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     if(applet!=null)\r
  52     {\r
  53       String treeFile = applet.getParameter("treeFile");\r
  54       if (treeFile != null)\r
  55       {\r
  56         try\r
  57         {\r
  58           treeFile = treeFile;\r
  59           jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
  60               getCodeBase() + treeFile, "URL");\r
  61           fin.parse();\r
  62 \r
  63           if (fin.getTree() != null)\r
  64           {\r
  65             TreePanel tp = null;\r
  66             tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
  67                                fin, "FromFile", applet.getCodeBase() + treeFile);\r
  68             jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
  69             addTreeMenuItem(tp, treeFile);\r
  70           }\r
  71         }\r
  72         catch (Exception ex)\r
  73         {\r
  74           ex.printStackTrace();\r
  75         }\r
  76       }\r
  77 \r
  78       String param = applet.getParameter("sortBy");\r
  79       if (param != null)\r
  80       {\r
  81         if (param.equalsIgnoreCase("Id"))\r
  82           sortIDMenuItem_actionPerformed(null);\r
  83         else if (param.equalsIgnoreCase("Pairwise Identity"))\r
  84           sortPairwiseMenuItem_actionPerformed(null);\r
  85       }\r
  86     }\r
  87 \r
  88     this.addWindowListener(new WindowAdapter()\r
  89     {\r
  90       public void windowClosing(WindowEvent e)\r
  91           {\r
  92             closeMenuItem_actionPerformed(null);\r
  93           }\r
  94     });\r
  95 \r
  96     viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
  97     {\r
  98      public void propertyChange(java.beans.PropertyChangeEvent evt)\r
  99      {\r
 100        if (evt.getPropertyName().equals("alignment"))\r
 101        {\r
 102          alignmentChanged();\r
 103        }\r
 104      }\r
 105    });\r
 106   }\r
 107 \r
 108   public void inputText_actionPerformed(ActionEvent e)\r
 109   {\r
 110     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);\r
 111     Frame frame = new Frame();\r
 112     frame.add(cap);\r
 113     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
 114   }\r
 115 \r
 116   protected void outputText_actionPerformed(ActionEvent e)\r
 117   {\r
 118     CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);\r
 119     Frame frame = new Frame();\r
 120     frame.add(cap);\r
 121     jalview.bin.JalviewLite.addFrame(frame,\r
 122                                      "Alignment output - " + e.getActionCommand(),\r
 123                                      600, 500);\r
 124     cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),\r
 125                                               viewport.getAlignment().\r
 126                                               getSequences()));\r
 127   }\r
 128 \r
 129   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 130   {\r
 131     PaintRefresher.components.remove(viewport.alignment);\r
 132     dispose();\r
 133     if(PaintRefresher.components.size()==0 && applet==null)\r
 134       System.exit(0);\r
 135   }\r
 136 \r
 137   Stack historyList = new Stack();\r
 138   Stack redoList = new Stack();\r
 139 \r
 140   void updateEditMenuBar()\r
 141   {\r
 142     if (historyList.size() > 0)\r
 143     {\r
 144       undoMenuItem.setEnabled(true);\r
 145       HistoryItem hi = (HistoryItem) historyList.peek();\r
 146       undoMenuItem.setLabel("Undo " + hi.getDescription());\r
 147     }\r
 148     else\r
 149     {\r
 150       undoMenuItem.setEnabled(false);\r
 151       undoMenuItem.setLabel("Undo");\r
 152     }\r
 153 \r
 154     if (redoList.size() > 0)\r
 155     {\r
 156       redoMenuItem.setEnabled(true);\r
 157       HistoryItem hi = (HistoryItem) redoList.peek();\r
 158       redoMenuItem.setLabel("Redo " + hi.getDescription());\r
 159     }\r
 160     else\r
 161     {\r
 162       redoMenuItem.setEnabled(false);\r
 163       redoMenuItem.setLabel("Redo");\r
 164     }\r
 165   }\r
 166 \r
 167   public void addHistoryItem(HistoryItem hi)\r
 168   {\r
 169     historyList.push(hi);\r
 170     updateEditMenuBar();\r
 171   }\r
 172 \r
 173   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 174   {\r
 175     HistoryItem hi = (HistoryItem) historyList.pop();\r
 176     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
 177                                   HistoryItem.HIDE));\r
 178     restoreHistoryItem(hi);\r
 179     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 180   }\r
 181 \r
 182   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 183   {\r
 184     HistoryItem hi = (HistoryItem) redoList.pop();\r
 185     restoreHistoryItem(hi);\r
 186     updateEditMenuBar();\r
 187     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 188   }\r
 189 \r
 190   // used by undo and redo\r
 191   void restoreHistoryItem(HistoryItem hi)\r
 192   {\r
 193     if (hi.getType() == HistoryItem.SORT)\r
 194     {\r
 195       for (int i = 0; i < hi.getSequences().size(); i++)\r
 196       {\r
 197         viewport.alignment.getSequences().setElementAt(hi.getSequences().\r
 198             elementAt(i), i);\r
 199       }\r
 200     }\r
 201     else\r
 202     {\r
 203       for (int i = 0; i < hi.getSequences().size(); i++)\r
