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     changeColour( null );\r
 639   }\r
 640 \r
 641 \r
 642   public void clustalColour_actionPerformed(ActionEvent e)\r
 643   {\r
 644     abovePIDThreshold.setSelected(false);\r
 645     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 646   }\r
 647 \r
 648   public void zappoColour_actionPerformed(ActionEvent e)\r
 649   {\r
 650     changeColour(new ZappoColourScheme());\r
 651   }\r
 652 \r
 653   public void taylorColour_actionPerformed(ActionEvent e)\r
 654   {\r
 655     changeColour(new TaylorColourScheme());\r
 656   }\r
 657 \r
 658 \r
 659   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 660   {\r
 661     changeColour( new HydrophobicColourScheme() );\r
 662   }\r
 663 \r
 664   public void helixColour_actionPerformed(ActionEvent e)\r
 665   {\r
 666     changeColour(new HelixColourScheme() );\r
 667   }\r
 668 \r
 669 \r
 670   public void strandColour_actionPerformed(ActionEvent e)\r
 671   {\r
 672     changeColour(new StrandColourScheme());\r
 673   }\r
 674 \r
 675 \r
 676   public void turnColour_actionPerformed(ActionEvent e)\r
 677   {\r
 678     changeColour(new TurnColourScheme());\r
 679   }\r
 680 \r
 681 \r
 682   public void buriedColour_actionPerformed(ActionEvent e)\r
 683   {\r
 684     changeColour(new BuriedColourScheme() );\r
 685   }\r
 686 \r
 687   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 688   {\r
 689     changeColour(new NucleotideColourScheme());\r
 690   }\r
 691 \r
 692 \r
 693   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 694   {\r
 695     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
 696   }\r
 697 \r
 698 \r
 699 \r
 700   void changeColour(ColourSchemeI cs)\r
 701   {\r
 702 \r
 703     if(viewport.getColourAppliesToAllGroups())\r
 704     {\r
 705       Vector groups = viewport.alignment.getGroups();\r
 706       for(int i=0; i<groups.size(); i++)\r
 707       {\r
 708         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 709         sg.cs = cs;\r
 710 \r
 711         if(abovePIDThreshold.isSelected())\r
 712           abovePIDThreshold_actionPerformed(null);\r
 713         else if( viewport.getConservationSelected() )\r
 714         {\r
 715           Conservation c = new Conservation("Group",\r
 716                                             ResidueProperties.propHash, 3,\r
 717                                             sg.sequences, sg.getStartRes(),\r
 718                                             sg.getEndRes());\r
 719           c.calculate();\r
 720           c.verdict(false, 100);\r
 721           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 722 \r
 723           sg.cs = ccs;\r
 724         }\r
 725 \r
 726       }\r
 727     }\r
 728 \r
 729 \r
 730     if ( viewport.getAbovePIDThreshold())\r
 731     {\r
 732       int threshold = 0;\r
 733       threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");\r
 734       Desktop.hideConservationSlider();\r
 735 \r
 736       if (cs instanceof ResidueColourScheme)\r
 737         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 738       else if (cs instanceof ScoreColourScheme)\r
 739         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 740 \r
 741       viewport.setGlobalColourScheme(cs);\r
 742 \r
 743     }\r
 744     else\r
 745     if (cs instanceof ResidueColourScheme)\r
 746       ( (ResidueColourScheme) cs).setThreshold(0);\r
 747     else if (cs instanceof ScoreColourScheme)\r
 748       ( (ScoreColourScheme) cs).setThreshold(0);\r
 749 \r
 750 \r
 751 \r
 752 \r
 753 if ( viewport.getConservationSelected() )\r
 754  {\r
 755    ConservationColourScheme ccs = null;\r
 756 \r
 757    Alignment al = (Alignment) viewport.alignment;\r
 758    Conservation c = new Conservation("All",\r
 759                                      ResidueProperties.propHash, 3,\r
 760                                      al.getSequences(), 0,\r
 761                                      al.getWidth());\r
 762 \r
 763    c.calculate();\r
 764    c.verdict(false, 100);\r
 765 \r
 766    ccs = new ConservationColourScheme(c, cs);\r
 767 \r
 768    int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,\r
 769        "Background");\r
 770 \r
 771    ccs.inc = threshold;\r
 772 \r
 773    viewport.setGlobalColourScheme(ccs);\r
 774 \r
 775   }\r
 776   else\r
 777        viewport.setGlobalColourScheme( cs );\r
 778 \r
 779     alignPanel.RefreshPanels();\r
 780   }\r
 781 \r
 782 \r
 783   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 784   {\r
 785     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 786 \r
 787     viewport.setAbovePIDThreshold(false);\r
 788     abovePIDThreshold.setSelected(false);\r
 789     Desktop.hidePIDSlider();\r
 790     if(!viewport.getConservationSelected())\r
 791       Desktop.hideConservationSlider();\r
 792 \r
 793    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 794    if(cs instanceof ConservationColourScheme )\r
