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 MCview.*;\r
  21 import java.awt.*;\r
  22 import java.awt.event.*;\r
  23 import java.awt.print.*;\r
  24 import javax.swing.*;\r
  25 import javax.swing.event.*;\r
  26 import java.util.*;\r
  27 import jalview.datamodel.SequenceI;\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 \r
  37     viewport = new AlignViewport(al,true,true,true,false);\r
  38     alignPanel = new AlignmentPanel(this, viewport);\r
  39     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
  40     fontNameMenuItem.setText(viewport.getFont().getName());\r
  41     fontSizeMenuItem.setText(viewport.getFont().getSize()+"");\r
  42 \r
  43     clustalColour.setSelected(true);\r
  44     clustalColour_actionPerformed(null);\r
  45   }\r
  46 \r
  47   protected void saveAs_actionPerformed(ActionEvent e)\r
  48   {\r
  49     JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);\r
  50     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
  51     chooser.setToolTipText("Save");\r
  52     int value = chooser.showSaveDialog(this);\r
  53     if(value == JFileChooser.APPROVE_OPTION)\r
  54     {\r
  55       String choice =  chooser.getSelectedFile().getPath();\r
  56       jalview.bin.Cache.LAST_DIRECTORY = choice;\r
  57       String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
  58       try{\r
  59         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
  60         out.println(output);\r
  61         out.close();\r
  62       }\r
  63       catch(Exception ex){}\r
  64     }\r
  65 \r
  66   }\r
  67 \r
  68   protected void outputText_actionPerformed(ActionEvent e)\r
  69   {\r
  70      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
  71      JInternalFrame frame = new JInternalFrame();\r
  72      cap.formatForOutput();\r
  73      frame.setContentPane(cap);\r
  74      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
  75      cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
  76   }\r
  77 \r
  78   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
  79   {\r
  80     HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
  81     htmlOutput = null;\r
  82   }\r
  83 \r
  84   public void printMenuItem_actionPerformed(ActionEvent e)\r
  85   {\r
  86     //Putting in a thread avoids Swing painting problems\r
  87     PrintThread thread = new PrintThread();\r
  88     thread.start();\r
  89   }\r
  90 \r
  91   class PrintThread extends Thread\r
  92   {\r
  93     public void run()\r
  94     {\r
  95       PrinterJob printJob = PrinterJob.getPrinterJob();\r
  96       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
  97       printJob.setPrintable(alignPanel, pf);\r
  98       if (printJob.printDialog())\r
  99       {\r
 100         try\r
 101         {\r
 102           printJob.print();\r
 103         }\r
 104         catch (Exception PrintException)\r
 105         {\r
 106           PrintException.printStackTrace();\r
 107         }\r
 108       }\r
 109     }\r
 110 \r
 111   }\r
 112 \r
 113 \r
 114 \r
 115 \r
 116   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 117   {\r
 118     try{\r
 119       this.setClosed(true);\r
 120     }catch(Exception ex){}\r
 121   }\r
 122 \r
 123   ArrayList  historyList = new ArrayList();\r
 124   ArrayList redoList = new ArrayList();\r
 125 \r
 126   void updateEditMenuBar()\r
 127   {\r
 128     if(historyList.size()>0)\r
 129      {\r
 130        undoMenuItem.setEnabled(true);\r
 131        Object [] history = (Object[])historyList.get(0);\r
 132        undoMenuItem.setText("Undo "+history[0]);\r
 133      }\r
 134     else\r
 135     {\r
 136       undoMenuItem.setEnabled(false);\r
 137       undoMenuItem.setText("Undo");\r
 138     }\r
 139 \r
 140     if(redoList.size()>0)\r
 141      {\r
 142        redoMenuItem.setEnabled(true);\r
 143        Object [] history = (Object[])redoList.get(0);\r
 144        redoMenuItem.setText("Redo "+history[0]);\r
 145      }\r
 146     else\r
 147     {\r
 148       redoMenuItem.setEnabled(false);\r
 149       redoMenuItem.setText("Redo");\r
 150     }\r
 151   }\r
 152 \r
 153   public void addHistoryItem(String type)\r
 154   {\r
 155     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 156     redoList.clear();\r
 157     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 158     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 159     {\r
 160       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 161                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 162     }\r