 204       {\r
 205         SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
 206         if (restore.getLength() == 0)\r
 207         {\r
 208           // log.System.out.println(hi.getHidden().elementAt(i));\r
 209           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 210           viewport.alignment.getSequences().insertElementAt(\r
 211               restore,\r
 212               hi.getAlignIndex(i));\r
 213         }\r
 214         else\r
 215         {\r
 216           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 217         }\r
 218       }\r
 219       if (hi.getType() == HistoryItem.PASTE)\r
 220       {\r
 221         for (int i = viewport.alignment.getHeight() - 1;\r
 222              i > hi.getSequences().size() - 1; i--)\r
 223         {\r
 224           viewport.alignment.deleteSequence(i);\r
 225         }\r
 226       }\r
 227     }\r
 228 \r
 229     updateEditMenuBar();\r
 230 \r
 231     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 232   }\r
 233 \r
 234   public void moveSelectedSequences(boolean up)\r
 235   {\r
 236     SequenceGroup sg = viewport.getSelectionGroup();\r
 237     if (sg == null)\r
 238     {\r
 239       return;\r
 240     }\r
 241 \r
 242     if (up)\r
 243     {\r
 244       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 245       {\r
 246         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 247         if (!sg.sequences.contains(seq))\r
 248         {\r
 249           continue;\r
 250         }\r
 251 \r
 252         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 253         if (sg.sequences.contains(temp))\r
 254         {\r
 255           continue;\r
 256         }\r
 257 \r
 258         viewport.alignment.getSequences().setElementAt(temp, i);\r
 259         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 260       }\r
 261     }\r
 262     else\r
 263     {\r
 264       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 265       {\r
 266         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 267         if (!sg.sequences.contains(seq))\r
 268         {\r
 269           continue;\r
 270         }\r
 271 \r
 272         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 273         if (sg.sequences.contains(temp))\r
 274         {\r
 275           continue;\r
 276         }\r
 277 \r
 278         viewport.alignment.getSequences().setElementAt(temp, i);\r
 279         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 280       }\r
 281     }\r
 282 \r
 283     alignPanel.repaint();\r
 284   }\r
 285 \r
 286   StringBuffer copiedSequences;\r
 287   protected void copy_actionPerformed(ActionEvent e)\r
 288   {\r
 289     if (viewport.getSelectionGroup() == null)\r
 290     {\r
 291       return;\r
 292     }\r
 293 \r
 294     SequenceGroup sg = viewport.getSelectionGroup();\r
 295     copiedSequences = new StringBuffer();\r
 296     Hashtable orderedSeqs = new Hashtable();\r
 297     for (int i = 0; i < sg.getSize(); i++)\r
 298     {\r
 299       SequenceI seq = sg.getSequenceAt(i);\r
 300       int index = viewport.alignment.findIndex(seq);\r
 301       orderedSeqs.put(index + "", seq);\r
 302     }\r
 303 \r
 304     int index = 0, startRes, endRes;\r
 305     char ch;\r
 306 \r
 307     for (int i = 0; i < sg.getSize(); i++)\r
 308     {\r
 309         SequenceI seq = null;\r
 310 \r
 311         while (seq == null)\r
 312         {\r
 313             if (orderedSeqs.containsKey(index + ""))\r
 314             {\r
 315                 seq = (SequenceI) orderedSeqs.get(index + "");\r
 316                 index++;\r
 317 \r
 318                 break;\r
 319             }\r
 320             else\r
 321             {\r
 322                 index++;\r
 323             }\r
 324         }\r
 325 \r
 326         //FIND START RES\r
 327         //Returns residue following index if gap\r
 328         startRes = seq.findPosition(sg.getStartRes());\r
 329 \r
 330         //FIND END RES\r
 331         //Need to find the residue preceeding index if gap\r
 332         endRes = 0;\r
 333 \r
 334         for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
 335         {\r
 336           ch = seq.getCharAt(j);\r
 337           if (!jalview.util.Comparison.isGap( (ch)))\r
 338           {\r
 339             endRes++;\r
 340           }\r
 341         }\r
 342 \r
 343         if(endRes>0)\r
 344         {\r
 345           endRes += seq.getStart() -1;\r
 346         }\r
 347 \r
 348         copiedSequences.append(seq.getName() + "\t" +\r
 349             startRes + "\t" +\r
 350             endRes + "\t" +\r
 351             seq.getSequence(sg.getStartRes(),\r
 352                 sg.getEndRes() + 1) + "\n");\r
 353     }\r
 354 \r
 355   }\r
 356 \r
 357   protected void pasteNew_actionPerformed(ActionEvent e)\r
 358   {\r
 359     paste(true);\r
 360   }\r
 361 \r
 362   protected void pasteThis_actionPerformed(ActionEvent e)\r
 363   {\r
 364     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
 365                                    HistoryItem.PASTE));\r
 366     paste(false);\r
 367   }\r
 368 \r
 369   void paste(boolean newAlignment)\r
 370   {\r
 371     try\r
 372     {\r
 373       if (copiedSequences == null)\r
 374       {\r
 375         return;\r
 376       }\r
 377 \r
