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     alignPanel.repaint();\r
 526     PaintRefresher.Refresh(null, viewport.alignment);\r
 527   }\r
 528 \r
 529   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 530   {\r
 531     SequenceGroup sg = viewport.getSelectionGroup();\r
 532     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 533     {\r
 534       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
 535     }\r
 536 \r
 537     PaintRefresher.Refresh(null, viewport.alignment);\r
 538   }\r
 539 \r
 540   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 541   {\r
 542     ColumnSelection colSel = viewport.getColumnSelection();\r
 543     if (colSel.size() > 0)\r
 544     {\r
 545       addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
 546                                      HistoryItem.HIDE));\r
 547       int min = colSel.getMin();\r
 548       viewport.getAlignment().trimLeft(min);\r
 549       colSel.compensateForEdit(0, min);\r
 550 \r
 551       if (viewport.getSelectionGroup() != null)\r
 552       {\r
 553         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 554       }\r
 555 \r
 556       Vector groups = viewport.alignment.getGroups();\r
 557       for (int i = 0; i < groups.size(); i++)\r
 558       {\r
 559         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 560         if (!sg.adjustForRemoveLeft(min))\r
 561         {\r
 562           viewport.alignment.deleteGroup(sg);\r
 563         }\r
 564       }\r
 565       resetAllColourSchemes();\r
 566       alignPanel.repaint();\r
 567     }\r
 568   }\r
 569 \r
 570   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 571   {\r
 572     ColumnSelection colSel = viewport.getColumnSelection();\r
 573     if (colSel.size() > 0)\r
 574     {\r
 575       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
 576                                      HistoryItem.HIDE));\r
 577       int max = colSel.getMax();\r
 578       viewport.getAlignment().trimRight(max);\r
 579       if (viewport.getSelectionGroup() != null)\r
 580       {\r
 581         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 582       }\r
 583 \r
 584       Vector groups = viewport.alignment.getGroups();\r
 585       for (int i = 0; i < groups.size(); i++)\r
 586       {\r
 587         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 588         if (!sg.adjustForRemoveRight(max))\r
 589         {\r
 590           viewport.alignment.deleteGroup(sg);\r
 591         }\r
 592       }\r
 593       resetAllColourSchemes();\r
 594       alignPanel.repaint();\r
 595     }\r
 596 \r
 597   }\r
 598 \r
 599   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 600   {\r
 601     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
 602                                    viewport.alignment,\r
 603                                    HistoryItem.HIDE));\r
 604 \r
 605     //This is to maintain viewport position on first residue\r
 606     //of first sequence\r
 607     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 608     int startRes = seq.findPosition(viewport.startRes);\r
 609 \r
 610     viewport.getAlignment().removeGaps();\r
 611 \r
 612     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 613 \r
 614     viewport.updateConservation();\r
 615     viewport.updateConsensus();\r
 616     resetAllColourSchemes();\r
 617     alignPanel.repaint();\r
 618   }\r
 619 \r
 620   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 621   {\r
 622     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
 623                                    HistoryItem.HIDE));\r
 624 \r
 625     //This is to maintain viewport position on first residue\r
 626     //of first sequence\r
 627     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 628     int startRes = seq.findPosition(viewport.startRes);\r
 629 \r
 630     SequenceI current;\r
 631     int jSize;\r
 632 \r
 633     Vector seqs=null;\r
 634 \r
 635     int start=0, end = viewport.alignment.getWidth();\r
 636 \r
 637     if (viewport.getSelectionGroup() != null\r
 638         && viewport.getSelectionGroup().sequences != null\r
 639         && viewport.getSelectionGroup().sequences.size()>0)\r
 640     {\r
 641       seqs = viewport.getSelectionGroup().sequences;\r
 642       start = viewport.getSelectionGroup().getStartRes();\r
 643       end = viewport.getSelectionGroup().getEndRes();\r
 644     }\r
 645     else\r
 646       seqs = viewport.alignment.getSequences();\r
 647 \r
 648     for (int i = 0; i <seqs.size(); i++)\r
 649     {\r
 650       current = (SequenceI)seqs.elementAt(i);\r
 651       jSize = current.getLength();\r
 652 \r
 653       int j = start;\r
 654       do\r
 655       {\r
 656         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 657         {\r
 658           current.deleteCharAt(j);\r
 659           j--;\r
 660           jSize--;\r
 661         }\r
 662         j++;\r
 663       }\r
 664       while(j < end && j < jSize) ;\r
 665     }\r
 666 \r
 667     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 668     viewport.updateConservation();\r
 669     viewport.updateConsensus();\r
