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.schemes.*;\r
  23 import jalview.datamodel.*;\r
  24 import jalview.analysis.*;\r
  25 import jalview.io.*;\r
  26 import java.awt.*;\r
  27 import java.awt.event.*;\r
  28 import java.util.*;\r
  29 import java.io.InputStreamReader;\r
  30 import java.io.BufferedReader;\r
  31 import java.net.URL;\r
  32 \r
  33 \r
  34 public class AlignFrame extends Frame\r
  35 {\r
  36   final AlignmentPanel alignPanel;\r
  37   public 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     try{\r
  46       jbInit();\r
  47     }catch(Exception ex)\r
  48     {\r
  49       ex.printStackTrace();\r
  50     }\r
  51     this.applet = applet;\r
  52     viewport = new AlignViewport(al, applet);\r
  53     alignPanel = new AlignmentPanel(this, viewport);\r
  54     add(alignPanel);\r
  55     alignPanel.validate();\r
  56 \r
  57     if(applet!=null)\r
  58     {\r
  59       String treeFile = applet.getParameter("treeFile");\r
  60       if (treeFile != null)\r
  61       {\r
  62         try\r
  63         {\r
  64           jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
  65               getCodeBase() + treeFile, "URL");\r
  66           fin.parse();\r
  67 \r
  68           if (fin.getTree() != null)\r
  69           {\r
  70             TreePanel tp = null;\r
  71             tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
  72                                fin, "FromFile", applet.getCodeBase() + treeFile);\r
  73             jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
  74             addTreeMenuItem(tp, treeFile);\r
  75           }\r
  76         }\r
  77         catch (Exception ex)\r
  78         {\r
  79           ex.printStackTrace();\r
  80         }\r
  81       }\r
  82 \r
  83       String param = applet.getParameter("sortBy");\r
  84       if (param != null)\r
  85       {\r
  86         if (param.equalsIgnoreCase("Id"))\r
  87           sortIDMenuItem_actionPerformed(null);\r
  88         else if (param.equalsIgnoreCase("Pairwise Identity"))\r
  89           sortPairwiseMenuItem_actionPerformed(null);\r
  90       }\r
  91 \r
  92       param = applet.getParameter("wrap");\r
  93       if (param != null)\r
  94       {\r
  95         if (param.equalsIgnoreCase("true"))\r
  96         {\r
  97           wrapMenuItem.setState(true);\r
  98           wrapMenuItem_actionPerformed(null);\r
  99         }\r
 100       }\r
 101 \r
 102       try\r
 103       {\r
 104         param = applet.getParameter("windowWidth");\r
 105         if (param != null)\r
 106         {\r
 107           int width = Integer.parseInt(param);\r
 108           NEW_WINDOW_WIDTH = width;\r
 109         }\r
 110         param = applet.getParameter("windowHeight");\r
 111         if (param != null)\r
 112         {\r
 113           int height = Integer.parseInt(param);\r
 114           NEW_WINDOW_HEIGHT = height;\r
 115         }\r
 116       }\r
 117       catch (Exception ex)\r
 118       {}\r
 119 \r
 120     }\r
 121 \r
 122     this.addWindowListener(new WindowAdapter()\r
 123     {\r
 124       public void windowClosing(WindowEvent e)\r
 125           {\r
 126             closeMenuItem_actionPerformed(null);\r
 127           }\r
 128     });\r
 129 \r
 130     viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
 131     {\r
 132      public void propertyChange(java.beans.PropertyChangeEvent evt)\r
 133      {\r
 134        if (evt.getPropertyName().equals("alignment"))\r
 135        {\r
 136          alignmentChanged();\r
 137        }\r
 138      }\r
 139    });\r
 140 \r
 141    jalview.bin.JalviewLite.addFrame(this, title,\r
 142                                     NEW_WINDOW_WIDTH,\r
 143                                     NEW_WINDOW_HEIGHT);\r
 144 \r
 145 \r
 146   }\r
 147 \r
 148 \r
 149   /**\r
 150    * DOCUMENT ME!\r
 151    *\r
 152    * @param String DOCUMENT ME!\r
 153    */\r
 154 \r
 155   public void parseFeaturesFile(String file)\r
 156   {\r
 157     try\r
 158     {\r
 159       URL url = new URL(file);\r
 160 \r
 161       BufferedReader in =  new BufferedReader(new InputStreamReader(url.openStream()));\r
 162       SequenceI seq = null;\r
 163       String line, type, desc, token;\r
 164 \r
 165       int index, start, end;\r
 166       StringTokenizer st;\r
 167       SequenceFeature sf;\r
 168       FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
 169       int lineNo = 0;\r
 170       while ( (line = in.readLine()) != null)\r
 171       {\r
 172         lineNo++;\r
 173         st = new StringTokenizer(line, "\t");\r
 174         if (st.countTokens() == 2)\r
 175         {\r
 176           type = st.nextToken();\r
 177           UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
 178           fr.setColour(type, ucs.findColour("A"));\r
 179           continue;\r
 180         }\r
 181 \r
 182         while (st.hasMoreElements())\r
 183         {\r
 184           desc = st.nextToken();\r
 185           token = st.nextToken();\r
 186           if (!token.equals("ID_NOT_SPECIFIED"))\r
 187           {\r
 188             index = viewport.alignment.findIndex(viewport.alignment.findName(\r
 189                 token));\r
 190             st.nextToken();\r
 191           }\r
 192           else\r
 193           {\r
 194             index = Integer.parseInt(st.nextToken());\r
 195           }\r
 196 \r
 197           start = Integer.parseInt(st.nextToken());\r
 198           end = Integer.parseInt(st.nextToken());\r
 199 \r
 200           seq = viewport.alignment.getSequenceAt(index);\r
 201           start = seq.findIndex(start) - 1;\r
 202           end = seq.findIndex(end) - 1;\r
 203 \r
 204           type = st.nextToken();\r
 205 \r
 206           if(fr.getColour(type)==null)\r
 207           {\r
 208             // Probably the old style groups file\r
 209             UserColourScheme ucs = new UserColourScheme(type);\r
 210             fr.setColour(type, ucs.findColour("A"));\r
 211           }\r
 212 \r
 213           sf = new SequenceFeature(type, desc, "", start, end);\r
 214 \r
 215           seq.addSequenceFeature(sf);\r
 216         }\r
 217       }\r
 218 \r
 219       viewport.showSequenceFeatures = true;\r
 220       ((Alignment)viewport.alignment).featuresAdded = true;\r
 221 \r
 222       alignPanel.repaint();\r
 223 \r
 224     }\r
 225     catch (Exception ex)\r
 226     {\r
 227       System.out.println("Error parsing groups file: " + ex);\r
 228     }\r
 229   }\r
 230 \r
 231 \r
 232   public void inputText_actionPerformed(ActionEvent e)\r
 233   {\r
 234     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);\r
 235     Frame frame = new Frame();\r
 236     frame.add(cap);\r
 237     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
 238   }\r
 239 \r
 240   protected void outputText_actionPerformed(ActionEvent e)\r
 241   {\r
 242     CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);\r
 243     Frame frame = new Frame();\r
 244     frame.add(cap);\r
 245     jalview.bin.JalviewLite.addFrame(frame,\r
 246                                      "Alignment output - " + e.getActionCommand(),\r
 247                                      600, 500);\r
 248     cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
 249                                               viewport.getAlignment().getSequences(),\r
 250                                                       viewport.showDBPrefix,\r
 251                                                       viewport.showJVSuffix));\r
 252   }\r
 253 \r
 254   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 255   {\r
 256     PaintRefresher.components.remove(viewport.alignment);\r
 257     if(PaintRefresher.components.size()==0 && applet==null)\r
 258       System.exit(0);\r
 259   }\r
 260 \r
 261   Stack historyList = new Stack();\r
 262   Stack redoList = new Stack();\r
 263 \r
 264   void updateEditMenuBar()\r
 265   {\r
 266     if (historyList.size() > 0)\r
 267     {\r
 268       undoMenuItem.setEnabled(true);\r
 269       HistoryItem hi = (HistoryItem) historyList.peek();\r
 270       undoMenuItem.setLabel("Undo " + hi.getDescription());\r
 271     }\r
 272     else\r
 273     {\r
 274       undoMenuItem.setEnabled(false);\r
 275       undoMenuItem.setLabel("Undo");\r
 276     }\r
 277 \r
 278     if (redoList.size() > 0)\r
 279     {\r
 280       redoMenuItem.setEnabled(true);\r
 281       HistoryItem hi = (HistoryItem) redoList.peek();\r
 282       redoMenuItem.setLabel("Redo " + hi.getDescription());\r
 283     }\r
 284     else\r
 285     {\r
 286       redoMenuItem.setEnabled(false);\r
 287       redoMenuItem.setLabel("Redo");\r
 288     }\r
 289   }\r
 290 \r
 291   public void addHistoryItem(HistoryItem hi)\r
 292   {\r
 293     historyList.push(hi);\r
 294     updateEditMenuBar();\r
 295   }\r
 296 \r
 297   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 298   {\r
 299     HistoryItem hi = (HistoryItem) historyList.pop();\r
 300     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
 301                                   HistoryItem.HIDE));\r
 302     restoreHistoryItem(hi);\r
 303     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 304   }\r
 305 \r
 306   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 307   {\r
 308     HistoryItem hi = (HistoryItem) redoList.pop();\r
 309     restoreHistoryItem(hi);\r
 310     updateEditMenuBar();\r
 311     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 312   }\r
 313 \r
 314   // used by undo and redo\r
 315   void restoreHistoryItem(HistoryItem hi)\r
 316   {\r
 317     if (hi.getType() == HistoryItem.SORT)\r
 318     {\r
 319       for (int i = 0; i < hi.getSequences().size(); i++)\r