 795      changeColour( ((ConservationColourScheme)cs).cs );\r
 796     else\r
 797       changeColour( cs );\r
 798   }\r
 799 \r
 800 \r
 801   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 802   {\r
 803     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
 804 \r
 805     conservationMenuItem.setSelected(false);\r
 806     viewport.setConservationSelected(false);\r
 807     Desktop.hideConservationSlider();\r
 808 \r
 809     if(!viewport.getAbovePIDThreshold())\r
 810       Desktop.hidePIDSlider();\r
 811 \r
 812 \r
 813     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 814     if(cs instanceof ConservationColourScheme )\r
 815         changeColour( ((ConservationColourScheme)cs).cs );\r
 816     else\r
 817         changeColour( cs );\r
 818 \r
 819   }\r
 820 \r
 821 \r
 822 \r
 823   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 824   {\r
 825     JInternalFrame frame = new JInternalFrame();\r
 826     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 827     frame.setContentPane(chooser);\r
 828     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 829     frame.setResizable(false);\r
 830     frame.setIconifiable(false);\r
 831     frame.setMaximizable(false);\r
 832   }\r
 833 \r
 834   public void PIDColour_actionPerformed(ActionEvent e)\r
 835   {\r
 836     changeColour( new PIDColourScheme() );\r
 837   }\r
 838 \r
 839 \r
 840   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 841   {\r
 842     changeColour(new Blosum62ColourScheme(viewport) );\r
 843   }\r
 844 \r
 845 \r
 846 \r
 847   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 848   {\r
 849     addHistoryItem("sort");\r
 850     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 851     alignPanel.RefreshPanels();\r
 852   }\r
 853 \r
 854   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 855   {\r
 856     addHistoryItem("sort");\r
 857     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 858     alignPanel.RefreshPanels();\r
 859   }\r
 860 \r
 861   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 862   {\r
 863     addHistoryItem("sort");\r
 864     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 865     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 866     alignPanel.RefreshPanels();\r
 867   }\r
 868 \r
 869   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 870   {\r
 871     addHistoryItem("sort");\r
 872     if(viewport.getCurrentTree()==null)\r
 873       return;\r
 874 \r
 875     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 876     alignPanel.RefreshPanels();\r
 877   }\r
 878 \r
 879   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 880   {\r
 881     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 882     JInternalFrame frame = new JInternalFrame();\r
 883     frame.setContentPane(sp);\r
 884     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
 885     frame.setMaximizable(false);\r
 886     frame.setResizable(false);\r
 887 \r
 888   }\r
 889 \r
 890   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 891   {\r
 892     if(viewport.getSelection().size()<2)\r
 893       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 894     else\r
 895     {\r
 896       JInternalFrame frame = new JInternalFrame();\r
 897       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 898       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 899     }\r
 900   }\r
 901 \r
 902   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 903   {\r
 904     if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)\r
 905        || viewport.getAlignment().getHeight()<4)\r
 906     {\r
 907       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 908                                     +"at least 4 input sequences.",\r
 909                                     "Sequence selection insufficient",\r
 910                                     JOptionPane.WARNING_MESSAGE);\r
 911       return;\r
 912     }\r
 913 \r
 914     try{\r
 915       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 916       JInternalFrame frame = new JInternalFrame();\r
 917       frame.setContentPane(pcaPanel);\r
 918       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 919    }catch(java.lang.OutOfMemoryError ex)\r
 920    {\r
 921      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 922                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 923    }\r
 924 \r
 925 \r
 926   }\r
 927 \r
 928   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 929   {\r
 930     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 931   }\r
 932 \r
 933   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 934   {\r
 935     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 936   }\r
 937 \r
 938 \r
 939   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 940   {\r
