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 import java.io.FileReader;\r
  33 \r
  34 public class AlignFrame\r
  35     extends GAlignFrame\r
  36 {\r
  37   final AlignmentPanel alignPanel;\r
  38   final AlignViewport viewport;\r
  39   int NEW_WINDOW_WIDTH = 700;\r
  40   int NEW_WINDOW_HEIGHT = 500;\r
  41   jalview.bin.JalviewLite applet;\r
  42 \r
  43 \r
  44   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title)\r
  45   {\r
  46     this.applet = applet;\r
  47     viewport = new AlignViewport(al, applet);\r
  48     alignPanel = new AlignmentPanel(this, viewport);\r
  49     add(alignPanel);\r
  50     alignPanel.validate();\r
  51 \r
  52     if(applet!=null)\r
  53     {\r
  54       String treeFile = applet.getParameter("treeFile");\r
  55       if (treeFile != null)\r
  56       {\r
  57         try\r
  58         {\r
  59           jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
  60               getCodeBase() + treeFile, "URL");\r
  61           fin.parse();\r
  62 \r
  63           if (fin.getTree() != null)\r
  64           {\r
  65             TreePanel tp = null;\r
  66             tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
  67                                fin, "FromFile", applet.getCodeBase() + treeFile);\r
  68             jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
  69             addTreeMenuItem(tp, treeFile);\r
  70           }\r
  71         }\r
  72         catch (Exception ex)\r
  73         {\r
  74           ex.printStackTrace();\r
  75         }\r
  76       }\r
  77 \r
  78       String param = applet.getParameter("sortBy");\r
  79       if (param != null)\r
  80       {\r
  81         if (param.equalsIgnoreCase("Id"))\r
  82           sortIDMenuItem_actionPerformed(null);\r
  83         else if (param.equalsIgnoreCase("Pairwise Identity"))\r
  84           sortPairwiseMenuItem_actionPerformed(null);\r
  85       }\r
  86 \r
  87       param = applet.getParameter("wrap");\r
  88       if (param != null)\r
  89       {\r
  90         if (param.equalsIgnoreCase("true"))\r
  91         {\r
  92           wrapMenuItem.setState(true);\r
  93           wrapMenuItem_actionPerformed(null);\r
  94         }\r
  95       }\r
  96 \r
  97       try\r
  98       {\r
  99         param = applet.getParameter("windowWidth");\r
 100         if (param != null)\r
 101         {\r
 102           int width = Integer.parseInt(param);\r
 103           NEW_WINDOW_WIDTH = width;\r
 104         }\r
 105         param = applet.getParameter("windowHeight");\r
 106         if (param != null)\r
 107         {\r
 108           int height = Integer.parseInt(param);\r
 109           NEW_WINDOW_HEIGHT = height;\r
 110         }\r
 111       }\r
 112       catch (Exception ex)\r
 113       {}\r
 114 \r
 115     }\r
 116 \r
 117     this.addWindowListener(new WindowAdapter()\r
 118     {\r
 119       public void windowClosing(WindowEvent e)\r
 120           {\r
 121             closeMenuItem_actionPerformed(null);\r
 122           }\r
 123     });\r
 124 \r
 125     viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
 126     {\r
 127      public void propertyChange(java.beans.PropertyChangeEvent evt)\r
 128      {\r
 129        if (evt.getPropertyName().equals("alignment"))\r
 130        {\r
 131          alignmentChanged();\r
 132        }\r
 133      }\r
 134    });\r
 135 \r
 136    jalview.bin.JalviewLite.addFrame(this, title,\r
 137                                     NEW_WINDOW_WIDTH,\r
 138                                     NEW_WINDOW_HEIGHT);\r
 139 \r
 140 \r
 141   }\r
 142 \r
 143 \r
 144   /**\r
 145    * DOCUMENT ME!\r
 146    *\r
 147    * @param String DOCUMENT ME!\r
 148    */\r
 149 \r
 150   public void parseGroupsFile(String file)\r
 151   {\r
 152     try\r
 153     {\r
 154       BufferedReader in = new BufferedReader(new FileReader(file));\r
 155       SequenceI seq = null;\r
 156       String line, text, token;\r
 157       UserColourScheme ucs;\r
 158       int index, start, end;\r
 159       StringTokenizer st;\r
 160       SequenceGroup sg;\r
 161       int lineNo = 0;\r
 162       while ( (line = in.readLine()) != null)\r
 163       {\r
 164         lineNo++;\r
 165         st = new StringTokenizer(line, "\t");\r
 166         if (st.countTokens() != 6)\r
 167         {\r
 168           System.out.println("Groups file " + file +\r
 169                              " is invalid. Read help file.\nLine: \n"\r
 170               +lineNo +": "+line);\r
 171           break;\r
 172         }\r
 173 \r
 174         while (st.hasMoreElements())\r
 175         {\r
 176           text = st.nextToken();\r
 177           token = st.nextToken();\r
 178           if (!token.equals("ID_NOT_SPECIFIED"))\r
 179           {\r
 180             index = viewport.alignment.findIndex(viewport.alignment.findName(\r
 181                 token));\r
 182             st.nextToken();\r
 183           }\r
 184           else\r
 185           {\r
 186             index = Integer.parseInt(st.nextToken());\r
 187           }\r
 188 \r
 189           start = Integer.parseInt(st.nextToken());\r
 190           end = Integer.parseInt(st.nextToken());\r
 191           ucs = new UserColourScheme(st.nextToken());\r
 192 \r
 193           seq = viewport.alignment.getSequenceAt(index);\r
 194           start = seq.findIndex(start) - 1;\r
 195           end = seq.findIndex(end) - 1;\r
 196 \r
 197           sg = new SequenceGroup(text, ucs, true, true, false, start, end);\r
 198           sg.addSequence(seq, false);\r
 199 \r
 200           viewport.alignment.addGroup(sg);\r
 201 \r
 202         }\r
 203       }\r
 204 \r
 205       alignPanel.repaint();\r
