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 \r
  43   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)\r
  44   {\r
  45     this.applet = applet;\r
  46     viewport = new AlignViewport(al, applet);\r
  47     alignPanel = new AlignmentPanel(this, viewport);\r
  48     add(alignPanel);\r
  49     alignPanel.validate();\r
  50 \r
  51     String treeFile = applet.getParameter("treeFile");\r
  52     if (treeFile != null)\r
  53     {\r
  54       try\r
  55       {\r
  56         treeFile = treeFile;\r
  57         jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
  58             getCodeBase() + treeFile, "URL");\r
  59         fin.parse();\r
  60 \r
  61         if (fin.getTree() != null)\r
  62         {\r
  63           TreePanel tp = null;\r
  64           tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
  65                              fin, "FromFile", applet.getCodeBase() + treeFile);\r
  66           jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
  67           addTreeMenuItem(tp, treeFile);\r
  68         }\r
  69       }\r
  70       catch (Exception ex)\r
  71       {\r
  72         ex.printStackTrace();\r
  73       }\r
  74     }\r
  75 \r
  76     String param = applet.getParameter("sortBy");\r
  77     if(param!=null)\r
  78     {\r
  79       if (param.equalsIgnoreCase("Id"))\r
  80         sortIDMenuItem_actionPerformed(null);\r
  81       else if (param.equalsIgnoreCase("Pairwise Identity"))\r
  82         sortPairwiseMenuItem_actionPerformed(null);\r
  83     }\r
  84 \r
  85     this.addWindowListener(new WindowAdapter()\r
  86     {\r
  87       public void windowClosing(WindowEvent e)\r
  88           {\r
  89             closeMenuItem_actionPerformed(null);\r
  90           }\r
  91     });\r
  92 \r
  93     viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
  94     {\r
  95      public void propertyChange(java.beans.PropertyChangeEvent evt)\r
  96      {\r
  97        if (evt.getPropertyName().equals("alignment"))\r
  98        {\r
  99          alignmentChanged();\r
 100        }\r
 101      }\r
 102    });\r
 103   }\r
 104 \r
 105   public void inputText_actionPerformed(ActionEvent e)\r
 106   {\r
 107     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);\r
 108     Frame frame = new Frame();\r
 109     frame.add(cap);\r
 110     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
 111   }\r
 112 \r
 113   protected void outputText_actionPerformed(ActionEvent e)\r
 114   {\r
 115     CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);\r
 116     Frame frame = new Frame();\r
 117     frame.add(cap);\r
 118     jalview.bin.JalviewLite.addFrame(frame,\r
 119                                      "Alignment output - " + e.getActionCommand(),\r
 120                                      600, 500);\r
 121     cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),\r
 122                                               viewport.getAlignment().\r
 123                                               getSequences()));\r
 124   }\r
 125 \r
 126   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 127   {\r
 128     PaintRefresher.components.remove(viewport.alignment);\r
 129     dispose();\r
 130   }\r
 131 \r
 132   Stack historyList = new Stack();\r
 133   Stack redoList = new Stack();\r
 134 \r
 135   void updateEditMenuBar()\r
 136   {\r
 137     if (historyList.size() > 0)\r
 138     {\r
 139       undoMenuItem.setEnabled(true);\r
 140       HistoryItem hi = (HistoryItem) historyList.peek();\r
 141       undoMenuItem.setLabel("Undo " + hi.getDescription());\r
 142     }\r
 143     else\r
 144     {\r
 145       undoMenuItem.setEnabled(false);\r
 146       undoMenuItem.setLabel("Undo");\r
 147     }\r
 148 \r
 149     if (redoList.size() > 0)\r
 150     {\r
 151       redoMenuItem.setEnabled(true);\r
 152       HistoryItem hi = (HistoryItem) redoList.peek();\r
 153       redoMenuItem.setLabel("Redo " + hi.getDescription());\r
 154     }\r
 155     else\r
 156     {\r
 157       redoMenuItem.setEnabled(false);\r
 158       redoMenuItem.setLabel("Redo");\r
 159     }\r
 160   }\r
 161 \r
 162   public void addHistoryItem(HistoryItem hi)\r
 163   {\r
 164     historyList.push(hi);\r
 165     updateEditMenuBar();\r
 166   }\r
 167 \r
 168   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 169   {\r
 170     HistoryItem hi = (HistoryItem) historyList.pop();\r
 171     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
 172                                   HistoryItem.HIDE));\r
 173     restoreHistoryItem(hi);\r
 174     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 175   }\r
 176 \r
 177   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 178   {\r
 179     HistoryItem hi = (HistoryItem) redoList.pop();\r
 180     restoreHistoryItem(hi);\r
 181     updateEditMenuBar();\r
 182     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 183   }\r
 184 \r
 185   // used by undo and redo\r
 186   void restoreHistoryItem(HistoryItem hi)\r
 187   {\r
 188     if (hi.getType() == HistoryItem.SORT)\r
 189     {\r
 190       for (int i = 0; i < hi.getSequences().size(); i++)\r
 191       {\r
 192         viewport.alignment.getSequences().setElementAt(hi.getSequences().\r
