src/jalview/appletgui/AlignFrame.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2006 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 \r
  42   String jalviewServletURL;\r
  43 \r
  44 \r
  45    public AlignFrame(AlignmentI al,\r
  46                      jalview.bin.JalviewLite applet,\r
  47                      String title,\r
  48                      boolean embedded)\r
  49   {\r
  50 \r
  51     jalviewServletURL = applet.getParameter("APPLICATION_URL");\r
  52 \r
  53     try{\r
  54       jbInit();\r
  55     }catch(Exception ex)\r
  56     {\r
  57       ex.printStackTrace();\r
  58     }\r
  59 \r
  60     viewport = new AlignViewport(al, applet);\r
  61     alignPanel = new AlignmentPanel(this, viewport);\r
  62 \r
  63     annotationPanelMenuItem.setState(viewport.showAnnotation);\r
  64 \r
  65     seqLimits.setState(viewport.showJVSuffix);\r
  66 \r
  67     if(applet!=null)\r
  68     {\r
  69       String param = applet.getParameter("sortBy");\r
  70       if (param != null)\r
  71       {\r
  72         if (param.equalsIgnoreCase("Id"))\r
  73           sortIDMenuItem_actionPerformed();\r
  74         else if (param.equalsIgnoreCase("Pairwise Identity"))\r
  75           sortPairwiseMenuItem_actionPerformed();\r
  76       }\r
  77 \r
  78       param = applet.getParameter("wrap");\r
  79       if (param != null)\r
  80       {\r
  81         if (param.equalsIgnoreCase("true"))\r
  82         {\r
  83           wrapMenuItem.setState(true);\r
  84           wrapMenuItem_actionPerformed();\r
  85         }\r
  86       }\r
  87 \r
  88       try\r
  89       {\r
  90         param = applet.getParameter("windowWidth");\r
  91         if (param != null)\r
  92         {\r
  93           int width = Integer.parseInt(param);\r
  94           NEW_WINDOW_WIDTH = width;\r
  95         }\r
  96         param = applet.getParameter("windowHeight");\r
  97         if (param != null)\r
  98         {\r
  99           int height = Integer.parseInt(param);\r
 100           NEW_WINDOW_HEIGHT = height;\r
 101         }\r
 102       }\r
 103       catch (Exception ex)\r
 104       {}\r
 105 \r
 106     }\r
 107 \r
 108    //Some JVMS send keyevents to Top frame or lowest panel,\r
 109    //Havent worked out why yet. So add to both this frame and seqCanvas for now\r
 110    this.addKeyListener(this);\r
 111    alignPanel.seqPanel.seqCanvas.addKeyListener(this);\r
 112    alignPanel.idPanel.idCanvas.addKeyListener(this);\r
 113    alignPanel.scalePanel.addKeyListener(this);\r
 114    alignPanel.annotationPanel.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       case KeyEvent.VK_H:\r
 333       {\r
 334         boolean toggleSeqs = !evt.isControlDown();\r
 335         boolean toggleCols = !evt.isShiftDown();\r
 336         boolean hide = false;\r
 337         SequenceGroup sg = viewport.getSelectionGroup();\r
 338 \r
 339         if(toggleSeqs)\r
 340         {\r
 341           if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())\r
 342           {\r
 343             hide = true;\r
 344             viewport.hideAllSelectedSeqs();\r
 345           }\r
 346           else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))\r
 347             viewport.showAllHiddenSeqs();\r
 348         }\r
 349 \r
 350         if(toggleCols)\r
 351         {\r
 352           if (viewport.colSel.getSelected().size() > 0)\r
 353           {\r
 354             viewport.hideSelectedColumns();\r
 355             if(!toggleSeqs)\r
 356                    viewport.selectionGroup = sg;\r
 357           }\r
 358           else if (!hide)\r
 359             viewport.showAllHiddenColumns();\r
 360         }\r
 361 \r
 362         alignPanel.repaint();\r
 363         break;\r
 364       }\r
 365 \r
 366     }\r
 367   }\r
 368   public void keyReleased(KeyEvent evt)\r
 369   {}\r
 370   public void keyTyped(KeyEvent evt)\r
 371   {}\r
 372 \r
 373 public void itemStateChanged(ItemEvent evt)\r
 374   {\r
 375     if(evt.getSource()==colourTextMenuItem)\r
 376             colourTextMenuItem_actionPerformed();\r
 377     else if(evt.getSource()==wrapMenuItem)\r
 378             wrapMenuItem_actionPerformed();\r
 379     else if(evt.getSource()==scaleAbove)\r
 380             scaleAbove_actionPerformed();\r
 381     else if(evt.getSource()==scaleLeft)\r
 382             scaleLeft_actionPerformed();\r
 383     else if(evt.getSource()==scaleRight)\r
 384             scaleRight_actionPerformed();\r
 385      else if(evt.getSource()==seqLimits)\r
 386       seqLimits_itemStateChanged();\r
 387     else if(evt.getSource()==viewBoxesMenuItem)\r
 388             viewBoxesMenuItem_actionPerformed();\r
 389     else if(evt.getSource()==viewTextMenuItem)\r
 390             viewTextMenuItem_actionPerformed();\r
 391     else if(evt.getSource()==renderGapsMenuItem)\r
 392             renderGapsMenuItem_actionPerformed();\r
 393     else if(evt.getSource()==annotationPanelMenuItem)\r
 394             annotationPanelMenuItem_actionPerformed();\r
 395       else if(evt.getSource()==sequenceFeatures)\r
 396       {\r
 397            viewport.showSequenceFeatures(sequenceFeatures.getState());\r
 398             alignPanel.seqPanel.seqCanvas.repaint();\r
 399       }\r
 400       else if(evt.getSource()==conservationMenuItem)\r
 401             conservationMenuItem_actionPerformed();\r
 402       else if(evt.getSource()==abovePIDThreshold)\r
 403             abovePIDThreshold_actionPerformed();\r
 404           else if(evt.getSource()==applyToAllGroups)\r
 405             applyToAllGroups_actionPerformed();\r
 406       else if(evt.getSource()==autoCalculate)\r
 407           viewport.autocalculateConsensus = autoCalculate.getState();\r
 408   }\r
 409  public void actionPerformed(ActionEvent evt)\r
 410  {\r
 411     Object source = evt.getSource();\r
 412 \r
 413     if(source==inputText)\r
 414       inputText_actionPerformed();\r
 415     else if(source==loadTree)\r
 416       loadTree_actionPerformed();\r
 417     else if(source==loadApplication)\r
 418       launchFullApplication();\r
 419     else if(source==closeMenuItem)\r
 420       closeMenuItem_actionPerformed();\r
 421     else if(source==copy)\r
 422       copy_actionPerformed();\r
 423     else if(source==undoMenuItem)\r
 424       undoMenuItem_actionPerformed();\r
 425     else if(source==redoMenuItem)\r
 426       redoMenuItem_actionPerformed();\r
 427     else if(source==inputText)\r
 428             inputText_actionPerformed();\r
 429     else if(source==closeMenuItem)\r
 430             closeMenuItem_actionPerformed();\r
 431     else if(source==undoMenuItem)\r
 432             undoMenuItem_actionPerformed();\r
 433     else if(source==redoMenuItem)\r
 434             redoMenuItem_actionPerformed();\r
 435     else if(source==copy)\r
 436             copy_actionPerformed();\r
 437     else if(source==pasteNew)\r
 438             pasteNew_actionPerformed();\r
 439     else if(source==pasteThis)\r
 440             pasteThis_actionPerformed();\r
 441     else if(source==cut)\r
 442             cut_actionPerformed();\r
 443     else if(source==delete)\r
 444             delete_actionPerformed();\r
 445     else if(source==deleteGroups)\r
 446             deleteGroups_actionPerformed();\r
 447     else if(source==selectAllSequenceMenuItem)\r
 448             selectAllSequenceMenuItem_actionPerformed();\r
 449     else if(source==deselectAllSequenceMenuItem)\r
 450             deselectAllSequenceMenuItem_actionPerformed();\r
 451     else if(source==invertSequenceMenuItem)\r
 452             invertSequenceMenuItem_actionPerformed();\r
 453     else if(source==invertColSel)\r
 454     { viewport.invertColumnSelection(); alignPanel.repaint(); }\r
 455     else if(source==remove2LeftMenuItem)\r
 456             remove2LeftMenuItem_actionPerformed();\r
 457     else if(source==remove2RightMenuItem)\r
 458             remove2RightMenuItem_actionPerformed();\r
 459     else if(source==removeGappedColumnMenuItem)\r
 460             removeGappedColumnMenuItem_actionPerformed();\r
 461     else if(source==removeAllGapsMenuItem)\r
 462             removeAllGapsMenuItem_actionPerformed();\r
 463     else if(source==findMenuItem)\r
 464             findMenuItem_actionPerformed();\r
 465     else if(source==font)\r
 466             font_actionPerformed();\r
 467     else if(source==showColumns)\r
 468     {\r
 469       viewport.showAllHiddenColumns(); alignPanel.repaint();\r
 470     }\r
 471     else if(source==showSeqs)\r
 472     {\r
 473       viewport.showAllHiddenSeqs();\r
 474     }\r
 475     else if(source == hideColumns)\r
 476     {\r
 477       viewport.hideSelectedColumns(); alignPanel.repaint();\r
 478     }\r
 479     else if(source == hideSequences && viewport.getSelectionGroup()!=null)\r
 480     {\r
 481       viewport.hideAllSelectedSeqs();\r
 482     }\r
 483     else if(source==featureSettings)\r
 484             featureSettings_actionPerformed();\r
 485     else if(source==overviewMenuItem)\r
 486             overviewMenuItem_actionPerformed();\r
 487     else if(source==noColourmenuItem)\r
 488             noColourmenuItem_actionPerformed();\r
 489     else if(source==clustalColour)\r
 490             clustalColour_actionPerformed();\r
 491     else if(source==zappoColour)\r
 492             zappoColour_actionPerformed();\r
 493     else if(source==taylorColour)\r
 494             taylorColour_actionPerformed();\r
 495     else if(source==hydrophobicityColour)\r
 496             hydrophobicityColour_actionPerformed();\r
 497     else if(source==helixColour)\r
 498             helixColour_actionPerformed();\r
 499     else if(source==strandColour)\r
 500             strandColour_actionPerformed();\r
 501     else if(source==turnColour)\r
 502             turnColour_actionPerformed();\r
 503     else if(source==buriedColour)\r
 504             buriedColour_actionPerformed();\r
 505     else if(source==nucleotideColour)\r
 506             nucleotideColour_actionPerformed();\r
 507     else if(source==modifyPID)\r
 508             modifyPID_actionPerformed();\r
 509     else if(source==modifyConservation)\r