 320       {\r
 321         viewport.alignment.getSequences().setElementAt(hi.getSequences().\r
 322             elementAt(i), i);\r
 323       }\r
 324     }\r
 325     else\r
 326     {\r
 327       for (int i = 0; i < hi.getSequences().size(); i++)\r
 328       {\r
 329         SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
 330         if (restore.getLength() == 0)\r
 331         {\r
 332           // log.System.out.println(hi.getHidden().elementAt(i));\r
 333           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 334           viewport.alignment.getSequences().insertElementAt(\r
 335               restore,\r
 336               hi.getAlignIndex(i));\r
 337         }\r
 338         else\r
 339         {\r
 340           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 341         }\r
 342       }\r
 343       if (hi.getType() == HistoryItem.PASTE)\r
 344       {\r
 345         for (int i = viewport.alignment.getHeight() - 1;\r
 346              i > hi.getSequences().size() - 1; i--)\r
 347         {\r
 348           viewport.alignment.deleteSequence(i);\r
 349         }\r
 350       }\r
 351     }\r
 352 \r
 353     updateEditMenuBar();\r
 354 \r
 355     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 356   }\r
 357 \r
 358   public void moveSelectedSequences(boolean up)\r
 359   {\r
 360     SequenceGroup sg = viewport.getSelectionGroup();\r
 361     if (sg == null)\r
 362     {\r
 363       return;\r
 364     }\r
 365 \r
 366     if (up)\r
 367     {\r
 368       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 369       {\r
 370         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 371         if (!sg.sequences.contains(seq))\r
 372         {\r
 373           continue;\r
 374         }\r
 375 \r
 376         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 377         if (sg.sequences.contains(temp))\r
 378         {\r
 379           continue;\r
 380         }\r
 381 \r
 382         viewport.alignment.getSequences().setElementAt(temp, i);\r
 383         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 384       }\r
 385     }\r
 386     else\r
 387     {\r
 388       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 389       {\r
 390         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 391         if (!sg.sequences.contains(seq))\r
 392         {\r
 393           continue;\r
 394         }\r
 395 \r
 396         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 397         if (sg.sequences.contains(temp))\r
 398         {\r
 399           continue;\r
 400         }\r
 401 \r
 402         viewport.alignment.getSequences().setElementAt(temp, i);\r
 403         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 404       }\r
 405     }\r
 406 \r
 407     alignPanel.repaint();\r
 408   }\r
 409 \r
 410   StringBuffer copiedSequences;\r
 411   protected void copy_actionPerformed(ActionEvent e)\r
 412   {\r
 413     if (viewport.getSelectionGroup() == null)\r
 414     {\r
 415       return;\r
 416     }\r
 417 \r
 418     SequenceGroup sg = viewport.getSelectionGroup();\r
 419     copiedSequences = new StringBuffer();\r
 420     Hashtable orderedSeqs = new Hashtable();\r
 421     for (int i = 0; i < sg.getSize(); i++)\r
 422     {\r
 423       SequenceI seq = sg.getSequenceAt(i);\r
 424       int index = viewport.alignment.findIndex(seq);\r
 425       orderedSeqs.put(index + "", seq);\r
 426     }\r
 427 \r
 428     int index = 0, startRes, endRes;\r
 429     char ch;\r
 430 \r
 431     for (int i = 0; i < sg.getSize(); i++)\r
 432     {\r
 433         SequenceI seq = null;\r
 434 \r
 435         while (seq == null)\r
 436         {\r
 437             if (orderedSeqs.containsKey(index + ""))\r
 438             {\r
 439                 seq = (SequenceI) orderedSeqs.get(index + "");\r
 440                 index++;\r
 441 \r
 442                 break;\r
 443             }\r
 444             else\r
 445             {\r
 446                 index++;\r
 447             }\r
 448         }\r
 449 \r
 450         //FIND START RES\r
 451         //Returns residue following index if gap\r
 452         startRes = seq.findPosition(sg.getStartRes());\r
 453 \r
 454         //FIND END RES\r
 455         //Need to find the residue preceeding index if gap\r
 456         endRes = 0;\r
 457 \r
 458         for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
 459         {\r
 460           ch = seq.getCharAt(j);\r
 461           if (!jalview.util.Comparison.isGap( (ch)))\r
 462           {\r
 463             endRes++;\r
 464           }\r
 465         }\r
 466 \r
 467         if(endRes>0)\r
 468         {\r
 469           endRes += seq.getStart() -1;\r
 470         }\r
 471 \r
 472         copiedSequences.append(seq.getName() + "\t" +\r
 473             startRes + "\t" +\r
 474             endRes + "\t" +\r
 475             seq.getSequence(sg.getStartRes(),\r
 476                 sg.getEndRes() + 1) + "\n");\r
 477     }\r
 478 \r
 479   }\r
 480 \r
 481   protected void pasteNew_actionPerformed(ActionEvent e)\r
 482   {\r
 483     paste(true);\r
 484   }\r
 485 \r
 486   protected void pasteThis_actionPerformed(ActionEvent e)\r
 487   {\r
 488     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
 489                                    HistoryItem.PASTE));\r
 490     paste(false);\r
 491   }\r
 492 \r
 493   void paste(boolean newAlignment)\r
 494   {\r
 495     try\r
 496     {\r
 497       if (copiedSequences == null)\r
 498       {\r
 499         return;\r
 500       }\r
 501 \r
 502       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 503       Vector seqs = new Vector();\r
 504       while (st.hasMoreElements())\r
 505       {\r
 506         String name = st.nextToken();\r
 507         int start = Integer.parseInt(st.nextToken());\r
 508         int end = Integer.parseInt(st.nextToken());\r
 509         Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
 510 \r
 511         if (!newAlignment)\r
 512         {\r
 513           viewport.alignment.addSequence(sequence);\r
 514         }\r
 515         else\r
 516         {\r
 517           seqs.addElement(sequence);\r
 518         }\r
 519       }\r
 520 \r
 521       if (newAlignment)\r
 522       {\r
 523         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 524         for (int i = 0; i < seqs.size(); i++)\r
 525         {\r
 526           newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
 527         }\r
 528 \r
 529         String newtitle = new String("Copied sequences");\r
 530         if (getTitle().startsWith("Copied sequences"))\r
 531         {\r
 532           newtitle = getTitle();\r
 533         }\r
 534         else\r
 535         {\r
 536           newtitle = newtitle.concat("- from " + getTitle());\r
 537         }\r
 538         AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle);\r
 539 \r
 540         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
 541                                          NEW_WINDOW_HEIGHT);\r
 542       }\r
 543       else\r
 544       {\r
 545         viewport.setEndSeq(viewport.alignment.getHeight());\r
 546         viewport.alignment.getWidth();\r
 547         viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 548       }\r
 549 \r
 550     }\r
 551     catch (Exception ex)\r
 552     {} // could be anything being pasted in here\r
 553 \r
 554   }\r
 555 \r
 556   protected void cut_actionPerformed(ActionEvent e)\r
 557   {\r
 558     copy_actionPerformed(null);\r
 559     delete_actionPerformed(null);\r
 560   }\r
 561 \r
 562   protected void delete_actionPerformed(ActionEvent e)\r
 563   {\r
 564     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
 565                                    HistoryItem.HIDE));\r
 566     if (viewport.getSelectionGroup() == null)\r
 567     {\r
 568       return;\r
 569     }\r
 570 \r
 571 \r
 572     SequenceGroup sg = viewport.getSelectionGroup();\r
 573     boolean allSequences = false;\r
 574     if(sg.sequences.size()==viewport.alignment.getHeight())\r
 575           allSequences = true;\r
 576 \r
 577     for (int i = 0; i < sg.sequences.size(); i++)\r
 578     {\r
 579       SequenceI seq = sg.getSequenceAt(i);\r
 580       int index = viewport.getAlignment().findIndex(seq);\r
 581       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 582 \r
 583       // If the cut affects all sequences, remove highlighted columns\r
 584       if (allSequences)\r
 585       {\r
 586         viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
 587                                                      sg.getEndRes() + 1);\r
 588       }\r
 589 \r
 590 \r
 591       if (seq.getSequence().length() < 1)\r
 592       {\r
 593         viewport.getAlignment().deleteSequence(seq);\r
 594       }\r
 595       else\r
 596       {\r
 597         viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 598       }\r
 599     }\r
 600 \r
 601     viewport.setSelectionGroup(null);\r
 602     viewport.alignment.deleteGroup(sg);\r
 603     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
 604     if (viewport.getAlignment().getHeight() < 1)\r
 605     {\r
 606       try\r
 607       {\r
 608         this.setVisible(false);\r
 609       }\r
 610       catch (Exception ex)\r
 611       {}\r
 612     }\r
 613     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 614 \r
 615   }\r
 616 \r
 617   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 618   {\r
 619     viewport.alignment.deleteAllGroups();\r
 620     viewport.setSelectionGroup(null);\r
 621 \r
 622     alignPanel.repaint();\r
 623   }\r
 624 \r
 625   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 626   {\r