 193             elementAt(i), i);\r
 194       }\r
 195     }\r
 196     else\r
 197     {\r
 198       for (int i = 0; i < hi.getSequences().size(); i++)\r
 199       {\r
 200         SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
 201         if (restore.getLength() == 0)\r
 202         {\r
 203           // log.System.out.println(hi.getHidden().elementAt(i));\r
 204           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 205           viewport.alignment.getSequences().insertElementAt(\r
 206               restore,\r
 207               hi.getAlignIndex(i));\r
 208         }\r
 209         else\r
 210         {\r
 211           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 212         }\r
 213       }\r
 214       if (hi.getType() == HistoryItem.PASTE)\r
 215       {\r
 216         for (int i = viewport.alignment.getHeight() - 1;\r
 217              i > hi.getSequences().size() - 1; i--)\r
 218         {\r
 219           viewport.alignment.deleteSequence(i);\r
 220         }\r
 221       }\r
 222     }\r
 223 \r
 224     updateEditMenuBar();\r
 225 \r
 226     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 227   }\r
 228 \r
 229   public void moveSelectedSequences(boolean up)\r
 230   {\r
 231     SequenceGroup sg = viewport.getSelectionGroup();\r
 232     if (sg == null)\r
 233     {\r
 234       return;\r
 235     }\r
 236 \r
 237     if (up)\r
 238     {\r
 239       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 240       {\r
 241         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 242         if (!sg.sequences.contains(seq))\r
 243         {\r
 244           continue;\r
 245         }\r
 246 \r
 247         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 248         if (sg.sequences.contains(temp))\r
 249         {\r
 250           continue;\r
 251         }\r
 252 \r
 253         viewport.alignment.getSequences().setElementAt(temp, i);\r
 254         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 255       }\r
 256     }\r
 257     else\r
 258     {\r
 259       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 260       {\r
 261         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 262         if (!sg.sequences.contains(seq))\r
 263         {\r
 264           continue;\r
 265         }\r
 266 \r
 267         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 268         if (sg.sequences.contains(temp))\r
 269         {\r
 270           continue;\r
 271         }\r
 272 \r
 273         viewport.alignment.getSequences().setElementAt(temp, i);\r
 274         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 275       }\r
 276     }\r
 277 \r
 278     alignPanel.repaint();\r
 279   }\r
 280 \r
 281   StringBuffer copiedSequences;\r
 282   protected void copy_actionPerformed(ActionEvent e)\r
 283   {\r
 284     if (viewport.getSelectionGroup() == null)\r
 285     {\r
 286       return;\r
 287     }\r
 288 \r
 289     SequenceGroup sg = viewport.getSelectionGroup();\r
 290     copiedSequences = new StringBuffer();\r
 291     Hashtable orderedSeqs = new Hashtable();\r
 292     for (int i = 0; i < sg.getSize(); i++)\r
 293     {\r
 294       SequenceI seq = sg.getSequenceAt(i);\r
 295       int index = viewport.alignment.findIndex(seq);\r
 296       orderedSeqs.put(index + "", seq);\r
 297     }\r
 298 \r
 299     int index = 0, startRes, endRes;\r
 300     char ch;\r
 301 \r
 302     for (int i = 0; i < sg.getSize(); i++)\r
 303     {\r
 304         SequenceI seq = null;\r
 305 \r
 306         while (seq == null)\r
 307         {\r
 308             if (orderedSeqs.containsKey(index + ""))\r
 309             {\r
 310                 seq = (SequenceI) orderedSeqs.get(index + "");\r
 311                 index++;\r
 312 \r
 313                 break;\r
 314             }\r
 315             else\r
 316             {\r
 317                 index++;\r
 318             }\r
 319         }\r
 320 \r
 321         //FIND START RES\r
 322         //Returns residue following index if gap\r
 323         startRes = seq.findPosition(sg.getStartRes());\r
 324 \r
 325         //FIND END RES\r
 326         //Need to find the residue preceeding index if gap\r
 327         endRes = 0;\r
 328 \r
 329         for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
 330         {\r
 331           ch = seq.getCharAt(j);\r
 332           if (!jalview.util.Comparison.isGap( (ch)))\r
 333           {\r
 334             endRes++;\r
 335           }\r
 336         }\r
 337 \r
 338         if(endRes>0)\r
 339         {\r
 340           endRes += seq.getStart() -1;\r
 341         }\r
 342 \r
 343         copiedSequences.append(seq.getName() + "\t" +\r
 344             startRes + "\t" +\r
 345             endRes + "\t" +\r
 346             seq.getSequence(sg.getStartRes(),\r
 347                 sg.getEndRes() + 1) + "\n");\r
 348     }\r
 349 \r
 350   }\r
 351 \r
 352   protected void pasteNew_actionPerformed(ActionEvent e)\r
 353   {\r
 354     paste(true);\r
 355   }\r
 356 \r
 357   protected void pasteThis_actionPerformed(ActionEvent e)\r
 358   {\r
 359     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
 360                                    HistoryItem.PASTE));\r
