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