src/jalview/appletgui/AlignFrame.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 \r
  20 package jalview.appletgui;\r
  21 \r
  22 import jalview.schemes.*;\r
  23 import jalview.datamodel.*;\r
  24 import jalview.analysis.*;\r
  25 import jalview.io.*;\r
  26 import java.awt.*;\r
  27 import java.awt.event.*;\r
  28 import java.util.*;\r
  29 import java.io.InputStreamReader;\r
  30 import java.io.BufferedReader;\r
  31 import java.net.URL;\r
  32 \r
  33 \r
  34 public class AlignFrame extends Frame implements ActionListener,\r
  35     ItemListener, KeyListener, MouseListener\r
  36 {\r
  37   public AlignmentPanel alignPanel;\r
  38   public 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   String jalviewServletURL;\r
  44 \r
  45 \r
  46    public AlignFrame(AlignmentI al,\r
  47                      jalview.bin.JalviewLite applet,\r
  48                      String title,\r
  49                      boolean embedded)\r
  50   {\r
  51 \r
  52     jalviewServletURL = applet.getParameter("APPLICATION_URL");\r
  53 \r
  54     try{\r
  55       jbInit();\r
  56     }catch(Exception ex)\r
  57     {\r
  58       ex.printStackTrace();\r
  59     }\r
  60 \r
  61     this.applet = applet;\r
  62     viewport = new AlignViewport(al, applet);\r
  63     alignPanel = new AlignmentPanel(this, viewport);\r
  64 \r
  65     annotationPanelMenuItem.setState(viewport.showAnnotation);\r
  66 \r
  67     seqLimits.setState(viewport.showJVSuffix);\r
  68 \r
  69     if(applet!=null)\r
  70     {\r
  71       String param = applet.getParameter("sortBy");\r
  72       if (param != null)\r
  73       {\r
  74         if (param.equalsIgnoreCase("Id"))\r
  75           sortIDMenuItem_actionPerformed();\r
  76         else if (param.equalsIgnoreCase("Pairwise Identity"))\r
  77           sortPairwiseMenuItem_actionPerformed();\r
  78       }\r
  79 \r
  80       param = applet.getParameter("wrap");\r
  81       if (param != null)\r
  82       {\r
  83         if (param.equalsIgnoreCase("true"))\r
  84         {\r
  85           wrapMenuItem.setState(true);\r
  86           wrapMenuItem_actionPerformed();\r
  87         }\r
  88       }\r
  89 \r
  90       try\r
  91       {\r
  92         param = applet.getParameter("windowWidth");\r
  93         if (param != null)\r
  94         {\r
  95           int width = Integer.parseInt(param);\r
  96           NEW_WINDOW_WIDTH = width;\r
  97         }\r
  98         param = applet.getParameter("windowHeight");\r
  99         if (param != null)\r
 100         {\r
 101           int height = Integer.parseInt(param);\r
 102           NEW_WINDOW_HEIGHT = height;\r
 103         }\r
 104       }\r
 105       catch (Exception ex)\r
 106       {}\r
 107 \r
 108     }\r
 109 \r
 110    //Some JVMS send keyevents to Top frame or lowest panel,\r
 111    //Havent worked out why yet. So add to both this frame and seqCanvas for now\r
 112    this.addKeyListener(this);\r
 113    alignPanel.seqPanel.seqCanvas.addKeyListener(this);\r
 114    alignPanel.idPanel.idCanvas.addKeyListener(this);\r
 115 \r
 116     viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
 117     {\r
 118      public void propertyChange(java.beans.PropertyChangeEvent evt)\r
 119      {\r
 120        if (evt.getPropertyName().equals("alignment"))\r
 121        {\r
 122          alignmentChanged();\r
 123        }\r
 124      }\r
 125    });\r
 126 \r
 127 \r
 128    if(embedded)\r
 129    {\r
 130      setEmbedded();\r
 131    }\r
 132    else\r
 133    {\r
 134      add(alignPanel, BorderLayout.CENTER);\r
 135      jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH,\r
 136                                       NEW_WINDOW_HEIGHT);\r
 137    }\r
 138    alignPanel.validate();\r
 139    alignPanel.repaint();\r
 140   }\r
 141   public AlignViewport getAlignViewport()\r
 142   {\r
 143     return viewport;\r
 144   }\r
 145 \r
 146   public SeqCanvas getSeqcanvas()\r
 147   {\r
 148     return alignPanel.seqPanel.seqCanvas;\r
 149   }\r
 150 \r
 151 \r
 152   /**\r
 153    * DOCUMENT ME!\r
 154    *\r
 155    * @param String DOCUMENT ME!\r
 156    */\r
 157 \r
 158   public void parseFeaturesFile(String file, String type)\r
 159   {\r
 160     Hashtable featureLinks = new Hashtable();\r
 161     boolean featuresFile = false;\r
 162     try{\r
 163       featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,\r
 164                                          alignPanel.seqPanel.seqCanvas.\r
 165                                          getFeatureRenderer().featureColours,\r
 166                                          featureLinks,\r
 167                                          true);\r
 168     }\r
 169     catch(Exception ex)\r
 170     {\r
 171       ex.printStackTrace();\r
 172     }\r
 173 \r
 174     if(featuresFile)\r
 175     {\r
 176       if(featureLinks.size()>0)\r
 177         alignPanel.seqPanel.seqCanvas\r
 178             .getFeatureRenderer().featureLinks = featureLinks;\r
 179       viewport.showSequenceFeatures = true;\r
 180       sequenceFeatures.setState(true);\r
 181       alignPanel.repaint();\r
 182     }\r
 183 \r
 184   }\r
 185 \r
 186 \r
 187   public void keyPressed(KeyEvent evt)\r
 188   {\r
 189     if (viewport.cursorMode\r
 190         && evt.getKeyCode() >= KeyEvent.VK_0\r
 191         && evt.getKeyCode() <= KeyEvent.VK_9)\r
 192     {\r
 193       alignPanel.seqPanel.numberPressed(evt.getKeyChar());\r
 194     }\r
 195 \r
 196     switch (evt.getKeyCode())\r
 197     {\r
 198       case 27: // escape key\r
 199         deselectAllSequenceMenuItem_actionPerformed();\r
 200         break;\r
 201       case KeyEvent.VK_X:\r
 202         if (evt.isControlDown() || evt.isMetaDown())\r
 203         {\r
 204           cut_actionPerformed();\r
 205         }\r
 206         break;\r
 207       case KeyEvent.VK_C:\r
 208         if (viewport.cursorMode && !evt.isControlDown())\r
 209         {\r
 210           alignPanel.seqPanel.setCursorColumn();\r
 211         }\r
 212         if (evt.isControlDown() || evt.isMetaDown())\r
 213         {\r
 214           copy_actionPerformed();\r
 215         }\r
 216         break;\r
 217       case KeyEvent.VK_V:\r
 218         if (evt.isControlDown() || evt.isMetaDown())\r
 219         {\r
 220           paste(true);\r
 221         }\r
 222         break;\r
 223       case KeyEvent.VK_A:\r
 224         if (evt.isControlDown() || evt.isMetaDown())\r
 225         {\r
 226           selectAllSequenceMenuItem_actionPerformed();\r
 227         }\r
 228         break;\r
 229       case KeyEvent.VK_DOWN:\r
 230         if(viewport.cursorMode)\r
 231         {\r
 232           alignPanel.seqPanel.moveCursor(0,1);\r
 233         }\r
 234         else\r
 235           moveSelectedSequences(false);\r
 236         break;\r
 237 \r
 238       case KeyEvent.VK_UP:\r
 239         if (viewport.cursorMode)\r
 240         {\r
 241           alignPanel.seqPanel.moveCursor(0,-1);\r
 242         }\r
 243         else\r
 244           moveSelectedSequences(true);\r
 245         break;\r
 246 \r
 247       case KeyEvent.VK_LEFT:\r
 248         if(viewport.cursorMode)\r
 249         {\r
 250           alignPanel.seqPanel.moveCursor(-1,0);\r
 251         }\r
 252         break;\r
 253 \r
 254       case KeyEvent.VK_RIGHT:\r
 255         if (viewport.cursorMode)\r
 256         {\r
 257           alignPanel.seqPanel.moveCursor(1,0);\r
 258         }\r
 259         break;\r
 260       case KeyEvent.VK_SPACE:\r
 261         if(viewport.cursorMode)\r
 262         {\r
 263           alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown());\r
 264         }\r
 265         break;\r
 266 \r
 267       case KeyEvent.VK_DELETE:\r
 268       case KeyEvent.VK_BACK_SPACE:\r
 269         if(viewport.cursorMode)\r
 270         {\r
 271           alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown());\r
 272         }\r
 273        else\r
 274         {\r
 275           cut_actionPerformed();\r
 276           alignPanel.seqPanel.seqCanvas.repaint();\r
 277         }\r
 278         break;\r
 279 \r
 280       case KeyEvent.VK_S:\r
 281         if(viewport.cursorMode)\r
 282         {\r
 283           alignPanel.seqPanel.setCursorRow();\r
 284         }\r
 285         break;\r
 286       case KeyEvent.VK_P:\r
 287         if(viewport.cursorMode)\r
 288         {\r
 289           alignPanel.seqPanel.setCursorPosition();\r
 290         }\r
 291         break;\r
 292 \r
 293       case KeyEvent.VK_ENTER:\r
 294       case KeyEvent.VK_COMMA:\r
 295         if(viewport.cursorMode)\r
 296         {\r
 297           alignPanel.seqPanel.setCursorRowAndColumn();\r
 298         }\r
 299         break;\r
 300 \r
 301       case KeyEvent.VK_Q:\r
 302         if(viewport.cursorMode)\r
 303         {\r
 304           alignPanel.seqPanel.setSelectionAreaAtCursor(true);\r
 305         }\r
 306         break;\r
 307       case KeyEvent.VK_M:\r
 308         if(viewport.cursorMode)\r
 309         {\r
 310           alignPanel.seqPanel.setSelectionAreaAtCursor(false);\r
 311         }\r
 312         break;\r
 313 \r
 314      case KeyEvent.VK_F2:\r
 315        viewport.cursorMode = ! viewport.cursorMode;\r
 316        statusBar.setText("Keyboard editing mode is "+\r
 317            (viewport.cursorMode ? "on" : "off"));\r
 318        if(viewport.cursorMode)\r
 319        {\r
 320          alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;\r
 321          alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;\r
 322        }\r
 323        alignPanel.seqPanel.seqCanvas.repaint();\r
 324        break;\r
 325 \r
 326       case KeyEvent.VK_F:\r
 327         if (evt.isControlDown())\r
 328         {\r
 329           findMenuItem_actionPerformed();\r
 330         }\r
 331         break;\r
 332     }\r
 333   }\r
 334   public void keyReleased(KeyEvent evt)\r
 335   {}\r
 336   public void keyTyped(KeyEvent evt)\r
 337   {}\r
 338 \r
 339 public void itemStateChanged(ItemEvent evt)\r
 340   {\r
 341     if(evt.getSource()==colourTextMenuItem)\r
 342             colourTextMenuItem_actionPerformed();\r
 343     else if(evt.getSource()==wrapMenuItem)\r
 344             wrapMenuItem_actionPerformed();\r
 345     else if(evt.getSource()==scaleAbove)\r
 346             scaleAbove_actionPerformed();\r
 347     else if(evt.getSource()==scaleLeft)\r
 348             scaleLeft_actionPerformed();\r
