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.net.URL;\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 parseFeaturesFile(String file)\r
 151   {\r
 152     try\r
 153     {\r
 154       URL url = new URL(file);\r
 155 \r
 156       BufferedReader in =  new BufferedReader(new InputStreamReader(url.openStream()));\r
 157       SequenceI seq = null;\r
 158       String line, type, desc, token;\r
 159 \r
 160       int index, start, end;\r
 161       StringTokenizer st;\r
 162       SequenceFeature sf;\r
 163       FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
 164       int lineNo = 0;\r
 165       while ( (line = in.readLine()) != null)\r
 166       {\r
 167         lineNo++;\r
 168         st = new StringTokenizer(line, "\t");\r
 169         if (st.countTokens() == 2)\r
 170         {\r
 171           type = st.nextToken();\r
 172           UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
 173           fr.setColour(type, ucs.findColour("A"));\r
 174           continue;\r
 175         }\r
 176 \r
 177         while (st.hasMoreElements())\r
 178         {\r
 179           desc = st.nextToken();\r
 180           token = st.nextToken();\r
 181           if (!token.equals("ID_NOT_SPECIFIED"))\r
 182           {\r
 183             index = viewport.alignment.findIndex(viewport.alignment.findName(\r
 184                 token));\r
 185             st.nextToken();\r
 186           }\r
 187           else\r
 188           {\r
 189             index = Integer.parseInt(st.nextToken());\r
 190           }\r
 191 \r
 192           start = Integer.parseInt(st.nextToken());\r
 193           end = Integer.parseInt(st.nextToken());\r
 194 \r
 195           seq = viewport.alignment.getSequenceAt(index);\r
 196           start = seq.findIndex(start) - 1;\r
 197           end = seq.findIndex(end) - 1;\r
 198 \r
 199           type = st.nextToken();\r
 200 \r
 201           if(fr.getColour(type)==null)\r
 202           {\r
 203             // Probably the old style groups file\r
 204             UserColourScheme ucs = new UserColourScheme(type);\r
 205             fr.setColour(type, ucs.findColour("A"));\r
 206           }\r
 207 \r
 208           sf = new SequenceFeature(type, desc, "", start, end);\r
 209 \r
 210           seq.addSequenceFeature(sf);\r
 211         }\r
 212       }\r
 213 \r
 214       viewport.showSequenceFeatures = true;\r
 215       ((Alignment)viewport.alignment).featuresAdded = true;\r
 216 \r
 217       alignPanel.repaint();\r
 218 \r
 219     }\r
 220     catch (Exception ex)\r
 221     {\r
 222       System.out.println("Error parsing groups file: " + ex);\r
 223     }\r
 224   }\r
 225 \r
 226 \r
 227   public void inputText_actionPerformed(ActionEvent e)\r
 228   {\r
 229     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);\r
 230     Frame frame = new Frame();\r
 231     frame.add(cap);\r
 232     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
 233   }\r
 234 \r
 235   protected void outputText_actionPerformed(ActionEvent e)\r
 236   {\r
 237     CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);\r
 238     Frame frame = new Frame();\r
 239     frame.add(cap);\r
 240     jalview.bin.JalviewLite.addFrame(frame,\r
 241                                      "Alignment output - " + e.getActionCommand(),\r
 242                                      600, 500);\r
 243     cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
 244                                               viewport.getAlignment().\r
 245                                               getSequences()));\r
 246   }\r
 247 \r
 248   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 249   {\r
 250     PaintRefresher.components.remove(viewport.alignment);\r
 251     dispose();\r
 252     if(PaintRefresher.components.size()==0 && applet==null)\r
 253       System.exit(0);\r
 254   }\r
 255 \r
 256   Stack historyList = new Stack();\r
 257   Stack redoList = new Stack();\r
 258 \r
 259   void updateEditMenuBar()\r
 260   {\r
 261     if (historyList.size() > 0)\r
 262     {\r
 263       undoMenuItem.setEnabled(true);\r
 264       HistoryItem hi = (HistoryItem) historyList.peek();\r
 265       undoMenuItem.setLabel("Undo " + hi.getDescription());\r
 266     }\r
 267     else\r
 268     {\r
 269       undoMenuItem.setEnabled(false);\r
 270       undoMenuItem.setLabel("Undo");\r
 271     }\r
 272 \r
 273     if (redoList.size() > 0)\r
 274     {\r
 275       redoMenuItem.setEnabled(true);\r
 276       HistoryItem hi = (HistoryItem) redoList.peek();\r
 277       redoMenuItem.setLabel("Redo " + hi.getDescription());\r
 278     }\r
 279     else\r
 280     {\r
 281       redoMenuItem.setEnabled(false);\r
 282       redoMenuItem.setLabel("Redo");\r
 283     }\r
 284   }\r
 285 \r
 286   public void addHistoryItem(HistoryItem hi)\r
 287   {\r
 288     historyList.push(hi);\r
 289     updateEditMenuBar();\r
 290   }\r
 291 \r
 292   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 293   {\r
 294     HistoryItem hi = (HistoryItem) historyList.pop();\r
 295     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
 296                                   HistoryItem.HIDE));\r
 297     restoreHistoryItem(hi);\r
 298     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 299   }\r
 300 \r
 301   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 302   {\r
 303     HistoryItem hi = (HistoryItem) redoList.pop();\r
 304     restoreHistoryItem(hi);\r