 163 \r
 164     historyList.add(0, new Object[]{type,  seq} );\r
 165     updateEditMenuBar();\r
 166   }\r
 167 \r
 168   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 169   {\r
 170     Object [] history = (Object[])historyList.remove(0);\r
 171     // add the redo state before continuing!!\r
 172     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 173     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 174     {\r
 175       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 176                             viewport.getAlignment().getSequenceAt(i).\r
 177                             getSequence());\r
 178     }\r
 179     /////////\r
 180 \r
 181     redoList.add(0, new Object[] {history[0], seq});\r
 182 \r
 183       seq = (SequenceI[]) history[1];\r
 184       viewport.setAlignment( new Alignment(seq) );\r
 185       updateEditMenuBar();\r
 186       alignPanel.RefreshPanels();\r
 187   }\r
 188 \r
 189 \r
 190   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 191   {\r
 192      Object [] history = (Object[])redoList.remove(0);\r
 193      SequenceI[] seq = (SequenceI[]) history[1];\r
 194      viewport.setAlignment( new Alignment(seq) );\r
 195      updateEditMenuBar();\r
 196      alignPanel.RefreshPanels();\r
 197   }\r
 198 \r
 199 \r
 200   public void groupsMenuItem_actionPerformed(ActionEvent e)\r
 201   {\r
 202     GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
 203     JInternalFrame frame = new JInternalFrame();\r
 204     frame.setContentPane(geditor);\r
 205     Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
 206     frame.setResizable(false);\r
 207   }\r
 208 \r
 209   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 210   {\r
 211     viewport.alignment.deleteAllGroups();\r
 212     viewport.getSelection().clear();\r
 213 \r
 214     alignPanel.RefreshPanels();\r
 215   }\r
 216 \r
 217 \r
 218 \r
 219   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 220   {\r
 221     Selection sel = viewport.getSelection();\r
 222     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 223       sel.addElement( viewport.getAlignment().getSequenceAt(i));\r
 224     PaintRefresher.Refresh(null);\r
 225   }\r
 226 \r
 227   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 228   {\r
 229     viewport.setRubberbandGroup(null);\r
 230     viewport.getSelection().clear();\r
 231     PaintRefresher.Refresh(null);\r
 232   }\r
 233 \r
 234   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 235   {\r
 236     Selection sel = viewport.getSelection();\r
 237     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 238     {\r
 239       if (sel.contains(viewport.getAlignment().getSequenceAt(i)))\r
 240         sel.removeElement(viewport.getAlignment().getSequenceAt(i));\r
 241       else\r
 242         sel.addElement(viewport.getAlignment().getSequenceAt(i));\r
 243     }\r
 244     PaintRefresher.Refresh(null);\r
 245   }\r
 246 \r
 247 \r
 248   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 249   {\r
 250     viewport.getColumnSelection().clear();\r
 251     repaint();\r
 252   }\r
 253 \r
 254   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 255   {\r
 256     addHistoryItem("delete columns");\r
 257     ColumnSelection colSel = viewport.getColumnSelection();\r
 258     if (colSel.size() > 0)\r
 259     {\r
 260       int min = colSel.getMin();\r
 261       viewport.getAlignment().trimLeft(min);\r
 262       colSel.compensateForEdit(0,min);\r
 263       alignPanel.RefreshPanels();\r
 264     }\r
 265   }\r
 266 \r
 267   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 268   {\r
 269     addHistoryItem("delete columns");\r
 270     ColumnSelection colSel = viewport.getColumnSelection();\r
 271     if (colSel.size() > 0)\r
 272     {\r
 273       int max = colSel.getMax();\r
 274       if(max>1)\r
 275         viewport.getAlignment().trimRight(max);\r
 276 \r
 277       alignPanel.RefreshPanels();\r
 278     }\r
 279 \r
 280   }\r
 281 \r
 282   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 283   {\r
 284     addHistoryItem("delete gapped columns");\r
 285     viewport.getAlignment().removeGaps();\r
 286     alignPanel.RefreshPanels();\r
 287   }\r
 288 \r
 289   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 290   {\r
 291     addHistoryItem("delete all gaps");\r
 292     SequenceI current;\r
 293     int jSize;\r