 206 \r
 207     }\r
 208     catch (Exception ex)\r
 209     {\r
 210       System.out.println("Error parsing groups file: " + ex);\r
 211     }\r
 212   }\r
 213 \r
 214 \r
 215   public void inputText_actionPerformed(ActionEvent e)\r
 216   {\r
 217     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);\r
 218     Frame frame = new Frame();\r
 219     frame.add(cap);\r
 220     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
 221   }\r
 222 \r
 223   protected void outputText_actionPerformed(ActionEvent e)\r
 224   {\r
 225     CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);\r
 226     Frame frame = new Frame();\r
 227     frame.add(cap);\r
 228     jalview.bin.JalviewLite.addFrame(frame,\r
 229                                      "Alignment output - " + e.getActionCommand(),\r
 230                                      600, 500);\r
 231     cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
 232                                               viewport.getAlignment().\r
 233                                               getSequences()));\r
 234   }\r
 235 \r
 236   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 237   {\r
 238     PaintRefresher.components.remove(viewport.alignment);\r
 239     dispose();\r
 240     if(PaintRefresher.components.size()==0 && applet==null)\r
 241       System.exit(0);\r
 242   }\r
 243 \r
 244   Stack historyList = new Stack();\r
 245   Stack redoList = new Stack();\r
 246 \r
 247   void updateEditMenuBar()\r
 248   {\r
 249     if (historyList.size() > 0)\r
 250     {\r
 251       undoMenuItem.setEnabled(true);\r
 252       HistoryItem hi = (HistoryItem) historyList.peek();\r
 253       undoMenuItem.setLabel("Undo " + hi.getDescription());\r
 254     }\r
 255     else\r
 256     {\r
 257       undoMenuItem.setEnabled(false);\r
 258       undoMenuItem.setLabel("Undo");\r
 259     }\r
 260 \r
 261     if (redoList.size() > 0)\r
 262     {\r
 263       redoMenuItem.setEnabled(true);\r
 264       HistoryItem hi = (HistoryItem) redoList.peek();\r
 265       redoMenuItem.setLabel("Redo " + hi.getDescription());\r
 266     }\r
 267     else\r
 268     {\r
 269       redoMenuItem.setEnabled(false);\r
 270       redoMenuItem.setLabel("Redo");\r
 271     }\r
 272   }\r
 273 \r
 274   public void addHistoryItem(HistoryItem hi)\r
 275   {\r
 276     historyList.push(hi);\r
 277     updateEditMenuBar();\r
 278   }\r
 279 \r
 280   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 281   {\r
 282     HistoryItem hi = (HistoryItem) historyList.pop();\r
 283     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
 284                                   HistoryItem.HIDE));\r
 285     restoreHistoryItem(hi);\r
 286     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 287   }\r
 288 \r
 289   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 290   {\r
 291     HistoryItem hi = (HistoryItem) redoList.pop();\r
 292     restoreHistoryItem(hi);\r
 293     updateEditMenuBar();\r
 294     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 295   }\r
 296 \r
 297   // used by undo and redo\r
 298   void restoreHistoryItem(HistoryItem hi)\r
 299   {\r
 300     if (hi.getType() == HistoryItem.SORT)\r
 301     {\r
 302       for (int i = 0; i < hi.getSequences().size(); i++)\r
 303       {\r
 304         viewport.alignment.getSequences().setElementAt(hi.getSequences().\r
 305             elementAt(i), i);\r
 306       }\r
 307     }\r
 308     else\r
 309     {\r
 310       for (int i = 0; i < hi.getSequences().size(); i++)\r
 311       {\r
 312         SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
 313         if (restore.getLength() == 0)\r
 314         {\r
 315           // log.System.out.println(hi.getHidden().elementAt(i));\r
 316           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 317           viewport.alignment.getSequences().insertElementAt(\r
 318               restore,\r
 319               hi.getAlignIndex(i));\r
 320         }\r
 321         else\r
 322         {\r
 323           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 324         }\r
 325       }\r
 326       if (hi.getType() == HistoryItem.PASTE)\r
 327       {\r
 328         for (int i = viewport.alignment.getHeight() - 1;\r
 329              i > hi.getSequences().size() - 1; i--)\r
 330         {\r
 331           viewport.alignment.deleteSequence(i);\r
 332         }\r
 333       }\r
 334     }\r
 335 \r
 336     updateEditMenuBar();\r
 337 \r
 338     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 339   }\r
 340 \r
 341   public void moveSelectedSequences(boolean up)\r
 342   {\r
 343     SequenceGroup sg = viewport.getSelectionGroup();\r
 344     if (sg == null)\r
 345     {\r
 346       return;\r
 347     }\r
 348 \r
 349     if (up)\r
 350     {\r
 351       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 352       {\r
 353         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 354         if (!sg.sequences.contains(seq))\r
 355         {\r
 356           continue;\r
 357         }\r
 358 \r
 359         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 360         if (sg.sequences.contains(temp))\r
 361         {\r
 362           continue;\r
 363         }\r
 364 \r
 365         viewport.alignment.getSequences().setElementAt(temp, i);\r
 366         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 367       }\r
 368     }\r
 369     else\r
 370     {\r
 371       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 372       {\r
 373         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 374         if (!sg.sequences.contains(seq))\r
 375         {\r
 376           continue;\r
 377         }\r
 378 \r
