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         resetAllColourSchemes();\r
 426         alignPanel.repaint();\r
 427       }\r
 428 \r
 429     }\r
 430     catch (Exception ex)\r
 431     {} // could be anything being pasted in here\r
 432 \r
 433   }\r
 434 \r
 435   protected void cut_actionPerformed(ActionEvent e)\r
 436   {\r
 437     copy_actionPerformed(null);\r
 438     delete_actionPerformed(null);\r
 439   }\r
 440 \r
 441   protected void delete_actionPerformed(ActionEvent e)\r
 442   {\r
 443     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
 444                                    HistoryItem.HIDE));\r
 445     if (viewport.getSelectionGroup() == null)\r
 446     {\r
 447       return;\r
 448     }\r
 449 \r
 450 \r
 451     SequenceGroup sg = viewport.getSelectionGroup();\r
 452     boolean allSequences = false;\r
 453     if(sg.sequences.size()==viewport.alignment.getHeight())\r
 454           allSequences = true;\r
 455 \r
 456     for (int i = 0; i < sg.sequences.size(); i++)\r
 457     {\r
 458       SequenceI seq = sg.getSequenceAt(i);\r
 459       int index = viewport.getAlignment().findIndex(seq);\r
 460       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 461 \r
 462       // If the cut affects all sequences, remove highlighted columns\r
 463       if (allSequences)\r
 464       {\r
 465         viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
 466                                                      sg.getEndRes() + 1);\r
 467       }\r
 468 \r
 469 \r
 470       if (seq.getSequence().length() < 1)\r
 471       {\r
 472         viewport.getAlignment().deleteSequence(seq);\r
 473       }\r
 474       else\r
 475       {\r
 476         viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 477       }\r
 478     }\r
 479 \r
 480     viewport.setSelectionGroup(null);\r
 481     viewport.alignment.deleteGroup(sg);\r
 482     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
 483     if (viewport.getAlignment().getHeight() < 1)\r
 484     {\r
 485       try\r
 486       {\r
 487         this.setVisible(false);\r
 488       }\r
 489       catch (Exception ex)\r
 490       {}\r
 491     }\r
 492     viewport.updateConservation();\r
 493     viewport.updateConsensus();\r
 494     resetAllColourSchemes();\r
 495     alignPanel.repaint();\r
 496 \r
 497   }\r
 498 \r
 499   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 500   {\r
 501     viewport.alignment.deleteAllGroups();\r
 502     viewport.setSelectionGroup(null);\r
 503 \r
 504     alignPanel.repaint();\r
 505   }\r
 506 \r
 507   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 508   {\r
 509     SequenceGroup sg = new SequenceGroup();\r
 510     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 511     {\r
 512       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
 513     }\r
 514     sg.setEndRes(viewport.alignment.getWidth()-1);\r
 515     viewport.setSelectionGroup(sg);\r
 516     alignPanel.repaint();\r
 517     PaintRefresher.Refresh(null, viewport.alignment);\r
 518   }\r
 519 \r
 520   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 521   {\r
 522     viewport.setSelectionGroup(null);\r
 523     viewport.getColumnSelection().clear();\r
 524     viewport.setSelectionGroup(null);\r
 525     PaintRefresher.Refresh(null, viewport.alignment);\r
 526   }\r
 527 \r
 528   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 529   {\r
 530     SequenceGroup sg = viewport.getSelectionGroup();\r
 531     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 532     {\r
 533       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
 534     }\r
 535 \r
 536     PaintRefresher.Refresh(null, viewport.alignment);\r
 537   }\r
 538 \r
 539   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 540   {\r
 541     ColumnSelection colSel = viewport.getColumnSelection();\r
 542     if (colSel.size() > 0)\r
 543     {\r
 544       addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
 545                                      HistoryItem.HIDE));\r
 546       int min = colSel.getMin();\r
 547       viewport.getAlignment().trimLeft(min);\r
 548       colSel.compensateForEdit(0, min);\r
 549 \r
 550       if (viewport.getSelectionGroup() != null)\r
 551       {\r
 552         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 553       }\r
 554 \r
 555       Vector groups = viewport.alignment.getGroups();\r
 556       for (int i = 0; i < groups.size(); i++)\r
 557       {\r
 558         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 559         if (!sg.adjustForRemoveLeft(min))\r
 560         {\r
 561           viewport.alignment.deleteGroup(sg);\r
 562         }\r
 563       }\r
 564       resetAllColourSchemes();\r
 565       alignPanel.repaint();\r
 566     }\r
 567   }\r
 568 \r
