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 jalview.commands.*;\r
  27 import java.awt.*;\r
  28 import java.awt.event.*;\r
  29 import java.util.*;\r
  30 import java.io.InputStreamReader;\r
  31 import java.io.BufferedReader;\r
  32 import java.net.URL;\r
  33 \r
  34 \r
  35 public class AlignFrame extends Frame implements ActionListener,\r
  36     ItemListener, KeyListener, MouseListener\r
  37 {\r
  38   public AlignmentPanel alignPanel;\r
  39   public AlignViewport viewport;\r
  40   int DEFAULT_WIDTH = 700;\r
  41   int DEFAULT_HEIGHT = 500;\r
  42 \r
  43   String jalviewServletURL;\r
  44 \r
  45 \r
  46    public AlignFrame(AlignmentI al,\r
  47                      jalview.bin.JalviewLite applet,\r
  48                      String title,\r
  49                      boolean embedded)\r
  50   {\r
  51 \r
  52     jalviewServletURL = applet.getParameter("APPLICATION_URL");\r
  53 \r
  54     try{\r
  55       jbInit();\r
  56     }catch(Exception ex)\r
  57     {\r
  58       ex.printStackTrace();\r
  59     }\r
  60 \r
  61     viewport = new AlignViewport(al, applet);\r
  62     alignPanel = new AlignmentPanel(this, viewport);\r
  63 \r
  64     viewport.updateConservation(alignPanel);\r
  65     viewport.updateConsensus(alignPanel);\r
  66 \r
  67     annotationPanelMenuItem.setState(viewport.showAnnotation);\r
  68 \r
  69     seqLimits.setState(viewport.showJVSuffix);\r
  70 \r
  71     if(applet!=null)\r
  72     {\r
  73       String param = applet.getParameter("sortBy");\r
  74       if (param != null)\r
  75       {\r
  76         if (param.equalsIgnoreCase("Id"))\r
  77           sortIDMenuItem_actionPerformed();\r
  78         else if (param.equalsIgnoreCase("Pairwise Identity"))\r
  79           sortPairwiseMenuItem_actionPerformed();\r
  80       }\r
  81 \r
  82       param = applet.getParameter("wrap");\r
  83       if (param != null)\r
  84       {\r
  85         if (param.equalsIgnoreCase("true"))\r
  86         {\r
  87           wrapMenuItem.setState(true);\r
  88           wrapMenuItem_actionPerformed();\r
  89         }\r
  90       }\r
  91 \r
  92       try\r
  93       {\r
  94         param = applet.getParameter("windowWidth");\r
  95         if (param != null)\r
  96         {\r
  97           int width = Integer.parseInt(param);\r
  98           DEFAULT_WIDTH = width;\r
  99         }\r
 100         param = applet.getParameter("windowHeight");\r
 101         if (param != null)\r
 102         {\r
 103           int height = Integer.parseInt(param);\r
 104           DEFAULT_HEIGHT = height;\r
 105         }\r
 106       }\r
 107       catch (Exception ex)\r
 108       {}\r
 109 \r
 110     }\r
 111 \r
 112    //Some JVMS send keyevents to Top frame or lowest panel,\r
 113    //Havent worked out why yet. So add to both this frame and seqCanvas for now\r
 114    this.addKeyListener(this);\r
 115    alignPanel.seqPanel.seqCanvas.addKeyListener(this);\r
 116    alignPanel.idPanel.idCanvas.addKeyListener(this);\r
 117    alignPanel.scalePanel.addKeyListener(this);\r
 118    alignPanel.annotationPanel.addKeyListener(this);\r
 119 \r
 120 \r
 121    if(embedded)\r
 122    {\r
 123      setEmbedded();\r
 124    }\r
 125    else\r
 126    {\r
 127      add(alignPanel, BorderLayout.CENTER);\r
 128      jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,\r
 129                                       DEFAULT_HEIGHT);\r
 130    }\r
 131    alignPanel.validate();\r
 132    alignPanel.repaint();\r
 133   }\r
 134   public AlignViewport getAlignViewport()\r
 135   {\r
 136     return viewport;\r
 137   }\r
 138 \r
 139   public SeqCanvas getSeqcanvas()\r
 140   {\r
 141     return alignPanel.seqPanel.seqCanvas;\r
 142   }\r
 143 \r
 144 \r
 145   /**\r
 146    * DOCUMENT ME!\r
 147    *\r
 148    * @param String DOCUMENT ME!\r
 149    */\r
 150 \r
 151   public void parseFeaturesFile(String file, String type)\r
 152   {\r
 153     Hashtable featureLinks = new Hashtable();\r
 154     boolean featuresFile = false;\r
 155     try{\r
 156       featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,\r
 157                                          alignPanel.seqPanel.seqCanvas.\r
 158                                          getFeatureRenderer().featureColours,\r
 159                                          featureLinks,\r
 160                                          true);\r
 161     }\r
 162     catch(Exception ex)\r
 163     {\r
 164       ex.printStackTrace();\r
 165     }\r
 166 \r
 167     if(featuresFile)\r
 168     {\r
 169       if(featureLinks.size()>0)\r
 170         alignPanel.seqPanel.seqCanvas\r
 171             .getFeatureRenderer().featureLinks = featureLinks;\r
 172       viewport.showSequenceFeatures = true;\r
 173       sequenceFeatures.setState(true);\r
 174       alignPanel.repaint();\r
 175     }\r
 176 \r
 177   }\r
 178 \r
 179 \r
 180   public void keyPressed(KeyEvent evt)\r
 181   {\r
 182     if (viewport.cursorMode\r
 183         && evt.getKeyCode() >= KeyEvent.VK_0\r
 184         && evt.getKeyCode() <= KeyEvent.VK_9)\r
 185     {\r
 186       alignPanel.seqPanel.numberPressed(evt.getKeyChar());\r
 187     }\r
 188 \r
 189     switch (evt.getKeyCode())\r
 190     {\r
 191       case 27: // escape key\r
 192         deselectAllSequenceMenuItem_actionPerformed();\r
 193         break;\r
 194       case KeyEvent.VK_X:\r
 195         if (evt.isControlDown() || evt.isMetaDown())\r
 196         {\r
 197           cut_actionPerformed();\r
 198         }\r
 199         break;\r
 200       case KeyEvent.VK_C:\r
 201         if (viewport.cursorMode && !evt.isControlDown())\r
 202         {\r
 203           alignPanel.seqPanel.setCursorColumn();\r
 204         }\r
 205         if (evt.isControlDown() || evt.isMetaDown())\r
 206         {\r
 207           copy_actionPerformed();\r
 208         }\r
 209         break;\r
 210       case KeyEvent.VK_V:\r
 211         if (evt.isControlDown())\r
 212         {\r
 213           paste(evt.isShiftDown());\r
 214         }\r
 215         break;\r
 216       case KeyEvent.VK_A:\r
 217         if (evt.isControlDown() || evt.isMetaDown())\r
 218         {\r
 219           selectAllSequenceMenuItem_actionPerformed();\r
 220         }\r
 221         break;\r
 222       case KeyEvent.VK_DOWN:\r
 223         if(viewport.cursorMode)\r
 224         {\r
 225           alignPanel.seqPanel.moveCursor(0,1);\r
 226         }\r
 227         else\r
 228           moveSelectedSequences(false);\r
 229         break;\r
 230 \r
 231       case KeyEvent.VK_UP:\r
 232         if (viewport.cursorMode)\r
 233         {\r
 234           alignPanel.seqPanel.moveCursor(0,-1);\r
 235         }\r
 236         else\r
 237           moveSelectedSequences(true);\r
 238         break;\r
 239 \r
 240       case KeyEvent.VK_LEFT:\r
 241         if(viewport.cursorMode)\r
 242         {\r
 243           alignPanel.seqPanel.moveCursor(-1,0);\r
 244         }\r
 245         break;\r
 246 \r
 247       case KeyEvent.VK_RIGHT:\r
 248         if (viewport.cursorMode)\r
 249         {\r
 250           alignPanel.seqPanel.moveCursor(1,0);\r
 251         }\r
 252         break;\r
 253       case KeyEvent.VK_SPACE:\r
 254         if(viewport.cursorMode)\r
 255         {\r
 256           alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()\r
 257                                                 || evt.isShiftDown()\r
 258                                                 || evt.isAltDown()\r
 259               );\r
 260         }\r
 261         break;\r
 262 \r
 263       case KeyEvent.VK_DELETE:\r
 264       case KeyEvent.VK_BACK_SPACE:\r
 265         if(viewport.cursorMode)\r
 266         {\r
 267           alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()\r
 268                                                 || evt.isShiftDown()\r
 269                                                 || evt.isAltDown());\r
 270         }\r
 271        else\r
 272         {\r
 273           cut_actionPerformed();\r
 274           alignPanel.seqPanel.seqCanvas.repaint();\r
 275         }\r
 276         break;\r
 277 \r
 278       case KeyEvent.VK_S:\r
 279         if(viewport.cursorMode)\r
 280         {\r
 281           alignPanel.seqPanel.setCursorRow();\r
 282         }\r
 283         break;\r
 284       case KeyEvent.VK_P:\r
 285         if(viewport.cursorMode)\r
 286         {\r
 287           alignPanel.seqPanel.setCursorPosition();\r
 288         }\r
 289         break;\r
 290 \r
 291       case KeyEvent.VK_ENTER:\r
 292       case KeyEvent.VK_COMMA:\r
 293         if(viewport.cursorMode)\r
 294         {\r
 295           alignPanel.seqPanel.setCursorRowAndColumn();\r
 296         }\r
 297         break;\r
 298 \r
 299       case KeyEvent.VK_Q:\r
 300         if(viewport.cursorMode)\r
 301         {\r
 302           alignPanel.seqPanel.setSelectionAreaAtCursor(true);\r
 303         }\r
 304         break;\r
 305       case KeyEvent.VK_M:\r
 306         if(viewport.cursorMode)\r
 307         {\r
 308           alignPanel.seqPanel.setSelectionAreaAtCursor(false);\r
 309         }\r
 310         break;\r
 311 \r
 312      case KeyEvent.VK_F2:\r
 313        viewport.cursorMode = ! viewport.cursorMode;\r
 314        statusBar.setText("Keyboard editing mode is "+\r
 315            (viewport.cursorMode ? "on" : "off"));\r
 316        if(viewport.cursorMode)\r
 317        {\r
 318          alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;\r
 319          alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;\r
 320        }\r
 321        break;\r
 322 \r
 323       case KeyEvent.VK_F:\r
 324         if (evt.isControlDown())\r
 325         {\r
 326           findMenuItem_actionPerformed();\r
 327         }\r
 328         break;\r
 329 \r
 330       case KeyEvent.VK_H:\r
 331       {\r
 332         boolean toggleSeqs = !evt.isControlDown();\r
 333         boolean toggleCols = !evt.isShiftDown();\r
 334         boolean hide = false;\r
 335         SequenceGroup sg = viewport.getSelectionGroup();\r
 336 \r
 337         if(toggleSeqs)\r
 338         {\r
 339           if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())\r
 340           {\r
 341             hide = true;\r
 342             viewport.hideAllSelectedSeqs();\r
 343           }\r
 344           else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))\r
 345             viewport.showAllHiddenSeqs();\r
 346         }\r
 347 \r
 348         if(toggleCols)\r
 349         {\r
 350           if (viewport.colSel.getSelected().size() > 0)\r
 351           {\r
 352             viewport.hideSelectedColumns();\r
 353             if(!toggleSeqs)\r
 354                    viewport.selectionGroup = sg;\r
 355           }\r
 356           else if (!hide)\r
 357             viewport.showAllHiddenColumns();\r
 358         }\r
 359         break;\r
 360       }\r
 361 \r
 362       case KeyEvent.VK_PAGE_UP:\r
 363         if (viewport.wrapAlignment)\r
 364           alignPanel.scrollUp(true);\r
 365         else\r
 366           alignPanel.setScrollValues(viewport.startRes,\r