 349     else if(evt.getSource()==scaleRight)\r
 350             scaleRight_actionPerformed();\r
 351      else if(evt.getSource()==seqLimits)\r
 352       seqLimits_itemStateChanged();\r
 353     else if(evt.getSource()==viewBoxesMenuItem)\r
 354             viewBoxesMenuItem_actionPerformed();\r
 355     else if(evt.getSource()==viewTextMenuItem)\r
 356             viewTextMenuItem_actionPerformed();\r
 357     else if(evt.getSource()==renderGapsMenuItem)\r
 358             renderGapsMenuItem_actionPerformed();\r
 359     else if(evt.getSource()==annotationPanelMenuItem)\r
 360             annotationPanelMenuItem_actionPerformed();\r
 361       else if(evt.getSource()==sequenceFeatures)\r
 362       {\r
 363            viewport.showSequenceFeatures(sequenceFeatures.getState());\r
 364             alignPanel.seqPanel.seqCanvas.repaint();\r
 365       }\r
 366       else if(evt.getSource()==conservationMenuItem)\r
 367             conservationMenuItem_actionPerformed();\r
 368       else if(evt.getSource()==abovePIDThreshold)\r
 369             abovePIDThreshold_actionPerformed();\r
 370           else if(evt.getSource()==applyToAllGroups)\r
 371             applyToAllGroups_actionPerformed();\r
 372       else if(evt.getSource()==autoCalculate)\r
 373           viewport.autocalculateConsensus = autoCalculate.getState();\r
 374   }\r
 375  public void actionPerformed(ActionEvent evt)\r
 376  {\r
 377     if(evt.getSource()==inputText)\r
 378       inputText_actionPerformed();\r
 379     else if(evt.getSource()==loadTree)\r
 380       loadTree_actionPerformed();\r
 381     else if(evt.getSource()==loadApplication)\r
 382       launchFullApplication();\r
 383     else if(evt.getSource()==closeMenuItem)\r
 384       closeMenuItem_actionPerformed();\r
 385     else if(evt.getSource()==copy)\r
 386       copy_actionPerformed();\r
 387     else if(evt.getSource()==undoMenuItem)\r
 388       undoMenuItem_actionPerformed();\r
 389     else if(evt.getSource()==redoMenuItem)\r
 390       redoMenuItem_actionPerformed();\r
 391     else if(evt.getSource()==inputText)\r
 392             inputText_actionPerformed();\r
 393     else if(evt.getSource()==closeMenuItem)\r
 394             closeMenuItem_actionPerformed();\r
 395     else if(evt.getSource()==undoMenuItem)\r
 396             undoMenuItem_actionPerformed();\r
 397     else if(evt.getSource()==redoMenuItem)\r
 398             redoMenuItem_actionPerformed();\r
 399     else if(evt.getSource()==copy)\r
 400             copy_actionPerformed();\r
 401     else if(evt.getSource()==pasteNew)\r
 402             pasteNew_actionPerformed();\r
 403     else if(evt.getSource()==pasteThis)\r
 404             pasteThis_actionPerformed();\r
 405     else if(evt.getSource()==cut)\r
 406             cut_actionPerformed();\r
 407     else if(evt.getSource()==delete)\r
 408             delete_actionPerformed();\r
 409     else if(evt.getSource()==deleteGroups)\r
 410             deleteGroups_actionPerformed();\r
 411     else if(evt.getSource()==selectAllSequenceMenuItem)\r
 412             selectAllSequenceMenuItem_actionPerformed();\r
 413     else if(evt.getSource()==deselectAllSequenceMenuItem)\r
 414             deselectAllSequenceMenuItem_actionPerformed();\r
 415     else if(evt.getSource()==invertSequenceMenuItem)\r
 416             invertSequenceMenuItem_actionPerformed();\r
 417     else if(evt.getSource()==remove2LeftMenuItem)\r
 418             remove2LeftMenuItem_actionPerformed();\r
 419     else if(evt.getSource()==remove2RightMenuItem)\r
 420             remove2RightMenuItem_actionPerformed();\r
 421     else if(evt.getSource()==removeGappedColumnMenuItem)\r
 422             removeGappedColumnMenuItem_actionPerformed();\r
 423     else if(evt.getSource()==removeAllGapsMenuItem)\r
 424             removeAllGapsMenuItem_actionPerformed();\r
 425     else if(evt.getSource()==findMenuItem)\r
 426             findMenuItem_actionPerformed();\r
 427     else if(evt.getSource()==font)\r
 428             font_actionPerformed();\r
 429     else if(evt.getSource()==featureSettings)\r
 430             featureSettings_actionPerformed();\r
 431     else if(evt.getSource()==overviewMenuItem)\r
 432             overviewMenuItem_actionPerformed();\r
 433     else if(evt.getSource()==noColourmenuItem)\r
 434             noColourmenuItem_actionPerformed();\r
 435     else if(evt.getSource()==clustalColour)\r
 436             clustalColour_actionPerformed();\r
 437     else if(evt.getSource()==zappoColour)\r
 438             zappoColour_actionPerformed();\r
 439     else if(evt.getSource()==taylorColour)\r
 440             taylorColour_actionPerformed();\r
 441     else if(evt.getSource()==hydrophobicityColour)\r
 442             hydrophobicityColour_actionPerformed();\r
 443     else if(evt.getSource()==helixColour)\r
 444             helixColour_actionPerformed();\r
 445     else if(evt.getSource()==strandColour)\r
 446             strandColour_actionPerformed();\r
 447     else if(evt.getSource()==turnColour)\r
 448             turnColour_actionPerformed();\r
 449     else if(evt.getSource()==buriedColour)\r
 450             buriedColour_actionPerformed();\r
 451     else if(evt.getSource()==nucleotideColour)\r
 452             nucleotideColour_actionPerformed();\r
 453     else if(evt.getSource()==modifyPID)\r
 454             modifyPID_actionPerformed();\r
 455     else if(evt.getSource()==modifyConservation)\r
 456             modifyConservation_actionPerformed();\r
 457     else if(evt.getSource()==userDefinedColour)\r
 458             userDefinedColour_actionPerformed();\r
 459     else if(evt.getSource()==PIDColour)\r
 460             PIDColour_actionPerformed();\r
 461     else if(evt.getSource()==BLOSUM62Colour)\r
 462             BLOSUM62Colour_actionPerformed();\r
 463     else if(evt.getSource()==annotationColour)\r
 464            new AnnotationColourChooser(viewport, alignPanel);\r
 465     else if(evt.getSource()==sortPairwiseMenuItem)\r
 466             sortPairwiseMenuItem_actionPerformed();\r
 467     else if(evt.getSource()==sortIDMenuItem)\r
 468             sortIDMenuItem_actionPerformed();\r
 469     else if(evt.getSource()==sortGroupMenuItem)\r
 470             sortGroupMenuItem_actionPerformed();\r
 471     else if(evt.getSource()==removeRedundancyMenuItem)\r
 472             removeRedundancyMenuItem_actionPerformed();\r
 473     else if(evt.getSource()==pairwiseAlignmentMenuItem)\r
 474             pairwiseAlignmentMenuItem_actionPerformed();\r
 475     else if(evt.getSource()==PCAMenuItem)\r
 476             PCAMenuItem_actionPerformed();\r
 477     else if(evt.getSource()==averageDistanceTreeMenuItem)\r
 478             averageDistanceTreeMenuItem_actionPerformed();\r
 479     else if(evt.getSource()==neighbourTreeMenuItem)\r
 480             neighbourTreeMenuItem_actionPerformed();\r
 481     else if(evt.getSource()==njTreeBlosumMenuItem)\r
 482             njTreeBlosumMenuItem_actionPerformed();\r
 483     else if(evt.getSource()==avDistanceTreeBlosumMenuItem)\r
 484             avTreeBlosumMenuItem_actionPerformed();\r
 485     else if(evt.getSource()==documentation)\r
 486             documentation_actionPerformed();\r
 487     else if(evt.getSource()==about)\r
 488             about_actionPerformed();\r
 489 \r
 490  }\r
 491 \r
 492   public void inputText_actionPerformed()\r
 493   {\r
 494     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
 495     Frame frame = new Frame();\r
 496     frame.add(cap);\r
 497     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
 498   }\r
 499 \r
 500   protected void outputText_actionPerformed(ActionEvent e)\r
 501   {\r
 502     CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
 503     Frame frame = new Frame();\r
 504     frame.add(cap);\r
 505     jalview.bin.JalviewLite.addFrame(frame,\r
 506                                      "Alignment output - " + e.getActionCommand(),\r
 507                                      600, 500);\r
 508     cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
 509                                               viewport.getAlignment().getSequences(),\r
 510                                                       viewport.showJVSuffix));\r
 511   }\r
 512 \r
 513   void launchFullApplication()\r
 514   {\r
 515     StringBuffer url = new StringBuffer(jalviewServletURL);\r
 516 \r
 517     url.append("?open="+\r
 518                appendProtocol( applet.getParameter("file") ) );\r
 519 \r
 520     if(applet.getParameter("features")!=null)\r
 521     {\r
 522       url.append( "&features=" );\r
 523       url.append( appendProtocol( applet.getParameter("features") ) );\r
 524     }\r
 525 \r
 526     if(applet.getParameter("defaultColour")!=null)\r
 527     {\r
 528       url.append("&colour=" +\r
 529                  removeWhiteSpace(applet.getParameter("defaultColour"))\r
 530           );\r
 531     }\r
 532 \r
 533     if(applet.getParameter("userDefinedColour")!=null)\r
 534     {\r
 535       url.append( "&colour=" +\r
 536                  removeWhiteSpace( applet.getParameter("userDefinedColour") )\r
 537          );\r
 538     }\r
 539 \r
 540     showURL(url.toString(), "FULL_APP");\r
 541   }\r
 542 \r
 543 \r
 544   String removeWhiteSpace(String colour)\r
 545   {\r
 546     StringBuffer sb = new StringBuffer();\r
 547     for (int i = 0; i < colour.length(); i++)\r
 548     {\r
 549       if (Character.isWhitespace(colour.charAt(i)))\r
 550         sb.append("%20");\r
 551       else\r
 552         sb.append(colour.charAt(i));\r
 553     }\r
 554 \r
 555     return sb.toString();\r
 556   }\r
 557 \r
 558 \r
 559   String appendProtocol(String url)\r
 560   {\r
 561     try{\r
 562        new URL(url);\r
 563     }catch(java.net.MalformedURLException ex)\r
 564     {\r
 565       url = applet.getCodeBase()+url;\r
 566     }\r
 567     return url;\r
 568   }\r
 569 \r
 570   public void closeMenuItem_actionPerformed()\r
 571   {\r
 572     PaintRefresher.components.remove(viewport.alignment);\r
 573     if(PaintRefresher.components.size()==0 && applet==null)\r
 574       System.exit(0);\r
 575 \r
 576     this.dispose();\r
 577   }\r
 578 \r
 579   Stack historyList = new Stack();\r
 580   Stack redoList = new Stack();\r
 581 \r
 582   void updateEditMenuBar()\r
 583   {\r
 584     if (historyList.size() > 0)\r
 585     {\r
