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   int NEW_WINDOW_WIDTH = 700;\r
  39   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, String title)\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       try\r
  98       {\r
  99         param = applet.getParameter("windowWidth");\r
 100         if (param != null)\r
 101         {\r
 102           int width = Integer.parseInt(param);\r
 103           NEW_WINDOW_WIDTH = width;\r
 104         }\r
 105         param = applet.getParameter("windowHeight");\r
 106         if (param != null)\r
 107         {\r
 108           int height = Integer.parseInt(param);\r
 109           NEW_WINDOW_HEIGHT = height;\r
 110         }\r
 111       }\r
 112       catch (Exception ex)\r
 113       {}\r
 114 \r
 115     }\r
 116 \r
 117     this.addWindowListener(new WindowAdapter()\r
 118     {\r
 119       public void windowClosing(WindowEvent e)\r
 120           {\r
 121             closeMenuItem_actionPerformed(null);\r
 122           }\r
 123     });\r
 124 \r
 125     viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
 126     {\r
 127      public void propertyChange(java.beans.PropertyChangeEvent evt)\r
 128      {\r
 129        if (evt.getPropertyName().equals("alignment"))\r
 130        {\r
 131          alignmentChanged();\r
 132        }\r
 133      }\r
 134    });\r
 135 \r
 136    jalview.bin.JalviewLite.addFrame(this, title,\r
 137                                     NEW_WINDOW_WIDTH,\r
 138                                     NEW_WINDOW_HEIGHT);\r
 139 \r
 140 \r
 141   }\r
 142 \r
 143   public void inputText_actionPerformed(ActionEvent e)\r
 144   {\r
 145     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);\r
 146     Frame frame = new Frame();\r
 147     frame.add(cap);\r
 148     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
 149   }\r
 150 \r
 151   protected void outputText_actionPerformed(ActionEvent e)\r
 152   {\r
 153     CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);\r
 154     Frame frame = new Frame();\r
 155     frame.add(cap);\r
 156     jalview.bin.JalviewLite.addFrame(frame,\r
 157                                      "Alignment output - " + e.getActionCommand(),\r
 158                                      600, 500);\r
 159     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),\r
 160                                               viewport.getAlignment().\r
 161                                               getSequences()));\r
 162   }\r
 163 \r
 164   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 165   {\r
 166     PaintRefresher.components.remove(viewport.alignment);\r
 167     dispose();\r
 168     if(PaintRefresher.components.size()==0 && applet==null)\r
 169       System.exit(0);\r
 170   }\r
 171 \r
 172   Stack historyList = new Stack();\r
 173   Stack redoList = new Stack();\r
 174 \r
 175   void updateEditMenuBar()\r
 176   {\r
 177     if (historyList.size() > 0)\r
 178     {\r
 179       undoMenuItem.setEnabled(true);\r
 180       HistoryItem hi = (HistoryItem) historyList.peek();\r
 181       undoMenuItem.setLabel("Undo " + hi.getDescription());\r
 182     }\r
 183     else\r
 184     {\r
 185       undoMenuItem.setEnabled(false);\r
 186       undoMenuItem.setLabel("Undo");\r
 187     }\r
 188 \r
 189     if (redoList.size() > 0)\r
 190     {\r
 191       redoMenuItem.setEnabled(true);\r
 192       HistoryItem hi = (HistoryItem) redoList.peek();\r
 193       redoMenuItem.setLabel("Redo " + hi.getDescription());\r
 194     }\r
 195     else\r
 196     {\r
 197       redoMenuItem.setEnabled(false);\r
 198       redoMenuItem.setLabel("Redo");\r
 199     }\r
 200   }\r
 201 \r
 202   public void addHistoryItem(HistoryItem hi)\r
 203   {\r
 204     historyList.push(hi);\r
 205     updateEditMenuBar();\r
 206   }\r
 207 \r
 208   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 209   {\r
 210     HistoryItem hi = (HistoryItem) historyList.pop();\r
 211     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
 212                                   HistoryItem.HIDE));\r
 213     restoreHistoryItem(hi);\r
 214     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 215   }\r
 216 \r
 217   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 218   {\r
 219     HistoryItem hi = (HistoryItem) redoList.pop();\r
 220     restoreHistoryItem(hi);\r
 221     updateEditMenuBar();\r
 222     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 223   }\r
 224 \r
 225   // used by undo and redo\r
 226   void restoreHistoryItem(HistoryItem hi)\r
 227   {\r
 228     if (hi.getType() == HistoryItem.SORT)\r
 229     {\r
 230       for (int i = 0; i < hi.getSequences().size(); i++)\r
 231       {\r
 232         viewport.alignment.getSequences().setElementAt(hi.getSequences().\r
 233             elementAt(i), i);\r
 234       }\r
 235     }\r
 236     else\r
 237     {\r
 238       for (int i = 0; i < hi.getSequences().size(); i++)\r
 239       {\r
 240         SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
 241         if (restore.getLength() == 0)\r
 242         {\r
 243           // log.System.out.println(hi.getHidden().elementAt(i));\r
