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().getSequences(),\r
 245                                                       viewport.showDBPrefix,\r
 246                                                       viewport.showJVSuffix));\r
 247   }\r
 248 \r
 249   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 250   {\r
 251     PaintRefresher.components.remove(viewport.alignment);\r
 252     dispose();\r
 253     if(PaintRefresher.components.size()==0 && applet==null)\r
 254       System.exit(0);\r
 255   }\r
 256 \r
 257   Stack historyList = new Stack();\r
 258   Stack redoList = new Stack();\r
 259 \r
 260   void updateEditMenuBar()\r
 261   {\r
 262     if (historyList.size() > 0)\r
 263     {\r
 264       undoMenuItem.setEnabled(true);\r
 265       HistoryItem hi = (HistoryItem) historyList.peek();\r
 266       undoMenuItem.setLabel("Undo " + hi.getDescription());\r
 267     }\r
 268     else\r
 269     {\r
 270       undoMenuItem.setEnabled(false);\r
 271       undoMenuItem.setLabel("Undo");\r
 272     }\r
 273 \r
 274     if (redoList.size() > 0)\r
 275     {\r
 276       redoMenuItem.setEnabled(true);\r
 277       HistoryItem hi = (HistoryItem) redoList.peek();\r
 278       redoMenuItem.setLabel("Redo " + hi.getDescription());\r
 279     }\r
 280     else\r
 281     {\r
 282       redoMenuItem.setEnabled(false);\r
 283       redoMenuItem.setLabel("Redo");\r
 284     }\r
 285   }\r
 286 \r
 287   public void addHistoryItem(HistoryItem hi)\r
 288   {\r
 289     historyList.push(hi);\r
 290     updateEditMenuBar();\r
 291   }\r
 292 \r
 293   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 294   {\r
 295     HistoryItem hi = (HistoryItem) historyList.pop();\r
 296     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
 297                                   HistoryItem.HIDE));\r
 298     restoreHistoryItem(hi);\r
 299     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 300   }\r
 301 \r
 302   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 303   {\r
 304     HistoryItem hi = (HistoryItem) redoList.pop();\r
 305     restoreHistoryItem(hi);\r
 306     updateEditMenuBar();\r
 307     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 308   }\r
 309 \r
 310   // used by undo and redo\r
 311   void restoreHistoryItem(HistoryItem hi)\r
 312   {\r
 313     if (hi.getType() == HistoryItem.SORT)\r
 314     {\r
 315       for (int i = 0; i < hi.getSequences().size(); i++)\r
 316       {\r
 317         viewport.alignment.getSequences().setElementAt(hi.getSequences().\r
 318             elementAt(i), i);\r
 319       }\r
 320     }\r
 321     else\r
 322     {\r
 323       for (int i = 0; i < hi.getSequences().size(); i++)\r
 324       {\r
 325         SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
 326         if (restore.getLength() == 0)\r
 327         {\r
 328           // log.System.out.println(hi.getHidden().elementAt(i));\r
 329           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 330           viewport.alignment.getSequences().insertElementAt(\r
 331               restore,\r
 332               hi.getAlignIndex(i));\r
 333         }\r
 334         else\r
 335         {\r
 336           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 337         }\r
 338       }\r
 339       if (hi.getType() == HistoryItem.PASTE)\r
 340       {\r
 341         for (int i = viewport.alignment.getHeight() - 1;\r
 342              i > hi.getSequences().size() - 1; i--)\r
 343         {\r
 344           viewport.alignment.deleteSequence(i);\r
 345         }\r
 346       }\r
 347     }\r
 348 \r
 349     updateEditMenuBar();\r
 350 \r
 351     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 352   }\r
 353 \r
 354   public void moveSelectedSequences(boolean up)\r
 355   {\r
 356     SequenceGroup sg = viewport.getSelectionGroup();\r
 357     if (sg == null)\r
 358     {\r
 359       return;\r
 360     }\r
 361 \r
 362     if (up)\r
 363     {\r
 364       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 365       {\r
 366         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 367         if (!sg.sequences.contains(seq))\r
 368         {\r
 369           continue;\r
 370         }\r
 371 \r
 372         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 373         if (sg.sequences.contains(temp))\r
 374         {\r
 375           continue;\r
 376         }\r
 377 \r
 378         viewport.alignment.getSequences().setElementAt(temp, i);\r
 379         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 380       }\r
 381     }\r
 382     else\r
 383     {\r
 384       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 385       {\r
 386         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 387         if (!sg.sequences.contains(seq))\r
 388         {\r
 389           continue;\r
 390         }\r
 391 \r
 392         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 393         if (sg.sequences.contains(temp))\r
 394         {\r
 395           continue;\r
 396         }\r
 397 \r
