src/jalview/appletgui/AlignFrame.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 \r
  20 package jalview.appletgui;\r
  21 \r
  22 import jalview.schemes.*;\r
  23 import jalview.datamodel.*;\r
  24 import jalview.analysis.*;\r
  25 import jalview.io.*;\r
  26 import jalview.commands.*;\r
  27 import java.awt.*;\r
  28 import java.awt.event.*;\r
  29 import java.util.*;\r
  30 import java.io.InputStreamReader;\r
  31 import java.io.BufferedReader;\r
  32 import java.net.URL;\r
  33 \r
  34 \r
  35 public class AlignFrame extends Frame implements ActionListener,\r
  36     ItemListener, KeyListener, MouseListener\r
  37 {\r
  38   public AlignmentPanel alignPanel;\r
  39   public AlignViewport viewport;\r
  40   int DEFAULT_WIDTH = 700;\r
  41   int DEFAULT_HEIGHT = 500;\r
  42 \r
  43   String jalviewServletURL;\r
  44 \r
  45 \r
  46    public AlignFrame(AlignmentI al,\r
  47                      jalview.bin.JalviewLite applet,\r
  48                      String title,\r
  49                      boolean embedded)\r
  50   {\r
  51 \r
  52     jalviewServletURL = applet.getParameter("APPLICATION_URL");\r
  53 \r
  54     try{\r
  55       jbInit();\r
  56     }catch(Exception ex)\r
  57     {\r
  58       ex.printStackTrace();\r
  59     }\r
  60 \r
  61     viewport = new AlignViewport(al, applet);\r
  62     alignPanel = new AlignmentPanel(this, viewport);\r
  63 \r
  64     viewport.updateConservation(alignPanel);\r
  65     viewport.updateConsensus(alignPanel);\r
  66 \r
  67     annotationPanelMenuItem.setState(viewport.showAnnotation);\r
  68 \r
  69     seqLimits.setState(viewport.showJVSuffix);\r
  70 \r
  71     if(applet!=null)\r
  72     {\r
  73       String param = applet.getParameter("sortBy");\r
  74       if (param != null)\r
  75       {\r
  76         if (param.equalsIgnoreCase("Id"))\r
  77           sortIDMenuItem_actionPerformed();\r
  78         else if (param.equalsIgnoreCase("Pairwise Identity"))\r
  79           sortPairwiseMenuItem_actionPerformed();\r
  80       }\r
  81 \r
  82       param = applet.getParameter("wrap");\r
  83       if (param != null)\r
  84       {\r
  85         if (param.equalsIgnoreCase("true"))\r
  86         {\r
  87           wrapMenuItem.setState(true);\r
  88           wrapMenuItem_actionPerformed();\r
  89         }\r
  90       }\r
  91 \r
  92       try\r
  93       {\r
  94         param = applet.getParameter("windowWidth");\r
  95         if (param != null)\r
  96         {\r
  97           int width = Integer.parseInt(param);\r
  98           DEFAULT_WIDTH = width;\r
  99         }\r
 100         param = applet.getParameter("windowHeight");\r
 101         if (param != null)\r
 102         {\r
 103           int height = Integer.parseInt(param);\r
 104           DEFAULT_HEIGHT = height;\r
 105         }\r
 106       }\r
 107       catch (Exception ex)\r
 108       {}\r
 109 \r
 110     }\r
 111 \r
 112    //Some JVMS send keyevents to Top frame or lowest panel,\r
 113    //Havent worked out why yet. So add to both this frame and seqCanvas for now\r
 114    this.addKeyListener(this);\r
 115    alignPanel.seqPanel.seqCanvas.addKeyListener(this);\r
 116    alignPanel.idPanel.idCanvas.addKeyListener(this);\r
 117    alignPanel.scalePanel.addKeyListener(this);\r
 118    alignPanel.annotationPanel.addKeyListener(this);\r
 119 \r
 120 \r
 121    if(embedded)\r
 122    {\r
 123      setEmbedded();\r
 124    }\r
 125    else\r
 126    {\r
 127      add(alignPanel, BorderLayout.CENTER);\r
 128      jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,\r
 129                                       DEFAULT_HEIGHT);\r
 130    }\r