 510             modifyConservation_actionPerformed();\r
 511     else if(source==userDefinedColour)\r
 512             userDefinedColour_actionPerformed();\r
 513     else if(source==PIDColour)\r
 514             PIDColour_actionPerformed();\r
 515     else if(source==BLOSUM62Colour)\r
 516             BLOSUM62Colour_actionPerformed();\r
 517     else if(source==annotationColour)\r
 518            new AnnotationColourChooser(viewport, alignPanel);\r
 519     else if(source==sortPairwiseMenuItem)\r
 520             sortPairwiseMenuItem_actionPerformed();\r
 521     else if(source==sortIDMenuItem)\r
 522             sortIDMenuItem_actionPerformed();\r
 523     else if(source==sortGroupMenuItem)\r
 524             sortGroupMenuItem_actionPerformed();\r
 525     else if(source==removeRedundancyMenuItem)\r
 526             removeRedundancyMenuItem_actionPerformed();\r
 527     else if(source==pairwiseAlignmentMenuItem)\r
 528             pairwiseAlignmentMenuItem_actionPerformed();\r
 529     else if(source==PCAMenuItem)\r
 530             PCAMenuItem_actionPerformed();\r
 531     else if(source==averageDistanceTreeMenuItem)\r
 532             averageDistanceTreeMenuItem_actionPerformed();\r
 533     else if(source==neighbourTreeMenuItem)\r
 534             neighbourTreeMenuItem_actionPerformed();\r
 535     else if(source==njTreeBlosumMenuItem)\r
 536             njTreeBlosumMenuItem_actionPerformed();\r
 537     else if(source==avDistanceTreeBlosumMenuItem)\r
 538             avTreeBlosumMenuItem_actionPerformed();\r
 539     else if(source==documentation)\r
 540             documentation_actionPerformed();\r
 541     else if(source==about)\r
 542             about_actionPerformed();\r
 543 \r
 544  }\r
 545 \r
 546   public void inputText_actionPerformed()\r
 547   {\r
 548     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
 549     Frame frame = new Frame();\r
 550     frame.add(cap);\r
 551     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
 552   }\r
 553 \r
 554   protected void outputText_actionPerformed(ActionEvent e)\r
 555   {\r
 556     CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
 557     Frame frame = new Frame();\r
 558     frame.add(cap);\r
 559     jalview.bin.JalviewLite.addFrame(frame,\r
 560                                      "Alignment output - " + e.getActionCommand(),\r
 561                                      600, 500);\r
 562     cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
 563                                               viewport.getAlignment().getSequences(),\r
 564                                                       viewport.showJVSuffix));\r
 565   }\r
 566 \r
 567   void launchFullApplication()\r
 568   {\r
 569     StringBuffer url = new StringBuffer(jalviewServletURL);\r
 570 \r
 571     url.append("?open="+\r
 572                appendProtocol( viewport.applet.getParameter("file") ) );\r
 573 \r
 574     if(viewport.applet.getParameter("features")!=null)\r
 575     {\r
 576       url.append( "&features=" );\r
 577       url.append( appendProtocol( viewport.applet.getParameter("features") ) );\r
 578     }\r
 579 \r
 580     if(viewport.applet.getParameter("annotations")!=null)\r
 581     {\r
 582       url.append( "&annotations=" );\r
 583       url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );\r
 584     }\r
 585 \r
 586     if(viewport.applet.getParameter("defaultColour")!=null)\r
 587     {\r
 588       url.append("&colour=" +\r
 589                  removeWhiteSpace(viewport.applet.getParameter("defaultColour"))\r
 590           );\r
 591     }\r
 592 \r
 593     if(viewport.applet.getParameter("userDefinedColour")!=null)\r
 594     {\r
 595       url.append( "&colour=" +\r
 596                  removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )\r
 597          );\r
 598     }\r
 599 \r
 600     showURL(url.toString(), "FULL_APP");\r
 601   }\r
 602 \r
 603 \r
 604   String removeWhiteSpace(String colour)\r
 605   {\r
 606     StringBuffer sb = new StringBuffer();\r
 607     for (int i = 0; i < colour.length(); i++)\r
 608     {\r
 609       if (Character.isWhitespace(colour.charAt(i)))\r
 610         sb.append("%20");\r
 611       else\r
 612         sb.append(colour.charAt(i));\r
 613     }\r
 614 \r
 615     return sb.toString();\r
 616   }\r
 617 \r
 618 \r
 619   String appendProtocol(String url)\r
 620   {\r
 621     try{\r
 622        new URL(url);\r
 623     }catch(java.net.MalformedURLException ex)\r
 624     {\r
 625       url = viewport.applet.getCodeBase()+url;\r
 626     }\r
 627     return url;\r
 628   }\r
 629 \r
 630   public void closeMenuItem_actionPerformed()\r
 631   {\r
 632     PaintRefresher.components.remove(viewport.alignment);\r
 633     if(PaintRefresher.components.size()==0 && viewport.applet==null)\r
 634       System.exit(0);\r
 635 \r
 636     this.dispose();\r
 637   }\r
 638 \r
 639   Stack historyList = new Stack();\r
 640   Stack redoList = new Stack();\r
 641 \r
 642   void updateEditMenuBar()\r
 643   {\r
 644     if (historyList.size() > 0)\r
 645     {\r
 646       undoMenuItem.setEnabled(true);\r
 647       HistoryItem hi = (HistoryItem) historyList.peek();\r
 648       undoMenuItem.setLabel("Undo " + hi.getDescription());\r
 649     }\r
 650     else\r
 651     {\r
 652       undoMenuItem.setEnabled(false);\r
 653       undoMenuItem.setLabel("Undo");\r
 654     }\r
 655 \r
 656     if (redoList.size() > 0)\r
 657     {\r
 658       redoMenuItem.setEnabled(true);\r
 659       HistoryItem hi = (HistoryItem) redoList.peek();\r
 660       redoMenuItem.setLabel("Redo " + hi.getDescription());\r
 661     }\r
 662     else\r
 663     {\r
 664       redoMenuItem.setEnabled(false);\r
 665       redoMenuItem.setLabel("Redo");\r
 666     }\r
 667   }\r
 668 \r
 669   public void addHistoryItem(HistoryItem hi)\r
 670   {\r
 671     historyList.push(hi);\r
 672     redoList.removeAllElements();\r
 673     updateEditMenuBar();\r
 674   }\r
 675 \r
 676   protected void undoMenuItem_actionPerformed()\r
 677   {\r
 678     HistoryItem nh,hi = (HistoryItem) historyList.pop();\r
 679     redoList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,\r
 680                                   HistoryItem.HIDE));\r
 681     if (hi.alColumnChanges!=null)\r
 682       nh.alColumnChanges=hi.alColumnChanges.getInverse();\r
 683     restoreHistoryItem(hi);\r
 684     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 685   }\r
 686 \r
 687   protected void redoMenuItem_actionPerformed()\r
 688   {\r
 689     HistoryItem nh,hi = (HistoryItem) redoList.pop();\r
 690     historyList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,\r
 691                                   HistoryItem.HIDE));\r
 692     if (hi.alColumnChanges!=null)\r
 693       nh.alColumnChanges=hi.alColumnChanges.getInverse();\r
 694     restoreHistoryItem(hi);\r
 695     updateEditMenuBar();\r
 696     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 697   }\r
 698 \r
 699   // used by undo and redo\r
 700   void restoreHistoryItem(HistoryItem hi)\r
 701   {\r
 702     hi.restore(viewport.getColumnSelection());\r
 703     updateEditMenuBar();\r
 704 \r
 705     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 706   }\r
 707 \r
 708   public void moveSelectedSequences(boolean up)\r
 709   {\r
 710     SequenceGroup sg = viewport.getSelectionGroup();\r
 711     if (sg == null)\r
 712     {\r
 713       return;\r
 714     }\r
 715 \r
 716     if (up)\r
 717     {\r
 718       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 719       {\r
 720         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 721         if (!sg.getSequences(false).contains(seq))\r
 722         {\r
 723           continue;\r
 724         }\r
 725 \r
 726         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 727         if (sg.getSequences(false).contains(temp))\r
 728         {\r
 729           continue;\r
 730         }\r
 731 \r
 732         viewport.alignment.getSequences().setElementAt(temp, i);\r
 733         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 734       }\r
 735     }\r
 736     else\r
 737     {\r
 738       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 739       {\r
 740         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 741         if (!sg.getSequences(true).contains(seq))\r
 742         {\r
 743           continue;\r
 744         }\r
 745 \r
 746         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 747         if (sg.getSequences(true).contains(temp))\r
 748         {\r
 749           continue;\r
 750         }\r
 751 \r
 752         viewport.alignment.getSequences().setElementAt(temp, i);\r
 753         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 754       }\r
 755     }\r
 756 \r
 757     alignPanel.repaint();\r
 758   }\r
 759 \r
 760   static StringBuffer copiedSequences;\r
 761   static Vector copiedHiddenColumns;\r
 762   protected void copy_actionPerformed()\r
 763   {\r
 764     if (viewport.getSelectionGroup() == null)\r
 765     {\r
 766       return;\r
 767     }\r
 768 \r
 769     SequenceGroup sg = viewport.getSelectionGroup();\r
 770     copiedSequences = new StringBuffer();\r
 771     Hashtable orderedSeqs = new Hashtable();\r
 772     for (int i = 0; i < sg.getSize(false); i++)\r
 773     {\r
 774       SequenceI seq = sg.getSequenceAt(i);\r
 775       int index = viewport.alignment.findIndex(seq);\r
 776       orderedSeqs.put(index + "", seq);\r
 777     }\r
 778 \r
 779     int index = 0, startRes, endRes;\r
 780     char ch;\r
 781 \r
 782     if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)\r
 783     {\r
 784       copiedHiddenColumns = new Vector();\r
 785       int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
 786       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();\r
 787            i++)\r
 788       {\r
 789         int[] region = (int[])\r
 790             viewport.getColumnSelection().getHiddenColumns().elementAt(i);\r
 791 \r
 792         copiedHiddenColumns.addElement(new int[]\r
 793                                  {region[0] - hiddenOffset,\r
