalFrame frame = new JInternalFrame();\r
 999     ClustalThread ct = new ClustalThread(frame);\r
1000     Thread t = new Thread(ct);\r
1001     t.start();\r
1002     frame.setContentPane(ct);\r
1003      Desktop.addInternalFrame(frame, title, 300, 80);\r
1004 \r
1005   }\r
1006 \r
1007   class ClustalThread extends JPanel implements Runnable\r
1008   {\r
1009     Image [] image;\r
1010     int imageIndex = 0;\r
1011     boolean webServiceRunning = false;\r
1012     JInternalFrame frame;\r
1013     public ClustalThread(JInternalFrame frame)\r
1014     {\r
1015       this.frame = frame;\r
1016       image = new Image[9];\r
1017       for(int i=0; i<9; i++)\r
1018       {\r
1019         java.net.URL url = getClass().getResource("/dna" + (i+1) + ".gif");\r
1020         if (url != null)\r
1021         {\r
1022           image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
1023           MediaTracker mt = new MediaTracker(this);\r
1024           mt.addImage(image[i], i);\r
1025           try{mt.waitForID(i);}\r
1026           catch(Exception ex){}\r
1027         }\r
1028       }\r
1029       DNATwirler twirler = new DNATwirler();\r
1030       twirler.start();\r
1031       webServiceRunning = true;\r
1032     }\r
1033 \r
1034     class DNATwirler extends Thread\r
1035     {\r
1036       public void run()\r
1037       {\r
1038         while(webServiceRunning)\r
1039         {\r
1040           try{\r
1041             Thread.sleep(100);\r
1042             imageIndex++;\r
1043             imageIndex %=9;\r
1044             repaint();\r
1045           }\r
1046           catch(Exception ex){}\r
1047         }\r
1048       }\r
1049     }\r
1050 \r
1051     // JBPNote\r
1052     // Should check to see if the server settings are valid\r
1053     // Need visual-delay indication here.\r
1054     public void run()\r
1055        {\r
1056          jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
1057          Vector sv = viewport.getAlignment().getSequences();\r
1058          SequenceI[] seqs = new SequenceI[sv.size()];\r
1059 \r
1060          int i = 0;\r
1061          do\r
1062          {\r
1063            seqs[i] = (SequenceI) sv.elementAt(i);\r
1064          }\r
1065          while (++i < sv.size());\r
1066 \r
1067          SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
1068 \r
1069          if (alignment != null)\r
1070          {\r
1071            AlignFrame af = new AlignFrame(new Alignment(alignment));\r
1072           af.clustalColour.setSelected(true);\r
1073           af.clustalColour_actionPerformed(null);\r
1074            Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
1075                                     700, 500); // JBPNote - is there a new window geom. property ?\r
1076          }\r
1077          else\r
1078            JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
1079                                          JOptionPane.WARNING_MESSAGE);\r
1080 \r
1081          webServiceRunning = false;\r
1082          try{\r
1083            frame.setClosed(true);\r
1084          }catch(Exception ex){}\r
1085        }\r
1086 \r
1087        public void paintComponent(Graphics g)\r
1088        {\r
1089          g.setColor(Color.white);\r
1090          g.fillRect(0,0,getWidth(), getHeight());\r
1091          if(image!=null)\r
1092          {\r
1093            g.drawImage(image[imageIndex],10,10,this);\r
1094          }\r
1095          g.setFont(new Font("Arial", Font.BOLD, 12));\r
1096          g.setColor(Color.black);\r
1097          g.drawString("Clustal Alignment Web Service running", 30,30);\r
1098        }\r
1099   }\r
1100 }\r