 379         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 380         if (sg.sequences.contains(temp))\r
 381         {\r
 382           continue;\r
 383         }\r
 384 \r
 385         viewport.alignment.getSequences().setElementAt(temp, i);\r
 386         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 387       }\r
 388     }\r
 389 \r
 390     alignPanel.repaint();\r
 391   }\r
 392 \r
 393   StringBuffer copiedSequences;\r
 394   protected void copy_actionPerformed(ActionEvent e)\r
 395   {\r
 396     if (viewport.getSelectionGroup() == null)\r
 397     {\r
 398       return;\r
 399     }\r
 400 \r
 401     SequenceGroup sg = viewport.getSelectionGroup();\r
 402     copiedSequences = new StringBuffer();\r
 403     Hashtable orderedSeqs = new Hashtable();\r
 404     for (int i = 0; i < sg.getSize(); i++)\r
 405     {\r
 406       SequenceI seq = sg.getSequenceAt(i);\r
 407       int index = viewport.alignment.findIndex(seq);\r
 408       orderedSeqs.put(index + "", seq);\r
 409     }\r
 410 \r
 411     int index = 0, startRes, endRes;\r
 412     char ch;\r
 413 \r
 414     for (int i = 0; i < sg.getSize(); i++)\r
 415     {\r
 416         SequenceI seq = null;\r
 417 \r
 418         while (seq == null)\r
 419         {\r
 420             if (orderedSeqs.containsKey(index + ""))\r
 421             {\r
 422                 seq = (SequenceI) orderedSeqs.get(index + "");\r
 423                 index++;\r
 424 \r
 425                 break;\r
 426             }\r
 427             else\r
 428             {\r
 429                 index++;\r
 430             }\r
 431         }\r
 432 \r
 433         //FIND START RES\r
 434         //Returns residue following index if gap\r
 435         startRes = seq.findPosition(sg.getStartRes());\r
 436 \r
 437         //FIND END RES\r
 438         //Need to find the residue preceeding index if gap\r
 439         endRes = 0;\r
 440 \r
 441         for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
 442         {\r
 443           ch = seq.getCharAt(j);\r
 444           if (!jalview.util.Comparison.isGap( (ch)))\r
 445           {\r
 446             endRes++;\r
 447           }\r
 448         }\r
 449 \r
 450         if(endRes>0)\r
 451         {\r
 452           endRes += seq.getStart() -1;\r
 453         }\r
 454 \r
 455         copiedSequences.append(seq.getName() + "\t" +\r
 456             startRes + "\t" +\r
 457             endRes + "\t" +\r
 458             seq.getSequence(sg.getStartRes(),\r
 459                 sg.getEndRes() + 1) + "\n");\r
 460     }\r
 461 \r
 462   }\r
 463 \r
 464   protected void pasteNew_actionPerformed(ActionEvent e)\r
 465   {\r
 466     paste(true);\r
 467   }\r
 468 \r
 469   protected void pasteThis_actionPerformed(ActionEvent e)\r
 470   {\r
 471     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
 472                                    HistoryItem.PASTE));\r
 473     paste(false);\r
 474   }\r
 475 \r
 476   void paste(boolean newAlignment)\r
 477   {\r
 478     try\r
 479     {\r
 480       if (copiedSequences == null)\r
 481       {\r
 482         return;\r
 483       }\r
 484 \r
 485       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 486       Vector seqs = new Vector();\r
 487       while (st.hasMoreElements())\r
 488       {\r
 489         String name = st.nextToken();\r
 490         int start = Integer.parseInt(st.nextToken());\r
 491         int end = Integer.parseInt(st.nextToken());\r
 492         Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
 493 \r
 494         if (!newAlignment)\r
 495         {\r
 496           viewport.alignment.addSequence(sequence);\r
 497         }\r
 498         else\r
 499         {\r
 500           seqs.addElement(sequence);\r
 501         }\r
 502       }\r
 503 \r
 504       if (newAlignment)\r
 505       {\r
 506         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 507         for (int i = 0; i < seqs.size(); i++)\r
 508         {\r
 509           newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
 510         }\r
 511 \r
 512         String newtitle = new String("Copied sequences");\r
 513         if (getTitle().startsWith("Copied sequences"))\r
 514         {\r
 515           newtitle = getTitle();\r
 516         }\r
 517         else\r
 518         {\r
 519           newtitle = newtitle.concat("- from " + getTitle());\r
 520         }\r
 521         AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle);\r
 522 \r
 523         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
 524                                          NEW_WINDOW_HEIGHT);\r
 525       }\r
 526       else\r
 527       {\r
 528         viewport.setEndSeq(viewport.alignment.getHeight());\r
 529         viewport.alignment.getWidth();\r
 530         viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 531       }\r
 532 \r
 533     }\r
 534     catch (Exception ex)\r
 535     {} // could be anything being pasted in here\r
 536 \r
 537   }\r
 538 \r
 539   protected void cut_actionPerformed(ActionEvent e)\r
 540   {\r
 541     copy_actionPerformed(null);\r
 542     delete_actionPerformed(null);\r
 543   }\r
 544 \r
 545   protected void delete_actionPerformed(ActionEvent e)\r
 546   {\r
 547     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
 548                                    HistoryItem.HIDE));\r
 549     if (viewport.getSelectionGroup() == null)\r
 550     {\r
 551       return;\r
 552     }\r
 553 \r
 554 \r
 555     SequenceGroup sg = viewport.getSelectionGroup();\r
 556     boolean allSequences = false;\r
 557     if(sg.sequences.size()==viewport.alignment.getHeight())\r
 558           allSequences = true;\r
 559 \r
