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        viewport.alignment.getGroups() );\r
 678 \r
 679     if(displayTextbox)\r
 680     {\r
 681 \r
 682       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
 683       Frame frame = new Frame();\r
 684       frame.add(cap);\r
 685       jalview.bin.JalviewLite.addFrame(frame,\r
 686                                        "Annotations",\r
 687                                        600, 500);\r
 688       cap.setText(annotation);\r
 689     }\r
 690 \r
 691     return annotation;\r
 692   }\r
 693 \r
 694   public String outputFeatures(boolean displayTextbox, String format)\r
 695   {\r
 696     String features;\r
 697     if (format.equalsIgnoreCase("Jalview"))\r
 698       features = new FeaturesFile().printJalviewFormat(\r
 699               viewport.alignment.getSequencesArray(),\r
 700               viewport.featuresDisplayed);\r
 701     else\r
 702       features = new FeaturesFile().printGFFFormat(\r
 703              viewport.alignment.getSequencesArray(),\r
 704              viewport.featuresDisplayed);\r
 705 \r
 706 \r
 707     if(displayTextbox)\r
 708     {\r
 709       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
 710       Frame frame = new Frame();\r
 711       frame.add(cap);\r
 712       jalview.bin.JalviewLite.addFrame(frame,\r
 713                                        "Features",\r
 714                                        600, 500);\r
 715 \r
 716       cap.setText(features);\r
 717     }\r
 718 \r
 719     return features;\r
 720   }\r
 721 \r
 722   void launchFullApplication()\r
 723   {\r
 724     StringBuffer url = new StringBuffer(jalviewServletURL);\r
 725 \r
 726     url.append("?open="+\r
 727                appendProtocol( viewport.applet.getParameter("file") ) );\r
 728 \r
 729     if(viewport.applet.getParameter("features")!=null)\r
 730     {\r
 731       url.append( "&features=" );\r
 732       url.append( appendProtocol( viewport.applet.getParameter("features") ) );\r
 733     }\r
 734 \r
 735     if(viewport.applet.getParameter("annotations")!=null)\r
 736     {\r
 737       url.append( "&annotations=" );\r
 738       url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );\r
 739     }\r
 740 \r
 741     if(viewport.applet.getParameter("jnetfile")!=null)\r
 742     {\r
 743       url.append( "&annotations=" );\r
 744       url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) );\r
 745     }\r
 746 \r
 747     if(viewport.applet.getParameter("defaultColour")!=null)\r
 748     {\r
 749       url.append("&colour=" +\r
 750                  removeWhiteSpace(viewport.applet.getParameter("defaultColour"))\r
 751           );\r
 752     }\r
 753 \r
 754     if(viewport.applet.getParameter("userDefinedColour")!=null)\r
 755     {\r
 756       url.append( "&colour=" +\r
 757                  removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )\r
 758          );\r
 759     }\r
 760 \r
 761     showURL(url.toString(), "FULL_APP");\r
 762   }\r
 763 \r
 764 \r
 765   String removeWhiteSpace(String colour)\r
 766   {\r
 767     StringBuffer sb = new StringBuffer();\r
 768     for (int i = 0; i < colour.length(); i++)\r
 769     {\r
 770       if (Character.isWhitespace(colour.charAt(i)))\r
 771         sb.append("%20");\r
 772       else\r
 773         sb.append(colour.charAt(i));\r
 774     }\r
 775 \r
 776     return sb.toString();\r
 777   }\r
 778 \r
 779 \r
 780   String appendProtocol(String url)\r
 781   {\r
 782     try{\r
 783        new URL(url);\r
 784     }catch(java.net.MalformedURLException ex)\r
 785     {\r
 786       url = viewport.applet.getCodeBase()+url;\r
 787     }\r
 788     return url;\r
 789   }\r
 790 \r
 791   public void closeMenuItem_actionPerformed()\r
 792   {\r
 793     PaintRefresher.RemoveComponent(alignPanel);\r
 794     PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);\r
 795     PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);\r
 796 \r
 797     if(PaintRefresher.components.size()==0 && viewport.applet==null)\r
 798       System.exit(0);\r
 799 \r
 800     this.dispose();\r
 801   }\r
 802 \r
 803 \r
 804   /**\r
 805    * DOCUMENT ME!\r
 806    */\r
 807   void updateEditMenuBar()\r
 808   {\r
 809 \r
 810     if (viewport.historyList.size() > 0)\r
 811     {\r
 812       undoMenuItem.setEnabled(true);\r
 813       CommandI command = (CommandI) viewport.historyList.peek();\r
 814       undoMenuItem.setLabel("Undo " + command.getDescription());\r
 815     }\r
 816     else\r
 817     {\r
 818       undoMenuItem.setEnabled(false);\r
 819       undoMenuItem.setLabel("Undo");\r
 820     }\r
 821 \r
 822     if (viewport.redoList.size() > 0)\r
 823     {\r
 824       redoMenuItem.setEnabled(true);\r
 825 \r
 826       CommandI command = (CommandI) viewport.redoList.peek();\r
 827       redoMenuItem.setLabel("Redo " + command.getDescription());\r
 828     }\r
 829     else\r
 830     {\r
 831       redoMenuItem.setEnabled(false);\r
 832       redoMenuItem.setLabel("Redo");\r
 833     }\r
 834   }\r
 835 \r
 836   public void addHistoryItem(CommandI command)\r
 837   {\r
 838     if(command.getSize()>0)\r
 839     {\r
 840       viewport.historyList.push(command);\r
 841       viewport.redoList.removeAllElements();\r
 842       updateEditMenuBar();\r
 843       viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
 844     }\r
 845   }\r
 846 \r
 847   /**\r
 848    * DOCUMENT ME!\r
 849    *\r
 850    * @param e DOCUMENT ME!\r
 851    */\r
 852   protected void undoMenuItem_actionPerformed()\r
 853   {\r
 854     if(viewport.historyList.size()<1)\r
 855       return;\r
 856 \r
 857     CommandI command = (CommandI)viewport.historyList.pop();\r
 858     viewport.redoList.push(command);\r
 859     command.undoCommand();\r
 860 \r
 861     AlignViewport originalSource = getOriginatingSource(command);\r
 862 \r
 863     originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
 864     updateEditMenuBar();\r
 865     originalSource.firePropertyChange("alignment", null,originalSource.alignment.getSequences());\r
 866   }\r
 867 \r
 868   /**\r
 869    * DOCUMENT ME!\r
 870    *\r
 871    * @param e DOCUMENT ME!\r
 872    */\r
 873   protected void redoMenuItem_actionPerformed()\r
 874   {\r
 875     if(viewport.redoList.size()<1)\r
 876       return;\r
 877 \r
 878     CommandI command = (CommandI) viewport.redoList.pop();\r
 879     viewport.historyList.push(command);\r
 880     command.doCommand();\r
 881 \r
 882     AlignViewport originalSource = getOriginatingSource(command);\r
 883     originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;\r
 884 \r
 885     updateEditMenuBar();\r
 886     originalSource.firePropertyChange("alignment", null, originalSource.alignment.getSequences());\r
 887   }\r
 888 \r
 889   AlignViewport getOriginatingSource(CommandI command)\r
 890   {\r
 891     AlignViewport originalSource = null;\r
 892     //For sequence removal and addition, we need to fire\r
 893    //the property change event FROM the viewport where the\r
 894    //original alignment was altered\r
 895    AlignmentI al = null;\r
 896     if (command instanceof EditCommand)\r
 897     {\r
 898       EditCommand editCommand = (EditCommand) command;\r
 899       al = editCommand.getAlignment();\r
 900       Vector comps = (Vector) PaintRefresher.components\r
 901           .get(viewport.getSequenceSetId());\r
 902       for (int i = 0; i < comps.size(); i++)\r
 903       {\r
 904         if (comps.elementAt(i) instanceof AlignmentPanel)\r
 905         {\r
 906           if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)\r
 907           {\r
 908             originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;\r
 909             break;\r
 910           }\r
 911         }\r
 912       }\r
 913     }\r
 914 \r
 915     if (originalSource == null)\r
 916     {\r
 917       //The original view is closed, we must validate\r
 918       //the current view against the closed view first\r
 919       if (al != null)\r
 920         PaintRefresher.validateSequences(al, viewport.alignment);\r
 921 \r
 922       originalSource = viewport;\r
 923     }\r
 924 \r
 925 \r
 926     return originalSource;\r
 927   }\r
 928 \r
 929   public void moveSelectedSequences(boolean up)\r
 930   {\r
 931     SequenceGroup sg = viewport.getSelectionGroup();\r
 932     if (sg == null)\r
 933     {\r
 934       return;\r
 935     }\r
 936 \r
 937     if (up)\r
 938     {\r
 939       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 940       {\r
 941         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 942         if (!sg.getSequences(null).contains(seq))\r