 305     updateEditMenuBar();\r
 306     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 307   }\r
 308 \r
 309   // used by undo and redo\r
 310   void restoreHistoryItem(HistoryItem hi)\r
 311   {\r
 312     if (hi.getType() == HistoryItem.SORT)\r
 313     {\r
 314       for (int i = 0; i < hi.getSequences().size(); i++)\r
 315       {\r
 316         viewport.alignment.getSequences().setElementAt(hi.getSequences().\r
 317             elementAt(i), i);\r
 318       }\r
 319     }\r
 320     else\r
 321     {\r
 322       for (int i = 0; i < hi.getSequences().size(); i++)\r
 323       {\r
 324         SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
 325         if (restore.getLength() == 0)\r
 326         {\r
 327           // log.System.out.println(hi.getHidden().elementAt(i));\r
 328           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 329           viewport.alignment.getSequences().insertElementAt(\r
 330               restore,\r
 331               hi.getAlignIndex(i));\r
 332         }\r
 333         else\r
 334         {\r
 335           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 336         }\r
 337       }\r
 338       if (hi.getType() == HistoryItem.PASTE)\r
 339       {\r
 340         for (int i = viewport.alignment.getHeight() - 1;\r
 341              i > hi.getSequences().size() - 1; i--)\r
 342         {\r
 343           viewport.alignment.deleteSequence(i);\r
 344         }\r
 345       }\r
 346     }\r
 347 \r
 348     updateEditMenuBar();\r
 349 \r
 350     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 351   }\r
 352 \r
 353   public void moveSelectedSequences(boolean up)\r
 354   {\r
 355     SequenceGroup sg = viewport.getSelectionGroup();\r
 356     if (sg == null)\r
 357     {\r
 358       return;\r
 359     }\r
 360 \r
 361     if (up)\r
 362     {\r
 363       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 364       {\r
 365         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 366         if (!sg.sequences.contains(seq))\r
 367         {\r
 368           continue;\r
 369         }\r
 370 \r
 371         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 372         if (sg.sequences.contains(temp))\r
 373         {\r
 374           continue;\r
 375         }\r
 376 \r
 377         viewport.alignment.getSequences().setElementAt(temp, i);\r
 378         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 379       }\r
 380     }\r
 381     else\r
 382     {\r
 383       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 384       {\r
 385         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 386         if (!sg.sequences.contains(seq))\r
 387         {\r
 388           continue;\r
 389         }\r
 390 \r
 391         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 392         if (sg.sequences.contains(temp))\r
 393         {\r
 394           continue;\r
 395         }\r
 396 \r
 397         viewport.alignment.getSequences().setElementAt(temp, i);\r
 398         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 399       }\r
 400     }\r
 401 \r
 402     alignPanel.repaint();\r
 403   }\r
 404 \r
 405   StringBuffer copiedSequences;\r
 406   protected void copy_actionPerformed(ActionEvent e)\r
 407   {\r
 408     if (viewport.getSelectionGroup() == null)\r
 409     {\r
 410       return;\r
 411     }\r
 412 \r
 413     SequenceGroup sg = viewport.getSelectionGroup();\r
 414     copiedSequences = new StringBuffer();\r
 415     Hashtable orderedSeqs = new Hashtable();\r
 416     for (int i = 0; i < sg.getSize(); i++)\r
 417     {\r
 418       SequenceI seq = sg.getSequenceAt(i);\r
 419       int index = viewport.alignment.findIndex(seq);\r
 420       orderedSeqs.put(index + "", seq);\r
 421     }\r
 422 \r
 423     int index = 0, startRes, endRes;\r
 424     char ch;\r
 425 \r
 426     for (int i = 0; i < sg.getSize(); i++)\r
 427     {\r
 428         SequenceI seq = null;\r
 429 \r
 430         while (seq == null)\r
 431         {\r
 432             if (orderedSeqs.containsKey(index + ""))\r
 433             {\r
 434                 seq = (SequenceI) orderedSeqs.get(index + "");\r
 435                 index++;\r
 436 \r
 437                 break;\r
 438             }\r
 439             else\r
 440             {\r
 441                 index++;\r
 442             }\r
 443         }\r
 444 \r
 445         //FIND START RES\r
 446         //Returns residue following index if gap\r
 447         startRes = seq.findPosition(sg.getStartRes());\r
 448 \r
 449         //FIND END RES\r
 450         //Need to find the residue preceeding index if gap\r
 451         endRes = 0;\r
 452 \r
 453         for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
 454         {\r
 455           ch = seq.getCharAt(j);\r
 456           if (!jalview.util.Comparison.isGap( (ch)))\r
 457           {\r
 458             endRes++;\r
 459           }\r
 460         }\r
 461 \r
 462         if(endRes>0)\r
 463         {\r
 464           endRes += seq.getStart() -1;\r
 465         }\r
 466 \r
 467         copiedSequences.append(seq.getName() + "\t" +\r
 468             startRes + "\t" +\r
 469             endRes + "\t" +\r
 470             seq.getSequence(sg.getStartRes(),\r
 471                 sg.getEndRes() + 1) + "\n");\r
 472     }\r
 473 \r
 474   }\r
 475 \r
 476   protected void pasteNew_actionPerformed(ActionEvent e)\r
 477   {\r
 478     paste(true);\r
