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     if (applet != null)\r
  53       jalviewServletURL = applet.getParameter("APPLICATION_URL");\r
  54 \r
  55     try{\r
  56       jbInit();\r
  57     }catch(Exception ex)\r
  58     {\r
  59       ex.printStackTrace();\r
  60     }\r
  61 \r
  62     viewport = new AlignViewport(al, applet);\r
  63     alignPanel = new AlignmentPanel(this, viewport);\r
  64 \r
  65     viewport.updateConservation(alignPanel);\r
  66     viewport.updateConsensus(alignPanel);\r
  67 \r
  68     annotationPanelMenuItem.setState(viewport.showAnnotation);\r
  69 \r
  70     seqLimits.setState(viewport.showJVSuffix);\r
  71 \r
  72     if(applet!=null)\r
  73     {\r
  74       String param = applet.getParameter("sortBy");\r
  75       if (param != null)\r
  76       {\r
  77         if (param.equalsIgnoreCase("Id"))\r
  78           sortIDMenuItem_actionPerformed();\r
  79         else if (param.equalsIgnoreCase("Pairwise Identity"))\r
  80           sortPairwiseMenuItem_actionPerformed();\r
  81       }\r
  82 \r
  83       param = applet.getParameter("wrap");\r
  84       if (param != null)\r
  85       {\r
  86         if (param.equalsIgnoreCase("true"))\r
  87         {\r
  88           wrapMenuItem.setState(true);\r
  89           wrapMenuItem_actionPerformed();\r
  90         }\r
  91       }\r
  92 \r
  93       try\r
  94       {\r
  95         param = applet.getParameter("windowWidth");\r
  96         if (param != null)\r
  97         {\r
  98           int width = Integer.parseInt(param);\r
  99           DEFAULT_WIDTH = width;\r
 100         }\r
 101         param = applet.getParameter("windowHeight");\r
 102         if (param != null)\r
 103         {\r
 104           int height = Integer.parseInt(param);\r
 105           DEFAULT_HEIGHT = height;\r
 106         }\r
 107       }\r
 108       catch (Exception ex)\r
 109       {}\r
 110 \r
 111     }\r
 112 \r
 113    //Some JVMS send keyevents to Top frame or lowest panel,\r
 114    //Havent worked out why yet. So add to both this frame and seqCanvas for now\r
 115    this.addKeyListener(this);\r
 116    alignPanel.seqPanel.seqCanvas.addKeyListener(this);\r
 117    alignPanel.idPanel.idCanvas.addKeyListener(this);\r
 118    alignPanel.scalePanel.addKeyListener(this);\r
 119    alignPanel.annotationPanel.addKeyListener(this);\r
 120 \r
 121 \r
 122    if(embedded)\r
 123    {\r
 124      setEmbedded();\r
 125    }\r
 126    else\r
 127    {\r
 128      add(alignPanel, BorderLayout.CENTER);\r
 129      jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,\r
 130                                       DEFAULT_HEIGHT);\r
 131    }\r
 132    alignPanel.validate();\r
 133    alignPanel.repaint();\r
 134   }\r
 135   public AlignViewport getAlignViewport()\r
 136   {\r
 137     return viewport;\r
 138   }\r
 139 \r
 140   public SeqCanvas getSeqcanvas()\r
 141   {\r
 142     return alignPanel.seqPanel.seqCanvas;\r
 143   }\r
 144 \r
 145 \r
 146   /**\r
 147    * DOCUMENT ME!\r
 148    *\r
 149    * @param String DOCUMENT ME!\r
 150    */\r
 151 \r
 152   public void parseFeaturesFile(String file, String type)\r
 153   {\r
 154     Hashtable featureLinks = new Hashtable();\r
 155     boolean featuresFile = false;\r
 156     try{\r
 157       featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,\r
 158                                          alignPanel.seqPanel.seqCanvas.\r
 159                                          getFeatureRenderer().featureColours,\r
 160                                          featureLinks,\r
 161                                          true);\r
 162     }\r
 163     catch(Exception ex)\r
 164     {\r
 165       ex.printStackTrace();\r
 166     }\r
 167 \r
 168     if(featuresFile)\r
 169     {\r
 170       if(featureLinks.size()>0)\r
 171         alignPanel.seqPanel.seqCanvas\r
 172             .getFeatureRenderer().featureLinks = featureLinks;\r
 173       viewport.showSequenceFeatures = true;\r
 174       sequenceFeatures.setState(true);\r
 175       alignPanel.repaint();\r
 176     }\r
 177 \r
 178   }\r
 179 \r
 180 \r
 181   public void keyPressed(KeyEvent evt)\r
 182   {\r
 183     if (viewport.cursorMode\r
 184         && evt.getKeyCode() >= KeyEvent.VK_0\r
 185         && evt.getKeyCode() <= KeyEvent.VK_9)\r
 186     {\r
 187       alignPanel.seqPanel.numberPressed(evt.getKeyChar());\r
 188     }\r
 189 \r
 190     switch (evt.getKeyCode())\r
 191     {\r
 192       case 27: // escape key\r
 193         deselectAllSequenceMenuItem_actionPerformed();\r
 194         break;\r
 195       case KeyEvent.VK_X:\r
 196         if (evt.isControlDown() || evt.isMetaDown())\r
 197         {\r
 198           cut_actionPerformed();\r
 199         }\r
 200         break;\r
 201       case KeyEvent.VK_C:\r
 202         if (viewport.cursorMode && !evt.isControlDown())\r
 203         {\r
 204           alignPanel.seqPanel.setCursorColumn();\r
 205         }\r
 206         if (evt.isControlDown() || evt.isMetaDown())\r
 207         {\r
 208           copy_actionPerformed();\r
 209         }\r
 210         break;\r
 211       case KeyEvent.VK_V:\r
 212         if (evt.isControlDown())\r
 213         {\r
 214           paste(evt.isShiftDown());\r
 215         }\r
 216         break;\r
 217       case KeyEvent.VK_A:\r
 218         if (evt.isControlDown() || evt.isMetaDown())\r
 219         {\r
 220           selectAllSequenceMenuItem_actionPerformed();\r
 221         }\r
 222         break;\r
 223       case KeyEvent.VK_DOWN:\r
 224         if(viewport.cursorMode)\r
 225         {\r
 226           alignPanel.seqPanel.moveCursor(0,1);\r
 227         }\r
 228         else\r
 229           moveSelectedSequences(false);\r
 230         break;\r
 231 \r
 232       case KeyEvent.VK_UP:\r
 233         if (viewport.cursorMode)\r
 234         {\r
 235           alignPanel.seqPanel.moveCursor(0,-1);\r
 236         }\r
 237         else\r
 238           moveSelectedSequences(true);\r
 239         break;\r
 240 \r
 241       case KeyEvent.VK_LEFT:\r
 242         if(viewport.cursorMode)\r
 243         {\r
 244           alignPanel.seqPanel.moveCursor(-1,0);\r
 245         }\r
 246         break;\r
 247 \r
 248       case KeyEvent.VK_RIGHT:\r
 249         if (viewport.cursorMode)\r
 250         {\r
 251           alignPanel.seqPanel.moveCursor(1,0);\r
 252         }\r
 253         break;\r
 254       case KeyEvent.VK_SPACE:\r
 255         if(viewport.cursorMode)\r
 256         {\r
 257           alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()\r
 258                                                 || evt.isShiftDown()\r
 259                                                 || evt.isAltDown()\r
 260               );\r
 261         }\r
 262         break;\r
 263 \r
 264       case KeyEvent.VK_DELETE:\r
 265       case KeyEvent.VK_BACK_SPACE:\r
 266         if(viewport.cursorMode)\r
 267         {\r
 268           alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()\r
 269                                                 || evt.isShiftDown()\r
 270                                                 || evt.isAltDown());\r
 271         }\r
 272        else\r
 273         {\r
 274           cut_actionPerformed();\r
 275           alignPanel.seqPanel.seqCanvas.repaint();\r
 276         }\r
 277         break;\r
 278 \r
 279       case KeyEvent.VK_S:\r
 280         if(viewport.cursorMode)\r
 281         {\r
 282           alignPanel.seqPanel.setCursorRow();\r
 283         }\r
 284         break;\r
 285       case KeyEvent.VK_P:\r
 286         if(viewport.cursorMode)\r
 287         {\r
 288           alignPanel.seqPanel.setCursorPosition();\r
 289         }\r
 290         break;\r
 291 \r
 292       case KeyEvent.VK_ENTER:\r
 293       case KeyEvent.VK_COMMA:\r
 294         if(viewport.cursorMode)\r
 295         {\r
 296           alignPanel.seqPanel.setCursorRowAndColumn();\r
 297         }\r
 298         break;\r
 299 \r
 300       case KeyEvent.VK_Q:\r
 301         if(viewport.cursorMode)\r
 302         {\r
 303           alignPanel.seqPanel.setSelectionAreaAtCursor(true);\r
 304         }\r
 305         break;\r
 306       case KeyEvent.VK_M:\r
 307         if(viewport.cursorMode)\r
 308         {\r
 309           alignPanel.seqPanel.setSelectionAreaAtCursor(false);\r
 310         }\r
 311         break;\r
 312 \r
 313      case KeyEvent.VK_F2:\r
 314        viewport.cursorMode = ! viewport.cursorMode;\r
 315        statusBar.setText("Keyboard editing mode is "+\r
 316            (viewport.cursorMode ? "on" : "off"));\r
 317        if(viewport.cursorMode)\r
 318        {\r
 319          alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;\r
 320          alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;\r
 321        }\r
 322        break;\r
 323 \r
 324       case KeyEvent.VK_F:\r
 325         if (evt.isControlDown())\r
 326         {\r
 327           findMenuItem_actionPerformed();\r
 328         }\r
 329         break;\r
 330 \r
 331       case KeyEvent.VK_H:\r
 332       {\r
 333         boolean toggleSeqs = !evt.isControlDown();\r
 334         boolean toggleCols = !evt.isShiftDown();\r
 335         boolean hide = false;\r
 336         SequenceGroup sg = viewport.getSelectionGroup();\r
 337 \r
 338         if(toggleSeqs)\r
 339         {\r
 340           if (sg != null && sg.getSize() != viewport.alignment.getHeight())\r
 341           {\r
 342             hide = true;\r
 343             viewport.hideAllSelectedSeqs();\r
 344           }\r
 345           else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))\r
 346             viewport.showAllHiddenSeqs();\r
 347         }\r
 348 \r
 349         if(toggleCols)\r
 350         {\r
 351           if (viewport.colSel.getSelected().size() > 0)\r
 352           {\r
 353             viewport.hideSelectedColumns();\r
 354             if(!toggleSeqs)\r
 355                    viewport.selectionGroup = sg;\r
 356           }\r
 357           else if (!hide)\r
 358             viewport.showAllHiddenColumns();\r
 359         }\r
 360         break;\r
 361       }\r
 362 \r
 363       case KeyEvent.VK_PAGE_UP:\r
 364         if (viewport.wrapAlignment)\r
 365           alignPanel.scrollUp(true);\r
 366         else\r
 367           alignPanel.setScrollValues(viewport.startRes,\r
 368                                      viewport.startSeq\r
 369                                      - viewport.endSeq + viewport.startSeq);\r
 370         break;\r
 371 \r
 372       case KeyEvent.VK_PAGE_DOWN:\r
 373         if (viewport.wrapAlignment)\r
 374           alignPanel.scrollUp(false);\r
 375         else\r
 376           alignPanel.setScrollValues(viewport.startRes,\r
 377                                      viewport.startSeq\r
 378                                      + viewport.endSeq - viewport.startSeq);\r
 379         break;\r
 380 \r
 381       case KeyEvent.VK_Z:\r
 382         if (evt.isControlDown())\r
 383         {\r
 384           undoMenuItem_actionPerformed();\r
 385         }\r
 386         break;\r
 387 \r
 388       case KeyEvent.VK_Y:\r
 389         if (evt.isControlDown())\r
 390         {\r
 391           redoMenuItem_actionPerformed();\r
 392         }\r
 393         break;\r
 394 \r
 395       case KeyEvent.VK_L:\r
 396         if (evt.isControlDown())\r
 397         {\r
 398           trimAlignment(true);\r
 399         }\r
 400         break;\r
 401 \r
 402       case KeyEvent.VK_R:\r