 560     for (int i = 0; i < sg.sequences.size(); i++)\r
 561     {\r
 562       SequenceI seq = sg.getSequenceAt(i);\r
 563       int index = viewport.getAlignment().findIndex(seq);\r
 564       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 565 \r
 566       // If the cut affects all sequences, remove highlighted columns\r
 567       if (allSequences)\r
 568       {\r
 569         viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
 570                                                      sg.getEndRes() + 1);\r
 571       }\r
 572 \r
 573 \r
 574       if (seq.getSequence().length() < 1)\r
 575       {\r
 576         viewport.getAlignment().deleteSequence(seq);\r
 577       }\r
 578       else\r
 579       {\r
 580         viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 581       }\r
 582     }\r
 583 \r
 584     viewport.setSelectionGroup(null);\r
 585     viewport.alignment.deleteGroup(sg);\r
 586     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
 587     if (viewport.getAlignment().getHeight() < 1)\r
 588     {\r
 589       try\r
 590       {\r
 591         this.setVisible(false);\r
 592       }\r
 593       catch (Exception ex)\r
 594       {}\r
 595     }\r
 596     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 597 \r
 598   }\r
 599 \r
 600   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 601   {\r
 602     viewport.alignment.deleteAllGroups();\r
 603     viewport.setSelectionGroup(null);\r
 604 \r
 605     alignPanel.repaint();\r
 606   }\r
 607 \r
 608   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 609   {\r
 610     SequenceGroup sg = new SequenceGroup();\r
 611     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 612     {\r
 613       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
 614     }\r
 615     sg.setEndRes(viewport.alignment.getWidth()-1);\r
 616     viewport.setSelectionGroup(sg);\r
 617     alignPanel.repaint();\r
 618     PaintRefresher.Refresh(null, viewport.alignment);\r
 619   }\r
 620 \r
 621   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 622   {\r
 623     viewport.setSelectionGroup(null);\r
 624     viewport.getColumnSelection().clear();\r
 625     viewport.setSelectionGroup(null);\r
 626     alignPanel.repaint();\r
 627     PaintRefresher.Refresh(null, viewport.alignment);\r
 628   }\r
 629 \r
 630   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 631   {\r
 632     SequenceGroup sg = viewport.getSelectionGroup();\r
 633     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 634     {\r
 635       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
 636     }\r
 637 \r
 638     PaintRefresher.Refresh(null, viewport.alignment);\r
 639   }\r
 640 \r
 641   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 642   {\r
 643     ColumnSelection colSel = viewport.getColumnSelection();\r
 644     if (colSel.size() > 0)\r
 645     {\r
 646       addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
 647                                      HistoryItem.HIDE));\r
 648       int min = colSel.getMin();\r
 649       viewport.getAlignment().trimLeft(min);\r
 650       colSel.compensateForEdit(0, min);\r
 651 \r
 652       if (viewport.getSelectionGroup() != null)\r
 653       {\r
 654         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 655       }\r
 656 \r
 657       Vector groups = viewport.alignment.getGroups();\r
 658       for (int i = 0; i < groups.size(); i++)\r
 659       {\r
 660         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 661         if (!sg.adjustForRemoveLeft(min))\r
 662         {\r
 663           viewport.alignment.deleteGroup(sg);\r
 664         }\r
 665       }\r
 666       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 667     }\r
 668   }\r
 669 \r
 670   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 671   {\r
 672     ColumnSelection colSel = viewport.getColumnSelection();\r
 673     if (colSel.size() > 0)\r
 674     {\r
 675       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
 676                                      HistoryItem.HIDE));\r
 677       int max = colSel.getMax();\r
 678       viewport.getAlignment().trimRight(max);\r
 679       if (viewport.getSelectionGroup() != null)\r
 680       {\r
 681         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 682       }\r
 683 \r
 684       Vector groups = viewport.alignment.getGroups();\r
 685       for (int i = 0; i < groups.size(); i++)\r
 686       {\r
 687         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 688         if (!sg.adjustForRemoveRight(max))\r
 689         {\r
 690           viewport.alignment.deleteGroup(sg);\r
 691         }\r
 692       }\r
 693       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 694     }\r
 695 \r
 696   }\r
 697 \r
 698   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 699   {\r
 700     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
 701                                    viewport.alignment,\r
 702                                    HistoryItem.HIDE));\r
 703 \r
 704     //This is to maintain viewport position on first residue\r
 705     //of first sequence\r
 706     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 707     int startRes = seq.findPosition(viewport.startRes);\r
 708 \r
 709     viewport.getAlignment().removeGaps();\r
 710 \r
 711     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 712 \r
 713     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 714   }\r
 715 \r
 716   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 717   {\r
 718     addHistoryItem(new HistoryItem("Remove Gaps", 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     SequenceI current;\r
 727     int jSize;\r