 378       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 379       Vector seqs = new Vector();\r
 380       while (st.hasMoreElements())\r
 381       {\r
 382         String name = st.nextToken();\r
 383         int start = Integer.parseInt(st.nextToken());\r
 384         int end = Integer.parseInt(st.nextToken());\r
 385         Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
 386 \r
 387         if (!newAlignment)\r
 388         {\r
 389           viewport.alignment.addSequence(sequence);\r
 390         }\r
 391         else\r
 392         {\r
 393           seqs.addElement(sequence);\r
 394         }\r
 395       }\r
 396 \r
 397       if (newAlignment)\r
 398       {\r
 399         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 400         for (int i = 0; i < seqs.size(); i++)\r
 401         {\r
 402           newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
 403         }\r
 404 \r
 405         AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);\r
 406         String newtitle = new String("Copied sequences");\r
 407         if (getTitle().startsWith("Copied sequences"))\r
 408         {\r
 409           newtitle = getTitle();\r
 410         }\r
 411         else\r
 412         {\r
 413           newtitle = newtitle.concat("- from " + getTitle());\r
 414         }\r
 415         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
 416                                          NEW_WINDOW_HEIGHT);\r
 417       }\r
 418       else\r
 419       {\r
 420         viewport.setEndSeq(viewport.alignment.getHeight());\r
 421         viewport.alignment.getWidth();\r
 422         viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 423       }\r
 424 \r
 425     }\r
 426     catch (Exception ex)\r
 427     {} // could be anything being pasted in here\r
 428 \r
 429   }\r
 430 \r
 431   protected void cut_actionPerformed(ActionEvent e)\r
 432   {\r
 433     copy_actionPerformed(null);\r
 434     delete_actionPerformed(null);\r
 435   }\r
 436 \r
 437   protected void delete_actionPerformed(ActionEvent e)\r
 438   {\r
 439     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
 440                                    HistoryItem.HIDE));\r
 441     if (viewport.getSelectionGroup() == null)\r
 442     {\r
 443       return;\r
 444     }\r
 445 \r
 446 \r
 447     SequenceGroup sg = viewport.getSelectionGroup();\r
 448     boolean allSequences = false;\r
 449     if(sg.sequences.size()==viewport.alignment.getHeight())\r
 450           allSequences = true;\r
 451 \r
 452     for (int i = 0; i < sg.sequences.size(); i++)\r
 453     {\r
 454       SequenceI seq = sg.getSequenceAt(i);\r
 455       int index = viewport.getAlignment().findIndex(seq);\r
 456       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 457 \r
 458       // If the cut affects all sequences, remove highlighted columns\r
 459       if (allSequences)\r
 460       {\r
 461         viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
 462                                                      sg.getEndRes() + 1);\r
 463       }\r
 464 \r
 465 \r
 466       if (seq.getSequence().length() < 1)\r
 467       {\r
 468         viewport.getAlignment().deleteSequence(seq);\r
 469       }\r
 470       else\r
 471       {\r
 472         viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 473       }\r
 474     }\r
 475 \r
 476     viewport.setSelectionGroup(null);\r
 477     viewport.alignment.deleteGroup(sg);\r
 478     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
 479     if (viewport.getAlignment().getHeight() < 1)\r
 480     {\r
 481       try\r
 482       {\r
 483         this.setVisible(false);\r
 484       }\r
 485       catch (Exception ex)\r
 486       {}\r
 487     }\r
 488     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 489 \r
 490   }\r
 491 \r
 492   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 493   {\r
 494     viewport.alignment.deleteAllGroups();\r
 495     viewport.setSelectionGroup(null);\r
 496 \r
 497     alignPanel.repaint();\r
 498   }\r
 499 \r
 500   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 501   {\r
 502     SequenceGroup sg = new SequenceGroup();\r
 503     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 504     {\r
 505       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
 506     }\r
 507     sg.setEndRes(viewport.alignment.getWidth()-1);\r
 508     viewport.setSelectionGroup(sg);\r
 509     alignPanel.repaint();\r
 510     PaintRefresher.Refresh(null, viewport.alignment);\r
 511   }\r
 512 \r
 513   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 514   {\r
 515     viewport.setSelectionGroup(null);\r
 516     viewport.getColumnSelection().clear();\r
 517     viewport.setSelectionGroup(null);\r
 518     alignPanel.repaint();\r
 519     PaintRefresher.Refresh(null, viewport.alignment);\r
 520   }\r
 521 \r
 522   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 523   {\r
 524     SequenceGroup sg = viewport.getSelectionGroup();\r
 525     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 526     {\r
 527       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
 528     }\r
 529 \r
 530     PaintRefresher.Refresh(null, viewport.alignment);\r
 531   }\r
 532 \r
 533   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 534   {\r