 943         {\r
 944           continue;\r
 945         }\r
 946 \r
 947         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 948         if (sg.getSequences(null).contains(temp))\r
 949         {\r
 950           continue;\r
 951         }\r
 952 \r
 953         viewport.alignment.getSequences().setElementAt(temp, i);\r
 954         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 955       }\r
 956     }\r
 957     else\r
 958     {\r
 959       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 960       {\r
 961         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 962         if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))\r
 963         {\r
 964           continue;\r
 965         }\r
 966 \r
 967         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 968         if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))\r
 969         {\r
 970           continue;\r
 971         }\r
 972 \r
 973         viewport.alignment.getSequences().setElementAt(temp, i);\r
 974         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 975       }\r
 976     }\r
 977 \r
 978     alignPanel.repaint();\r
 979   }\r
 980 \r
 981   static StringBuffer copiedSequences;\r
 982   static Vector copiedHiddenColumns;\r
 983   protected void copy_actionPerformed()\r
 984   {\r
 985     if (viewport.getSelectionGroup() == null)\r
 986     {\r
 987       return;\r
 988     }\r
 989 \r
 990     SequenceGroup sg = viewport.getSelectionGroup();\r
 991     copiedSequences = new StringBuffer();\r
 992     Hashtable orderedSeqs = new Hashtable();\r
 993     for (int i = 0; i < sg.getSize(); i++)\r
 994     {\r
 995       SequenceI seq = sg.getSequenceAt(i);\r
 996       int index = viewport.alignment.findIndex(seq);\r
 997       orderedSeqs.put(index + "", seq);\r
 998     }\r
 999 \r
1000     int index = 0, startRes, endRes;\r
1001     char ch;\r
1002 \r
1003     if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)\r
1004     {\r
1005       copiedHiddenColumns = new Vector();\r
1006       int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
1007       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();\r
1008            i++)\r
1009       {\r
1010         int[] region = (int[])\r
1011             viewport.getColumnSelection().getHiddenColumns().elementAt(i);\r
1012 \r
1013         copiedHiddenColumns.addElement(new int[]\r
1014                                  {region[0] - hiddenOffset,\r
1015                                  region[1] - hiddenOffset});\r
1016       }\r
1017     }\r
1018     else\r
1019       copiedHiddenColumns = null;\r
1020 \r
1021 \r
1022     for (int i = 0; i < sg.getSize(); i++)\r
1023     {\r
1024         SequenceI seq = null;\r
1025 \r
1026         while (seq == null)\r
1027         {\r
1028             if (orderedSeqs.containsKey(index + ""))\r
1029             {\r
1030                 seq = (SequenceI) orderedSeqs.get(index + "");\r
1031                 index++;\r
1032 \r
1033                 break;\r
1034             }\r
1035             else\r
1036             {\r
1037                 index++;\r
1038             }\r
1039         }\r
1040 \r
1041         //FIND START RES\r
1042         //Returns residue following index if gap\r
1043         startRes = seq.findPosition(sg.getStartRes());\r
1044 \r
1045         //FIND END RES\r
1046         //Need to find the residue preceeding index if gap\r
1047         endRes = 0;\r
1048 \r
1049         for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
1050         {\r
1051           ch = seq.getCharAt(j);\r
1052           if (!jalview.util.Comparison.isGap( (ch)))\r
1053           {\r
1054             endRes++;\r
1055           }\r
1056         }\r
1057 \r
1058         if(endRes>0)\r
1059         {\r
1060           endRes += seq.getStart() -1;\r
1061         }\r
1062 \r
1063         copiedSequences.append(seq.getName() + "\t" +\r
1064             startRes + "\t" +\r
1065             endRes + "\t" +\r
1066             seq.getSequenceAsString(sg.getStartRes(),\r
1067                 sg.getEndRes() + 1) + "\n");\r
1068     }\r
1069 \r
1070   }\r
1071 \r
1072   protected void pasteNew_actionPerformed()\r
1073   {\r
1074     paste(true);\r
1075   }\r
1076 \r
1077   protected void pasteThis_actionPerformed()\r
1078   {\r
1079     paste(false);\r
1080   }\r
1081 \r
1082   void paste(boolean newAlignment)\r
1083   {\r
1084     try\r
1085     {\r
1086 \r
1087       if (copiedSequences == null)\r
1088       {\r
1089         return;\r
1090       }\r
1091 \r
1092       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
1093       Vector seqs = new Vector();\r
1094       while (st.hasMoreElements())\r
1095       {\r
1096         String name = st.nextToken();\r
1097         int start = Integer.parseInt(st.nextToken());\r
1098         int end = Integer.parseInt(st.nextToken());\r
1099         seqs.addElement(new Sequence(name, st.nextToken(), start, end));\r
1100       }\r
1101       SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
1102       for (int i = 0; i < seqs.size(); i++)\r
1103       {\r
1104         newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
1105       }\r
1106 \r
1107       if (newAlignment)\r
1108       {\r
1109         String newtitle = new String("Copied sequences");\r
1110         if (getTitle().startsWith("Copied sequences"))\r
1111         {\r
1112           newtitle = getTitle();\r
1113         }\r
1114         else\r
1115         {\r
1116           newtitle = newtitle.concat("- from " + getTitle());\r
1117         }\r
1118         AlignFrame af = new AlignFrame(new Alignment(newSeqs),\r
1119                                        viewport.applet,\r
1120                                        newtitle,\r
1121                                        false);\r
1122         if (copiedHiddenColumns != null)\r
1123         {\r
1124           for (int i = 0; i < copiedHiddenColumns.size(); i++)\r
1125           {\r
1126             int[] region = (int[]) copiedHiddenColumns.elementAt(i);\r
1127             af.viewport.hideColumns(region[0], region[1]);\r
1128           }\r
1129         }\r
1130 \r
1131 \r
1132         jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,\r
1133                                          DEFAULT_HEIGHT);\r
1134       }\r
1135       else\r
1136       {\r
1137         addSequences(newSeqs);\r
1138       }\r
1139 \r
1140     }\r
1141     catch (Exception ex)\r
1142     {} // could be anything being pasted in here\r
1143 \r
1144   }\r
1145 \r
1146   void addSequences(SequenceI[] seqs)\r
1147   {\r
1148     for (int i = 0; i < seqs.length; i++)\r
1149     {\r
1150       viewport.alignment.addSequence(seqs[i]);\r
1151     }\r
1152 \r
1153     //!newAlignment\r
1154     addHistoryItem(new EditCommand(\r
1155         "Add sequences",\r
1156         EditCommand.PASTE,\r
1157         seqs,\r
1158         0,\r
1159         viewport.alignment.getWidth(),\r
1160         viewport.alignment)\r
1161         );\r
1162 \r
1163     viewport.setEndSeq(viewport.alignment.getHeight());\r
1164     viewport.alignment.getWidth();\r
1165     viewport.firePropertyChange("alignment", null,\r
1166                                 viewport.alignment.getSequences());\r
1167 \r
1168   }\r
1169 \r
1170   protected void cut_actionPerformed()\r
1171   {\r
1172     copy_actionPerformed();\r
1173     delete_actionPerformed();\r
1174   }\r
1175 \r
1176   protected void delete_actionPerformed()\r
1177   {\r
1178 \r
1179     SequenceGroup sg = viewport.getSelectionGroup();\r
1180     if (sg == null)\r
1181     {\r
1182       return;\r
1183     }\r
1184 \r
1185     Vector seqs = new Vector();\r
1186     SequenceI seq;\r
1187     for (int i = 0; i < sg.getSize(); i++)\r
1188     {\r
1189       seq = sg.getSequenceAt(i);\r
1190       seqs.addElement(seq);\r
1191     }\r
1192 \r
1193 \r
1194    // If the cut affects all sequences, remove highlighted columns\r
1195    if (sg.getSize() == viewport.alignment.getHeight())\r
1196    {\r
1197      viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
1198          sg.getEndRes() + 1);\r
1199    }\r
1200 \r
1201 \r
1202     SequenceI [] cut = new SequenceI[seqs.size()];\r
1203     for(int i=0; i<seqs.size(); i++)\r
1204       cut[i] = (SequenceI)seqs.elementAt(i);\r
1205 \r
1206 \r
1207     /*\r
1208     //ADD HISTORY ITEM\r
1209     */\r
1210     addHistoryItem(new EditCommand("Cut Sequences",\r
1211                                       EditCommand.CUT,\r
1212                                       cut,\r
1213                                       sg.getStartRes(),\r
1214                                       sg.getEndRes()-sg.getStartRes()+1,\r