 367                                      viewport.startSeq\r
 368                                      - viewport.endSeq + viewport.startSeq);\r
 369         break;\r
 370 \r
 371       case KeyEvent.VK_PAGE_DOWN:\r
 372         if (viewport.wrapAlignment)\r
 373           alignPanel.scrollUp(false);\r
 374         else\r
 375           alignPanel.setScrollValues(viewport.startRes,\r
 376                                      viewport.startSeq\r
 377                                      + viewport.endSeq - viewport.startSeq);\r
 378         break;\r
 379 \r
 380       case KeyEvent.VK_Z:\r
 381         if (evt.isControlDown())\r
 382         {\r
 383           undoMenuItem_actionPerformed();\r
 384         }\r
 385         break;\r
 386 \r
 387       case KeyEvent.VK_Y:\r
 388         if (evt.isControlDown())\r
 389         {\r
 390           redoMenuItem_actionPerformed();\r
 391         }\r
 392         break;\r
 393 \r
 394       case KeyEvent.VK_L:\r
 395         if (evt.isControlDown())\r
 396         {\r
 397           trimAlignment(true);\r
 398         }\r
 399         break;\r
 400 \r
 401       case KeyEvent.VK_R:\r
 402         if (evt.isControlDown())\r
 403         {\r
 404           trimAlignment(false);\r
 405         }\r
 406         break;\r
 407 \r
 408       case KeyEvent.VK_E:\r
 409         if (evt.isControlDown())\r
 410         {\r
 411           if (evt.isShiftDown())\r
 412             this.removeAllGapsMenuItem_actionPerformed();\r
 413           else\r
 414             removeGappedColumnMenuItem_actionPerformed();\r
 415         }\r
 416         break;\r
 417       case KeyEvent.VK_I:\r
 418         if (evt.isControlDown())\r
 419         {\r
 420           if (evt.isAltDown())\r
 421             viewport.invertColumnSelection();\r
 422           else\r
 423             this.invertSequenceMenuItem_actionPerformed();\r
 424         }\r
 425         break;\r
 426 \r
 427       case KeyEvent.VK_U:\r
 428         if (evt.isControlDown())\r
 429         {\r
 430           this.deleteGroups_actionPerformed();\r
 431         }\r
 432       break;\r
 433 \r
 434     case KeyEvent.VK_T:\r
 435       if (evt.isControlDown())\r
 436       {\r
 437        newView();\r
 438       }\r
 439       break;\r
 440 \r
 441 \r
 442       }\r
 443       alignPanel.repaint();\r
 444   }\r
 445   public void keyReleased(KeyEvent evt)\r
 446   {}\r
 447   public void keyTyped(KeyEvent evt)\r
 448   {}\r
 449 \r
 450 public void itemStateChanged(ItemEvent evt)\r
 451   {\r
 452     if(evt.getSource()==colourTextMenuItem)\r
 453             colourTextMenuItem_actionPerformed();\r
 454     else if(evt.getSource()==wrapMenuItem)\r
 455             wrapMenuItem_actionPerformed();\r
 456     else if(evt.getSource()==scaleAbove)\r
 457             viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 458     else if(evt.getSource()==scaleLeft)\r
 459             viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 460     else if(evt.getSource()==scaleRight)\r
 461             viewport.setScaleRightWrapped(scaleRight.getState());\r
 462      else if(evt.getSource()==seqLimits)\r
 463       seqLimits_itemStateChanged();\r
 464     else if(evt.getSource()==viewBoxesMenuItem)\r
 465             viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
 466     else if(evt.getSource()==viewTextMenuItem)\r
 467             viewport.setShowText(viewTextMenuItem.getState());\r
 468     else if(evt.getSource()==renderGapsMenuItem)\r
 469             viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 470     else if(evt.getSource()==annotationPanelMenuItem)\r
 471     {\r
 472       viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
 473       alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
 474     }\r
 475       else if(evt.getSource()==sequenceFeatures)\r
 476       {\r
 477            viewport.showSequenceFeatures(sequenceFeatures.getState());\r
 478             alignPanel.seqPanel.seqCanvas.repaint();\r
 479       }\r
 480       else if(evt.getSource()==conservationMenuItem)\r
 481             conservationMenuItem_actionPerformed();\r
 482       else if(evt.getSource()==abovePIDThreshold)\r
 483             abovePIDThreshold_actionPerformed();\r
 484       else if(evt.getSource()==applyToAllGroups)\r
 485             viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
 486       else if(evt.getSource()==autoCalculate)\r
 487           viewport.autocalculateConsensus = autoCalculate.getState();\r
 488 \r
 489       alignPanel.repaint();\r
 490   }\r
 491  public void actionPerformed(ActionEvent evt)\r
 492  {\r
 493     Object source = evt.getSource();\r
 494 \r
 495     if(source==inputText)\r
 496       inputText_actionPerformed();\r
 497     else if(source==loadTree)\r
 498       loadTree_actionPerformed();\r
 499     else if(source==loadApplication)\r
 500       launchFullApplication();\r
 501     else if(source==closeMenuItem)\r
 502       closeMenuItem_actionPerformed();\r
 503     else if(source==copy)\r
 504       copy_actionPerformed();\r
 505     else if(source==undoMenuItem)\r
 506       undoMenuItem_actionPerformed();\r
 507     else if(source==redoMenuItem)\r
 508       redoMenuItem_actionPerformed();\r
 509     else if(source==inputText)\r
 510             inputText_actionPerformed();\r
 511     else if(source==closeMenuItem)\r
 512             closeMenuItem_actionPerformed();\r
 513     else if(source==undoMenuItem)\r
 514             undoMenuItem_actionPerformed();\r
 515     else if(source==redoMenuItem)\r
 516             redoMenuItem_actionPerformed();\r
 517     else if(source==copy)\r
 518             copy_actionPerformed();\r
 519     else if(source==pasteNew)\r
 520             pasteNew_actionPerformed();\r
 521     else if(source==pasteThis)\r
 522             pasteThis_actionPerformed();\r
 523     else if(source==cut)\r
 524             cut_actionPerformed();\r
 525     else if(source==delete)\r
 526             delete_actionPerformed();\r
 527     else if(source==deleteGroups)\r
 528             deleteGroups_actionPerformed();\r
 529     else if(source==selectAllSequenceMenuItem)\r
 530             selectAllSequenceMenuItem_actionPerformed();\r
 531     else if(source==deselectAllSequenceMenuItem)\r
 532             deselectAllSequenceMenuItem_actionPerformed();\r
 533     else if(source==invertSequenceMenuItem)\r
 534             invertSequenceMenuItem_actionPerformed();\r
 535     else if(source==invertColSel)\r
 536     { viewport.invertColumnSelection(); alignPanel.repaint(); }\r
 537     else if(source==remove2LeftMenuItem)\r
 538             trimAlignment(true);\r
 539     else if(source==remove2RightMenuItem)\r
 540             trimAlignment(false);\r
 541     else if(source==removeGappedColumnMenuItem)\r
 542             removeGappedColumnMenuItem_actionPerformed();\r
 543     else if(source==removeAllGapsMenuItem)\r
 544             removeAllGapsMenuItem_actionPerformed();\r
 545     else if(source==findMenuItem)\r
 546             findMenuItem_actionPerformed();\r
 547     else if(source==font)\r
 548             new FontChooser(alignPanel);\r
 549     else if (source == newView)\r
 550       newView();\r
 551     else if(source==showColumns)\r
 552     {\r
 553       viewport.showAllHiddenColumns(); alignPanel.repaint();\r
 554     }\r
 555     else if(source==showSeqs)\r
 556     {\r
 557       viewport.showAllHiddenSeqs();\r
 558     }\r
 559     else if(source == hideColumns)\r
 560     {\r
 561       viewport.hideSelectedColumns(); alignPanel.repaint();\r
 562     }\r
 563     else if(source == hideSequences && viewport.getSelectionGroup()!=null)\r
 564     {\r
 565       viewport.hideAllSelectedSeqs();\r
 566     }\r
 567     else if(source==featureSettings)\r
 568             new FeatureSettings(alignPanel);\r
 569     else if(source==overviewMenuItem)\r
 570             overviewMenuItem_actionPerformed();\r
 571     else if(source==noColourmenuItem)\r
 572             changeColour(null);\r
 573     else if(source==clustalColour)\r
 574     {\r
 575       abovePIDThreshold.setState(false);\r
 576       changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
 577                                             viewport.alignment.getWidth()));\r
 578   }\r
 579     else if(source==zappoColour)\r
 580             changeColour(new ZappoColourScheme());\r
 581     else if(source==taylorColour)\r
 582             changeColour(new TaylorColourScheme());\r
 583     else if(source==hydrophobicityColour)\r
 584             changeColour(new HydrophobicColourScheme());\r
 585     else if(source==helixColour)\r
 586             changeColour(new HelixColourScheme());\r
 587     else if(source==strandColour)\r
 588             changeColour(new StrandColourScheme());\r
 589     else if(source==turnColour)\r
 590             changeColour(new TurnColourScheme());\r
 591     else if(source==buriedColour)\r
 592             changeColour(new BuriedColourScheme());\r
 593     else if(source==nucleotideColour)\r
 594             changeColour(new NucleotideColourScheme());\r
 595     else if(source==modifyPID)\r
 596             modifyPID_actionPerformed();\r
 597     else if(source==modifyConservation)\r
 598             modifyConservation_actionPerformed();\r
 599     else if(source==userDefinedColour)\r
 600             new UserDefinedColours(alignPanel, null);\r
 601     else if(source==PIDColour)\r
 602             changeColour(new PIDColourScheme());\r
 603     else if(source==BLOSUM62Colour)\r
 604             changeColour(new Blosum62ColourScheme());\r
 605     else if(source==annotationColour)\r
 606            new AnnotationColourChooser(viewport, alignPanel);\r
 607     else if(source==sortPairwiseMenuItem)\r
 608             sortPairwiseMenuItem_actionPerformed();\r
 609     else if(source==sortIDMenuItem)\r
 610             sortIDMenuItem_actionPerformed();\r
 611     else if(source==sortGroupMenuItem)\r
 612             sortGroupMenuItem_actionPerformed();\r
 613     else if(source==removeRedundancyMenuItem)\r
 614             removeRedundancyMenuItem_actionPerformed();\r
 615     else if(source==pairwiseAlignmentMenuItem)\r
 616             pairwiseAlignmentMenuItem_actionPerformed();\r
 617     else if(source==PCAMenuItem)\r
 618             PCAMenuItem_actionPerformed();\r
 619     else if(source==averageDistanceTreeMenuItem)\r
 620             averageDistanceTreeMenuItem_actionPerformed();\r
 621     else if(source==neighbourTreeMenuItem)\r
 622             neighbourTreeMenuItem_actionPerformed();\r
 623     else if(source==njTreeBlosumMenuItem)\r
 624             njTreeBlosumMenuItem_actionPerformed();\r
 625     else if(source==avDistanceTreeBlosumMenuItem)\r
 626             avTreeBlosumMenuItem_actionPerformed();\r
 627     else if(source==documentation)\r
 628             documentation_actionPerformed();\r
 629     else if(source==about)\r
 630             about_actionPerformed();\r
 631 \r
 632  }\r
 633 \r
 634   public void inputText_actionPerformed()\r
 635   {\r
 636     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
 637     Frame frame = new Frame();\r