 627     SequenceGroup sg = new SequenceGroup();\r
 628     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 629     {\r
 630       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
 631     }\r
 632     sg.setEndRes(viewport.alignment.getWidth()-1);\r
 633     viewport.setSelectionGroup(sg);\r
 634     alignPanel.repaint();\r
 635     PaintRefresher.Refresh(null, viewport.alignment);\r
 636   }\r
 637 \r
 638   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 639   {\r
 640     viewport.setSelectionGroup(null);\r
 641     viewport.getColumnSelection().clear();\r
 642     viewport.setSelectionGroup(null);\r
 643     alignPanel.repaint();\r
 644     PaintRefresher.Refresh(null, viewport.alignment);\r
 645   }\r
 646 \r
 647   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 648   {\r
 649     SequenceGroup sg = viewport.getSelectionGroup();\r
 650     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 651     {\r
 652       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
 653     }\r
 654 \r
 655     PaintRefresher.Refresh(null, viewport.alignment);\r
 656   }\r
 657 \r
 658   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 659   {\r
 660     ColumnSelection colSel = viewport.getColumnSelection();\r
 661     if (colSel.size() > 0)\r
 662     {\r
 663       addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
 664                                      HistoryItem.HIDE));\r
 665       int min = colSel.getMin();\r
 666       viewport.getAlignment().trimLeft(min);\r
 667       colSel.compensateForEdit(0, min);\r
 668 \r
 669       if (viewport.getSelectionGroup() != null)\r
 670       {\r
 671         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 672       }\r
 673 \r
 674       Vector groups = viewport.alignment.getGroups();\r
 675       for (int i = 0; i < groups.size(); i++)\r
 676       {\r
 677         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 678         if (!sg.adjustForRemoveLeft(min))\r
 679         {\r
 680           viewport.alignment.deleteGroup(sg);\r
 681         }\r
 682       }\r
 683       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 684     }\r
 685   }\r
 686 \r
 687   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 688   {\r
 689     ColumnSelection colSel = viewport.getColumnSelection();\r
 690     if (colSel.size() > 0)\r
 691     {\r
 692       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
 693                                      HistoryItem.HIDE));\r
 694       int max = colSel.getMax();\r
 695       viewport.getAlignment().trimRight(max);\r
 696       if (viewport.getSelectionGroup() != null)\r
 697       {\r
 698         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 699       }\r
 700 \r
 701       Vector groups = viewport.alignment.getGroups();\r
 702       for (int i = 0; i < groups.size(); i++)\r
 703       {\r
 704         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 705         if (!sg.adjustForRemoveRight(max))\r
 706         {\r
 707           viewport.alignment.deleteGroup(sg);\r
 708         }\r
 709       }\r
 710       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 711     }\r
 712 \r
 713   }\r
 714 \r
 715   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 716   {\r
 717     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
 718                                    viewport.alignment,\r
 719                                    HistoryItem.HIDE));\r
 720 \r
 721     //This is to maintain viewport position on first residue\r
 722     //of first sequence\r
 723     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 724     int startRes = seq.findPosition(viewport.startRes);\r
 725 \r
 726     viewport.getAlignment().removeGaps();\r
 727 \r
 728     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 729 \r
 730     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 731   }\r
 732 \r
 733   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 734   {\r
 735     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
 736                                    HistoryItem.HIDE));\r
 737 \r
 738     //This is to maintain viewport position on first residue\r
 739     //of first sequence\r
 740     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 741     int startRes = seq.findPosition(viewport.startRes);\r
 742 \r
 743     SequenceI current;\r
 744     int jSize;\r
 745 \r
 746     Vector seqs=null;\r
 747 \r
 748     int start=0, end = viewport.alignment.getWidth();\r
 749 \r
 750     if (viewport.getSelectionGroup() != null\r
 751         && viewport.getSelectionGroup().sequences != null\r
 752         && viewport.getSelectionGroup().sequences.size()>0)\r
 753     {\r
 754       seqs = viewport.getSelectionGroup().sequences;\r
 755       start = viewport.getSelectionGroup().getStartRes();\r
 756       end = viewport.getSelectionGroup().getEndRes()+1;\r
 757     }\r
 758     else\r
 759       seqs = viewport.alignment.getSequences();\r
 760 \r
 761     for (int i = 0; i < seqs.size(); i++)\r
 762     {\r
 763       current = (SequenceI) seqs.elementAt(i);\r
 764       jSize = current.getLength();\r
 765 \r
 766       // Removing a range is much quicker than removing gaps\r
 767       // one by one for long sequences\r
 768       int j = start;\r
 769       int rangeStart=-1, rangeEnd=-1;\r
 770 \r
 771       do\r
 772       {\r
 773         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 774         {\r
 775           if(rangeStart==-1)\r
 776            {\r
 777              rangeStart = j;\r
 778              rangeEnd = j+1;\r
 779            }\r
 780            else\r
 781            {\r
 782              rangeEnd++;\r
 783            }\r
 784            j++;\r
 785         }\r
 786         else\r
 787         {\r
 788           if(rangeStart>-1)\r
 789           {\r
 790             current.deleteChars(rangeStart, rangeEnd);\r
 791             j-=rangeEnd-rangeStart;\r
 792             jSize-=rangeEnd-rangeStart;\r
 793             rangeStart = -1;\r
 794             rangeEnd = -1;\r
 795           }\r
 796           else\r
 797             j++;\r
 798         }\r
 799       }\r
 800       while (j < end && j < jSize);\r
 801       if(rangeStart>-1)\r
 802       {\r
 803        current.deleteChars(rangeStart, rangeEnd);\r
 804       }\r
 805     }\r
 806     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 807     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 808   }\r
 809 \r
 810   public void alignmentChanged()\r
 811   {\r
 812     viewport.updateConsensus();\r
 813     viewport.updateConservation ();\r
 814     resetAllColourSchemes();\r
 815     if(alignPanel.overviewPanel!=null)\r
 816       alignPanel.overviewPanel.updateOverviewImage();\r
 817     alignPanel.repaint();\r
 818   }\r
 819 \r
 820   void resetAllColourSchemes()\r
 821   {\r
 822     ColourSchemeI cs = viewport.globalColourScheme;\r
 823     if(cs!=null)\r
 824     {\r
 825       if (cs instanceof ClustalxColourScheme)\r
 826       {\r
 827         ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
 828             resetClustalX(viewport.alignment.getSequences(),\r
 829                           viewport.alignment.getWidth());\r
 830       }\r
 831 \r
 832       cs.setConsensus(viewport.vconsensus);\r
 833       if (cs.conservationApplied())\r
 834       {\r
 835         Alignment al = (Alignment) viewport.alignment;\r
 836         Conservation c = new Conservation("All",\r
 837                                           ResidueProperties.propHash, 3,\r
 838                                           al.getSequences(), 0,\r
 839                                           al.getWidth() - 1);\r
 840         c.calculate();\r
 841         c.verdict(false, viewport.ConsPercGaps);\r
 842 \r
 843         cs.setConservation(c);\r
 844       }\r
 845     }\r
 846 \r
 847     int s, sSize = viewport.alignment.getGroups().size();\r
 848     for(s=0; s<sSize; s++)\r
 849     {\r
 850       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
 851       if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
 852       {\r
 853         ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
 854       }\r
 855       sg.recalcConservation();\r
 856     }\r
 857   }\r
 858 \r
 859 \r
 860 \r
 861   public void findMenuItem_actionPerformed(ActionEvent e)\r
 862   {\r
 863     new Finder(alignPanel);\r
 864   }\r
 865 \r
 866   public void font_actionPerformed(ActionEvent e)\r
 867   {\r
 868     new FontChooser(alignPanel);\r
 869   }\r
 870 \r
 871   public void dbref_actionPerformed(ItemEvent e)\r
 872   {\r
 873     viewport.showDBPrefix = dbref.getState();\r
 874     alignPanel.fontChanged();\r
 875     alignPanel.repaint();\r
 876   }\r
 877 \r
 878   public void seqLimits_itemStateChanged(ItemEvent e)\r
 879   {\r
 880     viewport.setShowJVSuffix(seqLimits.getState());\r
 881     alignPanel.fontChanged();\r
 882     alignPanel.repaint();\r
 883   }\r
 884 \r
 885 \r
 886   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 887   {\r
 888     viewport.setColourText(colourTextMenuItem.getState());\r
 889     alignPanel.repaint();\r
 890   }\r
 891 \r
 892   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 893   {\r
 894     viewport.setWrapAlignment(wrapMenuItem.getState());\r
 895     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
 896     scaleAbove.setEnabled(wrapMenuItem.getState());\r
 897     scaleLeft.setEnabled(wrapMenuItem.getState());\r
 898     scaleRight.setEnabled(wrapMenuItem.getState());\r
 899     alignPanel.repaint();\r
 900   }\r
 901 \r
 902   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 903   {\r
 904     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 905     alignPanel.repaint();\r