 361     paste(false);\r
 362   }\r
 363 \r
 364   void paste(boolean newAlignment)\r
 365   {\r
 366     try\r
 367     {\r
 368       if (copiedSequences == null)\r
 369       {\r
 370         return;\r
 371       }\r
 372 \r
 373       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 374       Vector seqs = new Vector();\r
 375       while (st.hasMoreElements())\r
 376       {\r
 377         String name = st.nextToken();\r
 378         int start = Integer.parseInt(st.nextToken());\r
 379         int end = Integer.parseInt(st.nextToken());\r
 380         Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
 381 \r
 382         if (!newAlignment)\r
 383         {\r
 384           viewport.alignment.addSequence(sequence);\r
 385         }\r
 386         else\r
 387         {\r
 388           seqs.addElement(sequence);\r
 389         }\r
 390       }\r
 391 \r
 392       if (newAlignment)\r
 393       {\r
 394         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 395         for (int i = 0; i < seqs.size(); i++)\r
 396         {\r
 397           newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
 398         }\r
 399 \r
 400         AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);\r
 401         String newtitle = new String("Copied sequences");\r
 402         if (getTitle().startsWith("Copied sequences"))\r
 403         {\r
 404           newtitle = getTitle();\r
 405         }\r
 406         else\r
 407         {\r
 408           newtitle = newtitle.concat("- from " + getTitle());\r
 409         }\r
 410         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
 411                                          NEW_WINDOW_HEIGHT);\r
 412       }\r
 413       else\r
 414       {\r
 415         viewport.setEndSeq(viewport.alignment.getHeight());\r
 416         viewport.alignment.getWidth();\r
 417         viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 418       }\r
 419 \r
 420     }\r
 421     catch (Exception ex)\r
 422     {} // could be anything being pasted in here\r
 423 \r
 424   }\r
 425 \r
 426   protected void cut_actionPerformed(ActionEvent e)\r
 427   {\r
 428     copy_actionPerformed(null);\r
 429     delete_actionPerformed(null);\r
 430   }\r
 431 \r
 432   protected void delete_actionPerformed(ActionEvent e)\r
 433   {\r
 434     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
 435                                    HistoryItem.HIDE));\r
 436     if (viewport.getSelectionGroup() == null)\r
 437     {\r
 438       return;\r
 439     }\r
 440 \r
 441 \r
 442     SequenceGroup sg = viewport.getSelectionGroup();\r
 443     boolean allSequences = false;\r
 444     if(sg.sequences.size()==viewport.alignment.getHeight())\r
 445           allSequences = true;\r
 446 \r
 447     for (int i = 0; i < sg.sequences.size(); i++)\r
 448     {\r
 449       SequenceI seq = sg.getSequenceAt(i);\r
 450       int index = viewport.getAlignment().findIndex(seq);\r
 451       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 452 \r
 453       // If the cut affects all sequences, remove highlighted columns\r
 454       if (allSequences)\r
 455       {\r
 456         viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
 457                                                      sg.getEndRes() + 1);\r
 458       }\r
 459 \r
 460 \r
 461       if (seq.getSequence().length() < 1)\r
 462       {\r
 463         viewport.getAlignment().deleteSequence(seq);\r
 464       }\r
 465       else\r
 466       {\r
 467         viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 468       }\r
 469     }\r
 470 \r
 471     viewport.setSelectionGroup(null);\r
 472     viewport.alignment.deleteGroup(sg);\r
 473     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
 474     if (viewport.getAlignment().getHeight() < 1)\r
 475     {\r
 476       try\r
 477       {\r
 478         this.setVisible(false);\r
 479       }\r
 480       catch (Exception ex)\r
 481       {}\r
 482     }\r
 483     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 484 \r
 485   }\r
 486 \r
 487   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 488   {\r
 489     viewport.alignment.deleteAllGroups();\r
 490     viewport.setSelectionGroup(null);\r
 491 \r
 492     alignPanel.repaint();\r
 493   }\r
 494 \r
 495   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 496   {\r
 497     SequenceGroup sg = new SequenceGroup();\r
 498     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 499     {\r
 500       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
 501     }\r
 502     sg.setEndRes(viewport.alignment.getWidth()-1);\r
 503     viewport.setSelectionGroup(sg);\r
 504     alignPanel.repaint();\r
 505     PaintRefresher.Refresh(null, viewport.alignment);\r
 506   }\r
 507 \r
 508   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 509   {\r
 510     viewport.setSelectionGroup(null);\r
 511     viewport.getColumnSelection().clear();\r
 512     viewport.setSelectionGroup(null);\r
 513     alignPanel.repaint();\r
 514     PaintRefresher.Refresh(null, viewport.alignment);\r
 515   }\r
 516 \r
 517   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 518   {\r