 569   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 570   {\r
 571     ColumnSelection colSel = viewport.getColumnSelection();\r
 572     if (colSel.size() > 0)\r
 573     {\r
 574       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
 575                                      HistoryItem.HIDE));\r
 576       int max = colSel.getMax();\r
 577       viewport.getAlignment().trimRight(max);\r
 578       if (viewport.getSelectionGroup() != null)\r
 579       {\r
 580         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 581       }\r
 582 \r
 583       Vector groups = viewport.alignment.getGroups();\r
 584       for (int i = 0; i < groups.size(); i++)\r
 585       {\r
 586         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 587         if (!sg.adjustForRemoveRight(max))\r
 588         {\r
 589           viewport.alignment.deleteGroup(sg);\r
 590         }\r
 591       }\r
 592       resetAllColourSchemes();\r
 593       alignPanel.repaint();\r
 594     }\r
 595 \r
 596   }\r
 597 \r
 598   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 599   {\r
 600     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
 601                                    viewport.alignment,\r
 602                                    HistoryItem.HIDE));\r
 603 \r
 604     //This is to maintain viewport position on first residue\r
 605     //of first sequence\r
 606     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 607     int startRes = seq.findPosition(viewport.startRes);\r
 608 \r
 609     viewport.getAlignment().removeGaps();\r
 610 \r
 611     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 612 \r
 613     viewport.updateConservation();\r
 614     viewport.updateConsensus();\r
 615     resetAllColourSchemes();\r
 616     alignPanel.repaint();\r
 617   }\r
 618 \r
 619   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 620   {\r
 621     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
 622                                    HistoryItem.HIDE));\r
 623 \r
 624     //This is to maintain viewport position on first residue\r
 625     //of first sequence\r
 626     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 627     int startRes = seq.findPosition(viewport.startRes);\r
 628 \r
 629     SequenceI current;\r
 630     int jSize;\r
 631 \r
 632     Vector seqs=null;\r
 633 \r
 634     int start=0, end = viewport.alignment.getWidth();\r
 635 \r
 636     if (viewport.getSelectionGroup() != null\r
 637         && viewport.getSelectionGroup().sequences != null\r
 638         && viewport.getSelectionGroup().sequences.size()>0)\r
 639     {\r
 640       seqs = viewport.getSelectionGroup().sequences;\r
 641       start = viewport.getSelectionGroup().getStartRes();\r
 642       end = viewport.getSelectionGroup().getEndRes();\r
 643     }\r
 644     else\r
 645       seqs = viewport.alignment.getSequences();\r
 646 \r
 647     for (int i = 0; i <seqs.size(); i++)\r
 648     {\r
 649       current = (SequenceI)seqs.elementAt(i);\r
 650       jSize = current.getLength();\r
 651 \r
 652       int j = start;\r
 653       do\r
 654       {\r
 655         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 656         {\r
 657           current.deleteCharAt(j);\r
 658           j--;\r
 659           jSize--;\r
 660         }\r
 661         j++;\r
 662       }\r
 663       while(j < end && j < jSize) ;\r
 664     }\r
 665 \r
 666     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 667     viewport.updateConservation();\r
 668     viewport.updateConsensus();\r
 669     resetAllColourSchemes();\r
 670     alignPanel.repaint();\r
 671   }\r
 672 \r
 673   void resetAllColourSchemes()\r
 674   {\r
 675     ColourSchemeI cs = viewport.globalColourScheme;\r
 676     if(cs!=null)\r
 677     {\r
 678         cs.setConsensus(viewport.vconsensus);\r
 679         if(cs.conservationApplied())\r
 680         {\r
 681           Alignment al = (Alignment) viewport.alignment;\r
 682           Conservation c = new Conservation("All",\r
 683                                             ResidueProperties.propHash, 3,\r
 684                                             al.getSequences(), 0,\r
 685                                             al.getWidth() - 1);\r
 686           c.calculate();\r
 687           c.verdict(false, viewport.ConsPercGaps);\r
 688 \r
 689           cs.setConservation(c);\r
 690         }\r
 691     }\r
 692 \r
 693     if(viewport.getGlobalColourScheme()!=null\r
 694        && viewport.getGlobalColourScheme() instanceof ClustalxColourScheme)\r
 695     {\r
 696       ((ClustalxColourScheme)viewport.getGlobalColourScheme()).\r
 697           resetClustalX(viewport.alignment.getSequences(),\r
 698                         viewport.alignment.getWidth());\r
 699     }\r
 700 \r
 701     int s, sSize = viewport.alignment.getGroups().size();\r