 244           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 245           viewport.alignment.getSequences().insertElementAt(\r
 246               restore,\r
 247               hi.getAlignIndex(i));\r
 248         }\r
 249         else\r
 250         {\r
 251           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 252         }\r
 253       }\r
 254       if (hi.getType() == HistoryItem.PASTE)\r
 255       {\r
 256         for (int i = viewport.alignment.getHeight() - 1;\r
 257              i > hi.getSequences().size() - 1; i--)\r
 258         {\r
 259           viewport.alignment.deleteSequence(i);\r
 260         }\r
 261       }\r
 262     }\r
 263 \r
 264     updateEditMenuBar();\r
 265 \r
 266     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 267   }\r
 268 \r
 269   public void moveSelectedSequences(boolean up)\r
 270   {\r
 271     SequenceGroup sg = viewport.getSelectionGroup();\r
 272     if (sg == null)\r
 273     {\r
 274       return;\r
 275     }\r
 276 \r
 277     if (up)\r
 278     {\r
 279       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 280       {\r
 281         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 282         if (!sg.sequences.contains(seq))\r
 283         {\r
 284           continue;\r
 285         }\r
 286 \r
 287         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 288         if (sg.sequences.contains(temp))\r
 289         {\r
 290           continue;\r
 291         }\r
 292 \r
 293         viewport.alignment.getSequences().setElementAt(temp, i);\r
 294         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 295       }\r
 296     }\r
 297     else\r
 298     {\r
 299       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 300       {\r
 301         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 302         if (!sg.sequences.contains(seq))\r
 303         {\r
 304           continue;\r
 305         }\r
 306 \r
 307         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 308         if (sg.sequences.contains(temp))\r
 309         {\r
 310           continue;\r
 311         }\r
 312 \r
 313         viewport.alignment.getSequences().setElementAt(temp, i);\r
 314         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 315       }\r
 316     }\r
 317 \r
 318     alignPanel.repaint();\r
 319   }\r
 320 \r
 321   StringBuffer copiedSequences;\r
 322   protected void copy_actionPerformed(ActionEvent e)\r
 323   {\r
 324     if (viewport.getSelectionGroup() == null)\r
 325     {\r
 326       return;\r
 327     }\r
 328 \r
 329     SequenceGroup sg = viewport.getSelectionGroup();\r
 330     copiedSequences = new StringBuffer();\r
 331     Hashtable orderedSeqs = new Hashtable();\r
 332     for (int i = 0; i < sg.getSize(); i++)\r
 333     {\r
 334       SequenceI seq = sg.getSequenceAt(i);\r
 335       int index = viewport.alignment.findIndex(seq);\r
 336       orderedSeqs.put(index + "", seq);\r
 337     }\r
 338 \r
 339     int index = 0, startRes, endRes;\r
 340     char ch;\r
 341 \r
 342     for (int i = 0; i < sg.getSize(); i++)\r
 343     {\r
 344         SequenceI seq = null;\r
 345 \r
 346         while (seq == null)\r
 347         {\r
 348             if (orderedSeqs.containsKey(index + ""))\r
 349             {\r
 350                 seq = (SequenceI) orderedSeqs.get(index + "");\r
 351                 index++;\r
 352 \r
 353                 break;\r
 354             }\r
 355             else\r
 356             {\r
 357                 index++;\r
 358             }\r
 359         }\r
 360 \r
 361         //FIND START RES\r
 362         //Returns residue following index if gap\r
 363         startRes = seq.findPosition(sg.getStartRes());\r
 364 \r
 365         //FIND END RES\r
 366         //Need to find the residue preceeding index if gap\r
 367         endRes = 0;\r
 368 \r
 369         for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
 370         {\r
 371           ch = seq.getCharAt(j);\r
 372           if (!jalview.util.Comparison.isGap( (ch)))\r
 373           {\r
 374             endRes++;\r
 375           }\r
 376         }\r
 377 \r
 378         if(endRes>0)\r
 379         {\r
 380           endRes += seq.getStart() -1;\r
 381         }\r
 382 \r
 383         copiedSequences.append(seq.getName() + "\t" +\r
 384             startRes + "\t" +\r
 385             endRes + "\t" +\r
 386             seq.getSequence(sg.getStartRes(),\r
 387                 sg.getEndRes() + 1) + "\n");\r
 388     }\r
 389 \r
 390   }\r
 391 \r
 392   protected void pasteNew_actionPerformed(ActionEvent e)\r
 393   {\r
 394     paste(true);\r
 395   }\r
 396 \r
 397   protected void pasteThis_actionPerformed(ActionEvent e)\r
 398   {\r
 399     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
 400                                    HistoryItem.PASTE));\r
 401     paste(false);\r
 402   }\r
 403 \r
 404   void paste(boolean newAlignment)\r
 405   {\r
 406     try\r
 407     {\r
 408       if (copiedSequences == null)\r
 409       {\r
 410         return;\r
 411       }\r
 412 \r
 413       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 414       Vector seqs = new Vector();\r
 415       while (st.hasMoreElements())\r
 416       {\r
