src/jalview/gui/AlignFrame.java

   1 /********************\r
   2  * 2004 Jalview Reengineered\r
   3  * Barton Group\r
   4  * Dundee University\r
   5  *\r
   6  * AM Waterhouse\r
   7  *******************/\r
   8 \r
   9 \r
  10 \r
  11 \r
  12 package jalview.gui;\r
  13 \r
  14 import jalview.jbgui.GAlignFrame;\r
  15 import jalview.schemes.*;\r
  16 import jalview.datamodel.*;\r
  17 import jalview.analysis.*;\r
  18 import jalview.io.*;\r
  19 import jalview.ws.*;\r
  20 import java.awt.*;\r
  21 import java.awt.event.*;\r
  22 import java.awt.print.*;\r
  23 import javax.swing.*;\r
  24 import javax.swing.event.*;\r
  25 import java.util.*;\r
  26 import  java.awt.datatransfer.*;\r
  27 \r
  28 \r
  29 public class AlignFrame extends GAlignFrame\r
  30 {\r
  31   final AlignmentPanel alignPanel;\r
  32   final AlignViewport viewport;\r
  33   public AlignFrame(AlignmentI al)\r
  34   {\r
  35     super();\r
  36     viewport = new AlignViewport(al,true,true,true,false);\r
  37 \r
  38     String fontName = jalview.bin.Cache.getProperty("FONT_NAME");\r
  39     String fontStyle= jalview.bin.Cache.getProperty("FONT_STYLE");\r
  40     String fontSize = jalview.bin.Cache.getProperty("FONT_SIZE");\r
  41     if(fontName!=null && fontStyle!=null && fontSize!=null)\r
  42       viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );\r
  43 \r
  44 \r
  45 \r
  46     alignPanel = new AlignmentPanel(this, viewport);\r
  47     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
  48 \r
  49     addInternalFrameListener(new InternalFrameAdapter()\r
  50    {\r
  51      public void internalFrameActivated(InternalFrameEvent evt)\r
  52      {\r
  53           javax.swing.SwingUtilities.invokeLater(new Runnable()\r
  54           {\r
  55             public void run()\r
  56             {      alignPanel.requestFocus();    }\r
  57           });\r
  58 \r
  59      }\r
  60    });\r
  61 \r
  62   }\r
  63 \r
  64   protected void saveAs_actionPerformed(ActionEvent e)\r
  65   {\r
  66     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
  67     chooser.setFileView(new JalviewFileView());\r
  68     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
  69     chooser.setToolTipText("Save");\r
  70     int value = chooser.showSaveDialog(this);\r
  71     if(value == JalviewFileChooser.APPROVE_OPTION)\r
  72     {\r
  73       String choice =  chooser.getSelectedFile().getPath();\r
  74       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
  75       String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
  76       try{\r
  77         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
  78         out.println(output);\r
  79         out.close();\r
  80       }\r
  81       catch(Exception ex){}\r
  82     }\r
  83 \r
  84   }\r
  85 \r
  86   protected void outputText_actionPerformed(ActionEvent e)\r
  87   {\r
  88      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
  89      JInternalFrame frame = new JInternalFrame();\r
  90      cap.formatForOutput();\r
  91      frame.setContentPane(cap);\r
  92      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
  93      cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
  94   }\r
  95 \r
  96   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
  97   {\r
  98     HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
  99     htmlOutput = null;\r
 100   }\r
 101 \r
 102   protected void createJPG_actionPerformed(ActionEvent e)\r
 103   {\r
 104 \r
 105     int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;\r
 106     int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();\r
 107 \r
 108 \r
 109     if(!viewport.getWrapAlignment())\r
 110     {\r
 111       height = viewport.alignment.getHeight() * viewport.charHeight;\r
 112       width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;\r
 113     }\r
 114 \r
 115     alignPanel.makeJPG( width, height);\r
 116   }\r
 117 \r
 118 \r
 119   public void printMenuItem_actionPerformed(ActionEvent e)\r
 120   {\r
 121     //Putting in a thread avoids Swing painting problems\r
 122     PrintThread thread = new PrintThread();\r
 123     thread.start();\r
 124   }\r
 125 \r
 126   class PrintThread extends Thread\r
 127   {\r
 128     public void run()\r
 129     {\r
 130       PrinterJob printJob = PrinterJob.getPrinterJob();\r
 131       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
