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     JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
  67     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
  68     chooser.setToolTipText("Save");\r
  69     int value = chooser.showSaveDialog(this);\r
  70     if(value == JFileChooser.APPROVE_OPTION)\r
  71     {\r
  72       String choice =  chooser.getSelectedFile().getPath();\r
  73       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
  74       String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());\r
  75       try{\r
  76         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );\r
  77         out.println(output);\r
  78         out.close();\r
  79       }\r
  80       catch(Exception ex){}\r
  81     }\r
  82 \r
  83   }\r
  84 \r
  85   protected void outputText_actionPerformed(ActionEvent e)\r
  86   {\r
  87      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
  88      JInternalFrame frame = new JInternalFrame();\r
  89      cap.formatForOutput();\r
  90      frame.setContentPane(cap);\r
  91      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);\r
  92      cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));\r
  93   }\r
  94 \r
  95   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
  96   {\r
  97     HTMLOutput htmlOutput = new HTMLOutput(viewport);\r
  98     htmlOutput = null;\r
  99   }\r
 100 \r
 101   protected void createJPG_actionPerformed(ActionEvent e)\r
 102   {\r
 103 \r
 104     int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;\r
 105     int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();\r
 106 \r
 107 \r
 108     if(!viewport.getWrapAlignment())\r
 109     {\r
 110       height = viewport.alignment.getHeight() * viewport.charHeight;\r
 111       width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;\r
 112     }\r
 113 \r
 114     alignPanel.makeJPG( width, height);\r
 115   }\r
 116 \r
 117 \r
 118   public void printMenuItem_actionPerformed(ActionEvent e)\r
 119   {\r
 120     //Putting in a thread avoids Swing painting problems\r
 121     PrintThread thread = new PrintThread();\r
 122     thread.start();\r
 123   }\r
 124 \r
 125   class PrintThread extends Thread\r
 126   {\r
 127     public void run()\r
 128     {\r
 129       PrinterJob printJob = PrinterJob.getPrinterJob();\r
 130       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
 131       printJob.setPrintable(alignPanel, pf);\r
 132       if (printJob.printDialog())\r
 133       {\r
 134         try\r
 135         {\r
 136           printJob.print();\r
 137         }\r
 138         catch (Exception PrintException)\r
 139         {\r
 140           PrintException.printStackTrace();\r
 141         }\r
 142       }\r
 143     }\r
 144 \r
 145   }\r
 146 \r
 147 \r
 148 \r
 149 \r
 150   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 151   {\r
 152     try{\r
 153       this.setClosed(true);\r
 154     }catch(Exception ex){}\r
 155   }\r
 156 \r
 157   Stack historyList = new Stack();\r
 158   Stack redoList = new Stack();\r
 159 \r
 160   void updateEditMenuBar()\r
 161   {\r
 162     if(historyList.size()>0)\r
 163      {\r
 164        undoMenuItem.setEnabled(true);\r
 165        Object [] history = (Object[])historyList.get(0);\r
 166        undoMenuItem.setText("Undo "+history[0]);\r
 167      }\r
 168     else\r
 169     {\r
 170       undoMenuItem.setEnabled(false);\r
 171       undoMenuItem.setText("Undo");\r
 172     }\r
 173 \r
 174     if(redoList.size()>0)\r
 175      {\r
 176        redoMenuItem.setEnabled(true);\r
 177        Object [] history = (Object[])redoList.get(0);\r
 178        redoMenuItem.setText("Redo "+history[0]);\r
 179      }\r
 180     else\r
 181     {\r
 182       redoMenuItem.setEnabled(false);\r
 183       redoMenuItem.setText("Redo");\r
 184     }\r
 185   }\r
 186 \r
 187   public void addHistoryItem(String type)\r
 188   {\r
 189     // must make sure we add new sequence objects her, not refs to the existing sequences\r
 190     redoList.clear();\r
 191     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 192     for(int i=0; i<viewport.getAlignment().getHeight(); i++)\r
 193     {\r