 403         if (evt.isControlDown())\r
 404         {\r
 405           trimAlignment(false);\r
 406         }\r
 407         break;\r
 408 \r
 409       case KeyEvent.VK_E:\r
 410         if (evt.isControlDown())\r
 411         {\r
 412           if (evt.isShiftDown())\r
 413             this.removeAllGapsMenuItem_actionPerformed();\r
 414           else\r
 415             removeGappedColumnMenuItem_actionPerformed();\r
 416         }\r
 417         break;\r
 418       case KeyEvent.VK_I:\r
 419         if (evt.isControlDown())\r
 420         {\r
 421           if (evt.isAltDown())\r
 422             viewport.invertColumnSelection();\r
 423           else\r
 424             this.invertSequenceMenuItem_actionPerformed();\r
 425         }\r
 426         break;\r
 427 \r
 428       case KeyEvent.VK_U:\r
 429         if (evt.isControlDown())\r
 430         {\r
 431           this.deleteGroups_actionPerformed();\r
 432         }\r
 433       break;\r
 434 \r
 435     case KeyEvent.VK_T:\r
 436       if (evt.isControlDown())\r
 437       {\r
 438        newView();\r
 439       }\r
 440       break;\r
 441 \r
 442 \r
 443       }\r
 444       alignPanel.repaint();\r
 445   }\r
 446   public void keyReleased(KeyEvent evt)\r
 447   {}\r
 448   public void keyTyped(KeyEvent evt)\r
 449   {}\r
 450 \r
 451 public void itemStateChanged(ItemEvent evt)\r
 452   {\r
 453     if(evt.getSource()==colourTextMenuItem)\r
 454             colourTextMenuItem_actionPerformed();\r
 455     else if(evt.getSource()==wrapMenuItem)\r
 456             wrapMenuItem_actionPerformed();\r
 457     else if(evt.getSource()==scaleAbove)\r
 458             viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 459     else if(evt.getSource()==scaleLeft)\r
 460             viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 461     else if(evt.getSource()==scaleRight)\r
 462             viewport.setScaleRightWrapped(scaleRight.getState());\r
 463      else if(evt.getSource()==seqLimits)\r
 464       seqLimits_itemStateChanged();\r
 465     else if(evt.getSource()==viewBoxesMenuItem)\r
 466             viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
 467     else if(evt.getSource()==viewTextMenuItem)\r
 468             viewport.setShowText(viewTextMenuItem.getState());\r
 469     else if(evt.getSource()==renderGapsMenuItem)\r
 470             viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 471     else if(evt.getSource()==annotationPanelMenuItem)\r
 472     {\r
 473       viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
 474       alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
 475     }\r
 476       else if(evt.getSource()==sequenceFeatures)\r
 477       {\r
 478            viewport.showSequenceFeatures(sequenceFeatures.getState());\r
 479             alignPanel.seqPanel.seqCanvas.repaint();\r
 480       }\r
 481       else if(evt.getSource()==conservationMenuItem)\r
 482             conservationMenuItem_actionPerformed();\r
 483       else if(evt.getSource()==abovePIDThreshold)\r
 484             abovePIDThreshold_actionPerformed();\r
 485       else if(evt.getSource()==applyToAllGroups)\r
 486             viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
 487       else if(evt.getSource()==autoCalculate)\r
 488           viewport.autocalculateConsensus = autoCalculate.getState();\r
 489 \r
 490       alignPanel.repaint();\r
 491   }\r
 492  public void actionPerformed(ActionEvent evt)\r
 493  {\r
 494     Object source = evt.getSource();\r
 495 \r
 496     if(source==inputText)\r
 497       inputText_actionPerformed();\r
 498     else if(source==loadTree)\r
 499       loadTree_actionPerformed();\r
 500     else if(source==loadApplication)\r
 501       launchFullApplication();\r
 502     else if (source == loadAnnotations)\r
 503       loadAnnotations();\r
 504     else if (source == outputAnnotations)\r
 505       outputAnnotations(true);\r
 506     else if(source == outputFeatures)\r
 507       outputFeatures(true, "Jalview");\r
 508     else if(source==closeMenuItem)\r
 509       closeMenuItem_actionPerformed();\r
 510     else if(source==copy)\r
 511       copy_actionPerformed();\r
 512     else if(source==undoMenuItem)\r
 513       undoMenuItem_actionPerformed();\r
 514     else if(source==redoMenuItem)\r
 515       redoMenuItem_actionPerformed();\r
 516     else if(source==inputText)\r
 517             inputText_actionPerformed();\r
 518     else if(source==closeMenuItem)\r
 519             closeMenuItem_actionPerformed();\r
 520     else if(source==undoMenuItem)\r
 521             undoMenuItem_actionPerformed();\r
 522     else if(source==redoMenuItem)\r
 523             redoMenuItem_actionPerformed();\r
 524     else if(source==copy)\r
 525             copy_actionPerformed();\r
 526     else if(source==pasteNew)\r
 527             pasteNew_actionPerformed();\r
 528     else if(source==pasteThis)\r
 529             pasteThis_actionPerformed();\r
 530     else if(source==cut)\r
 531             cut_actionPerformed();\r
 532     else if(source==delete)\r
 533             delete_actionPerformed();\r
 534     else if(source==deleteGroups)\r
 535             deleteGroups_actionPerformed();\r
 536     else if(source==selectAllSequenceMenuItem)\r
 537             selectAllSequenceMenuItem_actionPerformed();\r
 538     else if(source==deselectAllSequenceMenuItem)\r
 539             deselectAllSequenceMenuItem_actionPerformed();\r
 540     else if(source==invertSequenceMenuItem)\r
 541             invertSequenceMenuItem_actionPerformed();\r
 542     else if(source==invertColSel)\r
 543     { viewport.invertColumnSelection(); alignPanel.repaint(); }\r
 544     else if(source==remove2LeftMenuItem)\r
 545             trimAlignment(true);\r
 546     else if(source==remove2RightMenuItem)\r
 547             trimAlignment(false);\r
 548     else if(source==removeGappedColumnMenuItem)\r
 549             removeGappedColumnMenuItem_actionPerformed();\r
 550     else if(source==removeAllGapsMenuItem)\r
 551             removeAllGapsMenuItem_actionPerformed();\r
 552     else if(source==findMenuItem)\r
 553             findMenuItem_actionPerformed();\r
 554     else if(source==font)\r
 555             new FontChooser(alignPanel);\r
 556     else if (source == newView)\r
 557       newView();\r
 558     else if(source==showColumns)\r
 559     {\r
 560       viewport.showAllHiddenColumns(); alignPanel.repaint();\r
 561     }\r
 562     else if(source==showSeqs)\r
 563     {\r
 564       viewport.showAllHiddenSeqs();\r
 565     }\r
 566     else if(source == hideColumns)\r
 567     {\r
 568       viewport.hideSelectedColumns(); alignPanel.repaint();\r
 569     }\r
 570     else if(source == hideSequences && viewport.getSelectionGroup()!=null)\r
 571     {\r
 572       viewport.hideAllSelectedSeqs();\r
 573     }\r
 574     else if(source==featureSettings)\r
 575             new FeatureSettings(alignPanel);\r
 576     else if(source==overviewMenuItem)\r
 577             overviewMenuItem_actionPerformed();\r
 578     else if(source==noColourmenuItem)\r
 579             changeColour(null);\r
 580     else if(source==clustalColour)\r
 581     {\r
 582       abovePIDThreshold.setState(false);\r
 583       changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
 584                                             viewport.alignment.getWidth()));\r
 585   }\r
 586     else if(source==zappoColour)\r
 587             changeColour(new ZappoColourScheme());\r
 588     else if(source==taylorColour)\r
 589             changeColour(new TaylorColourScheme());\r
 590     else if(source==hydrophobicityColour)\r
 591             changeColour(new HydrophobicColourScheme());\r
 592     else if(source==helixColour)\r
 593             changeColour(new HelixColourScheme());\r
 594     else if(source==strandColour)\r
 595             changeColour(new StrandColourScheme());\r
 596     else if(source==turnColour)\r
 597             changeColour(new TurnColourScheme());\r
 598     else if(source==buriedColour)\r
 599             changeColour(new BuriedColourScheme());\r
 600     else if(source==nucleotideColour)\r
 601             changeColour(new NucleotideColourScheme());\r
 602     else if(source==modifyPID)\r
 603             modifyPID_actionPerformed();\r
 604     else if(source==modifyConservation)\r
 605             modifyConservation_actionPerformed();\r
 606     else if(source==userDefinedColour)\r
 607             new UserDefinedColours(alignPanel, null);\r
 608     else if(source==PIDColour)\r
 609             changeColour(new PIDColourScheme());\r
 610     else if(source==BLOSUM62Colour)\r
 611             changeColour(new Blosum62ColourScheme());\r
 612     else if(source==annotationColour)\r
 613            new AnnotationColourChooser(viewport, alignPanel);\r
 614     else if(source==sortPairwiseMenuItem)\r
 615             sortPairwiseMenuItem_actionPerformed();\r
 616     else if(source==sortIDMenuItem)\r
 617             sortIDMenuItem_actionPerformed();\r
 618     else if(source==sortGroupMenuItem)\r
 619             sortGroupMenuItem_actionPerformed();\r
 620     else if(source==removeRedundancyMenuItem)\r
 621             removeRedundancyMenuItem_actionPerformed();\r
 622     else if(source==pairwiseAlignmentMenuItem)\r
 623             pairwiseAlignmentMenuItem_actionPerformed();\r
 624     else if(source==PCAMenuItem)\r
 625             PCAMenuItem_actionPerformed();\r
 626     else if(source==averageDistanceTreeMenuItem)\r
 627             averageDistanceTreeMenuItem_actionPerformed();\r
 628     else if(source==neighbourTreeMenuItem)\r
 629             neighbourTreeMenuItem_actionPerformed();\r
 630     else if(source==njTreeBlosumMenuItem)\r
 631             njTreeBlosumMenuItem_actionPerformed();\r
 632     else if(source==avDistanceTreeBlosumMenuItem)\r
 633             avTreeBlosumMenuItem_actionPerformed();\r
 634     else if(source==documentation)\r
 635             documentation_actionPerformed();\r
 636     else if(source==about)\r
 637             about_actionPerformed();\r
 638 \r
 639  }\r
 640 \r
 641   public void inputText_actionPerformed()\r
 642   {\r
 643     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
 644     Frame frame = new Frame();\r
 645     frame.add(cap);\r
 646     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
 647   }\r
 648 \r
 649   protected void outputText_actionPerformed(ActionEvent e)\r
 650   {\r
 651     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
 652     Frame frame = new Frame();\r
 653     frame.add(cap);\r
 654     jalview.bin.JalviewLite.addFrame(frame,\r
 655                                      "Alignment output - " + e.getActionCommand(),\r
 656                                      600, 500);\r
 657     cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
 658                                               viewport.getAlignment(),\r
 659                                                       viewport.showJVSuffix));\r
 660   }\r
 661 \r
 662   public void loadAnnotations()\r
 663   {\r
 664     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
 665     cap.setText("Paste your features / annotations file here.");\r
 666     cap.setAnnotationImport();\r
 667     Frame frame = new Frame();\r
 668     frame.add(cap);\r
 669       jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);\r
 670 \r
 671   }\r
 672 \r
 673   public String outputAnnotations(boolean displayTextbox)\r
 674   {\r