 906   }\r
 907 \r
 908   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 909   {\r
 910     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 911     alignPanel.repaint();\r
 912   }\r
 913 \r
 914   protected void scaleRight_actionPerformed(ActionEvent e)\r
 915   {\r
 916     viewport.setScaleRightWrapped(scaleRight.getState());\r
 917     alignPanel.repaint();\r
 918   }\r
 919 \r
 920   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 921   {\r
 922     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
 923     alignPanel.repaint();\r
 924   }\r
 925 \r
 926   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 927   {\r
 928     viewport.setShowText(viewTextMenuItem.getState());\r
 929     alignPanel.repaint();\r
 930   }\r
 931 \r
 932   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 933   {\r
 934     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 935     alignPanel.repaint();\r
 936   }\r
 937 \r
 938   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 939   {\r
 940     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
 941     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
 942   }\r
 943 \r
 944   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 945   {\r
 946     if (alignPanel.overviewPanel != null)\r
 947     {\r
 948       return;\r
 949     }\r
 950 \r
 951     Frame frame = new Frame();\r
 952     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 953     frame.add(overview);\r
 954     // +50 must allow for applet frame window\r
 955     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
 956                                      overview.preferredSize().width,\r
 957                                      overview.preferredSize().height + 50);\r
 958 \r
 959     frame.pack();\r
 960     frame.addWindowListener(new WindowAdapter()\r
 961     {\r
 962       public void windowClosing(WindowEvent e)\r
 963       {\r
 964         alignPanel.setOverviewPanel(null);\r
 965       };\r
 966     });\r
 967 \r
 968     alignPanel.setOverviewPanel(overview);\r
 969 \r
 970   }\r
 971 \r
 972   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 973   {\r
 974     changeColour(null);\r
 975   }\r
 976 \r
 977   public void clustalColour_actionPerformed(ActionEvent e)\r
 978   {\r
 979     abovePIDThreshold.setState(false);\r
 980     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
 981                                           viewport.alignment.getWidth()));\r
 982   }\r
 983 \r
 984   public void zappoColour_actionPerformed(ActionEvent e)\r
 985   {\r
 986     changeColour(new ZappoColourScheme());\r
 987   }\r
 988 \r
 989   public void taylorColour_actionPerformed(ActionEvent e)\r
 990   {\r
 991     changeColour(new TaylorColourScheme());\r
 992   }\r
 993 \r
 994   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 995   {\r
 996     changeColour(new HydrophobicColourScheme());\r
 997   }\r
 998 \r
 999   public void helixColour_actionPerformed(ActionEvent e)\r
1000   {\r
1001     changeColour(new HelixColourScheme());\r
1002   }\r
1003 \r
1004   public void strandColour_actionPerformed(ActionEvent e)\r
1005   {\r
1006     changeColour(new StrandColourScheme());\r
1007   }\r
1008 \r
1009   public void turnColour_actionPerformed(ActionEvent e)\r
1010   {\r
1011     changeColour(new TurnColourScheme());\r
1012   }\r
1013 \r
1014   public void buriedColour_actionPerformed(ActionEvent e)\r
1015   {\r
1016     changeColour(new BuriedColourScheme());\r
1017   }\r
1018 \r
1019   public void nucleotideColour_actionPerformed(ActionEvent e)\r
1020   {\r
1021     changeColour(new NucleotideColourScheme());\r
1022   }\r
1023 \r
1024   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1025   {\r
1026     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
1027   }\r
1028 \r
1029   void changeColour(ColourSchemeI cs)\r
1030   {\r
1031     int threshold = 0;\r
1032 \r
1033     if(cs!=null)\r
1034     {\r
1035       if (viewport.getAbovePIDThreshold())\r
1036       {\r
1037         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
1038 \r
1039         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1040 \r
1041         viewport.setGlobalColourScheme(cs);\r
1042       }\r
1043       else\r
1044       {\r
1045         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1046       }\r
1047 \r
1048       if (viewport.getConservationSelected())\r
1049       {\r
1050 \r
1051         Alignment al = (Alignment) viewport.alignment;\r
1052         Conservation c = new Conservation("All",\r
1053                                           ResidueProperties.propHash, 3,\r
1054                                           al.getSequences(), 0,\r
1055                                           al.getWidth() - 1);\r
1056 \r
1057         c.calculate();\r
1058         c.verdict(false, viewport.ConsPercGaps);\r
1059 \r
1060         cs.setConservation(c);\r
1061 \r
1062         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
1063             "Background"));\r
1064 \r
1065       }\r
1066       else\r
1067       {\r
1068         cs.setConservation(null);\r
1069       }\r
1070 \r
1071       cs.setConsensus(viewport.vconsensus);\r
1072 \r
1073     }\r
1074     viewport.setGlobalColourScheme(cs);\r
1075 \r
1076     if (viewport.getColourAppliesToAllGroups())\r
1077     {\r
1078       Vector groups = viewport.alignment.getGroups();\r
1079       for (int i = 0; i < groups.size(); i++)\r
1080       {\r
1081         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1082 \r
1083         if(cs==null)\r
1084         {\r
1085           sg.cs = null;\r
1086           continue;\r
1087         }\r
1088         if (cs instanceof ClustalxColourScheme)\r
1089         {\r
1090           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
1091         }\r
1092         else\r
1093         {\r
1094           try\r
1095           {\r
1096             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
1097           }\r
1098           catch (Exception ex)\r
1099           {\r
1100             ex.printStackTrace();\r
1101             sg.cs = cs;\r
1102           }\r
1103         }\r
1104 \r
1105         if (viewport.getAbovePIDThreshold()\r
1106             || cs instanceof PIDColourScheme\r
1107             || cs instanceof Blosum62ColourScheme)\r
1108         {\r
1109           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1110           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
1111         }\r
1112         else\r
1113           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1114 \r
1115         if (viewport.getConservationSelected())\r
1116         {\r
1117           Conservation c = new Conservation("Group",\r
1118                                             ResidueProperties.propHash, 3,\r
1119                                             sg.sequences, 0,\r
1120                                             viewport.alignment.getWidth() - 1);\r
1121           c.calculate();\r
1122           c.verdict(false, viewport.ConsPercGaps);\r
1123           sg.cs.setConservation(c);\r
1124         }\r
1125         else\r
1126         {\r
1127           sg.cs.setConservation(null);\r
1128           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1129         }\r
1130 \r
1131       }\r
1132     }\r
1133 \r
1134 \r
1135     if (alignPanel.getOverviewPanel() != null)\r
1136     {\r
1137       alignPanel.getOverviewPanel().updateOverviewImage();\r
1138     }\r
1139 \r
1140     alignPanel.repaint();\r
1141   }\r
1142 \r
1143 \r
1144 \r
1145   protected void modifyPID_actionPerformed(ActionEvent e)\r
1146   {\r
1147     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
1148     {\r
1149       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
1150                                      "Background");\r
1151       SliderPanel.showPIDSlider();\r
1152     }\r
1153   }\r
1154 \r
1155   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1156   {\r
1157     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
1158     {\r
1159       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
1160                                         "Background");\r
1161       SliderPanel.showConservationSlider();\r
1162     }\r
1163   }\r
1164 \r
1165   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1166   {\r
1167     viewport.setConservationSelected(conservationMenuItem.getState());\r
1168 \r
1169     viewport.setAbovePIDThreshold(false);\r
1170     abovePIDThreshold.setState(false);\r
1171 \r
1172     changeColour(viewport.getGlobalColourScheme());\r
1173 \r
1174     modifyConservation_actionPerformed(null);\r
1175   }\r
1176 \r
1177   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1178   {\r
1179     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
1180 \r
1181     conservationMenuItem.setState(false);\r
1182     viewport.setConservationSelected(false);\r
1183 \r
1184     changeColour(viewport.getGlobalColourScheme());\r
1185 \r
1186     modifyPID_actionPerformed(null);\r
1187   }\r
1188 \r
1189   public void userDefinedColour_actionPerformed(ActionEvent e)\r
1190   {\r
1191     new UserDefinedColours(alignPanel, null);\r
1192   }\r
1193 \r
1194   public void PIDColour_actionPerformed(ActionEvent e)\r
1195   {\r
1196     changeColour(new PIDColourScheme());\r
1197   }\r
1198 \r
1199   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1200   {\r
1201     changeColour(new Blosum62ColourScheme());\r
1202   }\r
1203 \r
1204   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1205   {\r
1206     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1207                                    HistoryItem.SORT));\r