 479   }\r
 480 \r
 481   protected void pasteThis_actionPerformed(ActionEvent e)\r
 482   {\r
 483     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
 484                                    HistoryItem.PASTE));\r
 485     paste(false);\r
 486   }\r
 487 \r
 488   void paste(boolean newAlignment)\r
 489   {\r
 490     try\r
 491     {\r
 492       if (copiedSequences == null)\r
 493       {\r
 494         return;\r
 495       }\r
 496 \r
 497       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 498       Vector seqs = new Vector();\r
 499       while (st.hasMoreElements())\r
 500       {\r
 501         String name = st.nextToken();\r
 502         int start = Integer.parseInt(st.nextToken());\r
 503         int end = Integer.parseInt(st.nextToken());\r
 504         Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
 505 \r
 506         if (!newAlignment)\r
 507         {\r
 508           viewport.alignment.addSequence(sequence);\r
 509         }\r
 510         else\r
 511         {\r
 512           seqs.addElement(sequence);\r
 513         }\r
 514       }\r
 515 \r
 516       if (newAlignment)\r
 517       {\r
 518         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 519         for (int i = 0; i < seqs.size(); i++)\r
 520         {\r
 521           newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
 522         }\r
 523 \r
 524         String newtitle = new String("Copied sequences");\r
 525         if (getTitle().startsWith("Copied sequences"))\r
 526         {\r
 527           newtitle = getTitle();\r
 528         }\r
 529         else\r
 530         {\r
 531           newtitle = newtitle.concat("- from " + getTitle());\r
 532         }\r
 533         AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle);\r
 534 \r
 535         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
 536                                          NEW_WINDOW_HEIGHT);\r
 537       }\r
 538       else\r
 539       {\r
 540         viewport.setEndSeq(viewport.alignment.getHeight());\r
 541         viewport.alignment.getWidth();\r
 542         viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 543       }\r
 544 \r
 545     }\r
 546     catch (Exception ex)\r
 547     {} // could be anything being pasted in here\r
 548 \r
 549   }\r
 550 \r
 551   protected void cut_actionPerformed(ActionEvent e)\r
 552   {\r
 553     copy_actionPerformed(null);\r
 554     delete_actionPerformed(null);\r
 555   }\r
 556 \r
 557   protected void delete_actionPerformed(ActionEvent e)\r
 558   {\r
 559     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
 560                                    HistoryItem.HIDE));\r
 561     if (viewport.getSelectionGroup() == null)\r
 562     {\r
 563       return;\r
 564     }\r
 565 \r
 566 \r
 567     SequenceGroup sg = viewport.getSelectionGroup();\r
 568     boolean allSequences = false;\r
 569     if(sg.sequences.size()==viewport.alignment.getHeight())\r
 570           allSequences = true;\r
 571 \r
 572     for (int i = 0; i < sg.sequences.size(); i++)\r
 573     {\r
 574       SequenceI seq = sg.getSequenceAt(i);\r
 575       int index = viewport.getAlignment().findIndex(seq);\r
 576       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 577 \r
 578       // If the cut affects all sequences, remove highlighted columns\r
 579       if (allSequences)\r
 580       {\r
 581         viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
 582                                                      sg.getEndRes() + 1);\r
 583       }\r
 584 \r
 585 \r
 586       if (seq.getSequence().length() < 1)\r
 587       {\r
 588         viewport.getAlignment().deleteSequence(seq);\r
 589       }\r
 590       else\r
 591       {\r
 592         viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 593       }\r
 594     }\r
 595 \r
 596     viewport.setSelectionGroup(null);\r
 597     viewport.alignment.deleteGroup(sg);\r
 598     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
 599     if (viewport.getAlignment().getHeight() < 1)\r
 600     {\r
 601       try\r
 602       {\r
 603         this.setVisible(false);\r
 604       }\r
 605       catch (Exception ex)\r
 606       {}\r
 607     }\r
 608     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 609 \r
 610   }\r
 611 \r
 612   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 613   {\r
 614     viewport.alignment.deleteAllGroups();\r
 615     viewport.setSelectionGroup(null);\r
 616 \r
 617     alignPanel.repaint();\r
 618   }\r
 619 \r
 620   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 621   {\r
 622     SequenceGroup sg = new SequenceGroup();\r
 623     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 624     {\r
 625       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
 626     }\r
 627     sg.setEndRes(viewport.alignment.getWidth()-1);\r
 628     viewport.setSelectionGroup(sg);\r
 629     alignPanel.repaint();\r
 630     PaintRefresher.Refresh(null, viewport.alignment);\r
 631   }\r
 632 \r
 633   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 634   {\r
 635     viewport.setSelectionGroup(null);\r
 636     viewport.getColumnSelection().clear();\r
 637     viewport.setSelectionGroup(null);\r
 638     alignPanel.repaint();\r
 639     PaintRefresher.Refresh(null, viewport.alignment);\r
 640   }\r
 641 \r
 642   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 643   {\r
 644     SequenceGroup sg = viewport.getSelectionGroup();\r