 194       seq[i] = new Sequence( viewport.getAlignment().getSequenceAt(i).getName(),\r
 195                              viewport.getAlignment().getSequenceAt(i).getSequence());\r
 196     }\r
 197 \r
 198     historyList.add(0, new Object[]{type,  seq} );\r
 199     updateEditMenuBar();\r
 200   }\r
 201 \r
 202   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 203   {\r
 204     Object [] history = (Object[])historyList.remove(0);\r
 205     // add the redo state before continuing!!\r
 206     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];\r
 207     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
 208     {\r
 209       seq[i] = new Sequence(viewport.getAlignment().getSequenceAt(i).getName(),\r
 210                             viewport.getAlignment().getSequenceAt(i).\r
 211                             getSequence());\r
 212     }\r
 213     /////////\r
 214 \r
 215     redoList.add(0, new Object[] {history[0], seq});\r
 216 \r
 217       seq = (SequenceI[]) history[1];\r
 218       viewport.setAlignment( new Alignment(seq) );\r
 219       updateEditMenuBar();\r
 220       alignPanel.RefreshPanels();\r
 221   }\r
 222 \r
 223   public void moveSelectedSequences(boolean up)\r
 224   {\r
 225     SequenceGroup sg = viewport.getRubberbandGroup();\r
 226     if (sg == null)\r
 227       return;\r
 228 \r
 229     if (up)\r
 230     {\r
 231       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 232       {\r
 233         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 234         if (!sg.sequences.contains(seq))\r
 235           continue;\r
 236 \r
 237         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 238         if (sg.sequences.contains(temp))\r
 239           continue;\r
 240 \r
 241         viewport.alignment.getSequences().setElementAt(temp, i);\r
 242         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 243       }\r
 244     }\r
 245     else\r
 246     {\r
 247       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 248       {\r
 249         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 250         if (!sg.sequences.contains(seq))\r
 251           continue;\r
 252 \r
 253         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 254         if (sg.sequences.contains(temp))\r
 255           continue;\r
 256 \r
 257         viewport.alignment.getSequences().setElementAt(temp, i);\r
 258         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 259       }\r
 260     }\r
 261 \r
 262     alignPanel.RefreshPanels();\r
 263   }\r
 264 \r
 265 \r
 266 \r
 267   protected void copy_actionPerformed(ActionEvent e)\r
 268   {\r
 269    if(viewport.getRubberbandGroup()==null)\r
 270      return;\r
 271 \r
 272    SequenceGroup sg = viewport.getRubberbandGroup();\r
 273 \r
 274      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 275      StringBuffer buffer= new StringBuffer();\r
 276 \r
 277        for(int i=0; i<sg.getSize(); i++)\r
 278        {\r
 279          SequenceI seq = sg.getSequenceAt(i);\r
 280          buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"\r
 281                         +seq.findPosition( sg.getEndRes() )+ "\t"\r
 282                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");\r
 283        }\r
 284      c.setContents( new StringSelection( buffer.toString()) , null ) ;\r
 285 \r
 286   }\r
 287 \r
 288 \r
 289   protected void pasteNew_actionPerformed(ActionEvent e)\r
 290   {\r
 291     paste(true);\r
 292   }\r
 293 \r
 294   protected void pasteThis_actionPerformed(ActionEvent e)\r
 295   {\r
 296     addHistoryItem("Paste");\r
 297     paste(false);\r
 298   }\r
 299 \r
 300   void paste(boolean newAlignment)\r
 301   {\r
 302     try{\r
 303       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 304       Transferable contents = c.getContents(this);\r
 305       if (contents == null)\r
 306         return;\r
 307 \r
 308       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
 309       StringTokenizer st = new StringTokenizer(str);\r
 310       ArrayList seqs = new ArrayList();\r
 311       while (st.hasMoreElements())\r
 312       {\r
 313         String name = st.nextToken();\r
