src/jalview/appletgui/AlignFrame.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 \r
  20 package jalview.appletgui;\r
  21 \r
  22 import jalview.jbappletgui.GAlignFrame;\r
  23 import jalview.schemes.*;\r
  24 import jalview.datamodel.*;\r
  25 import jalview.analysis.*;\r
  26 import jalview.io.*;\r
  27 import java.awt.*;\r
  28 import java.awt.event.*;\r
  29 import java.util.*;\r
  30 import java.io.InputStreamReader;\r
  31 import java.io.BufferedReader;\r
  32 \r
  33 public class AlignFrame\r
  34     extends GAlignFrame\r
  35 {\r
  36   final AlignmentPanel alignPanel;\r
  37   final AlignViewport viewport;\r
  38   public static final int NEW_WINDOW_WIDTH = 700;\r
  39   public static final int NEW_WINDOW_HEIGHT = 500;\r
  40   jalview.bin.JalviewLite applet;\r
  41 \r
  42   public AlignFrame(AlignmentI al)\r
  43   {\r
  44     this.applet = null;\r
  45     viewport = new AlignViewport(al, null);\r
  46     alignPanel = new AlignmentPanel(this, viewport);\r
  47     add(alignPanel);\r
  48     alignPanel.validate();\r
  49 \r
  50     this.addWindowListener(new WindowAdapter()\r
  51     {\r
  52       public void windowClosing(WindowEvent e)\r
  53       {\r
  54         closeMenuItem_actionPerformed(null);\r
  55       }\r
  56     });\r
  57 \r
  58   }\r
  59 \r
  60 \r
  61   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)\r
  62   {\r
  63     this.applet = applet;\r
  64     viewport = new AlignViewport(al, applet);\r
  65     alignPanel = new AlignmentPanel(this, viewport);\r
  66     add(alignPanel);\r
  67     alignPanel.validate();\r
  68 \r
  69     String treeFile = applet.getParameter("treeFile");\r
  70     if (treeFile != null)\r
  71     {\r
  72       try\r
  73       {\r
  74         treeFile = treeFile;\r
  75         jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
  76             getCodeBase() + treeFile, "URL");\r
  77         fin.parse();\r
  78 \r
  79         if (fin.getTree() != null)\r
  80         {\r
  81           TreePanel tp = null;\r
  82           tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
  83                              fin, "FromFile", applet.getCodeBase() + treeFile);\r
  84           jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
  85           addTreeMenuItem(tp, treeFile);\r
  86         }\r
  87       }\r
  88       catch (Exception ex)\r
  89       {\r
  90         ex.printStackTrace();\r
  91       }\r
  92     }\r
  93 \r
  94     this.addWindowListener(new WindowAdapter()\r
  95     {\r
  96       public void windowClosing(WindowEvent e)\r
  97           {\r
  98             closeMenuItem_actionPerformed(null);\r
  99           }\r
 100     });\r
 101 \r
 102 \r
 103 \r
 104   }\r
 105 \r
 106   public void inputText_actionPerformed(ActionEvent e)\r
 107   {\r
 108     CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
 109     Frame frame = new Frame();\r
 110     frame.add(cap);\r
 111     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
 112   }\r
 113 \r
 114   protected void outputText_actionPerformed(ActionEvent e)\r
 115   {\r
 116     CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
 117     Frame frame = new Frame();\r
 118     frame.add(cap);\r
 119     jalview.bin.JalviewLite.addFrame(frame,\r
 120                                      "Alignment output - " + e.getActionCommand(),\r
 121                                      600, 500);\r
 122     cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),\r
 123                                               viewport.getAlignment().\r
 124                                               getSequences()));\r
 125   }\r
 126 \r
 127   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 128   {\r
 129     PaintRefresher.components.remove(viewport.alignment);\r
 130     dispose();\r
 131   }\r
 132 \r
 133   Stack historyList = new Stack();\r
 134   Stack redoList = new Stack();\r
 135 \r
 136   void updateEditMenuBar()\r
 137   {\r
 138     if (historyList.size() > 0)\r
 139     {\r
 140       undoMenuItem.setEnabled(true);\r
 141       HistoryItem hi = (HistoryItem) historyList.peek();\r
 142       undoMenuItem.setLabel("Undo " + hi.getDescription());\r
 143     }\r
 144     else\r
 145     {\r
 146       undoMenuItem.setEnabled(false);\r
 147       undoMenuItem.setLabel("Undo");\r
 148     }\r
 149 \r
 150     if (redoList.size() > 0)\r
 151     {\r
 152       redoMenuItem.setEnabled(true);\r
 153       HistoryItem hi = (HistoryItem) redoList.peek();\r
 154       redoMenuItem.setLabel("Redo " + hi.getDescription());\r
 155     }\r
 156     else\r
 157     {\r
 158       redoMenuItem.setEnabled(false);\r
 159       redoMenuItem.setLabel("Redo");\r
 160     }\r
 161   }\r
 162 \r
 163   public void addHistoryItem(HistoryItem hi)\r
 164   {\r
 165     historyList.push(hi);\r
 166     updateEditMenuBar();\r
 167   }\r
 168 \r
 169   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 170   {\r
 171     HistoryItem hi = (HistoryItem) historyList.pop();\r
 172     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
 173                                   HistoryItem.HIDE));\r
 174     restoreHistoryItem(hi);\r
 175     resetAllColourSchemes();\r
 176   }\r
 177 \r