 638     frame.add(cap);\r
 639     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
 640   }\r
 641 \r
 642   protected void outputText_actionPerformed(ActionEvent e)\r
 643   {\r
 644     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
 645     Frame frame = new Frame();\r
 646     frame.add(cap);\r
 647     jalview.bin.JalviewLite.addFrame(frame,\r
 648                                      "Alignment output - " + e.getActionCommand(),\r
 649                                      600, 500);\r
 650     cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
 651                                               viewport.getAlignment().getSequences(),\r
 652                                                       viewport.showJVSuffix));\r
 653   }\r
 654 \r
 655   void launchFullApplication()\r
 656   {\r
 657     StringBuffer url = new StringBuffer(jalviewServletURL);\r
 658 \r
 659     url.append("?open="+\r
 660                appendProtocol( viewport.applet.getParameter("file") ) );\r
 661 \r
 662     if(viewport.applet.getParameter("features")!=null)\r
 663     {\r
 664       url.append( "&features=" );\r
 665       url.append( appendProtocol( viewport.applet.getParameter("features") ) );\r
 666     }\r
 667 \r
 668     if(viewport.applet.getParameter("annotations")!=null)\r
 669     {\r
 670       url.append( "&annotations=" );\r
 671       url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );\r
 672     }\r
 673 \r
 674     if(viewport.applet.getParameter("jnetfile")!=null)\r
 675     {\r
 676       url.append( "&annotations=" );\r
 677       url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) );\r
 678     }\r
 679 \r
 680     if(viewport.applet.getParameter("defaultColour")!=null)\r
 681     {\r
 682       url.append("&colour=" +\r
 683                  removeWhiteSpace(viewport.applet.getParameter("defaultColour"))\r
 684           );\r
 685     }\r
 686 \r
 687     if(viewport.applet.getParameter("userDefinedColour")!=null)\r
 688     {\r
 689       url.append( "&colour=" +\r
 690                  removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )\r
 691          );\r
 692     }\r
 693 \r
 694     showURL(url.toString(), "FULL_APP");\r
 695   }\r
 696 \r
 697 \r
 698   String removeWhiteSpace(String colour)\r
 699   {\r
 700     StringBuffer sb = new StringBuffer();\r
 701     for (int i = 0; i < colour.length(); i++)\r
 702     {\r
 703       if (Character.isWhitespace(colour.charAt(i)))\r
 704         sb.append("%20");\r
 705       else\r
 706         sb.append(colour.charAt(i));\r
 707     }\r
 708 \r
 709     return sb.toString();\r
 710   }\r
 711 \r
 712 \r
 713   String appendProtocol(String url)\r
 714   {\r
 715     try{\r
 716        new URL(url);\r
 717     }catch(java.net.MalformedURLException ex)\r
 718     {\r
 719       url = viewport.applet.getCodeBase()+url;\r
 720     }\r
 721     return url;\r
 722   }\r
 723 \r
 724   public void closeMenuItem_actionPerformed()\r
 725   {\r
 726     PaintRefresher.RemoveComponent(alignPanel);\r
 727     PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);\r
 728     PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);\r
 729 \r
 730     if(PaintRefresher.components.size()==0 && viewport.applet==null)\r
 731       System.exit(0);\r
 732 \r
 733     this.dispose();\r
 734   }\r
 735 \r
 736 \r
 737   /**\r
 738    * DOCUMENT ME!\r
 739    */\r
 740   void updateEditMenuBar()\r
 741   {\r
 742 \r
 743     if (viewport.historyList.size() > 0)\r
 744     {\r
 745       undoMenuItem.setEnabled(true);\r
 746       CommandI command = (CommandI) viewport.historyList.peek();\r
 747       undoMenuItem.setLabel("Undo " + command.getDescription());\r
 748     }\r
 749     else\r
 750     {\r
 751       undoMenuItem.setEnabled(false);\r
 752       undoMenuItem.setLabel("Undo");\r
 753     }\r
 754 \r
 755     if (viewport.redoList.size() > 0)\r
 756     {\r
 757       redoMenuItem.setEnabled(true);\r
 758 \r
 759       CommandI command = (CommandI) viewport.redoList.peek();\r
 760       redoMenuItem.setLabel("Redo " + command.getDescription());\r
 761     }\r
 762     else\r
 763     {\r
 764       redoMenuItem.setEnabled(false);\r
 765       redoMenuItem.setLabel("Redo");\r
 766     }\r
 767   }\r
 768 \r
 769   public void addHistoryItem(CommandI command)\r
 770   {\r
 771     if(command.getSize()>0)\r
 772     {\r
 773       viewport.historyList.push(command);\r
 774       viewport.redoList.removeAllElements();\r
 775       updateEditMenuBar();\r
 776       viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
 777     }\r
 778   }\r
 779 \r
 780   /**\r
 781    * DOCUMENT ME!\r
 782    *\r
 783    * @param e DOCUMENT ME!\r
 784    */\r
 785   protected void undoMenuItem_actionPerformed()\r
 786   {\r
 787     if(viewport.historyList.size()<1)\r
 788       return;\r
 789 \r
 790     CommandI command = (CommandI)viewport.historyList.pop();\r
 791     viewport.redoList.push(command);\r
 792     command.undoCommand();\r
 793 \r
 794     AlignViewport originalSource = getOriginatingSource(command);\r
 795 \r
 796     originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
 797     updateEditMenuBar();\r
 798     originalSource.firePropertyChange("alignment", null,null);\r
 799   }\r
 800 \r
 801   /**\r
 802    * DOCUMENT ME!\r
 803    *\r
 804    * @param e DOCUMENT ME!\r
 805    */\r
 806   protected void redoMenuItem_actionPerformed()\r
 807   {\r
 808     if(viewport.redoList.size()<1)\r
 809       return;\r
 810 \r
 811     CommandI command = (CommandI) viewport.redoList.pop();\r
 812     viewport.historyList.push(command);\r
 813     command.doCommand();\r
 814 \r
 815     AlignViewport originalSource = getOriginatingSource(command);\r
 816     originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;\r
 817 \r
 818     updateEditMenuBar();\r
 819     originalSource.firePropertyChange("alignment", null, null);\r
 820   }\r
 821 \r
 822   AlignViewport getOriginatingSource(CommandI command)\r
 823   {\r
 824     AlignViewport originalSource = viewport;\r
 825     //For sequence removal and addition, we need to fire\r
 826    //the property change event FROM the viewport where the\r
 827    //original alignment was altered\r
 828     if (command instanceof EditCommand)\r
 829     {\r
 830       EditCommand editCommand = (EditCommand) command;\r
 831       AlignmentI al = editCommand.getAlignment();\r
 832       Vector comps = (Vector) PaintRefresher.components\r
 833           .get(viewport.getSequenceSetId());\r
 834       for (int i = 0; i < comps.size(); i++)\r
 835       {\r
 836         if (comps.elementAt(i) instanceof AlignmentPanel)\r
 837         {\r
 838           if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)\r
 839           {\r
 840             originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;\r
 841             break;\r
 842           }\r
 843         }\r
 844       }\r
 845     }\r
 846     return originalSource;\r
 847   }\r
 848 \r
 849   public void moveSelectedSequences(boolean up)\r
 850   {\r
 851     SequenceGroup sg = viewport.getSelectionGroup();\r
 852     if (sg == null)\r
 853     {\r
 854       return;\r
 855     }\r
 856 \r
 857     if (up)\r
 858     {\r
 859       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 860       {\r
 861         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 862         if (!sg.getSequences(false).contains(seq))\r
 863         {\r
 864           continue;\r
 865         }\r
 866 \r
 867         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 868         if (sg.getSequences(false).contains(temp))\r
 869         {\r
 870           continue;\r
 871         }\r
 872 \r
 873         viewport.alignment.getSequences().setElementAt(temp, i);\r
 874         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 875       }\r
 876     }\r
 877     else\r
 878     {\r
 879       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 880       {\r
 881         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 882         if (!sg.getSequences(true).contains(seq))\r
 883         {\r
 884           continue;\r
 885         }\r
 886 \r
 887         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 888         if (sg.getSequences(true).contains(temp))\r
 889         {\r
 890           continue;\r
 891         }\r
 892 \r
 893         viewport.alignment.getSequences().setElementAt(temp, i);\r
 894         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 895       }\r
 896     }\r
 897 \r
 898     alignPanel.repaint();\r
 899   }\r
 900 \r
 901   static StringBuffer copiedSequences;\r
 902   static Vector copiedHiddenColumns;\r
 903   protected void copy_actionPerformed()\r
 904   {\r
 905     if (viewport.getSelectionGroup() == null)\r
 906     {\r
 907       return;\r
 908     }\r
 909 \r
 910     SequenceGroup sg = viewport.getSelectionGroup();\r
 911     copiedSequences = new StringBuffer();\r
 912     Hashtable orderedSeqs = new Hashtable();\r
 913     for (int i = 0; i < sg.getSize(false); i++)\r
 914     {\r
 915       SequenceI seq = sg.getSequenceAt(i);\r
 916       int index = viewport.alignment.findIndex(seq);\r
 917       orderedSeqs.put(index + "", seq);\r
 918     }\r
 919 \r
 920     int index = 0, startRes, endRes;\r
 921     char ch;\r
 922 \r
 923     if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)\r
 924     {\r
 925       copiedHiddenColumns = new Vector();\r
 926       int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
 927       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();\r
 928            i++)\r
 929       {\r
 930         int[] region = (int[])\r
 931             viewport.getColumnSelection().getHiddenColumns().elementAt(i);\r
 932 \r
 933         copiedHiddenColumns.addElement(new int[]\r
 934                                  {region[0] - hiddenOffset,\r
 935                                  region[1] - hiddenOffset});\r
 936       }\r
 937     }\r
 938     else\r
 939       copiedHiddenColumns = null;\r
 940 \r
 941 \r
 942     for (int i = 0; i < sg.getSize(false); i++)\r
 943     {\r
 944         SequenceI seq = null;\r
 945 \r
 946         while (seq == null)\r
 947         {\r
 948             if (orderedSeqs.containsKey(index + ""))\r
 949             {\r
 950                 seq = (SequenceI) orderedSeqs.get(index + "");\r
 951                 index++;\r
 952 \r
 953                 break;\r
 954             }\r
 955             else\r
 956             {\r
 957                 index++;\r
 958             }\r
 959         }\r
 960 \r
 961         //FIND START RES\r
 962         //Returns residue following index if gap\r
 963         startRes = seq.findPosition(sg.getStartRes());\r
 964 \r
 965         //FIND END RES\r
 966         //Need to find the residue preceeding index if gap\r
 967         endRes = 0;\r
 968 \r
 969         for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
 970         {\r
 971           ch = seq.getCharAt(j);\r
 972           if (!jalview.util.Comparison.isGap( (ch)))\r
 973           {\r
 974             endRes++;\r