 586       undoMenuItem.setEnabled(true);\r
 587       HistoryItem hi = (HistoryItem) historyList.peek();\r
 588       undoMenuItem.setLabel("Undo " + hi.getDescription());\r
 589     }\r
 590     else\r
 591     {\r
 592       undoMenuItem.setEnabled(false);\r
 593       undoMenuItem.setLabel("Undo");\r
 594     }\r
 595 \r
 596     if (redoList.size() > 0)\r
 597     {\r
 598       redoMenuItem.setEnabled(true);\r
 599       HistoryItem hi = (HistoryItem) redoList.peek();\r
 600       redoMenuItem.setLabel("Redo " + hi.getDescription());\r
 601     }\r
 602     else\r
 603     {\r
 604       redoMenuItem.setEnabled(false);\r
 605       redoMenuItem.setLabel("Redo");\r
 606     }\r
 607   }\r
 608 \r
 609   public void addHistoryItem(HistoryItem hi)\r
 610   {\r
 611     historyList.push(hi);\r
 612     updateEditMenuBar();\r
 613   }\r
 614 \r
 615   protected void undoMenuItem_actionPerformed()\r
 616   {\r
 617     HistoryItem hi = (HistoryItem) historyList.pop();\r
 618     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
 619                                   HistoryItem.HIDE));\r
 620     restoreHistoryItem(hi);\r
 621     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 622   }\r
 623 \r
 624   protected void redoMenuItem_actionPerformed()\r
 625   {\r
 626     HistoryItem hi = (HistoryItem) redoList.pop();\r
 627     restoreHistoryItem(hi);\r
 628     updateEditMenuBar();\r
 629     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 630   }\r
 631 \r
 632   // used by undo and redo\r
 633   void restoreHistoryItem(HistoryItem hi)\r
 634   {\r
 635     hi.restore();\r
 636 \r
 637     updateEditMenuBar();\r
 638 \r
 639     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 640   }\r
 641 \r
 642   public void moveSelectedSequences(boolean up)\r
 643   {\r
 644     SequenceGroup sg = viewport.getSelectionGroup();\r
 645     if (sg == null)\r
 646     {\r
 647       return;\r
 648     }\r
 649 \r
 650     if (up)\r
 651     {\r
 652       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 653       {\r
 654         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 655         if (!sg.getSequences(false).contains(seq))\r
 656         {\r
 657           continue;\r
 658         }\r
 659 \r
 660         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 661         if (sg.getSequences(false).contains(temp))\r
 662         {\r
 663           continue;\r
 664         }\r
 665 \r
 666         viewport.alignment.getSequences().setElementAt(temp, i);\r
 667         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 668       }\r
 669     }\r
 670     else\r
 671     {\r
 672       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 673       {\r
 674         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 675         if (!sg.getSequences(true).contains(seq))\r
 676         {\r
 677           continue;\r
 678         }\r
 679 \r
 680         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 681         if (sg.getSequences(true).contains(temp))\r
 682         {\r
 683           continue;\r
 684         }\r
 685 \r
 686         viewport.alignment.getSequences().setElementAt(temp, i);\r
 687         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 688       }\r
 689     }\r
 690 \r
 691     alignPanel.repaint();\r
 692   }\r
 693 \r
 694   StringBuffer copiedSequences;\r
 695   protected void copy_actionPerformed()\r
 696   {\r
 697     if (viewport.getSelectionGroup() == null)\r
 698     {\r
 699       return;\r
 700     }\r
 701 \r
 702     SequenceGroup sg = viewport.getSelectionGroup();\r
 703     copiedSequences = new StringBuffer();\r
 704     Hashtable orderedSeqs = new Hashtable();\r
 705     for (int i = 0; i < sg.getSize(false); i++)\r
 706     {\r
 707       SequenceI seq = sg.getSequenceAt(i);\r
 708       int index = viewport.alignment.findIndex(seq);\r
 709       orderedSeqs.put(index + "", seq);\r
 710     }\r
 711 \r
 712     int index = 0, startRes, endRes;\r
 713     char ch;\r
 714 \r
 715     for (int i = 0; i < sg.getSize(false); i++)\r
 716     {\r
 717         SequenceI seq = null;\r
 718 \r
 719         while (seq == null)\r
 720         {\r
 721             if (orderedSeqs.containsKey(index + ""))\r
 722             {\r
 723                 seq = (SequenceI) orderedSeqs.get(index + "");\r
 724                 index++;\r
 725 \r
 726                 break;\r
 727             }\r
 728             else\r
 729             {\r
 730                 index++;\r
 731             }\r
 732         }\r
 733 \r
 734         //FIND START RES\r
 735         //Returns residue following index if gap\r
 736         startRes = seq.findPosition(sg.getStartRes());\r
 737 \r
 738         //FIND END RES\r
 739         //Need to find the residue preceeding index if gap\r
 740         endRes = 0;\r
 741 \r
 742         for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
 743         {\r
 744           ch = seq.getCharAt(j);\r
 745           if (!jalview.util.Comparison.isGap( (ch)))\r
 746           {\r
 747             endRes++;\r
 748           }\r
 749         }\r
 750 \r
 751         if(endRes>0)\r
 752         {\r
 753           endRes += seq.getStart() -1;\r
 754         }\r
 755 \r
 756         copiedSequences.append(seq.getName() + "\t" +\r
 757             startRes + "\t" +\r
 758             endRes + "\t" +\r
 759             seq.getSequence(sg.getStartRes(),\r
 760                 sg.getEndRes() + 1) + "\n");\r
 761     }\r
 762 \r
 763   }\r
 764 \r
 765   protected void pasteNew_actionPerformed()\r
 766   {\r
 767     paste(true);\r
 768   }\r
 769 \r
 770   protected void pasteThis_actionPerformed()\r
 771   {\r
 772     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
 773                                    HistoryItem.PASTE));\r
 774     paste(false);\r
 775   }\r
 776 \r
 777   void paste(boolean newAlignment)\r
 778   {\r
 779     try\r
 780     {\r
 781       if (copiedSequences == null)\r
 782       {\r
 783         return;\r
 784       }\r
 785 \r
 786       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 787       Vector seqs = new Vector();\r
 788       while (st.hasMoreElements())\r
 789       {\r
 790         String name = st.nextToken();\r
 791         int start = Integer.parseInt(st.nextToken());\r
 792         int end = Integer.parseInt(st.nextToken());\r
 793         Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
 794 \r
 795         if (!newAlignment)\r
 796         {\r
 797           viewport.alignment.addSequence(sequence);\r
 798         }\r
 799         else\r
 800         {\r
 801           seqs.addElement(sequence);\r
 802         }\r
 803       }\r
 804 \r
 805       if (newAlignment)\r
 806       {\r
 807         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 808         for (int i = 0; i < seqs.size(); i++)\r
 809         {\r
 810           newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
 811         }\r
 812 \r
 813         String newtitle = new String("Copied sequences");\r
 814         if (getTitle().startsWith("Copied sequences"))\r
 815         {\r
 816           newtitle = getTitle();\r
 817         }\r
 818         else\r
 819         {\r
 820           newtitle = newtitle.concat("- from " + getTitle());\r
 821         }\r
 822         AlignFrame af = new AlignFrame(new Alignment(newSeqs),\r
 823                                        applet,\r
 824                                        newtitle,\r
 825                                        false);\r
 826 \r
 827         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
 828                                          NEW_WINDOW_HEIGHT);\r
 829       }\r
 830       else\r
 831       {\r
 832         viewport.setEndSeq(viewport.alignment.getHeight());\r
 833         viewport.alignment.getWidth();\r
 834         viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 835       }\r
 836 \r
 837     }\r
 838     catch (Exception ex)\r
 839     {} // could be anything being pasted in here\r
 840 \r
 841   }\r
 842 \r
 843   protected void cut_actionPerformed()\r
 844   {\r
 845     copy_actionPerformed();\r
 846     delete_actionPerformed();\r
 847   }\r
 848 \r
 849   protected void delete_actionPerformed()\r
 850   {\r
 851     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
 852                                    HistoryItem.HIDE));\r
 853     if (viewport.getSelectionGroup() == null)\r
 854     {\r
 855       return;\r
 856     }\r
 857 \r
 858 \r
 859     SequenceGroup sg = viewport.getSelectionGroup();\r
 860     boolean allSequences = false;\r
 861     if(sg.getSize(false)==viewport.alignment.getHeight())\r
 862           allSequences = true;\r
 863 \r
 864     for (int i = 0; i < sg.getSize(false); i++)\r
 865     {\r
 866       SequenceI seq = sg.getSequenceAt(i);\r
 867       int index = viewport.getAlignment().findIndex(seq);\r
 868       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 869 \r
 870       // If the cut affects all sequences, remove highlighted columns\r
 871       if (allSequences)\r
 872       {\r
 873         viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
 874                                                      sg.getEndRes() + 1);\r
 875       }\r
 876 \r
 877 \r
 878       if (seq.getSequence().length() < 1)\r
 879       {\r
 880         viewport.getAlignment().deleteSequence(seq);\r
 881       }\r
 882       else\r
 883       {\r
 884         viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 885       }\r
 886     }\r
 887 \r
 888     viewport.setSelectionGroup(null);\r
 889     viewport.alignment.deleteGroup(sg);\r
 890     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
 891     if (viewport.getAlignment().getHeight() < 1)\r
 892     {\r
 893       try\r
 894       {\r
 895         this.setVisible(false);\r
 896       }\r
 897       catch (Exception ex)\r
 898       {}\r
 899     }\r
 900     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 901 \r
 902   }\r
 903 \r
 904   protected void deleteGroups_actionPerformed()\r
 905   {\r
 906     viewport.alignment.deleteAllGroups();\r
 907     viewport.setSelectionGroup(null);\r
 908 \r
 909     alignPanel.repaint();\r
 910   }\r
 911 \r
 912   public void selectAllSequenceMenuItem_actionPerformed()\r
 913   {\r
 914     SequenceGroup sg = new SequenceGroup();\r
 915     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 916     {\r