 178   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 179   {\r
 180     HistoryItem hi = (HistoryItem) redoList.pop();\r
 181     restoreHistoryItem(hi);\r
 182     updateEditMenuBar();\r
 183     viewport.updateConsensus();\r
 184     resetAllColourSchemes();\r
 185     alignPanel.repaint();\r
 186     alignPanel.repaint();\r
 187   }\r
 188 \r
 189   // used by undo and redo\r
 190   void restoreHistoryItem(HistoryItem hi)\r
 191   {\r
 192     if (hi.getType() == HistoryItem.SORT)\r
 193     {\r
 194       for (int i = 0; i < hi.getSequences().size(); i++)\r
 195       {\r
 196         viewport.alignment.getSequences().setElementAt(hi.getSequences().\r
 197             elementAt(i), i);\r
 198       }\r
 199     }\r
 200     else\r
 201     {\r
 202       for (int i = 0; i < hi.getSequences().size(); i++)\r
 203       {\r
 204         SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
 205         if (restore.getLength() == 0)\r
 206         {\r
 207           // log.System.out.println(hi.getHidden().elementAt(i));\r
 208           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 209           viewport.alignment.getSequences().insertElementAt(\r
 210               restore,\r
 211               hi.getAlignIndex(i));\r
 212         }\r
 213         else\r
 214         {\r
 215           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 216         }\r
 217       }\r
 218       if (hi.getType() == HistoryItem.PASTE)\r
 219       {\r
 220         for (int i = viewport.alignment.getHeight() - 1;\r
 221              i > hi.getSequences().size() - 1; i--)\r
 222         {\r
 223           viewport.alignment.deleteSequence(i);\r
 224         }\r
 225       }\r
 226     }\r
 227 \r
 228     updateEditMenuBar();\r
 229 \r
 230     viewport.updateConsensus();\r
 231     viewport.updateConservation();\r
 232     alignPanel.repaint();\r
 233   }\r
 234 \r
 235   public void moveSelectedSequences(boolean up)\r
 236   {\r
 237     SequenceGroup sg = viewport.getSelectionGroup();\r
 238     if (sg == null)\r
 239     {\r
 240       return;\r
 241     }\r
 242 \r
 243     if (up)\r
 244     {\r
 245       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 246       {\r
 247         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 248         if (!sg.sequences.contains(seq))\r
 249         {\r
 250           continue;\r
 251         }\r
 252 \r
 253         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 254         if (sg.sequences.contains(temp))\r
 255         {\r
 256           continue;\r
 257         }\r
 258 \r
 259         viewport.alignment.getSequences().setElementAt(temp, i);\r
 260         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 261       }\r
 262     }\r
 263     else\r
 264     {\r
 265       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 266       {\r
 267         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 268         if (!sg.sequences.contains(seq))\r
 269         {\r
 270           continue;\r
 271         }\r
 272 \r
 273         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 274         if (sg.sequences.contains(temp))\r
 275         {\r
 276           continue;\r
 277         }\r
 278 \r
 279         viewport.alignment.getSequences().setElementAt(temp, i);\r
 280         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 281       }\r
 282     }\r
 283 \r
 284     alignPanel.repaint();\r
 285   }\r
 286 \r
 287   StringBuffer copiedSequences;\r
 288   protected void copy_actionPerformed(ActionEvent e)\r
 289   {\r
 290     if (viewport.getSelectionGroup() == null)\r
 291     {\r
 292       return;\r
 293     }\r
 294 \r
 295     SequenceGroup sg = viewport.getSelectionGroup();\r
 296     copiedSequences = new StringBuffer();\r
 297     Hashtable orderedSeqs = new Hashtable();\r
 298     for (int i = 0; i < sg.getSize(); i++)\r
 299     {\r
 300       SequenceI seq = sg.getSequenceAt(i);\r
 301       int index = viewport.alignment.findIndex(seq);\r
 302       orderedSeqs.put(index + "", seq);\r
 303     }\r
 304 \r
 305     int index = 0, startRes, endRes;\r
 306     char ch;\r
 307 \r
 308     for (int i = 0; i < sg.getSize(); i++)\r
 309     {\r
 310         SequenceI seq = null;\r
 311 \r
 312         while (seq == null)\r
 313         {\r
 314             if (orderedSeqs.containsKey(index + ""))\r
 315             {\r
 316                 seq = (SequenceI) orderedSeqs.get(index + "");\r
 317                 index++;\r
 318 \r
 319                 break;\r
 320             }\r
 321             else\r
 322             {\r
 323                 index++;\r
 324             }\r
 325         }\r
 326 \r
 327         //FIND START RES\r
 328         //Returns residue following index if gap\r
 329         startRes = seq.findPosition(sg.getStartRes());\r
 330 \r
 331         //FIND END RES\r
 332         //Need to find the residue preceeding index if gap\r
 333         endRes = 0;\r
 334 \r
 335         for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
 336         {\r
 337           ch = seq.getCharAt(j);\r
 338           if (!jalview.util.Comparison.isGap( (ch)))\r
 339           {\r
 340             endRes++;\r
 341           }\r
 342         }\r
 343 \r