 675     String annotation = new AnnotationFile().printAnnotations(\r
 676       viewport.alignment.getAlignmentAnnotation() );\r
 677 \r
 678     if(displayTextbox)\r
 679     {\r
 680 \r
 681       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
 682       Frame frame = new Frame();\r
 683       frame.add(cap);\r
 684       jalview.bin.JalviewLite.addFrame(frame,\r
 685                                        "Annotations",\r
 686                                        600, 500);\r
 687       cap.setText(annotation);\r
 688     }\r
 689 \r
 690     return annotation;\r
 691   }\r
 692 \r
 693   public String outputFeatures(boolean displayTextbox, String format)\r
 694   {\r
 695     String features;\r
 696     if (format.equalsIgnoreCase("Jalview"))\r
 697       features = new FeaturesFile().printJalviewFormat(\r
 698               viewport.alignment.getSequencesArray(),\r
 699               viewport.featuresDisplayed);\r
 700     else\r
 701       features = new FeaturesFile().printGFFFormat(\r
 702              viewport.alignment.getSequencesArray(),\r
 703              viewport.featuresDisplayed);\r
 704 \r
 705 \r
 706     if(displayTextbox)\r
 707     {\r
 708       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
 709       Frame frame = new Frame();\r
 710       frame.add(cap);\r
 711       jalview.bin.JalviewLite.addFrame(frame,\r
 712                                        "Features",\r
 713                                        600, 500);\r
 714 \r
 715       cap.setText(features);\r
 716     }\r
 717 \r
 718     return features;\r
 719   }\r
 720 \r
 721   void launchFullApplication()\r
 722   {\r
 723     StringBuffer url = new StringBuffer(jalviewServletURL);\r
 724 \r
 725     url.append("?open="+\r
 726                appendProtocol( viewport.applet.getParameter("file") ) );\r
 727 \r
 728     if(viewport.applet.getParameter("features")!=null)\r
 729     {\r
 730       url.append( "&features=" );\r
 731       url.append( appendProtocol( viewport.applet.getParameter("features") ) );\r
 732     }\r
 733 \r
 734     if(viewport.applet.getParameter("annotations")!=null)\r
 735     {\r
 736       url.append( "&annotations=" );\r
 737       url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );\r
 738     }\r
 739 \r
 740     if(viewport.applet.getParameter("jnetfile")!=null)\r
 741     {\r
 742       url.append( "&annotations=" );\r
 743       url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) );\r
 744     }\r
 745 \r
 746     if(viewport.applet.getParameter("defaultColour")!=null)\r
 747     {\r
 748       url.append("&colour=" +\r
 749                  removeWhiteSpace(viewport.applet.getParameter("defaultColour"))\r
 750           );\r
 751     }\r
 752 \r
 753     if(viewport.applet.getParameter("userDefinedColour")!=null)\r
 754     {\r
 755       url.append( "&colour=" +\r
 756                  removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )\r
 757          );\r
 758     }\r
 759 \r
 760     showURL(url.toString(), "FULL_APP");\r
 761   }\r
 762 \r
 763 \r
 764   String removeWhiteSpace(String colour)\r
 765   {\r
 766     StringBuffer sb = new StringBuffer();\r
 767     for (int i = 0; i < colour.length(); i++)\r
 768     {\r
 769       if (Character.isWhitespace(colour.charAt(i)))\r
 770         sb.append("%20");\r
 771       else\r
 772         sb.append(colour.charAt(i));\r
 773     }\r
 774 \r
 775     return sb.toString();\r
 776   }\r
 777 \r
 778 \r
 779   String appendProtocol(String url)\r
 780   {\r
 781     try{\r
 782        new URL(url);\r
 783     }catch(java.net.MalformedURLException ex)\r
 784     {\r
 785       url = viewport.applet.getCodeBase()+url;\r
 786     }\r
 787     return url;\r
 788   }\r
 789 \r
 790   public void closeMenuItem_actionPerformed()\r
 791   {\r
 792     PaintRefresher.RemoveComponent(alignPanel);\r
 793     PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);\r
 794     PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);\r
 795 \r
 796     if(PaintRefresher.components.size()==0 && viewport.applet==null)\r
 797       System.exit(0);\r
 798 \r
 799     this.dispose();\r
 800   }\r
 801 \r
 802 \r
 803   /**\r
 804    * DOCUMENT ME!\r
 805    */\r
 806   void updateEditMenuBar()\r
 807   {\r
 808 \r
 809     if (viewport.historyList.size() > 0)\r
 810     {\r
 811       undoMenuItem.setEnabled(true);\r
 812       CommandI command = (CommandI) viewport.historyList.peek();\r
 813       undoMenuItem.setLabel("Undo " + command.getDescription());\r
 814     }\r
 815     else\r
 816     {\r
 817       undoMenuItem.setEnabled(false);\r
 818       undoMenuItem.setLabel("Undo");\r
 819     }\r
 820 \r
 821     if (viewport.redoList.size() > 0)\r
 822     {\r
 823       redoMenuItem.setEnabled(true);\r
 824 \r
 825       CommandI command = (CommandI) viewport.redoList.peek();\r
 826       redoMenuItem.setLabel("Redo " + command.getDescription());\r
 827     }\r
 828     else\r
 829     {\r
 830       redoMenuItem.setEnabled(false);\r
 831       redoMenuItem.setLabel("Redo");\r
 832     }\r
 833   }\r
 834 \r
 835   public void addHistoryItem(CommandI command)\r
 836   {\r
 837     if(command.getSize()>0)\r
 838     {\r
 839       viewport.historyList.push(command);\r
 840       viewport.redoList.removeAllElements();\r
 841       updateEditMenuBar();\r
 842       viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
 843     }\r
 844   }\r
 845 \r
 846   /**\r
 847    * DOCUMENT ME!\r
 848    *\r
 849    * @param e DOCUMENT ME!\r
 850    */\r
 851   protected void undoMenuItem_actionPerformed()\r
 852   {\r
 853     if(viewport.historyList.size()<1)\r
 854       return;\r
 855 \r
 856     CommandI command = (CommandI)viewport.historyList.pop();\r
 857     viewport.redoList.push(command);\r
 858     command.undoCommand();\r
 859 \r
 860     AlignViewport originalSource = getOriginatingSource(command);\r
 861 \r
 862     originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
 863     updateEditMenuBar();\r
 864     originalSource.firePropertyChange("alignment", null,originalSource.alignment.getSequences());\r
 865   }\r
 866 \r
 867   /**\r
 868    * DOCUMENT ME!\r
 869    *\r
 870    * @param e DOCUMENT ME!\r
 871    */\r
 872   protected void redoMenuItem_actionPerformed()\r
 873   {\r
 874     if(viewport.redoList.size()<1)\r
 875       return;\r
 876 \r
 877     CommandI command = (CommandI) viewport.redoList.pop();\r
 878     viewport.historyList.push(command);\r
 879     command.doCommand();\r
 880 \r
 881     AlignViewport originalSource = getOriginatingSource(command);\r
 882     originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;\r
 883 \r
 884     updateEditMenuBar();\r
 885     originalSource.firePropertyChange("alignment", null, originalSource.alignment.getSequences());\r
 886   }\r
 887 \r
 888   AlignViewport getOriginatingSource(CommandI command)\r
 889   {\r
 890     AlignViewport originalSource = null;\r
 891     //For sequence removal and addition, we need to fire\r
 892    //the property change event FROM the viewport where the\r
 893    //original alignment was altered\r
 894    AlignmentI al = null;\r
 895     if (command instanceof EditCommand)\r
 896     {\r
 897       EditCommand editCommand = (EditCommand) command;\r
 898       al = editCommand.getAlignment();\r
 899       Vector comps = (Vector) PaintRefresher.components\r
 900           .get(viewport.getSequenceSetId());\r
 901       for (int i = 0; i < comps.size(); i++)\r
 902       {\r
 903         if (comps.elementAt(i) instanceof AlignmentPanel)\r
 904         {\r
 905           if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)\r
 906           {\r
 907             originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;\r
 908             break;\r
 909           }\r
 910         }\r
 911       }\r
 912     }\r
 913 \r
 914     if (originalSource == null)\r
 915     {\r
 916       //The original view is closed, we must validate\r
 917       //the current view against the closed view first\r
 918       if (al != null)\r
 919         PaintRefresher.validateSequences(al, viewport.alignment);\r
 920 \r
 921       originalSource = viewport;\r
 922     }\r
 923 \r
 924 \r
 925     return originalSource;\r
 926   }\r
 927 \r
 928   public void moveSelectedSequences(boolean up)\r
 929   {\r
 930     SequenceGroup sg = viewport.getSelectionGroup();\r
 931     if (sg == null)\r
 932     {\r
 933       return;\r
 934     }\r
 935 \r
 936     if (up)\r
 937     {\r
 938       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 939       {\r
 940         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 941         if (!sg.getSequences(null).contains(seq))\r
 942         {\r
 943           continue;\r
 944         }\r
 945 \r
 946         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 947         if (sg.getSequences(null).contains(temp))\r
 948         {\r
 949           continue;\r
 950         }\r
 951 \r
 952         viewport.alignment.getSequences().setElementAt(temp, i);\r
 953         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 954       }\r
 955     }\r
 956     else\r
 957     {\r
 958       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 959       {\r
 960         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 961         if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))\r
 962         {\r
 963           continue;\r
 964         }\r
 965 \r
 966         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 967         if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))\r
 968         {\r
 969           continue;\r
 970         }\r
 971 \r
 972         viewport.alignment.getSequences().setElementAt(temp, i);\r
 973         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 974       }\r
 975     }\r
 976 \r
 977     alignPanel.repaint();\r
 978   }\r
 979 \r
 980   static StringBuffer copiedSequences;\r
 981   static Vector copiedHiddenColumns;\r
 982   protected void copy_actionPerformed()\r
 983   {\r
 984     if (viewport.getSelectionGroup() == null)\r
 985     {\r
 986       return;\r
 987     }\r
 988 \r
 989     SequenceGroup sg = viewport.getSelectionGroup();\r
 990     copiedSequences = new StringBuffer();\r
 991     Hashtable orderedSeqs = new Hashtable();\r
 992     for (int i = 0; i < sg.getSize(); i++)\r
 993     {\r
 994       SequenceI seq = sg.getSequenceAt(i);\r
 995       int index = viewport.alignment.findIndex(seq);\r
 996       orderedSeqs.put(index + "", seq);\r
 997     }\r
 998 \r
 999     int index = 0, startRes, endRes;\r
1000     char ch;\r
1001 \r
1002     if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)\r
1003     {\r
1004       copiedHiddenColumns = new Vector();\r
1005       int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
1006       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();\r
1007            i++)\r
1008       {\r
1009         int[] region = (int[])\r
1010             viewport.getColumnSelection().getHiddenColumns().elementAt(i);\r
1011 \r
1012         copiedHiddenColumns.addElement(new int[]\r
1013                                  {region[0] - hiddenOffset,\r
1014                                  region[1] - hiddenOffset});\r
1015       }\r
1016     }\r
1017     else\r
1018       copiedHiddenColumns = null;\r
1019 \r
1020 \r
1021     for (int i = 0; i < sg.getSize(); i++)\r
1022     {\r
1023         SequenceI seq = null;\r
1024 \r
1025         while (seq == null)\r
1026         {\r