 535     ColumnSelection colSel = viewport.getColumnSelection();\r
 536     if (colSel.size() > 0)\r
 537     {\r
 538       addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
 539                                      HistoryItem.HIDE));\r
 540       int min = colSel.getMin();\r
 541       viewport.getAlignment().trimLeft(min);\r
 542       colSel.compensateForEdit(0, min);\r
 543 \r
 544       if (viewport.getSelectionGroup() != null)\r
 545       {\r
 546         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 547       }\r
 548 \r
 549       Vector groups = viewport.alignment.getGroups();\r
 550       for (int i = 0; i < groups.size(); i++)\r
 551       {\r
 552         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 553         if (!sg.adjustForRemoveLeft(min))\r
 554         {\r
 555           viewport.alignment.deleteGroup(sg);\r
 556         }\r
 557       }\r
 558       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 559     }\r
 560   }\r
 561 \r
 562   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 563   {\r
 564     ColumnSelection colSel = viewport.getColumnSelection();\r
 565     if (colSel.size() > 0)\r
 566     {\r
 567       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
 568                                      HistoryItem.HIDE));\r
 569       int max = colSel.getMax();\r
 570       viewport.getAlignment().trimRight(max);\r
 571       if (viewport.getSelectionGroup() != null)\r
 572       {\r
 573         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 574       }\r
 575 \r
 576       Vector groups = viewport.alignment.getGroups();\r
 577       for (int i = 0; i < groups.size(); i++)\r
 578       {\r
 579         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 580         if (!sg.adjustForRemoveRight(max))\r
 581         {\r
 582           viewport.alignment.deleteGroup(sg);\r
 583         }\r
 584       }\r
 585       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 586     }\r
 587 \r
 588   }\r
 589 \r
 590   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 591   {\r
 592     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
 593                                    viewport.alignment,\r
 594                                    HistoryItem.HIDE));\r
 595 \r
 596     //This is to maintain viewport position on first residue\r
 597     //of first sequence\r
 598     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 599     int startRes = seq.findPosition(viewport.startRes);\r
 600 \r
 601     viewport.getAlignment().removeGaps();\r
 602 \r
 603     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 604 \r
 605     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 606   }\r
 607 \r
 608   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 609   {\r
 610     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
 611                                    HistoryItem.HIDE));\r
 612 \r
 613     //This is to maintain viewport position on first residue\r
 614     //of first sequence\r
 615     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 616     int startRes = seq.findPosition(viewport.startRes);\r
 617 \r
 618     SequenceI current;\r
 619     int jSize;\r
 620 \r
 621     Vector seqs=null;\r
 622 \r
 623     int start=0, end = viewport.alignment.getWidth();\r
 624 \r
 625     if (viewport.getSelectionGroup() != null\r
 626         && viewport.getSelectionGroup().sequences != null\r
 627         && viewport.getSelectionGroup().sequences.size()>0)\r
 628     {\r
 629       seqs = viewport.getSelectionGroup().sequences;\r
 630       start = viewport.getSelectionGroup().getStartRes();\r
 631       end = viewport.getSelectionGroup().getEndRes()+1;\r
 632     }\r
 633     else\r
 634       seqs = viewport.alignment.getSequences();\r
 635 \r
 636     for (int i = 0; i < seqs.size(); i++)\r
 637     {\r
 638       current = (SequenceI) seqs.elementAt(i);\r
 639       jSize = current.getLength();\r
 640 \r
 641       // Removing a range is much quicker than removing gaps\r
 642       // one by one for long sequences\r
 643       int j = start;\r
 644       int rangeStart=-1, rangeEnd=-1;\r
 645 \r
 646       do\r
 647       {\r
 648         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 649         {\r
 650           if(rangeStart==-1)\r
 651            {\r
 652              rangeStart = j;\r
 653              rangeEnd = j+1;\r
 654            }\r
 655            else\r
 656            {\r
 657              rangeEnd++;\r
 658            }\r
 659            j++;\r
 660         }\r
 661         else\r
 662         {\r
 663           if(rangeStart>-1)\r
 664           {\r
 665             current.deleteChars(rangeStart, rangeEnd);\r
 666             j-=rangeEnd-rangeStart;\r
 667             jSize-=rangeEnd-rangeStart;\r
 668             rangeStart = -1;\r
 669             rangeEnd = -1;\r
 670           }\r
 671           else\r
 672             j++;\r
 673         }\r
 674       }\r
 675       while (j < end && j < jSize);\r
 676       if(rangeStart>-1)\r
 677       {\r
 678        current.deleteChars(rangeStart, rangeEnd);\r
 679       }\r
 680     }\r
 681     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 682     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 683   }\r
 684 \r
 685   public void alignmentChanged()\r