 344         if(endRes>0)\r
 345         {\r
 346           endRes += seq.getStart() -1;\r
 347         }\r
 348 \r
 349         copiedSequences.append(seq.getName() + "\t" +\r
 350             startRes + "\t" +\r
 351             endRes + "\t" +\r
 352             seq.getSequence(sg.getStartRes(),\r
 353                 sg.getEndRes() + 1) + "\n");\r
 354     }\r
 355 \r
 356   }\r
 357 \r
 358   protected void pasteNew_actionPerformed(ActionEvent e)\r
 359   {\r
 360     paste(true);\r
 361   }\r
 362 \r
 363   protected void pasteThis_actionPerformed(ActionEvent e)\r
 364   {\r
 365     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
 366                                    HistoryItem.PASTE));\r
 367     paste(false);\r
 368   }\r
 369 \r
 370   void paste(boolean newAlignment)\r
 371   {\r
 372     try\r
 373     {\r
 374       if (copiedSequences == null)\r
 375       {\r
 376         return;\r
 377       }\r
 378 \r
 379       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 380       Vector seqs = new Vector();\r
 381       while (st.hasMoreElements())\r
 382       {\r
 383         String name = st.nextToken();\r
 384         int start = Integer.parseInt(st.nextToken());\r
 385         int end = Integer.parseInt(st.nextToken());\r
 386         Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
 387 \r
 388         if (!newAlignment)\r
 389         {\r
 390           viewport.alignment.addSequence(sequence);\r
 391         }\r
 392         else\r
 393         {\r
 394           seqs.addElement(sequence);\r
 395         }\r
 396       }\r
 397 \r
 398       if (newAlignment)\r
 399       {\r
 400         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 401         for (int i = 0; i < seqs.size(); i++)\r
 402         {\r
 403           newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
 404         }\r
 405 \r
 406         AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);\r
 407         String newtitle = new String("Copied sequences");\r
 408         if (getTitle().startsWith("Copied sequences"))\r
 409         {\r
 410           newtitle = getTitle();\r
 411         }\r
 412         else\r
 413         {\r
 414           newtitle = newtitle.concat("- from " + getTitle());\r
 415         }\r
 416         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
 417                                          NEW_WINDOW_HEIGHT);\r
 418       }\r
 419       else\r
 420       {\r
 421         viewport.setEndSeq(viewport.alignment.getHeight());\r
 422         viewport.alignment.getWidth();\r
 423         viewport.updateConservation();\r
 424         viewport.updateConsensus();\r
 425         alignPanel.repaint();\r
 426       }\r
 427 \r
 428     }\r
 429     catch (Exception ex)\r
 430     {} // could be anything being pasted in here\r
 431 \r
 432   }\r
 433 \r
 434   protected void cut_actionPerformed(ActionEvent e)\r
 435   {\r
 436     copy_actionPerformed(null);\r
 437     delete_actionPerformed(null);\r
 438   }\r
 439 \r
 440   protected void delete_actionPerformed(ActionEvent e)\r
 441   {\r
 442     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
 443                                    HistoryItem.HIDE));\r
 444     if (viewport.getSelectionGroup() == null)\r
 445     {\r
 446       return;\r
 447     }\r
 448 \r
 449 \r
 450     SequenceGroup sg = viewport.getSelectionGroup();\r
 451     boolean allSequences = false;\r
 452     if(sg.sequences.size()==viewport.alignment.getHeight())\r
 453           allSequences = true;\r
 454 \r
 455     for (int i = 0; i < sg.sequences.size(); i++)\r
 456     {\r
 457       SequenceI seq = sg.getSequenceAt(i);\r
 458       int index = viewport.getAlignment().findIndex(seq);\r
 459       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 460 \r
 461       // If the cut affects all sequences, remove highlighted columns\r
 462       if (allSequences)\r
 463       {\r
 464         viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
 465                                                      sg.getEndRes() + 1);\r
 466       }\r
 467 \r
 468 \r
 469       if (seq.getSequence().length() < 1)\r
 470       {\r
 471         viewport.getAlignment().deleteSequence(seq);\r
 472       }\r
 473       else\r
 474       {\r
 475         viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 476       }\r
 477     }\r
 478 \r
 479     viewport.setSelectionGroup(null);\r
 480     viewport.alignment.deleteGroup(sg);\r
 481     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
 482     if (viewport.getAlignment().getHeight() < 1)\r
 483     {\r
 484       try\r
 485       {\r
 486         this.setVisible(false);\r
 487       }\r
 488       catch (Exception ex)\r
 489       {}\r
 490     }\r
 491     viewport.updateConservation();\r
 492     viewport.updateConsensus();\r
 493     alignPanel.repaint();\r
 494 \r
 495   }\r
 496 \r
 497   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 498   {\r
 499     viewport.alignment.deleteAllGroups();\r
 500     viewport.setSelectionGroup(null);\r
 501 \r
 502     alignPanel.repaint();\r
 503   }\r
 504 \r
 505   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 506   {\r
 507     SequenceGroup sg = new SequenceGroup();\r