 645     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 646     {\r
 647       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
 648     }\r
 649 \r
 650     PaintRefresher.Refresh(null, viewport.alignment);\r
 651   }\r
 652 \r
 653   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 654   {\r
 655     ColumnSelection colSel = viewport.getColumnSelection();\r
 656     if (colSel.size() > 0)\r
 657     {\r
 658       addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
 659                                      HistoryItem.HIDE));\r
 660       int min = colSel.getMin();\r
 661       viewport.getAlignment().trimLeft(min);\r
 662       colSel.compensateForEdit(0, min);\r
 663 \r
 664       if (viewport.getSelectionGroup() != null)\r
 665       {\r
 666         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 667       }\r
 668 \r
 669       Vector groups = viewport.alignment.getGroups();\r
 670       for (int i = 0; i < groups.size(); i++)\r
 671       {\r
 672         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 673         if (!sg.adjustForRemoveLeft(min))\r
 674         {\r
 675           viewport.alignment.deleteGroup(sg);\r
 676         }\r
 677       }\r
 678       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 679     }\r
 680   }\r
 681 \r
 682   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 683   {\r
 684     ColumnSelection colSel = viewport.getColumnSelection();\r
 685     if (colSel.size() > 0)\r
 686     {\r
 687       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
 688                                      HistoryItem.HIDE));\r
 689       int max = colSel.getMax();\r
 690       viewport.getAlignment().trimRight(max);\r
 691       if (viewport.getSelectionGroup() != null)\r
 692       {\r
 693         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 694       }\r
 695 \r
 696       Vector groups = viewport.alignment.getGroups();\r
 697       for (int i = 0; i < groups.size(); i++)\r
 698       {\r
 699         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 700         if (!sg.adjustForRemoveRight(max))\r
 701         {\r
 702           viewport.alignment.deleteGroup(sg);\r
 703         }\r
 704       }\r
 705       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 706     }\r
 707 \r
 708   }\r
 709 \r
 710   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 711   {\r
 712     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
 713                                    viewport.alignment,\r
 714                                    HistoryItem.HIDE));\r
 715 \r
 716     //This is to maintain viewport position on first residue\r
 717     //of first sequence\r
 718     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 719     int startRes = seq.findPosition(viewport.startRes);\r
 720 \r
 721     viewport.getAlignment().removeGaps();\r
 722 \r
 723     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 724 \r
 725     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 726   }\r
 727 \r
 728   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 729   {\r
 730     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
 731                                    HistoryItem.HIDE));\r
 732 \r
 733     //This is to maintain viewport position on first residue\r
 734     //of first sequence\r
 735     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 736     int startRes = seq.findPosition(viewport.startRes);\r
 737 \r
 738     SequenceI current;\r
 739     int jSize;\r
 740 \r
 741     Vector seqs=null;\r
 742 \r
 743     int start=0, end = viewport.alignment.getWidth();\r
 744 \r
 745     if (viewport.getSelectionGroup() != null\r
 746         && viewport.getSelectionGroup().sequences != null\r
 747         && viewport.getSelectionGroup().sequences.size()>0)\r
 748     {\r
 749       seqs = viewport.getSelectionGroup().sequences;\r
 750       start = viewport.getSelectionGroup().getStartRes();\r
 751       end = viewport.getSelectionGroup().getEndRes()+1;\r
 752     }\r
 753     else\r
 754       seqs = viewport.alignment.getSequences();\r
 755 \r
 756     for (int i = 0; i < seqs.size(); i++)\r
 757     {\r
 758       current = (SequenceI) seqs.elementAt(i);\r
 759       jSize = current.getLength();\r
 760 \r
 761       // Removing a range is much quicker than removing gaps\r
 762       // one by one for long sequences\r
 763       int j = start;\r
 764       int rangeStart=-1, rangeEnd=-1;\r
 765 \r
 766       do\r
 767       {\r
 768         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 769         {\r
 770           if(rangeStart==-1)\r
 771            {\r
 772              rangeStart = j;\r
 773              rangeEnd = j+1;\r
 774            }\r
 775            else\r
 776            {\r
 777              rangeEnd++;\r
 778            }\r
 779            j++;\r
 780         }\r
 781         else\r
 782         {\r
 783           if(rangeStart>-1)\r
 784           {\r
 785             current.deleteChars(rangeStart, rangeEnd);\r
 786             j-=rangeEnd-rangeStart;\r
 787             jSize-=rangeEnd-rangeStart;\r
 788             rangeStart = -1;\r
 789             rangeEnd = -1;\r
 790           }\r
 791           else\r
 792             j++;\r
 793         }\r
 794       }\r
 795       while (j < end && j < jSize);\r
 796       if(rangeStart>-1)\r
 797       {\r
 798        current.deleteChars(rangeStart, rangeEnd);\r