1215                                       viewport.alignment));\r
1216 \r
1217 \r
1218     viewport.setSelectionGroup(null);\r
1219     viewport.alignment.deleteGroup(sg);\r
1220 \r
1221     viewport.firePropertyChange("alignment", null,\r
1222                                   viewport.getAlignment().getSequences());\r
1223 \r
1224     if (viewport.getAlignment().getHeight() < 1)\r
1225     {\r
1226         this.setVisible(false);\r
1227     }\r
1228   }\r
1229 \r
1230   protected void deleteGroups_actionPerformed()\r
1231   {\r
1232     viewport.alignment.deleteAllGroups();\r
1233     viewport.sequenceColours=null;\r
1234     viewport.setSelectionGroup(null);\r
1235 \r
1236     alignPanel.repaint();\r
1237   }\r
1238 \r
1239   public void selectAllSequenceMenuItem_actionPerformed()\r
1240   {\r
1241     SequenceGroup sg = new SequenceGroup();\r
1242     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
1243     {\r
1244       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
1245     }\r
1246     sg.setEndRes(viewport.alignment.getWidth()-1);\r
1247     viewport.setSelectionGroup(sg);\r
1248     alignPanel.repaint();\r
1249     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
1250   }\r
1251 \r
1252   public void deselectAllSequenceMenuItem_actionPerformed()\r
1253   {\r
1254     if(viewport.cursorMode)\r
1255     {\r
1256       alignPanel.seqPanel.keyboardNo1=null;\r
1257       alignPanel.seqPanel.keyboardNo2=null;\r
1258     }\r
1259     viewport.setSelectionGroup(null);\r
1260     viewport.getColumnSelection().clear();\r
1261     viewport.setSelectionGroup(null);\r
1262     alignPanel.idPanel.idCanvas.searchResults = null;\r
1263     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
1264     alignPanel.repaint();\r
1265     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
1266   }\r
1267 \r
1268   public void invertSequenceMenuItem_actionPerformed()\r
1269   {\r
1270     SequenceGroup sg = viewport.getSelectionGroup();\r
1271     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
1272     {\r
1273       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
1274     }\r
1275 \r
1276     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
1277   }\r
1278 \r
1279   void trimAlignment(boolean trimLeft)\r
1280   {\r
1281     ColumnSelection colSel = viewport.getColumnSelection();\r
1282     int column;\r
1283 \r
1284     if (colSel.size() > 0)\r
1285     {\r
1286       if(trimLeft)\r
1287         column = colSel.getMin();\r
1288       else\r
1289         column = colSel.getMax();\r
1290 \r
1291       SequenceI [] seqs;\r
1292       if(viewport.getSelectionGroup()!=null)\r
1293         seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
1294       else\r
1295         seqs = viewport.alignment.getSequencesArray();\r
1296 \r
1297 \r
1298       TrimRegionCommand trimRegion;\r
1299       if(trimLeft)\r
1300       {\r
1301         trimRegion = new TrimRegionCommand("Remove Left",\r
1302                                     TrimRegionCommand.TRIM_LEFT,\r
1303                                     seqs,\r
1304                                     column,\r
1305                                     viewport.alignment,\r
1306                                     viewport.colSel,\r
1307                                     viewport.selectionGroup);\r
1308         viewport.setStartRes(0);\r
1309       }\r
1310      else\r
1311      {\r
1312        trimRegion = new TrimRegionCommand("Remove Right",\r
1313                                    TrimRegionCommand.TRIM_RIGHT,\r
1314                                    seqs,\r
1315                                    column,\r
1316                                    viewport.alignment,\r
1317                                    viewport.colSel,\r
1318                                    viewport.selectionGroup);\r
1319      }\r
1320 \r
1321      statusBar.setText("Removed "+trimRegion.getSize()+" columns.");\r
1322 \r
1323 \r
1324       addHistoryItem(trimRegion);\r
1325 \r
1326       Vector groups = viewport.alignment.getGroups();\r
1327 \r
1328       for (int i = 0; i < groups.size(); i++)\r
1329       {\r
1330         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1331 \r
1332         if ( (trimLeft && !sg.adjustForRemoveLeft(column))\r
1333             || (!trimLeft && !sg.adjustForRemoveRight(column)))\r
1334         {\r
1335           viewport.alignment.deleteGroup(sg);\r
1336         }\r
1337       }\r
1338 \r
1339       viewport.firePropertyChange("alignment", null,\r
1340                                   viewport.getAlignment().getSequences());\r
1341     }\r
1342   }\r
1343 \r
1344 \r
1345   public void removeGappedColumnMenuItem_actionPerformed()\r
1346   {\r
1347     int start = 0, end = viewport.alignment.getWidth()-1;\r
1348 \r
1349     SequenceI[] seqs;\r
1350     if (viewport.getSelectionGroup() != null)\r
1351     {\r
1352       seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
1353       start = viewport.getSelectionGroup().getStartRes();\r
1354       end = viewport.getSelectionGroup().getEndRes();\r
1355     }\r
1356     else\r
1357       seqs = viewport.alignment.getSequencesArray();\r
1358 \r
1359 \r
1360     RemoveGapColCommand removeGapCols =\r
1361         new RemoveGapColCommand("Remove Gapped Columns",\r
1362                                 seqs,\r
1363                                 start, end,\r
1364                                 viewport.alignment);\r
1365 \r
1366     addHistoryItem(removeGapCols);\r
1367 \r
1368     statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");\r
1369 \r
1370     //This is to maintain viewport position on first residue\r
1371     //of first sequence\r
1372     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
1373     int startRes = seq.findPosition(viewport.startRes);\r
1374    // ShiftList shifts;\r
1375    // viewport.getAlignment().removeGaps(shifts=new ShiftList());\r
1376    // edit.alColumnChanges=shifts.getInverse();\r
1377    // if (viewport.hasHiddenColumns)\r
1378    //   viewport.getColumnSelection().compensateForEdits(shifts);\r
1379    viewport.setStartRes(seq.findIndex(startRes)-1);\r
1380    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1381 \r
1382   }\r
1383 \r
1384   public void removeAllGapsMenuItem_actionPerformed()\r
1385   {\r
1386     int start = 0, end = viewport.alignment.getWidth()-1;\r
1387 \r
1388     SequenceI[] seqs;\r
1389     if (viewport.getSelectionGroup() != null)\r
1390     {\r
1391       seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
1392       start = viewport.getSelectionGroup().getStartRes();\r
1393       end = viewport.getSelectionGroup().getEndRes();\r
1394     }\r
1395     else\r
1396       seqs = viewport.alignment.getSequencesArray();\r
1397 \r
1398     //This is to maintain viewport position on first residue\r
1399     //of first sequence\r
1400     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
1401     int startRes = seq.findPosition(viewport.startRes);\r
1402 \r
1403     addHistoryItem(new RemoveGapsCommand("Remove Gaps",\r
1404                                            seqs,\r
1405                                            start, end,\r
1406                      viewport.alignment));\r
1407 \r
1408     viewport.setStartRes(seq.findIndex(startRes)-1);\r
1409 \r
1410     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1411 \r
1412   }\r
1413 \r
1414   public void findMenuItem_actionPerformed()\r
1415   {\r
1416     new Finder(alignPanel);\r
1417   }\r
1418 \r
1419   public void newView()\r
1420   {\r
1421     AlignmentI newal;\r
1422     if (viewport.hasHiddenRows)\r
1423       newal = new Alignment(viewport.getAlignment().\r
1424                             getHiddenSequences()\r
1425                             .getFullAlignment().\r
1426                             getSequencesArray());\r
1427     else\r
1428       newal = new Alignment(viewport.alignment.getSequencesArray());\r
1429 \r
1430     if(viewport.alignment.getAlignmentAnnotation()!=null)\r
1431     {\r
1432       for(int i=0; i<viewport.alignment.getAlignmentAnnotation().length; i++)\r
1433       {\r
1434         if(!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)\r
1435         {\r
1436           newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);\r
1437         }\r
1438       }\r
1439     }\r
1440 \r
1441     AlignFrame newaf = new AlignFrame(newal,\r
1442                                       viewport.applet,\r
1443                                       "",\r
1444                                       false);\r
1445 \r
1446     newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();\r
