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 = null;\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    AlignmentI al = null;\r
 829     if (command instanceof EditCommand)\r
 830     {\r
 831       EditCommand editCommand = (EditCommand) command;\r
 832       al = editCommand.getAlignment();\r
 833       Vector comps = (Vector) PaintRefresher.components\r
 834           .get(viewport.getSequenceSetId());\r
 835       for (int i = 0; i < comps.size(); i++)\r
 836       {\r
 837         if (comps.elementAt(i) instanceof AlignmentPanel)\r
 838         {\r
 839           if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)\r
 840           {\r
 841             originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;\r
 842             break;\r
 843           }\r
 844         }\r
 845       }\r
 846     }\r
 847 \r
 848     if (originalSource == null)\r
 849     {\r
 850       //The original view is closed, we must validate\r
 851       //the current view against the closed view first\r
 852       if (al != null)\r
 853         PaintRefresher.validateSequences(al, viewport.alignment);\r
 854 \r
 855       originalSource = viewport;\r
 856     }\r
 857 \r
 858 \r
 859     return originalSource;\r
 860   }\r
 861 \r
 862   public void moveSelectedSequences(boolean up)\r
 863   {\r
 864     SequenceGroup sg = viewport.getSelectionGroup();\r
 865     if (sg == null)\r
 866     {\r
 867       return;\r
 868     }\r
 869 \r
 870     if (up)\r
 871     {\r
 872       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 873       {\r
 874         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 875         if (!sg.getSequences(false).contains(seq))\r
 876         {\r
 877           continue;\r
 878         }\r
 879 \r
 880         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 881         if (sg.getSequences(false).contains(temp))\r
 882         {\r
 883           continue;\r
 884         }\r
 885 \r
 886         viewport.alignment.getSequences().setElementAt(temp, i);\r
 887         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 888       }\r
 889     }\r
 890     else\r
 891     {\r
 892       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 893       {\r
 894         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 895         if (!sg.getSequences(true).contains(seq))\r
 896         {\r
 897           continue;\r
 898         }\r
 899 \r
 900         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 901         if (sg.getSequences(true).contains(temp))\r
 902         {\r
 903           continue;\r
 904         }\r
 905 \r
 906         viewport.alignment.getSequences().setElementAt(temp, i);\r
 907         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 908       }\r
 909     }\r
 910 \r
 911     alignPanel.repaint();\r
 912   }\r
 913 \r
 914   static StringBuffer copiedSequences;\r
 915   static Vector copiedHiddenColumns;\r
 916   protected void copy_actionPerformed()\r
 917   {\r
 918     if (viewport.getSelectionGroup() == null)\r
 919     {\r
 920       return;\r
 921     }\r
 922 \r
 923     SequenceGroup sg = viewport.getSelectionGroup();\r
 924     copiedSequences = new StringBuffer();\r
 925     Hashtable orderedSeqs = new Hashtable();\r
 926     for (int i = 0; i < sg.getSize(false); i++)\r
 927     {\r
 928       SequenceI seq = sg.getSequenceAt(i);\r
 929       int index = viewport.alignment.findIndex(seq);\r
 930       orderedSeqs.put(index + "", seq);\r
 931     }\r
 932 \r
 933     int index = 0, startRes, endRes;\r
 934     char ch;\r
 935 \r
 936     if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)\r
 937     {\r
 938       copiedHiddenColumns = new Vector();\r
 939       int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
 940       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();\r
 941            i++)\r
 942       {\r
 943         int[] region = (int[])\r
 944             viewport.getColumnSelection().getHiddenColumns().elementAt(i);\r
 945 \r
 946         copiedHiddenColumns.addElement(new int[]\r
 947                                  {region[0] - hiddenOffset,\r
 948                                  region[1] - hiddenOffset});\r
 949       }\r
 950     }\r
 951     else\r
 952       copiedHiddenColumns = null;\r
 953 \r
 954 \r
 955     for (int i = 0; i < sg.getSize(false); i++)\r
 956     {\r
 957         SequenceI seq = null;\r
 958 \r
 959         while (seq == null)\r
 960         {\r
 961             if (orderedSeqs.containsKey(index + ""))\r
 962             {\r
 963                 seq = (SequenceI) orderedSeqs.get(index + "");\r
 964                 index++;\r
 965 \r
 966                 break;\r
 967             }\r
 968             else\r
 969             {\r
 970                 index++;\r
 971             }\r
 972         }\r
 973 \r
 974         //FIND START RES\r
 975         //Returns residue following index if gap\r
 976         startRes = seq.findPosition(sg.getStartRes());\r
 977 \r
 978         //FIND END RES\r
 979         //Need to find the residue preceeding index if gap\r
 980         endRes = 0;\r
 981 \r
 982         for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
 983         {\r
 984           ch = seq.getCharAt(j);\r
 985           if (!jalview.util.Comparison.isGap( (ch)))\r
 986           {\r
 987             endRes++;\r
 988           }\r
 989         }\r
 990 \r
 991         if(endRes>0)\r
 992         {\r
 993           endRes += seq.getStart() -1;\r
 994         }\r
 995 \r
 996         copiedSequences.append(seq.getName() + "\t" +\r
 997             startRes + "\t" +\r
 998             endRes + "\t" +\r
 999             seq.getSequence(sg.getStartRes(),\r
1000                 sg.getEndRes() + 1) + "\n");\r
1001     }\r
1002 \r
1003   }\r
1004 \r
1005   protected void pasteNew_actionPerformed()\r
1006   {\r
1007     paste(true);\r
1008   }\r
1009 \r
1010   protected void pasteThis_actionPerformed()\r
1011   {\r
1012     paste(false);\r
1013   }\r
1014 \r
1015   void paste(boolean newAlignment)\r
1016   {\r
1017     try\r
1018     {\r
1019 \r
1020       if (copiedSequences == null)\r
1021       {\r
1022         return;\r
1023       }\r
1024 \r
1025       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
1026       Vector seqs = new Vector();\r
1027       while (st.hasMoreElements())\r
1028       {\r
1029         String name = st.nextToken();\r
1030         int start = Integer.parseInt(st.nextToken());\r
1031         int end = Integer.parseInt(st.nextToken());\r
1032         seqs.addElement(new Sequence(name, st.nextToken(), start, end));\r
1033       }\r
1034       SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
1035       for (int i = 0; i < seqs.size(); i++)\r
1036       {\r
1037         newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
1038       }\r
1039 \r
1040       if (newAlignment)\r
1041       {\r
1042         String newtitle = new String("Copied sequences");\r
1043         if (getTitle().startsWith("Copied sequences"))\r
1044         {\r
1045           newtitle = getTitle();\r
1046         }\r
1047         else\r
1048         {\r
1049           newtitle = newtitle.concat("- from " + getTitle());\r
1050         }\r
1051         AlignFrame af = new AlignFrame(new Alignment(newSeqs),\r
1052                                        viewport.applet,\r
1053                                        newtitle,\r
1054                                        false);\r
1055         if (copiedHiddenColumns != null)\r
1056         {\r
1057           for (int i = 0; i < copiedHiddenColumns.size(); i++)\r
1058           {\r
