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