 670     resetAllColourSchemes();\r
 671     alignPanel.repaint();\r
 672   }\r
 673 \r
 674   void resetAllColourSchemes()\r
 675   {\r
 676     ColourSchemeI cs = viewport.globalColourScheme;\r
 677     if(cs!=null)\r
 678     {\r
 679         cs.setConsensus(viewport.vconsensus);\r
 680         if(cs.conservationApplied())\r
 681         {\r
 682           Alignment al = (Alignment) viewport.alignment;\r
 683           Conservation c = new Conservation("All",\r
 684                                             ResidueProperties.propHash, 3,\r
 685                                             al.getSequences(), 0,\r
 686                                             al.getWidth() - 1);\r
 687           c.calculate();\r
 688           c.verdict(false, viewport.ConsPercGaps);\r
 689 \r
 690           cs.setConservation(c);\r
 691         }\r
 692     }\r
 693 \r
 694     if(viewport.getGlobalColourScheme()!=null\r
 695        && viewport.getGlobalColourScheme() instanceof ClustalxColourScheme)\r
 696     {\r
 697       ((ClustalxColourScheme)viewport.getGlobalColourScheme()).\r
 698           resetClustalX(viewport.alignment.getSequences(),\r
 699                         viewport.alignment.getWidth());\r
 700     }\r
 701 \r
 702     int s, sSize = viewport.alignment.getGroups().size();\r
 703     for(s=0; s<sSize; s++)\r
 704     {\r
 705       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
 706       if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
 707       {\r
 708         ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
 709       }\r
 710 \r
 711       sg.recalcConservation();\r
 712 \r
 713     }\r
 714   }\r
 715 \r
 716 \r
 717 \r
 718   public void findMenuItem_actionPerformed(ActionEvent e)\r
 719   {\r
 720     Finder finder = new Finder(alignPanel);\r
 721   }\r
 722 \r
 723   public void font_actionPerformed(ActionEvent e)\r
 724   {\r
 725     Frame frame = new Frame();\r
 726     FontChooser fc = new FontChooser(alignPanel, frame);\r
 727     frame.add(fc);\r
 728     jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);\r
 729 \r
 730   }\r
 731 \r
 732   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 733   {\r
 734     viewport.setShowFullId(fullSeqId.getState());\r
 735     alignPanel.fontChanged();\r
 736     alignPanel.repaint();\r
 737   }\r
 738 \r
 739   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 740   {\r
 741     viewport.setColourText(colourTextMenuItem.getState());\r
 742     alignPanel.repaint();\r
 743   }\r
 744 \r
 745   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 746   {\r
 747     viewport.setWrapAlignment(wrapMenuItem.getState());\r
 748     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
 749     scaleAbove.setEnabled(wrapMenuItem.getState());\r
 750     scaleLeft.setEnabled(wrapMenuItem.getState());\r
 751     scaleRight.setEnabled(wrapMenuItem.getState());\r
 752     alignPanel.repaint();\r
 753   }\r
 754 \r
 755   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 756   {\r
 757     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 758     alignPanel.repaint();\r
 759   }\r
 760 \r
 761   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 762   {\r
 763     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 764     alignPanel.repaint();\r
 765   }\r
 766 \r
 767   protected void scaleRight_actionPerformed(ActionEvent e)\r
 768   {\r
 769     viewport.setScaleRightWrapped(scaleRight.getState());\r
 770     alignPanel.repaint();\r
 771   }\r
 772 \r
 773   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 774   {\r
 775     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
 776     alignPanel.repaint();\r
 777   }\r
 778 \r
 779   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 780   {\r
 781     viewport.setShowText(viewTextMenuItem.getState());\r
 782     alignPanel.repaint();\r
 783   }\r
 784 \r
 785   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 786   {\r
 787     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 788     alignPanel.repaint();\r
 789   }\r
 790 \r
 791   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 792   {\r
 793     if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
 794     {\r
 795       annotationPanelMenuItem.setState(false);\r
 796       return;\r
 797     }\r
 798     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
 799     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
 800   }\r
 801 \r
 802   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 803   {\r
 804     if (alignPanel.overviewPanel != null)\r
 805     {\r
 806       return;\r
 807     }\r
 808 \r
 809     Frame frame = new Frame();\r
 810     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 811     frame.add(overview);\r
 812     // +50 must allow for applet frame window\r
 813     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
 814                                      overview.preferredSize().width,\r
 815                                      overview.preferredSize().height + 50);\r
 816 \r
 817     frame.pack();\r
 818     frame.addWindowListener(new WindowAdapter()\r
 819     {\r