 508     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 509     {\r
 510       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
 511     }\r
 512     sg.setEndRes(viewport.alignment.getWidth()-1);\r
 513     viewport.setSelectionGroup(sg);\r
 514     alignPanel.repaint();\r
 515     PaintRefresher.Refresh(null, viewport.alignment);\r
 516   }\r
 517 \r
 518   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 519   {\r
 520     viewport.setSelectionGroup(null);\r
 521     viewport.getColumnSelection().clear();\r
 522     viewport.setSelectionGroup(null);\r
 523     PaintRefresher.Refresh(null, viewport.alignment);\r
 524   }\r
 525 \r
 526   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 527   {\r
 528     SequenceGroup sg = viewport.getSelectionGroup();\r
 529     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 530     {\r
 531       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
 532     }\r
 533 \r
 534     PaintRefresher.Refresh(null, viewport.alignment);\r
 535   }\r
 536 \r
 537   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 538   {\r
 539     ColumnSelection colSel = viewport.getColumnSelection();\r
 540     if (colSel.size() > 0)\r
 541     {\r
 542       addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
 543                                      HistoryItem.HIDE));\r
 544       int min = colSel.getMin();\r
 545       viewport.getAlignment().trimLeft(min);\r
 546       colSel.compensateForEdit(0, min);\r
 547 \r
 548       if (viewport.getSelectionGroup() != null)\r
 549       {\r
 550         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 551       }\r
 552 \r
 553       Vector groups = viewport.alignment.getGroups();\r
 554       for (int i = 0; i < groups.size(); i++)\r
 555       {\r
 556         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 557         if (!sg.adjustForRemoveLeft(min))\r
 558         {\r
 559           viewport.alignment.deleteGroup(sg);\r
 560         }\r
 561       }\r
 562 \r
 563       alignPanel.repaint();\r
 564     }\r
 565   }\r
 566 \r
 567   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 568   {\r
 569     ColumnSelection colSel = viewport.getColumnSelection();\r
 570     if (colSel.size() > 0)\r
 571     {\r
 572       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
 573                                      HistoryItem.HIDE));\r
 574       int max = colSel.getMax();\r
 575       viewport.getAlignment().trimRight(max);\r
 576       if (viewport.getSelectionGroup() != null)\r
 577       {\r
 578         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 579       }\r
 580 \r
 581       Vector groups = viewport.alignment.getGroups();\r
 582       for (int i = 0; i < groups.size(); i++)\r
 583       {\r
 584         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 585         if (!sg.adjustForRemoveRight(max))\r
 586         {\r
 587           viewport.alignment.deleteGroup(sg);\r
 588         }\r
 589       }\r
 590 \r
 591       alignPanel.repaint();\r
 592     }\r
 593 \r
 594   }\r
 595 \r
 596   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 597   {\r
 598     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
 599                                    viewport.alignment,\r
 600                                    HistoryItem.HIDE));\r
 601 \r
 602     //This is to maintain viewport position on first residue\r
 603     //of first sequence\r
 604     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 605     int startRes = seq.findPosition(viewport.startRes);\r
 606 \r
 607     viewport.getAlignment().removeGaps();\r
 608 \r
 609     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 610 \r
 611     viewport.updateConservation();\r
 612     viewport.updateConsensus();\r
 613     resetAllColourSchemes();\r
 614     alignPanel.repaint();\r
 615   }\r
 616 \r
 617   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 618   {\r
 619     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
 620                                    HistoryItem.HIDE));\r
 621 \r
 622     //This is to maintain viewport position on first residue\r
 623     //of first sequence\r
 624     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 625     int startRes = seq.findPosition(viewport.startRes);\r
 626 \r
 627     SequenceI current;\r
 628     int jSize;\r
 629 \r
 630     Vector seqs=null;\r
 631 \r
 632     int start=0, end = viewport.alignment.getWidth();\r
 633 \r
 634     if (viewport.getSelectionGroup() != null\r
 635         && viewport.getSelectionGroup().sequences != null\r
 636         && viewport.getSelectionGroup().sequences.size()>0)\r
 637     {\r
 638       seqs = viewport.getSelectionGroup().sequences;\r
 639       start = viewport.getSelectionGroup().getStartRes();\r
 640       end = viewport.getSelectionGroup().getEndRes();\r
 641     }\r
 642     else\r
 643       seqs = viewport.alignment.getSequences();\r
 644 \r
 645     for (int i = 0; i <seqs.size(); i++)\r
 646     {\r
 647       current = (SequenceI)seqs.elementAt(i);\r
 648       jSize = current.getLength();\r
 649 \r
 650       int j = start;\r
 651       do\r
 652       {\r
 653         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 654         {\r