 799       }\r
 800     }\r
 801     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 802     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 803   }\r
 804 \r
 805   public void alignmentChanged()\r
 806   {\r
 807     viewport.updateConsensus();\r
 808     viewport.updateConservation ();\r
 809     resetAllColourSchemes();\r
 810     if(alignPanel.overviewPanel!=null)\r
 811       alignPanel.overviewPanel.updateOverviewImage();\r
 812     alignPanel.repaint();\r
 813   }\r
 814 \r
 815   void resetAllColourSchemes()\r
 816   {\r
 817     ColourSchemeI cs = viewport.globalColourScheme;\r
 818     if(cs!=null)\r
 819     {\r
 820       if (cs instanceof ClustalxColourScheme)\r
 821       {\r
 822         ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
 823             resetClustalX(viewport.alignment.getSequences(),\r
 824                           viewport.alignment.getWidth());\r
 825       }\r
 826 \r
 827       cs.setConsensus(viewport.vconsensus);\r
 828       if (cs.conservationApplied())\r
 829       {\r
 830         Alignment al = (Alignment) viewport.alignment;\r
 831         Conservation c = new Conservation("All",\r
 832                                           ResidueProperties.propHash, 3,\r
 833                                           al.getSequences(), 0,\r
 834                                           al.getWidth() - 1);\r
 835         c.calculate();\r
 836         c.verdict(false, viewport.ConsPercGaps);\r
 837 \r
 838         cs.setConservation(c);\r
 839       }\r
 840     }\r
 841 \r
 842     int s, sSize = viewport.alignment.getGroups().size();\r
 843     for(s=0; s<sSize; s++)\r
 844     {\r
 845       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
 846       if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
 847       {\r
 848         ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
 849       }\r
 850       sg.recalcConservation();\r
 851     }\r
 852   }\r
 853 \r
 854 \r
 855 \r
 856   public void findMenuItem_actionPerformed(ActionEvent e)\r
 857   {\r
 858     new Finder(alignPanel);\r
 859   }\r
 860 \r
 861   public void font_actionPerformed(ActionEvent e)\r
 862   {\r
 863     new FontChooser(alignPanel);\r
 864   }\r
 865 \r
 866   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 867   {\r
 868     viewport.setShowJVSuffix(fullSeqId.getState());\r
 869     alignPanel.fontChanged();\r
 870     alignPanel.repaint();\r
 871   }\r
 872 \r
 873   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 874   {\r
 875     viewport.setColourText(colourTextMenuItem.getState());\r
 876     alignPanel.repaint();\r
 877   }\r
 878 \r
 879   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 880   {\r
 881     viewport.setWrapAlignment(wrapMenuItem.getState());\r
 882     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
 883     scaleAbove.setEnabled(wrapMenuItem.getState());\r
 884     scaleLeft.setEnabled(wrapMenuItem.getState());\r
 885     scaleRight.setEnabled(wrapMenuItem.getState());\r
 886     alignPanel.repaint();\r
 887   }\r
 888 \r
 889   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 890   {\r
 891     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 892     alignPanel.repaint();\r
 893   }\r
 894 \r
 895   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 896   {\r
 897     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 898     alignPanel.repaint();\r
 899   }\r
 900 \r
 901   protected void scaleRight_actionPerformed(ActionEvent e)\r
 902   {\r
 903     viewport.setScaleRightWrapped(scaleRight.getState());\r
 904     alignPanel.repaint();\r
 905   }\r
 906 \r
 907   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 908   {\r
 909     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
 910     alignPanel.repaint();\r
 911   }\r
 912 \r
 913   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 914   {\r
 915     viewport.setShowText(viewTextMenuItem.getState());\r
 916     alignPanel.repaint();\r
 917   }\r
 918 \r
 919   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 920   {\r
 921     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 922     alignPanel.repaint();\r
 923   }\r
 924 \r
 925   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 926   {\r
 927     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
 928     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
 929   }\r
 930 \r
 931   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 932   {\r
 933     if (alignPanel.overviewPanel != null)\r
 934     {\r
 935       return;\r
 936     }\r
 937 \r
 938     Frame frame = new Frame();\r
 939     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 940     frame.add(overview);\r
 941     // +50 must allow for applet frame window\r
 942     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
 943                                      overview.preferredSize().width,\r
 944                                      overview.preferredSize().height + 50);\r
 945 \r
 946     frame.pack();\r
 947     frame.addWindowListener(new WindowAdapter()\r
 948     {\r
 949       public void windowClosing(WindowEvent e)\r
 950       {\r
 951         alignPanel.setOverviewPanel(null);\r
 952       };\r
 953     });\r
 954 \r
 955     alignPanel.setOverviewPanel(overview);\r
 956 \r
 957   }\r
 958 \r
 959   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 960   {\r
 961     changeColour(null);\r
 962   }\r