1059             int[] region = (int[]) copiedHiddenColumns.elementAt(i);\r
1060             af.viewport.hideColumns(region[0], region[1]);\r
1061           }\r
1062         }\r
1063 \r
1064 \r
1065         jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,\r
1066                                          DEFAULT_HEIGHT);\r
1067       }\r
1068       else\r
1069       {\r
1070         for (int i = 0; i < newSeqs.length; i++)\r
1071         {\r
1072           viewport.alignment.addSequence(newSeqs[i]);\r
1073         }\r
1074 \r
1075         //!newAlignment\r
1076         addHistoryItem(new EditCommand(\r
1077             "Add sequences",\r
1078             EditCommand.PASTE,\r
1079             newSeqs,\r
1080             0,\r
1081             viewport.alignment.getWidth(),\r
1082             viewport.alignment)\r
1083             );\r
1084 \r
1085         viewport.setEndSeq(viewport.alignment.getHeight());\r
1086         viewport.alignment.getWidth();\r
1087         viewport.firePropertyChange("alignment", null, null);\r
1088       }\r
1089 \r
1090     }\r
1091     catch (Exception ex)\r
1092     {} // could be anything being pasted in here\r
1093 \r
1094   }\r
1095 \r
1096   protected void cut_actionPerformed()\r
1097   {\r
1098     copy_actionPerformed();\r
1099     delete_actionPerformed();\r
1100   }\r
1101 \r
1102   protected void delete_actionPerformed()\r
1103   {\r
1104 \r
1105     SequenceGroup sg = viewport.getSelectionGroup();\r
1106     if (sg == null)\r
1107     {\r
1108       return;\r
1109     }\r
1110 \r
1111     Vector seqs = new Vector();\r
1112     SequenceI seq;\r
1113     for (int i = 0; i < sg.getSize(false); i++)\r
1114     {\r
1115       seq = sg.getSequenceAt(i);\r
1116       seqs.addElement(seq);\r
1117     }\r
1118 \r
1119 \r
1120    // If the cut affects all sequences, remove highlighted columns\r
1121    if (sg.getSize(false) == viewport.alignment.getHeight())\r
1122    {\r
1123      viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
1124          sg.getEndRes() + 1);\r
1125    }\r
1126 \r
1127 \r
1128     SequenceI [] cut = new SequenceI[seqs.size()];\r
1129     for(int i=0; i<seqs.size(); i++)\r
1130       cut[i] = (SequenceI)seqs.elementAt(i);\r
1131 \r
1132 \r
1133     /*\r
1134     //ADD HISTORY ITEM\r
1135     */\r
1136     addHistoryItem(new EditCommand("Cut Sequences",\r
1137                                       EditCommand.CUT,\r
1138                                       cut,\r
1139                                       sg.getStartRes(),\r
1140                                       sg.getEndRes()-sg.getStartRes()+1,\r
1141                                       viewport.alignment));\r
1142 \r
1143 \r
1144     viewport.setSelectionGroup(null);\r
1145     viewport.alignment.deleteGroup(sg);\r
1146 \r
1147     viewport.firePropertyChange("alignment", null,\r
1148                                   viewport.getAlignment().getSequences());\r
1149 \r
1150     if (viewport.getAlignment().getHeight() < 1)\r
1151     {\r
1152         this.setVisible(false);\r
1153     }\r
1154   }\r
1155 \r
1156   protected void deleteGroups_actionPerformed()\r
1157   {\r
1158     viewport.alignment.deleteAllGroups();\r
1159     viewport.sequenceColours=null;\r
1160     viewport.setSelectionGroup(null);\r
1161 \r
1162     alignPanel.repaint();\r
1163   }\r
1164 \r
1165   public void selectAllSequenceMenuItem_actionPerformed()\r
1166   {\r
1167     SequenceGroup sg = new SequenceGroup();\r
1168     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
1169     {\r
1170       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
1171     }\r
1172     sg.setEndRes(viewport.alignment.getWidth()-1);\r
1173     viewport.setSelectionGroup(sg);\r
1174     alignPanel.repaint();\r
1175     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
1176   }\r
1177 \r
1178   public void deselectAllSequenceMenuItem_actionPerformed()\r
1179   {\r
1180     if(viewport.cursorMode)\r
1181     {\r
1182       alignPanel.seqPanel.keyboardNo1=null;\r
1183       alignPanel.seqPanel.keyboardNo2=null;\r
1184     }\r
1185     viewport.setSelectionGroup(null);\r
1186     viewport.getColumnSelection().clear();\r
1187     viewport.setSelectionGroup(null);\r
1188     alignPanel.idPanel.idCanvas.searchResults = null;\r
1189     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
1190     alignPanel.repaint();\r
1191     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
1192   }\r
1193 \r
1194   public void invertSequenceMenuItem_actionPerformed()\r
1195   {\r
1196     SequenceGroup sg = viewport.getSelectionGroup();\r
1197     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
1198     {\r
1199       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
1200     }\r
1201 \r
1202     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
1203   }\r
1204 \r
1205   void trimAlignment(boolean trimLeft)\r
1206   {\r
1207     ColumnSelection colSel = viewport.getColumnSelection();\r
1208     int column;\r
1209 \r
1210     if (colSel.size() > 0)\r
1211     {\r
1212       if(trimLeft)\r
1213         column = colSel.getMin();\r
1214       else\r
1215         column = colSel.getMax();\r
1216 \r
1217       SequenceI [] seqs;\r
1218       if(viewport.getSelectionGroup()!=null)\r
1219         seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
1220       else\r
1221         seqs = viewport.alignment.getSequencesArray();\r
1222 \r
1223 \r
1224       TrimRegionCommand trimRegion;\r
1225       if(trimLeft)\r
1226       {\r
1227         trimRegion = new TrimRegionCommand("Remove Left",\r
1228                                     TrimRegionCommand.TRIM_LEFT,\r
1229                                     seqs,\r
1230                                     column,\r
1231                                     viewport.alignment,\r
1232                                     viewport.colSel,\r
1233                                     viewport.selectionGroup);\r
1234         viewport.setStartRes(0);\r
1235       }\r
1236      else\r
1237      {\r
1238        trimRegion = new TrimRegionCommand("Remove Right",\r
1239                                    TrimRegionCommand.TRIM_RIGHT,\r
1240                                    seqs,\r
1241                                    column,\r
1242                                    viewport.alignment,\r
1243                                    viewport.colSel,\r
1244                                    viewport.selectionGroup);\r
1245      }\r
1246 \r
1247      statusBar.setText("Removed "+trimRegion.getSize()+" columns.");\r
1248 \r
1249 \r
1250       addHistoryItem(trimRegion);\r
1251 \r
1252       Vector groups = viewport.alignment.getGroups();\r
1253 \r
1254       for (int i = 0; i < groups.size(); i++)\r
1255       {\r
1256         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1257 \r
1258         if ( (trimLeft && !sg.adjustForRemoveLeft(column))\r
1259             || (!trimLeft && !sg.adjustForRemoveRight(column)))\r
1260         {\r
1261           viewport.alignment.deleteGroup(sg);\r
1262         }\r
1263       }\r
1264 \r
1265       viewport.firePropertyChange("alignment", null,\r
1266                                   viewport.getAlignment().getSequences());\r
1267     }\r
1268   }\r
1269 \r
1270 \r
1271   public void removeGappedColumnMenuItem_actionPerformed()\r
1272   {\r
1273     int start = 0, end = viewport.alignment.getWidth()-1;\r
1274 \r
1275     SequenceI[] seqs;\r
1276     if (viewport.getSelectionGroup() != null)\r
1277     {\r
1278       seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
1279       start = viewport.getSelectionGroup().getStartRes();\r
1280       end = viewport.getSelectionGroup().getEndRes();\r