 917       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
 918     }\r
 919     sg.setEndRes(viewport.alignment.getWidth()-1);\r
 920     viewport.setSelectionGroup(sg);\r
 921     alignPanel.repaint();\r
 922     PaintRefresher.Refresh(null, viewport.alignment);\r
 923   }\r
 924 \r
 925   public void deselectAllSequenceMenuItem_actionPerformed()\r
 926   {\r
 927     if(viewport.cursorMode)\r
 928     {\r
 929       alignPanel.seqPanel.keyboardNo1=null;\r
 930       alignPanel.seqPanel.keyboardNo2=null;\r
 931     }\r
 932     viewport.setSelectionGroup(null);\r
 933     viewport.getColumnSelection().clear();\r
 934     viewport.setSelectionGroup(null);\r
 935     alignPanel.idPanel.idCanvas.searchResults = null;\r
 936     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
 937     alignPanel.repaint();\r
 938     PaintRefresher.Refresh(null, viewport.alignment);\r
 939   }\r
 940 \r
 941   public void invertSequenceMenuItem_actionPerformed()\r
 942   {\r
 943     SequenceGroup sg = viewport.getSelectionGroup();\r
 944     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 945     {\r
 946       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
 947     }\r
 948 \r
 949     PaintRefresher.Refresh(null, viewport.alignment);\r
 950   }\r
 951 \r
 952   public void remove2LeftMenuItem_actionPerformed()\r
 953   {\r
 954     ColumnSelection colSel = viewport.getColumnSelection();\r
 955     if (colSel.size() > 0)\r
 956     {\r
 957       addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
 958                                      HistoryItem.HIDE));\r
 959       int min = colSel.getMin();\r
 960       viewport.getAlignment().trimLeft(min);\r
 961       colSel.compensateForEdit(0, min);\r
 962 \r
 963       if (viewport.getSelectionGroup() != null)\r
 964       {\r
 965         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 966       }\r
 967 \r
 968       Vector groups = viewport.alignment.getGroups();\r
 969       for (int i = 0; i < groups.size(); i++)\r
 970       {\r
 971         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 972         if (!sg.adjustForRemoveLeft(min))\r
 973         {\r
 974           viewport.alignment.deleteGroup(sg);\r
 975         }\r
 976       }\r
 977       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 978     }\r
 979   }\r
 980 \r
 981   public void remove2RightMenuItem_actionPerformed()\r
 982   {\r
 983     ColumnSelection colSel = viewport.getColumnSelection();\r
 984     if (colSel.size() > 0)\r
 985     {\r
 986       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
 987                                      HistoryItem.HIDE));\r
 988       int max = colSel.getMax();\r
 989       viewport.getAlignment().trimRight(max);\r
 990       if (viewport.getSelectionGroup() != null)\r
 991       {\r
 992         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 993       }\r
 994 \r
 995       Vector groups = viewport.alignment.getGroups();\r
 996       for (int i = 0; i < groups.size(); i++)\r
 997       {\r
 998         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 999         if (!sg.adjustForRemoveRight(max))\r
1000         {\r
1001           viewport.alignment.deleteGroup(sg);\r
1002         }\r
1003       }\r
1004       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1005     }\r
1006 \r
1007   }\r
1008 \r
1009   public void removeGappedColumnMenuItem_actionPerformed()\r
1010   {\r
1011     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
1012                                    viewport.alignment,\r
1013                                    HistoryItem.HIDE));\r
1014 \r
1015     //This is to maintain viewport position on first residue\r
1016     //of first sequence\r
1017     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
1018     int startRes = seq.findPosition(viewport.startRes);\r
1019 \r
1020     viewport.getAlignment().removeGaps();\r
1021 \r
1022     viewport.setStartRes(seq.findIndex(startRes)-1);\r
1023 \r
1024     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1025   }\r
1026 \r
1027   public void removeAllGapsMenuItem_actionPerformed()\r
1028   {\r
1029     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
1030                                    HistoryItem.HIDE));\r
1031 \r
1032     //This is to maintain viewport position on first residue\r
1033     //of first sequence\r
1034     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
1035     int startRes = seq.findPosition(viewport.startRes);\r
1036 \r
1037     SequenceI current;\r
1038     int jSize;\r
1039 \r
1040     Vector seqs=null;\r
1041 \r
1042     int start=0, end = viewport.alignment.getWidth();\r
1043 \r
1044     if (viewport.getSelectionGroup() != null\r
1045         && viewport.getSelectionGroup().getSequences(false) != null\r
1046         && viewport.getSelectionGroup().getSize(false)>0)\r
1047     {\r
1048       seqs = viewport.getSelectionGroup().getSequences(true);\r
1049       start = viewport.getSelectionGroup().getStartRes();\r
1050       end = viewport.getSelectionGroup().getEndRes()+1;\r
1051     }\r
1052     else\r
1053       seqs = viewport.alignment.getSequences();\r
1054 \r
1055     for (int i = 0; i < seqs.size(); i++)\r
1056     {\r
1057       current = (SequenceI) seqs.elementAt(i);\r
1058       jSize = current.getLength();\r
1059 \r
1060       // Removing a range is much quicker than removing gaps\r
1061       // one by one for long sequences\r
1062       int j = start;\r
1063       int rangeStart=-1, rangeEnd=-1;\r
1064 \r
1065       do\r
1066       {\r
1067         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
1068         {\r
1069           if(rangeStart==-1)\r
1070            {\r
1071              rangeStart = j;\r
1072              rangeEnd = j+1;\r
1073            }\r
1074            else\r
1075            {\r
1076              rangeEnd++;\r
1077            }\r
1078            j++;\r
1079         }\r
1080         else\r
1081         {\r
1082           if(rangeStart>-1)\r
1083           {\r
1084             current.deleteChars(rangeStart, rangeEnd);\r
1085             j-=rangeEnd-rangeStart;\r
1086             jSize-=rangeEnd-rangeStart;\r
1087             rangeStart = -1;\r
1088             rangeEnd = -1;\r
1089           }\r
1090           else\r
1091             j++;\r
1092         }\r
1093       }\r
1094       while (j < end && j < jSize);\r
1095       if(rangeStart>-1)\r
1096       {\r
1097        current.deleteChars(rangeStart, rangeEnd);\r
1098       }\r
1099     }\r
1100     viewport.setStartRes(seq.findIndex(startRes)-1);\r
1101     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1102   }\r
1103 \r
1104   public void alignmentChanged()\r
1105   {\r
1106     viewport.alignment.padGaps();\r
1107     if(viewport.autocalculateConsensus)\r
1108     {\r
1109       viewport.updateConsensus();\r
1110       viewport.updateConservation();\r
1111     }\r
1112 \r
1113     resetAllColourSchemes();\r
1114     if(alignPanel.overviewPanel!=null)\r
1115       alignPanel.overviewPanel.updateOverviewImage();\r
1116 \r
1117     viewport.alignment.adjustSequenceAnnotations();\r
1118     alignPanel.repaint();\r
1119   }\r
1120 \r
1121   void resetAllColourSchemes()\r
1122   {\r
1123     ColourSchemeI cs = viewport.globalColourScheme;\r
1124     if(cs!=null)\r
1125     {\r
1126       if (cs instanceof ClustalxColourScheme)\r
1127       {\r
1128         ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
1129             resetClustalX(viewport.alignment.getSequences(),\r
1130                           viewport.alignment.getWidth());\r
1131       }\r
1132 \r
1133       cs.setConsensus(viewport.vconsensus);\r
1134       if (cs.conservationApplied())\r
1135       {\r
1136         Alignment al = (Alignment) viewport.alignment;\r
1137         Conservation c = new Conservation("All",\r
1138                                           ResidueProperties.propHash, 3,\r
1139                                           al.getSequences(), 0,\r
1140                                           al.getWidth() - 1);\r
1141         c.calculate();\r
1142         c.verdict(false, viewport.ConsPercGaps);\r
1143 \r
1144         cs.setConservation(c);\r
1145       }\r
1146     }\r
1147 \r
1148     int s, sSize = viewport.alignment.getGroups().size();\r
1149     for(s=0; s<sSize; s++)\r
1150     {\r
1151       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
1152       if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
1153       {\r
1154         ((ClustalxColourScheme)sg.cs).resetClustalX(\r
1155             sg.getSequences(true), sg.getWidth());\r
1156       }\r
1157       sg.recalcConservation();\r
1158     }\r
1159   }\r
1160 \r
1161 \r
1162 \r
1163   public void findMenuItem_actionPerformed()\r
1164   {\r
1165     new Finder(alignPanel);\r
1166   }\r
1167 \r
1168   public void font_actionPerformed()\r
1169   {\r
1170     new FontChooser(alignPanel);\r
1171   }\r
1172 \r
1173 \r
1174   public void seqLimits_itemStateChanged()\r
1175   {\r
1176     viewport.setShowJVSuffix(seqLimits.getState());\r
1177     alignPanel.fontChanged();\r
1178     alignPanel.repaint();\r
1179   }\r
1180 \r
1181 \r
1182   protected void colourTextMenuItem_actionPerformed()\r
1183   {\r
1184     viewport.setColourText(colourTextMenuItem.getState());\r
1185     alignPanel.repaint();\r
1186   }\r
1187 \r
1188   protected void wrapMenuItem_actionPerformed()\r
1189   {\r
1190     viewport.setWrapAlignment(wrapMenuItem.getState());\r
1191     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
1192     scaleAbove.setEnabled(wrapMenuItem.getState());\r
1193     scaleLeft.setEnabled(wrapMenuItem.getState());\r
1194     scaleRight.setEnabled(wrapMenuItem.getState());\r
1195     alignPanel.repaint();\r
1196   }\r
1197 \r
1198   protected void scaleAbove_actionPerformed()\r
1199   {\r
1200     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
1201     alignPanel.repaint();\r
1202   }\r
1203 \r
1204   protected void scaleLeft_actionPerformed()\r
1205   {\r
1206     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
1207     alignPanel.repaint();\r
1208   }\r
1209 \r
1210   protected void scaleRight_actionPerformed()\r
1211   {\r
1212     viewport.setScaleRightWrapped(scaleRight.getState());\r
1213     alignPanel.repaint();\r
1214   }\r
1215 \r
1216   public void viewBoxesMenuItem_actionPerformed()\r