 702     for(s=0; s<sSize; s++)\r
 703     {\r
 704       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
 705       if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
 706       {\r
 707         ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
 708       }\r
 709 \r
 710       sg.recalcConservation();\r
 711 \r
 712     }\r
 713   }\r
 714 \r
 715 \r
 716 \r
 717   public void findMenuItem_actionPerformed(ActionEvent e)\r
 718   {\r
 719     Finder finder = new Finder(alignPanel);\r
 720   }\r
 721 \r
 722   public void font_actionPerformed(ActionEvent e)\r
 723   {\r
 724     Frame frame = new Frame();\r
 725     FontChooser fc = new FontChooser(alignPanel, frame);\r
 726     frame.add(fc);\r
 727     jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);\r
 728 \r
 729   }\r
 730 \r
 731   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 732   {\r
 733     viewport.setShowFullId(fullSeqId.getState());\r
 734     alignPanel.fontChanged();\r
 735     alignPanel.repaint();\r
 736   }\r
 737 \r
 738   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 739   {\r
 740     viewport.setColourText(colourTextMenuItem.getState());\r
 741     alignPanel.repaint();\r
 742   }\r
 743 \r
 744   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 745   {\r
 746     viewport.setWrapAlignment(wrapMenuItem.getState());\r
 747     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
 748     scaleAbove.setEnabled(wrapMenuItem.getState());\r
 749     scaleLeft.setEnabled(wrapMenuItem.getState());\r
 750     scaleRight.setEnabled(wrapMenuItem.getState());\r
 751     alignPanel.repaint();\r
 752   }\r
 753 \r
 754   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 755   {\r
 756     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 757     alignPanel.repaint();\r
 758   }\r
 759 \r
 760   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 761   {\r
 762     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 763     alignPanel.repaint();\r
 764   }\r
 765 \r
 766   protected void scaleRight_actionPerformed(ActionEvent e)\r
 767   {\r
 768     viewport.setScaleRightWrapped(scaleRight.getState());\r
 769     alignPanel.repaint();\r
 770   }\r
 771 \r
 772   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 773   {\r
 774     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
 775     alignPanel.repaint();\r
 776   }\r
 777 \r
 778   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 779   {\r
 780     viewport.setShowText(viewTextMenuItem.getState());\r
 781     alignPanel.repaint();\r
 782   }\r
 783 \r
 784   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 785   {\r
 786     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 787     alignPanel.repaint();\r
 788   }\r
 789 \r
 790   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 791   {\r
 792     if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
 793     {\r
 794       annotationPanelMenuItem.setState(false);\r
 795       return;\r
 796     }\r
 797     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
 798     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
 799   }\r
 800 \r
 801   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 802   {\r
 803     if (alignPanel.overviewPanel != null)\r
 804     {\r
 805       return;\r
 806     }\r
 807 \r
 808     Frame frame = new Frame();\r
 809     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 810     frame.add(overview);\r
 811     // +50 must allow for applet frame window\r
 812     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
 813                                      overview.preferredSize().width,\r
 814                                      overview.preferredSize().height + 50);\r
 815 \r
 816     frame.pack();\r
 817     frame.addWindowListener(new WindowAdapter()\r
 818     {\r
 819       public void windowClosing(WindowEvent e)\r
 820       {\r
 821         alignPanel.setOverviewPanel(null);\r
 822       };\r
 823     });\r
 824 \r
 825     alignPanel.setOverviewPanel(overview);\r
 826 \r
 827   }\r
 828 \r
 829   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 830   {\r
 831     changeColour(null);\r
 832   }\r
 833 \r
 834   public void clustalColour_actionPerformed(ActionEvent e)\r
 835   {\r
 836     abovePIDThreshold.setState(false);\r
 837     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
 838                                           viewport.alignment.getWidth()));\r
 839   }\r
 840 \r
 841   public void zappoColour_actionPerformed(ActionEvent e)\r
 842   {\r
 843     changeColour(new ZappoColourScheme());\r
 844   }\r
 845 \r
 846   public void taylorColour_actionPerformed(ActionEvent e)\r
 847   {\r
 848     changeColour(new TaylorColourScheme());\r
 849   }\r
 850 \r
 851   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 852   {\r