1281     }\r
1282     else\r
1283       seqs = viewport.alignment.getSequencesArray();\r
1284 \r
1285 \r
1286     RemoveGapColCommand removeGapCols =\r
1287         new RemoveGapColCommand("Remove Gapped Columns",\r
1288                                 seqs,\r
1289                                 start, end,\r
1290                                 viewport.getGapCharacter());\r
1291 \r
1292     addHistoryItem(removeGapCols);\r
1293 \r
1294     statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");\r
1295 \r
1296     //This is to maintain viewport position on first residue\r
1297     //of first sequence\r
1298     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
1299     int startRes = seq.findPosition(viewport.startRes);\r
1300    // ShiftList shifts;\r
1301    // viewport.getAlignment().removeGaps(shifts=new ShiftList());\r
1302    // edit.alColumnChanges=shifts.getInverse();\r
1303    // if (viewport.hasHiddenColumns)\r
1304    //   viewport.getColumnSelection().compensateForEdits(shifts);\r
1305    viewport.setStartRes(seq.findIndex(startRes)-1);\r
1306    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1307 \r
1308   }\r
1309 \r
1310   public void removeAllGapsMenuItem_actionPerformed()\r
1311   {\r
1312     int start = 0, end = viewport.alignment.getWidth()-1;\r
1313 \r
1314     SequenceI[] seqs;\r
1315     if (viewport.getSelectionGroup() != null)\r
1316     {\r
1317       seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
1318       start = viewport.getSelectionGroup().getStartRes();\r
1319       end = viewport.getSelectionGroup().getEndRes();\r
1320     }\r
1321     else\r
1322       seqs = viewport.alignment.getSequencesArray();\r
1323 \r
1324     //This is to maintain viewport position on first residue\r
1325     //of first sequence\r
1326     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
1327     int startRes = seq.findPosition(viewport.startRes);\r
1328 \r
1329     addHistoryItem(new RemoveGapsCommand("Remove Gaps",\r
1330                                            seqs,\r
1331                                            start, end,\r
1332                      viewport.getGapCharacter()));\r
1333 \r
1334     viewport.setStartRes(seq.findIndex(startRes)-1);\r
1335 \r
1336     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1337 \r
1338   }\r
1339 \r
1340   public void findMenuItem_actionPerformed()\r
1341   {\r
1342     new Finder(alignPanel);\r
1343   }\r
1344 \r
1345   public void newView()\r
1346   {\r
1347     AlignmentI newal;\r
1348     if (viewport.hasHiddenRows)\r
1349       newal = new Alignment(viewport.getAlignment().\r
1350                             getHiddenSequences()\r
1351                             .getFullAlignment().\r
1352                             getSequencesArray());\r
1353     else\r
1354       newal = new Alignment(viewport.alignment.getSequencesArray());\r
1355 \r
1356     AlignFrame newaf = new AlignFrame(newal,\r
1357                                       viewport.applet,\r
1358                                       "",\r
1359                                       false);\r
1360 \r
1361     newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();\r
1362     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());\r
1363     PaintRefresher.Register(newaf.alignPanel,\r
1364                             newaf.alignPanel.av.getSequenceSetId());\r
1365 \r
1366     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,\r
1367                             newaf.alignPanel.av.getSequenceSetId());\r
1368     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,\r
1369                             newaf.alignPanel.av.getSequenceSetId());\r
1370 \r
1371     Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());\r
1372     int viewSize = -1;\r
1373     for (int i = 0; i < comps.size(); i++)\r
1374     {\r
1375       if (comps.elementAt(i) instanceof AlignmentPanel)\r
1376         viewSize++;\r
1377     }\r
1378 \r
1379     String title = new String(this.getTitle());\r
1380     if (title.indexOf("(View") > -1)\r
1381       title = title.substring(0, title.indexOf("(View"));\r
1382 \r
1383     title+= "(View "+viewSize+")";\r
1384 \r
1385     newaf.setTitle(title.toString());\r
1386 \r
1387 \r
1388     newaf.viewport.historyList = viewport.historyList;\r
1389     newaf.viewport.redoList = viewport.redoList;\r
1390 \r
1391    }\r
1392 \r
1393 \r
1394   public void seqLimits_itemStateChanged()\r
1395   {\r
1396     viewport.setShowJVSuffix(seqLimits.getState());\r
1397     alignPanel.fontChanged();\r
1398     alignPanel.repaint();\r
1399   }\r
1400 \r
1401 \r
1402   protected void colourTextMenuItem_actionPerformed()\r
1403   {\r
1404     viewport.setColourText(colourTextMenuItem.getState());\r
1405     alignPanel.repaint();\r
1406   }\r
1407 \r
1408   protected void wrapMenuItem_actionPerformed()\r
1409   {\r
1410     viewport.setWrapAlignment(wrapMenuItem.getState());\r
1411     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
1412     scaleAbove.setEnabled(wrapMenuItem.getState());\r
1413     scaleLeft.setEnabled(wrapMenuItem.getState());\r
1414     scaleRight.setEnabled(wrapMenuItem.getState());\r
1415     alignPanel.repaint();\r
1416   }\r
1417 \r
1418 \r
1419   public void overviewMenuItem_actionPerformed()\r
1420   {\r
1421     if (alignPanel.overviewPanel != null)\r
1422     {\r
1423       return;\r
1424     }\r
1425 \r
1426     Frame frame = new Frame();\r
1427     OverviewPanel overview = new OverviewPanel(alignPanel);\r
1428     frame.add(overview);\r
1429     // +50 must allow for applet frame window\r
1430     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
1431                                      overview.preferredSize().width,\r
1432                                      overview.preferredSize().height + 50);\r
1433 \r
1434     frame.pack();\r
1435     frame.addWindowListener(new WindowAdapter()\r
1436     {\r
1437       public void windowClosing(WindowEvent e)\r
1438       {\r
1439         alignPanel.setOverviewPanel(null);\r
1440       };\r
1441     });\r
1442 \r
1443     alignPanel.setOverviewPanel(overview);\r
1444 \r
1445   }\r
1446 \r
1447 \r
1448   void changeColour(ColourSchemeI cs)\r
1449   {\r
1450     int threshold = 0;\r
1451 \r
1452     if(cs!=null)\r
1453     {\r
1454       if (viewport.getAbovePIDThreshold())\r
1455       {\r
1456         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
1457 \r
1458         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1459 \r
1460         viewport.setGlobalColourScheme(cs);\r
1461       }\r
1462       else\r
1463       {\r
1464         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1465       }\r
1466 \r
1467       if (viewport.getConservationSelected())\r
1468       {\r
1469 \r
1470         Alignment al = (Alignment) viewport.alignment;\r
1471         Conservation c = new Conservation("All",\r
1472                                           ResidueProperties.propHash, 3,\r
1473                                           al.getSequences(), 0,\r
1474                                           al.getWidth() - 1);\r
1475 \r
1476         c.calculate();\r
1477         c.verdict(false, viewport.ConsPercGaps);\r
1478 \r
1479         cs.setConservation(c);\r
1480 \r
1481         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
1482             "Background"));\r
1483 \r
1484       }\r
1485       else\r
1486       {\r
1487         cs.setConservation(null);\r
1488       }\r
1489 \r
1490       cs.setConsensus(viewport.hconsensus);\r
1491 \r
1492     }\r
1493     viewport.setGlobalColourScheme(cs);\r
1494 \r