 728 \r
 729     Vector seqs=null;\r
 730 \r
 731     int start=0, end = viewport.alignment.getWidth();\r
 732 \r
 733     if (viewport.getSelectionGroup() != null\r
 734         && viewport.getSelectionGroup().sequences != null\r
 735         && viewport.getSelectionGroup().sequences.size()>0)\r
 736     {\r
 737       seqs = viewport.getSelectionGroup().sequences;\r
 738       start = viewport.getSelectionGroup().getStartRes();\r
 739       end = viewport.getSelectionGroup().getEndRes()+1;\r
 740     }\r
 741     else\r
 742       seqs = viewport.alignment.getSequences();\r
 743 \r
 744     for (int i = 0; i < seqs.size(); i++)\r
 745     {\r
 746       current = (SequenceI) seqs.elementAt(i);\r
 747       jSize = current.getLength();\r
 748 \r
 749       // Removing a range is much quicker than removing gaps\r
 750       // one by one for long sequences\r
 751       int j = start;\r
 752       int rangeStart=-1, rangeEnd=-1;\r
 753 \r
 754       do\r
 755       {\r
 756         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 757         {\r
 758           if(rangeStart==-1)\r
 759            {\r
 760              rangeStart = j;\r
 761              rangeEnd = j+1;\r
 762            }\r
 763            else\r
 764            {\r
 765              rangeEnd++;\r
 766            }\r
 767            j++;\r
 768         }\r
 769         else\r
 770         {\r
 771           if(rangeStart>-1)\r
 772           {\r
 773             current.deleteChars(rangeStart, rangeEnd);\r
 774             j-=rangeEnd-rangeStart;\r
 775             jSize-=rangeEnd-rangeStart;\r
 776             rangeStart = -1;\r
 777             rangeEnd = -1;\r
 778           }\r
 779           else\r
 780             j++;\r
 781         }\r
 782       }\r
 783       while (j < end && j < jSize);\r
 784       if(rangeStart>-1)\r
 785       {\r
 786        current.deleteChars(rangeStart, rangeEnd);\r
 787       }\r
 788     }\r
 789     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 790     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 791   }\r
 792 \r
 793   public void alignmentChanged()\r
 794   {\r
 795     viewport.updateConsensus();\r
 796     viewport.updateConservation ();\r
 797     resetAllColourSchemes();\r
 798     if(alignPanel.overviewPanel!=null)\r
 799       alignPanel.overviewPanel.updateOverviewImage();\r
 800     alignPanel.repaint();\r
 801   }\r
 802 \r
 803   void resetAllColourSchemes()\r
 804   {\r
 805     ColourSchemeI cs = viewport.globalColourScheme;\r
 806     if(cs!=null)\r
 807     {\r
 808       if (cs instanceof ClustalxColourScheme)\r
 809       {\r
 810         ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
 811             resetClustalX(viewport.alignment.getSequences(),\r
 812                           viewport.alignment.getWidth());\r
 813       }\r
 814 \r
 815       cs.setConsensus(viewport.vconsensus);\r
 816       if (cs.conservationApplied())\r
 817       {\r
 818         Alignment al = (Alignment) viewport.alignment;\r
 819         Conservation c = new Conservation("All",\r
 820                                           ResidueProperties.propHash, 3,\r
 821                                           al.getSequences(), 0,\r
 822                                           al.getWidth() - 1);\r
 823         c.calculate();\r
 824         c.verdict(false, viewport.ConsPercGaps);\r
 825 \r
 826         cs.setConservation(c);\r
 827       }\r
 828     }\r
 829 \r
 830     int s, sSize = viewport.alignment.getGroups().size();\r
 831     for(s=0; s<sSize; s++)\r
 832     {\r
 833       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
 834       if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
 835       {\r
 836         ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
 837       }\r
 838       sg.recalcConservation();\r
 839     }\r
 840   }\r
 841 \r
 842 \r
 843 \r
 844   public void findMenuItem_actionPerformed(ActionEvent e)\r
 845   {\r
 846     new Finder(alignPanel);\r
 847   }\r
 848 \r
 849   public void font_actionPerformed(ActionEvent e)\r
 850   {\r
 851     new FontChooser(alignPanel);\r
 852   }\r
 853 \r
 854   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 855   {\r
 856     viewport.setShowFullId(fullSeqId.getState());\r
 857     alignPanel.fontChanged();\r
 858     alignPanel.repaint();\r
 859   }\r
 860 \r
 861   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 862   {\r
 863     viewport.setColourText(colourTextMenuItem.getState());\r
 864     alignPanel.repaint();\r
 865   }\r
 866 \r
 867   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 868   {\r
 869     viewport.setWrapAlignment(wrapMenuItem.getState());\r
 870     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
 871     scaleAbove.setEnabled(wrapMenuItem.getState());\r
 872     scaleLeft.setEnabled(wrapMenuItem.getState());\r
 873     scaleRight.setEnabled(wrapMenuItem.getState());\r
 874     alignPanel.repaint();\r
 875   }\r
 876 \r
 877   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 878   {\r
 879     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 880     alignPanel.repaint();\r
 881   }\r
 882 \r
 883   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 884   {\r
 885     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 886     alignPanel.repaint();\r
 887   }\r
 888 \r
 889   protected void scaleRight_actionPerformed(ActionEvent e)\r
 890   {\r
 891     viewport.setScaleRightWrapped(scaleRight.getState());\r
 892     alignPanel.repaint();\r
 893   }\r
 894 \r
 895   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 896   {\r
 897     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
 898     alignPanel.repaint();\r