 853     changeColour(new HydrophobicColourScheme());\r
 854   }\r
 855 \r
 856   public void helixColour_actionPerformed(ActionEvent e)\r
 857   {\r
 858     changeColour(new HelixColourScheme());\r
 859   }\r
 860 \r
 861   public void strandColour_actionPerformed(ActionEvent e)\r
 862   {\r
 863     changeColour(new StrandColourScheme());\r
 864   }\r
 865 \r
 866   public void turnColour_actionPerformed(ActionEvent e)\r
 867   {\r
 868     changeColour(new TurnColourScheme());\r
 869   }\r
 870 \r
 871   public void buriedColour_actionPerformed(ActionEvent e)\r
 872   {\r
 873     changeColour(new BuriedColourScheme());\r
 874   }\r
 875 \r
 876   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 877   {\r
 878     changeColour(new NucleotideColourScheme());\r
 879   }\r
 880 \r
 881   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 882   {\r
 883     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
 884   }\r
 885 \r
 886   void changeColour(ColourSchemeI cs)\r
 887   {\r
 888     int threshold = 0;\r
 889 \r
 890     if(cs!=null)\r
 891     {\r
 892       if (viewport.getAbovePIDThreshold())\r
 893       {\r
 894         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 895 \r
 896         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
 897 \r
 898         viewport.setGlobalColourScheme(cs);\r
 899       }\r
 900       else\r
 901       {\r
 902         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
 903       }\r
 904 \r
 905       if (viewport.getConservationSelected())\r
 906       {\r
 907 \r
 908         Alignment al = (Alignment) viewport.alignment;\r
 909         Conservation c = new Conservation("All",\r
 910                                           ResidueProperties.propHash, 3,\r
 911                                           al.getSequences(), 0,\r
 912                                           al.getWidth() - 1);\r
 913 \r
 914         c.calculate();\r
 915         c.verdict(false, viewport.ConsPercGaps);\r
 916 \r
 917         cs.setConservation(c);\r
 918 \r
 919         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
 920             "Background"));\r
 921 \r
 922       }\r
 923       else\r
 924       {\r
 925         cs.setConservation(null);\r
 926       }\r
 927 \r
 928       cs.setConsensus(viewport.vconsensus);\r
 929 \r
 930     }\r
 931     viewport.setGlobalColourScheme(cs);\r
 932 \r
 933     if (viewport.getColourAppliesToAllGroups())\r
 934     {\r
 935       Vector groups = viewport.alignment.getGroups();\r
 936       for (int i = 0; i < groups.size(); i++)\r
 937       {\r
 938         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 939 \r
 940         if(cs==null)\r
 941         {\r
 942           sg.cs = null;\r
 943           continue;\r
 944         }\r
 945         if (cs instanceof ClustalxColourScheme)\r
 946         {\r
 947           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
 948         }\r
 949         else\r
 950         {\r
 951           try\r
 952           {\r
 953             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
 954           }\r
 955           catch (Exception ex)\r
 956           {\r
 957             ex.printStackTrace();\r
 958             sg.cs = cs;\r
 959           }\r
 960         }\r
 961 \r
 962         if (viewport.getAbovePIDThreshold()\r
 963             || cs instanceof PIDColourScheme\r
 964             || cs instanceof Blosum62ColourScheme)\r
 965         {\r
 966           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
 967           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 968         }\r
 969         else\r
 970           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
 971 \r
 972         if (viewport.getConservationSelected())\r
 973         {\r
 974           Conservation c = new Conservation("Group",\r
 975                                             ResidueProperties.propHash, 3,\r
 976                                             sg.sequences, 0,\r
 977                                             viewport.alignment.getWidth() - 1);\r
 978           c.calculate();\r
 979           c.verdict(false, viewport.ConsPercGaps);\r
 980           sg.cs.setConservation(c);\r
 981         }\r
 982         else\r
 983         {\r
 984           sg.cs.setConservation(null);\r
 985           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
 986         }\r
 987 \r
 988       }\r
 989     }\r
 990 \r
 991 \r
 992     if (alignPanel.getOverviewPanel() != null)\r
 993     {\r
 994       alignPanel.getOverviewPanel().updateOverviewImage();\r
 995     }\r
 996 \r
 997     alignPanel.repaint();\r
 998   }\r
 999 \r
1000 \r
1001 \r
1002   protected void modifyPID_actionPerformed(ActionEvent e)\r
1003   {\r
1004     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