 417         String name = st.nextToken();\r
 418         int start = Integer.parseInt(st.nextToken());\r
 419         int end = Integer.parseInt(st.nextToken());\r
 420         Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
 421 \r
 422         if (!newAlignment)\r
 423         {\r
 424           viewport.alignment.addSequence(sequence);\r
 425         }\r
 426         else\r
 427         {\r
 428           seqs.addElement(sequence);\r
 429         }\r
 430       }\r
 431 \r
 432       if (newAlignment)\r
 433       {\r
 434         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 435         for (int i = 0; i < seqs.size(); i++)\r
 436         {\r
 437           newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
 438         }\r
 439 \r
 440         String newtitle = new String("Copied sequences");\r
 441         if (getTitle().startsWith("Copied sequences"))\r
 442         {\r
 443           newtitle = getTitle();\r
 444         }\r
 445         else\r
 446         {\r
 447           newtitle = newtitle.concat("- from " + getTitle());\r
 448         }\r
 449         AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle);\r
 450 \r
 451         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
 452                                          NEW_WINDOW_HEIGHT);\r
 453       }\r
 454       else\r
 455       {\r
 456         viewport.setEndSeq(viewport.alignment.getHeight());\r
 457         viewport.alignment.getWidth();\r
 458         viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 459       }\r
 460 \r
 461     }\r
 462     catch (Exception ex)\r
 463     {} // could be anything being pasted in here\r
 464 \r
 465   }\r
 466 \r
 467   protected void cut_actionPerformed(ActionEvent e)\r
 468   {\r
 469     copy_actionPerformed(null);\r
 470     delete_actionPerformed(null);\r
 471   }\r
 472 \r
 473   protected void delete_actionPerformed(ActionEvent e)\r
 474   {\r
 475     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
 476                                    HistoryItem.HIDE));\r
 477     if (viewport.getSelectionGroup() == null)\r
 478     {\r
 479       return;\r
 480     }\r
 481 \r
 482 \r
 483     SequenceGroup sg = viewport.getSelectionGroup();\r
 484     boolean allSequences = false;\r
 485     if(sg.sequences.size()==viewport.alignment.getHeight())\r
 486           allSequences = true;\r
 487 \r
 488     for (int i = 0; i < sg.sequences.size(); i++)\r
 489     {\r
 490       SequenceI seq = sg.getSequenceAt(i);\r
 491       int index = viewport.getAlignment().findIndex(seq);\r
 492       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 493 \r
 494       // If the cut affects all sequences, remove highlighted columns\r
 495       if (allSequences)\r
 496       {\r
 497         viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
 498                                                      sg.getEndRes() + 1);\r
 499       }\r
 500 \r
 501 \r
 502       if (seq.getSequence().length() < 1)\r
 503       {\r
 504         viewport.getAlignment().deleteSequence(seq);\r
 505       }\r
 506       else\r
 507       {\r
 508         viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 509       }\r
 510     }\r
 511 \r
 512     viewport.setSelectionGroup(null);\r
 513     viewport.alignment.deleteGroup(sg);\r
 514     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
 515     if (viewport.getAlignment().getHeight() < 1)\r
 516     {\r
 517       try\r
 518       {\r
 519         this.setVisible(false);\r
 520       }\r
 521       catch (Exception ex)\r
 522       {}\r
 523     }\r
 524     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 525 \r
 526   }\r
 527 \r
 528   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 529   {\r
 530     viewport.alignment.deleteAllGroups();\r
 531     viewport.setSelectionGroup(null);\r
 532 \r
 533     alignPanel.repaint();\r
 534   }\r
 535 \r
 536   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 537   {\r
 538     SequenceGroup sg = new SequenceGroup();\r
 539     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 540     {\r
 541       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
 542     }\r
 543     sg.setEndRes(viewport.alignment.getWidth()-1);\r
 544     viewport.setSelectionGroup(sg);\r
 545     alignPanel.repaint();\r
 546     PaintRefresher.Refresh(null, viewport.alignment);\r
 547   }\r
 548 \r
 549   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 550   {\r
 551     viewport.setSelectionGroup(null);\r
 552     viewport.getColumnSelection().clear();\r
 553     viewport.setSelectionGroup(null);\r
 554     alignPanel.repaint();\r
 555     PaintRefresher.Refresh(null, viewport.alignment);\r
 556   }\r
 557 \r
 558   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 559   {\r
 560     SequenceGroup sg = viewport.getSelectionGroup();\r
 561     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 562     {\r
 563       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
 564     }\r
 565 \r
 566     PaintRefresher.Refresh(null, viewport.alignment);\r
 567   }\r
 568 \r
 569   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 570   {\r
 571     ColumnSelection colSel = viewport.getColumnSelection();\r