 131    alignPanel.validate();\r
 132    alignPanel.repaint();\r
 133   }\r
 134   public AlignViewport getAlignViewport()\r
 135   {\r
 136     return viewport;\r
 137   }\r
 138 \r
 139   public SeqCanvas getSeqcanvas()\r
 140   {\r
 141     return alignPanel.seqPanel.seqCanvas;\r
 142   }\r
 143 \r
 144 \r
 145   /**\r
 146    * DOCUMENT ME!\r
 147    *\r
 148    * @param String DOCUMENT ME!\r
 149    */\r
 150 \r
 151   public void parseFeaturesFile(String file, String type)\r
 152   {\r
 153     Hashtable featureLinks = new Hashtable();\r
 154     boolean featuresFile = false;\r
 155     try{\r
 156       featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,\r
 157                                          alignPanel.seqPanel.seqCanvas.\r
 158                                          getFeatureRenderer().featureColours,\r
 159                                          featureLinks,\r
 160                                          true);\r
 161     }\r
 162     catch(Exception ex)\r
 163     {\r
 164       ex.printStackTrace();\r
 165     }\r
 166 \r
 167     if(featuresFile)\r
 168     {\r
 169       if(featureLinks.size()>0)\r
 170         alignPanel.seqPanel.seqCanvas\r
 171             .getFeatureRenderer().featureLinks = featureLinks;\r
 172       viewport.showSequenceFeatures = true;\r
 173       sequenceFeatures.setState(true);\r
 174       alignPanel.repaint();\r
 175     }\r
 176 \r
 177   }\r
 178 \r
 179 \r
 180   public void keyPressed(KeyEvent evt)\r
 181   {\r
 182     if (viewport.cursorMode\r
 183         && evt.getKeyCode() >= KeyEvent.VK_0\r
 184         && evt.getKeyCode() <= KeyEvent.VK_9)\r
 185     {\r
 186       alignPanel.seqPanel.numberPressed(evt.getKeyChar());\r
 187     }\r
 188 \r
 189     switch (evt.getKeyCode())\r
 190     {\r
 191       case 27: // escape key\r
 192         deselectAllSequenceMenuItem_actionPerformed();\r
 193         break;\r
 194       case KeyEvent.VK_X:\r
 195         if (evt.isControlDown() || evt.isMetaDown())\r
 196         {\r
 197           cut_actionPerformed();\r
 198         }\r
 199         break;\r
 200       case KeyEvent.VK_C:\r
 201         if (viewport.cursorMode && !evt.isControlDown())\r
 202         {\r
 203           alignPanel.seqPanel.setCursorColumn();\r
 204         }\r
 205         if (evt.isControlDown() || evt.isMetaDown())\r
 206         {\r
 207           copy_actionPerformed();\r
 208         }\r
 209         break;\r
 210       case KeyEvent.VK_V:\r
 211         if (evt.isControlDown() || evt.isMetaDown())\r
 212         {\r
 213           paste(true);\r
 214         }\r
 215         break;\r
 216       case KeyEvent.VK_A:\r
 217         if (evt.isControlDown() || evt.isMetaDown())\r
 218         {\r
 219           selectAllSequenceMenuItem_actionPerformed();\r
 220         }\r
 221         break;\r
 222       case KeyEvent.VK_DOWN:\r
 223         if(viewport.cursorMode)\r
 224         {\r
 225           alignPanel.seqPanel.moveCursor(0,1);\r
 226         }\r
 227         else\r
 228           moveSelectedSequences(false);\r
 229         break;\r
 230 \r
 231       case KeyEvent.VK_UP:\r
 232         if (viewport.cursorMode)\r
 233         {\r
 234           alignPanel.seqPanel.moveCursor(0,-1);\r
 235         }\r
 236         else\r
 237           moveSelectedSequences(true);\r
 238         break;\r
 239 \r
 240       case KeyEvent.VK_LEFT:\r
 241         if(viewport.cursorMode)\r
 242         {\r
 243           alignPanel.seqPanel.moveCursor(-1,0);\r
 244         }\r
 245         break;\r
 246 \r
 247       case KeyEvent.VK_RIGHT:\r
 248         if (viewport.cursorMode)\r
 249         {\r