1208     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1209                               viewport.getAlignment().getSequenceAt(0));\r
1210     alignPanel.repaint();\r
1211   }\r
1212 \r
1213   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1214   {\r
1215     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1216                                    HistoryItem.SORT));\r
1217     AlignmentSorter.sortByID(viewport.getAlignment(), viewport.showDBPrefix);\r
1218     alignPanel.repaint();\r
1219   }\r
1220 \r
1221   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1222   {\r
1223     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1224                                    HistoryItem.SORT));\r
1225     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1226     alignPanel.repaint();\r
1227 \r
1228   }\r
1229 \r
1230   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1231   {\r
1232     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
1233     Frame frame = new Frame();\r
1234     frame.add(sp);\r
1235     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
1236                                      400, 120);\r
1237 \r
1238   }\r
1239 \r
1240   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1241   {\r
1242     if (viewport.getSelectionGroup().getSize() > 1)\r
1243     {\r
1244       Frame frame = new Frame();\r
1245       frame.add(new PairwiseAlignPanel(alignPanel));\r
1246       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1247     }\r
1248   }\r
1249 \r
1250   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
1251   {\r
1252     //are the sequences aligned?\r
1253     if (!viewport.alignment.isAligned())\r
1254     {\r
1255       SequenceI current;\r
1256       int Width = viewport.getAlignment().getWidth();\r
1257 \r
1258       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1259            i++)\r
1260       {\r
1261         current = viewport.getAlignment().getSequenceAt(i);\r
1262 \r
1263         if (current.getLength() < Width)\r
1264         {\r
1265           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1266         }\r
1267       }\r
1268       alignPanel.repaint();\r
1269     }\r
1270 \r
1271     if ( (viewport.getSelectionGroup() != null &&\r
1272           viewport.getSelectionGroup().getSize() < 4 &&\r
1273           viewport.getSelectionGroup().getSize() > 0)\r
1274         || viewport.getAlignment().getHeight() < 4)\r
1275     {\r
1276       return;\r
1277     }\r
1278 \r
1279     try\r
1280     {\r
1281       new PCAPanel(viewport);\r
1282     }\r
1283     catch (java.lang.OutOfMemoryError ex)\r
1284     {\r
1285     }\r
1286 \r
1287   }\r
1288 \r
1289   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1290   {\r
1291     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1292   }\r
1293 \r
1294   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1295   {\r
1296     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1297   }\r
1298 \r
1299   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1300   {\r
1301     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1302   }\r
1303 \r
1304   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1305   {\r
1306     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1307   }\r
1308 \r
1309   void NewTreePanel(String type, String pwType, String title)\r
1310   {\r
1311     //are the sequences aligned?\r
1312     if (!viewport.alignment.isAligned())\r
1313     {\r
1314       SequenceI current;\r
1315       int Width = viewport.getAlignment().getWidth();\r
1316 \r
1317       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1318            i++)\r
1319       {\r
1320         current = viewport.getAlignment().getSequenceAt(i);\r
1321 \r
1322         if (current.getLength() < Width)\r
1323         {\r
1324           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1325         }\r
1326       }\r
1327       alignPanel.repaint();\r
1328 \r
1329     }\r
1330 \r
1331     final TreePanel tp;\r
1332     if (viewport.getSelectionGroup() != null &&\r
1333         viewport.getSelectionGroup().getSize() > 3)\r
1334     {\r
1335       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1336                          pwType,\r
1337                          0, viewport.alignment.getWidth());\r
1338     }\r
1339     else\r
1340     {\r
1341       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1342                          type, pwType, 0, viewport.alignment.getWidth());\r
1343     }\r
1344 \r
1345     addTreeMenuItem(tp, title);\r
1346 \r
1347     jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1348   }\r
1349 \r
1350   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1351   {\r
1352     final MenuItem item = new MenuItem(title);\r
1353     sortByTreeMenu.add(item);\r
1354     item.addActionListener(new java.awt.event.ActionListener()\r
1355     {\r
1356       public void actionPerformed(ActionEvent e)\r
1357       {\r
1358         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1359                                        HistoryItem.SORT));\r
1360         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1361         alignPanel.repaint();\r
1362       }\r
1363     });\r
1364 \r
1365     treePanel.addWindowListener(new WindowAdapter()\r
1366     {\r
1367       public void windowClosing(WindowEvent e)\r
1368       {\r
1369         sortByTreeMenu.remove(item);\r
1370       };\r
1371     });\r
1372   }\r
1373 \r
1374   protected void documentation_actionPerformed(ActionEvent e)\r
1375   {\r
1376     showURL("http://www.jalview.org/help.html");\r
1377   }\r
1378 \r
1379   protected void about_actionPerformed(ActionEvent e)\r
1380   {\r
1381 \r
1382     class AboutPanel extends Canvas\r
1383     {\r
1384       String version;\r
1385       public AboutPanel(String version)\r
1386       { this.version = version; }\r
1387 \r
1388       public void paint(Graphics g)\r
1389       {\r
1390         g.setColor(Color.white);\r
1391         g.fillRect(0, 0, getSize().width, getSize().height);\r
1392         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1393         FontMetrics fm = g.getFontMetrics();\r
1394         int fh = fm.getHeight();\r
1395         int y = 5, x = 7;\r
1396         g.setColor(Color.black);\r
1397         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1398         g.drawString("Jalview - Release "+version, 200, y += fh);\r
1399         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1400         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1401                      x, y += fh * 2);\r
1402         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1403                      x, y += fh);\r
1404         g.drawString(\r
1405             "For any issues relating to Jalview, email help@jalview.org", x,\r
1406             y += fh);\r
1407         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1408         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1409                      x, y += fh);\r
1410         g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);\r
1411       }\r
1412     }\r
1413 \r
1414     String version = "test";\r
1415     java.net.URL url = getClass().getResource("/.build_properties");\r
1416     if (url != null)\r
1417     {\r
1418       try\r
1419       {\r
1420         BufferedReader reader = new BufferedReader(new InputStreamReader(\r
1421             url.openStream()));\r
1422         String line;\r
1423         while ( (line = reader.readLine()) != null)\r
1424         {\r
1425           if (line.indexOf("VERSION") > -1)\r
1426           {\r
1427             version = line.substring(line.indexOf("=") + 1);\r
1428           }\r
1429         }\r
1430       }\r
1431       catch (Exception ex)\r
1432       {\r
1433         ex.printStackTrace();\r
1434       }\r
1435     }\r
1436 \r
1437 \r
1438     Frame frame = new Frame();\r
1439     frame.add(new AboutPanel(version));\r
1440     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1441 \r
1442   }\r
1443 \r
1444   /**\r
1445    * Displays the given URL in a new browser window\r
1446    *\r
1447    * @param url URL to display in browser window.\r
1448    * <br>New window will be named "HELP_WINDOW"\r
1449    */\r
1450   public void showURL(String url)\r
1451   {\r
1452     showURL(url, "HELP");\r
1453   }\r
1454 \r
1455   public void showURL(String url, String target)\r
1456   {\r
1457     if (applet == null)\r
1458     {\r
1459       System.out.println("Not running as applet - no browser available.");\r
1460     }\r
1461     else\r
1462     {\r
1463       try\r
1464       {\r
1465         applet.getAppletContext().showDocument(new java.net.URL(url),\r
1466                                                target);\r
1467       }\r
1468       catch (Exception ex)\r
1469       {\r
1470         ex.printStackTrace();\r
1471       }\r
1472     }\r
1473   }\r
1474 \r
1475 \r
1476   //////////////////////////////////////////////////////////////////////////////////\r
1477   //JBuilder Graphics here\r
1478 \r
1479     protected MenuBar alignFrameMenuBar = new MenuBar();\r
1480     protected Menu fileMenu = new Menu();\r
1481     protected MenuItem closeMenuItem = new MenuItem();\r
1482     protected Menu editMenu = new Menu();\r
1483     protected Menu viewMenu = new Menu();\r
1484     protected Menu colourMenu = new Menu();\r
1485     protected Menu calculateMenu = new Menu();\r
1486     protected MenuItem selectAllSequenceMenuItem = new MenuItem();\r
1487     protected MenuItem deselectAllSequenceMenuItem = new MenuItem();\r
1488     protected MenuItem invertSequenceMenuItem = new MenuItem();\r
1489     protected MenuItem remove2LeftMenuItem = new MenuItem();\r
1490     protected MenuItem remove2RightMenuItem = new MenuItem();\r
