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   public void printMenuItem_actionPerformed(ActionEvent e)\r
  96   {\r
  97     //Putting in a thread avoids Swing painting problems\r
  98     PrintThread thread = new PrintThread();\r
  99     thread.start();\r
 100   }\r
 101 \r
 102   class PrintThread extends Thread\r
 103   {\r
 104     public void run()\r
 105     {\r
 106       PrinterJob printJob = PrinterJob.getPrinterJob();\r
 107       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
 108       printJob.setPrintable(alignPanel, pf);\r
 109       if (printJob.printDialog())\r
 110       {\r
 111         try\r
 112         {\r
 113           printJob.print();\r
 114         }\r
 115         catch (Exception PrintException)\r
 116         {\r
 117           PrintException.printStackTrace();\r
 118         }\r
 119       }\r
 120     }\r
 121 \r
 122   }\r
 123 \r
 124 \r
 125 \r
 126 \r
 127   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 128   {\r
 129     try{\r
 130       this.setClosed(true);\r
 131     }catch(Exception ex){}\r
 132   }\r
 133 \r
 134   ArrayList  historyList = new ArrayList();\r
 135   ArrayList redoList = new ArrayList();\r
 136 \r
 137   void updateEditMenuBar()\r
 138   {\r
 139     if(historyList.size()>0)\r
 140      {\r
 141        undoMenuItem.setEnabled(true);\r
 142        Object [] history = (Object[])historyList.get(0);\r
 143        undoMenuItem.setText("Undo "+history[0]);\r
 144      }\r
 145     else\r
 146     {\r
 147       undoMenuItem.setEnabled(false);\r
 148       undoMenuItem.setText("Undo");\r
 149     }\r
 150 \r
 151     if(redoList.size()>0)\r
 152      {\r
 153        redoMenuItem.setEnabled(true);\r
 154        Object [] history = (Object[])redoList.get(0);\r
 155        redoMenuItem.setText("Redo "+history[0]);\r
 156      }\r
 157     else\r
 158     {\r
 159       redoMenuItem.setEnabled(false);\r
 160       redoMenuItem.setText("Redo");\r
 161     }\r
 162   }\r
 163 \r
 164   public void addHistoryItem(String type)\r
 165   {\r
 166     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 167     redoList.clear();\r
 168     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 169     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 170     {\r
 171       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 172                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 173     }\r
 174 \r
 175     historyList.add(0, new Object[]{type,  seq} );\r
 176     updateEditMenuBar();\r
 177   }\r
 178 \r
 179   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 180   {\r
 181     Object [] history = (Object[])historyList.remove(0);\r
 182     // add the redo state before continuing!!\r
 183     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 184     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 185     {\r
 186       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 187                             viewport.getAlignment().getSequenceAt(i).\r
 188                             getSequence());\r
 189     }\r
 190     /////////\r
 191 \r
 192     redoList.add(0, new Object[] {history[0], seq});\r
 193 \r
 194       seq = (SequenceI[]) history[1];\r
 195       viewport.setAlignment( new Alignment(seq) );\r
 196       updateEditMenuBar();\r
 197       alignPanel.RefreshPanels();\r
 198   }\r
 199 \r
 200   public void moveSelectedSequences(boolean up)\r
 201   {\r
 202     SequenceGroup sg = viewport.getRubberbandGroup();\r
 203     if (sg == null)\r
 204       return;\r
 205 \r
 206     if (up)\r
 207     {\r
 208       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 209       {\r
 210         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 211         if (!sg.sequences.contains(seq))\r
 212           continue;\r
 213 \r
 214         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 215         if (sg.sequences.contains(temp))\r
 216           continue;\r
 217 \r
 218         viewport.alignment.getSequences().setElementAt(temp, i);\r
 219         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 220       }\r
 221     }\r
 222     else\r
 223     {\r
 224       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 225       {\r
 226         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 227         if (!sg.sequences.contains(seq))\r
 228           continue;\r
 229 \r
 230         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 231         if (sg.sequences.contains(temp))\r
 232           continue;\r
 233 \r
 234         viewport.alignment.getSequences().setElementAt(temp, i);\r
 235         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 236       }\r
 237     }\r
 238 \r
 239     alignPanel.RefreshPanels();\r