 250           alignPanel.seqPanel.moveCursor(1,0);\r
 251         }\r
 252         break;\r
 253       case KeyEvent.VK_SPACE:\r
 254         if(viewport.cursorMode)\r
 255         {\r
 256           alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()\r
 257                                                 || evt.isShiftDown()\r
 258                                                 || evt.isAltDown()\r
 259               );\r
 260         }\r
 261         break;\r
 262 \r
 263       case KeyEvent.VK_DELETE:\r
 264       case KeyEvent.VK_BACK_SPACE:\r
 265         if(viewport.cursorMode)\r
 266         {\r
 267           alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()\r
 268                                                 || evt.isShiftDown()\r
 269                                                 || evt.isAltDown()\r
 270               );\r
 271         }\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        alignPanel.seqPanel.seqCanvas.repaint();\r
 323        break;\r
 324 \r
 325       case KeyEvent.VK_F:\r
 326         if (evt.isControlDown())\r
 327         {\r
 328           findMenuItem_actionPerformed();\r
 329         }\r
 330         break;\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 \r
 361         alignPanel.repaint();\r
 362         break;\r
 363       }\r
 364       case KeyEvent.VK_PAGE_UP:\r
 365         if (viewport.wrapAlignment)\r
 366           alignPanel.scrollUp(true);\r
 367         else\r
 368           alignPanel.setScrollValues(viewport.startRes,\r
 369                                      viewport.startSeq\r
 370                                      - viewport.endSeq + viewport.startSeq);\r
 371         break;\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   }\r
 382   public void keyReleased(KeyEvent evt)\r
 383   {}\r
 384   public void keyTyped(KeyEvent evt)\r
 385   {}\r
 386 \r
 387 public void itemStateChanged(ItemEvent evt)\r
 388   {\r
 389     if(evt.getSource()==colourTextMenuItem)\r
 390             colourTextMenuItem_actionPerformed();\r
 391     else if(evt.getSource()==wrapMenuItem)\r
 392             wrapMenuItem_actionPerformed();\r
 393     else if(evt.getSource()==scaleAbove)\r
 394             scaleAbove_actionPerformed();\r
 395     else if(evt.getSource()==scaleLeft)\r
 396             scaleLeft_actionPerformed();\r
 397     else if(evt.getSource()==scaleRight)\r
 398             scaleRight_actionPerformed();\r
 399      else if(evt.getSource()==seqLimits)\r
 400       seqLimits_itemStateChanged();\r
 401     else if(evt.getSource()==viewBoxesMenuItem)\r
 402             viewBoxesMenuItem_actionPerformed();\r
 403     else if(evt.getSource()==viewTextMenuItem)\r
 404             viewTextMenuItem_actionPerformed();\r
 405     else if(evt.getSource()==renderGapsMenuItem)\r
 406             renderGapsMenuItem_actionPerformed();\r
 407     else if(evt.getSource()==annotationPanelMenuItem)\r
 408             annotationPanelMenuItem_actionPerformed();\r
 409       else if(evt.getSource()==sequenceFeatures)\r
 410       {\r
 411            viewport.showSequenceFeatures(sequenceFeatures.getState());\r
 412             alignPanel.seqPanel.seqCanvas.repaint();\r
 413       }\r
 414       else if(evt.getSource()==conservationMenuItem)\r
 415             conservationMenuItem_actionPerformed();\r
 416       else if(evt.getSource()==abovePIDThreshold)\r
 417             abovePIDThreshold_actionPerformed();\r
 418           else if(evt.getSource()==applyToAllGroups)\r
 419             applyToAllGroups_actionPerformed();\r
 420       else if(evt.getSource()==autoCalculate)\r
 421           viewport.autocalculateConsensus = autoCalculate.getState();\r