 294     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 295     {\r
 296       current = viewport.getAlignment().getSequenceAt(i);\r
 297       jSize = current.getLength();\r
 298       for (int j=0; j < jSize; j++)\r
 299         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 300         {\r
 301           current.deleteCharAt(j);\r
 302           j--;\r
 303           jSize--;\r
 304         }\r
 305     }\r
 306 \r
 307     alignPanel.RefreshPanels();\r
 308   }\r
 309 \r
 310   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 311   {\r
 312     char thisChar = '-';\r
 313     char nextChar = '.';\r
 314     if(viewport.getGapCharacter()=='-')\r
 315     {\r
 316       thisChar = '.';\r
 317       nextChar = '-';\r
 318     }\r
 319     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 320     viewport.setGapCharacter(thisChar);\r
 321     alignPanel.RefreshPanels();\r
 322   }\r
 323 \r
 324   public void findMenuItem_actionPerformed(ActionEvent e)\r
 325   {\r
 326     JOptionPane op = new JOptionPane();\r
 327     JInternalFrame frame =  op.createInternalFrame(this, "Find");\r
 328     Finder finder = new Finder(viewport, alignPanel, frame);\r
 329     frame.setClosable(true);\r
 330     frame.setContentPane(finder);\r
 331     frame.setSize(340,110);\r
 332     frame.setVisible(true);\r
 333   }\r
 334 \r
 335 \r
 336 \r
 337   public void fontNameMenuItem_actionPerformed(ActionEvent e)\r
 338   {\r
 339     String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
 340 \r
 341 \r
 342     String selection = JOptionPane.showInternalInputDialog(this,\r
 343                                 "Select font",\r
 344                                 "Font selection",\r
 345                                 JOptionPane.QUESTION_MESSAGE,\r
 346                                 null,fonts\r
 347                                 ,fontNameMenuItem.getText()).toString();\r
 348     if(selection!=null)\r
 349     {\r
 350        fontNameMenuItem.setText(selection);\r
 351        SetFont();\r
 352      }\r
 353 \r
 354   }\r
 355 \r
 356   public void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
 357   {\r
 358     String selection = JOptionPane.showInternalInputDialog(this,\r
 359                                 "Select font size",\r
 360                                 "Font size",\r
 361                                 JOptionPane.QUESTION_MESSAGE,\r
 362                                 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
 363                                 ,fontSizeMenuItem.getText()).toString();\r
 364     if(selection!=null)\r
 365      {\r
 366        fontSizeMenuItem.setText(selection);\r
 367        SetFont();\r
 368      }\r
 369   }\r
 370 \r
 371   public void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
 372   {\r
 373     String selection = JOptionPane.showInternalInputDialog(this,\r
 374                                 "Select font style",\r
 375                                 "Font style",\r
 376                                 JOptionPane.QUESTION_MESSAGE,\r
 377                                 null, new String[]{"plain", "bold", "italic"}\r
 378                                 ,fontStyleMenuItem.getText()).toString();\r
 379     if(selection!=null)\r
 380     {\r
 381       fontStyleMenuItem.setText(selection);\r
 382       SetFont();\r
 383     }\r
 384 \r
 385   }\r
 386 \r
 387   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 388   {\r
 389       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 390       alignPanel.RefreshPanels();\r
 391   }\r
 392 \r
 393   void SetFont()\r
 394   {\r
 395       int style = java.awt.Font.PLAIN;\r
 396       if(fontStyleMenuItem.getText().equals("bold"))\r
 397         style = java.awt.Font.BOLD;\r
 398       else if(fontStyleMenuItem.getText().equals("italic"))\r
 399         style = java.awt.Font.ITALIC;\r
 400 \r
 401       viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),\r
 402                                            style,\r
 403                                            Integer.parseInt(fontSizeMenuItem.getText())));\r
 404       alignPanel.RefreshPanels();\r
 405 \r
 406   }\r
 407 \r
 408   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 409   {\r
 410     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 411     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
 412   }\r
 413 \r
 414 \r
 415   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 416   {\r