 975           }\r
 976         }\r
 977 \r
 978         if(endRes>0)\r
 979         {\r
 980           endRes += seq.getStart() -1;\r
 981         }\r
 982 \r
 983         copiedSequences.append(seq.getName() + "\t" +\r
 984             startRes + "\t" +\r
 985             endRes + "\t" +\r
 986             seq.getSequence(sg.getStartRes(),\r
 987                 sg.getEndRes() + 1) + "\n");\r
 988     }\r
 989 \r
 990   }\r
 991 \r
 992   protected void pasteNew_actionPerformed()\r
 993   {\r
 994     paste(true);\r
 995   }\r
 996 \r
 997   protected void pasteThis_actionPerformed()\r
 998   {\r
 999     paste(false);\r
1000   }\r
1001 \r
1002   void paste(boolean newAlignment)\r
1003   {\r
1004     try\r
1005     {\r
1006 \r
1007       if (copiedSequences == null)\r
1008       {\r
1009         return;\r
1010       }\r
1011 \r
1012       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
1013       Vector seqs = new Vector();\r
1014       while (st.hasMoreElements())\r
1015       {\r
1016         String name = st.nextToken();\r
1017         int start = Integer.parseInt(st.nextToken());\r
1018         int end = Integer.parseInt(st.nextToken());\r
1019         seqs.addElement(new Sequence(name, st.nextToken(), start, end));\r
1020       }\r
1021       SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
1022       for (int i = 0; i < seqs.size(); i++)\r
1023       {\r
1024         newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
1025       }\r
1026 \r
1027       if (newAlignment)\r
1028       {\r
1029         String newtitle = new String("Copied sequences");\r
1030         if (getTitle().startsWith("Copied sequences"))\r
1031         {\r
1032           newtitle = getTitle();\r
1033         }\r
1034         else\r
1035         {\r
1036           newtitle = newtitle.concat("- from " + getTitle());\r
1037         }\r
1038         AlignFrame af = new AlignFrame(new Alignment(newSeqs),\r
1039                                        viewport.applet,\r
1040                                        newtitle,\r
1041                                        false);\r
1042         if (copiedHiddenColumns != null)\r
1043         {\r
1044           for (int i = 0; i < copiedHiddenColumns.size(); i++)\r
1045           {\r
1046             int[] region = (int[]) copiedHiddenColumns.elementAt(i);\r
1047             af.viewport.hideColumns(region[0], region[1]);\r
1048           }\r
1049         }\r
1050 \r
1051 \r
1052         jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,\r
1053                                          DEFAULT_HEIGHT);\r
1054       }\r
1055       else\r
1056       {\r
1057         for (int i = 0; i < newSeqs.length; i++)\r
1058         {\r
1059           viewport.alignment.addSequence(newSeqs[i]);\r
1060         }\r
1061 \r
1062         //!newAlignment\r
1063         addHistoryItem(new EditCommand(\r
1064             "Add sequences",\r
1065             EditCommand.PASTE,\r
1066             newSeqs,\r
1067             0,\r
1068             viewport.alignment.getWidth(),\r
1069             viewport.alignment)\r
1070             );\r
1071 \r
1072         viewport.setEndSeq(viewport.alignment.getHeight());\r
1073         viewport.alignment.getWidth();\r
1074         viewport.firePropertyChange("alignment", null, null);\r
1075       }\r
1076 \r
1077     }\r
1078     catch (Exception ex)\r
1079     {} // could be anything being pasted in here\r
1080 \r
1081   }\r
1082 \r
1083   protected void cut_actionPerformed()\r
1084   {\r
1085     copy_actionPerformed();\r
1086     delete_actionPerformed();\r
1087   }\r
1088 \r
1089   protected void delete_actionPerformed()\r
1090   {\r
1091 \r
1092     SequenceGroup sg = viewport.getSelectionGroup();\r
1093     if (sg == null)\r
1094     {\r
1095       return;\r
1096     }\r
1097 \r
1098     Vector seqs = new Vector();\r
1099     SequenceI seq;\r
1100     for (int i = 0; i < sg.getSize(false); i++)\r
1101     {\r
1102       seq = sg.getSequenceAt(i);\r
1103       seqs.addElement(seq);\r
1104     }\r
1105 \r
1106 \r
1107    // If the cut affects all sequences, remove highlighted columns\r
1108    if (sg.getSize(false) == viewport.alignment.getHeight())\r
1109    {\r
1110      viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
1111          sg.getEndRes() + 1);\r
1112    }\r
1113 \r
1114 \r
1115     SequenceI [] cut = new SequenceI[seqs.size()];\r
1116     for(int i=0; i<seqs.size(); i++)\r
1117       cut[i] = (SequenceI)seqs.elementAt(i);\r
1118 \r
1119 \r
1120     /*\r
1121     //ADD HISTORY ITEM\r
1122     */\r
1123     addHistoryItem(new EditCommand("Cut Sequences",\r
1124                                       EditCommand.CUT,\r
1125                                       cut,\r
1126                                       sg.getStartRes(),\r
1127                                       sg.getEndRes()-sg.getStartRes()+1,\r
1128                                       viewport.alignment));\r
1129 \r
1130 \r
1131     viewport.setSelectionGroup(null);\r
1132     viewport.alignment.deleteGroup(sg);\r
1133 \r
1134     viewport.firePropertyChange("alignment", null,\r
1135                                   viewport.getAlignment().getSequences());\r
1136 \r
1137     if (viewport.getAlignment().getHeight() < 1)\r
1138     {\r
1139         this.setVisible(false);\r
1140     }\r
1141   }\r
1142 \r
1143   protected void deleteGroups_actionPerformed()\r
1144   {\r
1145     viewport.alignment.deleteAllGroups();\r
1146     viewport.sequenceColours=null;\r
1147     viewport.setSelectionGroup(null);\r
1148 \r
1149     alignPanel.repaint();\r
1150   }\r
1151 \r
1152   public void selectAllSequenceMenuItem_actionPerformed()\r
1153   {\r
1154     SequenceGroup sg = new SequenceGroup();\r
1155     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
1156     {\r
1157       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
1158     }\r
1159     sg.setEndRes(viewport.alignment.getWidth()-1);\r
1160     viewport.setSelectionGroup(sg);\r
1161     alignPanel.repaint();\r
1162     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
1163   }\r
1164 \r
1165   public void deselectAllSequenceMenuItem_actionPerformed()\r
1166   {\r
1167     if(viewport.cursorMode)\r
1168     {\r
1169       alignPanel.seqPanel.keyboardNo1=null;\r
1170       alignPanel.seqPanel.keyboardNo2=null;\r
1171     }\r
1172     viewport.setSelectionGroup(null);\r
1173     viewport.getColumnSelection().clear();\r
1174     viewport.setSelectionGroup(null);\r
1175     alignPanel.idPanel.idCanvas.searchResults = null;\r
1176     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
1177     alignPanel.repaint();\r
1178     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
1179   }\r
1180 \r
1181   public void invertSequenceMenuItem_actionPerformed()\r
1182   {\r
1183     SequenceGroup sg = viewport.getSelectionGroup();\r
1184     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
1185     {\r
1186       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
1187     }\r
1188 \r
1189     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
1190   }\r
1191 \r
1192   void trimAlignment(boolean trimLeft)\r
1193   {\r
1194     ColumnSelection colSel = viewport.getColumnSelection();\r
1195     int column;\r
1196 \r
1197     if (colSel.size() > 0)\r
1198     {\r
1199       if(trimLeft)\r
1200         column = colSel.getMin();\r
1201       else\r
1202         column = colSel.getMax();\r
1203 \r
1204       SequenceI [] seqs;\r
1205       if(viewport.getSelectionGroup()!=null)\r
1206         seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
1207       else\r
1208         seqs = viewport.alignment.getSequencesArray();\r
1209 \r
1210 \r
1211       TrimRegionCommand trimRegion;\r
1212       if(trimLeft)\r
1213       {\r
1214         trimRegion = new TrimRegionCommand("Remove Left",\r
1215                                     TrimRegionCommand.TRIM_LEFT,\r
1216                                     seqs,\r
1217                                     column,\r
1218                                     viewport.alignment,\r
1219                                     viewport.colSel,\r
1220                                     viewport.selectionGroup);\r
1221         viewport.setStartRes(0);\r
1222       }\r
1223      else\r
1224      {\r
1225        trimRegion = new TrimRegionCommand("Remove Right",\r
1226                                    TrimRegionCommand.TRIM_RIGHT,\r
1227                                    seqs,\r
1228                                    column,\r
1229                                    viewport.alignment,\r
1230                                    viewport.colSel,\r
1231                                    viewport.selectionGroup);\r
1232      }\r
1233 \r
1234      statusBar.setText("Removed "+trimRegion.getSize()+" columns.");\r
1235 \r
1236 \r
1237       addHistoryItem(trimRegion);\r
1238 \r
1239       Vector groups = viewport.alignment.getGroups();\r
1240 \r
1241       for (int i = 0; i < groups.size(); i++)\r
1242       {\r
1243         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1244 \r
1245         if ( (trimLeft && !sg.adjustForRemoveLeft(column))\r
1246             || (!trimLeft && !sg.adjustForRemoveRight(column)))\r
1247         {\r
1248           viewport.alignment.deleteGroup(sg);\r
1249         }\r
1250       }\r
1251 \r
1252       viewport.firePropertyChange("alignment", null,\r
1253                                   viewport.getAlignment().getSequences());\r
1254     }\r
1255   }\r
1256 \r
1257 \r
1258   public void removeGappedColumnMenuItem_actionPerformed()\r
1259   {\r
1260     int start = 0, end = viewport.alignment.getWidth()-1;\r
1261 \r
1262     SequenceI[] seqs;\r
1263     if (viewport.getSelectionGroup() != null)\r
1264     {\r
1265       seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
1266       start = viewport.getSelectionGroup().getStartRes();\r
1267       end = viewport.getSelectionGroup().getEndRes();\r
1268     }\r
1269     else\r
1270       seqs = viewport.alignment.getSequencesArray();\r
1271 \r
1272 \r
1273     RemoveGapColCommand removeGapCols =\r
1274         new RemoveGapColCommand("Remove Gapped Columns",\r
1275                                 seqs,\r
1276                                 start, end,\r
1277                                 viewport.getGapCharacter());\r
1278 \r
1279     addHistoryItem(removeGapCols);\r
1280 \r
1281     statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");\r
1282 \r
1283     //This is to maintain viewport position on first residue\r
1284     //of first sequence\r
1285     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
1286     int startRes = seq.findPosition(viewport.startRes);\r
1287    // ShiftList shifts;\r
1288    // viewport.getAlignment().removeGaps(shifts=new ShiftList());\r
1289    // edit.alColumnChanges=shifts.getInverse();\r
1290    // if (viewport.hasHiddenColumns)\r
1291    //   viewport.getColumnSelection().compensateForEdits(shifts);\r
1292    viewport.setStartRes(seq.findIndex(startRes)-1);\r
1293    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1294 \r