1495     if (viewport.getColourAppliesToAllGroups())\r
1496     {\r
1497       Vector groups = viewport.alignment.getGroups();\r
1498       for (int i = 0; i < groups.size(); i++)\r
1499       {\r
1500         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1501 \r
1502         if(cs==null)\r
1503         {\r
1504           sg.cs = null;\r
1505           continue;\r
1506         }\r
1507         if (cs instanceof ClustalxColourScheme)\r
1508         {\r
1509           sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());\r
1510         }\r
1511         else\r
1512         {\r
1513           try\r
1514           {\r
1515             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
1516           }\r
1517           catch (Exception ex)\r
1518           {\r
1519             ex.printStackTrace();\r
1520             sg.cs = cs;\r
1521           }\r
1522         }\r
1523 \r
1524         if (viewport.getAbovePIDThreshold()\r
1525             || cs instanceof PIDColourScheme\r
1526             || cs instanceof Blosum62ColourScheme)\r
1527         {\r
1528           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1529           sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));\r
1530         }\r
1531         else\r
1532           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1533 \r
1534         if (viewport.getConservationSelected())\r
1535         {\r
1536           Conservation c = new Conservation("Group",\r
1537                                             ResidueProperties.propHash, 3,\r
1538                                             sg.getSequences(true), 0,\r
1539                                             viewport.alignment.getWidth() - 1);\r
1540           c.calculate();\r
1541           c.verdict(false, viewport.ConsPercGaps);\r
1542           sg.cs.setConservation(c);\r
1543         }\r
1544         else\r
1545         {\r
1546           sg.cs.setConservation(null);\r
1547           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1548         }\r
1549 \r
1550       }\r
1551     }\r
1552 \r
1553 \r
1554     if (alignPanel.getOverviewPanel() != null)\r
1555     {\r
1556       alignPanel.getOverviewPanel().updateOverviewImage();\r
1557     }\r
1558 \r
1559     alignPanel.repaint();\r
1560   }\r
1561 \r
1562 \r
1563 \r
1564   protected void modifyPID_actionPerformed()\r
1565   {\r
1566     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
1567     {\r
1568       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
1569                                      "Background");\r
1570       SliderPanel.showPIDSlider();\r
1571     }\r
1572   }\r
1573 \r
1574   protected void modifyConservation_actionPerformed()\r
1575   {\r
1576     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
1577     {\r
1578       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
1579                                         "Background");\r
1580       SliderPanel.showConservationSlider();\r
1581     }\r
1582   }\r
1583 \r
1584   protected void conservationMenuItem_actionPerformed()\r
1585   {\r
1586     viewport.setConservationSelected(conservationMenuItem.getState());\r
1587 \r
1588     viewport.setAbovePIDThreshold(false);\r
1589     abovePIDThreshold.setState(false);\r
1590 \r
1591     changeColour(viewport.getGlobalColourScheme());\r
1592 \r
1593     modifyConservation_actionPerformed();\r
1594   }\r
1595 \r
1596   public void abovePIDThreshold_actionPerformed()\r
1597   {\r
1598     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
1599 \r
1600     conservationMenuItem.setState(false);\r
1601     viewport.setConservationSelected(false);\r
1602 \r
1603     changeColour(viewport.getGlobalColourScheme());\r
1604 \r
1605     modifyPID_actionPerformed();\r
1606   }\r
1607 \r
1608 \r
1609 \r
1610   public void sortPairwiseMenuItem_actionPerformed()\r
1611   {\r
1612     SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();\r
1613     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1614                               viewport.getAlignment().getSequenceAt(0));\r
1615     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));\r
1616     alignPanel.repaint();\r
1617   }\r
1618 \r
1619   public void sortIDMenuItem_actionPerformed()\r
1620   {\r
1621   //  addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1622    //                                HistoryItem.SORT));\r
1623     AlignmentSorter.sortByID(viewport.getAlignment());\r
1624     alignPanel.repaint();\r
1625   }\r
1626 \r
1627   public void sortGroupMenuItem_actionPerformed()\r
1628   {\r
1629   //  addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1630   //                                 HistoryItem.SORT));\r
1631     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1632     alignPanel.repaint();\r
1633 \r
1634   }\r
1635 \r
1636   public void removeRedundancyMenuItem_actionPerformed()\r
1637   {\r
1638      new RedundancyPanel(alignPanel);\r
1639   }\r
1640 \r
1641   public void pairwiseAlignmentMenuItem_actionPerformed()\r
1642   {\r
1643     if (viewport.getSelectionGroup()!=null\r
1644         && viewport.getSelectionGroup().getSize(false) > 1)\r
1645     {\r
1646       Frame frame = new Frame();\r
1647       frame.add(new PairwiseAlignPanel(alignPanel));\r
1648       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1649     }\r
1650   }\r
1651 \r
1652   public void PCAMenuItem_actionPerformed()\r
1653   {\r
1654     //are the sequences aligned?\r
1655     if (!viewport.alignment.isAligned())\r
1656     {\r
1657       SequenceI current;\r
1658       int Width = viewport.getAlignment().getWidth();\r
1659 \r
1660       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1661            i++)\r
1662       {\r
1663         current = viewport.getAlignment().getSequenceAt(i);\r
1664 \r
1665         if (current.getLength() < Width)\r
1666         {\r
1667           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1668         }\r
1669       }\r
1670       alignPanel.repaint();\r
1671     }\r
1672 \r
1673     if ( (viewport.getSelectionGroup() != null &&\r
1674           viewport.getSelectionGroup().getSize(false) < 4 &&\r
1675           viewport.getSelectionGroup().getSize(false) > 0)\r
1676         || viewport.getAlignment().getHeight() < 4)\r
1677     {\r
1678       return;\r
1679     }\r
1680 \r
1681     try\r
1682     {\r
1683       new PCAPanel(viewport);\r
1684     }\r
1685     catch (java.lang.OutOfMemoryError ex)\r
1686     {\r
1687     }\r
1688 \r
1689   }\r
1690 \r
1691   public void averageDistanceTreeMenuItem_actionPerformed()\r
1692   {\r
1693     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1694   }\r
1695 \r
1696   public void neighbourTreeMenuItem_actionPerformed()\r
1697   {\r
1698     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1699   }\r
1700 \r
1701   protected void njTreeBlosumMenuItem_actionPerformed()\r
1702   {\r
1703     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1704   }\r
1705 \r
1706   protected void avTreeBlosumMenuItem_actionPerformed()\r
1707   {\r
1708     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1709   }\r
1710 \r
1711   void NewTreePanel(String type, String pwType, String title)\r
1712   {\r
1713     //are the sequences aligned?\r
1714     if (!viewport.alignment.isAligned())\r
1715     {\r
1716       SequenceI current;\r
1717       int Width = viewport.getAlignment().getWidth();\r
1718 \r
1719       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1720            i++)\r
1721       {\r
1722         current = viewport.getAlignment().getSequenceAt(i);\r
1723 \r
1724         if (current.getLength() < Width)\r
1725         {\r