 314         int start = Integer.parseInt(st.nextToken());\r
 315         int end = Integer.parseInt(st.nextToken());\r
 316         Sequence sequence = new Sequence(name,st.nextToken(), start, end);\r
 317 \r
 318         if(!newAlignment)\r
 319           viewport.alignment.addSequence(sequence);\r
 320         else\r
 321           seqs.add(sequence);\r
 322       }\r
 323 \r
 324       if(newAlignment)\r
 325       {\r
 326         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 327         seqs.toArray(newSeqs);\r
 328         AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
 329         int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;\r
 330         if (newHeight > 500)\r
 331           newHeight = 500;\r
 332         Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
 333       }\r
 334       else\r
 335       {\r
 336         viewport.setEndSeq(viewport.alignment.getHeight());\r
 337         viewport.alignment.getWidth();\r
 338         alignPanel.RefreshPanels();\r
 339       }\r
 340 \r
 341     }catch(Exception ex){}// could be anything being pasted in here\r
 342 \r
 343   }\r
 344 \r
 345 \r
 346   protected void cut_actionPerformed(ActionEvent e)\r
 347   {\r
 348     copy_actionPerformed(null);\r
 349     delete_actionPerformed(null);\r
 350   }\r
 351 \r
 352   protected void delete_actionPerformed(ActionEvent e)\r
 353   {\r
 354     addHistoryItem("Delete");\r
 355     if (viewport.getRubberbandGroup() == null)\r
 356       return;\r
 357 \r
 358      SequenceGroup sg = viewport.getRubberbandGroup();\r
 359      for (int i=0;i < sg.sequences.size(); i++)\r
 360      {\r
 361        SequenceI seq = sg.getSequenceAt(i);\r
 362        int index = viewport.getAlignment().findIndex(seq);\r
 363        seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);\r
 364 \r
 365        if(seq.getSequence().length()<1)\r
 366           viewport.getAlignment().deleteSequence(seq);\r
 367       else\r
 368           viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 369      }\r
 370 \r
 371      viewport.setRubberbandGroup(null);\r
 372      viewport.alignment.deleteGroup(sg);\r
 373      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
 374      if(viewport.getAlignment().getHeight()<1)\r
 375      try\r
 376      {\r
 377        this.setClosed(true);\r
 378      }catch(Exception ex){}\r
 379      alignPanel.RefreshPanels();\r
 380 \r
 381   }\r
 382 \r
 383 \r
 384 \r
 385   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 386   {\r
 387      Object [] history = (Object[])redoList.remove(0);\r
 388      SequenceI[] seq = (SequenceI[]) history[1];\r
 389      viewport.setAlignment( new Alignment(seq) );\r
 390      updateEditMenuBar();\r
 391      alignPanel.RefreshPanels();\r
 392   }\r
 393 \r
 394 \r
 395   public void groupsMenuItem_actionPerformed(ActionEvent e)\r
 396   {\r
 397     GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
 398     JInternalFrame frame = new JInternalFrame();\r
 399     frame.setContentPane(geditor);\r
 400     Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
 401     frame.setResizable(false);\r
 402   }\r
 403 \r
 404   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 405   {\r
 406     viewport.alignment.deleteAllGroups();\r
 407     viewport.getSelection().clear();\r
 408 \r
 409     alignPanel.RefreshPanels();\r
 410   }\r
 411 \r
 412 \r
 413 \r
 414   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 415   {\r
 416     Selection sel = viewport.getSelection();\r
 417     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 418       sel.addElement( viewport.getAlignment().getSequenceAt(i));\r
 419     PaintRefresher.Refresh(null);\r
 420   }\r
 421 \r
 422   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 423   {\r
 424     viewport.setRubberbandGroup(null);\r
 425     viewport.getSelection().clear();\r
 426     PaintRefresher.Refresh(null);\r
 427   }\r
 428 \r
 429   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 430   {\r
 431     Selection sel = viewport.getSelection();\r
 432     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
 433     {\r
 434       if (sel.contains(viewport.getAlignment().getSequenceAt(i)))\r