 686   {\r
 687     viewport.updateConsensus();\r
 688     viewport.updateConservation ();\r
 689     resetAllColourSchemes();\r
 690     if(alignPanel.overviewPanel!=null)\r
 691       alignPanel.overviewPanel.updateOverviewImage();\r
 692     alignPanel.repaint();\r
 693   }\r
 694 \r
 695   void resetAllColourSchemes()\r
 696   {\r
 697     ColourSchemeI cs = viewport.globalColourScheme;\r
 698     if(cs!=null)\r
 699     {\r
 700       if (cs instanceof ClustalxColourScheme)\r
 701       {\r
 702         ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
 703             resetClustalX(viewport.alignment.getSequences(),\r
 704                           viewport.alignment.getWidth());\r
 705       }\r
 706 \r
 707       cs.setConsensus(viewport.vconsensus);\r
 708       if (cs.conservationApplied())\r
 709       {\r
 710         Alignment al = (Alignment) viewport.alignment;\r
 711         Conservation c = new Conservation("All",\r
 712                                           ResidueProperties.propHash, 3,\r
 713                                           al.getSequences(), 0,\r
 714                                           al.getWidth() - 1);\r
 715         c.calculate();\r
 716         c.verdict(false, viewport.ConsPercGaps);\r
 717 \r
 718         cs.setConservation(c);\r
 719       }\r
 720     }\r
 721 \r
 722     int s, sSize = viewport.alignment.getGroups().size();\r
 723     for(s=0; s<sSize; s++)\r
 724     {\r
 725       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
 726       if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
 727       {\r
 728         ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
 729       }\r
 730       sg.recalcConservation();\r
 731     }\r
 732   }\r
 733 \r
 734 \r
 735 \r
 736   public void findMenuItem_actionPerformed(ActionEvent e)\r
 737   {\r
 738     Finder finder = new Finder(alignPanel);\r
 739   }\r
 740 \r
 741   public void font_actionPerformed(ActionEvent e)\r
 742   {\r
 743     Frame frame = new Frame();\r
 744     FontChooser fc = new FontChooser(alignPanel, frame);\r
 745     frame.add(fc);\r
 746     jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);\r
 747 \r
 748   }\r
 749 \r
 750   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 751   {\r
 752     viewport.setShowFullId(fullSeqId.getState());\r
 753     alignPanel.fontChanged();\r
 754     alignPanel.repaint();\r
 755   }\r
 756 \r
 757   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 758   {\r
 759     viewport.setColourText(colourTextMenuItem.getState());\r
 760     alignPanel.repaint();\r
 761   }\r
 762 \r
 763   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 764   {\r
 765     viewport.setWrapAlignment(wrapMenuItem.getState());\r
 766     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
 767     scaleAbove.setEnabled(wrapMenuItem.getState());\r
 768     scaleLeft.setEnabled(wrapMenuItem.getState());\r
 769     scaleRight.setEnabled(wrapMenuItem.getState());\r
 770     alignPanel.repaint();\r
 771   }\r
 772 \r
 773   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 774   {\r
 775     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 776     alignPanel.repaint();\r
 777   }\r
 778 \r
 779   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 780   {\r
 781     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 782     alignPanel.repaint();\r
 783   }\r
 784 \r
 785   protected void scaleRight_actionPerformed(ActionEvent e)\r
 786   {\r
 787     viewport.setScaleRightWrapped(scaleRight.getState());\r
 788     alignPanel.repaint();\r
 789   }\r
 790 \r
 791   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 792   {\r
 793     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
 794     alignPanel.repaint();\r
 795   }\r
 796 \r
 797   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 798   {\r
 799     viewport.setShowText(viewTextMenuItem.getState());\r
 800     alignPanel.repaint();\r
 801   }\r
 802 \r
 803   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 804   {\r
 805     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 806     alignPanel.repaint();\r
 807   }\r
 808 \r
 809   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 810   {\r
 811     if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
 812     {\r
 813       annotationPanelMenuItem.setState(false);\r
 814       return;\r
 815     }\r
 816     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
 817     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
 818   }\r
 819 \r
 820   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 821   {\r
 822     if (alignPanel.overviewPanel != null)\r
 823     {\r
 824       return;\r
 825     }\r
 826 \r
 827     Frame frame = new Frame();\r
 828     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 829     frame.add(overview);\r
 830     // +50 must allow for applet frame window\r
 831     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
 832                                      overview.preferredSize().width,\r
 833                                      overview.preferredSize().height + 50);\r
 834 \r
 835     frame.pack();\r
 836     frame.addWindowListener(new WindowAdapter()\r
 837     {\r
 838       public void windowClosing(WindowEvent e)\r
 839       {\r
 840         alignPanel.setOverviewPanel(null);\r