 655           current.deleteCharAt(j);\r
 656           j--;\r
 657           jSize--;\r
 658         }\r
 659         j++;\r
 660       }\r
 661       while(j < end && j < jSize) ;\r
 662     }\r
 663 \r
 664     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 665     viewport.updateConservation();\r
 666     viewport.updateConsensus();\r
 667     resetAllColourSchemes();\r
 668     alignPanel.repaint();\r
 669   }\r
 670 \r
 671   void resetAllColourSchemes()\r
 672   {\r
 673     ColourSchemeI cs = viewport.globalColourScheme;\r
 674     if(cs!=null)\r
 675     {\r
 676         cs.setConsensus(viewport.vconsensus);\r
 677         if(cs.conservationApplied())\r
 678         {\r
 679           Alignment al = (Alignment) viewport.alignment;\r
 680           Conservation c = new Conservation("All",\r
 681                                             ResidueProperties.propHash, 3,\r
 682                                             al.getSequences(), 0,\r
 683                                             al.getWidth() - 1);\r
 684           c.calculate();\r
 685           c.verdict(false, viewport.ConsPercGaps);\r
 686 \r
 687           cs.setConservation(c);\r
 688         }\r
 689     }\r
 690 \r
 691     if(viewport.getGlobalColourScheme()!=null\r
 692        && viewport.getGlobalColourScheme() instanceof ClustalxColourScheme)\r
 693     {\r
 694       ((ClustalxColourScheme)viewport.getGlobalColourScheme()).\r
 695           resetClustalX(viewport.alignment.getSequences(),\r
 696                         viewport.alignment.getWidth());\r
 697     }\r
 698 \r
 699     int s, sSize = viewport.alignment.getGroups().size();\r
 700     for(s=0; s<sSize; s++)\r
 701     {\r
 702       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
 703       if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
 704       {\r
 705         ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
 706       }\r
 707 \r
 708       sg.recalcConservation();\r
 709 \r
 710     }\r
 711   }\r
 712 \r
 713 \r
 714 \r
 715   public void findMenuItem_actionPerformed(ActionEvent e)\r
 716   {\r
 717     Finder finder = new Finder(alignPanel);\r
 718   }\r
 719 \r
 720   public void font_actionPerformed(ActionEvent e)\r
 721   {\r
 722     Frame frame = new Frame();\r
 723     FontChooser fc = new FontChooser(alignPanel, frame);\r
 724     frame.add(fc);\r
 725     jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);\r
 726 \r
 727   }\r
 728 \r
 729   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 730   {\r
 731     viewport.setShowFullId(fullSeqId.getState());\r
 732     alignPanel.fontChanged();\r
 733     alignPanel.repaint();\r
 734   }\r
 735 \r
 736   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 737   {\r
 738     viewport.setColourText(colourTextMenuItem.getState());\r
 739     alignPanel.repaint();\r
 740   }\r
 741 \r
 742   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 743   {\r
 744     viewport.setWrapAlignment(wrapMenuItem.getState());\r
 745     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
 746     scaleAbove.setEnabled(wrapMenuItem.getState());\r
 747     scaleLeft.setEnabled(wrapMenuItem.getState());\r
 748     scaleRight.setEnabled(wrapMenuItem.getState());\r
 749     alignPanel.repaint();\r
 750   }\r
 751 \r
 752   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 753   {\r
 754     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 755     alignPanel.repaint();\r
 756   }\r
 757 \r
 758   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 759   {\r
 760     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 761     alignPanel.repaint();\r
 762   }\r
 763 \r
 764   protected void scaleRight_actionPerformed(ActionEvent e)\r
 765   {\r
 766     viewport.setScaleRightWrapped(scaleRight.getState());\r
 767     alignPanel.repaint();\r
 768   }\r
 769 \r
 770   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 771   {\r
 772     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
 773     alignPanel.repaint();\r
 774   }\r
 775 \r
 776   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 777   {\r
 778     viewport.setShowText(viewTextMenuItem.getState());\r
 779     alignPanel.repaint();\r
 780   }\r
 781 \r
 782   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 783   {\r
 784     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 785     alignPanel.repaint();\r
 786   }\r
 787 \r
 788   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 789   {\r
 790     if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
 791     {\r
 792       annotationPanelMenuItem.setState(false);\r
 793       return;\r
 794     }\r
 795     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
 796     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
 797   }\r
 798 \r
 799   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 800   {\r
 801     if (alignPanel.overviewPanel != null)\r
 802     {\r
 803       return;\r
 804     }\r
 805 \r
 806     Frame frame = new Frame();\r
 807     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 808     frame.add(overview);\r
 809     // +50 must allow for applet frame window\r
 810     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