1295   }\r
1296 \r
1297   public void removeAllGapsMenuItem_actionPerformed()\r
1298   {\r
1299     int start = 0, end = viewport.alignment.getWidth()-1;\r
1300 \r
1301     SequenceI[] seqs;\r
1302     if (viewport.getSelectionGroup() != null)\r
1303     {\r
1304       seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
1305       start = viewport.getSelectionGroup().getStartRes();\r
1306       end = viewport.getSelectionGroup().getEndRes();\r
1307     }\r
1308     else\r
1309       seqs = viewport.alignment.getSequencesArray();\r
1310 \r
1311     //This is to maintain viewport position on first residue\r
1312     //of first sequence\r
1313     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
1314     int startRes = seq.findPosition(viewport.startRes);\r
1315 \r
1316     addHistoryItem(new RemoveGapsCommand("Remove Gaps",\r
1317                                            seqs,\r
1318                                            start, end,\r
1319                      viewport.getGapCharacter()));\r
1320 \r
1321     viewport.setStartRes(seq.findIndex(startRes)-1);\r
1322 \r
1323     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1324 \r
1325   }\r
1326 \r
1327   public void findMenuItem_actionPerformed()\r
1328   {\r
1329     new Finder(alignPanel);\r
1330   }\r
1331 \r
1332   public void newView()\r
1333   {\r
1334     AlignmentI newal;\r
1335     if (viewport.hasHiddenRows)\r
1336       newal = new Alignment(viewport.getAlignment().\r
1337                             getHiddenSequences()\r
1338                             .getFullAlignment().\r
1339                             getSequencesArray());\r
1340     else\r
1341       newal = new Alignment(viewport.alignment.getSequencesArray());\r
1342 \r
1343     AlignFrame newaf = new AlignFrame(newal,\r
1344                                       viewport.applet,\r
1345                                       "",\r
1346                                       false);\r
1347 \r
1348     newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();\r
1349     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());\r
1350     PaintRefresher.Register(newaf.alignPanel,\r
1351                             newaf.alignPanel.av.getSequenceSetId());\r
1352 \r
1353     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,\r
1354                             newaf.alignPanel.av.getSequenceSetId());\r
1355     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,\r
1356                             newaf.alignPanel.av.getSequenceSetId());\r
1357 \r
1358     Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());\r
1359     int viewSize = -1;\r
1360     for (int i = 0; i < comps.size(); i++)\r
1361     {\r
1362       if (comps.elementAt(i) instanceof AlignmentPanel)\r
1363         viewSize++;\r
1364     }\r
1365 \r
1366     StringBuffer title = new StringBuffer(this.getTitle());\r
1367     if (title.indexOf("(View") > -1)\r
1368       title.setLength(title.indexOf("(View"));\r
1369 \r
1370     title.append("(View ");\r
1371     title.append(viewSize);\r
1372     title.append(")");\r
1373 \r
1374     newaf.setTitle(title.toString());\r
1375 \r
1376 \r
1377     newaf.viewport.historyList = viewport.historyList;\r
1378     newaf.viewport.redoList = viewport.redoList;\r
1379 \r
1380    }\r
1381 \r
1382 \r
1383   public void seqLimits_itemStateChanged()\r
1384   {\r
1385     viewport.setShowJVSuffix(seqLimits.getState());\r
1386     alignPanel.fontChanged();\r
1387     alignPanel.repaint();\r
1388   }\r
1389 \r
1390 \r
1391   protected void colourTextMenuItem_actionPerformed()\r
1392   {\r
1393     viewport.setColourText(colourTextMenuItem.getState());\r
1394     alignPanel.repaint();\r
1395   }\r
1396 \r
1397   protected void wrapMenuItem_actionPerformed()\r
1398   {\r
1399     viewport.setWrapAlignment(wrapMenuItem.getState());\r
1400     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
1401     scaleAbove.setEnabled(wrapMenuItem.getState());\r
1402     scaleLeft.setEnabled(wrapMenuItem.getState());\r
1403     scaleRight.setEnabled(wrapMenuItem.getState());\r
1404     alignPanel.repaint();\r
1405   }\r
1406 \r
1407 \r
1408   public void overviewMenuItem_actionPerformed()\r
1409   {\r
1410     if (alignPanel.overviewPanel != null)\r
1411     {\r
1412       return;\r
1413     }\r
1414 \r
1415     Frame frame = new Frame();\r
1416     OverviewPanel overview = new OverviewPanel(alignPanel);\r
1417     frame.add(overview);\r
1418     // +50 must allow for applet frame window\r
1419     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
1420                                      overview.preferredSize().width,\r
1421                                      overview.preferredSize().height + 50);\r
1422 \r
1423     frame.pack();\r
1424     frame.addWindowListener(new WindowAdapter()\r
1425     {\r
1426       public void windowClosing(WindowEvent e)\r
1427       {\r
1428         alignPanel.setOverviewPanel(null);\r
1429       };\r
1430     });\r
1431 \r
1432     alignPanel.setOverviewPanel(overview);\r
1433 \r
1434   }\r
1435 \r
1436 \r
1437   void changeColour(ColourSchemeI cs)\r
1438   {\r
1439     int threshold = 0;\r
1440 \r
1441     if(cs!=null)\r
1442     {\r
1443       if (viewport.getAbovePIDThreshold())\r
1444       {\r
1445         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
1446 \r
1447         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1448 \r
1449         viewport.setGlobalColourScheme(cs);\r
1450       }\r
1451       else\r
1452       {\r
1453         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1454       }\r
1455 \r
1456       if (viewport.getConservationSelected())\r
1457       {\r
1458 \r
1459         Alignment al = (Alignment) viewport.alignment;\r
1460         Conservation c = new Conservation("All",\r
1461                                           ResidueProperties.propHash, 3,\r
1462                                           al.getSequences(), 0,\r
1463                                           al.getWidth() - 1);\r
1464 \r
1465         c.calculate();\r
1466         c.verdict(false, viewport.ConsPercGaps);\r
1467 \r
1468         cs.setConservation(c);\r
1469 \r
1470         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
1471             "Background"));\r
1472 \r
1473       }\r
1474       else\r
1475       {\r
1476         cs.setConservation(null);\r
1477       }\r
1478 \r
1479       cs.setConsensus(viewport.hconsensus);\r
1480 \r
1481     }\r
1482     viewport.setGlobalColourScheme(cs);\r
1483 \r
1484     if (viewport.getColourAppliesToAllGroups())\r
1485     {\r
1486       Vector groups = viewport.alignment.getGroups();\r
1487       for (int i = 0; i < groups.size(); i++)\r
1488       {\r
1489         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1490 \r
1491         if(cs==null)\r
1492         {\r
1493           sg.cs = null;\r
1494           continue;\r
1495         }\r
1496         if (cs instanceof ClustalxColourScheme)\r
1497         {\r
1498           sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());\r
1499         }\r
1500         else\r
1501         {\r
1502           try\r
1503           {\r
1504             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
1505           }\r
1506           catch (Exception ex)\r
1507           {\r
1508             ex.printStackTrace();\r
1509             sg.cs = cs;\r
1510           }\r
1511         }\r
1512 \r
1513         if (viewport.getAbovePIDThreshold()\r
1514             || cs instanceof PIDColourScheme\r
1515             || cs instanceof Blosum62ColourScheme)\r
1516         {\r
1517           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1518           sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));\r
1519         }\r
1520         else\r
1521           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1522 \r
1523         if (viewport.getConservationSelected())\r
1524         {\r
1525           Conservation c = new Conservation("Group",\r
1526                                             ResidueProperties.propHash, 3,\r
1527                                             sg.getSequences(true), 0,\r
1528                                             viewport.alignment.getWidth() - 1);\r
1529           c.calculate();\r
1530           c.verdict(false, viewport.ConsPercGaps);\r
1531           sg.cs.setConservation(c);\r
1532         }\r
1533         else\r
1534         {\r
1535           sg.cs.setConservation(null);\r
1536           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1537         }\r
1538 \r
1539       }\r
1540     }\r
1541 \r
1542 \r
1543     if (alignPanel.getOverviewPanel() != null)\r
1544     {\r
1545       alignPanel.getOverviewPanel().updateOverviewImage();\r
1546     }\r
1547 \r
1548     alignPanel.repaint();\r
1549   }\r
1550 \r
1551 \r
1552 \r
1553   protected void modifyPID_actionPerformed()\r
1554   {\r
1555     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
1556     {\r
1557       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
1558                                      "Background");\r
1559       SliderPanel.showPIDSlider();\r
1560     }\r
1561   }\r
1562 \r
1563   protected void modifyConservation_actionPerformed()\r
1564   {\r
1565     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
1566     {\r
1567       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
1568                                         "Background");\r
1569       SliderPanel.showConservationSlider();\r
1570     }\r
1571   }\r
1572 \r
1573   protected void conservationMenuItem_actionPerformed()\r
1574   {\r
1575     viewport.setConservationSelected(conservationMenuItem.getState());\r
1576 \r
1577     viewport.setAbovePIDThreshold(false);\r
1578     abovePIDThreshold.setState(false);\r
1579 \r
1580     changeColour(viewport.getGlobalColourScheme());\r
1581 \r
1582     modifyConservation_actionPerformed();\r
1583   }\r
1584 \r
1585   public void abovePIDThreshold_actionPerformed()\r
1586   {\r
1587     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
1588 \r
1589     conservationMenuItem.setState(false);\r
1590     viewport.setConservationSelected(false);\r
1591 \r
1592     changeColour(viewport.getGlobalColourScheme());\r
1593 \r
1594     modifyPID_actionPerformed();\r
1595   }\r
1596 \r
1597 \r
1598 \r
1599   public void sortPairwiseMenuItem_actionPerformed()\r
1600   {\r
1601     SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();\r
1602     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1603                               viewport.getAlignment().getSequenceAt(0));\r
1604     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));\r
1605     alignPanel.repaint();\r
1606   }\r
1607 \r
1608   public void sortIDMenuItem_actionPerformed()\r
1609   {\r
1610   //  addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1611    //                                HistoryItem.SORT));\r
1612     AlignmentSorter.sortByID(viewport.getAlignment());\r
1613     alignPanel.repaint();\r
1614   }\r
1615 \r
1616   public void sortGroupMenuItem_actionPerformed()\r
1617   {\r