 941     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 942   }\r
 943 \r
 944   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 945   {\r
 946     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 947   }\r
 948 \r
 949   void NewTreePanel(String type, String pwType, String title)\r
 950   {\r
 951     //are the sequences aligned?\r
 952     if(!viewport.alignment.isAligned())\r
 953     {\r
 954       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
 955                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
 956       return;\r
 957     }\r
 958 \r
 959     JInternalFrame frame = new javax.swing.JInternalFrame();\r
 960     TreePanel tp=null;\r
 961    if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
 962    {\r
 963      tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,\r
 964                          0, viewport.alignment.getWidth());\r
 965    }\r
 966    else\r
 967    {\r
 968      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 969                          type, pwType,  0, viewport.alignment.getWidth());\r
 970    }\r
 971 \r
 972    frame.setContentPane(tp);\r
 973    Desktop.addInternalFrame(frame, title, 600, 500);\r
 974   }\r
 975 \r
 976 \r
 977 \r
 978 \r
 979   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 980   {\r
 981     JInternalFrame frame = new JInternalFrame();\r
 982     ClustalThread ct = new ClustalThread(frame);\r
 983     Thread t = new Thread(ct);\r
 984     t.start();\r
 985     frame.setContentPane(ct);\r
 986      Desktop.addInternalFrame(frame, title, 300, 80);\r
 987 \r
 988   }\r
 989 \r
 990   class ClustalThread extends JPanel implements Runnable\r
 991   {\r
 992     Image [] image;\r
 993     int imageIndex = 0;\r
 994     boolean webServiceRunning = false;\r
 995     JInternalFrame frame;\r
 996     public ClustalThread(JInternalFrame frame)\r
 997     {\r
 998       this.frame = frame;\r
 999       image = new Image[9];\r
1000       for(int i=0; i<9; i++)\r
1001       {\r
1002         java.net.URL url = getClass().getResource("/dna" + (i+1) + ".gif");\r
1003         if (url != null)\r
1004         {\r
1005           image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
1006           MediaTracker mt = new MediaTracker(this);\r
1007           mt.addImage(image[i], i);\r
1008           try{mt.waitForID(i);}\r
1009           catch(Exception ex){}\r
1010         }\r
1011       }\r
1012       DNATwirler twirler = new DNATwirler();\r
1013       twirler.start();\r
1014       webServiceRunning = true;\r
1015     }\r
1016 \r
1017     class DNATwirler extends Thread\r
1018     {\r
1019       public void run()\r
1020       {\r
1021         while(webServiceRunning)\r
1022         {\r
1023           try{\r
1024             Thread.sleep(100);\r
1025             imageIndex++;\r
1026             imageIndex %=9;\r
1027             repaint();\r
1028           }\r
1029           catch(Exception ex){}\r
1030         }\r
1031       }\r
1032     }\r
1033 \r
1034     // JBPNote\r
1035     // Should check to see if the server settings are valid\r
1036     // Need visual-delay indication here.\r
1037     public void run()\r
1038        {\r
1039          jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
1040          Vector sv = viewport.getAlignment().getSequences();\r
1041          SequenceI[] seqs = new SequenceI[sv.size()];\r
1042 \r
1043          int i = 0;\r
1044          do\r
1045          {\r
1046            seqs[i] = (SequenceI) sv.elementAt(i);\r
1047          }\r
1048          while (++i < sv.size());\r
1049 \r
1050          SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
1051 \r
1052          if (alignment != null)\r
1053          {\r
1054            AlignFrame af = new AlignFrame(new Alignment(alignment));\r
1055           af.clustalColour.setSelected(true);\r
1056           af.clustalColour_actionPerformed(null);\r
1057            Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
1058                                     700, 500); // JBPNote - is there a new window geom. property ?\r
1059          }\r
1060          else\r
1061            JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
1062                                          JOptionPane.WARNING_MESSAGE);\r
1063 \r
1064          webServiceRunning = false;\r
1065          try{\r
1066            frame.setClosed(true);\r
1067          }catch(Exception ex){}\r
1068        }\r
1069 \r
1070        public void paintComponent(Graphics g)\r
1071        {\r
1072          g.setColor(Color.white);\r
1073          g.fillRect(0,0,getWidth(), getHeight());\r
1074          if(image!=null)\r
1075          {\r
1076            g.drawImage(image[imageIndex],10,10,this);\r
1077          }\r
1078          g.setFont(new Font("Arial", Font.BOLD, 12));\r
1079          g.setColor(Color.black);\r
1080          g.drawString("Clustal Alignment Web Service running", 30,30);\r
1081        }\r
1082   }\r
1083 }\r