 794                                  region[1] - hiddenOffset});\r
 795       }\r
 796     }\r
 797     else\r
 798       copiedHiddenColumns = null;\r
 799 \r
 800 \r
 801     for (int i = 0; i < sg.getSize(false); i++)\r
 802     {\r
 803         SequenceI seq = null;\r
 804 \r
 805         while (seq == null)\r
 806         {\r
 807             if (orderedSeqs.containsKey(index + ""))\r
 808             {\r
 809                 seq = (SequenceI) orderedSeqs.get(index + "");\r
 810                 index++;\r
 811 \r
 812                 break;\r
 813             }\r
 814             else\r
 815             {\r
 816                 index++;\r
 817             }\r
 818         }\r
 819 \r
 820         //FIND START RES\r
 821         //Returns residue following index if gap\r
 822         startRes = seq.findPosition(sg.getStartRes());\r
 823 \r
 824         //FIND END RES\r
 825         //Need to find the residue preceeding index if gap\r
 826         endRes = 0;\r
 827 \r
 828         for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
 829         {\r
 830           ch = seq.getCharAt(j);\r
 831           if (!jalview.util.Comparison.isGap( (ch)))\r
 832           {\r
 833             endRes++;\r
 834           }\r
 835         }\r
 836 \r
 837         if(endRes>0)\r
 838         {\r
 839           endRes += seq.getStart() -1;\r
 840         }\r
 841 \r
 842         copiedSequences.append(seq.getName() + "\t" +\r
 843             startRes + "\t" +\r
 844             endRes + "\t" +\r
 845             seq.getSequence(sg.getStartRes(),\r
 846                 sg.getEndRes() + 1) + "\n");\r
 847     }\r
 848 \r
 849   }\r
 850 \r
 851   protected void pasteNew_actionPerformed()\r
 852   {\r
 853     paste(true);\r
 854   }\r
 855 \r
 856   protected void pasteThis_actionPerformed()\r
 857   {\r
 858     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
 859                                    HistoryItem.PASTE));\r
 860     paste(false);\r
 861   }\r
 862 \r
 863   void paste(boolean newAlignment)\r
 864   {\r
 865     try\r
 866     {\r
 867       if (copiedSequences == null)\r
 868       {\r
 869         return;\r
 870       }\r
 871 \r
 872       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 873       Vector seqs = new Vector();\r
 874       while (st.hasMoreElements())\r
 875       {\r
 876         String name = st.nextToken();\r
 877         int start = Integer.parseInt(st.nextToken());\r
 878         int end = Integer.parseInt(st.nextToken());\r
 879         Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
 880 \r
 881         if (!newAlignment)\r
 882         {\r
 883           viewport.alignment.addSequence(sequence);\r
 884         }\r
 885         else\r
 886         {\r
 887           seqs.addElement(sequence);\r
 888         }\r
 889       }\r
 890 \r
 891       if (newAlignment)\r
 892       {\r
 893         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 894         for (int i = 0; i < seqs.size(); i++)\r
 895         {\r
 896           newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
 897         }\r
 898 \r
 899         String newtitle = new String("Copied sequences");\r
 900         if (getTitle().startsWith("Copied sequences"))\r
 901         {\r
 902           newtitle = getTitle();\r
 903         }\r
 904         else\r
 905         {\r
 906           newtitle = newtitle.concat("- from " + getTitle());\r
 907         }\r
 908         AlignFrame af = new AlignFrame(new Alignment(newSeqs),\r
 909                                        viewport.applet,\r
 910                                        newtitle,\r
 911                                        false);\r
 912         if (copiedHiddenColumns != null)\r
 913         {\r
 914           for (int i = 0; i < copiedHiddenColumns.size(); i++)\r
 915           {\r
 916             int[] region = (int[]) copiedHiddenColumns.elementAt(i);\r
 917             af.viewport.hideColumns(region[0], region[1]);\r
 918           }\r
 919         }\r
 920 \r
 921 \r
 922         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
 923                                          NEW_WINDOW_HEIGHT);\r
 924       }\r
 925       else\r
 926       {\r
 927         viewport.setEndSeq(viewport.alignment.getHeight());\r
 928         viewport.alignment.getWidth();\r
 929         viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 930       }\r
 931 \r
 932     }\r
 933     catch (Exception ex)\r
 934     {} // could be anything being pasted in here\r
 935 \r
 936   }\r
 937 \r
 938   protected void cut_actionPerformed()\r
 939   {\r
 940     copy_actionPerformed();\r
 941     delete_actionPerformed();\r
 942   }\r
 943 \r
 944   protected void delete_actionPerformed()\r
 945   {\r
 946     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
 947                                    HistoryItem.HIDE));\r
 948     if (viewport.getSelectionGroup() == null)\r
 949     {\r
 950       return;\r
 951     }\r
 952 \r
 953 \r
 954     SequenceGroup sg = viewport.getSelectionGroup();\r
 955     boolean allSequences = false;\r
 956     if(sg.getSize(false)==viewport.alignment.getHeight())\r
 957           allSequences = true;\r
 958 \r
 959     for (int i = 0; i < sg.getSize(false); i++)\r
 960     {\r
 961       SequenceI seq = sg.getSequenceAt(i);\r
 962       int index = viewport.getAlignment().findIndex(seq);\r
 963       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 964 \r
 965       // If the cut affects all sequences, remove highlighted columns\r
 966       if (allSequences)\r
 967       {\r
 968         viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
 969                                                      sg.getEndRes() + 1);\r
 970       }\r
 971 \r
 972 \r
 973       if (seq.getSequence().length() < 1)\r
 974       {\r
 975         viewport.getAlignment().deleteSequence(seq);\r
 976       }\r
 977       else\r
 978       {\r
 979         viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 980       }\r
 981     }\r
 982 \r
 983     viewport.setSelectionGroup(null);\r
 984     viewport.alignment.deleteGroup(sg);\r
 985     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
 986     if (viewport.getAlignment().getHeight() < 1)\r
 987     {\r
 988       try\r
 989       {\r
 990         this.setVisible(false);\r
 991       }\r
 992       catch (Exception ex)\r
 993       {}\r
 994     }\r
 995     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 996 \r
 997   }\r
 998 \r
 999   protected void deleteGroups_actionPerformed()\r
1000   {\r
1001     viewport.alignment.deleteAllGroups();\r
1002     viewport.setSelectionGroup(null);\r
1003 \r
1004     alignPanel.repaint();\r
1005   }\r
1006 \r
1007   public void selectAllSequenceMenuItem_actionPerformed()\r
1008   {\r
1009     SequenceGroup sg = new SequenceGroup();\r
1010     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
1011     {\r
1012       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
1013     }\r
1014     sg.setEndRes(viewport.alignment.getWidth()-1);\r
1015     viewport.setSelectionGroup(sg);\r
1016     alignPanel.repaint();\r
1017     PaintRefresher.Refresh(null, viewport.alignment);\r
1018   }\r
1019 \r
1020   public void deselectAllSequenceMenuItem_actionPerformed()\r
1021   {\r
1022     if(viewport.cursorMode)\r
1023     {\r
1024       alignPanel.seqPanel.keyboardNo1=null;\r
1025       alignPanel.seqPanel.keyboardNo2=null;\r
1026     }\r
1027     viewport.setSelectionGroup(null);\r
1028     viewport.getColumnSelection().clear();\r
1029     viewport.setSelectionGroup(null);\r
1030     alignPanel.idPanel.idCanvas.searchResults = null;\r
1031     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
1032     alignPanel.repaint();\r
1033     PaintRefresher.Refresh(null, viewport.alignment);\r
1034   }\r
1035 \r
1036   public void invertSequenceMenuItem_actionPerformed()\r
1037   {\r
1038     SequenceGroup sg = viewport.getSelectionGroup();\r
1039     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
1040     {\r
1041       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
1042     }\r
1043 \r
1044     PaintRefresher.Refresh(null, viewport.alignment);\r
1045   }\r
1046 \r
1047   public void remove2LeftMenuItem_actionPerformed()\r
1048   {\r
1049     ColumnSelection colSel = viewport.getColumnSelection();\r
1050     if (colSel.size() > 0)\r
1051     {\r
1052       HistoryItem edit;\r
1053       addHistoryItem(edit=new HistoryItem("Remove Left", viewport.alignment,\r
1054                                      HistoryItem.HIDE));\r
1055       int min = colSel.getMin();\r
1056       viewport.getAlignment().trimLeft(min);\r
1057       colSel.compensateForEdit(0, min);\r
1058       edit.addShift(0, min);\r
1059       if (viewport.getSelectionGroup() != null)\r
1060       {\r
1061         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
1062       }\r
1063 \r
1064       Vector groups = viewport.alignment.getGroups();\r
1065       for (int i = 0; i < groups.size(); i++)\r
1066       {\r
1067         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1068         if (!sg.adjustForRemoveLeft(min))\r
1069         {\r
1070           viewport.alignment.deleteGroup(sg);\r
1071         }\r
1072       }\r
1073       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1074     }\r
1075   }\r
1076 \r
1077   public void remove2RightMenuItem_actionPerformed()\r
1078   {\r
1079     ColumnSelection colSel = viewport.getColumnSelection();\r
1080     if (colSel.size() > 0)\r
1081     {\r
1082       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
1083                                      HistoryItem.HIDE));\r
1084       int max = colSel.getMax();\r
1085       viewport.getAlignment().trimRight(max);\r
1086 \r
1087       if (viewport.getSelectionGroup() != null)\r
1088       {\r
1089         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
1090       }\r
1091 \r
1092       Vector groups = viewport.alignment.getGroups();\r
1093       for (int i = 0; i < groups.size(); i++)\r
1094       {\r
1095         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1096         if (!sg.adjustForRemoveRight(max))\r