 422   }\r
 423  public void actionPerformed(ActionEvent evt)\r
 424  {\r
 425     Object source = evt.getSource();\r
 426 \r
 427     if(source==inputText)\r
 428       inputText_actionPerformed();\r
 429     else if(source==loadTree)\r
 430       loadTree_actionPerformed();\r
 431     else if(source==loadApplication)\r
 432       launchFullApplication();\r
 433     else if(source==closeMenuItem)\r
 434       closeMenuItem_actionPerformed();\r
 435     else if(source==copy)\r
 436       copy_actionPerformed();\r
 437     else if(source==undoMenuItem)\r
 438       undoMenuItem_actionPerformed();\r
 439     else if(source==redoMenuItem)\r
 440       redoMenuItem_actionPerformed();\r
 441     else if(source==inputText)\r
 442             inputText_actionPerformed();\r
 443     else if(source==closeMenuItem)\r
 444             closeMenuItem_actionPerformed();\r
 445     else if(source==undoMenuItem)\r
 446             undoMenuItem_actionPerformed();\r
 447     else if(source==redoMenuItem)\r
 448             redoMenuItem_actionPerformed();\r
 449     else if(source==copy)\r
 450             copy_actionPerformed();\r
 451     else if(source==pasteNew)\r
 452             pasteNew_actionPerformed();\r
 453     else if(source==pasteThis)\r
 454             pasteThis_actionPerformed();\r
 455     else if(source==cut)\r
 456             cut_actionPerformed();\r
 457     else if(source==delete)\r
 458             delete_actionPerformed();\r
 459     else if(source==deleteGroups)\r
 460             deleteGroups_actionPerformed();\r
 461     else if(source==selectAllSequenceMenuItem)\r
 462             selectAllSequenceMenuItem_actionPerformed();\r
 463     else if(source==deselectAllSequenceMenuItem)\r
 464             deselectAllSequenceMenuItem_actionPerformed();\r
 465     else if(source==invertSequenceMenuItem)\r
 466             invertSequenceMenuItem_actionPerformed();\r
 467     else if(source==invertColSel)\r
 468     { viewport.invertColumnSelection(); alignPanel.repaint(); }\r
 469     else if(source==remove2LeftMenuItem)\r
 470             trimAlignment(true);\r
 471     else if(source==remove2RightMenuItem)\r
 472             trimAlignment(false);\r
 473     else if(source==removeGappedColumnMenuItem)\r
 474             removeGappedColumnMenuItem_actionPerformed();\r
 475     else if(source==removeAllGapsMenuItem)\r
 476             removeAllGapsMenuItem_actionPerformed();\r
 477     else if(source==findMenuItem)\r
 478             findMenuItem_actionPerformed();\r
 479     else if(source==font)\r
 480             font_actionPerformed();\r
 481     else if(source==showColumns)\r
 482     {\r
 483       viewport.showAllHiddenColumns(); alignPanel.repaint();\r
 484     }\r
 485     else if(source==showSeqs)\r
 486     {\r
 487       viewport.showAllHiddenSeqs();\r
 488     }\r
 489     else if(source == hideColumns)\r
 490     {\r
 491       viewport.hideSelectedColumns(); alignPanel.repaint();\r
 492     }\r
 493     else if(source == hideSequences && viewport.getSelectionGroup()!=null)\r
 494     {\r
 495       viewport.hideAllSelectedSeqs();\r
 496     }\r
 497     else if(source==featureSettings)\r
 498             featureSettings_actionPerformed();\r
 499     else if(source==overviewMenuItem)\r
 500             overviewMenuItem_actionPerformed();\r
 501     else if(source==noColourmenuItem)\r
 502             noColourmenuItem_actionPerformed();\r
 503     else if(source==clustalColour)\r
 504             clustalColour_actionPerformed();\r
 505     else if(source==zappoColour)\r
 506             zappoColour_actionPerformed();\r
 507     else if(source==taylorColour)\r
