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