1027             if (orderedSeqs.containsKey(index + ""))\r
1028             {\r
1029                 seq = (SequenceI) orderedSeqs.get(index + "");\r
1030                 index++;\r
1031 \r
1032                 break;\r
1033             }\r
1034             else\r
1035             {\r
1036                 index++;\r
1037             }\r
1038         }\r
1039 \r
1040         //FIND START RES\r
1041         //Returns residue following index if gap\r
1042         startRes = seq.findPosition(sg.getStartRes());\r
1043 \r
1044         //FIND END RES\r
1045         //Need to find the residue preceeding index if gap\r
1046         endRes = 0;\r
1047 \r
1048         for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
1049         {\r
1050           ch = seq.getCharAt(j);\r
1051           if (!jalview.util.Comparison.isGap( (ch)))\r
1052           {\r
1053             endRes++;\r
1054           }\r
1055         }\r
1056 \r
1057         if(endRes>0)\r
1058         {\r
1059           endRes += seq.getStart() -1;\r
1060         }\r
1061 \r
1062         copiedSequences.append(seq.getName() + "\t" +\r
1063             startRes + "\t" +\r
1064             endRes + "\t" +\r
1065             seq.getSequenceAsString(sg.getStartRes(),\r
1066                 sg.getEndRes() + 1) + "\n");\r
1067     }\r
1068 \r
1069   }\r
1070 \r
1071   protected void pasteNew_actionPerformed()\r
1072   {\r
1073     paste(true);\r
1074   }\r
1075 \r
1076   protected void pasteThis_actionPerformed()\r
1077   {\r
1078     paste(false);\r
1079   }\r
1080 \r
1081   void paste(boolean newAlignment)\r
1082   {\r
1083     try\r
1084     {\r
1085 \r
1086       if (copiedSequences == null)\r
1087       {\r
1088         return;\r
1089       }\r
1090 \r
1091       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
1092       Vector seqs = new Vector();\r
1093       while (st.hasMoreElements())\r
1094       {\r
1095         String name = st.nextToken();\r
1096         int start = Integer.parseInt(st.nextToken());\r
1097         int end = Integer.parseInt(st.nextToken());\r
1098         seqs.addElement(new Sequence(name, st.nextToken(), start, end));\r
1099       }\r
1100       SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
1101       for (int i = 0; i < seqs.size(); i++)\r
1102       {\r
1103         newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
1104       }\r
1105 \r
1106       if (newAlignment)\r
1107       {\r
1108         String newtitle = new String("Copied sequences");\r
1109         if (getTitle().startsWith("Copied sequences"))\r
1110         {\r
1111           newtitle = getTitle();\r
1112         }\r
1113         else\r
1114         {\r
1115           newtitle = newtitle.concat("- from " + getTitle());\r
1116         }\r
1117         AlignFrame af = new AlignFrame(new Alignment(newSeqs),\r
1118                                        viewport.applet,\r
1119                                        newtitle,\r
1120                                        false);\r
1121         if (copiedHiddenColumns != null)\r
1122         {\r
1123           for (int i = 0; i < copiedHiddenColumns.size(); i++)\r
1124           {\r
1125             int[] region = (int[]) copiedHiddenColumns.elementAt(i);\r
1126             af.viewport.hideColumns(region[0], region[1]);\r
1127           }\r
1128         }\r
1129 \r
1130 \r
1131         jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,\r
1132                                          DEFAULT_HEIGHT);\r
1133       }\r
1134       else\r
1135       {\r
1136         addSequences(newSeqs);\r
1137       }\r
1138 \r
1139     }\r
1140     catch (Exception ex)\r
1141     {} // could be anything being pasted in here\r
1142 \r
1143   }\r
1144 \r
1145   void addSequences(SequenceI[] seqs)\r
1146   {\r
1147     for (int i = 0; i < seqs.length; i++)\r
1148     {\r
1149       viewport.alignment.addSequence(seqs[i]);\r
1150     }\r
1151 \r
1152     //!newAlignment\r
1153     addHistoryItem(new EditCommand(\r
1154         "Add sequences",\r
1155         EditCommand.PASTE,\r
1156         seqs,\r
1157         0,\r
1158         viewport.alignment.getWidth(),\r
1159         viewport.alignment)\r
1160         );\r
1161 \r
1162     viewport.setEndSeq(viewport.alignment.getHeight());\r
1163     viewport.alignment.getWidth();\r
1164     viewport.firePropertyChange("alignment", null,\r
1165                                 viewport.alignment.getSequences());\r
1166 \r
1167   }\r
1168 \r
1169   protected void cut_actionPerformed()\r
1170   {\r
1171     copy_actionPerformed();\r
1172     delete_actionPerformed();\r
1173   }\r
1174 \r
1175   protected void delete_actionPerformed()\r
1176   {\r
1177 \r
1178     SequenceGroup sg = viewport.getSelectionGroup();\r
1179     if (sg == null)\r
1180     {\r
1181       return;\r
1182     }\r
1183 \r
1184     Vector seqs = new Vector();\r
1185     SequenceI seq;\r
1186     for (int i = 0; i < sg.getSize(); i++)\r
1187     {\r
1188       seq = sg.getSequenceAt(i);\r
1189       seqs.addElement(seq);\r
1190     }\r
1191 \r
1192 \r
1193    // If the cut affects all sequences, remove highlighted columns\r
1194    if (sg.getSize() == viewport.alignment.getHeight())\r
1195    {\r
1196      viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
1197          sg.getEndRes() + 1);\r
1198    }\r
1199 \r
1200 \r
1201     SequenceI [] cut = new SequenceI[seqs.size()];\r
1202     for(int i=0; i<seqs.size(); i++)\r
1203       cut[i] = (SequenceI)seqs.elementAt(i);\r
1204 \r
1205 \r
1206     /*\r
1207     //ADD HISTORY ITEM\r
1208     */\r
1209     addHistoryItem(new EditCommand("Cut Sequences",\r
1210                                       EditCommand.CUT,\r
1211                                       cut,\r
1212                                       sg.getStartRes(),\r
1213                                       sg.getEndRes()-sg.getStartRes()+1,\r
1214                                       viewport.alignment));\r
1215 \r
1216 \r
1217     viewport.setSelectionGroup(null);\r
1218     viewport.alignment.deleteGroup(sg);\r
1219 \r
1220     viewport.firePropertyChange("alignment", null,\r
1221                                   viewport.getAlignment().getSequences());\r
1222 \r
1223     if (viewport.getAlignment().getHeight() < 1)\r
1224     {\r
1225         this.setVisible(false);\r
1226     }\r
1227   }\r
1228 \r
1229   protected void deleteGroups_actionPerformed()\r
1230   {\r
1231     viewport.alignment.deleteAllGroups();\r
1232     viewport.sequenceColours=null;\r
1233     viewport.setSelectionGroup(null);\r
1234 \r
1235     alignPanel.repaint();\r
1236   }\r
1237 \r
1238   public void selectAllSequenceMenuItem_actionPerformed()\r
1239   {\r
1240     SequenceGroup sg = new SequenceGroup();\r
1241     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
1242     {\r
1243       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
1244     }\r
1245     sg.setEndRes(viewport.alignment.getWidth()-1);\r
1246     viewport.setSelectionGroup(sg);\r
1247     alignPanel.repaint();\r
1248     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
1249   }\r
1250 \r
1251   public void deselectAllSequenceMenuItem_actionPerformed()\r
1252   {\r
1253     if(viewport.cursorMode)\r
1254     {\r
1255       alignPanel.seqPanel.keyboardNo1=null;\r
1256       alignPanel.seqPanel.keyboardNo2=null;\r
1257     }\r
1258     viewport.setSelectionGroup(null);\r
1259     viewport.getColumnSelection().clear();\r
1260     viewport.setSelectionGroup(null);\r
1261     alignPanel.idPanel.idCanvas.searchResults = null;\r
1262     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
1263     alignPanel.repaint();\r
1264     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
1265   }\r
1266 \r
1267   public void invertSequenceMenuItem_actionPerformed()\r
1268   {\r
1269     SequenceGroup sg = viewport.getSelectionGroup();\r
1270     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
1271     {\r
1272       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
1273     }\r
1274 \r
1275     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
1276   }\r
1277 \r
1278   void trimAlignment(boolean trimLeft)\r
1279   {\r
1280     ColumnSelection colSel = viewport.getColumnSelection();\r
1281     int column;\r
1282 \r
1283     if (colSel.size() > 0)\r
1284     {\r
1285       if(trimLeft)\r
1286         column = colSel.getMin();\r
1287       else\r
1288         column = colSel.getMax();\r
1289 \r
1290       SequenceI [] seqs;\r
1291       if(viewport.getSelectionGroup()!=null)\r
1292         seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
1293       else\r
1294         seqs = viewport.alignment.getSequencesArray();\r
1295 \r
1296 \r
1297       TrimRegionCommand trimRegion;\r
1298       if(trimLeft)\r
1299       {\r
1300         trimRegion = new TrimRegionCommand("Remove Left",\r
1301                                     TrimRegionCommand.TRIM_LEFT,\r
1302                                     seqs,\r
1303                                     column,\r
1304                                     viewport.alignment,\r
1305                                     viewport.colSel,\r
1306                                     viewport.selectionGroup);\r
1307         viewport.setStartRes(0);\r
1308       }\r
1309      else\r
1310      {\r
1311        trimRegion = new TrimRegionCommand("Remove Right",\r
1312                                    TrimRegionCommand.TRIM_RIGHT,\r
1313                                    seqs,\r
1314                                    column,\r
1315                                    viewport.alignment,\r
1316                                    viewport.colSel,\r
1317                                    viewport.selectionGroup);\r
1318      }\r
1319 \r
1320      statusBar.setText("Removed "+trimRegion.getSize()+" columns.");\r
1321 \r
1322 \r
1323       addHistoryItem(trimRegion);\r
1324 \r
1325       Vector groups = viewport.alignment.getGroups();\r
1326 \r
1327       for (int i = 0; i < groups.size(); i++)\r
1328       {\r
1329         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1330 \r
1331         if ( (trimLeft && !sg.adjustForRemoveLeft(column))\r
1332             || (!trimLeft && !sg.adjustForRemoveRight(column)))\r
1333         {\r
1334           viewport.alignment.deleteGroup(sg);\r
1335         }\r
1336       }\r
1337 \r
1338       viewport.firePropertyChange("alignment", null,\r
1339                                   viewport.getAlignment().getSequences());\r
1340     }\r
1341   }\r
1342 \r
1343 \r
1344   public void removeGappedColumnMenuItem_actionPerformed()\r
1345   {\r
1346     int start = 0, end = viewport.alignment.getWidth()-1;\r
1347 \r
1348     SequenceI[] seqs;\r
1349     if (viewport.getSelectionGroup() != null)\r
1350     {\r
1351       seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
1352       start = viewport.getSelectionGroup().getStartRes();\r
1353       end = viewport.getSelectionGroup().getEndRes();\r
1354     }\r
1355     else\r
1356       seqs = viewport.alignment.getSequencesArray();\r
1357 \r
1358 \r
1359     RemoveGapColCommand removeGapCols =\r
1360         new RemoveGapColCommand("Remove Gapped Columns",\r
1361                                 seqs,\r
1362                                 start, end,\r
1363                                 viewport.getGapCharacter());\r
1364 \r
1365     addHistoryItem(removeGapCols);\r
1366 \r
1367     statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");\r
1368 \r