 398         viewport.alignment.getSequences().setElementAt(temp, i);\r
 399         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 400       }\r
 401     }\r
 402 \r
 403     alignPanel.repaint();\r
 404   }\r
 405 \r
 406   StringBuffer copiedSequences;\r
 407   protected void copy_actionPerformed(ActionEvent e)\r
 408   {\r
 409     if (viewport.getSelectionGroup() == null)\r
 410     {\r
 411       return;\r
 412     }\r
 413 \r
 414     SequenceGroup sg = viewport.getSelectionGroup();\r
 415     copiedSequences = new StringBuffer();\r
 416     Hashtable orderedSeqs = new Hashtable();\r
 417     for (int i = 0; i < sg.getSize(); i++)\r
 418     {\r
 419       SequenceI seq = sg.getSequenceAt(i);\r
 420       int index = viewport.alignment.findIndex(seq);\r
 421       orderedSeqs.put(index + "", seq);\r
 422     }\r
 423 \r
 424     int index = 0, startRes, endRes;\r
 425     char ch;\r
 426 \r
 427     for (int i = 0; i < sg.getSize(); i++)\r
 428     {\r
 429         SequenceI seq = null;\r
 430 \r
 431         while (seq == null)\r
 432         {\r
 433             if (orderedSeqs.containsKey(index + ""))\r
 434             {\r
 435                 seq = (SequenceI) orderedSeqs.get(index + "");\r
 436                 index++;\r
 437 \r
 438                 break;\r
 439             }\r
 440             else\r
 441             {\r
 442                 index++;\r
 443             }\r
 444         }\r
 445 \r
 446         //FIND START RES\r
 447         //Returns residue following index if gap\r
 448         startRes = seq.findPosition(sg.getStartRes());\r
 449 \r
 450         //FIND END RES\r
 451         //Need to find the residue preceeding index if gap\r
 452         endRes = 0;\r
 453 \r
 454         for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
 455         {\r
 456           ch = seq.getCharAt(j);\r
 457           if (!jalview.util.Comparison.isGap( (ch)))\r
 458           {\r
 459             endRes++;\r
 460           }\r
 461         }\r
 462 \r
 463         if(endRes>0)\r
 464         {\r
 465           endRes += seq.getStart() -1;\r
 466         }\r
 467 \r
 468         copiedSequences.append(seq.getName() + "\t" +\r
 469             startRes + "\t" +\r
 470             endRes + "\t" +\r
 471             seq.getSequence(sg.getStartRes(),\r
 472                 sg.getEndRes() + 1) + "\n");\r
 473     }\r
 474 \r
 475   }\r
 476 \r
 477   protected void pasteNew_actionPerformed(ActionEvent e)\r
 478   {\r
 479     paste(true);\r
 480   }\r
 481 \r
 482   protected void pasteThis_actionPerformed(ActionEvent e)\r
 483   {\r
 484     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
 485                                    HistoryItem.PASTE));\r
 486     paste(false);\r
 487   }\r
 488 \r
 489   void paste(boolean newAlignment)\r
 490   {\r
 491     try\r
 492     {\r
 493       if (copiedSequences == null)\r
 494       {\r
 495         return;\r
 496       }\r
 497 \r
 498       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 499       Vector seqs = new Vector();\r
 500       while (st.hasMoreElements())\r
 501       {\r
 502         String name = st.nextToken();\r
 503         int start = Integer.parseInt(st.nextToken());\r
 504         int end = Integer.parseInt(st.nextToken());\r
 505         Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
 506 \r
 507         if (!newAlignment)\r
 508         {\r
 509           viewport.alignment.addSequence(sequence);\r
 510         }\r
 511         else\r
 512         {\r
 513           seqs.addElement(sequence);\r
 514         }\r
 515       }\r
 516 \r
 517       if (newAlignment)\r
 518       {\r
 519         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 520         for (int i = 0; i < seqs.size(); i++)\r
 521         {\r
 522           newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
 523         }\r
 524 \r
 525         String newtitle = new String("Copied sequences");\r
 526         if (getTitle().startsWith("Copied sequences"))\r
 527         {\r
 528           newtitle = getTitle();\r
 529         }\r
 530         else\r
 531         {\r
 532           newtitle = newtitle.concat("- from " + getTitle());\r
 533         }\r
 534         AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle);\r
 535 \r
 536         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
 537                                          NEW_WINDOW_HEIGHT);\r
 538       }\r
 539       else\r
 540       {\r
 541         viewport.setEndSeq(viewport.alignment.getHeight());\r
 542         viewport.alignment.getWidth();\r
 543         viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 544       }\r
 545 \r
 546     }\r
 547     catch (Exception ex)\r
 548     {} // could be anything being pasted in here\r
 549 \r
 550   }\r
 551 \r
 552   protected void cut_actionPerformed(ActionEvent e)\r
 553   {\r
 554     copy_actionPerformed(null);\r
 555     delete_actionPerformed(null);\r
 556   }\r
 557 \r
 558   protected void delete_actionPerformed(ActionEvent e)\r
 559   {\r