1217   {\r
1218     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
1219     alignPanel.repaint();\r
1220   }\r
1221 \r
1222   public void viewTextMenuItem_actionPerformed()\r
1223   {\r
1224     viewport.setShowText(viewTextMenuItem.getState());\r
1225     alignPanel.repaint();\r
1226   }\r
1227 \r
1228   protected void renderGapsMenuItem_actionPerformed()\r
1229   {\r
1230     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
1231     alignPanel.repaint();\r
1232   }\r
1233 \r
1234   public void annotationPanelMenuItem_actionPerformed()\r
1235   {\r
1236     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
1237     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
1238   }\r
1239 \r
1240   public void featureSettings_actionPerformed()\r
1241   {\r
1242     new FeatureSettings(viewport, alignPanel);\r
1243   }\r
1244 \r
1245   public void overviewMenuItem_actionPerformed()\r
1246   {\r
1247     if (alignPanel.overviewPanel != null)\r
1248     {\r
1249       return;\r
1250     }\r
1251 \r
1252     Frame frame = new Frame();\r
1253     OverviewPanel overview = new OverviewPanel(alignPanel);\r
1254     frame.add(overview);\r
1255     // +50 must allow for applet frame window\r
1256     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
1257                                      overview.preferredSize().width,\r
1258                                      overview.preferredSize().height + 50);\r
1259 \r
1260     frame.pack();\r
1261     frame.addWindowListener(new WindowAdapter()\r
1262     {\r
1263       public void windowClosing(WindowEvent e)\r
1264       {\r
1265         alignPanel.setOverviewPanel(null);\r
1266       };\r
1267     });\r
1268 \r
1269     alignPanel.setOverviewPanel(overview);\r
1270 \r
1271   }\r
1272 \r
1273   protected void noColourmenuItem_actionPerformed()\r
1274   {\r
1275     changeColour(null);\r
1276   }\r
1277 \r
1278   public void clustalColour_actionPerformed()\r
1279   {\r
1280     abovePIDThreshold.setState(false);\r
1281     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
1282                                           viewport.alignment.getWidth()));\r
1283   }\r
1284 \r
1285   public void zappoColour_actionPerformed()\r
1286   {\r
1287     changeColour(new ZappoColourScheme());\r
1288   }\r
1289 \r
1290   public void taylorColour_actionPerformed()\r
1291   {\r
1292     changeColour(new TaylorColourScheme());\r
1293   }\r
1294 \r
1295   public void hydrophobicityColour_actionPerformed()\r
1296   {\r
1297     changeColour(new HydrophobicColourScheme());\r
1298   }\r
1299 \r
1300   public void helixColour_actionPerformed()\r
1301   {\r
1302     changeColour(new HelixColourScheme());\r
1303   }\r
1304 \r
1305   public void strandColour_actionPerformed()\r
1306   {\r
1307     changeColour(new StrandColourScheme());\r
1308   }\r
1309 \r
1310   public void turnColour_actionPerformed()\r
1311   {\r
1312     changeColour(new TurnColourScheme());\r
1313   }\r
1314 \r
1315   public void buriedColour_actionPerformed()\r
1316   {\r
1317     changeColour(new BuriedColourScheme());\r
1318   }\r
1319 \r
1320   public void nucleotideColour_actionPerformed()\r
1321   {\r
1322     changeColour(new NucleotideColourScheme());\r
1323   }\r
1324 \r
1325   protected void applyToAllGroups_actionPerformed()\r
1326   {\r
1327     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
1328   }\r
1329 \r
1330   void changeColour(ColourSchemeI cs)\r
1331   {\r
1332     int threshold = 0;\r
1333 \r
1334     if(cs!=null)\r
1335     {\r
1336       if (viewport.getAbovePIDThreshold())\r
1337       {\r
1338         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
1339 \r
1340         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1341 \r
1342         viewport.setGlobalColourScheme(cs);\r
1343       }\r
1344       else\r
1345       {\r
1346         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1347       }\r
1348 \r
1349       if (viewport.getConservationSelected())\r
1350       {\r
1351 \r
1352         Alignment al = (Alignment) viewport.alignment;\r
1353         Conservation c = new Conservation("All",\r
1354                                           ResidueProperties.propHash, 3,\r
1355                                           al.getSequences(), 0,\r
1356                                           al.getWidth() - 1);\r
1357 \r
1358         c.calculate();\r
1359         c.verdict(false, viewport.ConsPercGaps);\r
1360 \r
1361         cs.setConservation(c);\r
1362 \r
1363         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
1364             "Background"));\r
1365 \r
1366       }\r
1367       else\r
1368       {\r
1369         cs.setConservation(null);\r
1370       }\r
1371 \r
1372       cs.setConsensus(viewport.vconsensus);\r
1373 \r
1374     }\r
1375     viewport.setGlobalColourScheme(cs);\r
1376 \r
1377     if (viewport.getColourAppliesToAllGroups())\r
1378     {\r
1379       Vector groups = viewport.alignment.getGroups();\r
1380       for (int i = 0; i < groups.size(); i++)\r
1381       {\r
1382         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1383 \r
1384         if(cs==null)\r
1385         {\r
1386           sg.cs = null;\r
1387           continue;\r
1388         }\r
1389         if (cs instanceof ClustalxColourScheme)\r
1390         {\r
1391           sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());\r
1392         }\r
1393         else\r
1394         {\r
1395           try\r
1396           {\r
1397             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
1398           }\r
1399           catch (Exception ex)\r
1400           {\r
1401             ex.printStackTrace();\r
1402             sg.cs = cs;\r
1403           }\r
1404         }\r
1405 \r
1406         if (viewport.getAbovePIDThreshold()\r
1407             || cs instanceof PIDColourScheme\r
1408             || cs instanceof Blosum62ColourScheme)\r
1409         {\r
1410           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1411           sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));\r
1412         }\r
1413         else\r
1414           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1415 \r
1416         if (viewport.getConservationSelected())\r
1417         {\r
1418           Conservation c = new Conservation("Group",\r
1419                                             ResidueProperties.propHash, 3,\r
1420                                             sg.getSequences(true), 0,\r
1421                                             viewport.alignment.getWidth() - 1);\r
1422           c.calculate();\r
1423           c.verdict(false, viewport.ConsPercGaps);\r
1424           sg.cs.setConservation(c);\r
1425         }\r
1426         else\r
1427         {\r
1428           sg.cs.setConservation(null);\r
1429           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1430         }\r
1431 \r
1432       }\r
1433     }\r
1434 \r
1435 \r
1436     if (alignPanel.getOverviewPanel() != null)\r
1437     {\r
1438       alignPanel.getOverviewPanel().updateOverviewImage();\r
1439     }\r
1440 \r
1441     alignPanel.repaint();\r
1442   }\r
1443 \r
1444 \r
1445 \r
1446   protected void modifyPID_actionPerformed()\r
1447   {\r
1448     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
1449     {\r
1450       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
1451                                      "Background");\r
1452       SliderPanel.showPIDSlider();\r
1453     }\r
1454   }\r
1455 \r
1456   protected void modifyConservation_actionPerformed()\r
1457   {\r
1458     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
1459     {\r
1460       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
1461                                         "Background");\r
1462       SliderPanel.showConservationSlider();\r
1463     }\r
1464   }\r
1465 \r
1466   protected void conservationMenuItem_actionPerformed()\r
1467   {\r
1468     viewport.setConservationSelected(conservationMenuItem.getState());\r
1469 \r
1470     viewport.setAbovePIDThreshold(false);\r
1471     abovePIDThreshold.setState(false);\r
1472 \r
1473     changeColour(viewport.getGlobalColourScheme());\r
1474 \r
1475     modifyConservation_actionPerformed();\r
1476   }\r
1477 \r
1478   public void abovePIDThreshold_actionPerformed()\r
1479   {\r
1480     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
1481 \r
1482     conservationMenuItem.setState(false);\r
1483     viewport.setConservationSelected(false);\r
1484 \r
1485     changeColour(viewport.getGlobalColourScheme());\r
1486 \r
1487     modifyPID_actionPerformed();\r
1488   }\r
1489 \r
1490   public void userDefinedColour_actionPerformed()\r
1491   {\r
1492     new UserDefinedColours(alignPanel, null);\r
1493   }\r
1494 \r
1495   public void PIDColour_actionPerformed()\r
1496   {\r
1497     changeColour(new PIDColourScheme());\r
1498   }\r
1499 \r
1500   public void BLOSUM62Colour_actionPerformed()\r
1501   {\r
1502     changeColour(new Blosum62ColourScheme());\r
1503   }\r
1504 \r
1505   public void sortPairwiseMenuItem_actionPerformed()\r
1506   {\r
1507     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1508                                    HistoryItem.SORT));\r
1509     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1510                               viewport.getAlignment().getSequenceAt(0));\r
1511     alignPanel.repaint();\r
1512   }\r
1513 \r
1514   public void sortIDMenuItem_actionPerformed()\r
1515   {\r
1516     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1517                                    HistoryItem.SORT));\r
1518     AlignmentSorter.sortByID(viewport.getAlignment());\r
1519     alignPanel.repaint();\r
1520   }\r
1521 \r
1522   public void sortGroupMenuItem_actionPerformed()\r
1523   {\r
1524     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1525                                    HistoryItem.SORT));\r
1526     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1527     alignPanel.repaint();\r
1528 \r
1529   }\r
1530 \r
1531   public void removeRedundancyMenuItem_actionPerformed()\r
1532   {\r
1533      new RedundancyPanel(alignPanel);\r
1534   }\r
1535 \r
1536   public void pairwiseAlignmentMenuItem_actionPerformed()\r
1537   {\r
1538     if (viewport.getSelectionGroup().getSize(false) > 1)\r
1539     {\r
1540       Frame frame = new Frame();\r
1541       frame.add(new PairwiseAlignPanel(alignPanel));\r