 132       printJob.setPrintable(alignPanel, pf);\r
 133       if (printJob.printDialog())\r
 134       {\r
 135         try\r
 136         {\r
 137           printJob.print();\r
 138         }\r
 139         catch (Exception PrintException)\r
 140         {\r
 141           PrintException.printStackTrace();\r
 142         }\r
 143       }\r
 144     }\r
 145 \r
 146   }\r
 147 \r
 148 \r
 149 \r
 150 \r
 151   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 152   {\r
 153     try{\r
 154       this.setClosed(true);\r
 155     }catch(Exception ex){}\r
 156   }\r
 157 \r
 158   Stack historyList = new Stack();\r
 159   Stack redoList = new Stack();\r
 160 \r
 161   void updateEditMenuBar()\r
 162   {\r
 163     if(historyList.size()>0)\r
 164      {\r
 165        undoMenuItem.setEnabled(true);\r
 166        Object [] history = (Object[])historyList.get(0);\r
 167        undoMenuItem.setText("Undo "+history[0]);\r
 168      }\r
 169     else\r
 170     {\r
 171       undoMenuItem.setEnabled(false);\r
 172       undoMenuItem.setText("Undo");\r
 173     }\r
 174 \r
 175     if(redoList.size()>0)\r
 176      {\r
 177        redoMenuItem.setEnabled(true);\r
 178        Object [] history = (Object[])redoList.get(0);\r
 179        redoMenuItem.setText("Redo "+history[0]);\r
 180      }\r
 181     else\r
 182     {\r
 183       redoMenuItem.setEnabled(false);\r
 184       redoMenuItem.setText("Redo");\r
 185     }\r
 186   }\r
 187 \r
 188   public void addHistoryItem(String type)\r
 189   {\r
 190     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 191     redoList.clear();\r
 192     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 193     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 194     {\r
 195       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 196                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 197     }\r
 198 \r
 199     historyList.add(0, new Object[]{type,  seq} );\r
 200     updateEditMenuBar();\r
 201   }\r
 202 \r
 203   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 204   {\r
 205     Object [] history = (Object[])historyList.remove(0);\r
 206     // add the redo state before continuing!!\r
 207     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 208     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 209     {\r
 210       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 211                             viewport.getAlignment().getSequenceAt(i).\r
 212                             getSequence());\r
 213     }\r
 214     /////////\r
 215 \r
 216     redoList.add(0, new Object[] {history[0], seq});\r
 217 \r
 218       seq = (SequenceI[]) history[1];\r
 219       viewport.setAlignment( new Alignment(seq) );\r
 220       updateEditMenuBar();\r
 221       alignPanel.RefreshPanels();\r
 222   }\r
 223 \r
 224   public void moveSelectedSequences(boolean up)\r
 225   {\r
 226     SequenceGroup sg = viewport.getSelectionGroup();\r
 227     if (sg == null)\r
 228       return;\r
 229 \r
 230     if (up)\r
 231     {\r
 232       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 233       {\r
 234         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 235         if (!sg.sequences.contains(seq))\r
 236           continue;\r
 237 \r
 238         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 239         if (sg.sequences.contains(temp))\r
 240           continue;\r
 241 \r
 242         viewport.alignment.getSequences().setElementAt(temp, i);\r
 243         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 244       }\r
 245     }\r
 246     else\r
 247     {\r
 248       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 249       {\r
 250         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 251         if (!sg.sequences.contains(seq))\r
 252           continue;\r
 253 \r
 254         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 255         if (sg.sequences.contains(temp))\r
 256           continue;\r
 257 \r
 258         viewport.alignment.getSequences().setElementAt(temp, i);\r
 259         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 260       }\r
 261     }\r
 262 \r
 263     alignPanel.RefreshPanels();\r
 264   }\r
 265 \r
 266 \r
 267 \r
 268   protected void copy_actionPerformed(ActionEvent e)\r
 269   {\r
 270    if(viewport.getSelectionGroup()==null)\r
