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