1542       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1543     }\r
1544   }\r
1545 \r
1546   public void PCAMenuItem_actionPerformed()\r
1547   {\r
1548     //are the sequences aligned?\r
1549     if (!viewport.alignment.isAligned())\r
1550     {\r
1551       SequenceI current;\r
1552       int Width = viewport.getAlignment().getWidth();\r
1553 \r
1554       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1555            i++)\r
1556       {\r
1557         current = viewport.getAlignment().getSequenceAt(i);\r
1558 \r
1559         if (current.getLength() < Width)\r
1560         {\r
1561           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1562         }\r
1563       }\r
1564       alignPanel.repaint();\r
1565     }\r
1566 \r
1567     if ( (viewport.getSelectionGroup() != null &&\r
1568           viewport.getSelectionGroup().getSize(false) < 4 &&\r
1569           viewport.getSelectionGroup().getSize(false) > 0)\r
1570         || viewport.getAlignment().getHeight() < 4)\r
1571     {\r
1572       return;\r
1573     }\r
1574 \r
1575     try\r
1576     {\r
1577       new PCAPanel(viewport);\r
1578     }\r
1579     catch (java.lang.OutOfMemoryError ex)\r
1580     {\r
1581     }\r
1582 \r
1583   }\r
1584 \r
1585   public void averageDistanceTreeMenuItem_actionPerformed()\r
1586   {\r
1587     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1588   }\r
1589 \r
1590   public void neighbourTreeMenuItem_actionPerformed()\r
1591   {\r
1592     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1593   }\r
1594 \r
1595   protected void njTreeBlosumMenuItem_actionPerformed()\r
1596   {\r
1597     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1598   }\r
1599 \r
1600   protected void avTreeBlosumMenuItem_actionPerformed()\r
1601   {\r
1602     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1603   }\r
1604 \r
1605   void NewTreePanel(String type, String pwType, String title)\r
1606   {\r
1607     //are the sequences aligned?\r
1608     if (!viewport.alignment.isAligned())\r
1609     {\r
1610       SequenceI current;\r
1611       int Width = viewport.getAlignment().getWidth();\r
1612 \r
1613       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1614            i++)\r
1615       {\r
1616         current = viewport.getAlignment().getSequenceAt(i);\r
1617 \r
1618         if (current.getLength() < Width)\r
1619         {\r
1620           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1621         }\r
1622       }\r
1623       alignPanel.repaint();\r
1624 \r
1625     }\r
1626 \r
1627     final TreePanel tp = new TreePanel(viewport,\r
1628                          type,\r
1629                          pwType);\r
1630 \r
1631     addTreeMenuItem(tp, title);\r
1632 \r
1633     jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1634   }\r
1635 \r
1636   void loadTree_actionPerformed()\r
1637   {\r
1638       CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
1639       cap.setText("Paste your Newick tree file here.");\r
1640       cap.treeImport = true;\r
1641       Frame frame = new Frame();\r
1642       frame.add(cap);\r
1643       jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);\r
1644   }\r
1645 \r
1646   public void loadTree(jalview.io.NewickFile tree, String treeFile)\r
1647   {\r
1648     TreePanel tp = new TreePanel(viewport,\r
1649                                  treeFile,\r
1650                                  "From File - ",\r
1651                                  tree);\r
1652     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
1653     addTreeMenuItem(tp, treeFile);\r
1654   }\r
1655 \r
1656   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1657   {\r
1658     final MenuItem item = new MenuItem(title);\r
1659     sortByTreeMenu.add(item);\r
1660     item.addActionListener(new java.awt.event.ActionListener()\r
1661     {\r
1662       public void actionPerformed(ActionEvent evt)\r
1663       {\r
1664         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1665                                        HistoryItem.SORT));\r
1666         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1667         alignPanel.repaint();\r
1668       }\r
1669     });\r
1670 \r
1671     treePanel.addWindowListener(new WindowAdapter()\r
1672     {\r
1673       public void windowClosing(WindowEvent e)\r
1674       {\r
1675         sortByTreeMenu.remove(item);\r
1676       };\r
1677     });\r
1678   }\r
1679 \r
1680   protected void documentation_actionPerformed()\r
1681   {\r
1682     showURL("http://www.jalview.org/help.html", "HELP");\r
1683   }\r
1684 \r
1685   protected void about_actionPerformed()\r
1686   {\r
1687 \r
1688     class AboutPanel extends Canvas\r
1689     {\r
1690       String version;\r
1691       public AboutPanel(String version)\r
1692       { this.version = version; }\r
1693 \r
1694       public void paint(Graphics g)\r
1695       {\r
1696         g.setColor(Color.white);\r
1697         g.fillRect(0, 0, getSize().width, getSize().height);\r
1698         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1699         FontMetrics fm = g.getFontMetrics();\r
1700         int fh = fm.getHeight();\r
1701         int y = 5, x = 7;\r
1702         g.setColor(Color.black);\r
1703         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1704         g.drawString("Jalview - Release "+version, 200, y += fh);\r
1705         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1706         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1707                      x, y += fh * 2);\r
1708         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1709                      x, y += fh);\r
1710         g.drawString(\r
1711             "For any issues relating to Jalview, email help@jalview.org", x,\r
1712             y += fh);\r
1713         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1714         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1715                      x, y += fh);\r
1716         g.drawString("Bioinformatics,  2004 20;426-7.", x, y += fh);\r
1717       }\r
1718     }\r
1719 \r
1720     String version = "test";\r
1721     java.net.URL url = getClass().getResource("/.build_properties");\r
1722     if (url != null)\r
1723     {\r
1724       try\r
1725       {\r
1726         BufferedReader reader = new BufferedReader(new InputStreamReader(\r
1727             url.openStream()));\r
1728         String line;\r
1729         while ( (line = reader.readLine()) != null)\r
1730         {\r
1731           if (line.indexOf("VERSION") > -1)\r
1732           {\r
1733             version = line.substring(line.indexOf("=") + 1);\r
1734           }\r
1735         }\r
1736       }\r
1737       catch (Exception ex)\r
1738       {\r
1739         ex.printStackTrace();\r
1740       }\r
1741     }\r
1742 \r
1743 \r
1744     Frame frame = new Frame();\r
1745     frame.add(new AboutPanel(version));\r
1746     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1747 \r
1748   }\r
1749 \r
1750   public void showURL(String url, String target)\r
1751   {\r
1752     if (applet == null)\r
1753     {\r
1754       System.out.println("Not running as applet - no browser available.");\r
1755     }\r
1756     else\r
1757     {\r
1758       try\r
1759       {\r
1760         System.out.println("Show url: "+url);\r
1761         applet.getAppletContext().showDocument(new java.net.URL(url),\r
1762                                                target);\r
1763       }\r
1764       catch (Exception ex)\r
1765       {\r
1766         ex.printStackTrace();\r
1767       }\r
1768     }\r
1769   }\r
1770 \r
1771 \r
1772   //////////////////////////////////////////////////////////////////////////////////\r
1773   //JBuilder Graphics here\r
1774 \r
1775     protected MenuBar alignFrameMenuBar = new MenuBar();\r
1776     protected Menu fileMenu = new Menu("File");\r
1777     protected MenuItem loadApplication = new MenuItem("View in Full Application");\r
1778     protected MenuItem loadTree = new MenuItem("Load Associated Tree");\r
1779     protected MenuItem closeMenuItem = new MenuItem("Close");\r
1780     protected Menu editMenu = new Menu("Edit");\r
1781     protected Menu viewMenu = new Menu("View");\r
1782     protected Menu colourMenu = new Menu("Colour");\r
1783     protected Menu calculateMenu = new Menu("Calculate");\r
1784     protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
1785     protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
1786     protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
1787     protected MenuItem remove2LeftMenuItem = new MenuItem();\r
1788     protected MenuItem remove2RightMenuItem = new MenuItem();\r
1789     protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
1790     protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
1791     protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
1792     protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
1793     protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
1794     protected MenuItem sortIDMenuItem = new MenuItem();\r
1795     protected MenuItem sortGroupMenuItem = new MenuItem();\r
1796     protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
1797     protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
1798     protected MenuItem PCAMenuItem = new MenuItem();\r
1799     protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
1800     protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
1801     BorderLayout borderLayout1 = new BorderLayout();\r
1802     public Label statusBar = new Label();\r
1803     protected Menu outputTextboxMenu = new Menu();\r
1804     protected MenuItem clustalColour = new MenuItem();\r
1805     protected MenuItem zappoColour = new MenuItem();\r
1806     protected MenuItem taylorColour = new MenuItem();\r
1807     protected MenuItem hydrophobicityColour = new MenuItem();\r
1808     protected MenuItem helixColour = new MenuItem();\r
1809     protected MenuItem strandColour = new MenuItem();\r
1810     protected MenuItem turnColour = new MenuItem();\r
1811     protected MenuItem buriedColour = new MenuItem();\r
1812     protected MenuItem userDefinedColour = new MenuItem();\r
1813     protected MenuItem PIDColour = new MenuItem();\r
1814     protected MenuItem BLOSUM62Colour = new MenuItem();\r
1815     MenuItem njTreeBlosumMenuItem = new MenuItem();\r