1005     {\r
1006       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
1007                                      "Background");\r
1008       SliderPanel.showPIDSlider();\r
1009     }\r
1010   }\r
1011 \r
1012   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1013   {\r
1014     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
1015     {\r
1016       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
1017                                         "Background");\r
1018       SliderPanel.showConservationSlider();\r
1019     }\r
1020   }\r
1021 \r
1022   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1023   {\r
1024     viewport.setConservationSelected(conservationMenuItem.getState());\r
1025 \r
1026     viewport.setAbovePIDThreshold(false);\r
1027     abovePIDThreshold.setState(false);\r
1028 \r
1029     changeColour(viewport.getGlobalColourScheme());\r
1030 \r
1031     modifyConservation_actionPerformed(null);\r
1032   }\r
1033 \r
1034   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1035   {\r
1036     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
1037 \r
1038     conservationMenuItem.setState(false);\r
1039     viewport.setConservationSelected(false);\r
1040 \r
1041     changeColour(viewport.getGlobalColourScheme());\r
1042 \r
1043     modifyPID_actionPerformed(null);\r
1044   }\r
1045 \r
1046   public void userDefinedColour_actionPerformed(ActionEvent e)\r
1047   {\r
1048     UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);\r
1049   }\r
1050 \r
1051   public void PIDColour_actionPerformed(ActionEvent e)\r
1052   {\r
1053     changeColour(new PIDColourScheme());\r
1054   }\r
1055 \r
1056   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1057   {\r
1058     changeColour(new Blosum62ColourScheme());\r
1059   }\r
1060 \r
1061   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1062   {\r
1063     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1064                                    HistoryItem.SORT));\r
1065     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1066                               viewport.getAlignment().getSequenceAt(0));\r
1067     alignPanel.repaint();\r
1068   }\r
1069 \r
1070   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1071   {\r
1072     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1073                                    HistoryItem.SORT));\r
1074     AlignmentSorter.sortByID(viewport.getAlignment());\r
1075     alignPanel.repaint();\r
1076   }\r
1077 \r
1078   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1079   {\r
1080     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1081                                    HistoryItem.SORT));\r
1082     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1083     alignPanel.repaint();\r
1084 \r
1085   }\r
1086 \r
1087   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1088   {\r
1089     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
1090     Frame frame = new Frame();\r
1091     frame.add(sp);\r
1092     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
1093                                      400, 120);\r
1094 \r
1095   }\r
1096 \r
1097   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1098   {\r
1099     if (viewport.getSelectionGroup().getSize() > 1)\r
1100     {\r
1101       Frame frame = new Frame();\r
1102       frame.add(new PairwiseAlignPanel(viewport));\r
1103       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1104     }\r
1105   }\r
1106 \r
1107   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
1108   {\r
1109 \r
1110     if ( (viewport.getSelectionGroup() != null &&\r
1111           viewport.getSelectionGroup().getSize() < 4 &&\r
1112           viewport.getSelectionGroup().getSize() > 0)\r
1113         || viewport.getAlignment().getHeight() < 4)\r
1114     {\r
1115       return;\r
1116     }\r
1117 \r
1118     try\r
1119     {\r
1120       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
1121       Frame frame = new Frame();\r
1122       frame.add(pcaPanel);\r
1123       jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",\r
1124                                        400, 400);\r
1125     }\r
1126     catch (java.lang.OutOfMemoryError ex)\r
1127     {\r
1128     }\r
1129 \r
1130   }\r
1131 \r
1132   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1133   {\r
1134     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1135   }\r
1136 \r
1137   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1138   {\r
1139     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1140   }\r
1141 \r
1142   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1143   {\r
1144     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1145   }\r
1146 \r
1147   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1148   {\r