 519     SequenceGroup sg = viewport.getSelectionGroup();\r
 520     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 521     {\r
 522       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
 523     }\r
 524 \r
 525     PaintRefresher.Refresh(null, viewport.alignment);\r
 526   }\r
 527 \r
 528   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 529   {\r
 530     ColumnSelection colSel = viewport.getColumnSelection();\r
 531     if (colSel.size() > 0)\r
 532     {\r
 533       addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
 534                                      HistoryItem.HIDE));\r
 535       int min = colSel.getMin();\r
 536       viewport.getAlignment().trimLeft(min);\r
 537       colSel.compensateForEdit(0, min);\r
 538 \r
 539       if (viewport.getSelectionGroup() != null)\r
 540       {\r
 541         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 542       }\r
 543 \r
 544       Vector groups = viewport.alignment.getGroups();\r
 545       for (int i = 0; i < groups.size(); i++)\r
 546       {\r
 547         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 548         if (!sg.adjustForRemoveLeft(min))\r
 549         {\r
 550           viewport.alignment.deleteGroup(sg);\r
 551         }\r
 552       }\r
 553       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 554     }\r
 555   }\r
 556 \r
 557   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 558   {\r
 559     ColumnSelection colSel = viewport.getColumnSelection();\r
 560     if (colSel.size() > 0)\r
 561     {\r
 562       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
 563                                      HistoryItem.HIDE));\r
 564       int max = colSel.getMax();\r
 565       viewport.getAlignment().trimRight(max);\r
 566       if (viewport.getSelectionGroup() != null)\r
 567       {\r
 568         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 569       }\r
 570 \r
 571       Vector groups = viewport.alignment.getGroups();\r
 572       for (int i = 0; i < groups.size(); i++)\r
 573       {\r
 574         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 575         if (!sg.adjustForRemoveRight(max))\r
 576         {\r
 577           viewport.alignment.deleteGroup(sg);\r
 578         }\r
 579       }\r
 580       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 581     }\r
 582 \r
 583   }\r
 584 \r
 585   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 586   {\r
 587     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
 588                                    viewport.alignment,\r
 589                                    HistoryItem.HIDE));\r
 590 \r
 591     //This is to maintain viewport position on first residue\r
 592     //of first sequence\r
 593     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 594     int startRes = seq.findPosition(viewport.startRes);\r
 595 \r
 596     viewport.getAlignment().removeGaps();\r
 597 \r
 598     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 599 \r
 600     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 601   }\r
 602 \r
 603   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 604   {\r
 605     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
 606                                    HistoryItem.HIDE));\r
 607 \r
 608     //This is to maintain viewport position on first residue\r
 609     //of first sequence\r
 610     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 611     int startRes = seq.findPosition(viewport.startRes);\r
 612 \r
 613     SequenceI current;\r
 614     int jSize;\r
 615 \r
 616     Vector seqs=null;\r
 617 \r
 618     int start=0, end = viewport.alignment.getWidth();\r
 619 \r
 620     if (viewport.getSelectionGroup() != null\r
 621         && viewport.getSelectionGroup().sequences != null\r
 622         && viewport.getSelectionGroup().sequences.size()>0)\r
 623     {\r
 624       seqs = viewport.getSelectionGroup().sequences;\r
 625       start = viewport.getSelectionGroup().getStartRes();\r
 626       end = viewport.getSelectionGroup().getEndRes()+1;\r
 627     }\r
 628     else\r
 629       seqs = viewport.alignment.getSequences();\r
 630 \r
 631     for (int i = 0; i < seqs.size(); i++)\r
 632     {\r
 633       current = (SequenceI) seqs.elementAt(i);\r
 634       jSize = current.getLength();\r
 635 \r
 636       // Removing a range is much quicker than removing gaps\r
 637       // one by one for long sequences\r
 638       int j = start;\r
 639       int rangeStart=-1, rangeEnd=-1;\r
 640 \r
 641       do\r
 642       {\r
 643         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 644         {\r
 645           if(rangeStart==-1)\r
 646            {\r
 647              rangeStart = j;\r
 648              rangeEnd = j+1;\r
 649            }\r
 650            else\r
 651            {\r
 652              rangeEnd++;\r
 653            }\r
 654            j++;\r
 655         }\r
 656         else\r
 657         {\r
 658           if(rangeStart>-1)\r
 659           {\r
 660             current.deleteChars(rangeStart, rangeEnd);\r
 661             j-=rangeEnd-rangeStart;\r
 662             jSize-=rangeEnd-rangeStart;\r
 663             rangeStart = -1;\r
 664             rangeEnd = -1;\r
 665           }\r