1726           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1727         }\r
1728       }\r
1729       alignPanel.repaint();\r
1730 \r
1731     }\r
1732 \r
1733     if ( (viewport.getSelectionGroup() != null &&\r
1734           viewport.getSelectionGroup().getSize(false) > 1)\r
1735       || (viewport.getSelectionGroup() == null\r
1736           && viewport.alignment.getHeight() > 1))\r
1737     {\r
1738       final TreePanel tp = new TreePanel(viewport,\r
1739                                          type,\r
1740                                          pwType);\r
1741 \r
1742       addTreeMenuItem(tp, title);\r
1743 \r
1744       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1745     }\r
1746   }\r
1747 \r
1748   void loadTree_actionPerformed()\r
1749   {\r
1750       CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
1751       cap.setText("Paste your Newick tree file here.");\r
1752       cap.setTreeImport();\r
1753       Frame frame = new Frame();\r
1754       frame.add(cap);\r
1755       jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);\r
1756   }\r
1757 \r
1758   public void loadTree(jalview.io.NewickFile tree, String treeFile)\r
1759   {\r
1760     TreePanel tp = new TreePanel(viewport,\r
1761                                  treeFile,\r
1762                                  "From File - ",\r
1763                                  tree);\r
1764     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
1765     addTreeMenuItem(tp, treeFile);\r
1766   }\r
1767 \r
1768   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1769   {\r
1770     final MenuItem item = new MenuItem(title);\r
1771     sortByTreeMenu.add(item);\r
1772     item.addActionListener(new java.awt.event.ActionListener()\r
1773     {\r
1774       public void actionPerformed(ActionEvent evt)\r
1775       {\r
1776       //  addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1777       //                                 HistoryItem.SORT));\r
1778         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1779         alignPanel.repaint();\r
1780       }\r
1781     });\r
1782 \r
1783     treePanel.addWindowListener(new WindowAdapter()\r
1784     {\r
1785       public void windowClosing(WindowEvent e)\r
1786       {\r
1787         sortByTreeMenu.remove(item);\r
1788       };\r
1789     });\r
1790   }\r
1791 \r
1792   protected void documentation_actionPerformed()\r
1793   {\r
1794     showURL("http://www.jalview.org/help.html", "HELP");\r
1795   }\r
1796 \r
1797   protected void about_actionPerformed()\r
1798   {\r
1799 \r
1800     class AboutPanel extends Canvas\r
1801     {\r
1802       String version;\r
1803       public AboutPanel(String version)\r
1804       { this.version = version; }\r
1805 \r
1806       public void paint(Graphics g)\r
1807       {\r
1808         g.setColor(Color.white);\r
1809         g.fillRect(0, 0, getSize().width, getSize().height);\r
1810         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1811         FontMetrics fm = g.getFontMetrics();\r
1812         int fh = fm.getHeight();\r
1813         int y = 5, x = 7;\r
1814         g.setColor(Color.black);\r
1815         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1816         g.drawString("Jalview - Release "+version, 200, y += fh);\r
1817         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1818         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1819                      x, y += fh * 2);\r
1820         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1821                      x, y += fh);\r
1822         g.drawString(\r
1823             "For any issues relating to Jalview, email help@jalview.org", x,\r
1824             y += fh);\r
1825         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1826         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1827                      x, y += fh);\r
1828         g.drawString("Bioinformatics,  2004 20;426-7.", x, y += fh);\r
1829       }\r
1830     }\r
1831 \r
1832     String version = "test";\r
1833     java.net.URL url = getClass().getResource("/.build_properties");\r
1834     if (url != null)\r
1835     {\r
1836       try\r
1837       {\r
1838         BufferedReader reader = new BufferedReader(new InputStreamReader(\r
1839             url.openStream()));\r
1840         String line;\r
1841         while ( (line = reader.readLine()) != null)\r
1842         {\r
1843           if (line.indexOf("VERSION") > -1)\r
1844           {\r
1845             version = line.substring(line.indexOf("=") + 1);\r
1846           }\r
1847         }\r
1848       }\r
1849       catch (Exception ex)\r
1850       {\r
1851         ex.printStackTrace();\r
1852       }\r
1853     }\r
1854 \r
1855 \r
1856     Frame frame = new Frame();\r
1857     frame.add(new AboutPanel(version));\r
1858     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1859 \r
1860   }\r
1861 \r
1862   public void showURL(String url, String target)\r
1863   {\r
1864     if (viewport.applet == null)\r
1865     {\r
1866       System.out.println("Not running as applet - no browser available.");\r
1867     }\r
1868     else\r
1869     {\r
1870       try\r
1871       {\r
1872         System.out.println("Show url: "+url);\r
1873         viewport.applet.getAppletContext().showDocument(new java.net.URL(url),\r
1874                                                target);\r
1875       }\r
1876       catch (Exception ex)\r
1877       {\r
1878         ex.printStackTrace();\r
1879       }\r
1880     }\r
1881   }\r
1882 \r
1883 \r
1884   //////////////////////////////////////////////////////////////////////////////////\r
1885   //JBuilder Graphics here\r
1886 \r
1887     protected MenuBar alignFrameMenuBar = new MenuBar();\r
1888     protected Menu fileMenu = new Menu("File");\r
1889     protected MenuItem loadApplication = new MenuItem("View in Full Application");\r
1890     protected MenuItem loadTree = new MenuItem("Load Associated Tree");\r
1891     protected MenuItem closeMenuItem = new MenuItem("Close");\r
1892     protected Menu editMenu = new Menu("Edit");\r
1893     protected Menu viewMenu = new Menu("View");\r
1894     protected Menu colourMenu = new Menu("Colour");\r
1895     protected Menu calculateMenu = new Menu("Calculate");\r
1896     protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
1897     protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
1898     protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
1899     protected MenuItem remove2LeftMenuItem = new MenuItem();\r
1900     protected MenuItem remove2RightMenuItem = new MenuItem();\r
1901     protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
1902     protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
1903     protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
1904     protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
1905     protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
1906     protected MenuItem sortIDMenuItem = new MenuItem();\r
1907     protected MenuItem sortGroupMenuItem = new MenuItem();\r
1908     protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
1909     protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
1910     protected MenuItem PCAMenuItem = new MenuItem();\r
1911     protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
1912     protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
1913     BorderLayout borderLayout1 = new BorderLayout();\r
1914     public Label statusBar = new Label();\r
1915     protected Menu outputTextboxMenu = new Menu();\r
1916     protected MenuItem clustalColour = new MenuItem();\r