 560     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
 561                                    HistoryItem.HIDE));\r
 562     if (viewport.getSelectionGroup() == null)\r
 563     {\r
 564       return;\r
 565     }\r
 566 \r
 567 \r
 568     SequenceGroup sg = viewport.getSelectionGroup();\r
 569     boolean allSequences = false;\r
 570     if(sg.sequences.size()==viewport.alignment.getHeight())\r
 571           allSequences = true;\r
 572 \r
 573     for (int i = 0; i < sg.sequences.size(); i++)\r
 574     {\r
 575       SequenceI seq = sg.getSequenceAt(i);\r
 576       int index = viewport.getAlignment().findIndex(seq);\r
 577       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 578 \r
 579       // If the cut affects all sequences, remove highlighted columns\r
 580       if (allSequences)\r
 581       {\r
 582         viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
 583                                                      sg.getEndRes() + 1);\r
 584       }\r
 585 \r
 586 \r
 587       if (seq.getSequence().length() < 1)\r
 588       {\r
 589         viewport.getAlignment().deleteSequence(seq);\r
 590       }\r
 591       else\r
 592       {\r
 593         viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 594       }\r
 595     }\r
 596 \r
 597     viewport.setSelectionGroup(null);\r
 598     viewport.alignment.deleteGroup(sg);\r
 599     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
 600     if (viewport.getAlignment().getHeight() < 1)\r
 601     {\r
 602       try\r
 603       {\r
 604         this.setVisible(false);\r
 605       }\r
 606       catch (Exception ex)\r
 607       {}\r
 608     }\r
 609     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 610 \r
 611   }\r
 612 \r
 613   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 614   {\r
 615     viewport.alignment.deleteAllGroups();\r
 616     viewport.setSelectionGroup(null);\r
 617 \r
 618     alignPanel.repaint();\r
 619   }\r
 620 \r
 621   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 622   {\r
 623     SequenceGroup sg = new SequenceGroup();\r
 624     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 625     {\r
 626       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
 627     }\r
 628     sg.setEndRes(viewport.alignment.getWidth()-1);\r
 629     viewport.setSelectionGroup(sg);\r
 630     alignPanel.repaint();\r
 631     PaintRefresher.Refresh(null, viewport.alignment);\r
 632   }\r
 633 \r
 634   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 635   {\r
 636     viewport.setSelectionGroup(null);\r
 637     viewport.getColumnSelection().clear();\r
 638     viewport.setSelectionGroup(null);\r
 639     alignPanel.repaint();\r
 640     PaintRefresher.Refresh(null, viewport.alignment);\r
 641   }\r
 642 \r
 643   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 644   {\r
 645     SequenceGroup sg = viewport.getSelectionGroup();\r
 646     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 647     {\r
 648       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
 649     }\r
 650 \r
 651     PaintRefresher.Refresh(null, viewport.alignment);\r
 652   }\r
 653 \r
 654   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 655   {\r
 656     ColumnSelection colSel = viewport.getColumnSelection();\r
 657     if (colSel.size() > 0)\r
 658     {\r
 659       addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
 660                                      HistoryItem.HIDE));\r
 661       int min = colSel.getMin();\r
 662       viewport.getAlignment().trimLeft(min);\r
 663       colSel.compensateForEdit(0, min);\r
 664 \r
 665       if (viewport.getSelectionGroup() != null)\r
 666       {\r
 667         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 668       }\r
 669 \r
 670       Vector groups = viewport.alignment.getGroups();\r
 671       for (int i = 0; i < groups.size(); i++)\r
 672       {\r
 673         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 674         if (!sg.adjustForRemoveLeft(min))\r
 675         {\r
 676           viewport.alignment.deleteGroup(sg);\r
 677         }\r
 678       }\r
 679       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 680     }\r
 681   }\r
 682 \r
 683   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 684   {\r
 685     ColumnSelection colSel = viewport.getColumnSelection();\r
 686     if (colSel.size() > 0)\r
 687     {\r
 688       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
 689                                      HistoryItem.HIDE));\r
 690       int max = colSel.getMax();\r
 691       viewport.getAlignment().trimRight(max);\r
 692       if (viewport.getSelectionGroup() != null)\r
 693       {\r
 694         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 695       }\r
 696 \r
 697       Vector groups = viewport.alignment.getGroups();\r
 698       for (int i = 0; i < groups.size(); i++)\r
 699       {\r
 700         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 701         if (!sg.adjustForRemoveRight(max))\r
 702         {\r