 841       };\r
 842     });\r
 843 \r
 844     alignPanel.setOverviewPanel(overview);\r
 845 \r
 846   }\r
 847 \r
 848   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 849   {\r
 850     changeColour(null);\r
 851   }\r
 852 \r
 853   public void clustalColour_actionPerformed(ActionEvent e)\r
 854   {\r
 855     abovePIDThreshold.setState(false);\r
 856     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
 857                                           viewport.alignment.getWidth()));\r
 858   }\r
 859 \r
 860   public void zappoColour_actionPerformed(ActionEvent e)\r
 861   {\r
 862     changeColour(new ZappoColourScheme());\r
 863   }\r
 864 \r
 865   public void taylorColour_actionPerformed(ActionEvent e)\r
 866   {\r
 867     changeColour(new TaylorColourScheme());\r
 868   }\r
 869 \r
 870   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 871   {\r
 872     changeColour(new HydrophobicColourScheme());\r
 873   }\r
 874 \r
 875   public void helixColour_actionPerformed(ActionEvent e)\r
 876   {\r
 877     changeColour(new HelixColourScheme());\r
 878   }\r
 879 \r
 880   public void strandColour_actionPerformed(ActionEvent e)\r
 881   {\r
 882     changeColour(new StrandColourScheme());\r
 883   }\r
 884 \r
 885   public void turnColour_actionPerformed(ActionEvent e)\r
 886   {\r
 887     changeColour(new TurnColourScheme());\r
 888   }\r
 889 \r
 890   public void buriedColour_actionPerformed(ActionEvent e)\r
 891   {\r
 892     changeColour(new BuriedColourScheme());\r
 893   }\r
 894 \r
 895   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 896   {\r
 897     changeColour(new NucleotideColourScheme());\r
 898   }\r
 899 \r
 900   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 901   {\r
 902     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
 903   }\r
 904 \r
 905   void changeColour(ColourSchemeI cs)\r
 906   {\r
 907     int threshold = 0;\r
 908 \r
 909     if(cs!=null)\r
 910     {\r
 911       if (viewport.getAbovePIDThreshold())\r
 912       {\r
 913         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 914 \r
 915         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
 916 \r
 917         viewport.setGlobalColourScheme(cs);\r
 918       }\r
 919       else\r
 920       {\r
 921         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
 922       }\r
 923 \r
 924       if (viewport.getConservationSelected())\r
 925       {\r
 926 \r
 927         Alignment al = (Alignment) viewport.alignment;\r
 928         Conservation c = new Conservation("All",\r
 929                                           ResidueProperties.propHash, 3,\r
 930                                           al.getSequences(), 0,\r
 931                                           al.getWidth() - 1);\r
 932 \r
 933         c.calculate();\r
 934         c.verdict(false, viewport.ConsPercGaps);\r
 935 \r
 936         cs.setConservation(c);\r
 937 \r
 938         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
 939             "Background"));\r
 940 \r
 941       }\r
 942       else\r
 943       {\r
 944         cs.setConservation(null);\r
 945       }\r
 946 \r
 947       cs.setConsensus(viewport.vconsensus);\r
 948 \r
 949     }\r
 950     viewport.setGlobalColourScheme(cs);\r
 951 \r
 952     if (viewport.getColourAppliesToAllGroups())\r
 953     {\r
 954       Vector groups = viewport.alignment.getGroups();\r
 955       for (int i = 0; i < groups.size(); i++)\r
 956       {\r
 957         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 958 \r
 959         if(cs==null)\r
 960         {\r
 961           sg.cs = null;\r
 962           continue;\r
 963         }\r
 964         if (cs instanceof ClustalxColourScheme)\r
 965         {\r
 966           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
 967         }\r
 968         else\r
 969         {\r
 970           try\r
 971           {\r
 972             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
 973           }\r
 974           catch (Exception ex)\r
 975           {\r
 976             ex.printStackTrace();\r
 977             sg.cs = cs;\r
 978           }\r
 979         }\r
 980 \r
 981         if (viewport.getAbovePIDThreshold()\r
 982             || cs instanceof PIDColourScheme\r
 983             || cs instanceof Blosum62ColourScheme)\r
 984         {\r
 985           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
 986           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 987         }\r
 988         else\r
 989           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
 990 \r
 991         if (viewport.getConservationSelected())\r
 992         {\r
 993           Conservation c = new Conservation("Group",\r
 994                                             ResidueProperties.propHash, 3,\r
 995                                             sg.sequences, 0,\r
 996                                             viewport.alignment.getWidth() - 1);\r
 997           c.calculate();\r
 998           c.verdict(false, viewport.ConsPercGaps);\r
 999           sg.cs.setConservation(c);\r
1000         }\r
1001         else\r
1002         {\r
1003           sg.cs.setConservation(null);\r
1004           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1005         }\r
1006 \r