 963 \r
 964   public void clustalColour_actionPerformed(ActionEvent e)\r
 965   {\r
 966     abovePIDThreshold.setState(false);\r
 967     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
 968                                           viewport.alignment.getWidth()));\r
 969   }\r
 970 \r
 971   public void zappoColour_actionPerformed(ActionEvent e)\r
 972   {\r
 973     changeColour(new ZappoColourScheme());\r
 974   }\r
 975 \r
 976   public void taylorColour_actionPerformed(ActionEvent e)\r
 977   {\r
 978     changeColour(new TaylorColourScheme());\r
 979   }\r
 980 \r
 981   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 982   {\r
 983     changeColour(new HydrophobicColourScheme());\r
 984   }\r
 985 \r
 986   public void helixColour_actionPerformed(ActionEvent e)\r
 987   {\r
 988     changeColour(new HelixColourScheme());\r
 989   }\r
 990 \r
 991   public void strandColour_actionPerformed(ActionEvent e)\r
 992   {\r
 993     changeColour(new StrandColourScheme());\r
 994   }\r
 995 \r
 996   public void turnColour_actionPerformed(ActionEvent e)\r
 997   {\r
 998     changeColour(new TurnColourScheme());\r
 999   }\r
1000 \r
1001   public void buriedColour_actionPerformed(ActionEvent e)\r
1002   {\r
1003     changeColour(new BuriedColourScheme());\r
1004   }\r
1005 \r
1006   public void nucleotideColour_actionPerformed(ActionEvent e)\r
1007   {\r
1008     changeColour(new NucleotideColourScheme());\r
1009   }\r
1010 \r
1011   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1012   {\r
1013     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
1014   }\r
1015 \r
1016   void changeColour(ColourSchemeI cs)\r
1017   {\r
1018     int threshold = 0;\r
1019 \r
1020     if(cs!=null)\r
1021     {\r
1022       if (viewport.getAbovePIDThreshold())\r
1023       {\r
1024         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
1025 \r
1026         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1027 \r
1028         viewport.setGlobalColourScheme(cs);\r
1029       }\r
1030       else\r
1031       {\r
1032         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1033       }\r
1034 \r
1035       if (viewport.getConservationSelected())\r
1036       {\r
1037 \r
1038         Alignment al = (Alignment) viewport.alignment;\r
1039         Conservation c = new Conservation("All",\r
1040                                           ResidueProperties.propHash, 3,\r
1041                                           al.getSequences(), 0,\r
1042                                           al.getWidth() - 1);\r
1043 \r
1044         c.calculate();\r
1045         c.verdict(false, viewport.ConsPercGaps);\r
1046 \r
1047         cs.setConservation(c);\r
1048 \r
1049         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
1050             "Background"));\r
1051 \r
1052       }\r
1053       else\r
1054       {\r
1055         cs.setConservation(null);\r
1056       }\r
1057 \r
1058       cs.setConsensus(viewport.vconsensus);\r
1059 \r
1060     }\r
1061     viewport.setGlobalColourScheme(cs);\r
1062 \r
1063     if (viewport.getColourAppliesToAllGroups())\r
1064     {\r
1065       Vector groups = viewport.alignment.getGroups();\r
1066       for (int i = 0; i < groups.size(); i++)\r
1067       {\r
1068         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1069 \r
1070         if(cs==null)\r
1071         {\r
1072           sg.cs = null;\r
1073           continue;\r
1074         }\r
1075         if (cs instanceof ClustalxColourScheme)\r
1076         {\r
1077           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
1078         }\r
1079         else\r
1080         {\r
1081           try\r
1082           {\r
1083             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
1084           }\r
1085           catch (Exception ex)\r
1086           {\r
1087             ex.printStackTrace();\r
1088             sg.cs = cs;\r
1089           }\r
1090         }\r
1091 \r
1092         if (viewport.getAbovePIDThreshold()\r
1093             || cs instanceof PIDColourScheme\r
1094             || cs instanceof Blosum62ColourScheme)\r
1095         {\r
1096           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1097           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
1098         }\r
1099         else\r
1100           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1101 \r
1102         if (viewport.getConservationSelected())\r
1103         {\r
1104           Conservation c = new Conservation("Group",\r
1105                                             ResidueProperties.propHash, 3,\r
1106                                             sg.sequences, 0,\r
1107                                             viewport.alignment.getWidth() - 1);\r
1108           c.calculate();\r
1109           c.verdict(false, viewport.ConsPercGaps);\r
1110           sg.cs.setConservation(c);\r
1111         }\r
1112         else\r
1113         {\r
1114           sg.cs.setConservation(null);\r
1115           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1116         }\r
1117 \r
1118       }\r
1119     }\r
1120 \r
1121 \r
1122     if (alignPanel.getOverviewPanel() != null)\r
1123     {\r
1124       alignPanel.getOverviewPanel().updateOverviewImage();\r
1125     }\r
1126 \r
1127     alignPanel.repaint();\r
1128   }\r
1129 \r
1130 \r
1131 \r
1132   protected void modifyPID_actionPerformed(ActionEvent e)\r
1133   {\r