 417     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 418     alignPanel.RefreshPanels();\r
 419   }\r
 420 \r
 421   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 422   {\r
 423     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 424     alignPanel.RefreshPanels();\r
 425   }\r
 426 \r
 427 \r
 428   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 429   {\r
 430     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 431     alignPanel.RefreshPanels();\r
 432   }\r
 433 \r
 434   public void secondaryStructure_actionPerformed(ActionEvent evt)\r
 435   {\r
 436     alignPanel.setSecondaryStructureVisible(secondaryStructure.isSelected());\r
 437   }\r
 438 \r
 439   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 440   {\r
 441     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
 442   }\r
 443 \r
 444   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 445   {\r
 446     if (alignPanel.overviewPanel != null)\r
 447       return;\r
 448 \r
 449     JInternalFrame frame = new JInternalFrame();\r
 450     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 451    try{\r
 452      overview = new OverviewPanel(alignPanel, viewport);\r
 453      frame.setContentPane(overview);\r
 454     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 455                              frame.getWidth(), frame.getHeight());\r
 456     frame.pack();\r
 457     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 458     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 459       {\r
 460             alignPanel.setOverviewPanel(null);\r
 461       };\r
 462     });\r
 463     alignPanel.setOverviewPanel( overview );\r
 464 \r
 465   }catch(java.lang.OutOfMemoryError ex)\r
 466    {\r
 467      JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 468                                    +"\nTry reducing the font size.",\r
 469                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 470    }\r
 471 \r
 472 \r
 473   }\r
 474 \r
 475   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 476   {\r
 477     viewport.setGlobalColourScheme( null );\r
 478     changeColour();\r
 479   }\r
 480 \r
 481 \r
 482   public void clustalColour_actionPerformed(ActionEvent e)\r
 483   {\r
 484     viewport.setGlobalColourScheme(\r
 485       new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 486     abovePIDThreshold.setSelected(false);\r
 487     changeColour();\r
 488   }\r
 489 \r
 490   public void zappoColour_actionPerformed(ActionEvent e)\r
 491   {\r
 492     viewport.setGlobalColourScheme(new ZappoColourScheme() );\r
 493     changeColour();\r
 494   }\r
 495 \r
 496   public void taylorColour_actionPerformed(ActionEvent e)\r
 497   {\r
 498     viewport.setGlobalColourScheme(new TaylorColourScheme() );\r
 499     changeColour();\r
 500   }\r
 501 \r
 502 \r
 503   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 504   {\r
 505     viewport.setGlobalColourScheme( new HydrophobicColourScheme() );\r
 506     changeColour();\r
 507   }\r
 508 \r
 509   public void helixColour_actionPerformed(ActionEvent e)\r
 510   {\r
 511     viewport.setGlobalColourScheme( new HelixColourScheme()  );\r
 512     changeColour();\r
 513   }\r
 514 \r
 515 \r
 516   public void strandColour_actionPerformed(ActionEvent e)\r
 517   {\r
 518     viewport.setGlobalColourScheme(new StrandColourScheme() );\r
 519     changeColour();\r
 520   }\r
 521 \r
 522 \r
 523   public void turnColour_actionPerformed(ActionEvent e)\r
 524   {\r
 525     viewport.setGlobalColourScheme(new TurnColourScheme() );\r
 526     changeColour();\r
 527   }\r
 528 \r
 529 \r
 530   public void buriedColour_actionPerformed(ActionEvent e)\r
 531   {\r
 532     viewport.setGlobalColourScheme( new BuriedColourScheme() );\r
 533     changeColour();\r
 534   }\r
 535 \r
 536   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 537   {\r
 538     viewport.setGlobalColourScheme( new NucleotideColourScheme() );\r
 539     changeColour();\r
 540   }\r
 541 \r
 542 \r
 543   void changeColour()\r
 544   {\r
 545     if(abovePIDThreshold.isSelected())\r
 546       abovePIDThreshold_actionPerformed(null);\r
 547     else if(conservationMenuItem.isSelected())\r
 548       conservationMenuItem_actionPerformed(null);\r
 549 \r
 550     alignPanel.RefreshPanels();\r
 551   }\r
 552 \r
 553 \r
 554   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 555   {\r
 556    if(abovePIDThreshold.isSelected())\r
 557    {\r
 558      abovePIDThreshold.setSelected(false);\r