 703           viewport.alignment.deleteGroup(sg);\r
 704         }\r
 705       }\r
 706       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 707     }\r
 708 \r
 709   }\r
 710 \r
 711   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 712   {\r
 713     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
 714                                    viewport.alignment,\r
 715                                    HistoryItem.HIDE));\r
 716 \r
 717     //This is to maintain viewport position on first residue\r
 718     //of first sequence\r
 719     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 720     int startRes = seq.findPosition(viewport.startRes);\r
 721 \r
 722     viewport.getAlignment().removeGaps();\r
 723 \r
 724     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 725 \r
 726     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 727   }\r
 728 \r
 729   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 730   {\r
 731     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
 732                                    HistoryItem.HIDE));\r
 733 \r
 734     //This is to maintain viewport position on first residue\r
 735     //of first sequence\r
 736     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 737     int startRes = seq.findPosition(viewport.startRes);\r
 738 \r
 739     SequenceI current;\r
 740     int jSize;\r
 741 \r
 742     Vector seqs=null;\r
 743 \r
 744     int start=0, end = viewport.alignment.getWidth();\r
 745 \r
 746     if (viewport.getSelectionGroup() != null\r
 747         && viewport.getSelectionGroup().sequences != null\r
 748         && viewport.getSelectionGroup().sequences.size()>0)\r
 749     {\r
 750       seqs = viewport.getSelectionGroup().sequences;\r
 751       start = viewport.getSelectionGroup().getStartRes();\r
 752       end = viewport.getSelectionGroup().getEndRes()+1;\r
 753     }\r
 754     else\r
 755       seqs = viewport.alignment.getSequences();\r
 756 \r
 757     for (int i = 0; i < seqs.size(); i++)\r
 758     {\r
 759       current = (SequenceI) seqs.elementAt(i);\r
 760       jSize = current.getLength();\r
 761 \r
 762       // Removing a range is much quicker than removing gaps\r
 763       // one by one for long sequences\r
 764       int j = start;\r
 765       int rangeStart=-1, rangeEnd=-1;\r
 766 \r
 767       do\r
 768       {\r
 769         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 770         {\r
 771           if(rangeStart==-1)\r
 772            {\r
 773              rangeStart = j;\r
 774              rangeEnd = j+1;\r
 775            }\r
 776            else\r
 777            {\r
 778              rangeEnd++;\r
 779            }\r
 780            j++;\r
 781         }\r
 782         else\r
 783         {\r
 784           if(rangeStart>-1)\r
 785           {\r
 786             current.deleteChars(rangeStart, rangeEnd);\r
 787             j-=rangeEnd-rangeStart;\r
 788             jSize-=rangeEnd-rangeStart;\r
 789             rangeStart = -1;\r
 790             rangeEnd = -1;\r
 791           }\r
 792           else\r
 793             j++;\r
 794         }\r
 795       }\r
 796       while (j < end && j < jSize);\r
 797       if(rangeStart>-1)\r
 798       {\r
 799        current.deleteChars(rangeStart, rangeEnd);\r
 800       }\r
 801     }\r
 802     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 803     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 804   }\r
 805 \r
 806   public void alignmentChanged()\r
 807   {\r
 808     viewport.updateConsensus();\r
 809     viewport.updateConservation ();\r
 810     resetAllColourSchemes();\r
 811     if(alignPanel.overviewPanel!=null)\r
 812       alignPanel.overviewPanel.updateOverviewImage();\r
 813     alignPanel.repaint();\r
 814   }\r
 815 \r
 816   void resetAllColourSchemes()\r
 817   {\r
 818     ColourSchemeI cs = viewport.globalColourScheme;\r
 819     if(cs!=null)\r
 820     {\r
 821       if (cs instanceof ClustalxColourScheme)\r
 822       {\r
 823         ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
 824             resetClustalX(viewport.alignment.getSequences(),\r
 825                           viewport.alignment.getWidth());\r
 826       }\r
 827 \r
 828       cs.setConsensus(viewport.vconsensus);\r
 829       if (cs.conservationApplied())\r
 830       {\r
 831         Alignment al = (Alignment) viewport.alignment;\r
 832         Conservation c = new Conservation("All",\r
 833                                           ResidueProperties.propHash, 3,\r
 834                                           al.getSequences(), 0,\r
 835                                           al.getWidth() - 1);\r
 836         c.calculate();\r
 837         c.verdict(false, viewport.ConsPercGaps);\r
 838 \r
 839         cs.setConservation(c);\r
 840       }\r
 841     }\r
 842 \r
 843     int s, sSize = viewport.alignment.getGroups().size();\r
 844     for(s=0; s<sSize; s++)\r
 845     {\r
 846       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
 847       if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