 820       public void windowClosing(WindowEvent e)\r
 821       {\r
 822         alignPanel.setOverviewPanel(null);\r
 823       };\r
 824     });\r
 825 \r
 826     alignPanel.setOverviewPanel(overview);\r
 827 \r
 828   }\r
 829 \r
 830   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 831   {\r
 832     changeColour(null);\r
 833   }\r
 834 \r
 835   public void clustalColour_actionPerformed(ActionEvent e)\r
 836   {\r
 837     abovePIDThreshold.setState(false);\r
 838     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
 839                                           viewport.alignment.getWidth()));\r
 840   }\r
 841 \r
 842   public void zappoColour_actionPerformed(ActionEvent e)\r
 843   {\r
 844     changeColour(new ZappoColourScheme());\r
 845   }\r
 846 \r
 847   public void taylorColour_actionPerformed(ActionEvent e)\r
 848   {\r
 849     changeColour(new TaylorColourScheme());\r
 850   }\r
 851 \r
 852   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 853   {\r
 854     changeColour(new HydrophobicColourScheme());\r
 855   }\r
 856 \r
 857   public void helixColour_actionPerformed(ActionEvent e)\r
 858   {\r
 859     changeColour(new HelixColourScheme());\r
 860   }\r
 861 \r
 862   public void strandColour_actionPerformed(ActionEvent e)\r
 863   {\r
 864     changeColour(new StrandColourScheme());\r
 865   }\r
 866 \r
 867   public void turnColour_actionPerformed(ActionEvent e)\r
 868   {\r
 869     changeColour(new TurnColourScheme());\r
 870   }\r
 871 \r
 872   public void buriedColour_actionPerformed(ActionEvent e)\r
 873   {\r
 874     changeColour(new BuriedColourScheme());\r
 875   }\r
 876 \r
 877   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 878   {\r
 879     changeColour(new NucleotideColourScheme());\r
 880   }\r
 881 \r
 882   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 883   {\r
 884     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
 885   }\r
 886 \r
 887   void changeColour(ColourSchemeI cs)\r
 888   {\r
 889     int threshold = 0;\r
 890 \r
 891     if(cs!=null)\r
 892     {\r
 893       if (viewport.getAbovePIDThreshold())\r
 894       {\r
 895         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 896 \r
 897         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
 898 \r
 899         viewport.setGlobalColourScheme(cs);\r
 900       }\r
 901       else\r
 902       {\r
 903         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
 904       }\r
 905 \r
 906       if (viewport.getConservationSelected())\r
 907       {\r
 908 \r
 909         Alignment al = (Alignment) viewport.alignment;\r
 910         Conservation c = new Conservation("All",\r
 911                                           ResidueProperties.propHash, 3,\r
 912                                           al.getSequences(), 0,\r
 913                                           al.getWidth() - 1);\r
 914 \r
 915         c.calculate();\r
 916         c.verdict(false, viewport.ConsPercGaps);\r
 917 \r
 918         cs.setConservation(c);\r
 919 \r
 920         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
 921             "Background"));\r
 922 \r
 923       }\r
 924       else\r
 925       {\r
 926         cs.setConservation(null);\r
 927       }\r
 928 \r
 929       cs.setConsensus(viewport.vconsensus);\r
 930 \r
 931     }\r
 932     viewport.setGlobalColourScheme(cs);\r
 933 \r
 934     if (viewport.getColourAppliesToAllGroups())\r
 935     {\r
 936       Vector groups = viewport.alignment.getGroups();\r
 937       for (int i = 0; i < groups.size(); i++)\r
 938       {\r
 939         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 940 \r
 941         if(cs==null)\r
 942         {\r
 943           sg.cs = null;\r
 944           continue;\r
 945         }\r
 946         if (cs instanceof ClustalxColourScheme)\r
 947         {\r
 948           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
 949         }\r
 950         else\r
 951         {\r
 952           try\r
 953           {\r
 954             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
 955           }\r
 956           catch (Exception ex)\r
 957           {\r
 958             ex.printStackTrace();\r
 959             sg.cs = cs;\r
 960           }\r
 961         }\r
 962 \r
 963         if (viewport.getAbovePIDThreshold()\r
 964             || cs instanceof PIDColourScheme\r
 965             || cs instanceof Blosum62ColourScheme)\r
 966         {\r
 967           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
 968           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 969         }\r
 970         else\r
 971           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
 972 \r
 973         if (viewport.getConservationSelected())\r
 974         {\r
 975           Conservation c = new Conservation("Group",\r
 976                                             ResidueProperties.propHash, 3,\r
 977                                             sg.sequences, 0,\r
 978                                             viewport.alignment.getWidth() - 1);\r
 979           c.calculate();\r
 980           c.verdict(false, viewport.ConsPercGaps);\r