1097         {\r
1098           viewport.alignment.deleteGroup(sg);\r
1099         }\r
1100       }\r
1101       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1102     }\r
1103 \r
1104   }\r
1105 \r
1106   public void removeGappedColumnMenuItem_actionPerformed()\r
1107   {\r
1108     HistoryItem edit;\r
1109     addHistoryItem(edit=new HistoryItem("Remove Gapped Columns",\r
1110                                    viewport.alignment,\r
1111                                    HistoryItem.HIDE));\r
1112 \r
1113     //This is to maintain viewport position on first residue\r
1114     //of first sequence\r
1115     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
1116     int startRes = seq.findPosition(viewport.startRes);\r
1117 \r
1118     viewport.getAlignment().removeGaps();\r
1119 \r
1120     viewport.setStartRes(seq.findIndex(startRes)-1);\r
1121 \r
1122     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1123   }\r
1124 \r
1125   public void removeAllGapsMenuItem_actionPerformed()\r
1126   {\r
1127     // TODO: hidden regions should not be touched by removeAllGaps - a minimal number of gaps will remain in alignment segments containing uneven length subsequences\r
1128     // TODO: columnSelection.compensateforedits should be called (and passed to history item)\r
1129     HistoryItem editgaps;\r
1130     addHistoryItem(editgaps=new HistoryItem("Remove Gaps", viewport.alignment,\r
1131                                    HistoryItem.HIDE));\r
1132 \r
1133     //This is to maintain viewport position on first residue\r
1134     //of first sequence\r
1135     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
1136     int startRes = seq.findPosition(viewport.startRes);\r
1137 \r
1138     SequenceI current;\r
1139     Vector seqs=null;\r
1140 \r
1141     int start=0, end = viewport.alignment.getWidth();\r
1142 \r
1143     if (viewport.getSelectionGroup() != null\r
1144         && viewport.getSelectionGroup().getSequences(false) != null\r
1145         && viewport.getSelectionGroup().getSize(false)>0)\r
1146     {\r
1147       seqs = viewport.getSelectionGroup().getSequences(true);\r
1148       start = viewport.getSelectionGroup().getStartRes();\r
1149       end = viewport.getSelectionGroup().getEndRes()+1;\r
1150     }\r
1151     else\r
1152       seqs = viewport.alignment.getSequences();\r
1153 \r
1154     /* Commented out regions below are partial implementation of todo above.\r
1155      * divide start,end into visible chunks, and for each:\r
1156      int diff=end-start+1;\r
1157      int diffmax=0;\r
1158      int dr[] = new int[seqs.size()];\r
1159      */\r
1160     for (int i = 0; i < seqs.size(); i++)\r
1161     {\r
1162       current = (SequenceI) seqs.elementAt(i);\r
1163       //dr[i]=\r
1164       current.removeGaps(start, end);\r
1165       /*if (d<diff) // can only shift\r
1166         diff=d;\r
1167       if (diffmax<d)\r
1168         diffmax=d;\r
1169         */\r
1170     }\r
1171     /* // after the end of each chunk -\r
1172      * if (diff>0) {\r
1173      // record shift for history.\r
1174       editgaps.addShift(start, diff);\r
1175       if (viewport.hasHiddenColumns && diffmax>diff) {\r
1176       // pad sequence\r
1177        StringBuffer gaps=new StringBuffer(diffmax);\r
1178        for (int i=0,j=diffmax-diff; i<j; i++)\r
1179        gaps.append(viewport.getGapCharacter());\r
1180        for (int i=0, j=seqs.size(); i<j; i++) {\r
1181        current = (SequenceI) seqs.elementAt(i);\r
1182        if (dr[i]-diff>0) {\r
1183        String sq = current.getSequence();\r
1184        current.setSequence(sq.substring(0, hcend-dr[i])+gaps.substring(0, dr[i]-diff)+sq.substring());\r
1185        }\r
1186        }\r
1187       }\r
1188       }*/\r
1189 \r
1190     viewport.setStartRes(seq.findIndex(startRes)-1);\r
1191     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1192   }\r
1193 \r
1194   public void alignmentChanged()\r
1195   {\r
1196     viewport.alignment.padGaps();\r
1197     if(viewport.autocalculateConsensus)\r
1198     {\r
1199       viewport.updateConsensus();\r
1200       viewport.updateConservation();\r
1201     }\r
1202 \r
1203     resetAllColourSchemes();\r
1204     if(alignPanel.overviewPanel!=null)\r
1205       alignPanel.overviewPanel.updateOverviewImage();\r
1206 \r
1207     viewport.alignment.adjustSequenceAnnotations();\r
1208     alignPanel.repaint();\r
1209   }\r
1210 \r
1211   void resetAllColourSchemes()\r
1212   {\r
1213     ColourSchemeI cs = viewport.globalColourScheme;\r
1214     if(cs!=null)\r
1215     {\r
1216       if (cs instanceof ClustalxColourScheme)\r
1217       {\r
1218         ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
1219             resetClustalX(viewport.alignment.getSequences(),\r
1220                           viewport.alignment.getWidth());\r
1221       }\r
1222 \r
1223       cs.setConsensus(viewport.vconsensus);\r
1224       if (cs.conservationApplied())\r
1225       {\r
1226         Alignment al = (Alignment) viewport.alignment;\r
1227         Conservation c = new Conservation("All",\r
1228                                           ResidueProperties.propHash, 3,\r
1229                                           al.getSequences(), 0,\r
1230                                           al.getWidth() - 1);\r
1231         c.calculate();\r
1232         c.verdict(false, viewport.ConsPercGaps);\r
1233 \r
1234         cs.setConservation(c);\r
1235       }\r
1236     }\r
1237 \r
1238     int s, sSize = viewport.alignment.getGroups().size();\r
1239     for(s=0; s<sSize; s++)\r
1240     {\r
1241       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
1242       if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
1243       {\r
1244         ((ClustalxColourScheme)sg.cs).resetClustalX(\r
1245             sg.getSequences(true), sg.getWidth());\r
1246       }\r
1247       sg.recalcConservation();\r
1248     }\r
1249   }\r
1250 \r
1251 \r
1252 \r
1253   public void findMenuItem_actionPerformed()\r
1254   {\r
1255     new Finder(alignPanel);\r
1256   }\r
1257 \r
1258   public void font_actionPerformed()\r
1259   {\r
1260     new FontChooser(alignPanel);\r
1261   }\r
1262 \r
1263 \r
1264   public void seqLimits_itemStateChanged()\r
1265   {\r
1266     viewport.setShowJVSuffix(seqLimits.getState());\r
1267     alignPanel.fontChanged();\r
1268     alignPanel.repaint();\r
1269   }\r
1270 \r
1271 \r
1272   protected void colourTextMenuItem_actionPerformed()\r
1273   {\r
1274     viewport.setColourText(colourTextMenuItem.getState());\r
1275     alignPanel.repaint();\r
1276   }\r
1277 \r
1278   protected void wrapMenuItem_actionPerformed()\r
1279   {\r
1280     viewport.setWrapAlignment(wrapMenuItem.getState());\r
1281     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
1282     scaleAbove.setEnabled(wrapMenuItem.getState());\r
1283     scaleLeft.setEnabled(wrapMenuItem.getState());\r
1284     scaleRight.setEnabled(wrapMenuItem.getState());\r
1285     alignPanel.repaint();\r
1286   }\r
1287 \r
1288 \r
1289   protected void scaleAbove_actionPerformed()\r
1290   {\r
1291     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
1292     alignPanel.repaint();\r
1293   }\r
1294 \r
1295   protected void scaleLeft_actionPerformed()\r
1296   {\r
1297     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
1298     alignPanel.repaint();\r
1299   }\r
1300 \r
1301   protected void scaleRight_actionPerformed()\r
1302   {\r
1303     viewport.setScaleRightWrapped(scaleRight.getState());\r
1304     alignPanel.repaint();\r
1305   }\r
1306 \r
1307   public void viewBoxesMenuItem_actionPerformed()\r
1308   {\r
1309     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
1310     alignPanel.repaint();\r
1311   }\r
1312 \r
1313   public void viewTextMenuItem_actionPerformed()\r
1314   {\r
1315     viewport.setShowText(viewTextMenuItem.getState());\r
1316     alignPanel.repaint();\r
1317   }\r
1318 \r
1319   protected void renderGapsMenuItem_actionPerformed()\r
1320   {\r
1321     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
1322     alignPanel.repaint();\r
1323   }\r
1324 \r
1325   public void annotationPanelMenuItem_actionPerformed()\r
1326   {\r
1327     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
1328     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
1329   }\r
1330 \r
1331   public void featureSettings_actionPerformed()\r
1332   {\r
1333     new FeatureSettings(viewport, alignPanel);\r
1334   }\r
1335 \r
1336   public void overviewMenuItem_actionPerformed()\r
1337   {\r
1338     if (alignPanel.overviewPanel != null)\r
1339     {\r
1340       return;\r
1341     }\r
1342 \r
1343     Frame frame = new Frame();\r
1344     OverviewPanel overview = new OverviewPanel(alignPanel);\r
1345     frame.add(overview);\r
1346     // +50 must allow for applet frame window\r
1347     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
1348                                      overview.preferredSize().width,\r
1349                                      overview.preferredSize().height + 50);\r
1350 \r
1351     frame.pack();\r
1352     frame.addWindowListener(new WindowAdapter()\r
1353     {\r
1354       public void windowClosing(WindowEvent e)\r
1355       {\r
1356         alignPanel.setOverviewPanel(null);\r
1357       };\r
1358     });\r
1359 \r
1360     alignPanel.setOverviewPanel(overview);\r
1361 \r
1362   }\r
1363 \r
1364   protected void noColourmenuItem_actionPerformed()\r
1365   {\r
1366     changeColour(null);\r
1367   }\r
1368 \r
1369   public void clustalColour_actionPerformed()\r
1370   {\r
1371     abovePIDThreshold.setState(false);\r
1372     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
1373                                           viewport.alignment.getWidth()));\r
1374   }\r
1375 \r
1376   public void zappoColour_actionPerformed()\r
1377   {\r
1378     changeColour(new ZappoColourScheme());\r
1379   }\r
1380 \r
1381   public void taylorColour_actionPerformed()\r
1382   {\r
1383     changeColour(new TaylorColourScheme());\r
1384   }\r
1385 \r
1386   public void hydrophobicityColour_actionPerformed()\r
1387   {\r
