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