 981           sg.cs.setConservation(c);\r
 982         }\r
 983         else\r
 984         {\r
 985           sg.cs.setConservation(null);\r
 986           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
 987         }\r
 988 \r
 989       }\r
 990     }\r
 991 \r
 992 \r
 993     if (alignPanel.getOverviewPanel() != null)\r
 994     {\r
 995       alignPanel.getOverviewPanel().updateOverviewImage();\r
 996     }\r
 997 \r
 998     alignPanel.repaint();\r
 999   }\r
1000 \r
1001 \r
1002 \r
1003   protected void modifyPID_actionPerformed(ActionEvent e)\r
1004   {\r
1005     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
1006     {\r
1007       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
1008                                      "Background");\r
1009       SliderPanel.showPIDSlider();\r
1010     }\r
1011   }\r
1012 \r
1013   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1014   {\r
1015     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
1016     {\r
1017       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
1018                                         "Background");\r
1019       SliderPanel.showConservationSlider();\r
1020     }\r
1021   }\r
1022 \r
1023   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1024   {\r
1025     viewport.setConservationSelected(conservationMenuItem.getState());\r
1026 \r
1027     viewport.setAbovePIDThreshold(false);\r
1028     abovePIDThreshold.setState(false);\r
1029 \r
1030     changeColour(viewport.getGlobalColourScheme());\r
1031 \r
1032     modifyConservation_actionPerformed(null);\r
1033   }\r
1034 \r
1035   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1036   {\r
1037     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
1038 \r
1039     conservationMenuItem.setState(false);\r
1040     viewport.setConservationSelected(false);\r
1041 \r
1042     changeColour(viewport.getGlobalColourScheme());\r
1043 \r
1044     modifyPID_actionPerformed(null);\r
1045   }\r
1046 \r
1047   public void userDefinedColour_actionPerformed(ActionEvent e)\r
1048   {\r
1049     UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);\r
1050   }\r
1051 \r
1052   public void PIDColour_actionPerformed(ActionEvent e)\r
1053   {\r
1054     changeColour(new PIDColourScheme());\r
1055   }\r
1056 \r
1057   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1058   {\r
1059     changeColour(new Blosum62ColourScheme());\r
1060   }\r
1061 \r
1062   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1063   {\r
1064     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1065                                    HistoryItem.SORT));\r
1066     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1067                               viewport.getAlignment().getSequenceAt(0));\r
1068     alignPanel.repaint();\r
1069   }\r
1070 \r
1071   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1072   {\r
1073     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1074                                    HistoryItem.SORT));\r
1075     AlignmentSorter.sortByID(viewport.getAlignment());\r
1076     alignPanel.repaint();\r
1077   }\r
1078 \r
1079   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1080   {\r
1081     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1082                                    HistoryItem.SORT));\r
1083     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1084     alignPanel.repaint();\r
1085 \r
1086   }\r
1087 \r
1088   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1089   {\r
1090     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
1091     Frame frame = new Frame();\r
1092     frame.add(sp);\r
1093     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
1094                                      400, 120);\r
1095 \r
1096   }\r
1097 \r
1098   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1099   {\r
1100     if (viewport.getSelectionGroup().getSize() > 1)\r
1101     {\r
1102       Frame frame = new Frame();\r
1103       frame.add(new PairwiseAlignPanel(viewport));\r
1104       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1105     }\r
1106   }\r
1107 \r
1108   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
1109   {\r
1110 \r
1111     if ( (viewport.getSelectionGroup() != null &&\r
1112           viewport.getSelectionGroup().getSize() < 4 &&\r
1113           viewport.getSelectionGroup().getSize() > 0)\r
1114         || viewport.getAlignment().getHeight() < 4)\r
1115     {\r
1116       return;\r
1117     }\r
1118 \r
1119     try\r
1120     {\r
1121       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
1122       Frame frame = new Frame();\r
1123       frame.add(pcaPanel);\r
1124       jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",\r
1125                                        400, 400);\r
1126     }\r
1127     catch (java.lang.OutOfMemoryError ex)\r
1128     {\r
1129     }\r
1130 \r
1131   }\r
1132 \r
1133   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1134   {\r
1135     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1136   }\r
1137 \r
1138   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1139   {\r
