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