1134     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
1135     {\r
1136       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
1137                                      "Background");\r
1138       SliderPanel.showPIDSlider();\r
1139     }\r
1140   }\r
1141 \r
1142   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1143   {\r
1144     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
1145     {\r
1146       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
1147                                         "Background");\r
1148       SliderPanel.showConservationSlider();\r
1149     }\r
1150   }\r
1151 \r
1152   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1153   {\r
1154     viewport.setConservationSelected(conservationMenuItem.getState());\r
1155 \r
1156     viewport.setAbovePIDThreshold(false);\r
1157     abovePIDThreshold.setState(false);\r
1158 \r
1159     changeColour(viewport.getGlobalColourScheme());\r
1160 \r
1161     modifyConservation_actionPerformed(null);\r
1162   }\r
1163 \r
1164   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1165   {\r
1166     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
1167 \r
1168     conservationMenuItem.setState(false);\r
1169     viewport.setConservationSelected(false);\r
1170 \r
1171     changeColour(viewport.getGlobalColourScheme());\r
1172 \r
1173     modifyPID_actionPerformed(null);\r
1174   }\r
1175 \r
1176   public void userDefinedColour_actionPerformed(ActionEvent e)\r
1177   {\r
1178     new UserDefinedColours(alignPanel, null);\r
1179   }\r
1180 \r
1181   public void PIDColour_actionPerformed(ActionEvent e)\r
1182   {\r
1183     changeColour(new PIDColourScheme());\r
1184   }\r
1185 \r
1186   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1187   {\r
1188     changeColour(new Blosum62ColourScheme());\r
1189   }\r
1190 \r
1191   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1192   {\r
1193     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1194                                    HistoryItem.SORT));\r
1195     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1196                               viewport.getAlignment().getSequenceAt(0));\r
1197     alignPanel.repaint();\r
1198   }\r
1199 \r
1200   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1201   {\r
1202     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1203                                    HistoryItem.SORT));\r
1204     AlignmentSorter.sortByID(viewport.getAlignment());\r
1205     alignPanel.repaint();\r
1206   }\r
1207 \r
1208   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1209   {\r
1210     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1211                                    HistoryItem.SORT));\r
1212     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1213     alignPanel.repaint();\r
1214 \r
1215   }\r
1216 \r
1217   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1218   {\r
1219     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
1220     Frame frame = new Frame();\r
1221     frame.add(sp);\r
1222     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
1223                                      400, 120);\r
1224 \r
1225   }\r
1226 \r
1227   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1228   {\r
1229     if (viewport.getSelectionGroup().getSize() > 1)\r
1230     {\r
1231       Frame frame = new Frame();\r
1232       frame.add(new PairwiseAlignPanel(alignPanel));\r
1233       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1234     }\r
1235   }\r
1236 \r
1237   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
1238   {\r
1239     //are the sequences aligned?\r
1240     if (!viewport.alignment.isAligned())\r
1241     {\r
1242       SequenceI current;\r
1243       int Width = viewport.getAlignment().getWidth();\r
1244 \r
1245       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1246            i++)\r
1247       {\r
1248         current = viewport.getAlignment().getSequenceAt(i);\r
1249 \r
1250         if (current.getLength() < Width)\r
1251         {\r
1252           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1253         }\r
1254       }\r
1255       alignPanel.repaint();\r
1256     }\r
1257 \r
1258     if ( (viewport.getSelectionGroup() != null &&\r
1259           viewport.getSelectionGroup().getSize() < 4 &&\r
1260           viewport.getSelectionGroup().getSize() > 0)\r
1261         || viewport.getAlignment().getHeight() < 4)\r
1262     {\r
1263       return;\r
1264     }\r
1265 \r
1266     try\r
1267     {\r
1268       new PCAPanel(viewport);\r
1269     }\r
1270     catch (java.lang.OutOfMemoryError ex)\r
1271     {\r
1272     }\r
1273 \r
1274   }\r
1275 \r
1276   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1277   {\r
1278     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1279   }\r
1280 \r
1281   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1282   {\r
1283     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1284   }\r
1285 \r
1286   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1287   {\r
1288     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1289   }\r
1290 \r
1291   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1292   {\r
1293     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1294   }\r
1295 \r
1296   void NewTreePanel(String type, String pwType, String title)\r
1297   {\r
1298     //are the sequences aligned?\r
1299     if (!viewport.alignment.isAligned())\r