1816     MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
1817     protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
1818     protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
1819     MenuItem overviewMenuItem = new MenuItem();\r
1820     protected MenuItem undoMenuItem = new MenuItem();\r
1821     protected MenuItem redoMenuItem = new MenuItem();\r
1822     protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
1823     MenuItem noColourmenuItem = new MenuItem();\r
1824     protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
1825     protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
1826     MenuItem findMenuItem = new MenuItem();\r
1827     Menu searchMenu = new Menu();\r
1828     protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
1829     protected MenuItem nucleotideColour = new MenuItem();\r
1830     MenuItem deleteGroups = new MenuItem();\r
1831     MenuItem delete = new MenuItem();\r
1832     MenuItem copy = new MenuItem();\r
1833     MenuItem cut = new MenuItem();\r
1834     Menu pasteMenu = new Menu();\r
1835     MenuItem pasteNew = new MenuItem();\r
1836     MenuItem pasteThis = new MenuItem();\r
1837     protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
1838     protected MenuItem font = new MenuItem();\r
1839     protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
1840     protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
1841     protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
1842     MenuItem modifyPID = new MenuItem();\r
1843     MenuItem modifyConservation = new MenuItem();\r
1844     protected CheckboxMenuItem autoCalculate\r
1845         = new CheckboxMenuItem("Autocalculate Consensus", true);\r
1846     protected Menu sortByTreeMenu = new Menu();\r
1847     Menu sort = new Menu();\r
1848     Menu calculate = new Menu();\r
1849     MenuItem inputText = new MenuItem();\r
1850     Menu helpMenu = new Menu();\r
1851     MenuItem documentation = new MenuItem();\r
1852     MenuItem about = new MenuItem();\r
1853     protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
1854   Panel embeddedMenu;\r
1855   Label embeddedEdit;\r
1856   Label embeddedSearch;\r
1857   Label embeddedView;\r
1858   Label embeddedColour;\r
1859   Label embeddedFile;\r
1860   Label embeddedHelp;\r
1861   Label embeddedCalculate;\r
1862   FlowLayout flowLayout1;\r
1863 \r
1864   private void jbInit() throws Exception {\r
1865 \r
1866       setMenuBar(alignFrameMenuBar);\r
1867 \r
1868       MenuItem item;\r
1869 \r
1870       // dynamically fill save as menu with available formats\r
1871       for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)\r
1872       {\r
1873 \r
1874         item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.\r
1875                             elementAt(\r
1876                                 i));\r
1877         item.addActionListener(new java.awt.event.ActionListener()\r
1878         {\r
1879           public void actionPerformed(ActionEvent e)\r
1880           {\r
1881             outputText_actionPerformed(e);\r
1882           }\r
1883         });\r
1884 \r
1885         outputTextboxMenu.add(item);\r
1886       }\r
1887         closeMenuItem.addActionListener(this);\r
1888         loadApplication.addActionListener(this);\r
1889 \r
1890         loadTree.addActionListener(this);\r
1891         selectAllSequenceMenuItem.addActionListener(this);\r
1892         deselectAllSequenceMenuItem.addActionListener(this);\r
1893         invertSequenceMenuItem.addActionListener(this);\r
1894         remove2LeftMenuItem.setLabel("Remove Left");\r
1895         remove2LeftMenuItem.addActionListener(this);\r
1896         remove2RightMenuItem.setLabel("Remove Right");\r
1897         remove2RightMenuItem.addActionListener(this);\r
1898         removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
1899         removeGappedColumnMenuItem.addActionListener(this);\r
1900         removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
1901         removeAllGapsMenuItem.addActionListener(this);\r
1902         viewBoxesMenuItem.setLabel("Boxes");\r
1903         viewBoxesMenuItem.setState(true);\r
1904         viewBoxesMenuItem.addItemListener(this);\r
1905         viewTextMenuItem.setLabel("Text");\r
1906         viewTextMenuItem.setState(true);\r
1907         viewTextMenuItem.addItemListener(this);\r
1908         sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
1909         sortPairwiseMenuItem.addActionListener(this);\r
1910         sortIDMenuItem.setLabel("by ID");\r
1911         sortIDMenuItem.addActionListener(this);\r
1912         sortGroupMenuItem.setLabel("by Group");\r
1913         sortGroupMenuItem.addActionListener(this);\r
1914         removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
1915         removeRedundancyMenuItem.addActionListener(this);\r
1916         pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
1917         pairwiseAlignmentMenuItem.addActionListener(this);\r
1918         PCAMenuItem.setLabel("Principal Component Analysis");\r
1919         PCAMenuItem.addActionListener(this);\r
1920         averageDistanceTreeMenuItem.setLabel(\r
1921             "Average Distance Using % Identity");\r
1922         averageDistanceTreeMenuItem.addActionListener(this);\r
1923         neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
1924         neighbourTreeMenuItem.addActionListener(this);\r
1925         alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
1926         statusBar.setBackground(Color.white);\r
1927         statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
1928         statusBar.setText("Status bar");\r
1929         outputTextboxMenu.setLabel("Output to Textbox");\r
1930         clustalColour.setLabel("Clustalx");\r
1931 \r
1932         clustalColour.addActionListener(this);\r
1933         zappoColour.setLabel("Zappo");\r
1934         zappoColour.addActionListener(this);\r
1935         taylorColour.setLabel("Taylor");\r
1936         taylorColour.addActionListener(this);\r
1937         hydrophobicityColour.setLabel("Hydrophobicity");\r
1938         hydrophobicityColour.addActionListener(this);\r
1939         helixColour.setLabel("Helix Propensity");\r
1940         helixColour.addActionListener(this);\r
1941         strandColour.setLabel("Strand Propensity");\r
1942         strandColour.addActionListener(this);\r
1943         turnColour.setLabel("Turn Propensity");\r
1944         turnColour.addActionListener(this);\r
1945         buriedColour.setLabel("Buried Index");\r
1946         buriedColour.addActionListener(this);\r
1947         userDefinedColour.setLabel("User Defined...");\r
1948         userDefinedColour.addActionListener(this);\r
1949         PIDColour.setLabel("Percentage Identity");\r
1950         PIDColour.addActionListener(this);\r
1951         BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
1952         BLOSUM62Colour.addActionListener(this);\r
1953         avDistanceTreeBlosumMenuItem.setLabel(\r
1954             "Average Distance Using BLOSUM62");\r
1955         avDistanceTreeBlosumMenuItem.addActionListener(this);\r
1956         njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
1957         njTreeBlosumMenuItem.addActionListener(this);\r
1958         annotationPanelMenuItem.setLabel("Show Annotations");\r
1959         annotationPanelMenuItem.addItemListener(this);\r
1960         colourTextMenuItem.setLabel("Colour Text");\r
1961         colourTextMenuItem.addItemListener(this);\r
1962         overviewMenuItem.setLabel("Overview Window");\r
1963         overviewMenuItem.addActionListener(this);\r
1964         undoMenuItem.setEnabled(false);\r
1965         undoMenuItem.setLabel("Undo");\r
1966         undoMenuItem.addActionListener(this);\r
1967         redoMenuItem.setEnabled(false);\r
1968         redoMenuItem.setLabel("Redo");\r
1969         redoMenuItem.addActionListener(this);\r
1970         conservationMenuItem.setLabel("by Conservation");\r
1971         conservationMenuItem.addItemListener(this);\r
1972         noColourmenuItem.setLabel("None");\r
1973         noColourmenuItem.addActionListener(this);\r
1974         wrapMenuItem.setLabel("Wrap");\r
1975         wrapMenuItem.addItemListener(this);\r
1976         renderGapsMenuItem.setLabel("Show Gaps");\r
1977         renderGapsMenuItem.setState(true);\r
1978         renderGapsMenuItem.addItemListener(this);\r
1979         findMenuItem.setLabel("Find...");\r
1980         findMenuItem.addActionListener(this);\r
1981         searchMenu.setLabel("Search");\r
1982 \r
1983         abovePIDThreshold.setLabel("Above Identity Threshold");\r
1984         abovePIDThreshold.addItemListener(this);\r
1985         nucleotideColour.setLabel("Nucleotide");\r
1986         nucleotideColour.addActionListener(this);\r
1987         deleteGroups.setLabel("Undefine Groups");\r
1988         deleteGroups.addActionListener(this);\r
1989         copy.setLabel("Copy");\r
1990         copy.addActionListener(this);\r
1991         cut.setLabel("Cut");\r
1992         cut.addActionListener(this);\r
1993         delete.setLabel("Delete");\r
1994         delete.addActionListener(this);\r
1995         pasteMenu.setLabel("Paste");\r
1996         pasteNew.setLabel("To New Alignment");\r
1997         pasteNew.addActionListener(this);\r
1998         pasteThis.setLabel("Add To This Alignment");\r
1999         pasteThis.addActionListener(this);\r
2000         applyToAllGroups.setLabel("Apply Colour To All Groups");\r
2001         applyToAllGroups.setState(true);\r
2002         applyToAllGroups.addItemListener(this);\r
2003         font.setLabel("Font...");\r
2004         font.addActionListener(this);\r
2005         scaleAbove.setLabel("Scale Above");\r
2006         scaleAbove.setState(true);\r
2007         scaleAbove.setEnabled(false);\r
2008         scaleAbove.addItemListener(this);\r
2009         scaleLeft.setEnabled(false);\r
2010         scaleLeft.setState(true);\r
2011         scaleLeft.setLabel("Scale Left");\r
2012         scaleLeft.addItemListener(this);\r
2013         scaleRight.setEnabled(false);\r
2014         scaleRight.setState(true);\r
2015         scaleRight.setLabel("Scale Right");\r
2016         scaleRight.addItemListener(this);\r
2017         modifyPID.setLabel("Modify Identity Threshold...");\r
2018         modifyPID.addActionListener(this);\r
2019         modifyConservation.setLabel("Modify Conservation Threshold...");\r