 848       {\r
 849         ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
 850       }\r
 851       sg.recalcConservation();\r
 852     }\r
 853   }\r
 854 \r
 855 \r
 856 \r
 857   public void findMenuItem_actionPerformed(ActionEvent e)\r
 858   {\r
 859     new Finder(alignPanel);\r
 860   }\r
 861 \r
 862   public void font_actionPerformed(ActionEvent e)\r
 863   {\r
 864     new FontChooser(alignPanel);\r
 865   }\r
 866 \r
 867   public void dbref_actionPerformed(ItemEvent e)\r
 868   {\r
 869     viewport.showDBPrefix = dbref.getState();\r
 870     alignPanel.fontChanged();\r
 871     alignPanel.repaint();\r
 872   }\r
 873 \r
 874   public void seqLimits_itemStateChanged(ItemEvent e)\r
 875   {\r
 876     viewport.setShowJVSuffix(seqLimits.getState());\r
 877     alignPanel.fontChanged();\r
 878     alignPanel.repaint();\r
 879   }\r
 880 \r
 881 \r
 882   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 883   {\r
 884     viewport.setColourText(colourTextMenuItem.getState());\r
 885     alignPanel.repaint();\r
 886   }\r
 887 \r
 888   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 889   {\r
 890     viewport.setWrapAlignment(wrapMenuItem.getState());\r
 891     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
 892     scaleAbove.setEnabled(wrapMenuItem.getState());\r
 893     scaleLeft.setEnabled(wrapMenuItem.getState());\r
 894     scaleRight.setEnabled(wrapMenuItem.getState());\r
 895     alignPanel.repaint();\r
 896   }\r
 897 \r
 898   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 899   {\r
 900     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 901     alignPanel.repaint();\r
 902   }\r
 903 \r
 904   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 905   {\r
 906     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 907     alignPanel.repaint();\r
 908   }\r
 909 \r
 910   protected void scaleRight_actionPerformed(ActionEvent e)\r
 911   {\r
 912     viewport.setScaleRightWrapped(scaleRight.getState());\r
 913     alignPanel.repaint();\r
 914   }\r
 915 \r
 916   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 917   {\r
 918     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
 919     alignPanel.repaint();\r
 920   }\r
 921 \r
 922   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 923   {\r
 924     viewport.setShowText(viewTextMenuItem.getState());\r
 925     alignPanel.repaint();\r
 926   }\r
 927 \r
 928   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 929   {\r
 930     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 931     alignPanel.repaint();\r
 932   }\r
 933 \r
 934   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 935   {\r
 936     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
 937     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
 938   }\r
 939 \r
 940   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 941   {\r
 942     if (alignPanel.overviewPanel != null)\r
 943     {\r
 944       return;\r
 945     }\r
 946 \r
 947     Frame frame = new Frame();\r
 948     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 949     frame.add(overview);\r
 950     // +50 must allow for applet frame window\r
 951     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
 952                                      overview.preferredSize().width,\r
 953                                      overview.preferredSize().height + 50);\r
 954 \r
 955     frame.pack();\r
 956     frame.addWindowListener(new WindowAdapter()\r
 957     {\r
 958       public void windowClosing(WindowEvent e)\r
 959       {\r
 960         alignPanel.setOverviewPanel(null);\r
 961       };\r
 962     });\r
 963 \r
 964     alignPanel.setOverviewPanel(overview);\r
 965 \r
 966   }\r
 967 \r
 968   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 969   {\r
 970     changeColour(null);\r
 971   }\r
 972 \r
 973   public void clustalColour_actionPerformed(ActionEvent e)\r
 974   {\r
 975     abovePIDThreshold.setState(false);\r
 976     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
 977                                           viewport.alignment.getWidth()));\r
 978   }\r
 979 \r
 980   public void zappoColour_actionPerformed(ActionEvent e)\r
 981   {\r
 982     changeColour(new ZappoColourScheme());\r
 983   }\r
 984 \r
 985   public void taylorColour_actionPerformed(ActionEvent e)\r
 986   {\r
 987     changeColour(new TaylorColourScheme());\r
 988   }\r
 989 \r
 990   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 991   {\r
 992     changeColour(new HydrophobicColourScheme());\r
 993   }\r
 994 \r
 995   public void helixColour_actionPerformed(ActionEvent e)\r
 996   {\r
 997     changeColour(new HelixColourScheme());\r
 998   }\r
 999 \r
1000   public void strandColour_actionPerformed(ActionEvent e)\r
1001   {\r
1002     changeColour(new StrandColourScheme());\r
1003   }\r
1004 \r
1005   public void turnColour_actionPerformed(ActionEvent e)\r
1006   {\r
1007     changeColour(new TurnColourScheme());\r
1008   }\r
1009 \r