 572     if (colSel.size() > 0)\r
 573     {\r
 574       addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
 575                                      HistoryItem.HIDE));\r
 576       int min = colSel.getMin();\r
 577       viewport.getAlignment().trimLeft(min);\r
 578       colSel.compensateForEdit(0, min);\r
 579 \r
 580       if (viewport.getSelectionGroup() != null)\r
 581       {\r
 582         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 583       }\r
 584 \r
 585       Vector groups = viewport.alignment.getGroups();\r
 586       for (int i = 0; i < groups.size(); i++)\r
 587       {\r
 588         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 589         if (!sg.adjustForRemoveLeft(min))\r
 590         {\r
 591           viewport.alignment.deleteGroup(sg);\r
 592         }\r
 593       }\r
 594       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 595     }\r
 596   }\r
 597 \r
 598   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 599   {\r
 600     ColumnSelection colSel = viewport.getColumnSelection();\r
 601     if (colSel.size() > 0)\r
 602     {\r
 603       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
 604                                      HistoryItem.HIDE));\r
 605       int max = colSel.getMax();\r
 606       viewport.getAlignment().trimRight(max);\r
 607       if (viewport.getSelectionGroup() != null)\r
 608       {\r
 609         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 610       }\r
 611 \r
 612       Vector groups = viewport.alignment.getGroups();\r
 613       for (int i = 0; i < groups.size(); i++)\r
 614       {\r
 615         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 616         if (!sg.adjustForRemoveRight(max))\r
 617         {\r
 618           viewport.alignment.deleteGroup(sg);\r
 619         }\r
 620       }\r
 621       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 622     }\r
 623 \r
 624   }\r
 625 \r
 626   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 627   {\r
 628     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
 629                                    viewport.alignment,\r
 630                                    HistoryItem.HIDE));\r
 631 \r
 632     //This is to maintain viewport position on first residue\r
 633     //of first sequence\r
 634     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 635     int startRes = seq.findPosition(viewport.startRes);\r
 636 \r
 637     viewport.getAlignment().removeGaps();\r
 638 \r
 639     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 640 \r
 641     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 642   }\r
 643 \r
 644   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 645   {\r
 646     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
 647                                    HistoryItem.HIDE));\r
 648 \r
 649     //This is to maintain viewport position on first residue\r
 650     //of first sequence\r
 651     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 652     int startRes = seq.findPosition(viewport.startRes);\r
 653 \r
 654     SequenceI current;\r
 655     int jSize;\r
 656 \r
 657     Vector seqs=null;\r
 658 \r
 659     int start=0, end = viewport.alignment.getWidth();\r
 660 \r
 661     if (viewport.getSelectionGroup() != null\r
 662         && viewport.getSelectionGroup().sequences != null\r
 663         && viewport.getSelectionGroup().sequences.size()>0)\r
 664     {\r
 665       seqs = viewport.getSelectionGroup().sequences;\r
 666       start = viewport.getSelectionGroup().getStartRes();\r
 667       end = viewport.getSelectionGroup().getEndRes()+1;\r
 668     }\r
 669     else\r
 670       seqs = viewport.alignment.getSequences();\r
 671 \r
 672     for (int i = 0; i < seqs.size(); i++)\r
 673     {\r
 674       current = (SequenceI) seqs.elementAt(i);\r
 675       jSize = current.getLength();\r
 676 \r
 677       // Removing a range is much quicker than removing gaps\r
 678       // one by one for long sequences\r
 679       int j = start;\r
 680       int rangeStart=-1, rangeEnd=-1;\r
 681 \r
 682       do\r
 683       {\r
 684         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 685         {\r
 686           if(rangeStart==-1)\r
 687            {\r
 688              rangeStart = j;\r
 689              rangeEnd = j+1;\r
 690            }\r
 691            else\r
 692            {\r
 693              rangeEnd++;\r
 694            }\r
 695            j++;\r
 696         }\r
 697         else\r
 698         {\r
 699           if(rangeStart>-1)\r
 700           {\r
 701             current.deleteChars(rangeStart, rangeEnd);\r
 702             j-=rangeEnd-rangeStart;\r
 703             jSize-=rangeEnd-rangeStart;\r
 704             rangeStart = -1;\r
 705             rangeEnd = -1;\r
 706           }\r
 707           else\r
 708             j++;\r
 709         }\r
 710       }\r
 711       while (j < end && j < jSize);\r
 712       if(rangeStart>-1)\r
 713       {\r
 714        current.deleteChars(rangeStart, rangeEnd);\r
 715       }\r
 716     }\r
 717     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 718     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 719   }\r