2020         modifyConservation.addActionListener(this);\r
2021         sortByTreeMenu.setLabel("By Tree Order");\r
2022         sort.setLabel("Sort");\r
2023         calculate.setLabel("Calculate Tree");\r
2024         autoCalculate.addItemListener(this);\r
2025         inputText.setLabel("Input from textbox");\r
2026         inputText.addActionListener(this);\r
2027 \r
2028         helpMenu.setLabel("Help");\r
2029         documentation.setLabel("Documentation");\r
2030         documentation.addActionListener(this);\r
2031 \r
2032         about.setLabel("About...");\r
2033         about.addActionListener(this);\r
2034           seqLimits.setState(true);\r
2035     seqLimits.setLabel("Show Sequence Limits");\r
2036     seqLimits.addItemListener(this);\r
2037     featureSettings.setLabel("Feature Settings...");\r
2038     featureSettings.addActionListener(this);\r
2039     sequenceFeatures.setLabel("Sequence Features");\r
2040     sequenceFeatures.addItemListener(this);\r
2041     sequenceFeatures.setState(false);\r
2042     annotationColour.setLabel("by Annotation...");\r
2043     annotationColour.addActionListener(this);\r
2044 \r
2045     alignFrameMenuBar.add(fileMenu);\r
2046         alignFrameMenuBar.add(editMenu);\r
2047         alignFrameMenuBar.add(searchMenu);\r
2048         alignFrameMenuBar.add(viewMenu);\r
2049         alignFrameMenuBar.add(colourMenu);\r
2050         alignFrameMenuBar.add(calculateMenu);\r
2051         alignFrameMenuBar.add(helpMenu);\r
2052         fileMenu.add(inputText);\r
2053         fileMenu.add(outputTextboxMenu);\r
2054         if(jalviewServletURL!=null)\r
2055           fileMenu.add(loadApplication);\r
2056         fileMenu.addSeparator();\r
2057         fileMenu.add(loadTree);\r
2058         fileMenu.add(closeMenuItem);\r
2059         editMenu.add(undoMenuItem);\r
2060         editMenu.add(redoMenuItem);\r
2061         editMenu.add(cut);\r
2062         editMenu.add(copy);\r
2063         editMenu.add(pasteMenu);\r
2064         editMenu.add(delete);\r
2065         editMenu.addSeparator();\r
2066         editMenu.add(selectAllSequenceMenuItem);\r
2067         editMenu.add(deselectAllSequenceMenuItem);\r
2068         editMenu.add(invertSequenceMenuItem);\r
2069         editMenu.add(deleteGroups);\r
2070         editMenu.addSeparator();\r
2071         editMenu.add(remove2LeftMenuItem);\r
2072         editMenu.add(remove2RightMenuItem);\r
2073         editMenu.add(removeGappedColumnMenuItem);\r
2074         editMenu.add(removeAllGapsMenuItem);\r
2075         editMenu.add(removeRedundancyMenuItem);\r
2076         searchMenu.add(findMenuItem);\r
2077         viewMenu.add(font);\r
2078         viewMenu.addSeparator();\r
2079     viewMenu.add(seqLimits);\r
2080         viewMenu.addSeparator();\r
2081     viewMenu.add(wrapMenuItem);\r
2082         viewMenu.add(scaleAbove);\r
2083         viewMenu.add(scaleLeft);\r
2084         viewMenu.add(scaleRight);\r
2085         viewMenu.addSeparator();\r
2086     viewMenu.add(viewBoxesMenuItem);\r
2087         viewMenu.add(viewTextMenuItem);\r
2088         viewMenu.add(colourTextMenuItem);\r
2089         viewMenu.add(renderGapsMenuItem);\r
2090         viewMenu.add(annotationPanelMenuItem);\r
2091     viewMenu.addSeparator();\r
2092         viewMenu.add(sequenceFeatures);\r
2093         viewMenu.add(featureSettings);\r
2094     viewMenu.addSeparator();\r
2095         viewMenu.add(overviewMenuItem);\r
2096         colourMenu.add(applyToAllGroups);\r
2097         colourMenu.addSeparator();\r
2098         colourMenu.add(noColourmenuItem);\r
2099         colourMenu.add(clustalColour);\r
2100         colourMenu.add(BLOSUM62Colour);\r
2101         colourMenu.add(PIDColour);\r
2102         colourMenu.add(zappoColour);\r
2103         colourMenu.add(taylorColour);\r
2104         colourMenu.add(hydrophobicityColour);\r
2105         colourMenu.add(helixColour);\r
2106         colourMenu.add(strandColour);\r
2107         colourMenu.add(turnColour);\r
2108         colourMenu.add(buriedColour);\r
2109         colourMenu.add(nucleotideColour);\r
2110         colourMenu.add(userDefinedColour);\r
2111         colourMenu.addSeparator();\r
2112         colourMenu.add(conservationMenuItem);\r
2113         colourMenu.add(modifyConservation);\r
2114         colourMenu.add(abovePIDThreshold);\r
2115         colourMenu.add(modifyPID);\r
2116     colourMenu.add(annotationColour);\r
2117     calculateMenu.add(sort);\r
2118         calculateMenu.add(calculate);\r
2119         calculateMenu.addSeparator();\r
2120         calculateMenu.add(pairwiseAlignmentMenuItem);\r
2121         calculateMenu.add(PCAMenuItem);\r
2122         calculateMenu.add(autoCalculate);\r
2123         this.add(statusBar, BorderLayout.SOUTH);\r
2124         pasteMenu.add(pasteNew);\r
2125         pasteMenu.add(pasteThis);\r
2126         sort.add(sortIDMenuItem);\r
2127         sort.add(sortByTreeMenu);\r
2128         sort.add(sortGroupMenuItem);\r
2129         sort.add(sortPairwiseMenuItem);\r
2130         calculate.add(averageDistanceTreeMenuItem);\r
2131         calculate.add(neighbourTreeMenuItem);\r
2132         calculate.add(avDistanceTreeBlosumMenuItem);\r
2133         calculate.add(njTreeBlosumMenuItem);\r
2134         helpMenu.add(documentation);\r
2135         helpMenu.add(about);\r
2136   }\r
2137 \r
2138   public void setEmbedded()\r
2139   {\r
2140 \r
2141     embeddedMenu = new Panel();\r
2142     embeddedEdit = new Label();\r
2143     embeddedSearch = new Label();\r
2144     embeddedView = new Label();\r
2145     embeddedColour = new Label();\r
2146     embeddedFile = new Label();\r
2147     embeddedHelp = new Label();\r
2148     embeddedCalculate = new Label();\r
2149     flowLayout1 = new FlowLayout();\r
2150     embeddedMenu.setBackground(Color.lightGray);\r
2151     embeddedMenu.setLayout(flowLayout1);\r
2152     embeddedEdit.setText("Edit");\r
2153     embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2154     embeddedSearch.setText("Search");\r
2155     embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2156     embeddedView.setText("View");\r
2157     embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2158     embeddedColour.setText("Colour");\r
2159     embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2160     embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2161     embeddedFile.setText("File");\r
2162     embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2163     embeddedHelp.setText("Help");\r
2164     embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2165     embeddedCalculate.setText("Calculate");\r
2166     embeddedMenu.add(embeddedFile);\r
2167     embeddedMenu.add(embeddedEdit);\r
2168     embeddedMenu.add(embeddedSearch);\r
2169     embeddedMenu.add(embeddedView);\r
2170     embeddedMenu.add(embeddedColour);\r
2171     embeddedMenu.add(embeddedCalculate);\r
2172     embeddedMenu.add(embeddedHelp);\r
2173     flowLayout1.setAlignment(FlowLayout.LEFT);\r
2174     flowLayout1.setHgap(2);\r
2175     flowLayout1.setVgap(0);\r
2176     embeddedFile.addMouseListener(this);\r
2177     embeddedEdit.addMouseListener(this);\r
2178     embeddedSearch.addMouseListener(this);\r
2179     embeddedView.addMouseListener(this);\r
2180     embeddedColour.addMouseListener(this);\r
2181     embeddedCalculate.addMouseListener(this);\r
2182     embeddedHelp.addMouseListener(this);\r
2183 \r
2184    // setVisible(false);\r
2185     fileMenu.remove(closeMenuItem);\r
2186     fileMenu.remove(3); // Seperator\r
2187 \r
2188     applet.setLayout(new BorderLayout());\r
2189     applet.add(embeddedMenu, BorderLayout.NORTH);\r
2190     applet.add(statusBar, BorderLayout.SOUTH);\r
2191    // applet.validate();\r
2192 \r
2193     alignPanel.setSize(applet.size().width, applet.size().height\r
2194                        - embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
2195 \r
2196      applet.add(alignPanel, BorderLayout.CENTER);\r
2197      applet.validate();\r
2198 \r
2199   }\r
2200 \r
2201 \r
2202 \r
2203   PopupMenu filePopup, editPopup, searchPopup,\r
2204       viewPopup, colourPopup, calculatePopup, helpPopup;\r
2205   MenuItem featureSettings = new MenuItem();\r
2206   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
2207   MenuItem annotationColour = new MenuItem();\r
2208 \r
2209   public void mousePressed(MouseEvent evt)\r
2210   {\r
2211     PopupMenu popup = null;\r
2212     Label source = (Label)evt.getSource();\r
2213     if(source==embeddedFile)\r
2214     {\r
2215       popup = filePopup = genPopupMenu(filePopup, fileMenu);\r
2216     }\r
2217     else if(source==embeddedEdit)\r
2218     {\r
2219       popup = editPopup = genPopupMenu(editPopup, editMenu);\r
2220     }\r
2221     else if(source==embeddedSearch)\r
2222     {\r
2223       popup = searchPopup = genPopupMenu(searchPopup, searchMenu);\r
2224     }\r
2225     else if(source==embeddedView)\r
2226     {\r
2227       popup = viewPopup = genPopupMenu(viewPopup, viewMenu);\r
2228     }\r
2229     else if(source==embeddedColour)\r
2230     {\r
2231       popup = colourPopup = genPopupMenu(colourPopup, colourMenu);\r
2232     }\r
2233     else if(source==embeddedCalculate)\r
2234     {\r
2235       popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);\r
2236     }\r
2237     else if(source==embeddedHelp)\r
2238     {\r
2239       popup = helpPopup = genPopupMenu(helpPopup, helpMenu);\r
2240     }\r
2241 \r
2242     embeddedMenu.add(popup);\r
2243     popup.show(embeddedMenu,\r
2244                source.getBounds().x,\r
2245                source.getBounds().y + source.getBounds().getSize().height);\r
2246   }\r
2247 \r
2248   PopupMenu genPopupMenu(PopupMenu popup, Menu original)\r
2249   {\r
2250     if(popup!=null)\r
2251     {\r
2252       return popup;\r
2253     }\r
2254     popup = new PopupMenu();\r
2255     int m, mSize = original.getItemCount();\r
2256     for(m=0; m<mSize; m++)\r
2257     {\r
2258       popup.add(original.getItem(m));\r
2259       mSize--;\r
2260       m--;\r
2261     }\r
2262 \r
2263     return popup;\r
2264   }\r
2265   public void mouseClicked(MouseEvent evt)\r
2266   {}\r
2267   public void mouseReleased(MouseEvent evt)\r
2268   {}\r
2269   public void mouseEntered(MouseEvent evt)\r
2270   {}\r
2271   public void mouseExited(MouseEvent evt)\r
2272   {}\r
2273 \r
2274 }\r
2275 \r