1447     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());\r
1448     PaintRefresher.Register(newaf.alignPanel,\r
1449                             newaf.alignPanel.av.getSequenceSetId());\r
1450 \r
1451     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,\r
1452                             newaf.alignPanel.av.getSequenceSetId());\r
1453     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,\r
1454                             newaf.alignPanel.av.getSequenceSetId());\r
1455 \r
1456     Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId());\r
1457     int viewSize = -1;\r
1458     for (int i = 0; i < comps.size(); i++)\r
1459     {\r
1460       if (comps.elementAt(i) instanceof AlignmentPanel)\r
1461         viewSize++;\r
1462     }\r
1463 \r
1464     String title = new String(this.getTitle());\r
1465     if (title.indexOf("(View") > -1)\r
1466       title = title.substring(0, title.indexOf("(View"));\r
1467 \r
1468     title+= "(View "+viewSize+")";\r
1469 \r
1470     newaf.setTitle(title.toString());\r
1471 \r
1472 \r
1473     newaf.viewport.historyList = viewport.historyList;\r
1474     newaf.viewport.redoList = viewport.redoList;\r
1475 \r
1476    }\r
1477 \r
1478 \r
1479   public void seqLimits_itemStateChanged()\r
1480   {\r
1481     viewport.setShowJVSuffix(seqLimits.getState());\r
1482     alignPanel.fontChanged();\r
1483     alignPanel.repaint();\r
1484   }\r
1485 \r
1486 \r
1487   protected void colourTextMenuItem_actionPerformed()\r
1488   {\r
1489     viewport.setColourText(colourTextMenuItem.getState());\r
1490     alignPanel.repaint();\r
1491   }\r
1492 \r
1493   protected void wrapMenuItem_actionPerformed()\r
1494   {\r
1495     viewport.setWrapAlignment(wrapMenuItem.getState());\r
1496     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
1497     scaleAbove.setEnabled(wrapMenuItem.getState());\r
1498     scaleLeft.setEnabled(wrapMenuItem.getState());\r
1499     scaleRight.setEnabled(wrapMenuItem.getState());\r
1500     alignPanel.repaint();\r
1501   }\r
1502 \r
1503 \r
1504   public void overviewMenuItem_actionPerformed()\r
1505   {\r
1506     if (alignPanel.overviewPanel != null)\r
1507     {\r
1508       return;\r
1509     }\r
1510 \r
1511     Frame frame = new Frame();\r
1512     OverviewPanel overview = new OverviewPanel(alignPanel);\r
1513     frame.add(overview);\r
1514     // +50 must allow for applet frame window\r
1515     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
1516                                      overview.preferredSize().width,\r
1517                                      overview.preferredSize().height + 50);\r
1518 \r
1519     frame.pack();\r
1520     frame.addWindowListener(new WindowAdapter()\r
1521     {\r
1522       public void windowClosing(WindowEvent e)\r
1523       {\r
1524         alignPanel.setOverviewPanel(null);\r
1525       };\r
1526     });\r
1527 \r
1528     alignPanel.setOverviewPanel(overview);\r
1529 \r
1530   }\r
1531 \r
1532 \r
1533   void changeColour(ColourSchemeI cs)\r
1534   {\r
1535     int threshold = 0;\r
1536 \r
1537     if(cs!=null)\r
1538     {\r
1539       if (viewport.getAbovePIDThreshold())\r
1540       {\r
1541         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
1542 \r
1543         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1544 \r
1545         viewport.setGlobalColourScheme(cs);\r
1546       }\r
1547       else\r
1548       {\r
1549         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1550       }\r
1551 \r
1552       if (viewport.getConservationSelected())\r
1553       {\r
1554 \r
1555         Alignment al = (Alignment) viewport.alignment;\r
1556         Conservation c = new Conservation("All",\r
1557                                           ResidueProperties.propHash, 3,\r
1558                                           al.getSequences(), 0,\r
1559                                           al.getWidth() - 1);\r
1560 \r
1561         c.calculate();\r
1562         c.verdict(false, viewport.ConsPercGaps);\r
1563 \r
1564         cs.setConservation(c);\r
1565 \r
1566         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
1567             "Background"));\r
1568 \r
1569       }\r
1570       else\r
1571       {\r
1572         cs.setConservation(null);\r
1573       }\r
1574 \r
1575       cs.setConsensus(viewport.hconsensus);\r
1576 \r
1577     }\r
1578     viewport.setGlobalColourScheme(cs);\r
1579 \r
1580     if (viewport.getColourAppliesToAllGroups())\r
1581     {\r
1582       Vector groups = viewport.alignment.getGroups();\r
1583       for (int i = 0; i < groups.size(); i++)\r
1584       {\r
1585         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1586 \r
1587         if(cs==null)\r
1588         {\r
1589           sg.cs = null;\r
1590           continue;\r
1591         }\r
1592         if (cs instanceof ClustalxColourScheme)\r
1593         {\r
1594           sg.cs = new ClustalxColourScheme(\r
1595               sg.getSequences(viewport.hiddenRepSequences),\r
1596               sg.getWidth());\r
1597         }\r
1598         else\r
1599         {\r
1600           try\r
1601           {\r
1602             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
1603           }\r
1604           catch (Exception ex)\r
1605           {\r
1606             ex.printStackTrace();\r
1607             sg.cs = cs;\r
1608           }\r
1609         }\r
1610 \r
1611         if (viewport.getAbovePIDThreshold()\r
1612             || cs instanceof PIDColourScheme\r
1613             || cs instanceof Blosum62ColourScheme)\r
1614         {\r
1615           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1616           sg.cs.setConsensus(AAFrequency.calculate(\r
1617               sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth()));\r
1618         }\r
1619         else\r
1620           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1621 \r
1622         if (viewport.getConservationSelected())\r
1623         {\r
1624           Conservation c = new Conservation("Group",\r
1625                                             ResidueProperties.propHash, 3,\r
1626                                             sg.getSequences(viewport.hiddenRepSequences), 0,\r
1627                                             viewport.alignment.getWidth() - 1);\r
1628           c.calculate();\r
1629           c.verdict(false, viewport.ConsPercGaps);\r
1630           sg.cs.setConservation(c);\r
1631         }\r
1632         else\r
1633         {\r
1634           sg.cs.setConservation(null);\r
1635           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1636         }\r
1637 \r
1638       }\r
1639     }\r
1640 \r
1641 \r
1642     if (alignPanel.getOverviewPanel() != null)\r
1643     {\r
1644       alignPanel.getOverviewPanel().updateOverviewImage();\r
1645     }\r
1646 \r
1647     alignPanel.repaint();\r
1648   }\r
1649 \r
1650 \r
1651 \r
1652   protected void modifyPID_actionPerformed()\r
1653   {\r
1654     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
1655     {\r
1656       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
1657                                      "Background");\r
1658       SliderPanel.showPIDSlider();\r
1659     }\r
1660   }\r
1661 \r
1662   protected void modifyConservation_actionPerformed()\r
1663   {\r
1664     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
1665     {\r
1666       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
1667                                         "Background");\r
1668       SliderPanel.showConservationSlider();\r
1669     }\r
1670   }\r
1671 \r
1672   protected void conservationMenuItem_actionPerformed()\r
1673   {\r
1674     viewport.setConservationSelected(conservationMenuItem.getState());\r
1675 \r
1676     viewport.setAbovePIDThreshold(false);\r
1677     abovePIDThreshold.setState(false);\r
1678 \r
1679     changeColour(viewport.getGlobalColourScheme());\r
1680 \r
1681     modifyConservation_actionPerformed();\r
1682   }\r
1683 \r
1684   public void abovePIDThreshold_actionPerformed()\r
1685   {\r
1686     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
1687 \r
1688     conservationMenuItem.setState(false);\r
1689     viewport.setConservationSelected(false);\r
1690 \r
1691     changeColour(viewport.getGlobalColourScheme());\r
1692 \r
1693     modifyPID_actionPerformed();\r
1694   }\r
1695 \r
1696 \r
1697 \r
1698   public void sortPairwiseMenuItem_actionPerformed()\r
1699   {\r
1700     SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();\r
1701     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1702                               viewport.getAlignment().getSequenceAt(0));\r