 720 \r
 721   public void alignmentChanged()\r
 722   {\r
 723     viewport.updateConsensus();\r
 724     viewport.updateConservation ();\r
 725     resetAllColourSchemes();\r
 726     if(alignPanel.overviewPanel!=null)\r
 727       alignPanel.overviewPanel.updateOverviewImage();\r
 728     alignPanel.repaint();\r
 729   }\r
 730 \r
 731   void resetAllColourSchemes()\r
 732   {\r
 733     ColourSchemeI cs = viewport.globalColourScheme;\r
 734     if(cs!=null)\r
 735     {\r
 736       if (cs instanceof ClustalxColourScheme)\r
 737       {\r
 738         ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
 739             resetClustalX(viewport.alignment.getSequences(),\r
 740                           viewport.alignment.getWidth());\r
 741       }\r
 742 \r
 743       cs.setConsensus(viewport.vconsensus);\r
 744       if (cs.conservationApplied())\r
 745       {\r
 746         Alignment al = (Alignment) viewport.alignment;\r
 747         Conservation c = new Conservation("All",\r
 748                                           ResidueProperties.propHash, 3,\r
 749                                           al.getSequences(), 0,\r
 750                                           al.getWidth() - 1);\r
 751         c.calculate();\r
 752         c.verdict(false, viewport.ConsPercGaps);\r
 753 \r
 754         cs.setConservation(c);\r
 755       }\r
 756     }\r
 757 \r
 758     int s, sSize = viewport.alignment.getGroups().size();\r
 759     for(s=0; s<sSize; s++)\r
 760     {\r
 761       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
 762       if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
 763       {\r
 764         ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
 765       }\r
 766       sg.recalcConservation();\r
 767     }\r
 768   }\r
 769 \r
 770 \r
 771 \r
 772   public void findMenuItem_actionPerformed(ActionEvent e)\r
 773   {\r
 774     Finder finder = new Finder(alignPanel);\r
 775   }\r
 776 \r
 777   public void font_actionPerformed(ActionEvent e)\r
 778   {\r
 779     new FontChooser(alignPanel);\r
 780   }\r
 781 \r
 782   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 783   {\r
 784     viewport.setShowFullId(fullSeqId.getState());\r
 785     alignPanel.fontChanged();\r
 786     alignPanel.repaint();\r
 787   }\r
 788 \r
 789   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 790   {\r
 791     viewport.setColourText(colourTextMenuItem.getState());\r
 792     alignPanel.repaint();\r
 793   }\r
 794 \r
 795   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 796   {\r
 797     viewport.setWrapAlignment(wrapMenuItem.getState());\r
 798     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
 799     scaleAbove.setEnabled(wrapMenuItem.getState());\r
 800     scaleLeft.setEnabled(wrapMenuItem.getState());\r
 801     scaleRight.setEnabled(wrapMenuItem.getState());\r
 802     alignPanel.repaint();\r
 803   }\r
 804 \r
 805   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 806   {\r
 807     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 808     alignPanel.repaint();\r
 809   }\r
 810 \r
 811   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 812   {\r
 813     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 814     alignPanel.repaint();\r
 815   }\r
 816 \r
 817   protected void scaleRight_actionPerformed(ActionEvent e)\r
 818   {\r
 819     viewport.setScaleRightWrapped(scaleRight.getState());\r
 820     alignPanel.repaint();\r
 821   }\r
 822 \r
 823   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 824   {\r
 825     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
 826     alignPanel.repaint();\r
 827   }\r
 828 \r
 829   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 830   {\r
 831     viewport.setShowText(viewTextMenuItem.getState());\r
 832     alignPanel.repaint();\r
 833   }\r
 834 \r
 835   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 836   {\r
 837     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 838     alignPanel.repaint();\r
 839   }\r
 840 \r
 841   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 842   {\r
 843     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
 844     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
 845   }\r
 846 \r
 847   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 848   {\r
 849     if (alignPanel.overviewPanel != null)\r
 850     {\r
 851       return;\r
 852     }\r
 853 \r
 854     Frame frame = new Frame();\r
 855     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 856     frame.add(overview);\r
 857     // +50 must allow for applet frame window\r
 858     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
 859                                      overview.preferredSize().width,\r
 860                                      overview.preferredSize().height + 50);\r
 861 \r
 862     frame.pack();\r
 863     frame.addWindowListener(new WindowAdapter()\r
 864     {\r
 865       public void windowClosing(WindowEvent e)\r
 866       {\r
 867         alignPanel.setOverviewPanel(null);\r
 868       };\r
 869     });\r
 870 \r
 871     alignPanel.setOverviewPanel(overview);\r
 872 \r
 873   }\r