1149     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1150   }\r
1151 \r
1152   void NewTreePanel(String type, String pwType, String title)\r
1153   {\r
1154     //are the sequences aligned?\r
1155     if (!viewport.alignment.isAligned())\r
1156     {\r
1157       SequenceI current;\r
1158       int Width = viewport.getAlignment().getWidth();\r
1159 \r
1160       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1161            i++)\r
1162       {\r
1163         current = viewport.getAlignment().getSequenceAt(i);\r
1164 \r
1165         if (current.getLength() < Width)\r
1166         {\r
1167           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1168         }\r
1169       }\r
1170       alignPanel.repaint();\r
1171 \r
1172     }\r
1173 \r
1174     final TreePanel tp;\r
1175     if (viewport.getSelectionGroup() != null &&\r
1176         viewport.getSelectionGroup().getSize() > 3)\r
1177     {\r
1178       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1179                          pwType,\r
1180                          0, viewport.alignment.getWidth());\r
1181     }\r
1182     else\r
1183     {\r
1184       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1185                          type, pwType, 0, viewport.alignment.getWidth());\r
1186     }\r
1187 \r
1188     addTreeMenuItem(tp, title);\r
1189 \r
1190     jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1191   }\r
1192 \r
1193   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1194   {\r
1195     final MenuItem item = new MenuItem(title);\r
1196     sortByTreeMenu.add(item);\r
1197     item.addActionListener(new java.awt.event.ActionListener()\r
1198     {\r
1199       public void actionPerformed(ActionEvent e)\r
1200       {\r
1201         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1202                                        HistoryItem.SORT));\r
1203         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1204         alignPanel.repaint();\r
1205       }\r
1206     });\r
1207 \r
1208     treePanel.addWindowListener(new WindowAdapter()\r
1209     {\r
1210       public void windowClosing(WindowEvent e)\r
1211       {\r
1212         sortByTreeMenu.remove(item);\r
1213       };\r
1214     });\r
1215   }\r
1216 \r
1217   protected void documentation_actionPerformed(ActionEvent e)\r
1218   {\r
1219     jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");\r
1220   }\r
1221 \r
1222   protected void about_actionPerformed(ActionEvent e)\r
1223   {\r
1224 \r
1225     class AboutPanel extends Canvas\r
1226     {\r
1227       String version;\r
1228       public AboutPanel(String version)\r
1229       { this.version = version; }\r
1230 \r
1231       public void paint(Graphics g)\r
1232       {\r
1233         g.setColor(Color.white);\r
1234         g.fillRect(0, 0, getSize().width, getSize().height);\r
1235         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1236         FontMetrics fm = g.getFontMetrics();\r
1237         int fh = fm.getHeight();\r
1238         int y = 5, x = 7;\r
1239         g.setColor(Color.black);\r
1240         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1241         g.drawString("Jalview - Release "+version, 200, y += fh);\r
1242         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1243         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1244                      x, y += fh * 2);\r
1245         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1246                      x, y += fh);\r
1247         g.drawString(\r
1248             "For any issues relating to Jalview, email help@jalview.org", x,\r
1249             y += fh);\r
1250         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1251         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1252                      x, y += fh);\r
1253         g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);\r
1254       }\r
1255     }\r
1256 \r
1257     String version = "test";\r
1258     java.net.URL url = getClass().getResource("/.build_properties");\r
1259     if (url != null)\r
1260     {\r
1261       try\r
1262       {\r
1263         BufferedReader reader = new BufferedReader(new InputStreamReader(\r
1264             url.openStream()));\r
1265         String line;\r
1266         while ( (line = reader.readLine()) != null)\r
1267         {\r
1268           if (line.indexOf("VERSION") > -1)\r
1269           {\r
1270             version = line.substring(line.indexOf("=") + 1);\r
1271           }\r
1272         }\r
1273       }\r
1274       catch (Exception ex)\r
1275       {\r
1276         ex.printStackTrace();\r
1277       }\r
1278     }\r
1279 \r
1280 \r
1281     Frame frame = new Frame();\r
1282     frame.add(new AboutPanel(version));\r
1283     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1284 \r
1285   }\r
1286 }\r