1618   //  addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1619   //                                 HistoryItem.SORT));\r
1620     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1621     alignPanel.repaint();\r
1622 \r
1623   }\r
1624 \r
1625   public void removeRedundancyMenuItem_actionPerformed()\r
1626   {\r
1627      new RedundancyPanel(alignPanel);\r
1628   }\r
1629 \r
1630   public void pairwiseAlignmentMenuItem_actionPerformed()\r
1631   {\r
1632     if (viewport.getSelectionGroup()!=null\r
1633         && viewport.getSelectionGroup().getSize(false) > 1)\r
1634     {\r
1635       Frame frame = new Frame();\r
1636       frame.add(new PairwiseAlignPanel(alignPanel));\r
1637       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1638     }\r
1639   }\r
1640 \r
1641   public void PCAMenuItem_actionPerformed()\r
1642   {\r
1643     //are the sequences aligned?\r
1644     if (!viewport.alignment.isAligned())\r
1645     {\r
1646       SequenceI current;\r
1647       int Width = viewport.getAlignment().getWidth();\r
1648 \r
1649       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1650            i++)\r
1651       {\r
1652         current = viewport.getAlignment().getSequenceAt(i);\r
1653 \r
1654         if (current.getLength() < Width)\r
1655         {\r
1656           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1657         }\r
1658       }\r
1659       alignPanel.repaint();\r
1660     }\r
1661 \r
1662     if ( (viewport.getSelectionGroup() != null &&\r
1663           viewport.getSelectionGroup().getSize(false) < 4 &&\r
1664           viewport.getSelectionGroup().getSize(false) > 0)\r
1665         || viewport.getAlignment().getHeight() < 4)\r
1666     {\r
1667       return;\r
1668     }\r
1669 \r
1670     try\r
1671     {\r
1672       new PCAPanel(viewport);\r
1673     }\r
1674     catch (java.lang.OutOfMemoryError ex)\r
1675     {\r
1676     }\r
1677 \r
1678   }\r
1679 \r
1680   public void averageDistanceTreeMenuItem_actionPerformed()\r
1681   {\r
1682     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1683   }\r
1684 \r
1685   public void neighbourTreeMenuItem_actionPerformed()\r
1686   {\r
1687     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1688   }\r
1689 \r
1690   protected void njTreeBlosumMenuItem_actionPerformed()\r
1691   {\r
1692     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1693   }\r
1694 \r
1695   protected void avTreeBlosumMenuItem_actionPerformed()\r
1696   {\r
1697     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1698   }\r
1699 \r
1700   void NewTreePanel(String type, String pwType, String title)\r
1701   {\r
1702     //are the sequences aligned?\r
1703     if (!viewport.alignment.isAligned())\r
1704     {\r
1705       SequenceI current;\r
1706       int Width = viewport.getAlignment().getWidth();\r
1707 \r
1708       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1709            i++)\r
1710       {\r
1711         current = viewport.getAlignment().getSequenceAt(i);\r
1712 \r
1713         if (current.getLength() < Width)\r
1714         {\r
1715           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1716         }\r
1717       }\r
1718       alignPanel.repaint();\r
1719 \r
1720     }\r
1721 \r
1722     if ( (viewport.getSelectionGroup() != null &&\r
1723           viewport.getSelectionGroup().getSize(false) > 1)\r
1724       || (viewport.getSelectionGroup() == null\r
1725           && viewport.alignment.getHeight() > 1))\r
1726     {\r
1727       final TreePanel tp = new TreePanel(viewport,\r
1728                                          type,\r
1729                                          pwType);\r
1730 \r
1731       addTreeMenuItem(tp, title);\r
1732 \r
1733       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1734     }\r
1735   }\r
1736 \r
1737   void loadTree_actionPerformed()\r
1738   {\r
1739       CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
1740       cap.setText("Paste your Newick tree file here.");\r
1741       cap.treeImport = true;\r
1742       Frame frame = new Frame();\r
1743       frame.add(cap);\r
1744       jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);\r
1745   }\r
1746 \r
1747   public void loadTree(jalview.io.NewickFile tree, String treeFile)\r
1748   {\r
1749     TreePanel tp = new TreePanel(viewport,\r
1750                                  treeFile,\r
1751                                  "From File - ",\r
1752                                  tree);\r
1753     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
1754     addTreeMenuItem(tp, treeFile);\r
1755   }\r
1756 \r
1757   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1758   {\r
1759     final MenuItem item = new MenuItem(title);\r
1760     sortByTreeMenu.add(item);\r
1761     item.addActionListener(new java.awt.event.ActionListener()\r
1762     {\r
1763       public void actionPerformed(ActionEvent evt)\r
1764       {\r
1765       //  addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1766       //                                 HistoryItem.SORT));\r
1767         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1768         alignPanel.repaint();\r
1769       }\r
1770     });\r
1771 \r
1772     treePanel.addWindowListener(new WindowAdapter()\r
1773     {\r
1774       public void windowClosing(WindowEvent e)\r
1775       {\r
1776         sortByTreeMenu.remove(item);\r
1777       };\r
1778     });\r
1779   }\r
1780 \r
1781   protected void documentation_actionPerformed()\r
1782   {\r
1783     showURL("http://www.jalview.org/help.html", "HELP");\r
1784   }\r
1785 \r
1786   protected void about_actionPerformed()\r
1787   {\r
1788 \r
1789     class AboutPanel extends Canvas\r
1790     {\r
1791       String version;\r
1792       public AboutPanel(String version)\r
1793       { this.version = version; }\r
1794 \r
1795       public void paint(Graphics g)\r
1796       {\r
1797         g.setColor(Color.white);\r
1798         g.fillRect(0, 0, getSize().width, getSize().height);\r
1799         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1800         FontMetrics fm = g.getFontMetrics();\r
1801         int fh = fm.getHeight();\r
1802         int y = 5, x = 7;\r
1803         g.setColor(Color.black);\r
1804         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1805         g.drawString("Jalview - Release "+version, 200, y += fh);\r
1806         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1807         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1808                      x, y += fh * 2);\r
1809         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1810                      x, y += fh);\r
1811         g.drawString(\r
1812             "For any issues relating to Jalview, email help@jalview.org", x,\r
1813             y += fh);\r
1814         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1815         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1816                      x, y += fh);\r
1817         g.drawString("Bioinformatics,  2004 20;426-7.", x, y += fh);\r
1818       }\r
1819     }\r
1820 \r
1821     String version = "test";\r
1822     java.net.URL url = getClass().getResource("/.build_properties");\r
1823     if (url != null)\r
1824     {\r
1825       try\r
1826       {\r
1827         BufferedReader reader = new BufferedReader(new InputStreamReader(\r
1828             url.openStream()));\r
1829         String line;\r
1830         while ( (line = reader.readLine()) != null)\r
1831         {\r
1832           if (line.indexOf("VERSION") > -1)\r
1833           {\r
1834             version = line.substring(line.indexOf("=") + 1);\r
1835           }\r
1836         }\r
1837       }\r
1838       catch (Exception ex)\r
1839       {\r
1840         ex.printStackTrace();\r
1841       }\r
1842     }\r
1843 \r
1844 \r
1845     Frame frame = new Frame();\r
1846     frame.add(new AboutPanel(version));\r
1847     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1848 \r
1849   }\r
1850 \r
1851   public void showURL(String url, String target)\r
1852   {\r
1853     if (viewport.applet == null)\r
1854     {\r
1855       System.out.println("Not running as applet - no browser available.");\r
1856     }\r
1857     else\r
1858     {\r
1859       try\r
1860       {\r
1861         System.out.println("Show url: "+url);\r
1862         viewport.applet.getAppletContext().showDocument(new java.net.URL(url),\r
1863                                                target);\r
1864       }\r
1865       catch (Exception ex)\r
1866       {\r
1867         ex.printStackTrace();\r
1868       }\r
1869     }\r
1870   }\r
1871 \r
1872 \r
1873   //////////////////////////////////////////////////////////////////////////////////\r
1874   //JBuilder Graphics here\r
1875 \r
1876     protected MenuBar alignFrameMenuBar = new MenuBar();\r
1877     protected Menu fileMenu = new Menu("File");\r
1878     protected MenuItem loadApplication = new MenuItem("View in Full Application");\r
1879     protected MenuItem loadTree = new MenuItem("Load Associated Tree");\r
1880     protected MenuItem closeMenuItem = new MenuItem("Close");\r
1881     protected Menu editMenu = new Menu("Edit");\r
1882     protected Menu viewMenu = new Menu("View");\r
1883     protected Menu colourMenu = new Menu("Colour");\r
1884     protected Menu calculateMenu = new Menu("Calculate");\r
1885     protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
1886     protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
1887     protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
1888     protected MenuItem remove2LeftMenuItem = new MenuItem();\r
1889     protected MenuItem remove2RightMenuItem = new MenuItem();\r
1890     protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
1891     protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
1892     protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
1893     protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
1894     protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
1895     protected MenuItem sortIDMenuItem = new MenuItem();\r
1896     protected MenuItem sortGroupMenuItem = new MenuItem();\r
1897     protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
1898     protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
1899     protected MenuItem PCAMenuItem = new MenuItem();\r
1900     protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
1901     protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
1902     BorderLayout borderLayout1 = new BorderLayout();\r
1903     public Label statusBar = new Label();\r
1904     protected Menu outputTextboxMenu = new Menu();\r
1905     protected MenuItem clustalColour = new MenuItem();\r
1906     protected MenuItem zappoColour = new MenuItem();\r
1907     protected MenuItem taylorColour = new MenuItem();\r
1908     protected MenuItem hydrophobicityColour = new MenuItem();\r
1909     protected MenuItem helixColour = new MenuItem();\r
1910     protected MenuItem strandColour = new MenuItem();\r
1911     protected MenuItem turnColour = new MenuItem();\r
1912     protected MenuItem buriedColour = new MenuItem();\r