 271      return;\r
 272 \r
 273    SequenceGroup sg = viewport.getSelectionGroup();\r
 274 \r
 275      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 276      StringBuffer buffer= new StringBuffer();\r
 277 \r
 278        for(int i=0; i<sg.getSize(); i++)\r
 279        {\r
 280          SequenceI seq = sg.getSequenceAt(i);\r
 281          buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
 282                         +seq.findPosition( sg.getEndRes() )+ "\t"\r
 283                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
 284        }\r
 285      c.setContents( new StringSelection( buffer.toString()) , null ) ;\r
 286 \r
 287   }\r
 288 \r
 289 \r
 290   protected void pasteNew_actionPerformed(ActionEvent e)\r
 291   {\r
 292     paste(true);\r
 293   }\r
 294 \r
 295   protected void pasteThis_actionPerformed(ActionEvent e)\r
 296   {\r
 297     addHistoryItem("Paste");\r
 298     paste(false);\r
 299   }\r
 300 \r
 301   void paste(boolean newAlignment)\r
 302   {\r
 303     try{\r
 304       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 305       Transferable contents = c.getContents(this);\r
 306       if (contents == null)\r
 307         return;\r
 308 \r
 309       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
 310       StringTokenizer st = new StringTokenizer(str);\r
 311       ArrayList seqs = new ArrayList();\r
 312       while (st.hasMoreElements())\r
 313       {\r
 314         String name = st.nextToken();\r
 315         int start = Integer.parseInt(st.nextToken());\r
 316         int end = Integer.parseInt(st.nextToken());\r
 317         Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
 318 \r
 319         if(!newAlignment)\r
 320           viewport.alignment.addSequence(sequence);\r
 321         else\r
 322           seqs.add(sequence);\r
 323       }\r
 324 \r
 325       if(newAlignment)\r
 326       {\r
 327         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 328         seqs.toArray(newSeqs);\r
 329         AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
 330         int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;\r
 331         if (newHeight > 500)\r
 332           newHeight = 500;\r
 333         Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
 334       }\r
 335       else\r
 336       {\r
 337         viewport.setEndSeq(viewport.alignment.getHeight());\r
 338         viewport.alignment.getWidth();\r
 339         alignPanel.RefreshPanels();\r
 340       }\r
 341 \r
 342     }catch(Exception ex){}// could be anything being pasted in here\r
 343 \r
 344   }\r
 345 \r
 346 \r
 347   protected void cut_actionPerformed(ActionEvent e)\r
 348   {\r
 349     copy_actionPerformed(null);\r
 350     delete_actionPerformed(null);\r
 351   }\r
 352 \r
 353   protected void delete_actionPerformed(ActionEvent e)\r
 354   {\r
 355     addHistoryItem("Delete");\r
 356     if (viewport.getSelectionGroup() == null)\r
 357       return;\r
 358 \r
 359      SequenceGroup sg = viewport.getSelectionGroup();\r
 360      for (int i=0;i < sg.sequences.size(); i++)\r
 361      {\r
 362        SequenceI seq = sg.getSequenceAt(i);\r
 363        int index = viewport.getAlignment().findIndex(seq);\r
 364        seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);\r
 365 \r
 366        if(seq.getSequence().length()<1)\r
 367           viewport.getAlignment().deleteSequence(seq);\r
 368       else\r
 369           viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 370      }\r
 371 \r
 372      viewport.setSelectionGroup(null);\r
 373      viewport.alignment.deleteGroup(sg);\r
 374      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
 375      if(viewport.getAlignment().getHeight()<1)\r
 376      try\r
 377      {\r
 378        this.setClosed(true);\r
 379      }catch(Exception ex){}\r
 380      alignPanel.RefreshPanels();\r
 381 \r
 382   }\r
 383 \r
 384 \r
 385 \r
 386   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 387   {\r
 388      Object [] history = (Object[])redoList.remove(0);\r
 389      SequenceI[] seq = (SequenceI[]) history[1];\r
 390      viewport.setAlignment( new Alignment(seq) );\r
 391      updateEditMenuBar();\r
 392      alignPanel.RefreshPanels();\r
 393   }\r
 394 \r
 395 \r
 396   public void groupsMenuItem_actionPerformed(ActionEvent e)\r
 397   {\r