 508             taylorColour_actionPerformed();\r
 509     else if(source==hydrophobicityColour)\r
 510             hydrophobicityColour_actionPerformed();\r
 511     else if(source==helixColour)\r
 512             helixColour_actionPerformed();\r
 513     else if(source==strandColour)\r
 514             strandColour_actionPerformed();\r
 515     else if(source==turnColour)\r
 516             turnColour_actionPerformed();\r
 517     else if(source==buriedColour)\r
 518             buriedColour_actionPerformed();\r
 519     else if(source==nucleotideColour)\r
 520             nucleotideColour_actionPerformed();\r
 521     else if(source==modifyPID)\r
 522             modifyPID_actionPerformed();\r
 523     else if(source==modifyConservation)\r
 524             modifyConservation_actionPerformed();\r
 525     else if(source==userDefinedColour)\r
 526             userDefinedColour_actionPerformed();\r
 527     else if(source==PIDColour)\r
 528             PIDColour_actionPerformed();\r
 529     else if(source==BLOSUM62Colour)\r
 530             BLOSUM62Colour_actionPerformed();\r
 531     else if(source==annotationColour)\r
 532            new AnnotationColourChooser(viewport, alignPanel);\r
 533     else if(source==sortPairwiseMenuItem)\r
 534             sortPairwiseMenuItem_actionPerformed();\r
 535     else if(source==sortIDMenuItem)\r
 536             sortIDMenuItem_actionPerformed();\r
 537     else if(source==sortGroupMenuItem)\r
 538             sortGroupMenuItem_actionPerformed();\r
 539     else if(source==removeRedundancyMenuItem)\r
 540             removeRedundancyMenuItem_actionPerformed();\r
 541     else if(source==pairwiseAlignmentMenuItem)\r
 542             pairwiseAlignmentMenuItem_actionPerformed();\r
 543     else if(source==PCAMenuItem)\r
 544             PCAMenuItem_actionPerformed();\r
 545     else if(source==averageDistanceTreeMenuItem)\r
 546             averageDistanceTreeMenuItem_actionPerformed();\r
 547     else if(source==neighbourTreeMenuItem)\r
 548             neighbourTreeMenuItem_actionPerformed();\r
 549     else if(source==njTreeBlosumMenuItem)\r
 550             njTreeBlosumMenuItem_actionPerformed();\r
 551     else if(source==avDistanceTreeBlosumMenuItem)\r
 552             avTreeBlosumMenuItem_actionPerformed();\r
 553     else if(source==documentation)\r
 554             documentation_actionPerformed();\r
 555     else if(source==about)\r
 556             about_actionPerformed();\r
 557 \r
 558  }\r
 559 \r
 560   public void inputText_actionPerformed()\r
 561   {\r
 562     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
 563     Frame frame = new Frame();\r
 564     frame.add(cap);\r
 565     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
 566   }\r
 567 \r
 568   protected void outputText_actionPerformed(ActionEvent e)\r
 569   {\r
 570     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
 571     Frame frame = new Frame();\r
 572     frame.add(cap);\r
 573     jalview.bin.JalviewLite.addFrame(frame,\r
 574                                      "Alignment output - " + e.getActionCommand(),\r
 575                                      600, 500);\r
 576     cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
 577                                               viewport.getAlignment().getSequences(),\r
 578                                                       viewport.showJVSuffix));\r
 579   }\r
 580 \r
 581   void launchFullApplication()\r
 582   {\r
 583     StringBuffer url = new StringBuffer(jalviewServletURL);\r
 584 \r
 585     url.append("?open="+\r
 586                appendProtocol( viewport.applet.getParameter("file") ) );\r
 587 \r