1388     changeColour(new HydrophobicColourScheme());\r
1389   }\r
1390 \r
1391   public void helixColour_actionPerformed()\r
1392   {\r
1393     changeColour(new HelixColourScheme());\r
1394   }\r
1395 \r
1396   public void strandColour_actionPerformed()\r
1397   {\r
1398     changeColour(new StrandColourScheme());\r
1399   }\r
1400 \r
1401   public void turnColour_actionPerformed()\r
1402   {\r
1403     changeColour(new TurnColourScheme());\r
1404   }\r
1405 \r
1406   public void buriedColour_actionPerformed()\r
1407   {\r
1408     changeColour(new BuriedColourScheme());\r
1409   }\r
1410 \r
1411   public void nucleotideColour_actionPerformed()\r
1412   {\r
1413     changeColour(new NucleotideColourScheme());\r
1414   }\r
1415 \r
1416   protected void applyToAllGroups_actionPerformed()\r
1417   {\r
1418     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
1419   }\r
1420 \r
1421   void changeColour(ColourSchemeI cs)\r
1422   {\r
1423     int threshold = 0;\r
1424 \r
1425     if(cs!=null)\r
1426     {\r
1427       if (viewport.getAbovePIDThreshold())\r
1428       {\r
1429         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
1430 \r
1431         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1432 \r
1433         viewport.setGlobalColourScheme(cs);\r
1434       }\r
1435       else\r
1436       {\r
1437         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1438       }\r
1439 \r
1440       if (viewport.getConservationSelected())\r
1441       {\r
1442 \r
1443         Alignment al = (Alignment) viewport.alignment;\r
1444         Conservation c = new Conservation("All",\r
1445                                           ResidueProperties.propHash, 3,\r
1446                                           al.getSequences(), 0,\r
1447                                           al.getWidth() - 1);\r
1448 \r
1449         c.calculate();\r
1450         c.verdict(false, viewport.ConsPercGaps);\r
1451 \r
1452         cs.setConservation(c);\r
1453 \r
1454         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
1455             "Background"));\r
1456 \r
1457       }\r
1458       else\r
1459       {\r
1460         cs.setConservation(null);\r
1461       }\r
1462 \r
1463       cs.setConsensus(viewport.vconsensus);\r
1464 \r
1465     }\r
1466     viewport.setGlobalColourScheme(cs);\r
1467 \r
1468     if (viewport.getColourAppliesToAllGroups())\r
1469     {\r
1470       Vector groups = viewport.alignment.getGroups();\r
1471       for (int i = 0; i < groups.size(); i++)\r
1472       {\r
1473         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1474 \r
1475         if(cs==null)\r
1476         {\r
1477           sg.cs = null;\r
1478           continue;\r
1479         }\r
1480         if (cs instanceof ClustalxColourScheme)\r
1481         {\r
1482           sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());\r
1483         }\r
1484         else\r
1485         {\r
1486           try\r
1487           {\r
1488             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
1489           }\r
1490           catch (Exception ex)\r
1491           {\r
1492             ex.printStackTrace();\r
1493             sg.cs = cs;\r
1494           }\r
1495         }\r
1496 \r
1497         if (viewport.getAbovePIDThreshold()\r
1498             || cs instanceof PIDColourScheme\r
1499             || cs instanceof Blosum62ColourScheme)\r
1500         {\r
1501           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1502           sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));\r
1503         }\r
1504         else\r
1505           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1506 \r
1507         if (viewport.getConservationSelected())\r
1508         {\r
1509           Conservation c = new Conservation("Group",\r
1510                                             ResidueProperties.propHash, 3,\r
1511                                             sg.getSequences(true), 0,\r
1512                                             viewport.alignment.getWidth() - 1);\r
1513           c.calculate();\r
1514           c.verdict(false, viewport.ConsPercGaps);\r
1515           sg.cs.setConservation(c);\r
1516         }\r
1517         else\r
1518         {\r
1519           sg.cs.setConservation(null);\r
1520           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1521         }\r
1522 \r
1523       }\r
1524     }\r
1525 \r
1526 \r
1527     if (alignPanel.getOverviewPanel() != null)\r
1528     {\r
1529       alignPanel.getOverviewPanel().updateOverviewImage();\r
1530     }\r
1531 \r
1532     alignPanel.repaint();\r
1533   }\r
1534 \r
1535 \r
1536 \r
1537   protected void modifyPID_actionPerformed()\r
1538   {\r
1539     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
1540     {\r
1541       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
1542                                      "Background");\r
1543       SliderPanel.showPIDSlider();\r
1544     }\r
1545   }\r
1546 \r
1547   protected void modifyConservation_actionPerformed()\r
1548   {\r
1549     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
1550     {\r
1551       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
1552                                         "Background");\r
1553       SliderPanel.showConservationSlider();\r
1554     }\r
1555   }\r
1556 \r
1557   protected void conservationMenuItem_actionPerformed()\r
1558   {\r
1559     viewport.setConservationSelected(conservationMenuItem.getState());\r
1560 \r
1561     viewport.setAbovePIDThreshold(false);\r
1562     abovePIDThreshold.setState(false);\r
1563 \r
1564     changeColour(viewport.getGlobalColourScheme());\r
1565 \r
1566     modifyConservation_actionPerformed();\r
1567   }\r
1568 \r
1569   public void abovePIDThreshold_actionPerformed()\r
1570   {\r
1571     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
1572 \r
1573     conservationMenuItem.setState(false);\r
1574     viewport.setConservationSelected(false);\r
1575 \r
1576     changeColour(viewport.getGlobalColourScheme());\r
1577 \r
1578     modifyPID_actionPerformed();\r
1579   }\r
1580 \r
1581   public void userDefinedColour_actionPerformed()\r
1582   {\r
1583     new UserDefinedColours(alignPanel, null);\r
1584   }\r
1585 \r
1586   public void PIDColour_actionPerformed()\r
1587   {\r
1588     changeColour(new PIDColourScheme());\r
1589   }\r
1590 \r
1591   public void BLOSUM62Colour_actionPerformed()\r
1592   {\r
1593     changeColour(new Blosum62ColourScheme());\r
1594   }\r
1595 \r
1596   public void sortPairwiseMenuItem_actionPerformed()\r
1597   {\r
1598     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1599                                    HistoryItem.SORT));\r
1600     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1601                               viewport.getAlignment().getSequenceAt(0));\r
1602     alignPanel.repaint();\r
1603   }\r
1604 \r
1605   public void sortIDMenuItem_actionPerformed()\r
1606   {\r
1607     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1608                                    HistoryItem.SORT));\r
1609     AlignmentSorter.sortByID(viewport.getAlignment());\r
1610     alignPanel.repaint();\r
1611   }\r
1612 \r
1613   public void sortGroupMenuItem_actionPerformed()\r
1614   {\r
1615     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1616                                    HistoryItem.SORT));\r
1617     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1618     alignPanel.repaint();\r
1619 \r
1620   }\r
1621 \r
1622   public void removeRedundancyMenuItem_actionPerformed()\r
1623   {\r
1624      new RedundancyPanel(alignPanel);\r
1625   }\r
1626 \r
1627   public void pairwiseAlignmentMenuItem_actionPerformed()\r
1628   {\r
1629     if (viewport.getSelectionGroup()!=null\r
1630         && viewport.getSelectionGroup().getSize(false) > 1)\r
1631     {\r
1632       Frame frame = new Frame();\r
1633       frame.add(new PairwiseAlignPanel(alignPanel));\r
1634       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1635     }\r
1636   }\r
1637 \r
1638   public void PCAMenuItem_actionPerformed()\r
1639   {\r
1640     //are the sequences aligned?\r
1641     if (!viewport.alignment.isAligned())\r
1642     {\r
1643       SequenceI current;\r
1644       int Width = viewport.getAlignment().getWidth();\r
1645 \r
1646       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1647            i++)\r
1648       {\r
1649         current = viewport.getAlignment().getSequenceAt(i);\r
1650 \r
1651         if (current.getLength() < Width)\r
1652         {\r
1653           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1654         }\r
1655       }\r
1656       alignPanel.repaint();\r
1657     }\r
1658 \r
1659     if ( (viewport.getSelectionGroup() != null &&\r
1660           viewport.getSelectionGroup().getSize(false) < 4 &&\r
1661           viewport.getSelectionGroup().getSize(false) > 0)\r
1662         || viewport.getAlignment().getHeight() < 4)\r
1663     {\r
1664       return;\r
1665     }\r
1666 \r
1667     try\r
1668     {\r
1669       new PCAPanel(viewport);\r
1670     }\r
1671     catch (java.lang.OutOfMemoryError ex)\r
1672     {\r
1673     }\r
1674 \r
1675   }\r
1676 \r
1677   public void averageDistanceTreeMenuItem_actionPerformed()\r
1678   {\r
1679     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1680   }\r
1681 \r
1682   public void neighbourTreeMenuItem_actionPerformed()\r
1683   {\r
1684     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1685   }\r
1686 \r
1687   protected void njTreeBlosumMenuItem_actionPerformed()\r
1688   {\r
1689     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1690   }\r
1691 \r
1692   protected void avTreeBlosumMenuItem_actionPerformed()\r
1693   {\r
1694     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1695   }\r
1696 \r
1697   void NewTreePanel(String type, String pwType, String title)\r
1698   {\r
1699     //are the sequences aligned?\r
1700     if (!viewport.alignment.isAligned())\r
1701     {\r
1702       SequenceI current;\r
1703       int Width = viewport.getAlignment().getWidth();\r
1704 \r
1705       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1706            i++)\r