 398     GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
 399     JInternalFrame frame = new JInternalFrame();\r
 400     frame.setContentPane(geditor);\r
 401     Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
 402     frame.setResizable(false);\r
 403   }\r
 404 \r
 405   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 406   {\r
 407     viewport.alignment.deleteAllGroups();\r
 408     viewport.setSelectionGroup(null);\r
 409 \r
 410     alignPanel.RefreshPanels();\r
 411   }\r
 412 \r
 413 \r
 414 \r
 415   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 416   {\r
 417     SequenceGroup sg = new SequenceGroup();\r
 418     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 419       sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
 420     sg.setEndRes(viewport.alignment.getWidth());\r
 421     viewport.setSelectionGroup(sg);\r
 422     PaintRefresher.Refresh(null);\r
 423   }\r
 424 \r
 425   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 426   {\r
 427     viewport.setSelectionGroup(null);\r
 428     PaintRefresher.Refresh(null);\r
 429   }\r
 430 \r
 431   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 432   {\r
 433     SequenceGroup sg = viewport.getSelectionGroup();\r
 434     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 435       sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
 436 \r
 437     PaintRefresher.Refresh(null);\r
 438   }\r
 439 \r
 440 \r
 441   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 442   {\r
 443     viewport.getColumnSelection().clear();\r
 444     repaint();\r
 445   }\r
 446 \r
 447   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 448   {\r
 449     addHistoryItem("delete columns");\r
 450     ColumnSelection colSel = viewport.getColumnSelection();\r
 451     if (colSel.size() > 0)\r
 452     {\r
 453       int min = colSel.getMin();\r
 454       viewport.getAlignment().trimLeft(min);\r
 455       colSel.compensateForEdit(0,min);\r
 456       alignPanel.RefreshPanels();\r
 457     }\r
 458   }\r
 459 \r
 460   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 461   {\r
 462     addHistoryItem("delete columns");\r
 463     ColumnSelection colSel = viewport.getColumnSelection();\r
 464     if (colSel.size() > 0)\r
 465     {\r
 466       int max = colSel.getMax();\r
 467       if(max>1)\r
 468         viewport.getAlignment().trimRight(max);\r
 469 \r
 470       alignPanel.RefreshPanels();\r
 471     }\r
 472 \r
 473   }\r
 474 \r
 475   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 476   {\r
 477     addHistoryItem("delete gapped columns");\r
 478     viewport.getAlignment().removeGaps();\r
 479     alignPanel.RefreshPanels();\r
 480   }\r
 481 \r
 482   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 483   {\r
 484     addHistoryItem("delete all gaps");\r
 485     SequenceI current;\r
 486     int jSize;\r
 487     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 488     {\r
 489       current = viewport.getAlignment().getSequenceAt(i);\r
 490       jSize = current.getLength();\r
 491       for (int j=0; j < jSize; j++)\r
 492         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 493         {\r
 494           current.deleteCharAt(j);\r
 495           j--;\r
 496           jSize--;\r
 497         }\r
 498     }\r
 499 \r
 500     alignPanel.RefreshPanels();\r
 501   }\r
 502 \r
 503   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 504   {\r
 505     char thisChar = '-';\r
 506     char nextChar = '.';\r
 507     if(viewport.getGapCharacter()=='-')\r
 508     {\r
 509       thisChar = '.';\r
 510       nextChar = '-';\r
 511     }\r
 512     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 513     viewport.setGapCharacter(thisChar);\r
 514     alignPanel.RefreshPanels();\r
 515   }\r
 516 \r
 517   public void findMenuItem_actionPerformed(ActionEvent e)\r
 518   {\r
 519       JInternalFrame frame = new JInternalFrame();\r
 520       Finder finder = new Finder(viewport, alignPanel, frame);\r
 521       frame.setContentPane(finder);\r
 522      Desktop.addInternalFrame(frame, "Find", 340,110);\r
 523 \r
 524   }\r
 525 \r
 526 \r
 527   public void font_actionPerformed(ActionEvent e)\r
 528   {\r
 529    // JOptionPane op = new JOptionPane();\r
 530     JInternalFrame frame = new JInternalFrame();\r
 531     FontChooser fc = new FontChooser( alignPanel, frame );\r