1010   public void buriedColour_actionPerformed(ActionEvent e)\r
1011   {\r
1012     changeColour(new BuriedColourScheme());\r
1013   }\r
1014 \r
1015   public void nucleotideColour_actionPerformed(ActionEvent e)\r
1016   {\r
1017     changeColour(new NucleotideColourScheme());\r
1018   }\r
1019 \r
1020   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1021   {\r
1022     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
1023   }\r
1024 \r
1025   void changeColour(ColourSchemeI cs)\r
1026   {\r
1027     int threshold = 0;\r
1028 \r
1029     if(cs!=null)\r
1030     {\r
1031       if (viewport.getAbovePIDThreshold())\r
1032       {\r
1033         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
1034 \r
1035         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1036 \r
1037         viewport.setGlobalColourScheme(cs);\r
1038       }\r
1039       else\r
1040       {\r
1041         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1042       }\r
1043 \r
1044       if (viewport.getConservationSelected())\r
1045       {\r
1046 \r
1047         Alignment al = (Alignment) viewport.alignment;\r
1048         Conservation c = new Conservation("All",\r
1049                                           ResidueProperties.propHash, 3,\r
1050                                           al.getSequences(), 0,\r
1051                                           al.getWidth() - 1);\r
1052 \r
1053         c.calculate();\r
1054         c.verdict(false, viewport.ConsPercGaps);\r
1055 \r
1056         cs.setConservation(c);\r
1057 \r
1058         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
1059             "Background"));\r
1060 \r
1061       }\r
1062       else\r
1063       {\r
1064         cs.setConservation(null);\r
1065       }\r
1066 \r
1067       cs.setConsensus(viewport.vconsensus);\r
1068 \r
1069     }\r
1070     viewport.setGlobalColourScheme(cs);\r
1071 \r
1072     if (viewport.getColourAppliesToAllGroups())\r
1073     {\r
1074       Vector groups = viewport.alignment.getGroups();\r
1075       for (int i = 0; i < groups.size(); i++)\r
1076       {\r
1077         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1078 \r
1079         if(cs==null)\r
1080         {\r
1081           sg.cs = null;\r
1082           continue;\r
1083         }\r
1084         if (cs instanceof ClustalxColourScheme)\r
1085         {\r
1086           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
1087         }\r
1088         else\r
1089         {\r
1090           try\r
1091           {\r
1092             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
1093           }\r
1094           catch (Exception ex)\r
1095           {\r
1096             ex.printStackTrace();\r
1097             sg.cs = cs;\r
1098           }\r
1099         }\r
1100 \r
1101         if (viewport.getAbovePIDThreshold()\r
1102             || cs instanceof PIDColourScheme\r
1103             || cs instanceof Blosum62ColourScheme)\r
1104         {\r
1105           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1106           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
1107         }\r
1108         else\r
1109           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1110 \r
1111         if (viewport.getConservationSelected())\r
1112         {\r
1113           Conservation c = new Conservation("Group",\r
1114                                             ResidueProperties.propHash, 3,\r
1115                                             sg.sequences, 0,\r
1116                                             viewport.alignment.getWidth() - 1);\r
1117           c.calculate();\r
1118           c.verdict(false, viewport.ConsPercGaps);\r
1119           sg.cs.setConservation(c);\r
1120         }\r
1121         else\r
1122         {\r
1123           sg.cs.setConservation(null);\r
1124           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1125         }\r
1126 \r
1127       }\r
1128     }\r
1129 \r
1130 \r
1131     if (alignPanel.getOverviewPanel() != null)\r
1132     {\r
1133       alignPanel.getOverviewPanel().updateOverviewImage();\r
1134     }\r
1135 \r
1136     alignPanel.repaint();\r
1137   }\r
1138 \r
1139 \r
1140 \r
1141   protected void modifyPID_actionPerformed(ActionEvent e)\r
1142   {\r
1143     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
1144     {\r
1145       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
1146                                      "Background");\r
1147       SliderPanel.showPIDSlider();\r
1148     }\r
1149   }\r
1150 \r
1151   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1152   {\r
1153     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
1154     {\r
1155       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
1156                                         "Background");\r
1157       SliderPanel.showConservationSlider();\r
1158     }\r
1159   }\r
1160 \r
1161   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1162   {\r
1163     viewport.setConservationSelected(conservationMenuItem.getState());\r
1164 \r