 899   }\r
 900 \r
 901   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 902   {\r
 903     viewport.setShowText(viewTextMenuItem.getState());\r
 904     alignPanel.repaint();\r
 905   }\r
 906 \r
 907   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 908   {\r
 909     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 910     alignPanel.repaint();\r
 911   }\r
 912 \r
 913   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 914   {\r
 915     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
 916     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
 917   }\r
 918 \r
 919   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 920   {\r
 921     if (alignPanel.overviewPanel != null)\r
 922     {\r
 923       return;\r
 924     }\r
 925 \r
 926     Frame frame = new Frame();\r
 927     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 928     frame.add(overview);\r
 929     // +50 must allow for applet frame window\r
 930     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
 931                                      overview.preferredSize().width,\r
 932                                      overview.preferredSize().height + 50);\r
 933 \r
 934     frame.pack();\r
 935     frame.addWindowListener(new WindowAdapter()\r
 936     {\r
 937       public void windowClosing(WindowEvent e)\r
 938       {\r
 939         alignPanel.setOverviewPanel(null);\r
 940       };\r
 941     });\r
 942 \r
 943     alignPanel.setOverviewPanel(overview);\r
 944 \r
 945   }\r
 946 \r
 947   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 948   {\r
 949     changeColour(null);\r
 950   }\r
 951 \r
 952   public void clustalColour_actionPerformed(ActionEvent e)\r
 953   {\r
 954     abovePIDThreshold.setState(false);\r
 955     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
 956                                           viewport.alignment.getWidth()));\r
 957   }\r
 958 \r
 959   public void zappoColour_actionPerformed(ActionEvent e)\r
 960   {\r
 961     changeColour(new ZappoColourScheme());\r
 962   }\r
 963 \r
 964   public void taylorColour_actionPerformed(ActionEvent e)\r
 965   {\r
 966     changeColour(new TaylorColourScheme());\r
 967   }\r
 968 \r
 969   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 970   {\r
 971     changeColour(new HydrophobicColourScheme());\r
 972   }\r
 973 \r
 974   public void helixColour_actionPerformed(ActionEvent e)\r
 975   {\r
 976     changeColour(new HelixColourScheme());\r
 977   }\r
 978 \r
 979   public void strandColour_actionPerformed(ActionEvent e)\r
 980   {\r
 981     changeColour(new StrandColourScheme());\r
 982   }\r
 983 \r
 984   public void turnColour_actionPerformed(ActionEvent e)\r
 985   {\r
 986     changeColour(new TurnColourScheme());\r
 987   }\r
 988 \r
 989   public void buriedColour_actionPerformed(ActionEvent e)\r
 990   {\r
 991     changeColour(new BuriedColourScheme());\r
 992   }\r
 993 \r
 994   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 995   {\r
 996     changeColour(new NucleotideColourScheme());\r
 997   }\r
 998 \r
 999   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1000   {\r
1001     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
1002   }\r
1003 \r
1004   void changeColour(ColourSchemeI cs)\r
1005   {\r
1006     int threshold = 0;\r
1007 \r
1008     if(cs!=null)\r
1009     {\r
1010       if (viewport.getAbovePIDThreshold())\r
1011       {\r
1012         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
1013 \r
1014         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1015 \r
1016         viewport.setGlobalColourScheme(cs);\r
1017       }\r
1018       else\r
1019       {\r
1020         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1021       }\r
1022 \r
1023       if (viewport.getConservationSelected())\r
1024       {\r
1025 \r
1026         Alignment al = (Alignment) viewport.alignment;\r
1027         Conservation c = new Conservation("All",\r
1028                                           ResidueProperties.propHash, 3,\r
1029                                           al.getSequences(), 0,\r
1030                                           al.getWidth() - 1);\r
1031 \r
1032         c.calculate();\r
1033         c.verdict(false, viewport.ConsPercGaps);\r
1034 \r
1035         cs.setConservation(c);\r
1036 \r
1037         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
1038             "Background"));\r
1039 \r
1040       }\r
1041       else\r
1042       {\r
1043         cs.setConservation(null);\r
1044       }\r
1045 \r
1046       cs.setConsensus(viewport.vconsensus);\r
1047 \r
1048     }\r
1049     viewport.setGlobalColourScheme(cs);\r
1050 \r
1051     if (viewport.getColourAppliesToAllGroups())\r
1052     {\r
1053       Vector groups = viewport.alignment.getGroups();\r
1054       for (int i = 0; i < groups.size(); i++)\r
1055       {\r
1056         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1057 \r
1058         if(cs==null)\r
1059         {\r
1060           sg.cs = null;\r
1061           continue;\r
1062         }\r
1063         if (cs instanceof ClustalxColourScheme)\r
1064         {\r
1065           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
1066         }\r
1067         else\r
1068         {\r
1069           try\r
1070           {\r
1071             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
1072           }\r
1073           catch (Exception ex)\r
1074           {\r
1075             ex.printStackTrace();\r
1076             sg.cs = cs;\r
1077           }\r
1078         }\r
1079 \r
1080         if (viewport.getAbovePIDThreshold()\r
1081             || cs instanceof PIDColourScheme\r