1369     //This is to maintain viewport position on first residue\r
1370     //of first sequence\r
1371     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
1372     int startRes = seq.findPosition(viewport.startRes);\r
1373    // ShiftList shifts;\r
1374    // viewport.getAlignment().removeGaps(shifts=new ShiftList());\r
1375    // edit.alColumnChanges=shifts.getInverse();\r
1376    // if (viewport.hasHiddenColumns)\r
1377    //   viewport.getColumnSelection().compensateForEdits(shifts);\r
1378    viewport.setStartRes(seq.findIndex(startRes)-1);\r
1379    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1380 \r
1381   }\r
1382 \r
1383   public void removeAllGapsMenuItem_actionPerformed()\r
1384   {\r
1385     int start = 0, end = viewport.alignment.getWidth()-1;\r
1386 \r
1387     SequenceI[] seqs;\r
1388     if (viewport.getSelectionGroup() != null)\r
1389     {\r
1390       seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
1391       start = viewport.getSelectionGroup().getStartRes();\r
1392       end = viewport.getSelectionGroup().getEndRes();\r
1393     }\r
1394     else\r
1395       seqs = viewport.alignment.getSequencesArray();\r
1396 \r
1397     //This is to maintain viewport position on first residue\r
1398     //of first sequence\r
1399     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
1400     int startRes = seq.findPosition(viewport.startRes);\r
1401 \r
1402     addHistoryItem(new RemoveGapsCommand("Remove Gaps",\r
1403                                            seqs,\r
1404                                            start, end,\r
1405                      viewport.getGapCharacter()));\r
1406 \r
1407     viewport.setStartRes(seq.findIndex(startRes)-1);\r
1408 \r
1409     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1410 \r
1411   }\r
1412 \r
1413   public void findMenuItem_actionPerformed()\r
1414   {\r
1415     new Finder(alignPanel);\r
1416   }\r
1417 \r
1418   public void newView()\r
1419   {\r
1420     AlignmentI newal;\r
1421     if (viewport.hasHiddenRows)\r
1422       newal = new Alignment(viewport.getAlignment().\r
1423                             getHiddenSequences()\r
1424                             .getFullAlignment().\r
1425                             getSequencesArray());\r
1426     else\r
1427       newal = new Alignment(viewport.alignment.getSequencesArray());\r
1428 \r
1429     AlignFrame newaf = new AlignFrame(newal,\r
1430                                       viewport.applet,\r
1431                                       "",\r
1432                                       false);\r
1433 \r
1434     newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();\r
1435     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());\r
1436     PaintRefresher.Register(newaf.alignPanel,\r
1437                             newaf.alignPanel.av.getSequenceSetId());\r
1438 \r
1439     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,\r
1440                             newaf.alignPanel.av.getSequenceSetId());\r
1441     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,\r
1442                             newaf.alignPanel.av.getSequenceSetId());\r
1443 \r
1444     Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());\r
1445     int viewSize = -1;\r
1446     for (int i = 0; i < comps.size(); i++)\r
1447     {\r
1448       if (comps.elementAt(i) instanceof AlignmentPanel)\r
1449         viewSize++;\r
1450     }\r
1451 \r
1452     String title = new String(this.getTitle());\r
1453     if (title.indexOf("(View") > -1)\r
1454       title = title.substring(0, title.indexOf("(View"));\r
1455 \r
1456     title+= "(View "+viewSize+")";\r
1457 \r
1458     newaf.setTitle(title.toString());\r
1459 \r
1460 \r
1461     newaf.viewport.historyList = viewport.historyList;\r
1462     newaf.viewport.redoList = viewport.redoList;\r
1463 \r
1464    }\r
1465 \r
1466 \r
1467   public void seqLimits_itemStateChanged()\r
1468   {\r
1469     viewport.setShowJVSuffix(seqLimits.getState());\r
1470     alignPanel.fontChanged();\r
1471     alignPanel.repaint();\r
1472   }\r
1473 \r
1474 \r
1475   protected void colourTextMenuItem_actionPerformed()\r
1476   {\r
1477     viewport.setColourText(colourTextMenuItem.getState());\r
1478     alignPanel.repaint();\r
1479   }\r
1480 \r
1481   protected void wrapMenuItem_actionPerformed()\r
1482   {\r
1483     viewport.setWrapAlignment(wrapMenuItem.getState());\r
1484     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
1485     scaleAbove.setEnabled(wrapMenuItem.getState());\r
1486     scaleLeft.setEnabled(wrapMenuItem.getState());\r
1487     scaleRight.setEnabled(wrapMenuItem.getState());\r
1488     alignPanel.repaint();\r
1489   }\r
1490 \r
1491 \r
1492   public void overviewMenuItem_actionPerformed()\r
1493   {\r
1494     if (alignPanel.overviewPanel != null)\r
1495     {\r
1496       return;\r
1497     }\r
1498 \r
1499     Frame frame = new Frame();\r
1500     OverviewPanel overview = new OverviewPanel(alignPanel);\r
1501     frame.add(overview);\r
1502     // +50 must allow for applet frame window\r
1503     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
1504                                      overview.preferredSize().width,\r
1505                                      overview.preferredSize().height + 50);\r
1506 \r
1507     frame.pack();\r
1508     frame.addWindowListener(new WindowAdapter()\r
1509     {\r
1510       public void windowClosing(WindowEvent e)\r
1511       {\r
1512         alignPanel.setOverviewPanel(null);\r
1513       };\r
1514     });\r
1515 \r
1516     alignPanel.setOverviewPanel(overview);\r
1517 \r
1518   }\r
1519 \r
1520 \r
1521   void changeColour(ColourSchemeI cs)\r
1522   {\r
1523     int threshold = 0;\r
1524 \r
1525     if(cs!=null)\r
1526     {\r
1527       if (viewport.getAbovePIDThreshold())\r
1528       {\r
1529         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
1530 \r
1531         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1532 \r
1533         viewport.setGlobalColourScheme(cs);\r
1534       }\r
1535       else\r
1536       {\r
1537         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1538       }\r
1539 \r
1540       if (viewport.getConservationSelected())\r
1541       {\r
1542 \r
1543         Alignment al = (Alignment) viewport.alignment;\r
1544         Conservation c = new Conservation("All",\r
1545                                           ResidueProperties.propHash, 3,\r
1546                                           al.getSequences(), 0,\r
1547                                           al.getWidth() - 1);\r
1548 \r
1549         c.calculate();\r
1550         c.verdict(false, viewport.ConsPercGaps);\r
1551 \r
1552         cs.setConservation(c);\r
1553 \r
1554         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
1555             "Background"));\r
1556 \r
1557       }\r
1558       else\r
1559       {\r
1560         cs.setConservation(null);\r
1561       }\r
1562 \r
1563       cs.setConsensus(viewport.hconsensus);\r
1564 \r
1565     }\r
1566     viewport.setGlobalColourScheme(cs);\r
1567 \r
1568     if (viewport.getColourAppliesToAllGroups())\r
1569     {\r
1570       Vector groups = viewport.alignment.getGroups();\r
1571       for (int i = 0; i < groups.size(); i++)\r
1572       {\r
1573         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1574 \r
1575         if(cs==null)\r
1576         {\r
1577           sg.cs = null;\r
1578           continue;\r
1579         }\r
1580         if (cs instanceof ClustalxColourScheme)\r
1581         {\r
1582           sg.cs = new ClustalxColourScheme(\r
1583               sg.getSequences(viewport.hiddenRepSequences),\r
1584               sg.getWidth());\r
1585         }\r
1586         else\r
1587         {\r
1588           try\r
1589           {\r
1590             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
1591           }\r
1592           catch (Exception ex)\r
1593           {\r
1594             ex.printStackTrace();\r
1595             sg.cs = cs;\r
1596           }\r
1597         }\r
1598 \r
1599         if (viewport.getAbovePIDThreshold()\r
1600             || cs instanceof PIDColourScheme\r
1601             || cs instanceof Blosum62ColourScheme)\r
1602         {\r
1603           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1604           sg.cs.setConsensus(AAFrequency.calculate(\r
1605               sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth()));\r
1606         }\r
1607         else\r
1608           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1609 \r
1610         if (viewport.getConservationSelected())\r
1611         {\r
1612           Conservation c = new Conservation("Group",\r
1613                                             ResidueProperties.propHash, 3,\r
1614                                             sg.getSequences(viewport.hiddenRepSequences), 0,\r
1615                                             viewport.alignment.getWidth() - 1);\r
1616           c.calculate();\r
1617           c.verdict(false, viewport.ConsPercGaps);\r
1618           sg.cs.setConservation(c);\r
1619         }\r
1620         else\r
1621         {\r
1622           sg.cs.setConservation(null);\r
1623           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1624         }\r
1625 \r
1626       }\r
1627     }\r
1628 \r
1629 \r
1630     if (alignPanel.getOverviewPanel() != null)\r
1631     {\r
1632       alignPanel.getOverviewPanel().updateOverviewImage();\r
1633     }\r
1634 \r
1635     alignPanel.repaint();\r
1636   }\r
1637 \r
1638 \r
1639 \r
1640   protected void modifyPID_actionPerformed()\r
1641   {\r
1642     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
1643     {\r
1644       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
1645                                      "Background");\r
1646       SliderPanel.showPIDSlider();\r
1647     }\r
1648   }\r
1649 \r
1650   protected void modifyConservation_actionPerformed()\r
1651   {\r
1652     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
1653     {\r
1654       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
1655                                         "Background");\r
1656       SliderPanel.showConservationSlider();\r
1657     }\r
1658   }\r
1659 \r
1660   protected void conservationMenuItem_actionPerformed()\r
1661   {\r
1662     viewport.setConservationSelected(conservationMenuItem.getState());\r
1663 \r
1664     viewport.setAbovePIDThreshold(false);\r
1665     abovePIDThreshold.setState(false);\r
1666 \r
1667     changeColour(viewport.getGlobalColourScheme());\r
1668 \r
1669     modifyConservation_actionPerformed();\r
1670   }\r
1671 \r
1672   public void abovePIDThreshold_actionPerformed()\r
1673   {\r
1674     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
1675 \r
1676     conservationMenuItem.setState(false);\r
1677     viewport.setConservationSelected(false);\r
1678 \r
1679     changeColour(viewport.getGlobalColourScheme());\r
1680 \r
1681     modifyPID_actionPerformed();\r
1682   }\r
1683 \r
1684 \r
1685 \r
1686   public void sortPairwiseMenuItem_actionPerformed()\r
1687   {\r
1688     SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();\r
1689     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1690                               viewport.getAlignment().getSequenceAt(0));\r
1691     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));\r
1692     alignPanel.repaint();\r
1693   }\r
1694 \r
1695   public void sortIDMenuItem_actionPerformed()\r
1696   {\r
