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