1165     viewport.setAbovePIDThreshold(false);\r
1166     abovePIDThreshold.setState(false);\r
1167 \r
1168     changeColour(viewport.getGlobalColourScheme());\r
1169 \r
1170     modifyConservation_actionPerformed(null);\r
1171   }\r
1172 \r
1173   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1174   {\r
1175     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
1176 \r
1177     conservationMenuItem.setState(false);\r
1178     viewport.setConservationSelected(false);\r
1179 \r
1180     changeColour(viewport.getGlobalColourScheme());\r
1181 \r
1182     modifyPID_actionPerformed(null);\r
1183   }\r
1184 \r
1185   public void userDefinedColour_actionPerformed(ActionEvent e)\r
1186   {\r
1187     new UserDefinedColours(alignPanel, null);\r
1188   }\r
1189 \r
1190   public void PIDColour_actionPerformed(ActionEvent e)\r
1191   {\r
1192     changeColour(new PIDColourScheme());\r
1193   }\r
1194 \r
1195   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1196   {\r
1197     changeColour(new Blosum62ColourScheme());\r
1198   }\r
1199 \r
1200   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1201   {\r
1202     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1203                                    HistoryItem.SORT));\r
1204     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1205                               viewport.getAlignment().getSequenceAt(0));\r
1206     alignPanel.repaint();\r
1207   }\r
1208 \r
1209   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1210   {\r
1211     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1212                                    HistoryItem.SORT));\r
1213     AlignmentSorter.sortByID(viewport.getAlignment());\r
1214     alignPanel.repaint();\r
1215   }\r
1216 \r
1217   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1218   {\r
1219     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1220                                    HistoryItem.SORT));\r
1221     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1222     alignPanel.repaint();\r
1223 \r
1224   }\r
1225 \r
1226   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1227   {\r
1228     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
1229     Frame frame = new Frame();\r
1230     frame.add(sp);\r
1231     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
1232                                      400, 120);\r
1233 \r
1234   }\r
1235 \r
1236   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1237   {\r
1238     if (viewport.getSelectionGroup().getSize() > 1)\r
1239     {\r
1240       Frame frame = new Frame();\r
1241       frame.add(new PairwiseAlignPanel(alignPanel));\r
1242       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1243     }\r
1244   }\r
1245 \r
1246   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
1247   {\r
1248     //are the sequences aligned?\r
1249     if (!viewport.alignment.isAligned())\r
1250     {\r
1251       SequenceI current;\r
1252       int Width = viewport.getAlignment().getWidth();\r
1253 \r
1254       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1255            i++)\r
1256       {\r
1257         current = viewport.getAlignment().getSequenceAt(i);\r
1258 \r
1259         if (current.getLength() < Width)\r
1260         {\r
1261           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1262         }\r
1263       }\r
1264       alignPanel.repaint();\r
1265     }\r
1266 \r
1267     if ( (viewport.getSelectionGroup() != null &&\r
1268           viewport.getSelectionGroup().getSize() < 4 &&\r
1269           viewport.getSelectionGroup().getSize() > 0)\r
1270         || viewport.getAlignment().getHeight() < 4)\r
1271     {\r
1272       return;\r
1273     }\r
1274 \r
1275     try\r
1276     {\r
1277       new PCAPanel(viewport);\r
1278     }\r
1279     catch (java.lang.OutOfMemoryError ex)\r
1280     {\r
1281     }\r
1282 \r
1283   }\r
1284 \r
1285   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1286   {\r
1287     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1288   }\r
1289 \r
1290   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1291   {\r
1292     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1293   }\r
1294 \r
1295   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1296   {\r
1297     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1298   }\r
1299 \r
1300   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1301   {\r
1302     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1303   }\r
1304 \r
1305   void NewTreePanel(String type, String pwType, String title)\r
1306   {\r
1307     //are the sequences aligned?\r
1308     if (!viewport.alignment.isAligned())\r
1309     {\r
1310       SequenceI current;\r
1311       int Width = viewport.getAlignment().getWidth();\r
1312 \r
1313       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1314            i++)\r
1315       {\r
1316         current = viewport.getAlignment().getSequenceAt(i);\r
1317 \r
1318         if (current.getLength() < Width)\r
1319         {\r