1917     protected MenuItem zappoColour = new MenuItem();\r
1918     protected MenuItem taylorColour = new MenuItem();\r
1919     protected MenuItem hydrophobicityColour = new MenuItem();\r
1920     protected MenuItem helixColour = new MenuItem();\r
1921     protected MenuItem strandColour = new MenuItem();\r
1922     protected MenuItem turnColour = new MenuItem();\r
1923     protected MenuItem buriedColour = new MenuItem();\r
1924     protected MenuItem userDefinedColour = new MenuItem();\r
1925     protected MenuItem PIDColour = new MenuItem();\r
1926     protected MenuItem BLOSUM62Colour = new MenuItem();\r
1927     MenuItem njTreeBlosumMenuItem = new MenuItem();\r
1928     MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
1929     protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
1930     protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
1931     MenuItem overviewMenuItem = new MenuItem();\r
1932     protected MenuItem undoMenuItem = new MenuItem();\r
1933     protected MenuItem redoMenuItem = new MenuItem();\r
1934     protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
1935     MenuItem noColourmenuItem = new MenuItem();\r
1936     protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
1937     protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
1938     MenuItem findMenuItem = new MenuItem();\r
1939   protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
1940     protected MenuItem nucleotideColour = new MenuItem();\r
1941     MenuItem deleteGroups = new MenuItem();\r
1942     MenuItem delete = new MenuItem();\r
1943     MenuItem copy = new MenuItem();\r
1944     MenuItem cut = new MenuItem();\r
1945     Menu pasteMenu = new Menu();\r
1946     MenuItem pasteNew = new MenuItem();\r
1947     MenuItem pasteThis = new MenuItem();\r
1948     protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
1949     protected MenuItem font = new MenuItem();\r
1950     protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
1951     protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
1952     protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
1953     MenuItem modifyPID = new MenuItem();\r
1954     MenuItem modifyConservation = new MenuItem();\r
1955     protected CheckboxMenuItem autoCalculate\r
1956         = new CheckboxMenuItem("Autocalculate Consensus", true);\r
1957     protected Menu sortByTreeMenu = new Menu();\r
1958     Menu sort = new Menu();\r
1959     Menu calculate = new Menu();\r
1960     MenuItem inputText = new MenuItem();\r
1961     Menu helpMenu = new Menu();\r
1962     MenuItem documentation = new MenuItem();\r
1963     MenuItem about = new MenuItem();\r
1964     protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
1965   Panel embeddedMenu;\r
1966   Label embeddedEdit;\r
1967   Label embeddedSelect;\r
1968   Label embeddedView;\r
1969   Label embeddedFormat;\r
1970   Label embeddedColour;\r
1971   Label embeddedFile;\r
1972   Label embeddedHelp;\r
1973   Label embeddedCalculate;\r
1974   FlowLayout flowLayout1;\r
1975 \r
1976   private void jbInit() throws Exception {\r
1977 \r
1978       setMenuBar(alignFrameMenuBar);\r
1979 \r
1980       MenuItem item;\r
1981 \r
1982       // dynamically fill save as menu with available formats\r
1983       for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
1984       {\r
1985 \r
1986         item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);\r
1987 \r
1988         item.addActionListener(new java.awt.event.ActionListener()\r
1989         {\r
1990           public void actionPerformed(ActionEvent e)\r
1991           {\r
1992             outputText_actionPerformed(e);\r
1993           }\r
1994         });\r
1995 \r
1996         outputTextboxMenu.add(item);\r
1997       }\r
1998         closeMenuItem.addActionListener(this);\r
1999         loadApplication.addActionListener(this);\r
2000 \r
2001         loadTree.addActionListener(this);\r
2002         selectAllSequenceMenuItem.addActionListener(this);\r
2003         deselectAllSequenceMenuItem.addActionListener(this);\r
2004         invertSequenceMenuItem.addActionListener(this);\r
2005         remove2LeftMenuItem.setLabel("Remove Left");\r
2006         remove2LeftMenuItem.addActionListener(this);\r
2007         remove2RightMenuItem.setLabel("Remove Right");\r
2008         remove2RightMenuItem.addActionListener(this);\r
2009         removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
2010         removeGappedColumnMenuItem.addActionListener(this);\r
2011         removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
2012         removeAllGapsMenuItem.addActionListener(this);\r
2013         viewBoxesMenuItem.setLabel("Boxes");\r
2014         viewBoxesMenuItem.setState(true);\r
2015         viewBoxesMenuItem.addItemListener(this);\r
2016         viewTextMenuItem.setLabel("Text");\r
2017         viewTextMenuItem.setState(true);\r
2018         viewTextMenuItem.addItemListener(this);\r
2019         sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
2020         sortPairwiseMenuItem.addActionListener(this);\r
2021         sortIDMenuItem.setLabel("by ID");\r
2022         sortIDMenuItem.addActionListener(this);\r
2023         sortGroupMenuItem.setLabel("by Group");\r
2024         sortGroupMenuItem.addActionListener(this);\r
2025         removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
2026         removeRedundancyMenuItem.addActionListener(this);\r
2027         pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
2028         pairwiseAlignmentMenuItem.addActionListener(this);\r
2029         PCAMenuItem.setLabel("Principal Component Analysis");\r
2030         PCAMenuItem.addActionListener(this);\r
2031         averageDistanceTreeMenuItem.setLabel(\r
2032             "Average Distance Using % Identity");\r
2033         averageDistanceTreeMenuItem.addActionListener(this);\r
2034         neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
2035         neighbourTreeMenuItem.addActionListener(this);\r
2036         alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
2037         statusBar.setBackground(Color.white);\r
2038         statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
2039         statusBar.setText("Status bar");\r
2040         outputTextboxMenu.setLabel("Output to Textbox");\r
2041         clustalColour.setLabel("Clustalx");\r
2042 \r
2043         clustalColour.addActionListener(this);\r
2044         zappoColour.setLabel("Zappo");\r
2045         zappoColour.addActionListener(this);\r
2046         taylorColour.setLabel("Taylor");\r
2047         taylorColour.addActionListener(this);\r
2048         hydrophobicityColour.setLabel("Hydrophobicity");\r
2049         hydrophobicityColour.addActionListener(this);\r
2050         helixColour.setLabel("Helix Propensity");\r
2051         helixColour.addActionListener(this);\r
2052         strandColour.setLabel("Strand Propensity");\r
2053         strandColour.addActionListener(this);\r
2054         turnColour.setLabel("Turn Propensity");\r
2055         turnColour.addActionListener(this);\r
2056         buriedColour.setLabel("Buried Index");\r
2057         buriedColour.addActionListener(this);\r
2058         userDefinedColour.setLabel("User Defined...");\r
2059         userDefinedColour.addActionListener(this);\r
2060         PIDColour.setLabel("Percentage Identity");\r
2061         PIDColour.addActionListener(this);\r
2062         BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
2063         BLOSUM62Colour.addActionListener(this);\r
2064         avDistanceTreeBlosumMenuItem.setLabel(\r
2065             "Average Distance Using BLOSUM62");\r