1913     protected MenuItem userDefinedColour = new MenuItem();\r
1914     protected MenuItem PIDColour = new MenuItem();\r
1915     protected MenuItem BLOSUM62Colour = new MenuItem();\r
1916     MenuItem njTreeBlosumMenuItem = new MenuItem();\r
1917     MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
1918     protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
1919     protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
1920     MenuItem overviewMenuItem = new MenuItem();\r
1921     protected MenuItem undoMenuItem = new MenuItem();\r
1922     protected MenuItem redoMenuItem = new MenuItem();\r
1923     protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
1924     MenuItem noColourmenuItem = new MenuItem();\r
1925     protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
1926     protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
1927     MenuItem findMenuItem = new MenuItem();\r
1928   protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
1929     protected MenuItem nucleotideColour = new MenuItem();\r
1930     MenuItem deleteGroups = new MenuItem();\r
1931     MenuItem delete = new MenuItem();\r
1932     MenuItem copy = new MenuItem();\r
1933     MenuItem cut = new MenuItem();\r
1934     Menu pasteMenu = new Menu();\r
1935     MenuItem pasteNew = new MenuItem();\r
1936     MenuItem pasteThis = new MenuItem();\r
1937     protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
1938     protected MenuItem font = new MenuItem();\r
1939     protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
1940     protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
1941     protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
1942     MenuItem modifyPID = new MenuItem();\r
1943     MenuItem modifyConservation = new MenuItem();\r
1944     protected CheckboxMenuItem autoCalculate\r
1945         = new CheckboxMenuItem("Autocalculate Consensus", true);\r
1946     protected Menu sortByTreeMenu = new Menu();\r
1947     Menu sort = new Menu();\r
1948     Menu calculate = new Menu();\r
1949     MenuItem inputText = new MenuItem();\r
1950     Menu helpMenu = new Menu();\r
1951     MenuItem documentation = new MenuItem();\r
1952     MenuItem about = new MenuItem();\r
1953     protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
1954   Panel embeddedMenu;\r
1955   Label embeddedEdit;\r
1956   Label embeddedSelect;\r
1957   Label embeddedView;\r
1958   Label embeddedFormat;\r
1959   Label embeddedColour;\r
1960   Label embeddedFile;\r
1961   Label embeddedHelp;\r
1962   Label embeddedCalculate;\r
1963   FlowLayout flowLayout1;\r
1964 \r
1965   private void jbInit() throws Exception {\r
1966 \r
1967       setMenuBar(alignFrameMenuBar);\r
1968 \r
1969       MenuItem item;\r
1970 \r
1971       // dynamically fill save as menu with available formats\r
1972       for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
1973       {\r
1974 \r
1975         item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);\r
1976 \r
1977         item.addActionListener(new java.awt.event.ActionListener()\r
1978         {\r
1979           public void actionPerformed(ActionEvent e)\r
1980           {\r
1981             outputText_actionPerformed(e);\r
1982           }\r
1983         });\r
1984 \r
1985         outputTextboxMenu.add(item);\r
1986       }\r
1987         closeMenuItem.addActionListener(this);\r
1988         loadApplication.addActionListener(this);\r
1989 \r
1990         loadTree.addActionListener(this);\r
1991         selectAllSequenceMenuItem.addActionListener(this);\r
1992         deselectAllSequenceMenuItem.addActionListener(this);\r
1993         invertSequenceMenuItem.addActionListener(this);\r
1994         remove2LeftMenuItem.setLabel("Remove Left");\r
1995         remove2LeftMenuItem.addActionListener(this);\r
1996         remove2RightMenuItem.setLabel("Remove Right");\r
1997         remove2RightMenuItem.addActionListener(this);\r
1998         removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
1999         removeGappedColumnMenuItem.addActionListener(this);\r
2000         removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
2001         removeAllGapsMenuItem.addActionListener(this);\r
2002         viewBoxesMenuItem.setLabel("Boxes");\r
2003         viewBoxesMenuItem.setState(true);\r
2004         viewBoxesMenuItem.addItemListener(this);\r
2005         viewTextMenuItem.setLabel("Text");\r
2006         viewTextMenuItem.setState(true);\r
2007         viewTextMenuItem.addItemListener(this);\r
2008         sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
2009         sortPairwiseMenuItem.addActionListener(this);\r
2010         sortIDMenuItem.setLabel("by ID");\r
2011         sortIDMenuItem.addActionListener(this);\r
2012         sortGroupMenuItem.setLabel("by Group");\r
2013         sortGroupMenuItem.addActionListener(this);\r
2014         removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
2015         removeRedundancyMenuItem.addActionListener(this);\r
2016         pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
2017         pairwiseAlignmentMenuItem.addActionListener(this);\r
2018         PCAMenuItem.setLabel("Principal Component Analysis");\r
2019         PCAMenuItem.addActionListener(this);\r
2020         averageDistanceTreeMenuItem.setLabel(\r
2021             "Average Distance Using % Identity");\r
2022         averageDistanceTreeMenuItem.addActionListener(this);\r
2023         neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
2024         neighbourTreeMenuItem.addActionListener(this);\r
2025         alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
2026         statusBar.setBackground(Color.white);\r
2027         statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
2028         statusBar.setText("Status bar");\r
2029         outputTextboxMenu.setLabel("Output to Textbox");\r
2030         clustalColour.setLabel("Clustalx");\r
2031 \r
2032         clustalColour.addActionListener(this);\r
2033         zappoColour.setLabel("Zappo");\r
2034         zappoColour.addActionListener(this);\r
2035         taylorColour.setLabel("Taylor");\r
2036         taylorColour.addActionListener(this);\r
2037         hydrophobicityColour.setLabel("Hydrophobicity");\r
2038         hydrophobicityColour.addActionListener(this);\r
2039         helixColour.setLabel("Helix Propensity");\r
2040         helixColour.addActionListener(this);\r
2041         strandColour.setLabel("Strand Propensity");\r
2042         strandColour.addActionListener(this);\r
2043         turnColour.setLabel("Turn Propensity");\r
2044         turnColour.addActionListener(this);\r
2045         buriedColour.setLabel("Buried Index");\r
2046         buriedColour.addActionListener(this);\r
2047         userDefinedColour.setLabel("User Defined...");\r
2048         userDefinedColour.addActionListener(this);\r
2049         PIDColour.setLabel("Percentage Identity");\r
2050         PIDColour.addActionListener(this);\r
2051         BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
2052         BLOSUM62Colour.addActionListener(this);\r
2053         avDistanceTreeBlosumMenuItem.setLabel(\r
2054             "Average Distance Using BLOSUM62");\r
2055         avDistanceTreeBlosumMenuItem.addActionListener(this);\r
2056         njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
2057         njTreeBlosumMenuItem.addActionListener(this);\r
2058         annotationPanelMenuItem.setLabel("Show Annotations");\r
2059         annotationPanelMenuItem.addItemListener(this);\r
2060         colourTextMenuItem.setLabel("Colour Text");\r
2061         colourTextMenuItem.addItemListener(this);\r
2062         overviewMenuItem.setLabel("Overview Window");\r
2063         overviewMenuItem.addActionListener(this);\r
2064         undoMenuItem.setEnabled(false);\r
2065         undoMenuItem.setLabel("Undo");\r
2066         undoMenuItem.addActionListener(this);\r
2067         redoMenuItem.setEnabled(false);\r
2068         redoMenuItem.setLabel("Redo");\r
2069         redoMenuItem.addActionListener(this);\r
2070         conservationMenuItem.setLabel("by Conservation");\r
2071         conservationMenuItem.addItemListener(this);\r
2072         noColourmenuItem.setLabel("None");\r
2073         noColourmenuItem.addActionListener(this);\r
2074         wrapMenuItem.setLabel("Wrap");\r
2075         wrapMenuItem.addItemListener(this);\r
2076         renderGapsMenuItem.setLabel("Show Gaps");\r
2077         renderGapsMenuItem.setState(true);\r
2078         renderGapsMenuItem.addItemListener(this);\r
2079         findMenuItem.setLabel("Find...");\r
2080         findMenuItem.addActionListener(this);\r
2081     abovePIDThreshold.setLabel("Above Identity Threshold");\r
2082         abovePIDThreshold.addItemListener(this);\r
2083         nucleotideColour.setLabel("Nucleotide");\r
2084         nucleotideColour.addActionListener(this);\r
2085         deleteGroups.setLabel("Undefine Groups");\r
2086         deleteGroups.addActionListener(this);\r
2087         copy.setLabel("Copy");\r
2088         copy.addActionListener(this);\r
2089         cut.setLabel("Cut");\r
2090         cut.addActionListener(this);\r
2091         delete.setLabel("Delete");\r
2092         delete.addActionListener(this);\r
2093         pasteMenu.setLabel("Paste");\r
2094         pasteNew.setLabel("To New Alignment");\r
2095         pasteNew.addActionListener(this);\r
2096         pasteThis.setLabel("Add To This Alignment");\r
2097         pasteThis.addActionListener(this);\r
2098         applyToAllGroups.setLabel("Apply Colour To All Groups");\r
2099         applyToAllGroups.setState(true);\r
2100         applyToAllGroups.addItemListener(this);\r
2101         font.setLabel("Font...");\r
2102         font.addActionListener(this);\r
2103         scaleAbove.setLabel("Scale Above");\r
2104         scaleAbove.setState(true);\r
2105         scaleAbove.setEnabled(false);\r
2106         scaleAbove.addItemListener(this);\r
2107         scaleLeft.setEnabled(false);\r
2108         scaleLeft.setState(true);\r
2109         scaleLeft.setLabel("Scale Left");\r
2110         scaleLeft.addItemListener(this);\r
2111         scaleRight.setEnabled(false);\r
2112         scaleRight.setState(true);\r
2113         scaleRight.setLabel("Scale Right");\r
2114         scaleRight.addItemListener(this);\r
2115         modifyPID.setLabel("Modify Identity Threshold...");\r
2116         modifyPID.addActionListener(this);\r
2117         modifyConservation.setLabel("Modify Conservation Threshold...");\r
2118         modifyConservation.addActionListener(this);\r
2119         sortByTreeMenu.setLabel("By Tree Order");\r
2120         sort.setLabel("Sort");\r
2121         calculate.setLabel("Calculate Tree");\r
2122         autoCalculate.addItemListener(this);\r
2123         inputText.setLabel("Input from textbox");\r
2124         inputText.addActionListener(this);\r
2125 \r
2126         helpMenu.setLabel("Help");\r
2127         documentation.setLabel("Documentation");\r
2128         documentation.addActionListener(this);\r
2129 \r
2130         about.setLabel("About...");\r