 435         sel.removeElement(viewport.getAlignment().getSequenceAt(i));\r
 436       else\r
 437         sel.addElement(viewport.getAlignment().getSequenceAt(i));\r
 438     }\r
 439     PaintRefresher.Refresh(null);\r
 440   }\r
 441 \r
 442 \r
 443   public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
 444   {\r
 445     viewport.getColumnSelection().clear();\r
 446     repaint();\r
 447   }\r
 448 \r
 449   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 450   {\r
 451     addHistoryItem("delete columns");\r
 452     ColumnSelection colSel = viewport.getColumnSelection();\r
 453     if (colSel.size() > 0)\r
 454     {\r
 455       int min = colSel.getMin();\r
 456       viewport.getAlignment().trimLeft(min);\r
 457       colSel.compensateForEdit(0,min);\r
 458       alignPanel.RefreshPanels();\r
 459     }\r
 460   }\r
 461 \r
 462   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 463   {\r
 464     addHistoryItem("delete columns");\r
 465     ColumnSelection colSel = viewport.getColumnSelection();\r
 466     if (colSel.size() > 0)\r
 467     {\r
 468       int max = colSel.getMax();\r
 469       if(max>1)\r
 470         viewport.getAlignment().trimRight(max);\r
 471 \r
 472       alignPanel.RefreshPanels();\r
 473     }\r
 474 \r
 475   }\r
 476 \r
 477   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 478   {\r
 479     addHistoryItem("delete gapped columns");\r
 480     viewport.getAlignment().removeGaps();\r
 481     alignPanel.RefreshPanels();\r
 482   }\r
 483 \r
 484   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 485   {\r
 486     addHistoryItem("delete all gaps");\r
 487     SequenceI current;\r
 488     int jSize;\r
 489     for (int i=0; i < viewport.getAlignment().getSequences().size();i++)\r
 490     {\r
 491       current = viewport.getAlignment().getSequenceAt(i);\r
 492       jSize = current.getLength();\r
 493       for (int j=0; j < jSize; j++)\r
 494         if(jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 495         {\r
 496           current.deleteCharAt(j);\r
 497           j--;\r
 498           jSize--;\r
 499         }\r
 500     }\r
 501 \r
 502     alignPanel.RefreshPanels();\r
 503   }\r
 504 \r
 505   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
 506   {\r
 507     char thisChar = '-';\r
 508     char nextChar = '.';\r
 509     if(viewport.getGapCharacter()=='-')\r
 510     {\r
 511       thisChar = '.';\r
 512       nextChar = '-';\r
 513     }\r
 514     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
 515     viewport.setGapCharacter(thisChar);\r
 516     alignPanel.RefreshPanels();\r
 517   }\r
 518 \r
 519   public void findMenuItem_actionPerformed(ActionEvent e)\r
 520   {\r
 521       JInternalFrame frame = new JInternalFrame();\r
 522       Finder finder = new Finder(viewport, alignPanel, frame);\r
 523       frame.setContentPane(finder);\r
 524      Desktop.addInternalFrame(frame, "Find", 340,110);\r
 525 \r
 526   }\r
 527 \r
 528 \r
 529   public void font_actionPerformed(ActionEvent e)\r
 530   {\r
 531    // JOptionPane op = new JOptionPane();\r
 532     JInternalFrame frame = new JInternalFrame();\r
 533     FontChooser fc = new FontChooser( alignPanel, frame );\r
 534     frame.setContentPane(fc);\r
 535     Desktop.addInternalFrame(frame, "Change Font", 480,100);\r
 536   }\r
 537 \r
 538   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 539   {\r
 540       viewport.setColourText( colourTextMenuItem.isSelected() );\r
 541       alignPanel.RefreshPanels();\r
 542   }\r
 543 \r
 544   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 545   {\r
 546     viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
 547     alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
 548   }\r
 549 \r
 550 \r
 551   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 552   {\r
 553     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
 554     alignPanel.RefreshPanels();\r
 555   }\r
 556 \r
 557   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 558   {\r
 559     viewport.setShowText( viewTextMenuItem.isSelected() );\r
 560     alignPanel.RefreshPanels();\r
 561   }\r
 562 \r