 588     if(viewport.applet.getParameter("features")!=null)\r
 589     {\r
 590       url.append( "&features=" );\r
 591       url.append( appendProtocol( viewport.applet.getParameter("features") ) );\r
 592     }\r
 593 \r
 594     if(viewport.applet.getParameter("annotations")!=null)\r
 595     {\r
 596       url.append( "&annotations=" );\r
 597       url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );\r
 598     }\r
 599 \r
 600     if(viewport.applet.getParameter("jnetfile")!=null)\r
 601     {\r
 602       url.append( "&annotations=" );\r
 603       url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) );\r
 604     }\r
 605 \r
 606     if(viewport.applet.getParameter("defaultColour")!=null)\r
 607     {\r
 608       url.append("&colour=" +\r
 609                  removeWhiteSpace(viewport.applet.getParameter("defaultColour"))\r
 610           );\r
 611     }\r
 612 \r
 613     if(viewport.applet.getParameter("userDefinedColour")!=null)\r
 614     {\r
 615       url.append( "&colour=" +\r
 616                  removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )\r
 617          );\r
 618     }\r
 619 \r
 620     showURL(url.toString(), "FULL_APP");\r
 621   }\r
 622 \r
 623 \r
 624   String removeWhiteSpace(String colour)\r
 625   {\r
 626     StringBuffer sb = new StringBuffer();\r
 627     for (int i = 0; i < colour.length(); i++)\r
 628     {\r
 629       if (Character.isWhitespace(colour.charAt(i)))\r
 630         sb.append("%20");\r
 631       else\r
 632         sb.append(colour.charAt(i));\r
 633     }\r
 634 \r
 635     return sb.toString();\r
 636   }\r
 637 \r
 638 \r
 639   String appendProtocol(String url)\r
 640   {\r
 641     try{\r
 642        new URL(url);\r
 643     }catch(java.net.MalformedURLException ex)\r
 644     {\r
 645       url = viewport.applet.getCodeBase()+url;\r
 646     }\r
 647     return url;\r
 648   }\r
 649 \r
 650   public void closeMenuItem_actionPerformed()\r
 651   {\r
 652     PaintRefresher.components.remove(viewport.alignment);\r
 653     if(PaintRefresher.components.size()==0 && viewport.applet==null)\r
 654       System.exit(0);\r
 655 \r
 656     this.dispose();\r
 657   }\r
 658 \r
 659 \r
 660   /**\r
 661    * DOCUMENT ME!\r
 662    */\r
 663   void updateEditMenuBar()\r
 664   {\r
 665 \r
 666     if (viewport.historyList.size() > 0)\r
 667     {\r
 668       undoMenuItem.setEnabled(true);\r
 669       CommandI command = (CommandI) viewport.historyList.peek();\r
 670       undoMenuItem.setLabel("Undo " + command.getDescription());\r
 671     }\r
 672     else\r
 673     {\r
 674       undoMenuItem.setEnabled(false);\r
 675       undoMenuItem.setLabel("Undo");\r
 676     }\r
 677 \r
 678     if (viewport.redoList.size() > 0)\r
 679     {\r
 680       redoMenuItem.setEnabled(true);\r
 681 \r
 682       CommandI command = (CommandI) viewport.redoList.peek();\r
 683       redoMenuItem.setLabel("Redo " + command.getDescription());\r
 684     }\r
 685     else\r
 686     {\r
 687       redoMenuItem.setEnabled(false);\r
 688       redoMenuItem.setLabel("Redo");\r
 689     }\r
 690   }\r
 691 \r
 692   public void addHistoryItem(CommandI command)\r
 693   {\r
 694     if(command.getSize()>0)\r
 695     {\r
 696       viewport.historyList.push(command);\r
 697       viewport.redoList.removeAllElements();\r
 698       updateEditMenuBar();\r
 699       viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
 700     }\r
 701   }\r
 702 \r
 703   protected void undoMenuItem_actionPerformed()\r
 704   {\r
 705     CommandI command = (CommandI)viewport.historyList.pop();\r
 706     viewport.redoList.push(command);\r
 707     command.undoCommand();\r