1140     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1141   }\r
1142 \r
1143   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1144   {\r
1145     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1146   }\r
1147 \r
1148   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1149   {\r
1150     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1151   }\r
1152 \r
1153   void NewTreePanel(String type, String pwType, String title)\r
1154   {\r
1155     //are the sequences aligned?\r
1156     if (!viewport.alignment.isAligned())\r
1157     {\r
1158       SequenceI current;\r
1159       int Width = viewport.getAlignment().getWidth();\r
1160 \r
1161       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1162            i++)\r
1163       {\r
1164         current = viewport.getAlignment().getSequenceAt(i);\r
1165 \r
1166         if (current.getLength() < Width)\r
1167         {\r
1168           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1169         }\r
1170       }\r
1171       alignPanel.repaint();\r
1172 \r
1173     }\r
1174 \r
1175     final TreePanel tp;\r
1176     if (viewport.getSelectionGroup() != null &&\r
1177         viewport.getSelectionGroup().getSize() > 3)\r
1178     {\r
1179       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1180                          pwType,\r
1181                          0, viewport.alignment.getWidth());\r
1182     }\r
1183     else\r
1184     {\r
1185       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1186                          type, pwType, 0, viewport.alignment.getWidth());\r
1187     }\r
1188 \r
1189     addTreeMenuItem(tp, title);\r
1190 \r
1191     jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1192   }\r
1193 \r
1194   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1195   {\r
1196     final MenuItem item = new MenuItem(title);\r
1197     sortByTreeMenu.add(item);\r
1198     item.addActionListener(new java.awt.event.ActionListener()\r
1199     {\r
1200       public void actionPerformed(ActionEvent e)\r
1201       {\r
1202         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1203                                        HistoryItem.SORT));\r
1204         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1205         alignPanel.repaint();\r
1206       }\r
1207     });\r
1208 \r
1209     treePanel.addWindowListener(new WindowAdapter()\r
1210     {\r
1211       public void windowClosing(WindowEvent e)\r
1212       {\r
1213         sortByTreeMenu.remove(item);\r
1214       };\r
1215     });\r
1216   }\r
1217 \r
1218   protected void documentation_actionPerformed(ActionEvent e)\r
1219   {\r
1220     jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");\r
1221   }\r
1222 \r
1223   protected void about_actionPerformed(ActionEvent e)\r
1224   {\r
1225 \r
1226     class AboutPanel extends Canvas\r
1227     {\r
1228       String version;\r
1229       public AboutPanel(String version)\r
1230       { this.version = version; }\r
1231 \r
1232       public void paint(Graphics g)\r
1233       {\r
1234         g.setColor(Color.white);\r
1235         g.fillRect(0, 0, getSize().width, getSize().height);\r
1236         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1237         FontMetrics fm = g.getFontMetrics();\r
1238         int fh = fm.getHeight();\r
1239         int y = 5, x = 7;\r
1240         g.setColor(Color.black);\r
1241         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1242         g.drawString("Jalview - Release "+version, 200, y += fh);\r
1243         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1244         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1245                      x, y += fh * 2);\r
1246         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1247                      x, y += fh);\r
1248         g.drawString(\r
1249             "For any issues relating to Jalview, email help@jalview.org", x,\r
1250             y += fh);\r
1251         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1252         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1253                      x, y += fh);\r
1254         g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);\r
1255       }\r
1256     }\r
1257 \r
1258     String version = "test";\r
1259     java.net.URL url = getClass().getResource("/.build_properties");\r
1260     if (url != null)\r
1261     {\r
1262       try\r
1263       {\r
1264         BufferedReader reader = new BufferedReader(new InputStreamReader(\r
1265             url.openStream()));\r
1266         String line;\r
1267         while ( (line = reader.readLine()) != null)\r
1268         {\r
1269           if (line.indexOf("VERSION") > -1)\r
1270           {\r
1271             version = line.substring(line.indexOf("=") + 1);\r
1272           }\r
1273         }\r
1274       }\r
1275       catch (Exception ex)\r
1276       {\r
1277         ex.printStackTrace();\r
1278       }\r
1279     }\r
1280 \r
1281 \r
1282     Frame frame = new Frame();\r
1283     frame.add(new AboutPanel(version));\r
1284     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1285 \r
1286   }\r
1287 }\r