 874 \r
 875   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 876   {\r
 877     changeColour(null);\r
 878   }\r
 879 \r
 880   public void clustalColour_actionPerformed(ActionEvent e)\r
 881   {\r
 882     abovePIDThreshold.setState(false);\r
 883     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
 884                                           viewport.alignment.getWidth()));\r
 885   }\r
 886 \r
 887   public void zappoColour_actionPerformed(ActionEvent e)\r
 888   {\r
 889     changeColour(new ZappoColourScheme());\r
 890   }\r
 891 \r
 892   public void taylorColour_actionPerformed(ActionEvent e)\r
 893   {\r
 894     changeColour(new TaylorColourScheme());\r
 895   }\r
 896 \r
 897   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 898   {\r
 899     changeColour(new HydrophobicColourScheme());\r
 900   }\r
 901 \r
 902   public void helixColour_actionPerformed(ActionEvent e)\r
 903   {\r
 904     changeColour(new HelixColourScheme());\r
 905   }\r
 906 \r
 907   public void strandColour_actionPerformed(ActionEvent e)\r
 908   {\r
 909     changeColour(new StrandColourScheme());\r
 910   }\r
 911 \r
 912   public void turnColour_actionPerformed(ActionEvent e)\r
 913   {\r
 914     changeColour(new TurnColourScheme());\r
 915   }\r
 916 \r
 917   public void buriedColour_actionPerformed(ActionEvent e)\r
 918   {\r
 919     changeColour(new BuriedColourScheme());\r
 920   }\r
 921 \r
 922   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 923   {\r
 924     changeColour(new NucleotideColourScheme());\r
 925   }\r
 926 \r
 927   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 928   {\r
 929     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
 930   }\r
 931 \r
 932   void changeColour(ColourSchemeI cs)\r
 933   {\r
 934     int threshold = 0;\r
 935 \r
 936     if(cs!=null)\r
 937     {\r
 938       if (viewport.getAbovePIDThreshold())\r
 939       {\r
 940         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 941 \r
 942         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
 943 \r
 944         viewport.setGlobalColourScheme(cs);\r
 945       }\r
 946       else\r
 947       {\r
 948         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
 949       }\r
 950 \r
 951       if (viewport.getConservationSelected())\r
 952       {\r
 953 \r
 954         Alignment al = (Alignment) viewport.alignment;\r
 955         Conservation c = new Conservation("All",\r
 956                                           ResidueProperties.propHash, 3,\r
 957                                           al.getSequences(), 0,\r
 958                                           al.getWidth() - 1);\r
 959 \r
 960         c.calculate();\r
 961         c.verdict(false, viewport.ConsPercGaps);\r
 962 \r
 963         cs.setConservation(c);\r
 964 \r
 965         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
 966             "Background"));\r
 967 \r
 968       }\r
 969       else\r
 970       {\r
 971         cs.setConservation(null);\r
 972       }\r
 973 \r
 974       cs.setConsensus(viewport.vconsensus);\r
 975 \r
 976     }\r
 977     viewport.setGlobalColourScheme(cs);\r
 978 \r
 979     if (viewport.getColourAppliesToAllGroups())\r
 980     {\r
 981       Vector groups = viewport.alignment.getGroups();\r
 982       for (int i = 0; i < groups.size(); i++)\r
 983       {\r
 984         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 985 \r
 986         if(cs==null)\r
 987         {\r
 988           sg.cs = null;\r
 989           continue;\r
 990         }\r
 991         if (cs instanceof ClustalxColourScheme)\r
 992         {\r
 993           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
 994         }\r
 995         else\r
 996         {\r
 997           try\r
 998           {\r
 999             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
1000           }\r
1001           catch (Exception ex)\r
1002           {\r
1003             ex.printStackTrace();\r
1004             sg.cs = cs;\r
1005           }\r
1006         }\r
1007 \r
1008         if (viewport.getAbovePIDThreshold()\r
1009             || cs instanceof PIDColourScheme\r
1010             || cs instanceof Blosum62ColourScheme)\r
1011         {\r
1012           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1013           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
1014         }\r
1015         else\r
1016           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1017 \r
1018         if (viewport.getConservationSelected())\r
1019         {\r
1020           Conservation c = new Conservation("Group",\r
1021                                             ResidueProperties.propHash, 3,\r
1022                                             sg.sequences, 0,\r
1023                                             viewport.alignment.getWidth() - 1);\r
1024           c.calculate();\r
1025           c.verdict(false, viewport.ConsPercGaps);\r
1026           sg.cs.setConservation(c);\r
1027         }\r
1028         else\r
1029         {\r
1030           sg.cs.setConservation(null);\r
1031           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1032         }\r
1033 \r
1034       }\r