1697   //  addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1698    //                                HistoryItem.SORT));\r
1699     AlignmentSorter.sortByID(viewport.getAlignment());\r
1700     alignPanel.repaint();\r
1701   }\r
1702 \r
1703   public void sortGroupMenuItem_actionPerformed()\r
1704   {\r
1705   //  addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1706   //                                 HistoryItem.SORT));\r
1707     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1708     alignPanel.repaint();\r
1709 \r
1710   }\r
1711 \r
1712   public void removeRedundancyMenuItem_actionPerformed()\r
1713   {\r
1714      new RedundancyPanel(alignPanel);\r
1715   }\r
1716 \r
1717   public void pairwiseAlignmentMenuItem_actionPerformed()\r
1718   {\r
1719     if (viewport.getSelectionGroup()!=null\r
1720         && viewport.getSelectionGroup().getSize() > 1)\r
1721     {\r
1722       Frame frame = new Frame();\r
1723       frame.add(new PairwiseAlignPanel(alignPanel));\r
1724       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1725     }\r
1726   }\r
1727 \r
1728   public void PCAMenuItem_actionPerformed()\r
1729   {\r
1730     //are the sequences aligned?\r
1731     if (!viewport.alignment.isAligned())\r
1732     {\r
1733       SequenceI current;\r
1734       int Width = viewport.getAlignment().getWidth();\r
1735 \r
1736       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1737            i++)\r
1738       {\r
1739         current = viewport.getAlignment().getSequenceAt(i);\r
1740 \r
1741         if (current.getLength() < Width)\r
1742         {\r
1743           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1744         }\r
1745       }\r
1746       alignPanel.repaint();\r
1747     }\r
1748 \r
1749     if ( (viewport.getSelectionGroup() != null &&\r
1750           viewport.getSelectionGroup().getSize() < 4 &&\r
1751           viewport.getSelectionGroup().getSize() > 0)\r
1752         || viewport.getAlignment().getHeight() < 4)\r
1753     {\r
1754       return;\r
1755     }\r
1756 \r
1757     try\r
1758     {\r
1759       new PCAPanel(viewport);\r
1760     }\r
1761     catch (java.lang.OutOfMemoryError ex)\r
1762     {\r
1763     }\r
1764 \r
1765   }\r
1766 \r
1767   public void averageDistanceTreeMenuItem_actionPerformed()\r
1768   {\r
1769     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1770   }\r
1771 \r
1772   public void neighbourTreeMenuItem_actionPerformed()\r
1773   {\r
1774     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1775   }\r
1776 \r
1777   protected void njTreeBlosumMenuItem_actionPerformed()\r
1778   {\r
1779     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1780   }\r
1781 \r
1782   protected void avTreeBlosumMenuItem_actionPerformed()\r
1783   {\r
1784     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
1785   }\r
1786 \r
1787   void NewTreePanel(String type, String pwType, String title)\r
1788   {\r
1789     //are the sequences aligned?\r
1790     if (!viewport.alignment.isAligned())\r
1791     {\r
1792       SequenceI current;\r
1793       int Width = viewport.getAlignment().getWidth();\r
1794 \r
1795       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1796            i++)\r
1797       {\r
1798         current = viewport.getAlignment().getSequenceAt(i);\r
1799 \r
1800         if (current.getLength() < Width)\r
1801         {\r
1802           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1803         }\r
1804       }\r
1805       alignPanel.repaint();\r
1806 \r
1807     }\r
1808 \r
1809     if ( (viewport.getSelectionGroup() != null &&\r
1810           viewport.getSelectionGroup().getSize() > 1)\r
1811       || (viewport.getSelectionGroup() == null\r
1812           && viewport.alignment.getHeight() > 1))\r
1813     {\r
1814       final TreePanel tp = new TreePanel(viewport,\r
1815                                          type,\r
1816                                          pwType);\r
1817 \r
1818       addTreeMenuItem(tp, title);\r
1819 \r
1820       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1821     }\r
1822   }\r
1823 \r
1824   void loadTree_actionPerformed()\r
1825   {\r
1826       CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
1827       cap.setText("Paste your Newick tree file here.");\r
1828       cap.setTreeImport();\r
1829       Frame frame = new Frame();\r
1830       frame.add(cap);\r
1831       jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);\r
1832   }\r
1833 \r
1834   public void loadTree(jalview.io.NewickFile tree, String treeFile)\r
1835   {\r
1836     TreePanel tp = new TreePanel(viewport,\r
1837                                  treeFile,\r
1838                                  "From File - ",\r
1839                                  tree);\r
1840     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
1841     addTreeMenuItem(tp, treeFile);\r
1842   }\r
1843 \r
1844   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1845   {\r
1846     final MenuItem item = new MenuItem(title);\r
1847     sortByTreeMenu.add(item);\r
1848     item.addActionListener(new java.awt.event.ActionListener()\r
1849     {\r
1850       public void actionPerformed(ActionEvent evt)\r
1851       {\r
1852       //  addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1853       //                                 HistoryItem.SORT));\r
1854         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1855         alignPanel.repaint();\r
1856       }\r
1857     });\r
1858 \r
1859     treePanel.addWindowListener(new WindowAdapter()\r
1860     {\r
1861       public void windowClosing(WindowEvent e)\r
1862       {\r
1863         sortByTreeMenu.remove(item);\r
1864       };\r
1865     });\r
1866   }\r
1867 \r
1868   protected void documentation_actionPerformed()\r
1869   {\r
1870     showURL("http://www.jalview.org/help.html", "HELP");\r
1871   }\r
1872 \r
1873   protected void about_actionPerformed()\r
1874   {\r
1875 \r
1876     class AboutPanel extends Canvas\r
1877     {\r
1878       String version;\r
1879       public AboutPanel(String version)\r
1880       { this.version = version; }\r
1881 \r
1882       public void paint(Graphics g)\r
1883       {\r
1884         g.setColor(Color.white);\r
1885         g.fillRect(0, 0, getSize().width, getSize().height);\r
1886         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1887         FontMetrics fm = g.getFontMetrics();\r
1888         int fh = fm.getHeight();\r
1889         int y = 5, x = 7;\r
1890         g.setColor(Color.black);\r
1891         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1892         g.drawString("Jalview - Release "+version, 200, y += fh);\r
1893         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1894         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1895                      x, y += fh * 2);\r
1896         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1897                      x, y += fh);\r
1898         g.drawString(\r
1899             "For any issues relating to Jalview, email help@jalview.org", x,\r
1900             y += fh);\r
1901         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1902         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1903                      x, y += fh);\r
1904         g.drawString("Bioinformatics,  2004 20;426-7.", x, y += fh);\r
1905       }\r
1906     }\r
1907 \r
1908     String version = "test";\r
1909     java.net.URL url = getClass().getResource("/.build_properties");\r
1910     if (url != null)\r
1911     {\r
1912       try\r
1913       {\r
1914         BufferedReader reader = new BufferedReader(new InputStreamReader(\r
1915             url.openStream()));\r
1916         String line;\r
1917         while ( (line = reader.readLine()) != null)\r
1918         {\r
1919           if (line.indexOf("VERSION") > -1)\r
1920           {\r
1921             version = line.substring(line.indexOf("=") + 1);\r
1922           }\r
1923         }\r
1924       }\r
1925       catch (Exception ex)\r
1926       {\r
1927         ex.printStackTrace();\r
1928       }\r
1929     }\r
1930 \r
1931 \r
1932     Frame frame = new Frame();\r
1933     frame.add(new AboutPanel(version));\r
1934     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1935 \r
1936   }\r
1937 \r
1938   public void showURL(String url, String target)\r
1939   {\r
1940     if (viewport.applet == null)\r
1941     {\r
1942       System.out.println("Not running as applet - no browser available.");\r
1943     }\r
1944     else\r
1945     {\r
1946       try\r
1947       {\r
1948         System.out.println("Show url: "+url);\r
1949         viewport.applet.getAppletContext().showDocument(new java.net.URL(url),\r
1950                                                target);\r
1951       }\r
1952       catch (Exception ex)\r
1953       {\r
1954         ex.printStackTrace();\r
1955       }\r
1956     }\r
1957   }\r
1958 \r
1959 \r
1960   //////////////////////////////////////////////////////////////////////////////////\r
1961   //JBuilder Graphics here\r
1962 \r
1963     protected MenuBar alignFrameMenuBar = new MenuBar();\r
1964     protected Menu fileMenu = new Menu("File");\r
1965     protected MenuItem loadApplication = new MenuItem("View in Full Application");\r
1966     protected MenuItem loadTree = new MenuItem("Load Associated Tree ...");\r
1967     protected MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");\r
1968     protected MenuItem outputFeatures = new MenuItem("Export Features ...");\r
1969     protected MenuItem outputAnnotations = new MenuItem("Export Annotations ...");\r
1970 \r
1971     protected MenuItem closeMenuItem = new MenuItem("Close");\r
1972     protected Menu editMenu = new Menu("Edit");\r
1973     protected Menu viewMenu = new Menu("View");\r
1974     protected Menu colourMenu = new Menu("Colour");\r
1975     protected Menu calculateMenu = new Menu("Calculate");\r
1976     protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
1977     protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
1978     protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
1979     protected MenuItem remove2LeftMenuItem = new MenuItem();\r
1980     protected MenuItem remove2RightMenuItem = new MenuItem();\r
1981     protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
1982     protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
1983     protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
1984     protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
1985     protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
1986     protected MenuItem sortIDMenuItem = new MenuItem();\r
1987     protected MenuItem sortGroupMenuItem = new MenuItem();\r
1988     protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
1989     protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
1990     protected MenuItem PCAMenuItem = new MenuItem();\r
1991     protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
1992     protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
1993     BorderLayout borderLayout1 = new BorderLayout();\r
1994     public Label statusBar = new Label();\r
1995     protected Menu outputTextboxMenu = new Menu();\r
1996     protected MenuItem clustalColour = new MenuItem();\r
1997     protected MenuItem zappoColour = new MenuItem();\r
1998     protected MenuItem taylorColour = new MenuItem();\r
1999     protected MenuItem hydrophobicityColour = new MenuItem();\r
2000     protected MenuItem helixColour = new MenuItem();\r