1491     protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
1492     protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
1493     protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
1494     protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
1495     protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
1496     protected MenuItem sortIDMenuItem = new MenuItem();\r
1497     protected MenuItem sortGroupMenuItem = new MenuItem();\r
1498     protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
1499     protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
1500     protected MenuItem PCAMenuItem = new MenuItem();\r
1501     protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
1502     protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
1503     BorderLayout borderLayout1 = new BorderLayout();\r
1504     public Label statusBar = new Label();\r
1505     protected Menu outputTextboxMenu = new Menu();\r
1506     protected MenuItem clustalColour = new MenuItem();\r
1507     protected MenuItem zappoColour = new MenuItem();\r
1508     protected MenuItem taylorColour = new MenuItem();\r
1509     protected MenuItem hydrophobicityColour = new MenuItem();\r
1510     protected MenuItem helixColour = new MenuItem();\r
1511     protected MenuItem strandColour = new MenuItem();\r
1512     protected MenuItem turnColour = new MenuItem();\r
1513     protected MenuItem buriedColour = new MenuItem();\r
1514     protected MenuItem userDefinedColour = new MenuItem();\r
1515     protected MenuItem PIDColour = new MenuItem();\r
1516     protected MenuItem BLOSUM62Colour = new MenuItem();\r
1517     MenuItem njTreeBlosumMenuItem = new MenuItem();\r
1518     MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
1519     protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
1520     protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
1521     MenuItem overviewMenuItem = new MenuItem();\r
1522     protected MenuItem undoMenuItem = new MenuItem();\r
1523     protected MenuItem redoMenuItem = new MenuItem();\r
1524     protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
1525     MenuItem noColourmenuItem = new MenuItem();\r
1526     protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
1527     protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
1528     MenuItem findMenuItem = new MenuItem();\r
1529     Menu searchMenu = new Menu();\r
1530     protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
1531     protected MenuItem nucleotideColour = new MenuItem();\r
1532     MenuItem deleteGroups = new MenuItem();\r
1533     MenuItem delete = new MenuItem();\r
1534     MenuItem copy = new MenuItem();\r
1535     MenuItem cut = new MenuItem();\r
1536     Menu Menu1 = new Menu();\r
1537     MenuItem pasteNew = new MenuItem();\r
1538     MenuItem pasteThis = new MenuItem();\r
1539     protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
1540     protected MenuItem font = new MenuItem();\r
1541     protected CheckboxMenuItem dbref = new CheckboxMenuItem();\r
1542     protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
1543     protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
1544     protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
1545     MenuItem modifyPID = new MenuItem();\r
1546     MenuItem modifyConservation = new MenuItem();\r
1547     protected Menu sortByTreeMenu = new Menu();\r
1548     Menu sort = new Menu();\r
1549     Menu calculate = new Menu();\r
1550     MenuItem inputText = new MenuItem();\r
1551     Menu helpMenu = new Menu();\r
1552     MenuItem documentation = new MenuItem();\r
1553     MenuItem about = new MenuItem();\r
1554     protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
1555 \r
1556     private void jbInit() throws Exception {\r
1557 \r
1558       setMenuBar(alignFrameMenuBar);\r
1559 \r
1560       MenuItem item;\r
1561 \r
1562       // dynamically fill save as menu with available formats\r
1563       for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)\r
1564       {\r
1565 \r
1566         item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.\r
1567                             elementAt(\r
1568                                 i));\r
1569         item.addActionListener(new java.awt.event.ActionListener()\r
1570         {\r
1571           public void actionPerformed(ActionEvent e)\r
1572           {\r
1573             outputText_actionPerformed(e);\r
1574           }\r
1575         });\r
1576 \r
1577         outputTextboxMenu.add(item);\r
1578       }\r
1579 \r
1580 \r
1581         fileMenu.setLabel("File");\r
1582         closeMenuItem.setLabel("Close");\r
1583         closeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
1584                 public void actionPerformed(ActionEvent e) {\r
1585                     closeMenuItem_actionPerformed(e);\r
1586                 }\r
1587             });\r
1588         editMenu.setLabel("Edit");\r
1589         viewMenu.setLabel("View");\r
1590         colourMenu.setLabel("Colour");\r
1591         calculateMenu.setLabel("Calculate");\r
1592         selectAllSequenceMenuItem.setLabel("Select all");\r
1593         selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
1594                 public void actionPerformed(ActionEvent e) {\r
1595                     selectAllSequenceMenuItem_actionPerformed(e);\r
1596                 }\r
1597             });\r
1598         deselectAllSequenceMenuItem.setLabel("Deselect All");\r
1599         deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
1600                 public void actionPerformed(ActionEvent e) {\r
1601                     deselectAllSequenceMenuItem_actionPerformed(e);\r
1602                 }\r
1603             });\r
1604         invertSequenceMenuItem.setLabel("Invert Selection");\r
1605         invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
1606                 public void actionPerformed(ActionEvent e) {\r
1607                     invertSequenceMenuItem_actionPerformed(e);\r
1608                 }\r
1609             });\r
1610         remove2LeftMenuItem.setLabel("Remove Left");\r
1611         remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
1612                 public void actionPerformed(ActionEvent e) {\r
1613                     remove2LeftMenuItem_actionPerformed(e);\r
1614                 }\r
1615             });\r
1616         remove2RightMenuItem.setLabel("Remove Right");\r
1617         remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
1618                 public void actionPerformed(ActionEvent e) {\r
1619                     remove2RightMenuItem_actionPerformed(e);\r
1620                 }\r
1621             });\r
1622         removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
1623         removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
1624                 public void actionPerformed(ActionEvent e) {\r
1625                     removeGappedColumnMenuItem_actionPerformed(e);\r
1626                 }\r
1627             });\r
1628         removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
1629         removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
1630                 public void actionPerformed(ActionEvent e) {\r
1631                     removeAllGapsMenuItem_actionPerformed(e);\r
1632                 }\r
1633             });\r
1634         viewBoxesMenuItem.setLabel("Boxes");\r
1635         viewBoxesMenuItem.setState(true);\r
1636         viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
1637                 public void itemStateChanged(ItemEvent e) {\r
1638                     viewBoxesMenuItem_actionPerformed(null);\r
1639                 }\r
1640             });\r
1641         viewTextMenuItem.setLabel("Text");\r
1642         viewTextMenuItem.setState(true);\r
1643         viewTextMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
1644                 public void itemStateChanged(ItemEvent e) {\r
1645                     viewTextMenuItem_actionPerformed(null);\r
1646                 }\r
1647             });\r
1648         sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
1649         sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
1650                 public void actionPerformed(ActionEvent e) {\r
1651                     sortPairwiseMenuItem_actionPerformed(e);\r
1652                 }\r
1653             });\r
1654         sortIDMenuItem.setLabel("by ID");\r
1655         sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
1656                 public void actionPerformed(ActionEvent e) {\r
1657                     sortIDMenuItem_actionPerformed(e);\r
1658                 }\r
1659             });\r
1660         sortGroupMenuItem.setLabel("by Group");\r
1661         sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
1662                 public void actionPerformed(ActionEvent e) {\r
1663                     sortGroupMenuItem_actionPerformed(e);\r
1664                 }\r
1665             });\r
1666         removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
1667         removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
1668                 public void actionPerformed(ActionEvent e) {\r
1669                     removeRedundancyMenuItem_actionPerformed(e);\r
1670                 }\r
1671             });\r
1672         pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
1673         pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
1674                 public void actionPerformed(ActionEvent e) {\r
1675                     pairwiseAlignmentMenuItem_actionPerformed(e);\r
1676                 }\r
1677             });\r
1678         PCAMenuItem.setLabel("Principal Component Analysis");\r