 666           else\r
 667             j++;\r
 668         }\r
 669       }\r
 670       while (j < end && j < jSize);\r
 671       if(rangeStart>-1)\r
 672       {\r
 673        current.deleteChars(rangeStart, rangeEnd);\r
 674       }\r
 675     }\r
 676     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 677     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 678   }\r
 679 \r
 680   public void alignmentChanged()\r
 681   {\r
 682     viewport.updateConsensus();\r
 683     viewport.updateConservation ();\r
 684     resetAllColourSchemes();\r
 685     if(alignPanel.overviewPanel!=null)\r
 686       alignPanel.overviewPanel.updateOverviewImage();\r
 687     alignPanel.repaint();\r
 688   }\r
 689 \r
 690   void resetAllColourSchemes()\r
 691   {\r
 692     ColourSchemeI cs = viewport.globalColourScheme;\r
 693     if(cs!=null)\r
 694     {\r
 695       if (cs 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       cs.setConsensus(viewport.vconsensus);\r
 703       if (cs.conservationApplied())\r
 704       {\r
 705         Alignment al = (Alignment) viewport.alignment;\r
 706         Conservation c = new Conservation("All",\r
 707                                           ResidueProperties.propHash, 3,\r
 708                                           al.getSequences(), 0,\r
 709                                           al.getWidth() - 1);\r
 710         c.calculate();\r
 711         c.verdict(false, viewport.ConsPercGaps);\r
 712 \r
 713         cs.setConservation(c);\r
 714       }\r
 715     }\r
 716 \r
 717     int s, sSize = viewport.alignment.getGroups().size();\r
 718     for(s=0; s<sSize; s++)\r
 719     {\r
 720       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
 721       if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
 722       {\r
 723         ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
 724       }\r
 725       sg.recalcConservation();\r
 726     }\r
 727   }\r
 728 \r
 729 \r
 730 \r
 731   public void findMenuItem_actionPerformed(ActionEvent e)\r
 732   {\r
 733     Finder finder = new Finder(alignPanel);\r
 734   }\r
 735 \r
 736   public void font_actionPerformed(ActionEvent e)\r
 737   {\r
 738     Frame frame = new Frame();\r
 739     FontChooser fc = new FontChooser(alignPanel, frame);\r
 740     frame.add(fc);\r
 741     jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);\r
 742 \r
 743   }\r
 744 \r
 745   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 746   {\r
 747     viewport.setShowFullId(fullSeqId.getState());\r
 748     alignPanel.fontChanged();\r
 749     alignPanel.repaint();\r
 750   }\r
 751 \r
 752   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 753   {\r
 754     viewport.setColourText(colourTextMenuItem.getState());\r
 755     alignPanel.repaint();\r
 756   }\r
 757 \r
 758   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 759   {\r
 760     viewport.setWrapAlignment(wrapMenuItem.getState());\r
 761     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
 762     scaleAbove.setEnabled(wrapMenuItem.getState());\r
 763     scaleLeft.setEnabled(wrapMenuItem.getState());\r
 764     scaleRight.setEnabled(wrapMenuItem.getState());\r
 765     alignPanel.repaint();\r
 766   }\r
 767 \r
 768   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 769   {\r
 770     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 771     alignPanel.repaint();\r
 772   }\r
 773 \r
 774   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 775   {\r
 776     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 777     alignPanel.repaint();\r
 778   }\r
 779 \r
 780   protected void scaleRight_actionPerformed(ActionEvent e)\r
 781   {\r
 782     viewport.setScaleRightWrapped(scaleRight.getState());\r
 783     alignPanel.repaint();\r
 784   }\r
 785 \r
 786   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 787   {\r
 788     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
 789     alignPanel.repaint();\r
 790   }\r
 791 \r
 792   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 793   {\r
 794     viewport.setShowText(viewTextMenuItem.getState());\r
 795     alignPanel.repaint();\r
 796   }\r
 797 \r
 798   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 799   {\r
 800     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 801     alignPanel.repaint();\r
 802   }\r
 803 \r
 804   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 805   {\r
 806     if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
 807     {\r
 808       annotationPanelMenuItem.setState(false);\r
 809       return;\r
 810     }\r
 811     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
 812     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
 813   }\r
 814 \r
 815   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 816   {\r
 817     if (alignPanel.overviewPanel != null)\r
 818     {\r
 819       return;\r
 820     }\r
 821 \r
 822     Frame frame = new Frame();\r
 823     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 824     frame.add(overview);\r
 825     // +50 must allow for applet frame window\r
 826     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
 827                                      overview.preferredSize().width,\r