2001     protected MenuItem strandColour = new MenuItem();\r
2002     protected MenuItem turnColour = new MenuItem();\r
2003     protected MenuItem buriedColour = new MenuItem();\r
2004     protected MenuItem userDefinedColour = new MenuItem();\r
2005     protected MenuItem PIDColour = new MenuItem();\r
2006     protected MenuItem BLOSUM62Colour = new MenuItem();\r
2007     MenuItem njTreeBlosumMenuItem = new MenuItem();\r
2008     MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
2009     protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
2010     protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
2011     MenuItem overviewMenuItem = new MenuItem();\r
2012     protected MenuItem undoMenuItem = new MenuItem();\r
2013     protected MenuItem redoMenuItem = new MenuItem();\r
2014     protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
2015     MenuItem noColourmenuItem = new MenuItem();\r
2016     protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
2017     protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
2018     MenuItem findMenuItem = new MenuItem();\r
2019   protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
2020     protected MenuItem nucleotideColour = new MenuItem();\r
2021     MenuItem deleteGroups = new MenuItem();\r
2022     MenuItem delete = new MenuItem();\r
2023     MenuItem copy = new MenuItem();\r
2024     MenuItem cut = new MenuItem();\r
2025     Menu pasteMenu = new Menu();\r
2026     MenuItem pasteNew = new MenuItem();\r
2027     MenuItem pasteThis = new MenuItem();\r
2028     protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
2029     protected MenuItem font = new MenuItem();\r
2030     protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
2031     protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
2032     protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
2033     MenuItem modifyPID = new MenuItem();\r
2034     MenuItem modifyConservation = new MenuItem();\r
2035     protected CheckboxMenuItem autoCalculate\r
2036         = new CheckboxMenuItem("Autocalculate Consensus", true);\r
2037     protected Menu sortByTreeMenu = new Menu();\r
2038     Menu sort = new Menu();\r
2039     Menu calculate = new Menu();\r
2040     MenuItem inputText = new MenuItem();\r
2041     Menu helpMenu = new Menu();\r
2042     MenuItem documentation = new MenuItem();\r
2043     MenuItem about = new MenuItem();\r
2044     protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
2045   Panel embeddedMenu;\r
2046   Label embeddedEdit;\r
2047   Label embeddedSelect;\r
2048   Label embeddedView;\r
2049   Label embeddedFormat;\r
2050   Label embeddedColour;\r
2051   Label embeddedFile;\r
2052   Label embeddedHelp;\r
2053   Label embeddedCalculate;\r
2054   FlowLayout flowLayout1;\r
2055 \r
2056   private void jbInit() throws Exception {\r
2057 \r
2058       setMenuBar(alignFrameMenuBar);\r
2059 \r
2060       MenuItem item;\r
2061 \r
2062       // dynamically fill save as menu with available formats\r
2063       for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
2064       {\r
2065 \r
2066         item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);\r
2067 \r
2068         item.addActionListener(new java.awt.event.ActionListener()\r
2069         {\r
2070           public void actionPerformed(ActionEvent e)\r
2071           {\r
2072             outputText_actionPerformed(e);\r
2073           }\r
2074         });\r
2075 \r
2076         outputTextboxMenu.add(item);\r
2077       }\r
2078         closeMenuItem.addActionListener(this);\r
2079         loadApplication.addActionListener(this);\r
2080 \r
2081         loadTree.addActionListener(this);\r
2082         loadAnnotations.addActionListener(this);\r
2083         outputFeatures.addActionListener(this);\r
2084         outputAnnotations.addActionListener(this);\r
2085         selectAllSequenceMenuItem.addActionListener(this);\r
2086         deselectAllSequenceMenuItem.addActionListener(this);\r
2087         invertSequenceMenuItem.addActionListener(this);\r
2088         remove2LeftMenuItem.setLabel("Remove Left");\r
2089         remove2LeftMenuItem.addActionListener(this);\r
2090         remove2RightMenuItem.setLabel("Remove Right");\r
2091         remove2RightMenuItem.addActionListener(this);\r
2092         removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
2093         removeGappedColumnMenuItem.addActionListener(this);\r
2094         removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
2095         removeAllGapsMenuItem.addActionListener(this);\r
2096         viewBoxesMenuItem.setLabel("Boxes");\r
2097         viewBoxesMenuItem.setState(true);\r
2098         viewBoxesMenuItem.addItemListener(this);\r
2099         viewTextMenuItem.setLabel("Text");\r
2100         viewTextMenuItem.setState(true);\r
2101         viewTextMenuItem.addItemListener(this);\r
2102         sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
2103         sortPairwiseMenuItem.addActionListener(this);\r
2104         sortIDMenuItem.setLabel("by ID");\r
2105         sortIDMenuItem.addActionListener(this);\r
2106         sortGroupMenuItem.setLabel("by Group");\r
2107         sortGroupMenuItem.addActionListener(this);\r
2108         removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
2109         removeRedundancyMenuItem.addActionListener(this);\r
2110         pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
2111         pairwiseAlignmentMenuItem.addActionListener(this);\r
2112         PCAMenuItem.setLabel("Principal Component Analysis");\r
2113         PCAMenuItem.addActionListener(this);\r
2114         averageDistanceTreeMenuItem.setLabel(\r
2115             "Average Distance Using % Identity");\r
2116         averageDistanceTreeMenuItem.addActionListener(this);\r
2117         neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
2118         neighbourTreeMenuItem.addActionListener(this);\r
2119         statusBar.setBackground(Color.white);\r
2120         statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
2121         statusBar.setText("Status bar");\r
2122         outputTextboxMenu.setLabel("Output to Textbox");\r
2123         clustalColour.setLabel("Clustalx");\r
2124 \r
2125         clustalColour.addActionListener(this);\r
2126         zappoColour.setLabel("Zappo");\r
2127         zappoColour.addActionListener(this);\r
2128         taylorColour.setLabel("Taylor");\r
2129         taylorColour.addActionListener(this);\r
2130         hydrophobicityColour.setLabel("Hydrophobicity");\r
2131         hydrophobicityColour.addActionListener(this);\r
2132         helixColour.setLabel("Helix Propensity");\r
2133         helixColour.addActionListener(this);\r
2134         strandColour.setLabel("Strand Propensity");\r
2135         strandColour.addActionListener(this);\r
2136         turnColour.setLabel("Turn Propensity");\r
2137         turnColour.addActionListener(this);\r
2138         buriedColour.setLabel("Buried Index");\r
2139         buriedColour.addActionListener(this);\r
2140         userDefinedColour.setLabel("User Defined...");\r
2141         userDefinedColour.addActionListener(this);\r
2142         PIDColour.setLabel("Percentage Identity");\r
2143         PIDColour.addActionListener(this);\r
2144         BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
2145         BLOSUM62Colour.addActionListener(this);\r
2146         avDistanceTreeBlosumMenuItem.setLabel(\r
2147             "Average Distance Using BLOSUM62");\r
2148         avDistanceTreeBlosumMenuItem.addActionListener(this);\r
2149         njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
2150         njTreeBlosumMenuItem.addActionListener(this);\r
2151         annotationPanelMenuItem.setLabel("Show Annotations");\r
2152         annotationPanelMenuItem.addItemListener(this);\r
2153         colourTextMenuItem.setLabel("Colour Text");\r
2154         colourTextMenuItem.addItemListener(this);\r
2155         overviewMenuItem.setLabel("Overview Window");\r
2156         overviewMenuItem.addActionListener(this);\r
2157         undoMenuItem.setEnabled(false);\r
2158         undoMenuItem.setLabel("Undo");\r
2159         undoMenuItem.addActionListener(this);\r
2160         redoMenuItem.setEnabled(false);\r
2161         redoMenuItem.setLabel("Redo");\r
2162         redoMenuItem.addActionListener(this);\r
2163         conservationMenuItem.setLabel("by Conservation");\r
2164         conservationMenuItem.addItemListener(this);\r
2165         noColourmenuItem.setLabel("None");\r
2166         noColourmenuItem.addActionListener(this);\r
2167         wrapMenuItem.setLabel("Wrap");\r
2168         wrapMenuItem.addItemListener(this);\r
2169         renderGapsMenuItem.setLabel("Show Gaps");\r
2170         renderGapsMenuItem.setState(true);\r
2171         renderGapsMenuItem.addItemListener(this);\r
2172         findMenuItem.setLabel("Find...");\r
2173         findMenuItem.addActionListener(this);\r
2174     abovePIDThreshold.setLabel("Above Identity Threshold");\r
2175         abovePIDThreshold.addItemListener(this);\r
2176         nucleotideColour.setLabel("Nucleotide");\r
2177         nucleotideColour.addActionListener(this);\r
2178         deleteGroups.setLabel("Undefine Groups");\r
2179         deleteGroups.addActionListener(this);\r
2180         copy.setLabel("Copy");\r
2181         copy.addActionListener(this);\r
2182         cut.setLabel("Cut");\r
2183         cut.addActionListener(this);\r
2184         delete.setLabel("Delete");\r
2185         delete.addActionListener(this);\r
2186         pasteMenu.setLabel("Paste");\r
2187         pasteNew.setLabel("To New Alignment");\r
2188         pasteNew.addActionListener(this);\r
2189         pasteThis.setLabel("Add To This Alignment");\r
2190         pasteThis.addActionListener(this);\r
2191         applyToAllGroups.setLabel("Apply Colour To All Groups");\r
2192         applyToAllGroups.setState(true);\r
2193         applyToAllGroups.addItemListener(this);\r
2194         font.setLabel("Font...");\r
2195         font.addActionListener(this);\r
2196         scaleAbove.setLabel("Scale Above");\r
2197         scaleAbove.setState(true);\r
2198         scaleAbove.setEnabled(false);\r
2199         scaleAbove.addItemListener(this);\r
2200         scaleLeft.setEnabled(false);\r
2201         scaleLeft.setState(true);\r
2202         scaleLeft.setLabel("Scale Left");\r
2203         scaleLeft.addItemListener(this);\r
2204         scaleRight.setEnabled(false);\r
2205         scaleRight.setState(true);\r
2206         scaleRight.setLabel("Scale Right");\r
2207         scaleRight.addItemListener(this);\r
2208         modifyPID.setLabel("Modify Identity Threshold...");\r
2209         modifyPID.addActionListener(this);\r
2210         modifyConservation.setLabel("Modify Conservation Threshold...");\r
2211         modifyConservation.addActionListener(this);\r
2212         sortByTreeMenu.setLabel("By Tree Order");\r
2213         sort.setLabel("Sort");\r
2214         calculate.setLabel("Calculate Tree");\r
2215         autoCalculate.addItemListener(this);\r
2216         inputText.setLabel("Input from textbox");\r
2217         inputText.addActionListener(this);\r
2218 \r
2219         helpMenu.setLabel("Help");\r
2220         documentation.setLabel("Documentation");\r
2221         documentation.addActionListener(this);\r
2222 \r
2223         about.setLabel("About...");\r
2224         about.addActionListener(this);\r
2225           seqLimits.setState(true);\r