 563 \r
 564   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 565   {\r
 566     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 567     alignPanel.RefreshPanels();\r
 568   }\r
 569 \r
 570   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 571   {\r
 572     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 573     if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)\r
 574     {\r
 575          AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);\r
 576          ((Alignment)viewport.alignment).featuresAdded = true;\r
 577     }\r
 578     alignPanel.RefreshPanels();\r
 579   }\r
 580 \r
 581   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
 582   {\r
 583     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
 584   }\r
 585 \r
 586   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 587   {\r
 588     if (alignPanel.overviewPanel != null)\r
 589       return;\r
 590 \r
 591     JInternalFrame frame = new JInternalFrame();\r
 592     OverviewPanel overview = alignPanel.getOverviewPanel();\r
 593    try{\r
 594      overview = new OverviewPanel(alignPanel, viewport);\r
 595      frame.setContentPane(overview);\r
 596     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 597                              frame.getWidth(), frame.getHeight());\r
 598     frame.pack();\r
 599     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 600     { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 601       {\r
 602             alignPanel.setOverviewPanel(null);\r
 603       };\r
 604     });\r
 605     alignPanel.setOverviewPanel( overview );\r
 606 \r
 607   }catch(java.lang.OutOfMemoryError ex)\r
 608    {\r
 609      JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!"\r
 610                                    +"\nTry reducing the font size.",\r
 611                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 612    }\r
 613 \r
 614 \r
 615   }\r
 616 \r
 617   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 618   {\r
 619     changeColour( null );\r
 620   }\r
 621 \r
 622 \r
 623   public void clustalColour_actionPerformed(ActionEvent e)\r
 624   {\r
 625     abovePIDThreshold.setSelected(false);\r
 626     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 627   }\r
 628 \r
 629   public void zappoColour_actionPerformed(ActionEvent e)\r
 630   {\r
 631     changeColour(new ZappoColourScheme());\r
 632   }\r
 633 \r
 634   public void taylorColour_actionPerformed(ActionEvent e)\r
 635   {\r
 636     changeColour(new TaylorColourScheme());\r
 637   }\r
 638 \r
 639 \r
 640   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 641   {\r
 642     changeColour( new HydrophobicColourScheme() );\r
 643   }\r
 644 \r
 645   public void helixColour_actionPerformed(ActionEvent e)\r
 646   {\r
 647     changeColour(new HelixColourScheme() );\r
 648   }\r
 649 \r
 650 \r
 651   public void strandColour_actionPerformed(ActionEvent e)\r
 652   {\r
 653     changeColour(new StrandColourScheme());\r
 654   }\r
 655 \r
 656 \r
 657   public void turnColour_actionPerformed(ActionEvent e)\r
 658   {\r
 659     changeColour(new TurnColourScheme());\r
 660   }\r
 661 \r
 662 \r
 663   public void buriedColour_actionPerformed(ActionEvent e)\r
 664   {\r
 665     changeColour(new BuriedColourScheme() );\r
 666   }\r
 667 \r
 668   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 669   {\r
 670     changeColour(new NucleotideColourScheme());\r
 671   }\r
 672 \r
 673 \r
 674   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 675   {\r
 676     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
 677   }\r
 678 \r
 679 \r
 680 \r
 681   void changeColour(ColourSchemeI cs)\r
 682   {\r
 683 \r
 684     if(viewport.getColourAppliesToAllGroups())\r
 685     {\r
 686       Vector groups = viewport.alignment.getGroups();\r
 687       for(int i=0; i<groups.size(); i++)\r
 688       {\r
 689         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
 690         sg.cs = cs;\r
 691 \r
 692         if(abovePIDThreshold.isSelected())\r
 693           abovePIDThreshold_actionPerformed(null);\r
 694         else if( viewport.getConservationSelected() )\r
 695         {\r