2131         about.addActionListener(this);\r
2132           seqLimits.setState(true);\r
2133     seqLimits.setLabel("Show Sequence Limits");\r
2134     seqLimits.addItemListener(this);\r
2135     featureSettings.setLabel("Feature Settings...");\r
2136     featureSettings.addActionListener(this);\r
2137     sequenceFeatures.setLabel("Sequence Features");\r
2138     sequenceFeatures.addItemListener(this);\r
2139     sequenceFeatures.setState(false);\r
2140     annotationColour.setLabel("by Annotation...");\r
2141     annotationColour.addActionListener(this);\r
2142     invertSequenceMenuItem.setLabel("Invert Sequence Selection");\r
2143     invertColSel.setLabel("Invert Column Selection");\r
2144     menu1.setLabel("Show");\r
2145     showColumns.setLabel("All Columns ");\r
2146     showSeqs.setLabel("All Sequences");\r
2147     menu2.setLabel("Hide");\r
2148     hideColumns.setLabel("Selected Columns");\r
2149     hideSequences.setLabel("Selected Sequences");\r
2150     invertColSel.addActionListener(this);\r
2151     showColumns.addActionListener(this);\r
2152     showSeqs.addActionListener(this);\r
2153     hideColumns.addActionListener(this);\r
2154     hideSequences.addActionListener(this);\r
2155     formatMenu.setLabel("Format");\r
2156     selectMenu.setLabel("Select");\r
2157     newView.setLabel("New View");\r
2158     newView.addActionListener(this);\r
2159     alignFrameMenuBar.add(fileMenu);\r
2160         alignFrameMenuBar.add(editMenu);\r
2161     alignFrameMenuBar.add(selectMenu);\r
2162     alignFrameMenuBar.add(viewMenu);\r
2163     alignFrameMenuBar.add(formatMenu);\r
2164     alignFrameMenuBar.add(colourMenu);\r
2165         alignFrameMenuBar.add(calculateMenu);\r
2166         alignFrameMenuBar.add(helpMenu);\r
2167         fileMenu.add(inputText);\r
2168         fileMenu.add(outputTextboxMenu);\r
2169         if(jalviewServletURL!=null)\r
2170           fileMenu.add(loadApplication);\r
2171         fileMenu.addSeparator();\r
2172         fileMenu.add(loadTree);\r
2173         fileMenu.add(closeMenuItem);\r
2174         editMenu.add(undoMenuItem);\r
2175         editMenu.add(redoMenuItem);\r
2176         editMenu.add(cut);\r
2177         editMenu.add(copy);\r
2178         editMenu.add(pasteMenu);\r
2179         editMenu.add(delete);\r
2180     editMenu.addSeparator();\r
2181         editMenu.add(remove2LeftMenuItem);\r
2182         editMenu.add(remove2RightMenuItem);\r
2183         editMenu.add(removeGappedColumnMenuItem);\r
2184         editMenu.add(removeAllGapsMenuItem);\r
2185         editMenu.add(removeRedundancyMenuItem);\r
2186     viewMenu.add(newView);\r
2187     viewMenu.addSeparator();\r
2188     viewMenu.add(menu1);\r
2189     viewMenu.add(menu2);\r
2190     viewMenu.addSeparator();\r
2191     viewMenu.add(annotationPanelMenuItem);\r
2192     viewMenu.addSeparator();\r
2193         viewMenu.add(sequenceFeatures);\r
2194         viewMenu.add(featureSettings);\r
2195     viewMenu.addSeparator();\r
2196         viewMenu.add(overviewMenuItem);\r
2197         colourMenu.add(applyToAllGroups);\r
2198         colourMenu.addSeparator();\r
2199         colourMenu.add(noColourmenuItem);\r
2200         colourMenu.add(clustalColour);\r
2201         colourMenu.add(BLOSUM62Colour);\r
2202         colourMenu.add(PIDColour);\r
2203         colourMenu.add(zappoColour);\r
2204         colourMenu.add(taylorColour);\r
2205         colourMenu.add(hydrophobicityColour);\r
2206         colourMenu.add(helixColour);\r
2207         colourMenu.add(strandColour);\r
2208         colourMenu.add(turnColour);\r
2209         colourMenu.add(buriedColour);\r
2210         colourMenu.add(nucleotideColour);\r
2211         colourMenu.add(userDefinedColour);\r
2212         colourMenu.addSeparator();\r
2213         colourMenu.add(conservationMenuItem);\r
2214         colourMenu.add(modifyConservation);\r
2215         colourMenu.add(abovePIDThreshold);\r
2216         colourMenu.add(modifyPID);\r
2217     colourMenu.add(annotationColour);\r
2218     calculateMenu.add(sort);\r
2219         calculateMenu.add(calculate);\r
2220         calculateMenu.addSeparator();\r
2221         calculateMenu.add(pairwiseAlignmentMenuItem);\r
2222         calculateMenu.add(PCAMenuItem);\r
2223         calculateMenu.add(autoCalculate);\r
2224         this.add(statusBar, BorderLayout.SOUTH);\r
2225         pasteMenu.add(pasteNew);\r
2226         pasteMenu.add(pasteThis);\r
2227         sort.add(sortIDMenuItem);\r
2228         sort.add(sortByTreeMenu);\r
2229         sort.add(sortGroupMenuItem);\r
2230         sort.add(sortPairwiseMenuItem);\r
2231         calculate.add(averageDistanceTreeMenuItem);\r
2232         calculate.add(neighbourTreeMenuItem);\r
2233         calculate.add(avDistanceTreeBlosumMenuItem);\r
2234         calculate.add(njTreeBlosumMenuItem);\r
2235         helpMenu.add(documentation);\r
2236         helpMenu.add(about);\r
2237     menu1.add(showColumns);\r
2238     menu1.add(showSeqs);\r
2239     menu2.add(hideColumns);\r
2240     menu2.add(hideSequences);\r
2241     formatMenu.add(font);\r
2242     formatMenu.add(seqLimits);\r
2243     formatMenu.add(wrapMenuItem);\r
2244     formatMenu.add(scaleAbove);\r
2245     formatMenu.add(scaleLeft);\r
2246     formatMenu.add(scaleRight);\r
2247     formatMenu.add(viewBoxesMenuItem);\r
2248     formatMenu.add(viewTextMenuItem);\r
2249     formatMenu.add(colourTextMenuItem);\r
2250     formatMenu.add(renderGapsMenuItem);\r
2251     selectMenu.add(findMenuItem);\r
2252     selectMenu.addSeparator();\r
2253     selectMenu.add(selectAllSequenceMenuItem);\r
2254     selectMenu.add(deselectAllSequenceMenuItem);\r
2255     selectMenu.add(invertSequenceMenuItem);\r
2256     selectMenu.add(invertColSel);\r
2257     selectMenu.add(deleteGroups);\r
2258   }\r
2259 \r
2260   public void setEmbedded()\r
2261   {\r
2262 \r
2263     embeddedMenu = new Panel();\r
2264     embeddedEdit = new Label("Edit");\r
2265     embeddedSelect = new Label("Select");\r
2266     embeddedView = new Label("View");\r
2267     embeddedFormat = new Label("Format");\r
2268     embeddedColour = new Label("Colour");\r
2269     embeddedFile = new Label("File");\r
2270     embeddedHelp = new Label("Help");\r
2271     embeddedCalculate = new Label("Calculate");\r
2272     flowLayout1 = new FlowLayout();\r
2273     embeddedMenu.setBackground(Color.lightGray);\r
2274     embeddedMenu.setLayout(flowLayout1);\r
2275     embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2276     embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2277     embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2278     embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2279     embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2280     embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2281     embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2282     embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2283     embeddedMenu.add(embeddedFile);\r
2284     embeddedMenu.add(embeddedEdit);\r
2285     embeddedMenu.add(embeddedSelect);\r
2286     embeddedMenu.add(embeddedView);\r
2287     embeddedMenu.add(embeddedFormat);\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     embeddedSelect.addMouseListener(this);\r
2297     embeddedView.addMouseListener(this);\r
2298     embeddedFormat.addMouseListener(this);\r
2299     embeddedColour.addMouseListener(this);\r
2300     embeddedCalculate.addMouseListener(this);\r
2301     embeddedHelp.addMouseListener(this);\r
2302 \r
2303    // setVisible(false);\r
2304     fileMenu.remove(closeMenuItem);\r
2305     fileMenu.remove(3); // Seperator\r
2306 \r
2307     viewport.applet.setLayout(new BorderLayout());\r
2308     viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
2309     viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
2310    // viewport.applet.validate();\r
2311 \r
2312     alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height\r
2313                        - embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
2314 \r
2315      viewport.applet.add(alignPanel, BorderLayout.CENTER);\r
2316      viewport.applet.validate();\r
2317 \r
2318   }\r
2319 \r
2320 \r
2321 \r
2322   PopupMenu filePopup, editPopup, searchPopup,\r
2323       viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup;\r
2324   MenuItem featureSettings = new MenuItem();\r
2325   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
2326   MenuItem annotationColour = new MenuItem();\r
2327   MenuItem invertColSel = new MenuItem();\r
2328   Menu menu1 = new Menu();\r
2329   MenuItem showColumns = new MenuItem();\r
2330   MenuItem showSeqs = new MenuItem();\r
2331   Menu menu2 = new Menu();\r
2332   MenuItem hideColumns = new MenuItem();\r
2333   MenuItem hideSequences = new MenuItem();\r
2334   Menu formatMenu = new Menu();\r
2335   Menu selectMenu = new Menu();\r
2336   MenuItem newView = new MenuItem();\r
2337 \r
2338   public void mousePressed(MouseEvent evt)\r
2339   {\r
2340     PopupMenu popup = null;\r
2341     Label source = (Label)evt.getSource();\r
2342     if(source==embeddedFile)\r
2343     {\r
2344       popup = filePopup = genPopupMenu(filePopup, fileMenu);\r
2345     }\r
2346     else if(source==embeddedEdit)\r
2347     {\r
2348       popup = editPopup = genPopupMenu(editPopup, editMenu);\r
2349     }\r
2350     else if(source==embeddedSelect)\r
2351     {\r
2352       popup = searchPopup = genPopupMenu(searchPopup, selectMenu);\r
2353     }\r
2354     else if(source==embeddedView)\r
2355     {\r
2356       popup = viewPopup = genPopupMenu(viewPopup, viewMenu);\r
2357     }\r
2358     else if (source ==embeddedFormat)\r
2359     {\r
2360       popup = formatPopup = genPopupMenu(formatPopup, formatMenu);\r
2361     }\r
2362     else if(source==embeddedColour)\r
2363     {\r
2364       popup = colourPopup = genPopupMenu(colourPopup, colourMenu);\r
2365     }\r
2366     else if(source==embeddedCalculate)\r
2367     {\r
2368       popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);\r
2369     }\r
2370     else if(source==embeddedHelp)\r
2371     {\r
2372       popup = helpPopup = genPopupMenu(helpPopup, helpMenu);\r
2373     }\r
2374 \r
2375     embeddedMenu.add(popup);\r
2376     popup.show(embeddedMenu,\r
2377                source.getBounds().x,\r
2378                source.getBounds().y + source.getBounds().getSize().height);\r
2379   }\r
2380 \r
2381   PopupMenu genPopupMenu(PopupMenu popup, Menu original)\r
2382   {\r
2383     if(popup!=null)\r
2384     {\r
2385       return popup;\r
2386     }\r
2387     popup = new PopupMenu();\r
2388     int m, mSize = original.getItemCount();\r
2389     for(m=0; m<mSize; m++)\r
2390     {\r
2391       popup.add(original.getItem(m));\r
2392       mSize--;\r
2393       m--;\r
2394     }\r
2395 \r
2396     return popup;\r
2397   }\r
2398   public void mouseClicked(MouseEvent evt)\r
2399   {}\r
2400   public void mouseReleased(MouseEvent evt)\r
2401   {}\r
2402   public void mouseEntered(MouseEvent evt)\r
2403   {}\r
2404   public void mouseExited(MouseEvent evt)\r
2405   {}\r
2406 \r
2407 }\r
2408 \r