1007       }\r
1008     }\r
1009 \r
1010 \r
1011     if (alignPanel.getOverviewPanel() != null)\r
1012     {\r
1013       alignPanel.getOverviewPanel().updateOverviewImage();\r
1014     }\r
1015 \r
1016     alignPanel.repaint();\r
1017   }\r
1018 \r
1019 \r
1020 \r
1021   protected void modifyPID_actionPerformed(ActionEvent e)\r
1022   {\r
1023     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
1024     {\r
1025       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
1026                                      "Background");\r
1027       SliderPanel.showPIDSlider();\r
1028     }\r
1029   }\r
1030 \r
1031   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1032   {\r
1033     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
1034     {\r
1035       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
1036                                         "Background");\r
1037       SliderPanel.showConservationSlider();\r
1038     }\r
1039   }\r
1040 \r
1041   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1042   {\r
1043     viewport.setConservationSelected(conservationMenuItem.getState());\r
1044 \r
1045     viewport.setAbovePIDThreshold(false);\r
1046     abovePIDThreshold.setState(false);\r
1047 \r
1048     changeColour(viewport.getGlobalColourScheme());\r
1049 \r
1050     modifyConservation_actionPerformed(null);\r
1051   }\r
1052 \r
1053   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1054   {\r
1055     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
1056 \r
1057     conservationMenuItem.setState(false);\r
1058     viewport.setConservationSelected(false);\r
1059 \r
1060     changeColour(viewport.getGlobalColourScheme());\r
1061 \r
1062     modifyPID_actionPerformed(null);\r
1063   }\r
1064 \r
1065   public void userDefinedColour_actionPerformed(ActionEvent e)\r
1066   {\r
1067     UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);\r
1068   }\r
1069 \r
1070   public void PIDColour_actionPerformed(ActionEvent e)\r
1071   {\r
1072     changeColour(new PIDColourScheme());\r
1073   }\r
1074 \r
1075   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1076   {\r
1077     changeColour(new Blosum62ColourScheme());\r
1078   }\r
1079 \r
1080   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1081   {\r
1082     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1083                                    HistoryItem.SORT));\r
1084     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1085                               viewport.getAlignment().getSequenceAt(0));\r
1086     alignPanel.repaint();\r
1087   }\r
1088 \r
1089   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1090   {\r
1091     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1092                                    HistoryItem.SORT));\r
1093     AlignmentSorter.sortByID(viewport.getAlignment());\r
1094     alignPanel.repaint();\r
1095   }\r
1096 \r
1097   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1098   {\r
1099     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1100                                    HistoryItem.SORT));\r
1101     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1102     alignPanel.repaint();\r
1103 \r
1104   }\r
1105 \r
1106   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1107   {\r
1108     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
1109     Frame frame = new Frame();\r
1110     frame.add(sp);\r
1111     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
1112                                      400, 120);\r
1113 \r
1114   }\r
1115 \r
1116   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1117   {\r
1118     if (viewport.getSelectionGroup().getSize() > 1)\r
1119     {\r
1120       Frame frame = new Frame();\r
1121       frame.add(new PairwiseAlignPanel(alignPanel));\r
1122       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1123     }\r
1124   }\r
1125 \r
1126   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
1127   {\r
1128     //are the sequences aligned?\r
1129     if (!viewport.alignment.isAligned())\r
1130     {\r
1131       SequenceI current;\r
1132       int Width = viewport.getAlignment().getWidth();\r
1133 \r
1134       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1135            i++)\r
1136       {\r
1137         current = viewport.getAlignment().getSequenceAt(i);\r
1138 \r
1139         if (current.getLength() < Width)\r
1140         {\r
1141           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1142         }\r
1143       }\r
1144       alignPanel.repaint();\r
1145     }\r
1146 \r
1147     if ( (viewport.getSelectionGroup() != null &&\r
1148           viewport.getSelectionGroup().getSize() < 4 &&\r
1149           viewport.getSelectionGroup().getSize() > 0)\r
1150         || viewport.getAlignment().getHeight() < 4)\r
1151     {\r
1152       return;\r
1153     }\r
1154 \r
1155     try\r
1156     {\r
1157       PCAPanel pcaPanel = new PCAPanel(viewport);\r
1158       Frame frame = new Frame();\r
1159       frame.add(pcaPanel);\r
1160       jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",\r
1161                                        400, 400);\r
1162     }\r
1163     catch (java.lang.OutOfMemoryError ex)\r
1164     {\r
1165     }\r
1166 \r
1167   }\r
1168 \r
1169   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1170   {\r