 811                                      overview.preferredSize().width,\r
 812                                      overview.preferredSize().height + 50);\r
 813 \r
 814     frame.pack();\r
 815     frame.addWindowListener(new WindowAdapter()\r
 816     {\r
 817       public void windowClosing(WindowEvent e)\r
 818       {\r
 819         alignPanel.setOverviewPanel(null);\r
 820       };\r
 821     });\r
 822 \r
 823     alignPanel.setOverviewPanel(overview);\r
 824 \r
 825   }\r
 826 \r
 827   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 828   {\r
 829     changeColour(null);\r
 830   }\r
 831 \r
 832   public void clustalColour_actionPerformed(ActionEvent e)\r
 833   {\r
 834     abovePIDThreshold.setState(false);\r
 835     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
 836                                           viewport.alignment.getWidth()));\r
 837   }\r
 838 \r
 839   public void zappoColour_actionPerformed(ActionEvent e)\r
 840   {\r
 841     changeColour(new ZappoColourScheme());\r
 842   }\r
 843 \r
 844   public void taylorColour_actionPerformed(ActionEvent e)\r
 845   {\r
 846     changeColour(new TaylorColourScheme());\r
 847   }\r
 848 \r
 849   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 850   {\r
 851     changeColour(new HydrophobicColourScheme());\r
 852   }\r
 853 \r
 854   public void helixColour_actionPerformed(ActionEvent e)\r
 855   {\r
 856     changeColour(new HelixColourScheme());\r
 857   }\r
 858 \r
 859   public void strandColour_actionPerformed(ActionEvent e)\r
 860   {\r
 861     changeColour(new StrandColourScheme());\r
 862   }\r
 863 \r
 864   public void turnColour_actionPerformed(ActionEvent e)\r
 865   {\r
 866     changeColour(new TurnColourScheme());\r
 867   }\r
 868 \r
 869   public void buriedColour_actionPerformed(ActionEvent e)\r
 870   {\r
 871     changeColour(new BuriedColourScheme());\r
 872   }\r
 873 \r
 874   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 875   {\r
 876     changeColour(new NucleotideColourScheme());\r
 877   }\r
 878 \r
 879   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 880   {\r
 881     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
 882   }\r
 883 \r
 884   void changeColour(ColourSchemeI cs)\r
 885   {\r
 886     int threshold = 0;\r
 887 \r
 888     if(cs!=null)\r
 889     {\r
 890       if (viewport.getAbovePIDThreshold())\r
 891       {\r
 892         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 893 \r
 894         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
 895 \r
 896         viewport.setGlobalColourScheme(cs);\r
 897       }\r
 898       else\r
 899       {\r
 900         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
 901       }\r
 902 \r
 903       if (viewport.getConservationSelected())\r
 904       {\r
 905 \r
 906         Alignment al = (Alignment) viewport.alignment;\r
 907         Conservation c = new Conservation("All",\r
 908                                           ResidueProperties.propHash, 3,\r
 909                                           al.getSequences(), 0,\r
 910                                           al.getWidth() - 1);\r
 911 \r
 912         c.calculate();\r
 913         c.verdict(false, viewport.ConsPercGaps);\r
 914 \r
 915         cs.setConservation(c);\r
 916 \r
 917         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
 918             "Background"));\r
 919 \r
 920       }\r
 921       else\r
 922       {\r
 923         cs.setConservation(null);\r
 924       }\r
 925 \r
 926       cs.setConsensus(viewport.vconsensus);\r
 927 \r
 928     }\r
 929     viewport.setGlobalColourScheme(cs);\r
 930 \r
 931     if (viewport.getColourAppliesToAllGroups())\r
 932     {\r
 933       Vector groups = viewport.alignment.getGroups();\r
 934       for (int i = 0; i < groups.size(); i++)\r
 935       {\r
 936         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 937 \r
 938         if(cs==null)\r
 939         {\r
 940           sg.cs = null;\r
 941           continue;\r
 942         }\r
 943         if (cs instanceof ClustalxColourScheme)\r
 944         {\r
 945           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
 946         }\r
 947         else\r
 948         {\r
 949           try\r
 950           {\r
 951             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
 952           }\r
 953           catch (Exception ex)\r
 954           {\r
 955             ex.printStackTrace();\r
 956             sg.cs = cs;\r
 957           }\r
 958         }\r
 959 \r
 960         if (viewport.getAbovePIDThreshold()\r
 961             || cs instanceof PIDColourScheme\r
 962             || cs instanceof Blosum62ColourScheme)\r
 963         {\r
 964           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
 965           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 966         }\r
 967         else\r
 968           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
 969 \r
 970         if (viewport.getConservationSelected())\r
 971         {\r
 972           Conservation c = new Conservation("Group",\r
 973                                             ResidueProperties.propHash, 3,\r
 974                                             sg.sequences, 0,\r