 696           Conservation c = new Conservation("Group",\r
 697                                             ResidueProperties.propHash, 3,\r
 698                                             sg.sequences, sg.getStartRes(),\r
 699                                             sg.getEndRes());\r
 700           c.calculate();\r
 701           c.verdict(false, 100);\r
 702           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 703 \r
 704           sg.cs = ccs;\r
 705         }\r
 706 \r
 707       }\r
 708     }\r
 709 \r
 710 \r
 711     if ( viewport.getAbovePIDThreshold())\r
 712     {\r
 713       int threshold = 0;\r
 714       threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background");\r
 715       Desktop.hideConservationSlider();\r
 716 \r
 717       if (cs instanceof ResidueColourScheme)\r
 718         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 719       else if (cs instanceof ScoreColourScheme)\r
 720         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 721 \r
 722       viewport.setGlobalColourScheme(cs);\r
 723 \r
 724     }\r
 725     else\r
 726     if (cs instanceof ResidueColourScheme)\r
 727       ( (ResidueColourScheme) cs).setThreshold(0);\r
 728     else if (cs instanceof ScoreColourScheme)\r
 729       ( (ScoreColourScheme) cs).setThreshold(0);\r
 730 \r
 731 \r
 732 \r
 733 \r
 734 if ( viewport.getConservationSelected() )\r
 735  {\r
 736    ConservationColourScheme ccs = null;\r
 737 \r
 738    Alignment al = (Alignment) viewport.alignment;\r
 739    Conservation c = new Conservation("All",\r
 740                                      ResidueProperties.propHash, 3,\r
 741                                      al.getSequences(), 0,\r
 742                                      al.getWidth());\r
 743 \r
 744    c.calculate();\r
 745    c.verdict(false, 100);\r
 746 \r
 747    ccs = new ConservationColourScheme(c, cs);\r
 748 \r
 749    int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,\r
 750        "Background");\r
 751 \r
 752    ccs.inc = threshold;\r
 753 \r
 754    viewport.setGlobalColourScheme(ccs);\r
 755 \r
 756   }\r
 757   else\r
 758        viewport.setGlobalColourScheme( cs );\r
 759 \r
 760     alignPanel.RefreshPanels();\r
 761   }\r
 762 \r
 763 \r
 764   protected  void conservationMenuItem_actionPerformed(ActionEvent e)\r
 765   {\r
 766     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
 767 \r
 768     viewport.setAbovePIDThreshold(false);\r
 769     abovePIDThreshold.setSelected(false);\r
 770     Desktop.hidePIDSlider();\r
 771     if(!viewport.getConservationSelected())\r
 772       Desktop.hideConservationSlider();\r
 773 \r
 774    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 775    if(cs instanceof ConservationColourScheme )\r
 776      changeColour( ((ConservationColourScheme)cs).cs );\r
 777     else\r
 778       changeColour( cs );\r
 779   }\r
 780 \r
 781 \r
 782   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 783   {\r
 784     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
 785 \r
 786     conservationMenuItem.setSelected(false);\r
 787     viewport.setConservationSelected(false);\r
 788     Desktop.hideConservationSlider();\r
 789 \r
 790     if(!viewport.getAbovePIDThreshold())\r
 791       Desktop.hidePIDSlider();\r
 792 \r
 793 \r
 794     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 795     if(cs instanceof ConservationColourScheme )\r
 796         changeColour( ((ConservationColourScheme)cs).cs );\r
 797     else\r
 798         changeColour( cs );\r
 799 \r
 800   }\r
 801 \r
 802 \r
 803 \r
 804   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 805   {\r
 806     JInternalFrame frame = new JInternalFrame();\r
 807     UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
 808     frame.setContentPane(chooser);\r
 809     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
 810     frame.setResizable(false);\r
 811     frame.setIconifiable(false);\r
 812     frame.setMaximizable(false);\r
 813   }\r
 814 \r
 815   public void PIDColour_actionPerformed(ActionEvent e)\r
 816   {\r
 817     changeColour( new PIDColourScheme() );\r
 818   }\r
 819 \r
 820 \r
