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