1171     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1172   }\r
1173 \r
1174   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1175   {\r
1176     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1177   }\r
1178 \r
1179   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1180   {\r
1181     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1182   }\r
1183 \r
1184   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1185   {\r
1186     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1187   }\r
1188 \r
1189   void NewTreePanel(String type, String pwType, String title)\r
1190   {\r
1191     //are the sequences aligned?\r
1192     if (!viewport.alignment.isAligned())\r
1193     {\r
1194       SequenceI current;\r
1195       int Width = viewport.getAlignment().getWidth();\r
1196 \r
1197       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1198            i++)\r
1199       {\r
1200         current = viewport.getAlignment().getSequenceAt(i);\r
1201 \r
1202         if (current.getLength() < Width)\r
1203         {\r
1204           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1205         }\r
1206       }\r
1207       alignPanel.repaint();\r
1208 \r
1209     }\r
1210 \r
1211     final TreePanel tp;\r
1212     if (viewport.getSelectionGroup() != null &&\r
1213         viewport.getSelectionGroup().getSize() > 3)\r
1214     {\r
1215       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1216                          pwType,\r
1217                          0, viewport.alignment.getWidth());\r
1218     }\r
1219     else\r
1220     {\r
1221       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1222                          type, pwType, 0, viewport.alignment.getWidth());\r
1223     }\r
1224 \r
1225     addTreeMenuItem(tp, title);\r
1226 \r
1227     jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1228   }\r
1229 \r
1230   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1231   {\r
1232     final MenuItem item = new MenuItem(title);\r
1233     sortByTreeMenu.add(item);\r
1234     item.addActionListener(new java.awt.event.ActionListener()\r
1235     {\r
1236       public void actionPerformed(ActionEvent e)\r
1237       {\r
1238         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1239                                        HistoryItem.SORT));\r
1240         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1241         alignPanel.repaint();\r
1242       }\r
1243     });\r
1244 \r
1245     treePanel.addWindowListener(new WindowAdapter()\r
1246     {\r
1247       public void windowClosing(WindowEvent e)\r
1248       {\r
1249         sortByTreeMenu.remove(item);\r
1250       };\r
1251     });\r
1252   }\r
1253 \r
1254   protected void documentation_actionPerformed(ActionEvent e)\r
1255   {\r
1256     jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");\r
1257   }\r
1258 \r
1259   protected void about_actionPerformed(ActionEvent e)\r
1260   {\r
1261 \r
1262     class AboutPanel extends Canvas\r
1263     {\r
1264       String version;\r
1265       public AboutPanel(String version)\r
1266       { this.version = version; }\r
1267 \r
1268       public void paint(Graphics g)\r
1269       {\r
1270         g.setColor(Color.white);\r
1271         g.fillRect(0, 0, getSize().width, getSize().height);\r
1272         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1273         FontMetrics fm = g.getFontMetrics();\r
1274         int fh = fm.getHeight();\r
1275         int y = 5, x = 7;\r
1276         g.setColor(Color.black);\r
1277         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1278         g.drawString("Jalview - Release "+version, 200, y += fh);\r
1279         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1280         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1281                      x, y += fh * 2);\r
1282         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1283                      x, y += fh);\r
1284         g.drawString(\r
1285             "For any issues relating to Jalview, email help@jalview.org", x,\r
1286             y += fh);\r
1287         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1288         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1289                      x, y += fh);\r
1290         g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);\r
1291       }\r
1292     }\r
1293 \r
1294     String version = "test";\r
1295     java.net.URL url = getClass().getResource("/.build_properties");\r
1296     if (url != null)\r
1297     {\r
1298       try\r
1299       {\r
1300         BufferedReader reader = new BufferedReader(new InputStreamReader(\r
1301             url.openStream()));\r
1302         String line;\r
1303         while ( (line = reader.readLine()) != null)\r
1304         {\r
1305           if (line.indexOf("VERSION") > -1)\r
1306           {\r
1307             version = line.substring(line.indexOf("=") + 1);\r
1308           }\r
1309         }\r
1310       }\r
1311       catch (Exception ex)\r
1312       {\r
1313         ex.printStackTrace();\r
1314       }\r
1315     }\r
1316 \r
1317 \r
1318     Frame frame = new Frame();\r
1319     frame.add(new AboutPanel(version));\r
1320     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1321 \r
1322   }\r
1323 }\r