 821   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
 822   {\r
 823     changeColour(new Blosum62ColourScheme(viewport) );\r
 824   }\r
 825 \r
 826 \r
 827 \r
 828   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
 829   {\r
 830     addHistoryItem("sort");\r
 831     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
 832     alignPanel.RefreshPanels();\r
 833   }\r
 834 \r
 835   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
 836   {\r
 837     addHistoryItem("sort");\r
 838     AlignmentSorter.sortByID( viewport.getAlignment() );\r
 839     alignPanel.RefreshPanels();\r
 840   }\r
 841 \r
 842   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
 843   {\r
 844     addHistoryItem("sort");\r
 845     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
 846     AlignmentSorter.sortGroups(viewport.getAlignment());\r
 847     alignPanel.RefreshPanels();\r
 848   }\r
 849 \r
 850   public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)\r
 851   {\r
 852     addHistoryItem("sort");\r
 853     if(viewport.getCurrentTree()==null)\r
 854       return;\r
 855 \r
 856     AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree());\r
 857     alignPanel.RefreshPanels();\r
 858   }\r
 859 \r
 860   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
 861   {\r
 862     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
 863     JInternalFrame frame = new JInternalFrame();\r
 864     frame.setContentPane(sp);\r
 865     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100);\r
 866     frame.setMaximizable(false);\r
 867     frame.setResizable(false);\r
 868 \r
 869   }\r
 870 \r
 871   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
 872   {\r
 873     if(viewport.getSelection().size()<2)\r
 874       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
 875     else\r
 876     {\r
 877       JInternalFrame frame = new JInternalFrame();\r
 878       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
 879       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
 880     }\r
 881   }\r
 882 \r
 883   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
 884   {\r
 885     if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)\r
 886        || viewport.getAlignment().getHeight()<4)\r
 887     {\r
 888       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
 889                                     +"at least 4 input sequences.",\r
 890                                     "Sequence selection insufficient",\r
 891                                     JOptionPane.WARNING_MESSAGE);\r
 892       return;\r
 893     }\r
 894 \r
 895     try{\r
 896       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
 897       JInternalFrame frame = new JInternalFrame();\r
 898       frame.setContentPane(pcaPanel);\r
 899       Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400);\r
 900    }catch(java.lang.OutOfMemoryError ex)\r
 901    {\r
 902      JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!",\r
 903                                    "Out of memory", JOptionPane.WARNING_MESSAGE);\r
 904    }\r
 905 \r
 906 \r
 907   }\r
 908 \r
 909   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
 910   {\r
 911     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
 912   }\r
 913 \r
 914   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
 915   {\r
 916     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
 917   }\r
 918 \r
 919 \r
 920   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 921   {\r
 922     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
 923   }\r
 924 \r
 925   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
 926   {\r
 927     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
 928   }\r
 929 \r
 930   void NewTreePanel(String type, String pwType, String title)\r
 931   {\r
 932     //are the sequences aligned?\r
 933     if(!viewport.alignment.isAligned())\r
 934     {\r
 935       JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",\r
 936                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
 937       return;\r
 938     }\r
 939 \r
 940     TreePanel tp=null;\r
 941    if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