 975                                             viewport.alignment.getWidth() - 1);\r
 976           c.calculate();\r
 977           c.verdict(false, viewport.ConsPercGaps);\r
 978           sg.cs.setConservation(c);\r
 979         }\r
 980         else\r
 981         {\r
 982           sg.cs.setConservation(null);\r
 983           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
 984         }\r
 985 \r
 986       }\r
 987     }\r
 988 \r
 989 \r
 990     if (alignPanel.getOverviewPanel() != null)\r
 991     {\r
 992       alignPanel.getOverviewPanel().updateOverviewImage();\r
 993     }\r
 994 \r
 995     alignPanel.repaint();\r
 996   }\r
 997 \r
 998 \r
 999 \r
1000   protected void modifyPID_actionPerformed(ActionEvent e)\r
1001   {\r
1002     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
1003     {\r
1004       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
1005                                      "Background");\r
1006       SliderPanel.showPIDSlider();\r
1007     }\r
1008   }\r
1009 \r
1010   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1011   {\r
1012     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
1013     {\r
1014       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
1015                                         "Background");\r
1016       SliderPanel.showConservationSlider();\r
1017     }\r
1018   }\r
1019 \r
1020   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1021   {\r
1022     viewport.setConservationSelected(conservationMenuItem.getState());\r
1023 \r
1024     viewport.setAbovePIDThreshold(false);\r
1025     abovePIDThreshold.setState(false);\r
1026 \r
1027     changeColour(viewport.getGlobalColourScheme());\r
1028 \r
1029     modifyConservation_actionPerformed(null);\r
1030   }\r
1031 \r
1032   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1033   {\r
1034     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
1035 \r
1036     conservationMenuItem.setState(false);\r
1037     viewport.setConservationSelected(false);\r
1038 \r
1039     changeColour(viewport.getGlobalColourScheme());\r
1040 \r
1041     modifyPID_actionPerformed(null);\r
1042   }\r
1043 \r
1044   public void userDefinedColour_actionPerformed(ActionEvent e)\r
1045   {\r
1046     UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);\r
1047   }\r
1048 \r
1049   public void PIDColour_actionPerformed(ActionEvent e)\r
1050   {\r
1051     changeColour(new PIDColourScheme());\r
1052   }\r
1053 \r
1054   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1055   {\r
1056     changeColour(new Blosum62ColourScheme());\r
1057   }\r
1058 \r
1059   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1060   {\r
1061     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1062                                    HistoryItem.SORT));\r
1063     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1064                               viewport.getAlignment().getSequenceAt(0));\r
1065     alignPanel.repaint();\r
1066   }\r
1067 \r
1068   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1069   {\r
1070     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1071                                    HistoryItem.SORT));\r
1072     AlignmentSorter.sortByID(viewport.getAlignment());\r
1073     alignPanel.repaint();\r
1074   }\r
1075 \r
1076   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1077   {\r
1078     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1079                                    HistoryItem.SORT));\r
1080     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1081     alignPanel.repaint();\r
1082 \r
1083   }\r
1084 \r
1085   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1086   {\r
1087     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
1088     Frame frame = new Frame();\r
1089     frame.add(sp);\r
1090     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
1091                                      400, 120);\r
1092 \r
1093   }\r
1094 \r
1095   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1096   {\r
1097     if (viewport.getSelectionGroup().getSize() > 1)\r
1098     {\r
1099       Frame frame = new Frame();\r
1100       frame.add(new PairwiseAlignPanel(viewport));\r
1101       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1102     }\r
1103   }\r
1104 \r
1105   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
1106   {\r
1107 \r
1108     if ( (viewport.getSelectionGroup() != null &&\r
1109           viewport.getSelectionGroup().getSize() < 4 &&\r
1110           viewport.getSelectionGroup().getSize() > 0)\r
1111         || viewport.getAlignment().getHeight() < 4)\r
1112     {\r
1113       return;\r
1114     }\r
1115 \r
1116     try\r
1117     {\r
1118       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
1119       Frame frame = new Frame();\r
1120       frame.add(pcaPanel);\r
1121       jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",\r
1122                                        400, 400);\r
1123     }\r
1124     catch (java.lang.OutOfMemoryError ex)\r
1125     {\r
1126     }\r
1127 \r
1128   }\r
1129 \r
1130   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1131   {\r
1132     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1133   }\r