 240   }\r
 241 \r
 242 \r
 243 \r
 244   protected void copy_actionPerformed(ActionEvent e)\r
 245   {\r
 246    if(viewport.getRubberbandGroup()==null)\r
 247      return;\r
 248 \r
 249    SequenceGroup sg = viewport.getRubberbandGroup();\r
 250 \r
 251      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 252      StringBuffer buffer= new StringBuffer();\r
 253 \r
 254        for(int i=0; i<sg.getSize(); i++)\r
 255        {\r
 256          SequenceI seq = sg.getSequenceAt(i);\r
 257          buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
 258                         +seq.findPosition( sg.getEndRes() )+ "\t"\r
 259                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
 260        }\r
 261      c.setContents( new StringSelection( buffer.toString()) , null ) ;\r
 262 \r
 263   }\r
 264 \r
 265 \r
 266   protected void pasteNew_actionPerformed(ActionEvent e)\r
 267   {\r
 268     paste(true);\r
 269   }\r
 270 \r
 271   protected void pasteThis_actionPerformed(ActionEvent e)\r
 272   {\r
 273     paste(false);\r
 274   }\r
 275 \r
 276   void paste(boolean newAlignment)\r
 277   {\r
 278     try{\r
 279       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 280       Transferable contents = c.getContents(this);\r
 281       if (contents == null)\r
 282         return;\r
 283 \r
 284       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
 285       StringTokenizer st = new StringTokenizer(str);\r
 286       ArrayList seqs = new ArrayList();\r
 287       while (st.hasMoreElements())\r
 288       {\r
 289         String name = st.nextToken();\r
 290         int start = Integer.parseInt(st.nextToken());\r
 291         int end = Integer.parseInt(st.nextToken());\r
 292         Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
 293 \r
 294         if(!newAlignment)\r
 295           viewport.alignment.addSequence(sequence);\r
 296         else\r
 297           seqs.add(sequence);\r
 298       }\r
 299 \r
 300       if(newAlignment)\r
 301       {\r
 302         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 303         seqs.toArray(newSeqs);\r
 304         AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
 305         int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;\r
 306         if (newHeight > 500)\r
 307           newHeight = 500;\r
 308         Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
 309       }\r
 310       else\r
 311       {\r
 312         viewport.setEndSeq(viewport.alignment.getHeight());\r
 313         viewport.alignment.getWidth();\r
 314         alignPanel.RefreshPanels();\r
 315       }\r
 316 \r
 317     }catch(Exception ex){}// could be anything being pasted in here\r
 318 \r
 319   }\r
 320 \r
 321 \r
 322   protected void cut_actionPerformed(ActionEvent e)\r
 323   {\r
 324     copy_actionPerformed(null);\r
 325     delete_actionPerformed(null);\r
 326   }\r
 327 \r
 328   protected void delete_actionPerformed(ActionEvent e)\r
 329   {\r
 330     if (viewport.getRubberbandGroup() == null)\r
 331       return;\r
 332 \r
 333      SequenceGroup sg = viewport.getRubberbandGroup();\r
 334      for (int i=0;i < sg.sequences.size(); i++)\r
 335              viewport.getAlignment().deleteSequence(sg.getSequenceAt(i));\r
 336 \r
 337      viewport.alignment.deleteGroup(sg);\r
 338      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
 339      if(viewport.getAlignment().getHeight()<1)\r
 340      try\r
 341      {\r
 342        this.setClosed(true);\r
 343      }catch(Exception ex){}\r
 344      alignPanel.RefreshPanels();\r
 345 \r
 346   }\r
 347 \r
 348 \r
 349 \r
 350   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 351   {\r
 352      Object [] history = (Object[])redoList.remove(0);\r
 353      SequenceI[] seq = (SequenceI[]) history[1];\r
 354      viewport.setAlignment( new Alignment(seq) );\r
 355      updateEditMenuBar();\r
 356      alignPanel.RefreshPanels();\r
 357   }\r
 358 \r
 359 \r
 360   public void groupsMenuItem_actionPerformed(ActionEvent e)\r
 361   {\r
 362     GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
 363     JInternalFrame frame = new JInternalFrame();\r
 364     frame.setContentPane(geditor);\r
 365     Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
 366     frame.setResizable(false);\r
 367   }\r
 368 \r
 369   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 370   {\r
 371     viewport.alignment.deleteAllGroups();\r
 372     viewport.getSelection().clear();\r
 373 \r
 374     alignPanel.RefreshPanels();\r
 375   }\r
 376 \r
 377 \r
 378 \r
 379   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 380   {\r
 381     Selection sel = viewport.getSelection();\r