1703     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));\r
1704     alignPanel.repaint();\r
1705   }\r
1706 \r
1707   public void sortIDMenuItem_actionPerformed()\r
1708   {\r
1709   //  addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1710    //                                HistoryItem.SORT));\r
1711     AlignmentSorter.sortByID(viewport.getAlignment());\r
1712     alignPanel.repaint();\r
1713   }\r
1714 \r
1715   public void sortGroupMenuItem_actionPerformed()\r
1716   {\r
1717   //  addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1718   //                                 HistoryItem.SORT));\r
1719     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1720     alignPanel.repaint();\r
1721 \r
1722   }\r
1723 \r
1724   public void removeRedundancyMenuItem_actionPerformed()\r
1725   {\r
1726      new RedundancyPanel(alignPanel);\r
1727   }\r
1728 \r
1729   public void pairwiseAlignmentMenuItem_actionPerformed()\r
1730   {\r
1731     if (viewport.getSelectionGroup()!=null\r
1732         && viewport.getSelectionGroup().getSize() > 1)\r
1733     {\r
1734       Frame frame = new Frame();\r
1735       frame.add(new PairwiseAlignPanel(alignPanel));\r
1736       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1737     }\r
1738   }\r
1739 \r
1740   public void PCAMenuItem_actionPerformed()\r
1741   {\r
1742     //are the sequences aligned?\r
1743     if (!viewport.alignment.isAligned())\r
1744     {\r
1745       SequenceI current;\r
1746       int Width = viewport.getAlignment().getWidth();\r
1747 \r
1748       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1749            i++)\r
1750       {\r
1751         current = viewport.getAlignment().getSequenceAt(i);\r
1752 \r
1753         if (current.getLength() < Width)\r
1754         {\r
1755           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1756         }\r
1757       }\r
1758       alignPanel.repaint();\r
1759     }\r
1760 \r
1761     if ( (viewport.getSelectionGroup() != null &&\r
1762           viewport.getSelectionGroup().getSize() < 4 &&\r
1763           viewport.getSelectionGroup().getSize() > 0)\r
1764         || viewport.getAlignment().getHeight() < 4)\r
1765     {\r
1766       return;\r
1767     }\r
1768 \r
1769     try\r
1770     {\r
1771       new PCAPanel(viewport);\r
1772     }\r
1773     catch (java.lang.OutOfMemoryError ex)\r
1774     {\r
1775     }\r
1776 \r
1777   }\r
1778 \r
1779   public void averageDistanceTreeMenuItem_actionPerformed()\r
1780   {\r
1781     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1782   }\r
1783 \r
1784   public void neighbourTreeMenuItem_actionPerformed()\r
1785   {\r
1786     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1787   }\r
1788 \r
1789   protected void njTreeBlosumMenuItem_actionPerformed()\r
1790   {\r
1791     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1792   }\r
1793 \r
1794   protected void avTreeBlosumMenuItem_actionPerformed()\r
1795   {\r
1796     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
1797   }\r
1798 \r
1799   void NewTreePanel(String type, String pwType, String title)\r
1800   {\r
1801     //are the sequences aligned?\r
1802     if (!viewport.alignment.isAligned())\r
1803     {\r
1804       SequenceI current;\r
1805       int Width = viewport.getAlignment().getWidth();\r
1806 \r
1807       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1808            i++)\r
1809       {\r
1810         current = viewport.getAlignment().getSequenceAt(i);\r
1811 \r
1812         if (current.getLength() < Width)\r
1813         {\r
1814           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1815         }\r
1816       }\r
1817       alignPanel.repaint();\r
1818 \r
1819     }\r
1820 \r
1821     if ( (viewport.getSelectionGroup() != null &&\r
1822           viewport.getSelectionGroup().getSize() > 1)\r
1823       || (viewport.getSelectionGroup() == null\r
1824           && viewport.alignment.getHeight() > 1))\r
1825     {\r
1826       final TreePanel tp = new TreePanel(viewport,\r
1827                                          type,\r
1828                                          pwType);\r
1829 \r
1830       addTreeMenuItem(tp, title);\r
1831 \r
1832       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1833     }\r
1834   }\r
1835 \r
1836   void loadTree_actionPerformed()\r
1837   {\r
1838       CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
1839       cap.setText("Paste your Newick tree file here.");\r
1840       cap.setTreeImport();\r
1841       Frame frame = new Frame();\r
1842       frame.add(cap);\r
1843       jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);\r
1844   }\r
1845 \r
1846   public void loadTree(jalview.io.NewickFile tree, String treeFile)\r
1847   {\r
1848     TreePanel tp = new TreePanel(viewport,\r
1849                                  treeFile,\r
1850                                  "From File - ",\r
1851                                  tree);\r
1852     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
1853     addTreeMenuItem(tp, treeFile);\r
1854   }\r
1855 \r
1856   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1857   {\r
1858     final MenuItem item = new MenuItem(title);\r
1859     sortByTreeMenu.add(item);\r
1860     item.addActionListener(new java.awt.event.ActionListener()\r
1861     {\r
1862       public void actionPerformed(ActionEvent evt)\r
1863       {\r
1864       //  addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1865       //                                 HistoryItem.SORT));\r
1866         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1867         alignPanel.repaint();\r
1868       }\r
1869     });\r
1870 \r
1871     treePanel.addWindowListener(new WindowAdapter()\r
1872     {\r
1873       public void windowClosing(WindowEvent e)\r
1874       {\r
1875         sortByTreeMenu.remove(item);\r
1876       };\r
1877     });\r
1878   }\r
1879 \r
1880   protected void documentation_actionPerformed()\r
1881   {\r
1882     showURL("http://www.jalview.org/help.html", "HELP");\r
1883   }\r
1884 \r
1885   protected void about_actionPerformed()\r
1886   {\r
1887 \r
1888     class AboutPanel extends Canvas\r
1889     {\r
1890       String version;\r
1891       public AboutPanel(String version)\r
1892       { this.version = version; }\r
1893 \r
1894       public void paint(Graphics g)\r
1895       {\r
1896         g.setColor(Color.white);\r
1897         g.fillRect(0, 0, getSize().width, getSize().height);\r
1898         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1899         FontMetrics fm = g.getFontMetrics();\r
1900         int fh = fm.getHeight();\r
1901         int y = 5, x = 7;\r
1902         g.setColor(Color.black);\r
1903         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1904         g.drawString("Jalview - Release "+version, 200, y += fh);\r
1905         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1906         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1907                      x, y += fh * 2);\r
1908         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1909                      x, y += fh);\r
1910         g.drawString(\r
1911             "For any issues relating to Jalview, email help@jalview.org", x,\r
1912             y += fh);\r
1913         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1914         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1915                      x, y += fh);\r
1916         g.drawString("Bioinformatics,  2004 20;426-7.", x, y += fh);\r
1917       }\r
1918     }\r
1919 \r
1920     String version = "test";\r
1921     java.net.URL url = getClass().getResource("/.build_properties");\r
1922     if (url != null)\r
1923     {\r
1924       try\r
1925       {\r
1926         BufferedReader reader = new BufferedReader(new InputStreamReader(\r
1927             url.openStream()));\r
1928         String line;\r
1929         while ( (line = reader.readLine()) != null)\r
1930         {\r
1931           if (line.indexOf("VERSION") > -1)\r
1932           {\r
1933             version = line.substring(line.indexOf("=") + 1);\r
1934           }\r
1935         }\r
1936       }\r
1937       catch (Exception ex)\r
1938       {\r
1939         ex.printStackTrace();\r
1940       }\r
1941     }\r
1942 \r
1943 \r
1944     Frame frame = new Frame();\r
1945     frame.add(new AboutPanel(version));\r
1946     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1947 \r
1948   }\r
1949 \r
1950   public void showURL(String url, String target)\r
1951   {\r
1952     if (viewport.applet == null)\r
1953     {\r
1954       System.out.println("Not running as applet - no browser available.");\r