 532     frame.setContentPane(fc);\r
 533     Desktop.addInternalFrame(frame, "Change Font", 480,100);\r
 534   }\r
 535 \r
 536   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 537   {\r
 538       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 539       alignPanel.RefreshPanels();\r
 540   }\r
 541 \r
 542   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 543   {\r
 544     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 545     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
 546   }\r
 547 \r
 548 \r
 549   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 550   {\r
 551     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 552     alignPanel.RefreshPanels();\r
 553   }\r
 554 \r
 555   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 556   {\r
 557     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 558     alignPanel.RefreshPanels();\r
 559   }\r
 560 \r
 561 \r
 562   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 563   {\r
 564     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 565     alignPanel.RefreshPanels();\r
 566   }\r
 567 \r
 568   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 569   {\r
 570     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 571     if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
 572     {\r
 573          AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);\r
 574          ((Alignment)viewport.alignment).featuresAdded = true;\r
 575     }\r
 576     alignPanel.RefreshPanels();\r
 577   }\r
 578 \r
 579   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 580   {\r
 581     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
 582   }\r
 583 \r
 584   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 585   {\r
 586     if (alignPanel.overviewPanel != null)\r
 587       return;\r
 588 \r
 589     JInternalFrame frame = new JInternalFrame();\r
 590     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 591    try{\r
 592      overview = new OverviewPanel(alignPanel, viewport);\r
 593      frame.setContentPane(overview);\r
 594     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 595                              frame.getWidth(), frame.getHeight());\r
 596     frame.pack();\r
 597     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 598     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 599       {\r
 600             alignPanel.setOverviewPanel(null);\r
 601       };\r
 602     });\r
 603     alignPanel.setOverviewPanel( overview );\r
 604 \r
 605   }catch(java.lang.OutOfMemoryError ex)\r
 606    {\r
 607      JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 608                                    +"\nTry reducing the font size.",\r
 609                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 610    }\r
 611 \r
 612 \r
 613   }\r
 614 \r
 615   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 616   {\r
 617     changeColour( null );\r
 618   }\r
 619 \r
 620 \r
 621   public void clustalColour_actionPerformed(ActionEvent e)\r
 622   {\r
 623     abovePIDThreshold.setSelected(false);\r
 624     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 625   }\r
 626 \r
 627   public void zappoColour_actionPerformed(ActionEvent e)\r
 628   {\r
 629     changeColour(new ZappoColourScheme());\r
 630   }\r
 631 \r
 632   public void taylorColour_actionPerformed(ActionEvent e)\r
 633   {\r
 634     changeColour(new TaylorColourScheme());\r
 635   }\r
 636 \r
 637 \r
 638   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 639   {\r
 640     changeColour( new HydrophobicColourScheme() );\r
 641   }\r
 642 \r
 643   public void helixColour_actionPerformed(ActionEvent e)\r
 644   {\r
 645     changeColour(new HelixColourScheme() );\r
 646   }\r
 647 \r
 648 \r
 649   public void strandColour_actionPerformed(ActionEvent e)\r
 650   {\r
 651     changeColour(new StrandColourScheme());\r
 652   }\r
 653 \r
 654 \r
 655   public void turnColour_actionPerformed(ActionEvent e)\r
 656   {\r
 657     changeColour(new TurnColourScheme());\r
 658   }\r
 659 \r
 660 \r
 661   public void buriedColour_actionPerformed(ActionEvent e)\r
 662   {\r
 663     changeColour(new BuriedColourScheme() );\r
 664   }\r
 665 \r
 666   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 667   {\r
 668     changeColour(new NucleotideColourScheme());\r
 669   }\r
 670 \r
 671 \r