2066         avDistanceTreeBlosumMenuItem.addActionListener(this);\r
2067         njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
2068         njTreeBlosumMenuItem.addActionListener(this);\r
2069         annotationPanelMenuItem.setLabel("Show Annotations");\r
2070         annotationPanelMenuItem.addItemListener(this);\r
2071         colourTextMenuItem.setLabel("Colour Text");\r
2072         colourTextMenuItem.addItemListener(this);\r
2073         overviewMenuItem.setLabel("Overview Window");\r
2074         overviewMenuItem.addActionListener(this);\r
2075         undoMenuItem.setEnabled(false);\r
2076         undoMenuItem.setLabel("Undo");\r
2077         undoMenuItem.addActionListener(this);\r
2078         redoMenuItem.setEnabled(false);\r
2079         redoMenuItem.setLabel("Redo");\r
2080         redoMenuItem.addActionListener(this);\r
2081         conservationMenuItem.setLabel("by Conservation");\r
2082         conservationMenuItem.addItemListener(this);\r
2083         noColourmenuItem.setLabel("None");\r
2084         noColourmenuItem.addActionListener(this);\r
2085         wrapMenuItem.setLabel("Wrap");\r
2086         wrapMenuItem.addItemListener(this);\r
2087         renderGapsMenuItem.setLabel("Show Gaps");\r
2088         renderGapsMenuItem.setState(true);\r
2089         renderGapsMenuItem.addItemListener(this);\r
2090         findMenuItem.setLabel("Find...");\r
2091         findMenuItem.addActionListener(this);\r
2092     abovePIDThreshold.setLabel("Above Identity Threshold");\r
2093         abovePIDThreshold.addItemListener(this);\r
2094         nucleotideColour.setLabel("Nucleotide");\r
2095         nucleotideColour.addActionListener(this);\r
2096         deleteGroups.setLabel("Undefine Groups");\r
2097         deleteGroups.addActionListener(this);\r
2098         copy.setLabel("Copy");\r
2099         copy.addActionListener(this);\r
2100         cut.setLabel("Cut");\r
2101         cut.addActionListener(this);\r
2102         delete.setLabel("Delete");\r
2103         delete.addActionListener(this);\r
2104         pasteMenu.setLabel("Paste");\r
2105         pasteNew.setLabel("To New Alignment");\r
2106         pasteNew.addActionListener(this);\r
2107         pasteThis.setLabel("Add To This Alignment");\r
2108         pasteThis.addActionListener(this);\r
2109         applyToAllGroups.setLabel("Apply Colour To All Groups");\r
2110         applyToAllGroups.setState(true);\r
2111         applyToAllGroups.addItemListener(this);\r
2112         font.setLabel("Font...");\r
2113         font.addActionListener(this);\r
2114         scaleAbove.setLabel("Scale Above");\r
2115         scaleAbove.setState(true);\r
2116         scaleAbove.setEnabled(false);\r
2117         scaleAbove.addItemListener(this);\r
2118         scaleLeft.setEnabled(false);\r
2119         scaleLeft.setState(true);\r
2120         scaleLeft.setLabel("Scale Left");\r
2121         scaleLeft.addItemListener(this);\r
2122         scaleRight.setEnabled(false);\r
2123         scaleRight.setState(true);\r
2124         scaleRight.setLabel("Scale Right");\r
2125         scaleRight.addItemListener(this);\r
2126         modifyPID.setLabel("Modify Identity Threshold...");\r
2127         modifyPID.addActionListener(this);\r
2128         modifyConservation.setLabel("Modify Conservation Threshold...");\r
2129         modifyConservation.addActionListener(this);\r
2130         sortByTreeMenu.setLabel("By Tree Order");\r
2131         sort.setLabel("Sort");\r
2132         calculate.setLabel("Calculate Tree");\r
2133         autoCalculate.addItemListener(this);\r
2134         inputText.setLabel("Input from textbox");\r
2135         inputText.addActionListener(this);\r
2136 \r
2137         helpMenu.setLabel("Help");\r
2138         documentation.setLabel("Documentation");\r
2139         documentation.addActionListener(this);\r
2140 \r
2141         about.setLabel("About...");\r
2142         about.addActionListener(this);\r
2143           seqLimits.setState(true);\r
2144     seqLimits.setLabel("Show Sequence Limits");\r
2145     seqLimits.addItemListener(this);\r
2146     featureSettings.setLabel("Feature Settings...");\r
2147     featureSettings.addActionListener(this);\r
2148     sequenceFeatures.setLabel("Sequence Features");\r
2149     sequenceFeatures.addItemListener(this);\r
2150     sequenceFeatures.setState(false);\r
2151     annotationColour.setLabel("by Annotation...");\r
2152     annotationColour.addActionListener(this);\r
2153     invertSequenceMenuItem.setLabel("Invert Sequence Selection");\r
2154     invertColSel.setLabel("Invert Column Selection");\r
2155     menu1.setLabel("Show");\r
2156     showColumns.setLabel("All Columns ");\r
2157     showSeqs.setLabel("All Sequences");\r
2158     menu2.setLabel("Hide");\r
2159     hideColumns.setLabel("Selected Columns");\r
2160     hideSequences.setLabel("Selected Sequences");\r
2161     invertColSel.addActionListener(this);\r
2162     showColumns.addActionListener(this);\r
2163     showSeqs.addActionListener(this);\r
2164     hideColumns.addActionListener(this);\r
2165     hideSequences.addActionListener(this);\r
2166     formatMenu.setLabel("Format");\r
2167     selectMenu.setLabel("Select");\r
2168     newView.setLabel("New View");\r
2169     newView.addActionListener(this);\r
2170     alignFrameMenuBar.add(fileMenu);\r
2171         alignFrameMenuBar.add(editMenu);\r
2172     alignFrameMenuBar.add(selectMenu);\r
2173     alignFrameMenuBar.add(viewMenu);\r
2174     alignFrameMenuBar.add(formatMenu);\r
2175     alignFrameMenuBar.add(colourMenu);\r
2176         alignFrameMenuBar.add(calculateMenu);\r
2177         alignFrameMenuBar.add(helpMenu);\r
2178         fileMenu.add(inputText);\r
2179         fileMenu.add(outputTextboxMenu);\r
2180         if(jalviewServletURL!=null)\r
2181           fileMenu.add(loadApplication);\r
2182         fileMenu.addSeparator();\r
2183         fileMenu.add(loadTree);\r
2184         fileMenu.add(closeMenuItem);\r
2185         editMenu.add(undoMenuItem);\r
2186         editMenu.add(redoMenuItem);\r
2187         editMenu.add(cut);\r
2188         editMenu.add(copy);\r
2189         editMenu.add(pasteMenu);\r
2190         editMenu.add(delete);\r
2191     editMenu.addSeparator();\r
2192         editMenu.add(remove2LeftMenuItem);\r
2193         editMenu.add(remove2RightMenuItem);\r
2194         editMenu.add(removeGappedColumnMenuItem);\r
2195         editMenu.add(removeAllGapsMenuItem);\r
2196         editMenu.add(removeRedundancyMenuItem);\r
2197     viewMenu.add(newView);\r
2198     viewMenu.addSeparator();\r
2199     viewMenu.add(menu1);\r
2200     viewMenu.add(menu2);\r
2201     viewMenu.addSeparator();\r
2202     viewMenu.add(annotationPanelMenuItem);\r
2203     viewMenu.addSeparator();\r
2204         viewMenu.add(sequenceFeatures);\r
2205         viewMenu.add(featureSettings);\r
2206     viewMenu.addSeparator();\r
2207         viewMenu.add(overviewMenuItem);\r
2208         colourMenu.add(applyToAllGroups);\r
2209         colourMenu.addSeparator();\r
2210         colourMenu.add(noColourmenuItem);\r
2211         colourMenu.add(clustalColour);\r
2212         colourMenu.add(BLOSUM62Colour);\r
2213         colourMenu.add(PIDColour);\r
2214         colourMenu.add(zappoColour);\r
2215         colourMenu.add(taylorColour);\r
2216         colourMenu.add(hydrophobicityColour);\r
2217         colourMenu.add(helixColour);\r
2218         colourMenu.add(strandColour);\r
2219         colourMenu.add(turnColour);\r
2220         colourMenu.add(buriedColour);\r
2221         colourMenu.add(nucleotideColour);\r
2222         colourMenu.add(userDefinedColour);\r
2223         colourMenu.addSeparator();\r
