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