1707       {\r
1708         current = viewport.getAlignment().getSequenceAt(i);\r
1709 \r
1710         if (current.getLength() < Width)\r
1711         {\r
1712           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1713         }\r
1714       }\r
1715       alignPanel.repaint();\r
1716 \r
1717     }\r
1718 \r
1719     if ( (viewport.getSelectionGroup() != null &&\r
1720           viewport.getSelectionGroup().getSize(false) > 1)\r
1721       || (viewport.getSelectionGroup() == null\r
1722           && viewport.alignment.getHeight() > 1))\r
1723     {\r
1724       final TreePanel tp = new TreePanel(viewport,\r
1725                                          type,\r
1726                                          pwType);\r
1727 \r
1728       addTreeMenuItem(tp, title);\r
1729 \r
1730       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1731     }\r
1732   }\r
1733 \r
1734   void loadTree_actionPerformed()\r
1735   {\r
1736       CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
1737       cap.setText("Paste your Newick tree file here.");\r
1738       cap.treeImport = true;\r
1739       Frame frame = new Frame();\r
1740       frame.add(cap);\r
1741       jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);\r
1742   }\r
1743 \r
1744   public void loadTree(jalview.io.NewickFile tree, String treeFile)\r
1745   {\r
1746     TreePanel tp = new TreePanel(viewport,\r
1747                                  treeFile,\r
1748                                  "From File - ",\r
1749                                  tree);\r
1750     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
1751     addTreeMenuItem(tp, treeFile);\r
1752   }\r
1753 \r
1754   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1755   {\r
1756     final MenuItem item = new MenuItem(title);\r
1757     sortByTreeMenu.add(item);\r
1758     item.addActionListener(new java.awt.event.ActionListener()\r
1759     {\r
1760       public void actionPerformed(ActionEvent evt)\r
1761       {\r
1762         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1763                                        HistoryItem.SORT));\r
1764         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1765         alignPanel.repaint();\r
1766       }\r
1767     });\r
1768 \r
1769     treePanel.addWindowListener(new WindowAdapter()\r
1770     {\r
1771       public void windowClosing(WindowEvent e)\r
1772       {\r
1773         sortByTreeMenu.remove(item);\r
1774       };\r
1775     });\r
1776   }\r
1777 \r
1778   protected void documentation_actionPerformed()\r
1779   {\r
1780     showURL("http://www.jalview.org/help.html", "HELP");\r
1781   }\r
1782 \r
1783   protected void about_actionPerformed()\r
1784   {\r
1785 \r
1786     class AboutPanel extends Canvas\r
1787     {\r
1788       String version;\r
1789       public AboutPanel(String version)\r
1790       { this.version = version; }\r
1791 \r
1792       public void paint(Graphics g)\r
1793       {\r
1794         g.setColor(Color.white);\r
1795         g.fillRect(0, 0, getSize().width, getSize().height);\r
1796         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1797         FontMetrics fm = g.getFontMetrics();\r
1798         int fh = fm.getHeight();\r
1799         int y = 5, x = 7;\r
1800         g.setColor(Color.black);\r
1801         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1802         g.drawString("Jalview - Release "+version, 200, y += fh);\r
1803         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1804         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1805                      x, y += fh * 2);\r
1806         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1807                      x, y += fh);\r
1808         g.drawString(\r
1809             "For any issues relating to Jalview, email help@jalview.org", x,\r
1810             y += fh);\r
1811         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1812         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1813                      x, y += fh);\r
1814         g.drawString("Bioinformatics,  2004 20;426-7.", x, y += fh);\r
1815       }\r
1816     }\r
1817 \r
1818     String version = "test";\r
1819     java.net.URL url = getClass().getResource("/.build_properties");\r
1820     if (url != null)\r
1821     {\r
1822       try\r
1823       {\r
1824         BufferedReader reader = new BufferedReader(new InputStreamReader(\r
1825             url.openStream()));\r
1826         String line;\r
1827         while ( (line = reader.readLine()) != null)\r
1828         {\r
1829           if (line.indexOf("VERSION") > -1)\r
1830           {\r
1831             version = line.substring(line.indexOf("=") + 1);\r
1832           }\r
1833         }\r
1834       }\r
1835       catch (Exception ex)\r
1836       {\r
1837         ex.printStackTrace();\r
1838       }\r
1839     }\r
1840 \r
1841 \r
1842     Frame frame = new Frame();\r
1843     frame.add(new AboutPanel(version));\r
1844     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1845 \r
1846   }\r
1847 \r
1848   public void showURL(String url, String target)\r
1849   {\r
1850     if (viewport.applet == null)\r
1851     {\r
1852       System.out.println("Not running as applet - no browser available.");\r
1853     }\r
1854     else\r
1855     {\r
1856       try\r
1857       {\r
1858         System.out.println("Show url: "+url);\r
1859         viewport.applet.getAppletContext().showDocument(new java.net.URL(url),\r
1860                                                target);\r
1861       }\r
1862       catch (Exception ex)\r
1863       {\r
1864         ex.printStackTrace();\r
1865       }\r
1866     }\r
1867   }\r
1868 \r
1869 \r
1870   //////////////////////////////////////////////////////////////////////////////////\r
1871   //JBuilder Graphics here\r
1872 \r
1873     protected MenuBar alignFrameMenuBar = new MenuBar();\r
1874     protected Menu fileMenu = new Menu("File");\r
1875     protected MenuItem loadApplication = new MenuItem("View in Full Application");\r
1876     protected MenuItem loadTree = new MenuItem("Load Associated Tree");\r
1877     protected MenuItem closeMenuItem = new MenuItem("Close");\r
1878     protected Menu editMenu = new Menu("Edit");\r
1879     protected Menu viewMenu = new Menu("View");\r
1880     protected Menu colourMenu = new Menu("Colour");\r
1881     protected Menu calculateMenu = new Menu("Calculate");\r
1882     protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
1883     protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
1884     protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
1885     protected MenuItem remove2LeftMenuItem = new MenuItem();\r
1886     protected MenuItem remove2RightMenuItem = new MenuItem();\r
1887     protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
1888     protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
1889     protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
1890     protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
1891     protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
1892     protected MenuItem sortIDMenuItem = new MenuItem();\r
1893     protected MenuItem sortGroupMenuItem = new MenuItem();\r
1894     protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
1895     protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
1896     protected MenuItem PCAMenuItem = new MenuItem();\r
1897     protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
1898     protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
1899     BorderLayout borderLayout1 = new BorderLayout();\r
1900     public Label statusBar = new Label();\r
1901     protected Menu outputTextboxMenu = new Menu();\r
1902     protected MenuItem clustalColour = new MenuItem();\r
1903     protected MenuItem zappoColour = new MenuItem();\r
1904     protected MenuItem taylorColour = new MenuItem();\r
1905     protected MenuItem hydrophobicityColour = new MenuItem();\r
1906     protected MenuItem helixColour = new MenuItem();\r
1907     protected MenuItem strandColour = new MenuItem();\r
1908     protected MenuItem turnColour = new MenuItem();\r
1909     protected MenuItem buriedColour = new MenuItem();\r
1910     protected MenuItem userDefinedColour = new MenuItem();\r
1911     protected MenuItem PIDColour = new MenuItem();\r
1912     protected MenuItem BLOSUM62Colour = new MenuItem();\r
1913     MenuItem njTreeBlosumMenuItem = new MenuItem();\r
1914     MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
1915     protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
1916     protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
1917     MenuItem overviewMenuItem = new MenuItem();\r
1918     protected MenuItem undoMenuItem = new MenuItem();\r
1919     protected MenuItem redoMenuItem = new MenuItem();\r
1920     protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
1921     MenuItem noColourmenuItem = new MenuItem();\r
1922     protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
1923     protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
1924     MenuItem findMenuItem = new MenuItem();\r
1925     Menu searchMenu = new Menu();\r
1926     protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
1927     protected MenuItem nucleotideColour = new MenuItem();\r
1928     MenuItem deleteGroups = new MenuItem();\r
1929     MenuItem delete = new MenuItem();\r
1930     MenuItem copy = new MenuItem();\r
1931     MenuItem cut = new MenuItem();\r
1932     Menu pasteMenu = new Menu();\r
1933     MenuItem pasteNew = new MenuItem();\r
1934     MenuItem pasteThis = new MenuItem();\r
1935     protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
1936     protected MenuItem font = new MenuItem();\r
1937     protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
1938     protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
1939     protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
1940     MenuItem modifyPID = new MenuItem();\r
1941     MenuItem modifyConservation = new MenuItem();\r
1942     protected CheckboxMenuItem autoCalculate\r