2224         colourMenu.add(conservationMenuItem);\r
2225         colourMenu.add(modifyConservation);\r
2226         colourMenu.add(abovePIDThreshold);\r
2227         colourMenu.add(modifyPID);\r
2228     colourMenu.add(annotationColour);\r
2229     calculateMenu.add(sort);\r
2230         calculateMenu.add(calculate);\r
2231         calculateMenu.addSeparator();\r
2232         calculateMenu.add(pairwiseAlignmentMenuItem);\r
2233         calculateMenu.add(PCAMenuItem);\r
2234         calculateMenu.add(autoCalculate);\r
2235         this.add(statusBar, BorderLayout.SOUTH);\r
2236         pasteMenu.add(pasteNew);\r
2237         pasteMenu.add(pasteThis);\r
2238         sort.add(sortIDMenuItem);\r
2239         sort.add(sortByTreeMenu);\r
2240         sort.add(sortGroupMenuItem);\r
2241         sort.add(sortPairwiseMenuItem);\r
2242         calculate.add(averageDistanceTreeMenuItem);\r
2243         calculate.add(neighbourTreeMenuItem);\r
2244         calculate.add(avDistanceTreeBlosumMenuItem);\r
2245         calculate.add(njTreeBlosumMenuItem);\r
2246         helpMenu.add(documentation);\r
2247         helpMenu.add(about);\r
2248     menu1.add(showColumns);\r
2249     menu1.add(showSeqs);\r
2250     menu2.add(hideColumns);\r
2251     menu2.add(hideSequences);\r
2252     formatMenu.add(font);\r
2253     formatMenu.add(seqLimits);\r
2254     formatMenu.add(wrapMenuItem);\r
2255     formatMenu.add(scaleAbove);\r
2256     formatMenu.add(scaleLeft);\r
2257     formatMenu.add(scaleRight);\r
2258     formatMenu.add(viewBoxesMenuItem);\r
2259     formatMenu.add(viewTextMenuItem);\r
2260     formatMenu.add(colourTextMenuItem);\r
2261     formatMenu.add(renderGapsMenuItem);\r
2262     selectMenu.add(findMenuItem);\r
2263     selectMenu.addSeparator();\r
2264     selectMenu.add(selectAllSequenceMenuItem);\r
2265     selectMenu.add(deselectAllSequenceMenuItem);\r
2266     selectMenu.add(invertSequenceMenuItem);\r
2267     selectMenu.add(invertColSel);\r
2268     selectMenu.add(deleteGroups);\r
2269   }\r
2270 \r
2271   public void setEmbedded()\r
2272   {\r
2273 \r
2274     embeddedMenu = new Panel();\r
2275     embeddedEdit = new Label("Edit");\r
2276     embeddedSelect = new Label("Select");\r
2277     embeddedView = new Label("View");\r
2278     embeddedFormat = new Label("Format");\r
2279     embeddedColour = new Label("Colour");\r
2280     embeddedFile = new Label("File");\r
2281     embeddedHelp = new Label("Help");\r
2282     embeddedCalculate = new Label("Calculate");\r
2283     flowLayout1 = new FlowLayout();\r
2284     embeddedMenu.setBackground(Color.lightGray);\r
2285     embeddedMenu.setLayout(flowLayout1);\r
2286     embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2287     embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2288     embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2289     embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2290     embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2291     embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2292     embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2293     embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2294     embeddedMenu.add(embeddedFile);\r
2295     embeddedMenu.add(embeddedEdit);\r
2296     embeddedMenu.add(embeddedSelect);\r
2297     embeddedMenu.add(embeddedView);\r
2298     embeddedMenu.add(embeddedFormat);\r
2299     embeddedMenu.add(embeddedColour);\r
2300     embeddedMenu.add(embeddedCalculate);\r
2301     embeddedMenu.add(embeddedHelp);\r
2302     flowLayout1.setAlignment(FlowLayout.LEFT);\r
2303     flowLayout1.setHgap(2);\r
2304     flowLayout1.setVgap(0);\r
2305     embeddedFile.addMouseListener(this);\r
2306     embeddedEdit.addMouseListener(this);\r
2307     embeddedSelect.addMouseListener(this);\r
2308     embeddedView.addMouseListener(this);\r
2309     embeddedFormat.addMouseListener(this);\r
2310     embeddedColour.addMouseListener(this);\r
2311     embeddedCalculate.addMouseListener(this);\r
2312     embeddedHelp.addMouseListener(this);\r
2313 \r
2314    // setVisible(false);\r
2315     fileMenu.remove(closeMenuItem);\r
2316     fileMenu.remove(3); // Seperator\r
2317 \r
2318     viewport.applet.setLayout(new BorderLayout());\r
2319     viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
2320     viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
2321    // viewport.applet.validate();\r
2322 \r
2323     alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height\r
2324                        - embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
2325 \r
2326      viewport.applet.add(alignPanel, BorderLayout.CENTER);\r
2327      viewport.applet.validate();\r
2328 \r
2329   }\r
2330 \r
2331 \r
2332 \r
2333   PopupMenu filePopup, editPopup, searchPopup,\r
2334       viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup;\r
2335   MenuItem featureSettings = new MenuItem();\r
2336   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
2337   MenuItem annotationColour = new MenuItem();\r
2338   MenuItem invertColSel = new MenuItem();\r
2339   Menu menu1 = new Menu();\r
2340   MenuItem showColumns = new MenuItem();\r
2341   MenuItem showSeqs = new MenuItem();\r
2342   Menu menu2 = new Menu();\r
2343   MenuItem hideColumns = new MenuItem();\r
2344   MenuItem hideSequences = new MenuItem();\r
2345   Menu formatMenu = new Menu();\r
2346   Menu selectMenu = new Menu();\r
2347   MenuItem newView = new MenuItem();\r
2348 \r
2349   public void mousePressed(MouseEvent evt)\r
2350   {\r
2351     PopupMenu popup = null;\r
2352     Label source = (Label)evt.getSource();\r
2353     if(source==embeddedFile)\r
2354     {\r
2355       popup = filePopup = genPopupMenu(filePopup, fileMenu);\r
2356     }\r
2357     else if(source==embeddedEdit)\r
2358     {\r
2359       popup = editPopup = genPopupMenu(editPopup, editMenu);\r
2360     }\r
2361     else if(source==embeddedSelect)\r
2362     {\r
2363       popup = searchPopup = genPopupMenu(searchPopup, selectMenu);\r
2364     }\r
2365     else if(source==embeddedView)\r
2366     {\r
2367       popup = viewPopup = genPopupMenu(viewPopup, viewMenu);\r
2368     }\r
2369     else if (source ==embeddedFormat)\r
2370     {\r
2371       popup = formatPopup = genPopupMenu(formatPopup, formatMenu);\r
2372     }\r
2373     else if(source==embeddedColour)\r
2374     {\r
2375       popup = colourPopup = genPopupMenu(colourPopup, colourMenu);\r
2376     }\r
2377     else if(source==embeddedCalculate)\r
2378     {\r
2379       popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);\r
2380     }\r
2381     else if(source==embeddedHelp)\r
2382     {\r
2383       popup = helpPopup = genPopupMenu(helpPopup, helpMenu);\r
2384     }\r
2385 \r
2386     embeddedMenu.add(popup);\r
2387     popup.show(embeddedMenu,\r
2388                source.getBounds().x,\r
2389                source.getBounds().y + source.getBounds().getSize().height);\r
2390   }\r
2391 \r
2392   PopupMenu genPopupMenu(PopupMenu popup, Menu original)\r
2393   {\r
2394     if(popup!=null)\r
2395     {\r
2396       return popup;\r
2397     }\r
2398     popup = new PopupMenu();\r
2399     int m, mSize = original.getItemCount();\r
2400     for(m=0; m<mSize; m++)\r
2401     {\r
2402       popup.add(original.getItem(m));\r
2403       mSize--;\r
2404       m--;\r
2405     }\r
2406 \r
2407     return popup;\r
2408   }\r
2409   public void mouseClicked(MouseEvent evt)\r
2410   {}\r
2411   public void mouseReleased(MouseEvent evt)\r
2412   {}\r
2413   public void mouseEntered(MouseEvent evt)\r
2414   {}\r
2415   public void mouseExited(MouseEvent evt)\r
2416   {}\r
2417 \r
2418 }\r
2419 \r