1320           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1321         }\r
1322       }\r
1323       alignPanel.repaint();\r
1324 \r
1325     }\r
1326 \r
1327     final TreePanel tp;\r
1328     if (viewport.getSelectionGroup() != null &&\r
1329         viewport.getSelectionGroup().getSize() > 3)\r
1330     {\r
1331       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1332                          pwType,\r
1333                          0, viewport.alignment.getWidth());\r
1334     }\r
1335     else\r
1336     {\r
1337       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1338                          type, pwType, 0, viewport.alignment.getWidth());\r
1339     }\r
1340 \r
1341     addTreeMenuItem(tp, title);\r
1342 \r
1343     jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1344   }\r
1345 \r
1346   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1347   {\r
1348     final MenuItem item = new MenuItem(title);\r
1349     sortByTreeMenu.add(item);\r
1350     item.addActionListener(new java.awt.event.ActionListener()\r
1351     {\r
1352       public void actionPerformed(ActionEvent e)\r
1353       {\r
1354         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1355                                        HistoryItem.SORT));\r
1356         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1357         alignPanel.repaint();\r
1358       }\r
1359     });\r
1360 \r
1361     treePanel.addWindowListener(new WindowAdapter()\r
1362     {\r
1363       public void windowClosing(WindowEvent e)\r
1364       {\r
1365         sortByTreeMenu.remove(item);\r
1366       };\r
1367     });\r
1368   }\r
1369 \r
1370   protected void documentation_actionPerformed(ActionEvent e)\r
1371   {\r
1372     showURL("http://www.jalview.org/help.html");\r
1373   }\r
1374 \r
1375   protected void about_actionPerformed(ActionEvent e)\r
1376   {\r
1377 \r
1378     class AboutPanel extends Canvas\r
1379     {\r
1380       String version;\r
1381       public AboutPanel(String version)\r
1382       { this.version = version; }\r
1383 \r
1384       public void paint(Graphics g)\r
1385       {\r
1386         g.setColor(Color.white);\r
1387         g.fillRect(0, 0, getSize().width, getSize().height);\r
1388         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1389         FontMetrics fm = g.getFontMetrics();\r
1390         int fh = fm.getHeight();\r
1391         int y = 5, x = 7;\r
1392         g.setColor(Color.black);\r
1393         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1394         g.drawString("Jalview - Release "+version, 200, y += fh);\r
1395         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1396         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1397                      x, y += fh * 2);\r
1398         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1399                      x, y += fh);\r
1400         g.drawString(\r
1401             "For any issues relating to Jalview, email help@jalview.org", x,\r
1402             y += fh);\r
1403         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1404         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1405                      x, y += fh);\r
1406         g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);\r
1407       }\r
1408     }\r
1409 \r
1410     String version = "test";\r
1411     java.net.URL url = getClass().getResource("/.build_properties");\r
1412     if (url != null)\r
1413     {\r
1414       try\r
1415       {\r
1416         BufferedReader reader = new BufferedReader(new InputStreamReader(\r
1417             url.openStream()));\r
1418         String line;\r
1419         while ( (line = reader.readLine()) != null)\r
1420         {\r
1421           if (line.indexOf("VERSION") > -1)\r
1422           {\r
1423             version = line.substring(line.indexOf("=") + 1);\r
1424           }\r
1425         }\r
1426       }\r
1427       catch (Exception ex)\r
1428       {\r
1429         ex.printStackTrace();\r
1430       }\r
1431     }\r
1432 \r
1433 \r
1434     Frame frame = new Frame();\r
1435     frame.add(new AboutPanel(version));\r
1436     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1437 \r
1438   }\r
1439 \r
1440   /**\r
1441    * Displays the given URL in a new browser window\r
1442    *\r
1443    * @param url URL to display in browser window.\r
1444    * <br>New window will be named "HELP_WINDOW"\r
1445    */\r
1446   public void showURL(String url)\r
1447   {\r
1448     showURL(url, "HELP");\r
1449   }\r
1450 \r
1451   public void showURL(String url, String target)\r
1452   {\r
1453     if (applet == null)\r
1454     {\r
1455       System.out.println("Not running as applet - no browser available.");\r
1456     }\r
1457     else\r
1458     {\r
1459       try\r
1460       {\r
1461         applet.getAppletContext().showDocument(new java.net.URL(url),\r
1462                                                target);\r
1463       }\r
1464       catch (Exception ex)\r
1465       {\r
1466         ex.printStackTrace();\r
1467       }\r
1468     }\r
1469   }\r
1470 \r
1471 }\r