1679         PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
1680                 public void actionPerformed(ActionEvent e) {\r
1681                     PCAMenuItem_actionPerformed(e);\r
1682                 }\r
1683             });\r
1684         averageDistanceTreeMenuItem.setLabel(\r
1685             "Average Distance Using % Identity");\r
1686         averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
1687                 public void actionPerformed(ActionEvent e) {\r
1688                     averageDistanceTreeMenuItem_actionPerformed(e);\r
1689                 }\r
1690             });\r
1691         neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
1692         neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
1693                 public void actionPerformed(ActionEvent e) {\r
1694                     neighbourTreeMenuItem_actionPerformed(e);\r
1695                 }\r
1696             });\r
1697         alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
1698         statusBar.setBackground(Color.white);\r
1699         statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
1700         statusBar.setText("Status bar");\r
1701         outputTextboxMenu.setLabel("Output to Textbox");\r
1702         clustalColour.setLabel("Clustalx");\r
1703 \r
1704         clustalColour.addActionListener(new java.awt.event.ActionListener() {\r
1705                 public void actionPerformed(ActionEvent e) {\r
1706                     clustalColour_actionPerformed(e);\r
1707                 }\r
1708             });\r
1709         zappoColour.setLabel("Zappo");\r
1710         zappoColour.addActionListener(new java.awt.event.ActionListener() {\r
1711                 public void actionPerformed(ActionEvent e) {\r
1712                     zappoColour_actionPerformed(e);\r
1713                 }\r
1714             });\r
1715         taylorColour.setLabel("Taylor");\r
1716         taylorColour.addActionListener(new java.awt.event.ActionListener() {\r
1717                 public void actionPerformed(ActionEvent e) {\r
1718                     taylorColour_actionPerformed(e);\r
1719                 }\r
1720             });\r
1721         hydrophobicityColour.setLabel("Hydrophobicity");\r
1722         hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {\r
1723                 public void actionPerformed(ActionEvent e) {\r
1724                     hydrophobicityColour_actionPerformed(e);\r
1725                 }\r
1726             });\r
1727         helixColour.setLabel("Helix Propensity");\r
1728         helixColour.addActionListener(new java.awt.event.ActionListener() {\r
1729                 public void actionPerformed(ActionEvent e) {\r
1730                     helixColour_actionPerformed(e);\r
1731                 }\r
1732             });\r
1733         strandColour.setLabel("Strand Propensity");\r
1734         strandColour.addActionListener(new java.awt.event.ActionListener() {\r
1735                 public void actionPerformed(ActionEvent e) {\r
1736                     strandColour_actionPerformed(e);\r
1737                 }\r
1738             });\r
1739         turnColour.setLabel("Turn Propensity");\r
1740         turnColour.addActionListener(new java.awt.event.ActionListener() {\r
1741                 public void actionPerformed(ActionEvent e) {\r
1742                     turnColour_actionPerformed(e);\r
1743                 }\r
1744             });\r
1745         buriedColour.setLabel("Buried Index");\r
1746         buriedColour.addActionListener(new java.awt.event.ActionListener() {\r
1747                 public void actionPerformed(ActionEvent e) {\r
1748                     buriedColour_actionPerformed(e);\r
1749                 }\r
1750             });\r
1751         userDefinedColour.setLabel("User Defined...");\r
1752         userDefinedColour.addActionListener(new java.awt.event.ActionListener() {\r
1753                 public void actionPerformed(ActionEvent e) {\r
1754                     userDefinedColour_actionPerformed(e);\r
1755                 }\r
1756             });\r
1757         PIDColour.setLabel("Percentage Identity");\r
1758         PIDColour.addActionListener(new java.awt.event.ActionListener() {\r
1759                 public void actionPerformed(ActionEvent e) {\r
1760                     PIDColour_actionPerformed(e);\r
1761                 }\r
1762             });\r
1763         BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
1764         BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {\r
1765                 public void actionPerformed(ActionEvent e) {\r
1766                     BLOSUM62Colour_actionPerformed(e);\r
1767                 }\r
1768             });\r
1769         avDistanceTreeBlosumMenuItem.setLabel(\r
1770             "Average Distance Using BLOSUM62");\r
1771         avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
1772                 public void actionPerformed(ActionEvent e) {\r
1773                     avTreeBlosumMenuItem_actionPerformed(e);\r
1774                 }\r
1775             });\r
1776         njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
1777         njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
1778                 public void actionPerformed(ActionEvent e) {\r
1779                     njTreeBlosumMenuItem_actionPerformed(e);\r
1780                 }\r
1781             });\r
1782         annotationPanelMenuItem.setActionCommand("");\r
1783         annotationPanelMenuItem.setState(true);\r
1784         annotationPanelMenuItem.setLabel("Show Annotations");\r
1785         annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
1786                 public void itemStateChanged(ItemEvent e) {\r
1787                     annotationPanelMenuItem_actionPerformed(null);\r
1788                 }\r
1789             });\r
1790         colourTextMenuItem.setLabel("Colour Text");\r
1791         colourTextMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
1792                 public void itemStateChanged(ItemEvent e) {\r
1793                     colourTextMenuItem_actionPerformed(null);\r
1794                 }\r
1795             });\r
1796         overviewMenuItem.setLabel("Overview Window");\r
1797         overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
1798                 public void actionPerformed(ActionEvent e) {\r
1799                     overviewMenuItem_actionPerformed(e);\r
1800                 }\r
1801             });\r
1802         undoMenuItem.setEnabled(false);\r
1803         undoMenuItem.setLabel("Undo");\r
1804         undoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
1805                 public void actionPerformed(ActionEvent e) {\r
1806                     undoMenuItem_actionPerformed(e);\r
1807                 }\r
1808             });\r
1809         redoMenuItem.setEnabled(false);\r
1810         redoMenuItem.setLabel("Redo");\r
1811         redoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
1812                 public void actionPerformed(ActionEvent e) {\r
1813                     redoMenuItem_actionPerformed(e);\r
1814                 }\r
1815             });\r
1816         conservationMenuItem.setLabel("by Conservation");\r
1817         conservationMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
1818                 public void itemStateChanged(ItemEvent e) {\r
1819                     conservationMenuItem_actionPerformed(null);\r
1820                 }\r
1821             });\r
1822         noColourmenuItem.setLabel("None");\r
1823         noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {\r
1824                 public void actionPerformed(ActionEvent e) {\r
1825                     noColourmenuItem_actionPerformed(e);\r
1826                 }\r
1827             });\r
1828         wrapMenuItem.setLabel("Wrap");\r
1829         wrapMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
1830                 public void itemStateChanged(ItemEvent e) {\r
1831                     wrapMenuItem_actionPerformed(null);\r
1832                 }\r
1833             });\r
1834         renderGapsMenuItem.setLabel("Show Gaps");\r
1835         renderGapsMenuItem.setState(true);\r
1836         renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
1837                 public void itemStateChanged(ItemEvent e) {\r
1838                     renderGapsMenuItem_actionPerformed(null);\r
1839                 }\r
1840             });\r
1841         findMenuItem.setLabel("Find...");\r
1842         findMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
1843                 public void actionPerformed(ActionEvent e) {\r
1844                     findMenuItem_actionPerformed(e);\r
1845                 }\r
1846             });\r
1847         searchMenu.setLabel("Search");\r
1848 \r
1849         abovePIDThreshold.setLabel("Above Identity Threshold");\r
1850         abovePIDThreshold.addItemListener(new java.awt.event.ItemListener() {\r
1851                 public void itemStateChanged(ItemEvent e) {\r
1852                     abovePIDThreshold_actionPerformed(null);\r
1853                 }\r
1854             });\r
1855         nucleotideColour.setLabel("Nucleotide");\r
1856         nucleotideColour.addActionListener(new java.awt.event.ActionListener() {\r
1857                 public void actionPerformed(ActionEvent e) {\r
1858                     nucleotideColour_actionPerformed(e);\r
1859                 }\r
1860             });\r
1861         deleteGroups.setLabel("Undefine Groups");\r
1862         deleteGroups.addActionListener(new java.awt.event.ActionListener() {\r
1863                 public void actionPerformed(ActionEvent e) {\r