 382     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 383       sel.addElement( viewport.getAlignment().getSequenceAt(i));\r
 384     PaintRefresher.Refresh(null);\r
 385   }\r
 386 \r
 387   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 388   {\r
 389     viewport.setRubberbandGroup(null);\r
 390     viewport.getSelection().clear();\r
 391     PaintRefresher.Refresh(null);\r
 392   }\r
 393 \r
 394   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 395   {\r
 396     Selection sel = viewport.getSelection();\r
 397     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 398     {\r
 399       if (sel.contains(viewport.getAlignment().getSequenceAt(i)))\r
 400         sel.removeElement(viewport.getAlignment().getSequenceAt(i));\r
 401       else\r
 402         sel.addElement(viewport.getAlignment().getSequenceAt(i));\r
 403     }\r
 404     PaintRefresher.Refresh(null);\r
 405   }\r
 406 \r
 407 \r
 408   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 409   {\r
 410     viewport.getColumnSelection().clear();\r
 411     repaint();\r
 412   }\r
 413 \r
 414   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 415   {\r
 416     addHistoryItem("delete columns");\r
 417     ColumnSelection colSel = viewport.getColumnSelection();\r
 418     if (colSel.size() > 0)\r
 419     {\r
 420       int min = colSel.getMin();\r
 421       viewport.getAlignment().trimLeft(min);\r
 422       colSel.compensateForEdit(0,min);\r
 423       alignPanel.RefreshPanels();\r
 424     }\r
 425   }\r
 426 \r
 427   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 428   {\r
 429     addHistoryItem("delete columns");\r
 430     ColumnSelection colSel = viewport.getColumnSelection();\r
 431     if (colSel.size() > 0)\r
 432     {\r
 433       int max = colSel.getMax();\r
 434       if(max>1)\r
 435         viewport.getAlignment().trimRight(max);\r
 436 \r
 437       alignPanel.RefreshPanels();\r
 438     }\r
 439 \r
 440   }\r
 441 \r
 442   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 443   {\r
 444     addHistoryItem("delete gapped columns");\r
 445     viewport.getAlignment().removeGaps();\r
 446     alignPanel.RefreshPanels();\r
 447   }\r
 448 \r
 449   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 450   {\r
 451     addHistoryItem("delete all gaps");\r
 452     SequenceI current;\r
 453     int jSize;\r
 454     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 455     {\r
 456       current = viewport.getAlignment().getSequenceAt(i);\r
 457       jSize = current.getLength();\r
 458       for (int j=0; j < jSize; j++)\r
 459         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 460         {\r
 461           current.deleteCharAt(j);\r
 462           j--;\r
 463           jSize--;\r
 464         }\r
 465     }\r
 466 \r
 467     alignPanel.RefreshPanels();\r
 468   }\r
 469 \r
 470   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 471   {\r
 472     char thisChar = '-';\r
 473     char nextChar = '.';\r
 474     if(viewport.getGapCharacter()=='-')\r
 475     {\r
 476       thisChar = '.';\r
 477       nextChar = '-';\r
 478     }\r
 479     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 480     viewport.setGapCharacter(thisChar);\r
 481     alignPanel.RefreshPanels();\r
 482   }\r
 483 \r
 484   public void findMenuItem_actionPerformed(ActionEvent e)\r
 485   {\r
 486     JOptionPane op = new JOptionPane();\r
 487     JInternalFrame frame =  op.createInternalFrame(this, "Find");\r
 488     Finder finder = new Finder(viewport, alignPanel, frame);\r
 489     frame.setClosable(true);\r
 490     frame.setContentPane(finder);\r
 491     frame.setSize(340,110);\r
 492     frame.setVisible(true);\r
 493   }\r
 494 \r
 495 \r
 496 \r
 497   public void fontNameMenuItem_actionPerformed(ActionEvent e)\r
 498   {\r
 499     String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
 500 \r
 501 \r
 502     String selection = JOptionPane.showInternalInputDialog(this,\r
 503                                 "Select font",\r
 504                                 "Font selection",\r
 505                                 JOptionPane.QUESTION_MESSAGE,\r
 506                                 null,fonts\r
 507                                 ,fontNameMenuItem.getText()).toString();\r
 508     if(selection!=null)\r
 509     {\r
 510        fontNameMenuItem.setText(selection);\r
 511        SetFont();\r
 512      }\r
 513 \r
 514   }\r
 515 \r
 516   public void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
 517   {\r
 518     String selection = JOptionPane.showInternalInputDialog(this,\r
 519                                 "Select font size",\r
 520                                 "Font size",\r
 521                                 JOptionPane.QUESTION_MESSAGE,\r