 828                                      overview.preferredSize().height + 50);\r
 829 \r
 830     frame.pack();\r
 831     frame.addWindowListener(new WindowAdapter()\r
 832     {\r
 833       public void windowClosing(WindowEvent e)\r
 834       {\r
 835         alignPanel.setOverviewPanel(null);\r
 836       };\r
 837     });\r
 838 \r
 839     alignPanel.setOverviewPanel(overview);\r
 840 \r
 841   }\r
 842 \r
 843   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 844   {\r
 845     changeColour(null);\r
 846   }\r
 847 \r
 848   public void clustalColour_actionPerformed(ActionEvent e)\r
 849   {\r
 850     abovePIDThreshold.setState(false);\r
 851     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
 852                                           viewport.alignment.getWidth()));\r
 853   }\r
 854 \r
 855   public void zappoColour_actionPerformed(ActionEvent e)\r
 856   {\r
 857     changeColour(new ZappoColourScheme());\r
 858   }\r
 859 \r
 860   public void taylorColour_actionPerformed(ActionEvent e)\r
 861   {\r
 862     changeColour(new TaylorColourScheme());\r
 863   }\r
 864 \r
 865   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 866   {\r
 867     changeColour(new HydrophobicColourScheme());\r
 868   }\r
 869 \r
 870   public void helixColour_actionPerformed(ActionEvent e)\r
 871   {\r
 872     changeColour(new HelixColourScheme());\r
 873   }\r
 874 \r
 875   public void strandColour_actionPerformed(ActionEvent e)\r
 876   {\r
 877     changeColour(new StrandColourScheme());\r
 878   }\r
 879 \r
 880   public void turnColour_actionPerformed(ActionEvent e)\r
 881   {\r
 882     changeColour(new TurnColourScheme());\r
 883   }\r
 884 \r
 885   public void buriedColour_actionPerformed(ActionEvent e)\r
 886   {\r
 887     changeColour(new BuriedColourScheme());\r
 888   }\r
 889 \r
 890   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 891   {\r
 892     changeColour(new NucleotideColourScheme());\r
 893   }\r
 894 \r
 895   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 896   {\r
 897     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
 898   }\r
 899 \r
 900   void changeColour(ColourSchemeI cs)\r
 901   {\r
 902     int threshold = 0;\r
 903 \r
 904     if(cs!=null)\r
 905     {\r
 906       if (viewport.getAbovePIDThreshold())\r
 907       {\r
 908         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 909 \r
 910         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
 911 \r
 912         viewport.setGlobalColourScheme(cs);\r
 913       }\r
 914       else\r
 915       {\r
 916         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
 917       }\r
 918 \r
 919       if (viewport.getConservationSelected())\r
 920       {\r
 921 \r
 922         Alignment al = (Alignment) viewport.alignment;\r
 923         Conservation c = new Conservation("All",\r
 924                                           ResidueProperties.propHash, 3,\r
 925                                           al.getSequences(), 0,\r
 926                                           al.getWidth() - 1);\r
 927 \r
 928         c.calculate();\r
 929         c.verdict(false, viewport.ConsPercGaps);\r
 930 \r
 931         cs.setConservation(c);\r
 932 \r
 933         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
 934             "Background"));\r
 935 \r
 936       }\r
 937       else\r
 938       {\r
 939         cs.setConservation(null);\r
 940       }\r
 941 \r
 942       cs.setConsensus(viewport.vconsensus);\r
 943 \r
 944     }\r
 945     viewport.setGlobalColourScheme(cs);\r
 946 \r
 947     if (viewport.getColourAppliesToAllGroups())\r
 948     {\r
 949       Vector groups = viewport.alignment.getGroups();\r
 950       for (int i = 0; i < groups.size(); i++)\r
 951       {\r
 952         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 953 \r
 954         if(cs==null)\r
 955         {\r
 956           sg.cs = null;\r
 957           continue;\r
 958         }\r
 959         if (cs instanceof ClustalxColourScheme)\r
 960         {\r
 961           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
 962         }\r
 963         else\r
 964         {\r
 965           try\r
 966           {\r
 967             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
 968           }\r
 969           catch (Exception ex)\r
 970           {\r
 971             ex.printStackTrace();\r
 972             sg.cs = cs;\r
 973           }\r
 974         }\r
 975 \r
 976         if (viewport.getAbovePIDThreshold()\r
 977             || cs instanceof PIDColourScheme\r
 978             || cs instanceof Blosum62ColourScheme)\r
 979         {\r
 980           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
 981           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 982         }\r
 983         else\r
 984           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
 985 \r
 986         if (viewport.getConservationSelected())\r
 987         {\r
 988           Conservation c = new Conservation("Group",\r
 989                                             ResidueProperties.propHash, 3,\r
 990                                             sg.sequences, 0,\r