 559      Desktop.hidePIDSlider();\r
 560    }\r
 561 \r
 562    viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 563 \r
 564    ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
 565 \r
 566    ConservationColourScheme ccs = null;\r
 567    if (oldCs instanceof ConservationColourScheme)\r
 568          ccs = (ConservationColourScheme) oldCs;\r
 569 \r
 570        if (conservationMenuItem.isSelected())\r
 571        {\r
 572          Alignment al = (Alignment) viewport.alignment;\r
 573          Conservation c = new Conservation("All",\r
 574                                            ResidueProperties.propHash, 3,\r
 575                                            al.getSequences(), 0,\r
 576                                            al.getWidth());\r
 577 \r
 578          c.calculate();\r
 579          c.verdict(false, 100);\r
 580 \r
 581          if (ccs != null)\r
 582            ccs = new ConservationColourScheme(c, ccs.cs);\r
 583          else\r
 584            ccs = new ConservationColourScheme(c, oldCs);\r
 585 \r
 586 \r
 587          int threshold = Desktop.setConservationSliderSource(alignPanel, ccs, "Background");\r
 588 \r
 589          ccs.inc = threshold;\r
 590 \r
 591          if (ccs.cs instanceof ResidueColourScheme)\r
 592            ((ResidueColourScheme) ccs.cs).setThreshold(0);\r
 593          else if (ccs.cs instanceof ScoreColourScheme)\r
 594            ((ScoreColourScheme)ccs.cs).setThreshold(0);\r
 595 \r
 596          viewport.setGlobalColourScheme(ccs);\r
 597 \r
 598 \r
 599        }\r
 600        else if (oldCs instanceof ConservationColourScheme)\r
 601        {\r
 602          /// ie, if we remove ConservationColourScheme from backgroundColour\r
 603          oldCs = ccs.cs;\r
 604          viewport.setGlobalColourScheme(oldCs);\r
 605          Desktop.hideConservationSlider();\r
 606        }\r
 607 \r
 608        if(e!=null)\r
 609          alignPanel.RefreshPanels();\r
 610   }\r
 611 \r
 612 \r
 613   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 614   {\r
 615       if(conservationMenuItem.isSelected())\r
 616         conservationMenuItem.setSelected(false);\r
 617 \r
 618       ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
 619       int threshold = 0;\r
 620       if (oldCs instanceof ConservationColourScheme)\r
 621      {\r
 622        ConservationColourScheme ccs = (ConservationColourScheme) oldCs;\r
 623        oldCs = ccs.cs;\r
 624      }\r
 625 \r
 626      if(abovePIDThreshold.isSelected())\r
 627      {\r
 628        threshold = Desktop.setPIDSliderSource(alignPanel, oldCs, "Background");\r
 629        Desktop.hideConservationSlider();\r
 630      }\r
 631      else\r
 632        Desktop.hidePIDSlider();\r
 633 \r
 634       if (oldCs instanceof ResidueColourScheme)\r
 635           ((ResidueColourScheme) oldCs).setThreshold(threshold);\r
 636       else if (oldCs instanceof ScoreColourScheme)\r
 637           ((ScoreColourScheme)oldCs).setThreshold(threshold);\r
 638 \r
 639     viewport.setGlobalColourScheme(oldCs);\r
 640      if(e!=null)\r
 641         alignPanel.RefreshPanels();\r
 642   }\r
 643 \r
 644 \r
 645 \r
 646   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 647   {\r
 648     JInternalFrame frame = new JInternalFrame();\r
 649     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 650     frame.setContentPane(chooser);\r
 651     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 652     frame.setResizable(false);\r
 653     frame.setIconifiable(false);\r
 654     frame.setMaximizable(false);\r
 655   }\r
 656 \r
 657   public void PIDColour_actionPerformed(ActionEvent e)\r
 658   {\r
 659     viewport.setGlobalColourScheme( new PIDColourScheme() );\r
 660     alignPanel.setColourScheme( );\r
 661   }\r
 662 \r
 663 \r
 664   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 665   {\r
 666     viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport)  );\r
 667     changeColour();\r
 668   }\r
 669 \r
 670 \r
 671 \r
 672   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 673   {\r
 674     addHistoryItem("sort");\r
 675     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 676     alignPanel.RefreshPanels();\r
 677   }\r
 678 \r
 679   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 680   {\r
 681     addHistoryItem("sort");\r
 682     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 683     alignPanel.RefreshPanels();\r
 684   }\r
 685 \r