 522                                 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
 523                                 ,fontSizeMenuItem.getText()).toString();\r
 524     if(selection!=null)\r
 525      {\r
 526        fontSizeMenuItem.setText(selection);\r
 527        SetFont();\r
 528      }\r
 529   }\r
 530 \r
 531   public void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
 532   {\r
 533     String selection = JOptionPane.showInternalInputDialog(this,\r
 534                                 "Select font style",\r
 535                                 "Font style",\r
 536                                 JOptionPane.QUESTION_MESSAGE,\r
 537                                 null, new String[]{"plain", "bold", "italic"}\r
 538                                 ,fontStyleMenuItem.getText()).toString();\r
 539     if(selection!=null)\r
 540     {\r
 541       fontStyleMenuItem.setText(selection);\r
 542       SetFont();\r
 543     }\r
 544 \r
 545   }\r
 546 \r
 547   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 548   {\r
 549       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 550       alignPanel.RefreshPanels();\r
 551   }\r
 552 \r
 553   void SetFont()\r
 554   {\r
 555       int style = java.awt.Font.PLAIN;\r
 556       if(fontStyleMenuItem.getText().equals("bold"))\r
 557         style = java.awt.Font.BOLD;\r
 558       else if(fontStyleMenuItem.getText().equals("italic"))\r
 559         style = java.awt.Font.ITALIC;\r
 560 \r
 561       viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),\r
 562                                            style,\r
 563                                            Integer.parseInt(fontSizeMenuItem.getText())));\r
 564       alignPanel.RefreshPanels();\r
 565 \r
 566   }\r
 567 \r
 568   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 569   {\r
 570     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 571     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
 572   }\r
 573 \r
 574 \r
 575   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 576   {\r
 577     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 578     alignPanel.RefreshPanels();\r
 579   }\r
 580 \r
 581   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 582   {\r
 583     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 584     alignPanel.RefreshPanels();\r
 585   }\r
 586 \r
 587 \r
 588   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 589   {\r
 590     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 591     alignPanel.RefreshPanels();\r
 592   }\r
 593 \r
 594   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 595   {\r
 596     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 597     alignPanel.RefreshPanels();\r
 598   }\r
 599 \r
 600   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 601   {\r
 602     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
 603   }\r
 604 \r
 605   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 606   {\r
 607     if (alignPanel.overviewPanel != null)\r
 608       return;\r
 609 \r
 610     JInternalFrame frame = new JInternalFrame();\r
 611     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 612    try{\r
 613      overview = new OverviewPanel(alignPanel, viewport);\r
 614      frame.setContentPane(overview);\r
 615     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 616                              frame.getWidth(), frame.getHeight());\r
 617     frame.pack();\r
 618     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 619     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 620       {\r
 621             alignPanel.setOverviewPanel(null);\r
 622       };\r
 623     });\r
 624     alignPanel.setOverviewPanel( overview );\r
 625 \r
 626   }catch(java.lang.OutOfMemoryError ex)\r
 627    {\r
 628      JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 629                                    +"\nTry reducing the font size.",\r
 630                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 631    }\r
 632 \r
 633 \r
 634   }\r
 635 \r
 636   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 637   {\r
 638     viewport.setGlobalColourScheme( null );\r
 639     changeColour();\r
 640   }\r
 641 \r
 642 \r
 643   public void clustalColour_actionPerformed(ActionEvent e)\r
 644   {\r
 645     viewport.setGlobalColourScheme(\r
 646       new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 647     abovePIDThreshold.setSelected(false);\r
 648     changeColour();\r
 649   }\r
 650 \r
 651   public void zappoColour_actionPerformed(ActionEvent e)\r
 652   {\r
 653     viewport.setGlobalColourScheme(new ZappoColourScheme() );\r
 654     changeColour();\r