 991                                             viewport.alignment.getWidth() - 1);\r
 992           c.calculate();\r
 993           c.verdict(false, viewport.ConsPercGaps);\r
 994           sg.cs.setConservation(c);\r
 995         }\r
 996         else\r
 997         {\r
 998           sg.cs.setConservation(null);\r
 999           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1000         }\r
1001 \r
1002       }\r
1003     }\r
1004 \r
1005 \r
1006     if (alignPanel.getOverviewPanel() != null)\r
1007     {\r
1008       alignPanel.getOverviewPanel().updateOverviewImage();\r
1009     }\r
1010 \r
1011     alignPanel.repaint();\r
1012   }\r
1013 \r
1014 \r
1015 \r
1016   protected void modifyPID_actionPerformed(ActionEvent e)\r
1017   {\r
1018     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
1019     {\r
1020       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
1021                                      "Background");\r
1022       SliderPanel.showPIDSlider();\r
1023     }\r
1024   }\r
1025 \r
1026   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1027   {\r
1028     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
1029     {\r
1030       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
1031                                         "Background");\r
1032       SliderPanel.showConservationSlider();\r
1033     }\r
1034   }\r
1035 \r
1036   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1037   {\r
1038     viewport.setConservationSelected(conservationMenuItem.getState());\r
1039 \r
1040     viewport.setAbovePIDThreshold(false);\r
1041     abovePIDThreshold.setState(false);\r
1042 \r
1043     changeColour(viewport.getGlobalColourScheme());\r
1044 \r
1045     modifyConservation_actionPerformed(null);\r
1046   }\r
1047 \r
1048   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1049   {\r
1050     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
1051 \r
1052     conservationMenuItem.setState(false);\r
1053     viewport.setConservationSelected(false);\r
1054 \r
1055     changeColour(viewport.getGlobalColourScheme());\r
1056 \r
1057     modifyPID_actionPerformed(null);\r
1058   }\r
1059 \r
1060   public void userDefinedColour_actionPerformed(ActionEvent e)\r
1061   {\r
1062     UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);\r
1063   }\r
1064 \r
1065   public void PIDColour_actionPerformed(ActionEvent e)\r
1066   {\r
1067     changeColour(new PIDColourScheme());\r
1068   }\r
1069 \r
1070   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1071   {\r
1072     changeColour(new Blosum62ColourScheme());\r
1073   }\r
1074 \r
1075   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1076   {\r
1077     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1078                                    HistoryItem.SORT));\r
1079     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1080                               viewport.getAlignment().getSequenceAt(0));\r
1081     alignPanel.repaint();\r
1082   }\r
1083 \r
1084   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1085   {\r
1086     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1087                                    HistoryItem.SORT));\r
1088     AlignmentSorter.sortByID(viewport.getAlignment());\r
1089     alignPanel.repaint();\r
1090   }\r
1091 \r
1092   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1093   {\r
1094     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1095                                    HistoryItem.SORT));\r
1096     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1097     alignPanel.repaint();\r
1098 \r
1099   }\r
1100 \r
1101   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1102   {\r
1103     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
1104     Frame frame = new Frame();\r
1105     frame.add(sp);\r
1106     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
1107                                      400, 120);\r
1108 \r
1109   }\r
1110 \r
1111   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1112   {\r
1113     if (viewport.getSelectionGroup().getSize() > 1)\r
1114     {\r
1115       Frame frame = new Frame();\r
1116       frame.add(new PairwiseAlignPanel(alignPanel));\r
1117       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1118     }\r
1119   }\r
1120 \r
1121   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
1122   {\r
1123 \r
1124     if ( (viewport.getSelectionGroup() != null &&\r
1125           viewport.getSelectionGroup().getSize() < 4 &&\r
1126           viewport.getSelectionGroup().getSize() > 0)\r
1127         || viewport.getAlignment().getHeight() < 4)\r
1128     {\r
1129       return;\r
1130     }\r
1131 \r
1132     try\r
1133     {\r
1134       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
1135       Frame frame = new Frame();\r
1136       frame.add(pcaPanel);\r
1137       jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",\r
1138                                        400, 400);\r
1139     }\r
1140     catch (java.lang.OutOfMemoryError ex)\r
1141     {\r
1142     }\r
1143 \r
1144   }\r
1145 \r
1146   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1147   {\r
1148     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1149   }\r