 686   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 687   {\r
 688     addHistoryItem("sort");\r
 689     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 690     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 691     alignPanel.RefreshPanels();\r
 692   }\r
 693 \r
 694   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 695   {\r
 696     addHistoryItem("sort");\r
 697     if(viewport.getCurrentTree()==null)\r
 698       return;\r
 699 \r
 700     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 701     alignPanel.RefreshPanels();\r
 702   }\r
 703 \r
 704   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 705   {\r
 706     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 707     JInternalFrame frame = new JInternalFrame();\r
 708     frame.setContentPane(sp);\r
 709     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
 710     frame.setMaximizable(false);\r
 711     frame.setResizable(false);\r
 712 \r
 713   }\r
 714 \r
 715   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 716   {\r
 717     if(viewport.getSelection().size()<2)\r
 718       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 719     else\r
 720     {\r
 721       JInternalFrame frame = new JInternalFrame();\r
 722       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 723       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 724     }\r
 725   }\r
 726 \r
 727   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 728   {\r
 729     if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)\r
 730        || viewport.getAlignment().getHeight()<4)\r
 731     {\r
 732       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 733                                     +"at least 4 input sequences.",\r
 734                                     "Sequence selection insufficient",\r
 735                                     JOptionPane.WARNING_MESSAGE);\r
 736       return;\r
 737     }\r
 738 \r
 739     try{\r
 740       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 741       JInternalFrame frame = new JInternalFrame();\r
 742       frame.setContentPane(pcaPanel);\r
 743       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 744    }catch(java.lang.OutOfMemoryError ex)\r
 745    {\r
 746      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 747                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 748    }\r
 749 \r
 750 \r
 751   }\r
 752 \r
 753   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 754   {\r
 755     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 756   }\r
 757 \r
 758   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 759   {\r
 760     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 761   }\r
 762 \r
 763 \r
 764   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 765   {\r
 766     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 767   }\r
 768 \r
 769   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 770   {\r
 771     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 772   }\r
 773 \r
 774   void NewTreePanel(String type, String pwType, String title)\r
 775   {\r
 776     JInternalFrame frame = new javax.swing.JInternalFrame();\r
 777     TreePanel tp=null;\r
 778    if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
 779    {\r
 780      tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,\r
 781                          viewport.getStartRes(), viewport.getEndRes());\r
 782    }\r
 783    else\r
 784    {\r
 785      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 786                          type, pwType, viewport.getStartRes(),\r
 787                          viewport.getEndRes());\r
 788    }\r
 789 \r
 790    frame.setContentPane(tp);\r
 791    Desktop.addInternalFrame(frame, title, 600, 500);\r
 792   }\r
 793 \r
 794 \r
 795 \r
 796 \r
 797   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 798   {\r
 799     JInternalFrame frame = new JInternalFrame();\r
 800     ClustalThread ct = new ClustalThread(frame);\r
 801     Thread t = new Thread(ct);\r
 802     t.start();\r
 803     frame.setContentPane(ct);\r
 804      Desktop.addInternalFrame(frame, title, 300, 80);\r
 805 \r
 806   }\r
 807 \r
 808   class ClustalThread extends JPanel implements Runnable\r
 809   {\r
 810     Image [] image;\r
 811     int imageIndex = 0;\r
 812     boolean webServiceRunning = false;\r
 813     JInternalFrame frame;\r
 814     public ClustalThread(JInternalFrame frame)\r
 815     {\r
 816       this.frame = frame;\r