1082             || cs instanceof Blosum62ColourScheme)\r
1083         {\r
1084           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1085           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
1086         }\r
1087         else\r
1088           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1089 \r
1090         if (viewport.getConservationSelected())\r
1091         {\r
1092           Conservation c = new Conservation("Group",\r
1093                                             ResidueProperties.propHash, 3,\r
1094                                             sg.sequences, 0,\r
1095                                             viewport.alignment.getWidth() - 1);\r
1096           c.calculate();\r
1097           c.verdict(false, viewport.ConsPercGaps);\r
1098           sg.cs.setConservation(c);\r
1099         }\r
1100         else\r
1101         {\r
1102           sg.cs.setConservation(null);\r
1103           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1104         }\r
1105 \r
1106       }\r
1107     }\r
1108 \r
1109 \r
1110     if (alignPanel.getOverviewPanel() != null)\r
1111     {\r
1112       alignPanel.getOverviewPanel().updateOverviewImage();\r
1113     }\r
1114 \r
1115     alignPanel.repaint();\r
1116   }\r
1117 \r
1118 \r
1119 \r
1120   protected void modifyPID_actionPerformed(ActionEvent e)\r
1121   {\r
1122     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
1123     {\r
1124       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
1125                                      "Background");\r
1126       SliderPanel.showPIDSlider();\r
1127     }\r
1128   }\r
1129 \r
1130   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1131   {\r
1132     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
1133     {\r
1134       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
1135                                         "Background");\r
1136       SliderPanel.showConservationSlider();\r
1137     }\r
1138   }\r
1139 \r
1140   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1141   {\r
1142     viewport.setConservationSelected(conservationMenuItem.getState());\r
1143 \r
1144     viewport.setAbovePIDThreshold(false);\r
1145     abovePIDThreshold.setState(false);\r
1146 \r
1147     changeColour(viewport.getGlobalColourScheme());\r
1148 \r
1149     modifyConservation_actionPerformed(null);\r
1150   }\r
1151 \r
1152   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1153   {\r
1154     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
1155 \r
1156     conservationMenuItem.setState(false);\r
1157     viewport.setConservationSelected(false);\r
1158 \r
1159     changeColour(viewport.getGlobalColourScheme());\r
1160 \r
1161     modifyPID_actionPerformed(null);\r
1162   }\r
1163 \r
1164   public void userDefinedColour_actionPerformed(ActionEvent e)\r
1165   {\r
1166     new UserDefinedColours(alignPanel, null);\r
1167   }\r
1168 \r
1169   public void PIDColour_actionPerformed(ActionEvent e)\r
1170   {\r
1171     changeColour(new PIDColourScheme());\r
1172   }\r
1173 \r
1174   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1175   {\r
1176     changeColour(new Blosum62ColourScheme());\r
1177   }\r
1178 \r
1179   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1180   {\r
1181     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1182                                    HistoryItem.SORT));\r
1183     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1184                               viewport.getAlignment().getSequenceAt(0));\r
1185     alignPanel.repaint();\r
1186   }\r
1187 \r
1188   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1189   {\r
1190     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1191                                    HistoryItem.SORT));\r
1192     AlignmentSorter.sortByID(viewport.getAlignment());\r
1193     alignPanel.repaint();\r
1194   }\r
1195 \r
1196   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1197   {\r
1198     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1199                                    HistoryItem.SORT));\r
1200     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1201     alignPanel.repaint();\r
1202 \r
1203   }\r
1204 \r
1205   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1206   {\r
1207     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
1208     Frame frame = new Frame();\r
1209     frame.add(sp);\r
1210     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
1211                                      400, 120);\r
1212 \r
1213   }\r
1214 \r
1215   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1216   {\r
1217     if (viewport.getSelectionGroup().getSize() > 1)\r
1218     {\r
1219       Frame frame = new Frame();\r
1220       frame.add(new PairwiseAlignPanel(alignPanel));\r
1221       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1222     }\r
1223   }\r
1224 \r
1225   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
1226   {\r
1227     //are the sequences aligned?\r
1228     if (!viewport.alignment.isAligned())\r
1229     {\r
1230       SequenceI current;\r
1231       int Width = viewport.getAlignment().getWidth();\r
1232 \r
1233       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1234            i++)\r
1235       {\r
1236         current = viewport.getAlignment().getSequenceAt(i);\r
1237 \r
1238         if (current.getLength() < Width)\r
1239         {\r
1240           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1241         }\r
1242       }\r
1243       alignPanel.repaint();\r
1244     }\r
1245 \r
1246     if ( (viewport.getSelectionGroup() != null &&\r
1247           viewport.getSelectionGroup().getSize() < 4 &&\r