1955     }\r
1956     else\r
1957     {\r
1958       try\r
1959       {\r
1960         System.out.println("Show url: "+url);\r
1961         viewport.applet.getAppletContext().showDocument(new java.net.URL(url),\r
1962                                                target);\r
1963       }\r
1964       catch (Exception ex)\r
1965       {\r
1966         ex.printStackTrace();\r
1967       }\r
1968     }\r
1969   }\r
1970 \r
1971 \r
1972   //////////////////////////////////////////////////////////////////////////////////\r
1973   //JBuilder Graphics here\r
1974 \r
1975     protected MenuBar alignFrameMenuBar = new MenuBar();\r
1976     protected Menu fileMenu = new Menu("File");\r
1977     protected MenuItem loadApplication = new MenuItem("View in Full Application");\r
1978     protected MenuItem loadTree = new MenuItem("Load Associated Tree ...");\r
1979     protected MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");\r
1980     protected MenuItem outputFeatures = new MenuItem("Export Features ...");\r
1981     protected MenuItem outputAnnotations = new MenuItem("Export Annotations ...");\r
1982 \r
1983     protected MenuItem closeMenuItem = new MenuItem("Close");\r
1984     protected Menu editMenu = new Menu("Edit");\r
1985     protected Menu viewMenu = new Menu("View");\r
1986     protected Menu colourMenu = new Menu("Colour");\r
1987     protected Menu calculateMenu = new Menu("Calculate");\r
1988     protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
1989     protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
1990     protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
1991     protected MenuItem remove2LeftMenuItem = new MenuItem();\r
1992     protected MenuItem remove2RightMenuItem = new MenuItem();\r
1993     protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
1994     protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
1995     protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
1996     protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
1997     protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
1998     protected MenuItem sortIDMenuItem = new MenuItem();\r
1999     protected MenuItem sortGroupMenuItem = new MenuItem();\r
2000     protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
2001     protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
2002     protected MenuItem PCAMenuItem = new MenuItem();\r
2003     protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
2004     protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
2005     BorderLayout borderLayout1 = new BorderLayout();\r
2006     public Label statusBar = new Label();\r
2007     protected Menu outputTextboxMenu = new Menu();\r
2008     protected MenuItem clustalColour = new MenuItem();\r
2009     protected MenuItem zappoColour = new MenuItem();\r
2010     protected MenuItem taylorColour = new MenuItem();\r
2011     protected MenuItem hydrophobicityColour = new MenuItem();\r
2012     protected MenuItem helixColour = new MenuItem();\r
2013     protected MenuItem strandColour = new MenuItem();\r
2014     protected MenuItem turnColour = new MenuItem();\r
2015     protected MenuItem buriedColour = new MenuItem();\r
2016     protected MenuItem userDefinedColour = new MenuItem();\r
2017     protected MenuItem PIDColour = new MenuItem();\r
2018     protected MenuItem BLOSUM62Colour = new MenuItem();\r
2019     MenuItem njTreeBlosumMenuItem = new MenuItem();\r
2020     MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
2021     protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
2022     protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
2023     MenuItem overviewMenuItem = new MenuItem();\r
2024     protected MenuItem undoMenuItem = new MenuItem();\r
2025     protected MenuItem redoMenuItem = new MenuItem();\r
2026     protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
2027     MenuItem noColourmenuItem = new MenuItem();\r
2028     protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
2029     protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
2030     MenuItem findMenuItem = new MenuItem();\r
2031   protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
2032     protected MenuItem nucleotideColour = new MenuItem();\r
2033     MenuItem deleteGroups = new MenuItem();\r
2034     MenuItem delete = new MenuItem();\r
2035     MenuItem copy = new MenuItem();\r
2036     MenuItem cut = new MenuItem();\r
2037     Menu pasteMenu = new Menu();\r
2038     MenuItem pasteNew = new MenuItem();\r
2039     MenuItem pasteThis = new MenuItem();\r
2040     protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
2041     protected MenuItem font = new MenuItem();\r
2042     protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
2043     protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
2044     protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
2045     MenuItem modifyPID = new MenuItem();\r
2046     MenuItem modifyConservation = new MenuItem();\r
2047     protected CheckboxMenuItem autoCalculate\r
2048         = new CheckboxMenuItem("Autocalculate Consensus", true);\r
2049     protected Menu sortByTreeMenu = new Menu();\r
2050     Menu sort = new Menu();\r
2051     Menu calculate = new Menu();\r
2052     MenuItem inputText = new MenuItem();\r
2053     Menu helpMenu = new Menu();\r
2054     MenuItem documentation = new MenuItem();\r
2055     MenuItem about = new MenuItem();\r
2056     protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
2057   Panel embeddedMenu;\r
2058   Label embeddedEdit;\r
2059   Label embeddedSelect;\r
2060   Label embeddedView;\r
2061   Label embeddedFormat;\r
2062   Label embeddedColour;\r
2063   Label embeddedFile;\r
2064   Label embeddedHelp;\r
2065   Label embeddedCalculate;\r
2066   FlowLayout flowLayout1;\r
2067 \r
2068   private void jbInit() throws Exception {\r
2069 \r
2070       setMenuBar(alignFrameMenuBar);\r
2071 \r
2072       MenuItem item;\r
2073 \r
2074       // dynamically fill save as menu with available formats\r
2075       for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
2076       {\r
2077 \r
2078         item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);\r
2079 \r
2080         item.addActionListener(new java.awt.event.ActionListener()\r
2081         {\r
2082           public void actionPerformed(ActionEvent e)\r
2083           {\r
2084             outputText_actionPerformed(e);\r
2085           }\r
2086         });\r
2087 \r
2088         outputTextboxMenu.add(item);\r
2089       }\r
2090         closeMenuItem.addActionListener(this);\r
2091         loadApplication.addActionListener(this);\r
2092 \r
2093         loadTree.addActionListener(this);\r
2094         loadAnnotations.addActionListener(this);\r
2095         outputFeatures.addActionListener(this);\r
2096         outputAnnotations.addActionListener(this);\r
2097         selectAllSequenceMenuItem.addActionListener(this);\r
2098         deselectAllSequenceMenuItem.addActionListener(this);\r
2099         invertSequenceMenuItem.addActionListener(this);\r
2100         remove2LeftMenuItem.setLabel("Remove Left");\r
2101         remove2LeftMenuItem.addActionListener(this);\r
2102         remove2RightMenuItem.setLabel("Remove Right");\r
2103         remove2RightMenuItem.addActionListener(this);\r
2104         removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
2105         removeGappedColumnMenuItem.addActionListener(this);\r
2106         removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
2107         removeAllGapsMenuItem.addActionListener(this);\r
2108         viewBoxesMenuItem.setLabel("Boxes");\r
2109         viewBoxesMenuItem.setState(true);\r
2110         viewBoxesMenuItem.addItemListener(this);\r
2111         viewTextMenuItem.setLabel("Text");\r
2112         viewTextMenuItem.setState(true);\r
2113         viewTextMenuItem.addItemListener(this);\r
2114         sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
2115         sortPairwiseMenuItem.addActionListener(this);\r
2116         sortIDMenuItem.setLabel("by ID");\r
2117         sortIDMenuItem.addActionListener(this);\r
2118         sortGroupMenuItem.setLabel("by Group");\r
2119         sortGroupMenuItem.addActionListener(this);\r
2120         removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
2121         removeRedundancyMenuItem.addActionListener(this);\r
2122         pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
2123         pairwiseAlignmentMenuItem.addActionListener(this);\r
2124         PCAMenuItem.setLabel("Principal Component Analysis");\r
2125         PCAMenuItem.addActionListener(this);\r