1943         = new CheckboxMenuItem("Autocalculate Consensus", true);\r
1944     protected Menu sortByTreeMenu = new Menu();\r
1945     Menu sort = new Menu();\r
1946     Menu calculate = new Menu();\r
1947     MenuItem inputText = new MenuItem();\r
1948     Menu helpMenu = new Menu();\r
1949     MenuItem documentation = new MenuItem();\r
1950     MenuItem about = new MenuItem();\r
1951     protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
1952   Panel embeddedMenu;\r
1953   Label embeddedEdit;\r
1954   Label embeddedSearch;\r
1955   Label embeddedView;\r
1956   Label embeddedColour;\r
1957   Label embeddedFile;\r
1958   Label embeddedHelp;\r
1959   Label embeddedCalculate;\r
1960   FlowLayout flowLayout1;\r
1961 \r
1962   private void jbInit() throws Exception {\r
1963 \r
1964       setMenuBar(alignFrameMenuBar);\r
1965 \r
1966       MenuItem item;\r
1967 \r
1968       // dynamically fill save as menu with available formats\r
1969       for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
1970       {\r
1971 \r
1972         item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);\r
1973 \r
1974         item.addActionListener(new java.awt.event.ActionListener()\r
1975         {\r
1976           public void actionPerformed(ActionEvent e)\r
1977           {\r
1978             outputText_actionPerformed(e);\r
1979           }\r
1980         });\r
1981 \r
1982         outputTextboxMenu.add(item);\r
1983       }\r
1984         closeMenuItem.addActionListener(this);\r
1985         loadApplication.addActionListener(this);\r
1986 \r
1987         loadTree.addActionListener(this);\r
1988         selectAllSequenceMenuItem.addActionListener(this);\r
1989         deselectAllSequenceMenuItem.addActionListener(this);\r
1990         invertSequenceMenuItem.addActionListener(this);\r
1991         remove2LeftMenuItem.setLabel("Remove Left");\r
1992         remove2LeftMenuItem.addActionListener(this);\r
1993         remove2RightMenuItem.setLabel("Remove Right");\r
1994         remove2RightMenuItem.addActionListener(this);\r
1995         removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
1996         removeGappedColumnMenuItem.addActionListener(this);\r
1997         removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
1998         removeAllGapsMenuItem.addActionListener(this);\r
1999         viewBoxesMenuItem.setLabel("Boxes");\r
2000         viewBoxesMenuItem.setState(true);\r
2001         viewBoxesMenuItem.addItemListener(this);\r
2002         viewTextMenuItem.setLabel("Text");\r
2003         viewTextMenuItem.setState(true);\r
2004         viewTextMenuItem.addItemListener(this);\r
2005         sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
2006         sortPairwiseMenuItem.addActionListener(this);\r
2007         sortIDMenuItem.setLabel("by ID");\r
2008         sortIDMenuItem.addActionListener(this);\r
2009         sortGroupMenuItem.setLabel("by Group");\r
2010         sortGroupMenuItem.addActionListener(this);\r
2011         removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
2012         removeRedundancyMenuItem.addActionListener(this);\r
2013         pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
2014         pairwiseAlignmentMenuItem.addActionListener(this);\r
2015         PCAMenuItem.setLabel("Principal Component Analysis");\r
2016         PCAMenuItem.addActionListener(this);\r
2017         averageDistanceTreeMenuItem.setLabel(\r
2018             "Average Distance Using % Identity");\r
2019         averageDistanceTreeMenuItem.addActionListener(this);\r
2020         neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
2021         neighbourTreeMenuItem.addActionListener(this);\r
2022         alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
2023         statusBar.setBackground(Color.white);\r
2024         statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
2025         statusBar.setText("Status bar");\r
2026         outputTextboxMenu.setLabel("Output to Textbox");\r
2027         clustalColour.setLabel("Clustalx");\r
2028 \r
2029         clustalColour.addActionListener(this);\r
2030         zappoColour.setLabel("Zappo");\r
2031         zappoColour.addActionListener(this);\r
2032         taylorColour.setLabel("Taylor");\r
2033         taylorColour.addActionListener(this);\r
2034         hydrophobicityColour.setLabel("Hydrophobicity");\r
2035         hydrophobicityColour.addActionListener(this);\r
2036         helixColour.setLabel("Helix Propensity");\r
2037         helixColour.addActionListener(this);\r
2038         strandColour.setLabel("Strand Propensity");\r
2039         strandColour.addActionListener(this);\r
2040         turnColour.setLabel("Turn Propensity");\r
2041         turnColour.addActionListener(this);\r
2042         buriedColour.setLabel("Buried Index");\r
2043         buriedColour.addActionListener(this);\r
2044         userDefinedColour.setLabel("User Defined...");\r
2045         userDefinedColour.addActionListener(this);\r
2046         PIDColour.setLabel("Percentage Identity");\r
2047         PIDColour.addActionListener(this);\r
2048         BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
2049         BLOSUM62Colour.addActionListener(this);\r
2050         avDistanceTreeBlosumMenuItem.setLabel(\r
2051             "Average Distance Using BLOSUM62");\r
2052         avDistanceTreeBlosumMenuItem.addActionListener(this);\r
2053         njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
2054         njTreeBlosumMenuItem.addActionListener(this);\r
2055         annotationPanelMenuItem.setLabel("Show Annotations");\r
2056         annotationPanelMenuItem.addItemListener(this);\r
2057         colourTextMenuItem.setLabel("Colour Text");\r
2058         colourTextMenuItem.addItemListener(this);\r
2059         overviewMenuItem.setLabel("Overview Window");\r
2060         overviewMenuItem.addActionListener(this);\r
2061         undoMenuItem.setEnabled(false);\r
2062         undoMenuItem.setLabel("Undo");\r
2063         undoMenuItem.addActionListener(this);\r
2064         redoMenuItem.setEnabled(false);\r
2065         redoMenuItem.setLabel("Redo");\r
2066         redoMenuItem.addActionListener(this);\r
2067         conservationMenuItem.setLabel("by Conservation");\r
2068         conservationMenuItem.addItemListener(this);\r
2069         noColourmenuItem.setLabel("None");\r
2070         noColourmenuItem.addActionListener(this);\r
2071         wrapMenuItem.setLabel("Wrap");\r
2072         wrapMenuItem.addItemListener(this);\r
2073         renderGapsMenuItem.setLabel("Show Gaps");\r
2074         renderGapsMenuItem.setState(true);\r
2075         renderGapsMenuItem.addItemListener(this);\r
2076         findMenuItem.setLabel("Find...");\r
2077         findMenuItem.addActionListener(this);\r
2078         searchMenu.setLabel("Search");\r
2079 \r
2080         abovePIDThreshold.setLabel("Above Identity Threshold");\r
2081         abovePIDThreshold.addItemListener(this);\r
2082         nucleotideColour.setLabel("Nucleotide");\r
2083         nucleotideColour.addActionListener(this);\r
2084         deleteGroups.setLabel("Undefine Groups");\r
2085         deleteGroups.addActionListener(this);\r
2086         copy.setLabel("Copy");\r
2087         copy.addActionListener(this);\r
2088         cut.setLabel("Cut");\r
2089         cut.addActionListener(this);\r
2090         delete.setLabel("Delete");\r
2091         delete.addActionListener(this);\r
2092         pasteMenu.setLabel("Paste");\r
2093         pasteNew.setLabel("To New Alignment");\r
2094         pasteNew.addActionListener(this);\r
2095         pasteThis.setLabel("Add To This Alignment");\r
2096         pasteThis.addActionListener(this);\r
2097         applyToAllGroups.setLabel("Apply Colour To All Groups");\r
2098         applyToAllGroups.setState(true);\r
2099         applyToAllGroups.addItemListener(this);\r
2100         font.setLabel("Font...");\r
2101         font.addActionListener(this);\r
2102         scaleAbove.setLabel("Scale Above");\r
2103         scaleAbove.setState(true);\r
2104         scaleAbove.setEnabled(false);\r
2105         scaleAbove.addItemListener(this);\r
2106         scaleLeft.setEnabled(false);\r
2107         scaleLeft.setState(true);\r
2108         scaleLeft.setLabel("Scale Left");\r
2109         scaleLeft.addItemListener(this);\r
2110         scaleRight.setEnabled(false);\r
2111         scaleRight.setState(true);\r
2112         scaleRight.setLabel("Scale Right");\r
2113         scaleRight.addItemListener(this);\r
2114         modifyPID.setLabel("Modify Identity Threshold...");\r
2115         modifyPID.addActionListener(this);\r
2116         modifyConservation.setLabel("Modify Conservation Threshold...");\r
2117         modifyConservation.addActionListener(this);\r
2118         sortByTreeMenu.setLabel("By Tree Order");\r
2119         sort.setLabel("Sort");\r
2120         calculate.setLabel("Calculate Tree");\r
2121         autoCalculate.addItemListener(this);\r
2122         inputText.setLabel("Input from textbox");\r
2123         inputText.addActionListener(this);\r
2124 \r
2125         helpMenu.setLabel("Help");\r
2126         documentation.setLabel("Documentation");\r
2127         documentation.addActionListener(this);\r
2128 \r
2129         about.setLabel("About...");\r
2130         about.addActionListener(this);\r
2131           seqLimits.setState(true);\r
2132     seqLimits.setLabel("Show Sequence Limits");\r
2133     seqLimits.addItemListener(this);\r
2134     featureSettings.setLabel("Feature Settings...");\r
2135     featureSettings.addActionListener(this);\r
2136     sequenceFeatures.setLabel("Sequence Features");\r
2137     sequenceFeatures.addItemListener(this);\r
2138     sequenceFeatures.setState(false);\r
2139     annotationColour.setLabel("by Annotation...");\r
2140     annotationColour.addActionListener(this);\r
2141     invertSequenceMenuItem.setLabel("Invert Sequence Selection");\r
2142     invertColSel.setLabel("Invert Column Selection");\r
2143     menu1.setLabel("Show");\r
2144     showColumns.setLabel("All Columns ");\r
2145     showSeqs.setLabel("All Sequences");\r
2146     menu2.setLabel("Hide");\r