1248           viewport.getSelectionGroup().getSize() > 0)\r
1249         || viewport.getAlignment().getHeight() < 4)\r
1250     {\r
1251       return;\r
1252     }\r
1253 \r
1254     try\r
1255     {\r
1256       new PCAPanel(viewport);\r
1257     }\r
1258     catch (java.lang.OutOfMemoryError ex)\r
1259     {\r
1260     }\r
1261 \r
1262   }\r
1263 \r
1264   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1265   {\r
1266     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1267   }\r
1268 \r
1269   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1270   {\r
1271     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1272   }\r
1273 \r
1274   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1275   {\r
1276     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1277   }\r
1278 \r
1279   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1280   {\r
1281     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1282   }\r
1283 \r
1284   void NewTreePanel(String type, String pwType, String title)\r
1285   {\r
1286     //are the sequences aligned?\r
1287     if (!viewport.alignment.isAligned())\r
1288     {\r
1289       SequenceI current;\r
1290       int Width = viewport.getAlignment().getWidth();\r
1291 \r
1292       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1293            i++)\r
1294       {\r
1295         current = viewport.getAlignment().getSequenceAt(i);\r
1296 \r
1297         if (current.getLength() < Width)\r
1298         {\r
1299           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1300         }\r
1301       }\r
1302       alignPanel.repaint();\r
1303 \r
1304     }\r
1305 \r
1306     final TreePanel tp;\r
1307     if (viewport.getSelectionGroup() != null &&\r
1308         viewport.getSelectionGroup().getSize() > 3)\r
1309     {\r
1310       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1311                          pwType,\r
1312                          0, viewport.alignment.getWidth());\r
1313     }\r
1314     else\r
1315     {\r
1316       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1317                          type, pwType, 0, viewport.alignment.getWidth());\r
1318     }\r
1319 \r
1320     addTreeMenuItem(tp, title);\r
1321 \r
1322     jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1323   }\r
1324 \r
1325   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1326   {\r
1327     final MenuItem item = new MenuItem(title);\r
1328     sortByTreeMenu.add(item);\r
1329     item.addActionListener(new java.awt.event.ActionListener()\r
1330     {\r
1331       public void actionPerformed(ActionEvent e)\r
1332       {\r
1333         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1334                                        HistoryItem.SORT));\r
1335         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1336         alignPanel.repaint();\r
1337       }\r
1338     });\r
1339 \r
1340     treePanel.addWindowListener(new WindowAdapter()\r
1341     {\r
1342       public void windowClosing(WindowEvent e)\r
1343       {\r
1344         sortByTreeMenu.remove(item);\r
1345       };\r
1346     });\r
1347   }\r
1348 \r
1349   protected void documentation_actionPerformed(ActionEvent e)\r
1350   {\r
1351     jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");\r
1352   }\r
1353 \r
1354   protected void about_actionPerformed(ActionEvent e)\r
1355   {\r
1356 \r
1357     class AboutPanel extends Canvas\r
1358     {\r
1359       String version;\r
1360       public AboutPanel(String version)\r
1361       { this.version = version; }\r
1362 \r
1363       public void paint(Graphics g)\r
1364       {\r
1365         g.setColor(Color.white);\r
1366         g.fillRect(0, 0, getSize().width, getSize().height);\r
1367         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1368         FontMetrics fm = g.getFontMetrics();\r
1369         int fh = fm.getHeight();\r
1370         int y = 5, x = 7;\r
1371         g.setColor(Color.black);\r
1372         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1373         g.drawString("Jalview - Release "+version, 200, y += fh);\r
1374         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1375         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1376                      x, y += fh * 2);\r
1377         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1378                      x, y += fh);\r
1379         g.drawString(\r
1380             "For any issues relating to Jalview, email help@jalview.org", x,\r
1381             y += fh);\r
1382         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1383         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1384                      x, y += fh);\r
1385         g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);\r
1386       }\r
1387     }\r
1388 \r
1389     String version = "test";\r
1390     java.net.URL url = getClass().getResource("/.build_properties");\r
1391     if (url != null)\r
1392     {\r
1393       try\r
1394       {\r
1395         BufferedReader reader = new BufferedReader(new InputStreamReader(\r
1396             url.openStream()));\r
1397         String line;\r
1398         while ( (line = reader.readLine()) != null)\r
1399         {\r
1400           if (line.indexOf("VERSION") > -1)\r
1401           {\r
1402             version = line.substring(line.indexOf("=") + 1);\r
1403           }\r
1404         }\r
1405       }\r
1406       catch (Exception ex)\r
1407       {\r
1408         ex.printStackTrace();\r
1409       }\r
1410     }\r
1411 \r
1412 \r
1413     Frame frame = new Frame();\r
1414     frame.add(new AboutPanel(version));\r
1415     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1416 \r
1417   }\r
1418 }\r