1864                     deleteGroups_actionPerformed(e);\r
1865                 }\r
1866             });\r
1867         copy.setLabel("Copy");\r
1868         copy.addActionListener(new java.awt.event.ActionListener() {\r
1869                 public void actionPerformed(ActionEvent e) {\r
1870                     copy_actionPerformed(e);\r
1871                 }\r
1872             });\r
1873         cut.setLabel("Cut");\r
1874         cut.addActionListener(new java.awt.event.ActionListener() {\r
1875                 public void actionPerformed(ActionEvent e) {\r
1876                     cut_actionPerformed(e);\r
1877                 }\r
1878             });\r
1879         delete.setLabel("Delete");\r
1880         delete.addActionListener(new java.awt.event.ActionListener() {\r
1881                 public void actionPerformed(ActionEvent e) {\r
1882                     delete_actionPerformed(e);\r
1883                 }\r
1884             });\r
1885         Menu1.setLabel("Paste");\r
1886         pasteNew.setLabel("To New Alignment");\r
1887         pasteNew.addActionListener(new java.awt.event.ActionListener() {\r
1888                 public void actionPerformed(ActionEvent e) {\r
1889                     pasteNew_actionPerformed(e);\r
1890                 }\r
1891             });\r
1892         pasteThis.setLabel("Add To This Alignment");\r
1893         pasteThis.addActionListener(new java.awt.event.ActionListener() {\r
1894                 public void actionPerformed(ActionEvent e) {\r
1895                     pasteThis_actionPerformed(e);\r
1896                 }\r
1897             });\r
1898         applyToAllGroups.setLabel("Apply Colour To All Groups");\r
1899         applyToAllGroups.setState(true);\r
1900         applyToAllGroups.addItemListener(new java.awt.event.ItemListener() {\r
1901                 public void itemStateChanged(ItemEvent e) {\r
1902                     applyToAllGroups_actionPerformed(null);\r
1903                 }\r
1904             });\r
1905         font.setLabel("Font...");\r
1906         font.addActionListener(new java.awt.event.ActionListener() {\r
1907                 public void actionPerformed(ActionEvent e) {\r
1908                     font_actionPerformed(e);\r
1909                 }\r
1910             });\r
1911     dbref.setLabel("ShowSequence DB Refs");\r
1912     dbref.setActionCommand("");\r
1913     dbref.setState(true);\r
1914     dbref.addItemListener(new java.awt.event.ItemListener() {\r
1915                 public void itemStateChanged(ItemEvent e) {\r
1916         dbref_actionPerformed(e);\r
1917       }\r
1918             });\r
1919         scaleAbove.setLabel("Scale Above");\r
1920         scaleAbove.setState(true);\r
1921         scaleAbove.addItemListener(new java.awt.event.ItemListener() {\r
1922                 public void itemStateChanged(ItemEvent e) {\r
1923                     scaleAbove_actionPerformed(null);\r
1924                 }\r
1925             });\r
1926         scaleLeft.setEnabled(false);\r
1927         scaleLeft.setState(true);\r
1928         scaleLeft.setLabel("Scale Left");\r
1929         scaleLeft.addItemListener(new java.awt.event.ItemListener() {\r
1930                 public void itemStateChanged(ItemEvent e) {\r
1931                     scaleLeft_actionPerformed(null);\r
1932                 }\r
1933             });\r
1934         scaleRight.setEnabled(false);\r
1935         scaleRight.setState(true);\r
1936         scaleRight.setLabel("Scale Right");\r
1937         scaleRight.addItemListener(new java.awt.event.ItemListener() {\r
1938                 public void itemStateChanged(ItemEvent e) {\r
1939                     scaleRight_actionPerformed(null);\r
1940                 }\r
1941             });\r
1942         modifyPID.setLabel("Modify Identity Threshold...");\r
1943         modifyPID.addActionListener(new java.awt.event.ActionListener() {\r
1944                 public void actionPerformed(ActionEvent e) {\r
1945                     modifyPID_actionPerformed(e);\r
1946                 }\r
1947             });\r
1948         modifyConservation.setLabel("Modify Conservation Threshold...");\r
1949         modifyConservation.addActionListener(new java.awt.event.ActionListener() {\r
1950                 public void actionPerformed(ActionEvent e) {\r
1951                     modifyConservation_actionPerformed(e);\r
1952                 }\r
1953             });\r
1954         sortByTreeMenu.setLabel("By Tree Order");\r
1955         sort.setLabel("Sort");\r
1956         calculate.setLabel("Calculate Tree");\r
1957         inputText.setLabel("Input from textbox");\r
1958         inputText.addActionListener(new java.awt.event.ActionListener() {\r
1959                 public void actionPerformed(ActionEvent e) {\r
1960                     inputText_actionPerformed(e);\r
1961                 }\r
1962             });\r
1963 \r
1964         helpMenu.setLabel("Help");\r
1965         documentation.setLabel("Documentation");\r
1966         documentation.addActionListener(new java.awt.event.ActionListener() {\r
1967                 public void actionPerformed(ActionEvent e) {\r
1968                     documentation_actionPerformed(e);\r
1969                 }\r
1970             });\r
1971 \r
1972         about.setLabel("About...");\r
1973         about.addActionListener(new java.awt.event.ActionListener() {\r
1974                 public void actionPerformed(ActionEvent e) {\r
1975                     about_actionPerformed(e);\r
1976                 }\r
1977             });\r
1978           seqLimits.setState(true);\r
1979     seqLimits.setLabel("Show Sequence Limits");\r
1980     seqLimits.addItemListener(new ItemListener()\r
1981     {\r
1982       public void itemStateChanged(ItemEvent e)\r
1983       {\r
1984         seqLimits_itemStateChanged(e);\r
1985       }\r
1986     });\r
1987 \r
1988     alignFrameMenuBar.add(fileMenu);\r
1989         alignFrameMenuBar.add(editMenu);\r
1990         alignFrameMenuBar.add(searchMenu);\r
1991         alignFrameMenuBar.add(viewMenu);\r
1992         alignFrameMenuBar.add(colourMenu);\r
1993         alignFrameMenuBar.add(calculateMenu);\r
1994         alignFrameMenuBar.add(helpMenu);\r
1995         fileMenu.add(inputText);\r
1996         fileMenu.add(outputTextboxMenu);\r
1997         fileMenu.addSeparator();\r
1998         fileMenu.add(closeMenuItem);\r
1999         editMenu.add(undoMenuItem);\r
2000         editMenu.add(redoMenuItem);\r
2001         editMenu.add(cut);\r
2002         editMenu.add(copy);\r
2003         editMenu.add(Menu1);\r
2004         editMenu.add(delete);\r
2005         editMenu.addSeparator();\r
2006         editMenu.add(selectAllSequenceMenuItem);\r
2007         editMenu.add(deselectAllSequenceMenuItem);\r
2008         editMenu.add(invertSequenceMenuItem);\r
2009         editMenu.add(deleteGroups);\r
2010         editMenu.addSeparator();\r
2011         editMenu.add(remove2LeftMenuItem);\r
2012         editMenu.add(remove2RightMenuItem);\r
2013         editMenu.add(removeGappedColumnMenuItem);\r
2014         editMenu.add(removeAllGapsMenuItem);\r
2015         editMenu.add(removeRedundancyMenuItem);\r
2016         searchMenu.add(findMenuItem);\r
2017         viewMenu.add(font);\r
2018         viewMenu.addSeparator();\r
2019         viewMenu.add(dbref);\r
2020         viewMenu.add(seqLimits);\r
2021         viewMenu.addSeparator();\r
2022     viewMenu.add(wrapMenuItem);\r
2023         viewMenu.add(scaleAbove);\r
2024         viewMenu.add(scaleLeft);\r
2025         viewMenu.add(scaleRight);\r
2026         viewMenu.addSeparator();\r
2027     viewMenu.add(viewBoxesMenuItem);\r
2028         viewMenu.add(viewTextMenuItem);\r
2029         viewMenu.add(colourTextMenuItem);\r
2030         viewMenu.add(renderGapsMenuItem);\r
2031         viewMenu.add(annotationPanelMenuItem);\r
2032         viewMenu.addSeparator();\r
2033         viewMenu.add(overviewMenuItem);\r
2034         colourMenu.add(applyToAllGroups);\r
2035         colourMenu.addSeparator();\r
2036         colourMenu.add(noColourmenuItem);\r
2037         colourMenu.add(clustalColour);\r
2038         colourMenu.add(BLOSUM62Colour);\r
2039         colourMenu.add(PIDColour);\r
2040         colourMenu.add(zappoColour);\r
2041         colourMenu.add(taylorColour);\r
2042         colourMenu.add(hydrophobicityColour);\r
2043         colourMenu.add(helixColour);\r
2044         colourMenu.add(strandColour);\r
2045         colourMenu.add(turnColour);\r
2046         colourMenu.add(buriedColour);\r
2047         colourMenu.add(nucleotideColour);\r
2048         colourMenu.add(userDefinedColour);\r
2049         colourMenu.addSeparator();\r
2050         colourMenu.add(conservationMenuItem);\r
2051         colourMenu.add(modifyConservation);\r
2052         colourMenu.add(abovePIDThreshold);\r
2053         colourMenu.add(modifyPID);\r
2054         calculateMenu.add(sort);\r
2055         calculateMenu.add(calculate);\r
2056         calculateMenu.addSeparator();\r
2057         calculateMenu.add(pairwiseAlignmentMenuItem);\r
2058         calculateMenu.add(PCAMenuItem);\r
2059         this.add(statusBar, BorderLayout.SOUTH);\r
2060         Menu1.add(pasteNew);\r
2061         Menu1.add(pasteThis);\r
2062         sort.add(sortIDMenuItem);\r
2063         sort.add(sortByTreeMenu);\r
2064         sort.add(sortGroupMenuItem);\r
2065         sort.add(sortPairwiseMenuItem);\r
2066         calculate.add(averageDistanceTreeMenuItem);\r
2067         calculate.add(neighbourTreeMenuItem);\r
2068         calculate.add(avDistanceTreeBlosumMenuItem);\r
2069         calculate.add(njTreeBlosumMenuItem);\r
2070         helpMenu.add(documentation);\r
2071         helpMenu.add(about);\r
2072     }\r
2073 }\r
2074 \r