 655   }\r
 656 \r
 657   public void taylorColour_actionPerformed(ActionEvent e)\r
 658   {\r
 659     viewport.setGlobalColourScheme(new TaylorColourScheme() );\r
 660     changeColour();\r
 661   }\r
 662 \r
 663 \r
 664   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 665   {\r
 666     viewport.setGlobalColourScheme( new HydrophobicColourScheme() );\r
 667     changeColour();\r
 668   }\r
 669 \r
 670   public void helixColour_actionPerformed(ActionEvent e)\r
 671   {\r
 672     viewport.setGlobalColourScheme( new HelixColourScheme()  );\r
 673     changeColour();\r
 674   }\r
 675 \r
 676 \r
 677   public void strandColour_actionPerformed(ActionEvent e)\r
 678   {\r
 679     viewport.setGlobalColourScheme(new StrandColourScheme() );\r
 680     changeColour();\r
 681   }\r
 682 \r
 683 \r
 684   public void turnColour_actionPerformed(ActionEvent e)\r
 685   {\r
 686     viewport.setGlobalColourScheme(new TurnColourScheme() );\r
 687     changeColour();\r
 688   }\r
 689 \r
 690 \r
 691   public void buriedColour_actionPerformed(ActionEvent e)\r
 692   {\r
 693     viewport.setGlobalColourScheme( new BuriedColourScheme() );\r
 694     changeColour();\r
 695   }\r
 696 \r
 697   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 698   {\r
 699     viewport.setGlobalColourScheme( new NucleotideColourScheme() );\r
 700     changeColour();\r
 701   }\r
 702 \r
 703 \r
 704   void changeColour()\r
 705   {\r
 706     if(abovePIDThreshold.isSelected())\r
 707       abovePIDThreshold_actionPerformed(null);\r
 708     else if(conservationMenuItem.isSelected())\r
 709       conservationMenuItem_actionPerformed(null);\r
 710 \r
 711     alignPanel.RefreshPanels();\r
 712   }\r
 713 \r
 714 \r
 715   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 716   {\r
 717    if(abovePIDThreshold.isSelected())\r
 718    {\r
 719      abovePIDThreshold.setSelected(false);\r
 720      Desktop.hidePIDSlider();\r
 721    }\r
 722 \r
 723    viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 724 \r
 725    ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
 726 \r
 727    ConservationColourScheme ccs = null;\r
 728    if (oldCs instanceof ConservationColourScheme)\r
 729          ccs = (ConservationColourScheme) oldCs;\r
 730 \r
 731        if (conservationMenuItem.isSelected())\r
 732        {\r
 733          Alignment al = (Alignment) viewport.alignment;\r
 734          Conservation c = new Conservation("All",\r
 735                                            ResidueProperties.propHash, 3,\r
 736                                            al.getSequences(), 0,\r
 737                                            al.getWidth());\r
 738 \r
 739          c.calculate();\r
 740          c.verdict(false, 100);\r
 741 \r
 742          if (ccs != null)\r
 743            ccs = new ConservationColourScheme(c, ccs.cs);\r
 744          else\r
 745            ccs = new ConservationColourScheme(c, oldCs);\r
 746 \r
 747 \r
 748          int threshold = Desktop.setConservationSliderSource(alignPanel, ccs, "Background");\r
 749 \r
 750          ccs.inc = threshold;\r
 751 \r
 752          if (ccs.cs instanceof ResidueColourScheme)\r
 753            ((ResidueColourScheme) ccs.cs).setThreshold(0);\r
 754          else if (ccs.cs instanceof ScoreColourScheme)\r
 755            ((ScoreColourScheme)ccs.cs).setThreshold(0);\r
 756 \r
 757          viewport.setGlobalColourScheme(ccs);\r
 758 \r
 759 \r
 760        }\r
 761        else if (oldCs instanceof ConservationColourScheme)\r
 762        {\r
 763          /// ie, if we remove ConservationColourScheme from backgroundColour\r
 764          oldCs = ccs.cs;\r
 765          viewport.setGlobalColourScheme(oldCs);\r
 766          Desktop.hideConservationSlider();\r
 767        }\r
 768 \r
 769        if(e!=null)\r
 770          alignPanel.RefreshPanels();\r
 771   }\r
 772 \r
 773 \r
 774   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 775   {\r
 776       if(conservationMenuItem.isSelected())\r
 777         conservationMenuItem.setSelected(false);\r
 778 \r
 779       ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
 780       int threshold = 0;\r
 781       if (oldCs instanceof ConservationColourScheme)\r
 782      {\r
 783        ConservationColourScheme ccs = (ConservationColourScheme) oldCs;\r
 784        oldCs = ccs.cs;\r
 785      }\r
 786 \r
 787      if(abovePIDThreshold.isSelected())\r
 788      {\r
 789        threshold = Desktop.setPIDSliderSource(alignPanel, oldCs, "Background");\r
 790        Desktop.hideConservationSlider();\r
 791      }\r
 792      else\r
 793        Desktop.hidePIDSlider();\r
 794 \r
 795       if (oldCs instanceof ResidueColourScheme)\r