 942    {\r
 943      tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,\r
 944                          0, viewport.alignment.getWidth());\r
 945    }\r
 946    else\r
 947    {\r
 948      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
 949                          type, pwType,  0, viewport.alignment.getWidth());\r
 950    }\r
 951 \r
 952    Desktop.addInternalFrame(tp, title, 600, 500);\r
 953   }\r
 954 \r
 955 \r
 956 \r
 957 \r
 958   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
 959   {\r
 960     JInternalFrame frame = new JInternalFrame();\r
 961     ClustalThread ct = new ClustalThread(frame);\r
 962     Thread t = new Thread(ct);\r
 963     t.start();\r
 964     frame.setContentPane(ct);\r
 965      Desktop.addInternalFrame(frame, title, 300, 80);\r
 966 \r
 967   }\r
 968 \r
 969   class ClustalThread extends JPanel implements Runnable\r
 970   {\r
 971     Image [] image;\r
 972     int imageIndex = 0;\r
 973     boolean webServiceRunning = false;\r
 974     JInternalFrame frame;\r
 975     public ClustalThread(JInternalFrame frame)\r
 976     {\r
 977       this.frame = frame;\r
 978       image = new Image[9];\r
 979       for(int i=0; i<9; i++)\r
 980       {\r
 981         java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");\r
 982         if (url != null)\r
 983         {\r
 984           image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
 985           MediaTracker mt = new MediaTracker(this);\r
 986           mt.addImage(image[i], i);\r
 987           try{mt.waitForID(i);}\r
 988           catch(Exception ex){}\r
 989         }\r
 990       }\r
 991       DNATwirler twirler = new DNATwirler();\r
 992       twirler.start();\r
 993       webServiceRunning = true;\r
 994     }\r
 995 \r
 996     class DNATwirler extends Thread\r
 997     {\r
 998       public void run()\r
 999       {\r
1000         while(webServiceRunning)\r
1001         {\r
1002           try{\r
1003             Thread.sleep(100);\r
1004             imageIndex++;\r
1005             imageIndex %=9;\r
1006             repaint();\r
1007           }\r
1008           catch(Exception ex){}\r
1009         }\r
1010       }\r
1011     }\r
1012 \r
1013     // JBPNote\r
1014     // Should check to see if the server settings are valid\r
1015     // Need visual-delay indication here.\r
1016     public void run()\r
1017        {\r
1018          jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();\r
1019          Vector sv = viewport.getAlignment().getSequences();\r
1020          SequenceI[] seqs = new SequenceI[sv.size()];\r
1021 \r
1022          int i = 0;\r
1023          do\r
1024          {\r
1025            seqs[i] = (SequenceI) sv.elementAt(i);\r
1026          }\r
1027          while (++i < sv.size());\r
1028 \r
1029          SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method\r
1030 \r
1031          if (alignment != null)\r
1032          {\r
1033            AlignFrame af = new AlignFrame(new Alignment(alignment));\r
1034           af.clustalColour.setSelected(true);\r
1035           af.clustalColour_actionPerformed(null);\r
1036            Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),\r
1037                                     700, 500); // JBPNote - is there a new window geom. property ?\r
1038          }\r
1039          else\r
1040            JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",\r
1041                                          JOptionPane.WARNING_MESSAGE);\r
1042 \r
1043          webServiceRunning = false;\r
1044          try{\r
1045            frame.setClosed(true);\r
1046          }catch(Exception ex){}\r
1047        }\r
1048 \r
1049        public void paintComponent(Graphics g)\r
1050        {\r
1051          g.setColor(Color.white);\r
1052          g.fillRect(0,0,getWidth(), getHeight());\r
1053          if(image!=null)\r
1054          {\r
1055            g.drawImage(image[imageIndex],10,10,this);\r
1056          }\r
1057          g.setFont(new Font("Arial", Font.BOLD, 12));\r
1058          g.setColor(Color.black);\r
1059          g.drawString("Clustal Alignment Web Service running", 30,30);\r
1060        }\r
1061   }\r
1062 }\r