1035     }\r
1036 \r
1037 \r
1038     if (alignPanel.getOverviewPanel() != null)\r
1039     {\r
1040       alignPanel.getOverviewPanel().updateOverviewImage();\r
1041     }\r
1042 \r
1043     alignPanel.repaint();\r
1044   }\r
1045 \r
1046 \r
1047 \r
1048   protected void modifyPID_actionPerformed(ActionEvent e)\r
1049   {\r
1050     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
1051     {\r
1052       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
1053                                      "Background");\r
1054       SliderPanel.showPIDSlider();\r
1055     }\r
1056   }\r
1057 \r
1058   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1059   {\r
1060     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
1061     {\r
1062       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
1063                                         "Background");\r
1064       SliderPanel.showConservationSlider();\r
1065     }\r
1066   }\r
1067 \r
1068   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1069   {\r
1070     viewport.setConservationSelected(conservationMenuItem.getState());\r
1071 \r
1072     viewport.setAbovePIDThreshold(false);\r
1073     abovePIDThreshold.setState(false);\r
1074 \r
1075     changeColour(viewport.getGlobalColourScheme());\r
1076 \r
1077     modifyConservation_actionPerformed(null);\r
1078   }\r
1079 \r
1080   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1081   {\r
1082     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
1083 \r
1084     conservationMenuItem.setState(false);\r
1085     viewport.setConservationSelected(false);\r
1086 \r
1087     changeColour(viewport.getGlobalColourScheme());\r
1088 \r
1089     modifyPID_actionPerformed(null);\r
1090   }\r
1091 \r
1092   public void userDefinedColour_actionPerformed(ActionEvent e)\r
1093   {\r
1094     UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);\r
1095   }\r
1096 \r
1097   public void PIDColour_actionPerformed(ActionEvent e)\r
1098   {\r
1099     changeColour(new PIDColourScheme());\r
1100   }\r
1101 \r
1102   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1103   {\r
1104     changeColour(new Blosum62ColourScheme());\r
1105   }\r
1106 \r
1107   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1108   {\r
1109     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1110                                    HistoryItem.SORT));\r
1111     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1112                               viewport.getAlignment().getSequenceAt(0));\r
1113     alignPanel.repaint();\r
1114   }\r
1115 \r
1116   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1117   {\r
1118     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1119                                    HistoryItem.SORT));\r
1120     AlignmentSorter.sortByID(viewport.getAlignment());\r
1121     alignPanel.repaint();\r
1122   }\r
1123 \r
1124   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1125   {\r
1126     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1127                                    HistoryItem.SORT));\r
1128     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1129     alignPanel.repaint();\r
1130 \r
1131   }\r
1132 \r
1133   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1134   {\r
1135     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
1136     Frame frame = new Frame();\r
1137     frame.add(sp);\r
1138     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
1139                                      400, 120);\r
1140 \r
1141   }\r
1142 \r
1143   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1144   {\r
1145     if (viewport.getSelectionGroup().getSize() > 1)\r
1146     {\r
1147       Frame frame = new Frame();\r
1148       frame.add(new PairwiseAlignPanel(alignPanel));\r
1149       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1150     }\r
1151   }\r
1152 \r
1153   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
1154   {\r
1155     //are the sequences aligned?\r
1156     if (!viewport.alignment.isAligned())\r
1157     {\r
1158       SequenceI current;\r
1159       int Width = viewport.getAlignment().getWidth();\r
1160 \r
1161       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1162            i++)\r
1163       {\r
1164         current = viewport.getAlignment().getSequenceAt(i);\r
1165 \r
1166         if (current.getLength() < Width)\r
1167         {\r
1168           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1169         }\r
1170       }\r
1171       alignPanel.repaint();\r
1172     }\r
1173 \r
1174     if ( (viewport.getSelectionGroup() != null &&\r
1175           viewport.getSelectionGroup().getSize() < 4 &&\r
1176           viewport.getSelectionGroup().getSize() > 0)\r
1177         || viewport.getAlignment().getHeight() < 4)\r
1178     {\r
1179       return;\r
1180     }\r
1181 \r
1182     try\r
1183     {\r
1184       new PCAPanel(viewport);\r
1185     }\r
1186     catch (java.lang.OutOfMemoryError ex)\r
1187     {\r
1188     }\r
1189 \r
1190   }\r
1191 \r
1192   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1193   {\r
1194     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1195   }\r
1196 \r