 672   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 673   {\r
 674     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
 675   }\r
 676 \r
 677 \r
 678 \r
 679   void changeColour(ColourSchemeI cs)\r
 680   {\r
 681 \r
 682     if(viewport.getColourAppliesToAllGroups())\r
 683     {\r
 684       Vector groups = viewport.alignment.getGroups();\r
 685       for(int i=0; i<groups.size(); i++)\r
 686       {\r
 687         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 688         sg.cs = cs;\r
 689 \r
 690         if(abovePIDThreshold.isSelected())\r
 691           abovePIDThreshold_actionPerformed(null);\r
 692         else if( viewport.getConservationSelected() )\r
 693         {\r
 694           Conservation c = new Conservation("Group",\r
 695                                             ResidueProperties.propHash, 3,\r
 696                                             sg.sequences, sg.getStartRes(),\r
 697                                             sg.getEndRes());\r
 698           c.calculate();\r
 699           c.verdict(false, 100);\r
 700           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 701 \r
 702           sg.cs = ccs;\r
 703         }\r
 704 \r
 705       }\r
 706     }\r
 707 \r
 708 \r
 709     if ( viewport.getAbovePIDThreshold())\r
 710     {\r
 711       int threshold = 0;\r
 712       threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");\r
 713       Desktop.hideConservationSlider();\r
 714 \r
 715       if (cs instanceof ResidueColourScheme)\r
 716         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 717       else if (cs instanceof ScoreColourScheme)\r
 718         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 719 \r
 720       viewport.setGlobalColourScheme(cs);\r
 721 \r
 722     }\r
 723     else\r
 724     if (cs instanceof ResidueColourScheme)\r
 725       ( (ResidueColourScheme) cs).setThreshold(0);\r
 726     else if (cs instanceof ScoreColourScheme)\r
 727       ( (ScoreColourScheme) cs).setThreshold(0);\r
 728 \r
 729 \r
 730 \r
 731 \r
 732 if ( viewport.getConservationSelected() )\r
 733  {\r
 734    ConservationColourScheme ccs = null;\r
 735 \r
 736    Alignment al = (Alignment) viewport.alignment;\r
 737    Conservation c = new Conservation("All",\r
 738                                      ResidueProperties.propHash, 3,\r
 739                                      al.getSequences(), 0,\r
 740                                      al.getWidth());\r
 741 \r
 742    c.calculate();\r
 743    c.verdict(false, 100);\r
 744 \r
 745    ccs = new ConservationColourScheme(c, cs);\r
 746 \r
 747    int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,\r
 748        "Background");\r
 749 \r
 750    ccs.inc = threshold;\r
 751 \r
 752    viewport.setGlobalColourScheme(ccs);\r
 753 \r
 754   }\r
 755   else\r
 756        viewport.setGlobalColourScheme( cs );\r
 757 \r
 758     alignPanel.RefreshPanels();\r
 759   }\r
 760 \r
 761 \r
 762   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 763   {\r
 764     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 765 \r
 766     viewport.setAbovePIDThreshold(false);\r
 767     abovePIDThreshold.setSelected(false);\r
 768     Desktop.hidePIDSlider();\r
 769     if(!viewport.getConservationSelected())\r
 770       Desktop.hideConservationSlider();\r
 771 \r
 772    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 773    if(cs instanceof ConservationColourScheme )\r
 774      changeColour( ((ConservationColourScheme)cs).cs );\r
 775     else\r
 776       changeColour( cs );\r
 777   }\r
 778 \r
 779 \r
 780   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 781   {\r
 782     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
 783 \r
 784     conservationMenuItem.setSelected(false);\r
 785     viewport.setConservationSelected(false);\r
 786     Desktop.hideConservationSlider();\r
 787 \r
 788     if(!viewport.getAbovePIDThreshold())\r
 789       Desktop.hidePIDSlider();\r
 790 \r
 791 \r
 792     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 793     if(cs instanceof ConservationColourScheme )\r
 794         changeColour( ((ConservationColourScheme)cs).cs );\r
 795     else\r
 796         changeColour( cs );\r
 797 \r
 798   }\r
 799 \r
 800 \r
 801 \r
 802   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 803   {\r
 804     JInternalFrame frame = new JInternalFrame();\r