1150 \r
1151   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1152   {\r
1153     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1154   }\r
1155 \r
1156   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1157   {\r
1158     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1159   }\r
1160 \r
1161   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1162   {\r
1163     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1164   }\r
1165 \r
1166   void NewTreePanel(String type, String pwType, String title)\r
1167   {\r
1168     //are the sequences aligned?\r
1169     if (!viewport.alignment.isAligned())\r
1170     {\r
1171       SequenceI current;\r
1172       int Width = viewport.getAlignment().getWidth();\r
1173 \r
1174       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1175            i++)\r
1176       {\r
1177         current = viewport.getAlignment().getSequenceAt(i);\r
1178 \r
1179         if (current.getLength() < Width)\r
1180         {\r
1181           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1182         }\r
1183       }\r
1184       alignPanel.repaint();\r
1185 \r
1186     }\r
1187 \r
1188     final TreePanel tp;\r
1189     if (viewport.getSelectionGroup() != null &&\r
1190         viewport.getSelectionGroup().getSize() > 3)\r
1191     {\r
1192       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1193                          pwType,\r
1194                          0, viewport.alignment.getWidth());\r
1195     }\r
1196     else\r
1197     {\r
1198       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1199                          type, pwType, 0, viewport.alignment.getWidth());\r
1200     }\r
1201 \r
1202     addTreeMenuItem(tp, title);\r
1203 \r
1204     jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1205   }\r
1206 \r
1207   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1208   {\r
1209     final MenuItem item = new MenuItem(title);\r
1210     sortByTreeMenu.add(item);\r
1211     item.addActionListener(new java.awt.event.ActionListener()\r
1212     {\r
1213       public void actionPerformed(ActionEvent e)\r
1214       {\r
1215         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1216                                        HistoryItem.SORT));\r
1217         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1218         alignPanel.repaint();\r
1219       }\r
1220     });\r
1221 \r
1222     treePanel.addWindowListener(new WindowAdapter()\r
1223     {\r
1224       public void windowClosing(WindowEvent e)\r
1225       {\r
1226         sortByTreeMenu.remove(item);\r
1227       };\r
1228     });\r
1229   }\r
1230 \r
1231   protected void documentation_actionPerformed(ActionEvent e)\r
1232   {\r
1233     jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");\r
1234   }\r
1235 \r
1236   protected void about_actionPerformed(ActionEvent e)\r
1237   {\r
1238 \r
1239     class AboutPanel extends Canvas\r
1240     {\r
1241       String version;\r
1242       public AboutPanel(String version)\r
1243       { this.version = version; }\r
1244 \r
1245       public void paint(Graphics g)\r
1246       {\r
1247         g.setColor(Color.white);\r
1248         g.fillRect(0, 0, getSize().width, getSize().height);\r
1249         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1250         FontMetrics fm = g.getFontMetrics();\r
1251         int fh = fm.getHeight();\r
1252         int y = 5, x = 7;\r
1253         g.setColor(Color.black);\r
1254         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1255         g.drawString("Jalview - Release "+version, 200, y += fh);\r
1256         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1257         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1258                      x, y += fh * 2);\r
1259         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1260                      x, y += fh);\r
1261         g.drawString(\r
1262             "For any issues relating to Jalview, email help@jalview.org", x,\r
1263             y += fh);\r
1264         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1265         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1266                      x, y += fh);\r
1267         g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);\r
1268       }\r
1269     }\r
1270 \r
1271     String version = "test";\r
1272     java.net.URL url = getClass().getResource("/.build_properties");\r
1273     if (url != null)\r
1274     {\r
1275       try\r
1276       {\r
1277         BufferedReader reader = new BufferedReader(new InputStreamReader(\r
1278             url.openStream()));\r
1279         String line;\r
1280         while ( (line = reader.readLine()) != null)\r
1281         {\r
1282           if (line.indexOf("VERSION") > -1)\r
1283           {\r
1284             version = line.substring(line.indexOf("=") + 1);\r
1285           }\r
1286         }\r
1287       }\r
1288       catch (Exception ex)\r
1289       {\r
1290         ex.printStackTrace();\r
1291       }\r
1292     }\r
1293 \r
1294 \r
1295     Frame frame = new Frame();\r
1296     frame.add(new AboutPanel(version));\r
1297     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1298 \r
1299   }\r
1300 }\r