 796           ((ResidueColourScheme) oldCs).setThreshold(threshold);\r
 797       else if (oldCs instanceof ScoreColourScheme)\r
 798           ((ScoreColourScheme)oldCs).setThreshold(threshold);\r
 799 \r
 800     viewport.setGlobalColourScheme(oldCs);\r
 801      if(e!=null)\r
 802         alignPanel.RefreshPanels();\r
 803   }\r
 804 \r
 805 \r
 806 \r
 807   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 808   {\r
 809     JInternalFrame frame = new JInternalFrame();\r
 810     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 811     frame.setContentPane(chooser);\r
 812     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 813     frame.setResizable(false);\r
 814     frame.setIconifiable(false);\r
 815     frame.setMaximizable(false);\r
 816   }\r
 817 \r
 818   public void PIDColour_actionPerformed(ActionEvent e)\r
 819   {\r
 820     viewport.setGlobalColourScheme( new PIDColourScheme() );\r
 821     alignPanel.setColourScheme( );\r
 822   }\r
 823 \r
 824 \r
 825   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 826   {\r
 827     viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport)  );\r
 828     changeColour();\r
 829   }\r
 830 \r
 831 \r
 832 \r
 833   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 834   {\r
 835     addHistoryItem("sort");\r
 836     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 837     alignPanel.RefreshPanels();\r
 838   }\r
 839 \r
 840   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 841   {\r
 842     addHistoryItem("sort");\r
 843     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 844     alignPanel.RefreshPanels();\r
 845   }\r
 846 \r
 847   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 848   {\r
 849     addHistoryItem("sort");\r
 850     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 851     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 852     alignPanel.RefreshPanels();\r
 853   }\r
 854 \r
 855   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 856   {\r
 857     addHistoryItem("sort");\r
 858     if(viewport.getCurrentTree()==null)\r
 859       return;\r
 860 \r
 861     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 862     alignPanel.RefreshPanels();\r
 863   }\r
 864 \r
 865   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 866   {\r
 867     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 868     JInternalFrame frame = new JInternalFrame();\r
 869     frame.setContentPane(sp);\r
 870     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
 871     frame.setMaximizable(false);\r
 872     frame.setResizable(false);\r
 873 \r
 874   }\r
 875 \r
 876   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 877   {\r
 878     if(viewport.getSelection().size()<2)\r
 879       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 880     else\r
 881     {\r
 882       JInternalFrame frame = new JInternalFrame();\r
 883       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 884       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 885     }\r
 886   }\r
 887 \r
 888   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 889   {\r
 890     if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)\r
 891        || viewport.getAlignment().getHeight()<4)\r
 892     {\r
 893       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 894                                     +"at least 4 input sequences.",\r
 895                                     "Sequence selection insufficient",\r
 896                                     JOptionPane.WARNING_MESSAGE);\r
 897       return;\r
 898     }\r
 899 \r
 900     try{\r
 901       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 902       JInternalFrame frame = new JInternalFrame();\r
 903       frame.setContentPane(pcaPanel);\r
 904       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 905    }catch(java.lang.OutOfMemoryError ex)\r
 906    {\r
 907      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 908                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 909    }\r
 910 \r
 911 \r
 912   }\r
 913 \r
 914   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 915   {\r
 916     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 917   }\r
 918 \r
 919   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 920   {\r
 921     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 922   }\r
 923 \r
 924 \r
 925   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 926   {\r
 927     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 928   }\r
 929 \r
 930   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 931   {\r
 932     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 933   }\r
 934 \r
 935   void NewTreePanel(String type, String pwType, String title)\r