2226     seqLimits.setLabel("Show Sequence Limits");\r
2227     seqLimits.addItemListener(this);\r
2228     featureSettings.setLabel("Feature Settings...");\r
2229     featureSettings.addActionListener(this);\r
2230     sequenceFeatures.setLabel("Sequence Features");\r
2231     sequenceFeatures.addItemListener(this);\r
2232     sequenceFeatures.setState(false);\r
2233     annotationColour.setLabel("by Annotation...");\r
2234     annotationColour.addActionListener(this);\r
2235     invertSequenceMenuItem.setLabel("Invert Sequence Selection");\r
2236     invertColSel.setLabel("Invert Column Selection");\r
2237     menu1.setLabel("Show");\r
2238     showColumns.setLabel("All Columns ");\r
2239     showSeqs.setLabel("All Sequences");\r
2240     menu2.setLabel("Hide");\r
2241     hideColumns.setLabel("Selected Columns");\r
2242     hideSequences.setLabel("Selected Sequences");\r
2243     invertColSel.addActionListener(this);\r
2244     showColumns.addActionListener(this);\r
2245     showSeqs.addActionListener(this);\r
2246     hideColumns.addActionListener(this);\r
2247     hideSequences.addActionListener(this);\r
2248     formatMenu.setLabel("Format");\r
2249     selectMenu.setLabel("Select");\r
2250     newView.setLabel("New View");\r
2251     newView.addActionListener(this);\r
2252     alignFrameMenuBar.add(fileMenu);\r
2253         alignFrameMenuBar.add(editMenu);\r
2254     alignFrameMenuBar.add(selectMenu);\r
2255     alignFrameMenuBar.add(viewMenu);\r
2256     alignFrameMenuBar.add(formatMenu);\r
2257     alignFrameMenuBar.add(colourMenu);\r
2258         alignFrameMenuBar.add(calculateMenu);\r
2259         alignFrameMenuBar.add(helpMenu);\r
2260 \r
2261         fileMenu.add(inputText);\r
2262         fileMenu.add(loadTree);\r
2263         fileMenu.add(loadAnnotations);\r
2264 \r
2265         fileMenu.addSeparator();\r
2266         fileMenu.add(outputTextboxMenu);\r
2267         fileMenu.add(outputFeatures);\r
2268         fileMenu.add(outputAnnotations);\r
2269 \r
2270         if(jalviewServletURL!=null)\r
2271           fileMenu.add(loadApplication);\r
2272 \r
2273         fileMenu.addSeparator();\r
2274         fileMenu.add(closeMenuItem);\r
2275 \r
2276         editMenu.add(undoMenuItem);\r
2277         editMenu.add(redoMenuItem);\r
2278         editMenu.add(cut);\r
2279         editMenu.add(copy);\r
2280         editMenu.add(pasteMenu);\r
2281         editMenu.add(delete);\r
2282         editMenu.addSeparator();\r
2283         editMenu.add(remove2LeftMenuItem);\r
2284         editMenu.add(remove2RightMenuItem);\r
2285         editMenu.add(removeGappedColumnMenuItem);\r
2286         editMenu.add(removeAllGapsMenuItem);\r
2287         editMenu.add(removeRedundancyMenuItem);\r
2288     viewMenu.add(newView);\r
2289     viewMenu.addSeparator();\r
2290     viewMenu.add(menu1);\r
2291     viewMenu.add(menu2);\r
2292     viewMenu.addSeparator();\r
2293     viewMenu.add(annotationPanelMenuItem);\r
2294     viewMenu.addSeparator();\r
2295         viewMenu.add(sequenceFeatures);\r
2296         viewMenu.add(featureSettings);\r
2297     viewMenu.addSeparator();\r
2298         viewMenu.add(overviewMenuItem);\r
2299         colourMenu.add(applyToAllGroups);\r
2300         colourMenu.addSeparator();\r
2301         colourMenu.add(noColourmenuItem);\r
2302         colourMenu.add(clustalColour);\r
2303         colourMenu.add(BLOSUM62Colour);\r
2304         colourMenu.add(PIDColour);\r
2305         colourMenu.add(zappoColour);\r
2306         colourMenu.add(taylorColour);\r
2307         colourMenu.add(hydrophobicityColour);\r
2308         colourMenu.add(helixColour);\r
2309         colourMenu.add(strandColour);\r
2310         colourMenu.add(turnColour);\r
2311         colourMenu.add(buriedColour);\r
2312         colourMenu.add(nucleotideColour);\r
2313         colourMenu.add(userDefinedColour);\r
2314         colourMenu.addSeparator();\r
2315         colourMenu.add(conservationMenuItem);\r
2316         colourMenu.add(modifyConservation);\r
2317         colourMenu.add(abovePIDThreshold);\r
2318         colourMenu.add(modifyPID);\r
2319     colourMenu.add(annotationColour);\r
2320     calculateMenu.add(sort);\r
2321         calculateMenu.add(calculate);\r
2322         calculateMenu.addSeparator();\r
2323         calculateMenu.add(pairwiseAlignmentMenuItem);\r
2324         calculateMenu.add(PCAMenuItem);\r
2325         calculateMenu.add(autoCalculate);\r
2326         this.add(statusBar, BorderLayout.SOUTH);\r
2327         pasteMenu.add(pasteNew);\r
2328         pasteMenu.add(pasteThis);\r
2329         sort.add(sortIDMenuItem);\r
2330         sort.add(sortByTreeMenu);\r
2331         sort.add(sortGroupMenuItem);\r
2332         sort.add(sortPairwiseMenuItem);\r
2333         calculate.add(averageDistanceTreeMenuItem);\r
2334         calculate.add(neighbourTreeMenuItem);\r
2335         calculate.add(avDistanceTreeBlosumMenuItem);\r
2336         calculate.add(njTreeBlosumMenuItem);\r
2337         helpMenu.add(documentation);\r
2338         helpMenu.add(about);\r
2339     menu1.add(showColumns);\r
2340     menu1.add(showSeqs);\r
2341     menu2.add(hideColumns);\r
2342     menu2.add(hideSequences);\r
2343     formatMenu.add(font);\r
2344     formatMenu.add(seqLimits);\r
2345     formatMenu.add(wrapMenuItem);\r
2346     formatMenu.add(scaleAbove);\r
2347     formatMenu.add(scaleLeft);\r
2348     formatMenu.add(scaleRight);\r
2349     formatMenu.add(viewBoxesMenuItem);\r
2350     formatMenu.add(viewTextMenuItem);\r
2351     formatMenu.add(colourTextMenuItem);\r
2352     formatMenu.add(renderGapsMenuItem);\r
2353     selectMenu.add(findMenuItem);\r
2354     selectMenu.addSeparator();\r
2355     selectMenu.add(selectAllSequenceMenuItem);\r
2356     selectMenu.add(deselectAllSequenceMenuItem);\r
2357     selectMenu.add(invertSequenceMenuItem);\r
2358     selectMenu.add(invertColSel);\r
2359     selectMenu.add(deleteGroups);\r
2360   }\r
2361 \r
2362   public void setEmbedded()\r
2363   {\r
2364 \r
2365     embeddedMenu = new Panel();\r
2366     embeddedEdit = new Label("Edit");\r
2367     embeddedSelect = new Label("Select");\r
2368     embeddedView = new Label("View");\r
2369     embeddedFormat = new Label("Format");\r
2370     embeddedColour = new Label("Colour");\r
2371     embeddedFile = new Label("File");\r
2372     embeddedHelp = new Label("Help");\r
2373     embeddedCalculate = new Label("Calculate");\r
2374     flowLayout1 = new FlowLayout();\r
2375     embeddedMenu.setBackground(Color.lightGray);\r
2376     embeddedMenu.setLayout(flowLayout1);\r
2377     embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2378     embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2379     embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2380     embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2381     embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2382     embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2383     embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2384     embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2385     embeddedMenu.add(embeddedFile);\r
2386     embeddedMenu.add(embeddedEdit);\r
2387     embeddedMenu.add(embeddedSelect);\r
2388     embeddedMenu.add(embeddedView);\r
2389     embeddedMenu.add(embeddedFormat);\r
2390     embeddedMenu.add(embeddedColour);\r
2391     embeddedMenu.add(embeddedCalculate);\r
2392     embeddedMenu.add(embeddedHelp);\r
2393     flowLayout1.setAlignment(FlowLayout.LEFT);\r
2394     flowLayout1.setHgap(2);\r
2395     flowLayout1.setVgap(0);\r
2396     embeddedFile.addMouseListener(this);\r
2397     embeddedEdit.addMouseListener(this);\r
2398     embeddedSelect.addMouseListener(this);\r
2399     embeddedView.addMouseListener(this);\r
2400     embeddedFormat.addMouseListener(this);\r
2401     embeddedColour.addMouseListener(this);\r
2402     embeddedCalculate.addMouseListener(this);\r
2403     embeddedHelp.addMouseListener(this);\r
2404 \r
2405     fileMenu.remove(closeMenuItem);\r
2406     fileMenu.remove(3); // Seperator\r
2407 \r
2408     viewport.applet.setLayout(new BorderLayout());\r
2409     viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
2410     viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
2411 \r
2412     alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height\r
2413                        - embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
2414 \r
2415      viewport.applet.add(alignPanel, BorderLayout.CENTER);\r
2416      viewport.applet.validate();\r
2417 \r
2418   }\r
2419 \r
2420 \r
2421 \r
2422   PopupMenu filePopup, editPopup, searchPopup,\r
2423       viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup;\r
2424   MenuItem featureSettings = new MenuItem();\r
2425   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
2426   MenuItem annotationColour = new MenuItem();\r
2427   MenuItem invertColSel = new MenuItem();\r
2428   Menu menu1 = new Menu();\r
2429   MenuItem showColumns = new MenuItem();\r
2430   MenuItem showSeqs = new MenuItem();\r
2431   Menu menu2 = new Menu();\r
2432   MenuItem hideColumns = new MenuItem();\r
2433   MenuItem hideSequences = new MenuItem();\r
2434   Menu formatMenu = new Menu();\r
2435   Menu selectMenu = new Menu();\r
2436   MenuItem newView = new MenuItem();\r
2437 \r
2438   public void mousePressed(MouseEvent evt)\r
2439   {\r
2440     PopupMenu popup = null;\r
2441     Label source = (Label)evt.getSource();\r
2442     if(source==embeddedFile)\r
2443     {\r
2444       popup = filePopup = genPopupMenu(filePopup, fileMenu);\r
2445     }\r
2446     else if(source==embeddedEdit)\r
2447     {\r
2448       popup = editPopup = genPopupMenu(editPopup, editMenu);\r
2449     }\r
2450     else if(source==embeddedSelect)\r
2451     {\r
2452       popup = searchPopup = genPopupMenu(searchPopup, selectMenu);\r
2453     }\r
2454     else if(source==embeddedView)\r
2455     {\r
2456       popup = viewPopup = genPopupMenu(viewPopup, viewMenu);\r
2457     }\r
2458     else if (source ==embeddedFormat)\r
2459     {\r
2460       popup = formatPopup = genPopupMenu(formatPopup, formatMenu);\r
2461     }\r
2462     else if(source==embeddedColour)\r
2463     {\r
2464       popup = colourPopup = genPopupMenu(colourPopup, colourMenu);\r
2465     }\r
2466     else if(source==embeddedCalculate)\r
2467     {\r
2468       popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);\r
2469     }\r
2470     else if(source==embeddedHelp)\r
2471     {\r
2472       popup = helpPopup = genPopupMenu(helpPopup, helpMenu);\r
2473     }\r
2474 \r
2475     embeddedMenu.add(popup);\r
2476     popup.show(embeddedMenu,\r
2477                source.getBounds().x,\r
2478                source.getBounds().y + source.getBounds().getSize().height);\r
2479   }\r
2480 \r
2481   PopupMenu genPopupMenu(PopupMenu popup, Menu original)\r
2482   {\r
2483     if(popup!=null)\r
2484     {\r
2485       return popup;\r
2486     }\r
2487     popup = new PopupMenu();\r
2488     int m, mSize = original.getItemCount();\r
2489     for(m=0; m<mSize; m++)\r
2490     {\r
2491       popup.add(original.getItem(m));\r
2492       mSize--;\r
2493       m--;\r
2494     }\r
2495 \r
2496     return popup;\r
2497   }\r
2498   public void mouseClicked(MouseEvent evt)\r
2499   {}\r
2500   public void mouseReleased(MouseEvent evt)\r
2501   {}\r
2502   public void mouseEntered(MouseEvent evt)\r
2503   {}\r
2504   public void mouseExited(MouseEvent evt)\r
2505   {}\r
2506 \r
2507 }\r
2508 \r