2126         averageDistanceTreeMenuItem.setLabel(\r
2127             "Average Distance Using % Identity");\r
2128         averageDistanceTreeMenuItem.addActionListener(this);\r
2129         neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
2130         neighbourTreeMenuItem.addActionListener(this);\r
2131         statusBar.setBackground(Color.white);\r
2132         statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
2133         statusBar.setText("Status bar");\r
2134         outputTextboxMenu.setLabel("Output to Textbox");\r
2135         clustalColour.setLabel("Clustalx");\r
2136 \r
2137         clustalColour.addActionListener(this);\r
2138         zappoColour.setLabel("Zappo");\r
2139         zappoColour.addActionListener(this);\r
2140         taylorColour.setLabel("Taylor");\r
2141         taylorColour.addActionListener(this);\r
2142         hydrophobicityColour.setLabel("Hydrophobicity");\r
2143         hydrophobicityColour.addActionListener(this);\r
2144         helixColour.setLabel("Helix Propensity");\r
2145         helixColour.addActionListener(this);\r
2146         strandColour.setLabel("Strand Propensity");\r
2147         strandColour.addActionListener(this);\r
2148         turnColour.setLabel("Turn Propensity");\r
2149         turnColour.addActionListener(this);\r
2150         buriedColour.setLabel("Buried Index");\r
2151         buriedColour.addActionListener(this);\r
2152         userDefinedColour.setLabel("User Defined...");\r
2153         userDefinedColour.addActionListener(this);\r
2154         PIDColour.setLabel("Percentage Identity");\r
2155         PIDColour.addActionListener(this);\r
2156         BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
2157         BLOSUM62Colour.addActionListener(this);\r
2158         avDistanceTreeBlosumMenuItem.setLabel(\r
2159             "Average Distance Using BLOSUM62");\r
2160         avDistanceTreeBlosumMenuItem.addActionListener(this);\r
2161         njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
2162         njTreeBlosumMenuItem.addActionListener(this);\r
2163         annotationPanelMenuItem.setLabel("Show Annotations");\r
2164         annotationPanelMenuItem.addItemListener(this);\r
2165         colourTextMenuItem.setLabel("Colour Text");\r
2166         colourTextMenuItem.addItemListener(this);\r
2167         overviewMenuItem.setLabel("Overview Window");\r
2168         overviewMenuItem.addActionListener(this);\r
2169         undoMenuItem.setEnabled(false);\r
2170         undoMenuItem.setLabel("Undo");\r
2171         undoMenuItem.addActionListener(this);\r
2172         redoMenuItem.setEnabled(false);\r
2173         redoMenuItem.setLabel("Redo");\r
2174         redoMenuItem.addActionListener(this);\r
2175         conservationMenuItem.setLabel("by Conservation");\r
2176         conservationMenuItem.addItemListener(this);\r
2177         noColourmenuItem.setLabel("None");\r
2178         noColourmenuItem.addActionListener(this);\r
2179         wrapMenuItem.setLabel("Wrap");\r
2180         wrapMenuItem.addItemListener(this);\r
2181         renderGapsMenuItem.setLabel("Show Gaps");\r
2182         renderGapsMenuItem.setState(true);\r
2183         renderGapsMenuItem.addItemListener(this);\r
2184         findMenuItem.setLabel("Find...");\r
2185         findMenuItem.addActionListener(this);\r
2186     abovePIDThreshold.setLabel("Above Identity Threshold");\r
2187         abovePIDThreshold.addItemListener(this);\r
2188         nucleotideColour.setLabel("Nucleotide");\r
2189         nucleotideColour.addActionListener(this);\r
2190         deleteGroups.setLabel("Undefine Groups");\r
2191         deleteGroups.addActionListener(this);\r
2192         copy.setLabel("Copy");\r
2193         copy.addActionListener(this);\r
2194         cut.setLabel("Cut");\r
2195         cut.addActionListener(this);\r
2196         delete.setLabel("Delete");\r
2197         delete.addActionListener(this);\r
2198         pasteMenu.setLabel("Paste");\r
2199         pasteNew.setLabel("To New Alignment");\r
2200         pasteNew.addActionListener(this);\r
2201         pasteThis.setLabel("Add To This Alignment");\r
2202         pasteThis.addActionListener(this);\r
2203         applyToAllGroups.setLabel("Apply Colour To All Groups");\r
2204         applyToAllGroups.setState(true);\r
2205         applyToAllGroups.addItemListener(this);\r
2206         font.setLabel("Font...");\r
2207         font.addActionListener(this);\r
2208         scaleAbove.setLabel("Scale Above");\r
2209         scaleAbove.setState(true);\r
2210         scaleAbove.setEnabled(false);\r
2211         scaleAbove.addItemListener(this);\r
2212         scaleLeft.setEnabled(false);\r
2213         scaleLeft.setState(true);\r
2214         scaleLeft.setLabel("Scale Left");\r
2215         scaleLeft.addItemListener(this);\r
2216         scaleRight.setEnabled(false);\r
2217         scaleRight.setState(true);\r
2218         scaleRight.setLabel("Scale Right");\r
2219         scaleRight.addItemListener(this);\r
2220         modifyPID.setLabel("Modify Identity Threshold...");\r
2221         modifyPID.addActionListener(this);\r
2222         modifyConservation.setLabel("Modify Conservation Threshold...");\r
2223         modifyConservation.addActionListener(this);\r
2224         sortByTreeMenu.setLabel("By Tree Order");\r
2225         sort.setLabel("Sort");\r
2226         calculate.setLabel("Calculate Tree");\r
2227         autoCalculate.addItemListener(this);\r
2228         inputText.setLabel("Input from textbox");\r
2229         inputText.addActionListener(this);\r
2230 \r
2231         helpMenu.setLabel("Help");\r
2232         documentation.setLabel("Documentation");\r
2233         documentation.addActionListener(this);\r
2234 \r
2235         about.setLabel("About...");\r
2236         about.addActionListener(this);\r
2237           seqLimits.setState(true);\r
2238     seqLimits.setLabel("Show Sequence Limits");\r
2239     seqLimits.addItemListener(this);\r
2240     featureSettings.setLabel("Feature Settings...");\r
2241     featureSettings.addActionListener(this);\r
2242     sequenceFeatures.setLabel("Sequence Features");\r
2243     sequenceFeatures.addItemListener(this);\r
2244     sequenceFeatures.setState(false);\r
2245     annotationColour.setLabel("by Annotation...");\r
2246     annotationColour.addActionListener(this);\r
2247     invertSequenceMenuItem.setLabel("Invert Sequence Selection");\r
2248     invertColSel.setLabel("Invert Column Selection");\r
2249     menu1.setLabel("Show");\r
2250     showColumns.setLabel("All Columns ");\r
2251     showSeqs.setLabel("All Sequences");\r
2252     menu2.setLabel("Hide");\r
2253     hideColumns.setLabel("Selected Columns");\r
2254     hideSequences.setLabel("Selected Sequences");\r
2255     invertColSel.addActionListener(this);\r
2256     showColumns.addActionListener(this);\r
2257     showSeqs.addActionListener(this);\r
2258     hideColumns.addActionListener(this);\r
2259     hideSequences.addActionListener(this);\r
2260     formatMenu.setLabel("Format");\r
2261     selectMenu.setLabel("Select");\r
2262     newView.setLabel("New View");\r
2263     newView.addActionListener(this);\r
2264     alignFrameMenuBar.add(fileMenu);\r
2265         alignFrameMenuBar.add(editMenu);\r
2266     alignFrameMenuBar.add(selectMenu);\r
2267     alignFrameMenuBar.add(viewMenu);\r
2268     alignFrameMenuBar.add(formatMenu);\r
2269     alignFrameMenuBar.add(colourMenu);\r
2270         alignFrameMenuBar.add(calculateMenu);\r
2271         alignFrameMenuBar.add(helpMenu);\r
2272 \r
2273         fileMenu.add(inputText);\r
2274         fileMenu.add(loadTree);\r
2275         fileMenu.add(loadAnnotations);\r
2276 \r
2277         fileMenu.addSeparator();\r
2278         fileMenu.add(outputTextboxMenu);\r
2279         fileMenu.add(outputFeatures);\r
2280         fileMenu.add(outputAnnotations);\r
2281 \r
2282         if(jalviewServletURL!=null)\r
2283           fileMenu.add(loadApplication);\r
2284 \r
2285         fileMenu.addSeparator();\r
2286         fileMenu.add(closeMenuItem);\r
2287 \r
2288         editMenu.add(undoMenuItem);\r
2289         editMenu.add(redoMenuItem);\r
2290         editMenu.add(cut);\r
2291         editMenu.add(copy);\r
2292         editMenu.add(pasteMenu);\r
2293         editMenu.add(delete);\r
2294         editMenu.addSeparator();\r
2295         editMenu.add(remove2LeftMenuItem);\r
2296         editMenu.add(remove2RightMenuItem);\r
2297         editMenu.add(removeGappedColumnMenuItem);\r
2298         editMenu.add(removeAllGapsMenuItem);\r
2299         editMenu.add(removeRedundancyMenuItem);\r
2300     viewMenu.add(newView);\r
2301     viewMenu.addSeparator();\r