1300     {\r
1301       SequenceI current;\r
1302       int Width = viewport.getAlignment().getWidth();\r
1303 \r
1304       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1305            i++)\r
1306       {\r
1307         current = viewport.getAlignment().getSequenceAt(i);\r
1308 \r
1309         if (current.getLength() < Width)\r
1310         {\r
1311           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1312         }\r
1313       }\r
1314       alignPanel.repaint();\r
1315 \r
1316     }\r
1317 \r
1318     final TreePanel tp;\r
1319     if (viewport.getSelectionGroup() != null &&\r
1320         viewport.getSelectionGroup().getSize() > 3)\r
1321     {\r
1322       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1323                          pwType,\r
1324                          0, viewport.alignment.getWidth());\r
1325     }\r
1326     else\r
1327     {\r
1328       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1329                          type, pwType, 0, viewport.alignment.getWidth());\r
1330     }\r
1331 \r
1332     addTreeMenuItem(tp, title);\r
1333 \r
1334     jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1335   }\r
1336 \r
1337   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1338   {\r
1339     final MenuItem item = new MenuItem(title);\r
1340     sortByTreeMenu.add(item);\r
1341     item.addActionListener(new java.awt.event.ActionListener()\r
1342     {\r
1343       public void actionPerformed(ActionEvent e)\r
1344       {\r
1345         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1346                                        HistoryItem.SORT));\r
1347         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1348         alignPanel.repaint();\r
1349       }\r
1350     });\r
1351 \r
1352     treePanel.addWindowListener(new WindowAdapter()\r
1353     {\r
1354       public void windowClosing(WindowEvent e)\r
1355       {\r
1356         sortByTreeMenu.remove(item);\r
1357       };\r
1358     });\r
1359   }\r
1360 \r
1361   protected void documentation_actionPerformed(ActionEvent e)\r
1362   {\r
1363     showURL("http://www.jalview.org/help.html");\r
1364   }\r
1365 \r
1366   protected void about_actionPerformed(ActionEvent e)\r
1367   {\r
1368 \r
1369     class AboutPanel extends Canvas\r
1370     {\r
1371       String version;\r
1372       public AboutPanel(String version)\r
1373       { this.version = version; }\r
1374 \r
1375       public void paint(Graphics g)\r
1376       {\r
1377         g.setColor(Color.white);\r
1378         g.fillRect(0, 0, getSize().width, getSize().height);\r
1379         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1380         FontMetrics fm = g.getFontMetrics();\r
1381         int fh = fm.getHeight();\r
1382         int y = 5, x = 7;\r
1383         g.setColor(Color.black);\r
1384         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1385         g.drawString("Jalview - Release "+version, 200, y += fh);\r
1386         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1387         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1388                      x, y += fh * 2);\r
1389         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1390                      x, y += fh);\r
1391         g.drawString(\r
1392             "For any issues relating to Jalview, email help@jalview.org", x,\r
1393             y += fh);\r
1394         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1395         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1396                      x, y += fh);\r
1397         g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);\r
1398       }\r
1399     }\r
1400 \r
1401     String version = "test";\r
1402     java.net.URL url = getClass().getResource("/.build_properties");\r
1403     if (url != null)\r
1404     {\r
1405       try\r
1406       {\r
1407         BufferedReader reader = new BufferedReader(new InputStreamReader(\r
1408             url.openStream()));\r
1409         String line;\r
1410         while ( (line = reader.readLine()) != null)\r
1411         {\r
1412           if (line.indexOf("VERSION") > -1)\r
1413           {\r
1414             version = line.substring(line.indexOf("=") + 1);\r
1415           }\r
1416         }\r
1417       }\r
1418       catch (Exception ex)\r
1419       {\r
1420         ex.printStackTrace();\r
1421       }\r
1422     }\r
1423 \r
1424 \r
1425     Frame frame = new Frame();\r
1426     frame.add(new AboutPanel(version));\r
1427     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1428 \r
1429   }\r
1430 \r
1431   /**\r
1432    * Displays the given URL in a new browser window\r
1433    *\r
1434    * @param url URL to display in browser window.\r
1435    * <br>New window will be named "HELP_WINDOW"\r
1436    */\r
1437   public void showURL(String url)\r
1438   {\r
1439     showURL(url, "HELP");\r
1440   }\r
1441 \r
1442   public void showURL(String url, String target)\r
1443   {\r
1444     if (applet == null)\r
1445     {\r
1446       System.out.println("Not running as applet - no browser available.");\r
1447     }\r
1448     else\r
1449     {\r
1450       try\r
1451       {\r
1452         applet.getAppletContext().showDocument(new java.net.URL(url),\r
1453                                                target);\r
1454       }\r
1455       catch (Exception ex)\r
1456       {\r
1457         ex.printStackTrace();\r
1458       }\r
1459     }\r
1460   }\r
1461 \r
1462 }\r