 936   {\r
 937     //are the sequences aligned?\r
 938     if(!viewport.alignment.isAligned())\r
 939     {\r
 940       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
 941                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
 942       return;\r
 943     }\r
 944 \r
 945     JInternalFrame frame = new javax.swing.JInternalFrame();\r
 946     TreePanel tp=null;\r
 947    if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
 948    {\r
 949      tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,\r
 950                          viewport.getStartRes(), viewport.getEndRes());\r
 951    }\r
 952    else\r
 953    {\r
 954      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 955                          type, pwType, viewport.getStartRes(),\r
 956                          viewport.getEndRes());\r
 957    }\r
 958 \r
 959    frame.setContentPane(tp);\r
 960    Desktop.addInternalFrame(frame, title, 600, 500);\r
 961   }\r
 962 \r
 963 \r
 964 \r
 965 \r
 966   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 967   {\r
 968     JInternalFrame frame = new JInternalFrame();\r
 969     ClustalThread ct = new ClustalThread(frame);\r
 970     Thread t = new Thread(ct);\r
 971     t.start();\r
 972     frame.setContentPane(ct);\r
 973      Desktop.addInternalFrame(frame, title, 300, 80);\r
 974 \r
 975   }\r
 976 \r
 977   class ClustalThread extends JPanel implements Runnable\r
 978   {\r
 979     Image [] image;\r
 980     int imageIndex = 0;\r
 981     boolean webServiceRunning = false;\r
 982     JInternalFrame frame;\r
 983     public ClustalThread(JInternalFrame frame)\r
 984     {\r
 985       this.frame = frame;\r
 986       image = new Image[9];\r
 987       for(int i=0; i<9; i++)\r
 988       {\r
 989         java.net.URL url = getClass().getResource("/dna" + (i+1) + ".gif");\r
 990         if (url != null)\r
 991         {\r
 992           image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
 993           MediaTracker mt = new MediaTracker(this);\r
 994           mt.addImage(image[i], i);\r
 995           try{mt.waitForID(i);}\r
 996           catch(Exception ex){}\r
 997         }\r
 998       }\r
 999       DNATwirler twirler = new DNATwirler();\r
1000       twirler.start();\r
1001       webServiceRunning = true;\r
1002     }\r
1003 \r
1004     class DNATwirler extends Thread\r
1005     {\r
1006       public void run()\r
1007       {\r
1008         while(webServiceRunning)\r
1009         {\r
1010           try{\r
1011             Thread.sleep(100);\r
1012             imageIndex++;\r
1013             imageIndex %=9;\r
1014             repaint();\r
1015           }\r
1016           catch(Exception ex){}\r
1017         }\r
1018       }\r
1019     }\r
1020 \r
1021     // JBPNote\r
1022     // Should check to see if the server settings are valid\r
1023     // Need visual-delay indication here.\r
1024     public void run()\r
1025        {\r
1026          jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
1027          Vector sv = viewport.getAlignment().getSequences();\r
1028          SequenceI[] seqs = new SequenceI[sv.size()];\r
1029 \r
1030          int i = 0;\r
1031          do\r
1032          {\r
1033            seqs[i] = (SequenceI) sv.elementAt(i);\r
1034          }\r
1035          while (++i < sv.size());\r
1036 \r
1037          SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
1038 \r
1039          if (alignment != null)\r
1040          {\r
1041            AlignFrame af = new AlignFrame(new Alignment(alignment));\r
1042           af.clustalColour.setSelected(true);\r
1043           af.clustalColour_actionPerformed(null);\r
1044            Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
1045                                     700, 500); // JBPNote - is there a new window geom. property ?\r
1046          }\r
1047          else\r
1048            JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
1049                                          JOptionPane.WARNING_MESSAGE);\r
1050 \r
1051          webServiceRunning = false;\r
1052          try{\r
1053            frame.setClosed(true);\r
1054          }catch(Exception ex){}\r
1055        }\r
1056 \r
1057        public void paintComponent(Graphics g)\r
1058        {\r
1059          g.setColor(Color.white);\r
1060          g.fillRect(0,0,getWidth(), getHeight());\r
1061          if(image!=null)\r
1062          {\r
1063            g.drawImage(image[imageIndex],10,10,this);\r
1064          }\r
1065          g.setFont(new Font("Arial", Font.BOLD, 12));\r
1066          g.setColor(Color.black);\r
1067          g.drawString("Clustal Alignment Web Service running", 30,30);\r
1068        }\r
1069   }\r
1070 }\r