 805     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 806     frame.setContentPane(chooser);\r
 807     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 808     frame.setResizable(false);\r
 809     frame.setIconifiable(false);\r
 810     frame.setMaximizable(false);\r
 811   }\r
 812 \r
 813   public void PIDColour_actionPerformed(ActionEvent e)\r
 814   {\r
 815     changeColour( new PIDColourScheme() );\r
 816   }\r
 817 \r
 818 \r
 819   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 820   {\r
 821     changeColour(new Blosum62ColourScheme(viewport) );\r
 822   }\r
 823 \r
 824 \r
 825 \r
 826   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 827   {\r
 828     addHistoryItem("sort");\r
 829     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 830     alignPanel.RefreshPanels();\r
 831   }\r
 832 \r
 833   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 834   {\r
 835     addHistoryItem("sort");\r
 836     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 837     alignPanel.RefreshPanels();\r
 838   }\r
 839 \r
 840   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 841   {\r
 842     addHistoryItem("sort");\r
 843     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 844     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 845     alignPanel.RefreshPanels();\r
 846   }\r
 847 \r
 848   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 849   {\r
 850     addHistoryItem("sort");\r
 851     if(viewport.getCurrentTree()==null)\r
 852       return;\r
 853 \r
 854     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 855     alignPanel.RefreshPanels();\r
 856   }\r
 857 \r
 858   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 859   {\r
 860     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 861     JInternalFrame frame = new JInternalFrame();\r
 862     frame.setContentPane(sp);\r
 863     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
 864     frame.setMaximizable(false);\r
 865     frame.setResizable(false);\r
 866 \r
 867   }\r
 868 \r
 869   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 870   {\r
 871     if(viewport.getSelectionGroup().getSize()<2)\r
 872       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 873     else\r
 874     {\r
 875       JInternalFrame frame = new JInternalFrame();\r
 876       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 877       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 878     }\r
 879   }\r
 880 \r
 881   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 882   {\r
 883 \r
 884     if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
 885        || viewport.getAlignment().getHeight()<4)\r
 886     {\r
 887       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 888                                     +"at least 4 input sequences.",\r
 889                                     "Sequence selection insufficient",\r
 890                                     JOptionPane.WARNING_MESSAGE);\r
 891       return;\r
 892     }\r
 893 \r
 894     try{\r
 895       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 896       JInternalFrame frame = new JInternalFrame();\r
 897       frame.setContentPane(pcaPanel);\r
 898       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 899    }catch(java.lang.OutOfMemoryError ex)\r
 900    {\r
 901      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 902                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 903    }\r
 904 \r
 905 \r
 906   }\r
 907 \r
 908   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 909   {\r
 910     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 911   }\r
 912 \r
 913   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 914   {\r
 915     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 916   }\r
 917 \r
 918 \r
 919   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 920   {\r
 921     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 922   }\r
 923 \r
 924   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 925   {\r
 926     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 927   }\r
 928 \r
 929   void NewTreePanel(String type, String pwType, String title)\r
 930   {\r
 931     //are the sequences aligned?\r
 932     if(!viewport.alignment.isAligned())\r
 933     {\r
 934       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