2302     viewMenu.add(menu1);\r
2303     viewMenu.add(menu2);\r
2304     viewMenu.addSeparator();\r
2305     viewMenu.add(annotationPanelMenuItem);\r
2306     viewMenu.addSeparator();\r
2307         viewMenu.add(sequenceFeatures);\r
2308         viewMenu.add(featureSettings);\r
2309     viewMenu.addSeparator();\r
2310         viewMenu.add(overviewMenuItem);\r
2311         colourMenu.add(applyToAllGroups);\r
2312         colourMenu.addSeparator();\r
2313         colourMenu.add(noColourmenuItem);\r
2314         colourMenu.add(clustalColour);\r
2315         colourMenu.add(BLOSUM62Colour);\r
2316         colourMenu.add(PIDColour);\r
2317         colourMenu.add(zappoColour);\r
2318         colourMenu.add(taylorColour);\r
2319         colourMenu.add(hydrophobicityColour);\r
2320         colourMenu.add(helixColour);\r
2321         colourMenu.add(strandColour);\r
2322         colourMenu.add(turnColour);\r
2323         colourMenu.add(buriedColour);\r
2324         colourMenu.add(nucleotideColour);\r
2325         colourMenu.add(userDefinedColour);\r
2326         colourMenu.addSeparator();\r
2327         colourMenu.add(conservationMenuItem);\r
2328         colourMenu.add(modifyConservation);\r
2329         colourMenu.add(abovePIDThreshold);\r
2330         colourMenu.add(modifyPID);\r
2331     colourMenu.add(annotationColour);\r
2332     calculateMenu.add(sort);\r
2333         calculateMenu.add(calculate);\r
2334         calculateMenu.addSeparator();\r
2335         calculateMenu.add(pairwiseAlignmentMenuItem);\r
2336         calculateMenu.add(PCAMenuItem);\r
2337         calculateMenu.add(autoCalculate);\r
2338         this.add(statusBar, BorderLayout.SOUTH);\r
2339         pasteMenu.add(pasteNew);\r
2340         pasteMenu.add(pasteThis);\r
2341         sort.add(sortIDMenuItem);\r
2342         sort.add(sortByTreeMenu);\r
2343         sort.add(sortGroupMenuItem);\r
2344         sort.add(sortPairwiseMenuItem);\r
2345         calculate.add(averageDistanceTreeMenuItem);\r
2346         calculate.add(neighbourTreeMenuItem);\r
2347         calculate.add(avDistanceTreeBlosumMenuItem);\r
2348         calculate.add(njTreeBlosumMenuItem);\r
2349         helpMenu.add(documentation);\r
2350         helpMenu.add(about);\r
2351     menu1.add(showColumns);\r
2352     menu1.add(showSeqs);\r
2353     menu2.add(hideColumns);\r
2354     menu2.add(hideSequences);\r
2355     formatMenu.add(font);\r
2356     formatMenu.add(seqLimits);\r
2357     formatMenu.add(wrapMenuItem);\r
2358     formatMenu.add(scaleAbove);\r
2359     formatMenu.add(scaleLeft);\r
2360     formatMenu.add(scaleRight);\r
2361     formatMenu.add(viewBoxesMenuItem);\r
2362     formatMenu.add(viewTextMenuItem);\r
2363     formatMenu.add(colourTextMenuItem);\r
2364     formatMenu.add(renderGapsMenuItem);\r
2365     selectMenu.add(findMenuItem);\r
2366     selectMenu.addSeparator();\r
2367     selectMenu.add(selectAllSequenceMenuItem);\r
2368     selectMenu.add(deselectAllSequenceMenuItem);\r
2369     selectMenu.add(invertSequenceMenuItem);\r
2370     selectMenu.add(invertColSel);\r
2371     selectMenu.add(deleteGroups);\r
2372   }\r
2373 \r
2374   public void setEmbedded()\r
2375   {\r
2376 \r
2377     embeddedMenu = new Panel();\r
2378     embeddedEdit = new Label("Edit");\r
2379     embeddedSelect = new Label("Select");\r
2380     embeddedView = new Label("View");\r
2381     embeddedFormat = new Label("Format");\r
2382     embeddedColour = new Label("Colour");\r
2383     embeddedFile = new Label("File");\r
2384     embeddedHelp = new Label("Help");\r
2385     embeddedCalculate = new Label("Calculate");\r
2386     flowLayout1 = new FlowLayout();\r
2387     embeddedMenu.setBackground(Color.lightGray);\r
2388     embeddedMenu.setLayout(flowLayout1);\r
2389     embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2390     embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2391     embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2392     embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2393     embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2394     embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2395     embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2396     embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2397     embeddedMenu.add(embeddedFile);\r
2398     embeddedMenu.add(embeddedEdit);\r
2399     embeddedMenu.add(embeddedSelect);\r
2400     embeddedMenu.add(embeddedView);\r
2401     embeddedMenu.add(embeddedFormat);\r
2402     embeddedMenu.add(embeddedColour);\r
2403     embeddedMenu.add(embeddedCalculate);\r
2404     embeddedMenu.add(embeddedHelp);\r
2405     flowLayout1.setAlignment(FlowLayout.LEFT);\r
2406     flowLayout1.setHgap(2);\r
2407     flowLayout1.setVgap(0);\r
2408     embeddedFile.addMouseListener(this);\r
2409     embeddedEdit.addMouseListener(this);\r
2410     embeddedSelect.addMouseListener(this);\r
2411     embeddedView.addMouseListener(this);\r
2412     embeddedFormat.addMouseListener(this);\r
2413     embeddedColour.addMouseListener(this);\r
2414     embeddedCalculate.addMouseListener(this);\r
2415     embeddedHelp.addMouseListener(this);\r
2416 \r
2417     fileMenu.remove(closeMenuItem);\r
2418     fileMenu.remove(3); // Seperator\r
2419 \r
2420     viewport.applet.setLayout(new BorderLayout());\r
2421     viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
2422     viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
2423 \r
2424     alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height\r
2425                        - embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
2426 \r
2427      viewport.applet.add(alignPanel, BorderLayout.CENTER);\r
2428      viewport.applet.validate();\r
2429 \r
2430   }\r
2431 \r
2432 \r
2433 \r
2434   PopupMenu filePopup, editPopup, searchPopup,\r
2435       viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup;\r
2436   MenuItem featureSettings = new MenuItem();\r
2437   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
2438   MenuItem annotationColour = new MenuItem();\r
2439   MenuItem invertColSel = new MenuItem();\r
2440   Menu menu1 = new Menu();\r
2441   MenuItem showColumns = new MenuItem();\r
2442   MenuItem showSeqs = new MenuItem();\r
2443   Menu menu2 = new Menu();\r
2444   MenuItem hideColumns = new MenuItem();\r
2445   MenuItem hideSequences = new MenuItem();\r
2446   Menu formatMenu = new Menu();\r
2447   Menu selectMenu = new Menu();\r
2448   MenuItem newView = new MenuItem();\r
2449 \r
2450   public void mousePressed(MouseEvent evt)\r
2451   {\r
2452     PopupMenu popup = null;\r
2453     Label source = (Label)evt.getSource();\r
2454     if(source==embeddedFile)\r
2455     {\r
2456       popup = filePopup = genPopupMenu(filePopup, fileMenu);\r
2457     }\r
2458     else if(source==embeddedEdit)\r
2459     {\r
2460       popup = editPopup = genPopupMenu(editPopup, editMenu);\r
2461     }\r
2462     else if(source==embeddedSelect)\r
2463     {\r
2464       popup = searchPopup = genPopupMenu(searchPopup, selectMenu);\r
2465     }\r
2466     else if(source==embeddedView)\r
2467     {\r
2468       popup = viewPopup = genPopupMenu(viewPopup, viewMenu);\r
2469     }\r
2470     else if (source ==embeddedFormat)\r
2471     {\r
2472       popup = formatPopup = genPopupMenu(formatPopup, formatMenu);\r
2473     }\r
2474     else if(source==embeddedColour)\r
2475     {\r
2476       popup = colourPopup = genPopupMenu(colourPopup, colourMenu);\r
2477     }\r
2478     else if(source==embeddedCalculate)\r
2479     {\r
2480       popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);\r
2481     }\r
2482     else if(source==embeddedHelp)\r
2483     {\r
2484       popup = helpPopup = genPopupMenu(helpPopup, helpMenu);\r
2485     }\r
2486 \r
2487     embeddedMenu.add(popup);\r
2488     popup.show(embeddedMenu,\r
2489                source.getBounds().x,\r
2490                source.getBounds().y + source.getBounds().getSize().height);\r
2491   }\r
2492 \r
2493   PopupMenu genPopupMenu(PopupMenu popup, Menu original)\r
2494   {\r
2495     if(popup!=null)\r
2496     {\r
2497       return popup;\r
2498     }\r
2499     popup = new PopupMenu();\r
2500     int m, mSize = original.getItemCount();\r
2501     for(m=0; m<mSize; m++)\r
2502     {\r
2503       popup.add(original.getItem(m));\r
2504       mSize--;\r
2505       m--;\r
2506     }\r
2507 \r
2508     return popup;\r
2509   }\r
2510   public void mouseClicked(MouseEvent evt)\r
2511   {}\r
2512   public void mouseReleased(MouseEvent evt)\r
2513   {}\r
2514   public void mouseEntered(MouseEvent evt)\r
2515   {}\r
2516   public void mouseExited(MouseEvent evt)\r
2517   {}\r
2518 \r
2519 }\r
2520 \r