2147     hideColumns.setLabel("Selected Columns");\r
2148     hideSequences.setLabel("Selected Sequences");\r
2149     invertColSel.addActionListener(this);\r
2150     showColumns.addActionListener(this);\r
2151     showSeqs.addActionListener(this);\r
2152     hideColumns.addActionListener(this);\r
2153     hideSequences.addActionListener(this);\r
2154 \r
2155 \r
2156     alignFrameMenuBar.add(fileMenu);\r
2157         alignFrameMenuBar.add(editMenu);\r
2158         alignFrameMenuBar.add(searchMenu);\r
2159         alignFrameMenuBar.add(viewMenu);\r
2160         alignFrameMenuBar.add(colourMenu);\r
2161         alignFrameMenuBar.add(calculateMenu);\r
2162         alignFrameMenuBar.add(helpMenu);\r
2163         fileMenu.add(inputText);\r
2164         fileMenu.add(outputTextboxMenu);\r
2165         if(jalviewServletURL!=null)\r
2166           fileMenu.add(loadApplication);\r
2167         fileMenu.addSeparator();\r
2168         fileMenu.add(loadTree);\r
2169         fileMenu.add(closeMenuItem);\r
2170         editMenu.add(undoMenuItem);\r
2171         editMenu.add(redoMenuItem);\r
2172         editMenu.add(cut);\r
2173         editMenu.add(copy);\r
2174         editMenu.add(pasteMenu);\r
2175         editMenu.add(delete);\r
2176         editMenu.addSeparator();\r
2177         editMenu.add(selectAllSequenceMenuItem);\r
2178         editMenu.add(deselectAllSequenceMenuItem);\r
2179         editMenu.add(invertSequenceMenuItem);\r
2180     editMenu.add(invertColSel);\r
2181     editMenu.add(deleteGroups);\r
2182         editMenu.addSeparator();\r
2183         editMenu.add(remove2LeftMenuItem);\r
2184         editMenu.add(remove2RightMenuItem);\r
2185         editMenu.add(removeGappedColumnMenuItem);\r
2186         editMenu.add(removeAllGapsMenuItem);\r
2187         editMenu.add(removeRedundancyMenuItem);\r
2188         searchMenu.add(findMenuItem);\r
2189         viewMenu.add(font);\r
2190         viewMenu.addSeparator();\r
2191     viewMenu.add(menu1);\r
2192     viewMenu.add(menu2);\r
2193     viewMenu.addSeparator();\r
2194     viewMenu.add(wrapMenuItem);\r
2195         viewMenu.add(scaleAbove);\r
2196         viewMenu.add(scaleLeft);\r
2197         viewMenu.add(scaleRight);\r
2198         viewMenu.addSeparator();\r
2199     viewMenu.add(seqLimits);\r
2200     viewMenu.add(viewBoxesMenuItem);\r
2201         viewMenu.add(viewTextMenuItem);\r
2202         viewMenu.add(colourTextMenuItem);\r
2203         viewMenu.add(renderGapsMenuItem);\r
2204         viewMenu.add(annotationPanelMenuItem);\r
2205     viewMenu.addSeparator();\r
2206         viewMenu.add(sequenceFeatures);\r
2207         viewMenu.add(featureSettings);\r
2208     viewMenu.addSeparator();\r
2209         viewMenu.add(overviewMenuItem);\r
2210         colourMenu.add(applyToAllGroups);\r
2211         colourMenu.addSeparator();\r
2212         colourMenu.add(noColourmenuItem);\r
2213         colourMenu.add(clustalColour);\r
2214         colourMenu.add(BLOSUM62Colour);\r
2215         colourMenu.add(PIDColour);\r
2216         colourMenu.add(zappoColour);\r
2217         colourMenu.add(taylorColour);\r
2218         colourMenu.add(hydrophobicityColour);\r
2219         colourMenu.add(helixColour);\r
2220         colourMenu.add(strandColour);\r
2221         colourMenu.add(turnColour);\r
2222         colourMenu.add(buriedColour);\r
2223         colourMenu.add(nucleotideColour);\r
2224         colourMenu.add(userDefinedColour);\r
2225         colourMenu.addSeparator();\r
2226         colourMenu.add(conservationMenuItem);\r
2227         colourMenu.add(modifyConservation);\r
2228         colourMenu.add(abovePIDThreshold);\r
2229         colourMenu.add(modifyPID);\r
2230     colourMenu.add(annotationColour);\r
2231     calculateMenu.add(sort);\r
2232         calculateMenu.add(calculate);\r
2233         calculateMenu.addSeparator();\r
2234         calculateMenu.add(pairwiseAlignmentMenuItem);\r
2235         calculateMenu.add(PCAMenuItem);\r
2236         calculateMenu.add(autoCalculate);\r
2237         this.add(statusBar, BorderLayout.SOUTH);\r
2238         pasteMenu.add(pasteNew);\r
2239         pasteMenu.add(pasteThis);\r
2240         sort.add(sortIDMenuItem);\r
2241         sort.add(sortByTreeMenu);\r
2242         sort.add(sortGroupMenuItem);\r
2243         sort.add(sortPairwiseMenuItem);\r
2244         calculate.add(averageDistanceTreeMenuItem);\r
2245         calculate.add(neighbourTreeMenuItem);\r
2246         calculate.add(avDistanceTreeBlosumMenuItem);\r
2247         calculate.add(njTreeBlosumMenuItem);\r
2248         helpMenu.add(documentation);\r
2249         helpMenu.add(about);\r
2250     menu1.add(showColumns);\r
2251     menu1.add(showSeqs);\r
2252     menu2.add(hideColumns);\r
2253     menu2.add(hideSequences);\r
2254   }\r
2255 \r
2256   public void setEmbedded()\r
2257   {\r
2258 \r
2259     embeddedMenu = new Panel();\r
2260     embeddedEdit = new Label();\r
2261     embeddedSearch = new Label();\r
2262     embeddedView = new Label();\r
2263     embeddedColour = new Label();\r
2264     embeddedFile = new Label();\r
2265     embeddedHelp = new Label();\r
2266     embeddedCalculate = new Label();\r
2267     flowLayout1 = new FlowLayout();\r
2268     embeddedMenu.setBackground(Color.lightGray);\r
2269     embeddedMenu.setLayout(flowLayout1);\r
2270     embeddedEdit.setText("Edit");\r
2271     embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2272     embeddedSearch.setText("Search");\r
2273     embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2274     embeddedView.setText("View");\r
2275     embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2276     embeddedColour.setText("Colour");\r
2277     embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2278     embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2279     embeddedFile.setText("File");\r
2280     embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2281     embeddedHelp.setText("Help");\r
2282     embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2283     embeddedCalculate.setText("Calculate");\r
2284     embeddedMenu.add(embeddedFile);\r
2285     embeddedMenu.add(embeddedEdit);\r
2286     embeddedMenu.add(embeddedSearch);\r
2287     embeddedMenu.add(embeddedView);\r
2288     embeddedMenu.add(embeddedColour);\r
2289     embeddedMenu.add(embeddedCalculate);\r
2290     embeddedMenu.add(embeddedHelp);\r
2291     flowLayout1.setAlignment(FlowLayout.LEFT);\r
2292     flowLayout1.setHgap(2);\r
2293     flowLayout1.setVgap(0);\r
2294     embeddedFile.addMouseListener(this);\r
2295     embeddedEdit.addMouseListener(this);\r
2296     embeddedSearch.addMouseListener(this);\r
2297     embeddedView.addMouseListener(this);\r
2298     embeddedColour.addMouseListener(this);\r
2299     embeddedCalculate.addMouseListener(this);\r
2300     embeddedHelp.addMouseListener(this);\r
2301 \r
2302    // setVisible(false);\r
2303     fileMenu.remove(closeMenuItem);\r
2304     fileMenu.remove(3); // Seperator\r
2305 \r
2306     viewport.applet.setLayout(new BorderLayout());\r
2307     viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
2308     viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
2309    // viewport.applet.validate();\r
2310 \r
2311     alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height\r
2312                        - embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
2313 \r
2314      viewport.applet.add(alignPanel, BorderLayout.CENTER);\r
2315      viewport.applet.validate();\r
2316 \r
2317   }\r
2318 \r
2319 \r
2320 \r
2321   PopupMenu filePopup, editPopup, searchPopup,\r
2322       viewPopup, colourPopup, calculatePopup, helpPopup;\r
2323   MenuItem featureSettings = new MenuItem();\r
2324   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
2325   MenuItem annotationColour = new MenuItem();\r
2326   MenuItem invertColSel = new MenuItem();\r
2327   Menu menu1 = new Menu();\r
2328   MenuItem showColumns = new MenuItem();\r
2329   MenuItem showSeqs = new MenuItem();\r
2330   Menu menu2 = new Menu();\r
2331   MenuItem hideColumns = new MenuItem();\r
2332   MenuItem hideSequences = new MenuItem();\r
2333 \r
2334   public void mousePressed(MouseEvent evt)\r
2335   {\r
2336     PopupMenu popup = null;\r
2337     Label source = (Label)evt.getSource();\r
2338     if(source==embeddedFile)\r
2339     {\r
2340       popup = filePopup = genPopupMenu(filePopup, fileMenu);\r
2341     }\r
2342     else if(source==embeddedEdit)\r
2343     {\r
2344       popup = editPopup = genPopupMenu(editPopup, editMenu);\r
2345     }\r
2346     else if(source==embeddedSearch)\r
2347     {\r
2348       popup = searchPopup = genPopupMenu(searchPopup, searchMenu);\r
2349     }\r
2350     else if(source==embeddedView)\r
2351     {\r
2352       popup = viewPopup = genPopupMenu(viewPopup, viewMenu);\r
2353     }\r
2354     else if(source==embeddedColour)\r
2355     {\r
2356       popup = colourPopup = genPopupMenu(colourPopup, colourMenu);\r
2357     }\r
2358     else if(source==embeddedCalculate)\r
2359     {\r
2360       popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);\r
2361     }\r
2362     else if(source==embeddedHelp)\r
2363     {\r
2364       popup = helpPopup = genPopupMenu(helpPopup, helpMenu);\r
2365     }\r
2366 \r
2367     embeddedMenu.add(popup);\r
2368     popup.show(embeddedMenu,\r
2369                source.getBounds().x,\r
2370                source.getBounds().y + source.getBounds().getSize().height);\r
2371   }\r
2372 \r
2373   PopupMenu genPopupMenu(PopupMenu popup, Menu original)\r
2374   {\r
2375     if(popup!=null)\r
2376     {\r
2377       return popup;\r
2378     }\r
2379     popup = new PopupMenu();\r
2380     int m, mSize = original.getItemCount();\r
2381     for(m=0; m<mSize; m++)\r
2382     {\r
2383       popup.add(original.getItem(m));\r
2384       mSize--;\r
2385       m--;\r
2386     }\r
2387 \r
2388     return popup;\r
2389   }\r
2390   public void mouseClicked(MouseEvent evt)\r
2391   {}\r
2392   public void mouseReleased(MouseEvent evt)\r
2393   {}\r
2394   public void mouseEntered(MouseEvent evt)\r
2395   {}\r
2396   public void mouseExited(MouseEvent evt)\r
2397   {}\r
2398 \r
2399 }\r
2400 \r