 817       image = new Image[9];\r
 818       for(int i=0; i<9; i++)\r
 819       {\r
 820         java.net.URL url = getClass().getResource("/dna" + (i+1) + ".gif");\r
 821         if (url != null)\r
 822         {\r
 823           image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
 824           MediaTracker mt = new MediaTracker(this);\r
 825           mt.addImage(image[i], i);\r
 826           try{mt.waitForID(i);}\r
 827           catch(Exception ex){}\r
 828         }\r
 829       }\r
 830       DNATwirler twirler = new DNATwirler();\r
 831       twirler.start();\r
 832       webServiceRunning = true;\r
 833     }\r
 834 \r
 835     class DNATwirler extends Thread\r
 836     {\r
 837       public void run()\r
 838       {\r
 839         while(webServiceRunning)\r
 840         {\r
 841           try{\r
 842             Thread.sleep(100);\r
 843             imageIndex++;\r
 844             imageIndex %=9;\r
 845             repaint();\r
 846           }\r
 847           catch(Exception ex){}\r
 848         }\r
 849       }\r
 850     }\r
 851 \r
 852     // JBPNote\r
 853     // Should check to see if the server settings are valid\r
 854     // Need visual-delay indication here.\r
 855     public void run()\r
 856        {\r
 857          jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
 858          Vector sv = viewport.getAlignment().getSequences();\r
 859          SequenceI[] seqs = new SequenceI[sv.size()];\r
 860 \r
 861          int i = 0;\r
 862          do\r
 863          {\r
 864            seqs[i] = (SequenceI) sv.elementAt(i);\r
 865          }\r
 866          while (++i < sv.size());\r
 867 \r
 868          SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
 869 \r
 870          if (alignment != null)\r
 871          {\r
 872            AlignFrame af = new AlignFrame(new Alignment(alignment));\r
 873            Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
 874                                     700, 500); // JBPNote - is there a new window geom. property ?\r
 875          }\r
 876          else\r
 877            JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
 878                                          JOptionPane.WARNING_MESSAGE);\r
 879 \r
 880          webServiceRunning = false;\r
 881          try{\r
 882            frame.setClosed(true);\r
 883          }catch(Exception ex){}\r
 884        }\r
 885 \r
 886        public void paintComponent(Graphics g)\r
 887        {\r
 888          g.setColor(Color.white);\r
 889          g.fillRect(0,0,getWidth(), getHeight());\r
 890          if(image!=null)\r
 891          {\r
 892            g.drawImage(image[imageIndex],10,10,this);\r
 893          }\r
 894          g.setFont(new Font("Arial", Font.BOLD, 12));\r
 895          g.setColor(Color.black);\r
 896          g.drawString("Clustal Alignment Web Service running", 30,30);\r
 897        }\r
 898 \r
 899 \r
 900   }\r
 901 \r
 902 \r
 903   public void pdbTest_actionPerformed(ActionEvent e)\r
 904   {\r
 905    String reply =\r
 906        JOptionPane.showInternalInputDialog(this, "Enter pdb code",\r
 907                                            "PDB test viewer", JOptionPane.QUESTION_MESSAGE);\r
 908 \r
 909    String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";\r
 910    if (reply.length()>1)\r
 911      url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id="+reply;\r
 912 \r
 913    try\r
 914    {\r
 915      PDBfile pdb = new PDBfile(url,\r
 916                                "URL");\r
 917     Sequence seq = (Sequence)viewport.getAlignment().getSequenceAt(0);\r
 918     seq.setPDBfile(pdb);\r
 919      ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).isVisible = true;\r
 920      ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).sequence = seq;\r
 921   // ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).colourBySequence();\r
 922 \r
 923      rotCanvas rc = new rotCanvas(pdb);\r
 924      JInternalFrame frame = new JInternalFrame();\r
 925      frame.setContentPane(rc);\r
 926      Desktop.addInternalFrame(frame, url, 400,400);\r
 927    }\r
 928    catch (Exception ex)\r
 929    {\r
 930      ex.printStackTrace();\r
 931    }\r
 932 \r
 933   }\r
 934 \r
 935 \r
 936   public void doKeyPressed(KeyEvent evt)\r
 937   {\r
 938 \r
 939     System.out.println(evt.getKeyChar());\r
 940     if(evt.isControlDown() && evt.getKeyChar()=='f')\r
 941       findMenuItem_actionPerformed(null);\r
 942 \r
 943   }\r
 944 \r
 945 \r
 946 }\r