1197   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1198   {\r
1199     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1200   }\r
1201 \r
1202   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1203   {\r
1204     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1205   }\r
1206 \r
1207   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1208   {\r
1209     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1210   }\r
1211 \r
1212   void NewTreePanel(String type, String pwType, String title)\r
1213   {\r
1214     //are the sequences aligned?\r
1215     if (!viewport.alignment.isAligned())\r
1216     {\r
1217       SequenceI current;\r
1218       int Width = viewport.getAlignment().getWidth();\r
1219 \r
1220       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1221            i++)\r
1222       {\r
1223         current = viewport.getAlignment().getSequenceAt(i);\r
1224 \r
1225         if (current.getLength() < Width)\r
1226         {\r
1227           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1228         }\r
1229       }\r
1230       alignPanel.repaint();\r
1231 \r
1232     }\r
1233 \r
1234     final TreePanel tp;\r
1235     if (viewport.getSelectionGroup() != null &&\r
1236         viewport.getSelectionGroup().getSize() > 3)\r
1237     {\r
1238       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1239                          pwType,\r
1240                          0, viewport.alignment.getWidth());\r
1241     }\r
1242     else\r
1243     {\r
1244       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1245                          type, pwType, 0, viewport.alignment.getWidth());\r
1246     }\r
1247 \r
1248     addTreeMenuItem(tp, title);\r
1249 \r
1250     jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1251   }\r
1252 \r
1253   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1254   {\r
1255     final MenuItem item = new MenuItem(title);\r
1256     sortByTreeMenu.add(item);\r
1257     item.addActionListener(new java.awt.event.ActionListener()\r
1258     {\r
1259       public void actionPerformed(ActionEvent e)\r
1260       {\r
1261         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1262                                        HistoryItem.SORT));\r
1263         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1264         alignPanel.repaint();\r
1265       }\r
1266     });\r
1267 \r
1268     treePanel.addWindowListener(new WindowAdapter()\r
1269     {\r
1270       public void windowClosing(WindowEvent e)\r
1271       {\r
1272         sortByTreeMenu.remove(item);\r
1273       };\r
1274     });\r
1275   }\r
1276 \r
1277   protected void documentation_actionPerformed(ActionEvent e)\r
1278   {\r
1279     jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");\r
1280   }\r
1281 \r
1282   protected void about_actionPerformed(ActionEvent e)\r
1283   {\r
1284 \r
1285     class AboutPanel extends Canvas\r
1286     {\r
1287       String version;\r
1288       public AboutPanel(String version)\r
1289       { this.version = version; }\r
1290 \r
1291       public void paint(Graphics g)\r
1292       {\r
1293         g.setColor(Color.white);\r
1294         g.fillRect(0, 0, getSize().width, getSize().height);\r
1295         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1296         FontMetrics fm = g.getFontMetrics();\r
1297         int fh = fm.getHeight();\r
1298         int y = 5, x = 7;\r
1299         g.setColor(Color.black);\r
1300         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1301         g.drawString("Jalview - Release "+version, 200, y += fh);\r
1302         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1303         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1304                      x, y += fh * 2);\r
1305         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1306                      x, y += fh);\r
1307         g.drawString(\r
1308             "For any issues relating to Jalview, email help@jalview.org", x,\r
1309             y += fh);\r
1310         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1311         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1312                      x, y += fh);\r
1313         g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);\r
1314       }\r
1315     }\r
1316 \r
1317     String version = "test";\r
1318     java.net.URL url = getClass().getResource("/.build_properties");\r
1319     if (url != null)\r
1320     {\r
1321       try\r
1322       {\r
1323         BufferedReader reader = new BufferedReader(new InputStreamReader(\r
1324             url.openStream()));\r
1325         String line;\r
1326         while ( (line = reader.readLine()) != null)\r
1327         {\r
1328           if (line.indexOf("VERSION") > -1)\r
1329           {\r
1330             version = line.substring(line.indexOf("=") + 1);\r
1331           }\r
1332         }\r
1333       }\r
1334       catch (Exception ex)\r
1335       {\r
1336         ex.printStackTrace();\r
1337       }\r
1338     }\r
1339 \r
1340 \r
1341     Frame frame = new Frame();\r
1342     frame.add(new AboutPanel(version));\r
1343     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1344 \r
1345   }\r
1346 }\r