1134 \r
1135   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1136   {\r
1137     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1138   }\r
1139 \r
1140   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1141   {\r
1142     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1143   }\r
1144 \r
1145   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1146   {\r
1147     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1148   }\r
1149 \r
1150   void NewTreePanel(String type, String pwType, String title)\r
1151   {\r
1152     //are the sequences aligned?\r
1153     if (!viewport.alignment.isAligned())\r
1154     {\r
1155       SequenceI current;\r
1156       int Width = viewport.getAlignment().getWidth();\r
1157 \r
1158       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1159            i++)\r
1160       {\r
1161         current = viewport.getAlignment().getSequenceAt(i);\r
1162 \r
1163         if (current.getLength() < Width)\r
1164         {\r
1165           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1166         }\r
1167       }\r
1168       alignPanel.repaint();\r
1169 \r
1170     }\r
1171 \r
1172     final TreePanel tp;\r
1173     if (viewport.getSelectionGroup() != null &&\r
1174         viewport.getSelectionGroup().getSize() > 3)\r
1175     {\r
1176       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1177                          pwType,\r
1178                          0, viewport.alignment.getWidth());\r
1179     }\r
1180     else\r
1181     {\r
1182       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1183                          type, pwType, 0, viewport.alignment.getWidth());\r
1184     }\r
1185 \r
1186     addTreeMenuItem(tp, title);\r
1187 \r
1188     jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1189   }\r
1190 \r
1191   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1192   {\r
1193     final MenuItem item = new MenuItem(title);\r
1194     sortByTreeMenu.add(item);\r
1195     item.addActionListener(new java.awt.event.ActionListener()\r
1196     {\r
1197       public void actionPerformed(ActionEvent e)\r
1198       {\r
1199         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1200                                        HistoryItem.SORT));\r
1201         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1202         alignPanel.repaint();\r
1203       }\r
1204     });\r
1205 \r
1206     treePanel.addWindowListener(new WindowAdapter()\r
1207     {\r
1208       public void windowClosing(WindowEvent e)\r
1209       {\r
1210         sortByTreeMenu.remove(item);\r
1211       };\r
1212     });\r
1213   }\r
1214 \r
1215   protected void documentation_actionPerformed(ActionEvent e)\r
1216   {\r
1217     jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");\r
1218   }\r
1219 \r
1220   protected void about_actionPerformed(ActionEvent e)\r
1221   {\r
1222 \r
1223     class AboutPanel extends Canvas\r
1224     {\r
1225       String version;\r
1226       public AboutPanel(String version)\r
1227       { this.version = version; }\r
1228 \r
1229       public void paint(Graphics g)\r
1230       {\r
1231         g.setColor(Color.white);\r
1232         g.fillRect(0, 0, getSize().width, getSize().height);\r
1233         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1234         FontMetrics fm = g.getFontMetrics();\r
1235         int fh = fm.getHeight();\r
1236         int y = 5, x = 7;\r
1237         g.setColor(Color.black);\r
1238         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1239         g.drawString("Jalview - Release "+version, 200, y += fh);\r
1240         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1241         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1242                      x, y += fh * 2);\r
1243         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1244                      x, y += fh);\r
1245         g.drawString(\r
1246             "For any issues relating to Jalview, email help@jalview.org", x,\r
1247             y += fh);\r
1248         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1249         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1250                      x, y += fh);\r
1251         g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);\r
1252       }\r
1253     }\r
1254 \r
1255     String version = "test";\r
1256     java.net.URL url = getClass().getResource("/.build_properties");\r
1257     if (url != null)\r
1258     {\r
1259       try\r
1260       {\r
1261         BufferedReader reader = new BufferedReader(new InputStreamReader(\r
1262             url.openStream()));\r
1263         String line;\r
1264         while ( (line = reader.readLine()) != null)\r
1265         {\r
1266           if (line.indexOf("VERSION") > -1)\r
1267           {\r
1268             version = line.substring(line.indexOf("=") + 1);\r
1269           }\r
1270         }\r
1271       }\r
1272       catch (Exception ex)\r
1273       {\r
1274         ex.printStackTrace();\r
1275       }\r
1276     }\r
1277 \r
1278 \r
1279     Frame frame = new Frame();\r
1280     frame.add(new AboutPanel(version));\r
1281     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1282 \r
1283   }\r
1284 }\r