 935                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
 936       return;\r
 937     }\r
 938 \r
 939     TreePanel tp=null;\r
 940    if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)\r
 941    {\r
 942      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,\r
 943                          0, viewport.alignment.getWidth());\r
 944    }\r
 945    else\r
 946    {\r
 947      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 948                          type, pwType,  0, viewport.alignment.getWidth());\r
 949    }\r
 950 \r
 951    Desktop.addInternalFrame(tp, title, 600, 500);\r
 952   }\r
 953 \r
 954 \r
 955 \r
 956 \r
 957   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 958   {\r
 959     JInternalFrame frame = new JInternalFrame();\r
 960     ClustalThread ct = new ClustalThread(frame);\r
 961     Thread t = new Thread(ct);\r
 962     t.start();\r
 963     frame.setContentPane(ct);\r
 964      Desktop.addInternalFrame(frame, title, 300, 80);\r
 965 \r
 966   }\r
 967 \r
 968   class ClustalThread extends JPanel implements Runnable\r
 969   {\r
 970     Image [] image;\r
 971     int imageIndex = 0;\r
 972     boolean webServiceRunning = false;\r
 973     JInternalFrame frame;\r
 974     public ClustalThread(JInternalFrame frame)\r
 975     {\r
 976       this.frame = frame;\r
 977       image = new Image[9];\r
 978       for(int i=0; i<9; i++)\r
 979       {\r
 980         java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");\r
 981         if (url != null)\r
 982         {\r
 983           image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
 984           MediaTracker mt = new MediaTracker(this);\r
 985           mt.addImage(image[i], i);\r
 986           try{mt.waitForID(i);}\r
 987           catch(Exception ex){}\r
 988         }\r
 989       }\r
 990       DNATwirler twirler = new DNATwirler();\r
 991       twirler.start();\r
 992       webServiceRunning = true;\r
 993     }\r
 994 \r
 995     class DNATwirler extends Thread\r
 996     {\r
 997       public void run()\r
 998       {\r
 999         while(webServiceRunning)\r
1000         {\r
1001           try{\r
1002             Thread.sleep(100);\r
1003             imageIndex++;\r
1004             imageIndex %=9;\r
1005             repaint();\r
1006           }\r
1007           catch(Exception ex){}\r
1008         }\r
1009       }\r
1010     }\r
1011 \r
1012     // JBPNote\r
1013     // Should check to see if the server settings are valid\r
1014     // Need visual-delay indication here.\r
1015     public void run()\r
1016        {\r
1017          jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
1018          Vector sv = viewport.getAlignment().getSequences();\r
1019          SequenceI[] seqs = new SequenceI[sv.size()];\r
1020 \r
1021          int i = 0;\r
1022          do\r
1023          {\r
1024            seqs[i] = (SequenceI) sv.elementAt(i);\r
1025          }\r
1026          while (++i < sv.size());\r
1027 \r
1028          SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
1029 \r
1030          if (alignment != null)\r
1031          {\r
1032            AlignFrame af = new AlignFrame(new Alignment(alignment));\r
1033           af.clustalColour.setSelected(true);\r
1034           af.clustalColour_actionPerformed(null);\r
1035            Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
1036                                     700, 500); // JBPNote - is there a new window geom. property ?\r
1037          }\r
1038          else\r
1039            JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
1040                                          JOptionPane.WARNING_MESSAGE);\r
1041 \r
1042          webServiceRunning = false;\r
1043          try{\r
1044            frame.setClosed(true);\r
1045          }catch(Exception ex){}\r
1046        }\r
1047 \r
1048        public void paintComponent(Graphics g)\r
1049        {\r
1050          g.setColor(Color.white);\r
1051          g.fillRect(0,0,getWidth(), getHeight());\r
1052          if(image!=null)\r
1053          {\r
1054            g.drawImage(image[imageIndex],10,10,this);\r
1055          }\r
1056          g.setFont(new Font("Arial", Font.BOLD, 12));\r
1057          g.setColor(Color.black);\r
1058          g.drawString("Clustal Alignment Web Service running", 30,30);\r
1059        }\r
1060   }\r
1061 }\r