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