 708 \r
 709     viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
 710     updateEditMenuBar();\r
 711     viewport.firePropertyChange("alignment", null,\r
 712                                 viewport.getAlignment().getSequences());\r
 713   }\r
 714 \r
 715   protected void redoMenuItem_actionPerformed()\r
 716   {\r
 717     CommandI command = (CommandI) viewport.redoList.pop();\r
 718     viewport.historyList.push(command);\r
 719     command.doCommand();\r
 720     viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;\r
 721 \r
 722     updateEditMenuBar();\r
 723     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 724   }\r
 725 \r
 726 \r
 727   public void moveSelectedSequences(boolean up)\r
 728   {\r
 729     SequenceGroup sg = viewport.getSelectionGroup();\r
 730     if (sg == null)\r
 731     {\r
 732       return;\r
 733     }\r
 734 \r
 735     if (up)\r
 736     {\r
 737       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 738       {\r
 739         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 740         if (!sg.getSequences(false).contains(seq))\r
 741         {\r
 742           continue;\r
 743         }\r
 744 \r
 745         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 746         if (sg.getSequences(false).contains(temp))\r
 747         {\r
 748           continue;\r
 749         }\r
 750 \r
 751         viewport.alignment.getSequences().setElementAt(temp, i);\r
 752         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 753       }\r
 754     }\r
 755     else\r
 756     {\r
 757       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 758       {\r
 759         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 760         if (!sg.getSequences(true).contains(seq))\r
 761         {\r
 762           continue;\r
 763         }\r
 764 \r
 765         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 766         if (sg.getSequences(true).contains(temp))\r
 767         {\r
 768           continue;\r
 769         }\r
 770 \r
 771         viewport.alignment.getSequences().setElementAt(temp, i);\r
 772         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 773       }\r
 774     }\r
 775 \r
 776     alignPanel.repaint();\r
 777   }\r
 778 \r
 779   static StringBuffer copiedSequences;\r
 780   static Vector copiedHiddenColumns;\r
 781   protected void copy_actionPerformed()\r
 782   {\r
 783     if (viewport.getSelectionGroup() == null)\r
 784     {\r
 785       return;\r
 786     }\r
 787 \r
 788     SequenceGroup sg = viewport.getSelectionGroup();\r
 789     copiedSequences = new StringBuffer();\r
 790     Hashtable orderedSeqs = new Hashtable();\r
 791     for (int i = 0; i < sg.getSize(false); i++)\r
 792     {\r
 793       SequenceI seq = sg.getSequenceAt(i);\r
 794       int index = viewport.alignment.findIndex(seq);\r
 795       orderedSeqs.put(index + "", seq);\r
 796     }\r
 797 \r
 798     int index = 0, startRes, endRes;\r
 799     char ch;\r
 800 \r
 801     if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)\r
 802     {\r
 803       copiedHiddenColumns = new Vector();\r
 804       int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
 805       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();\r
 806            i++)\r
 807       {\r
 808         int[] region = (int[])\r
 809             viewport.getColumnSelection().getHiddenColumns().elementAt(i);\r
 810 \r
 811         copiedHiddenColumns.addElement(new int[]\r
 812                                  {region[0] - hiddenOffset,\r
 813                                  region[1] - hiddenOffset});\r
 814       }\r
 815     }\r
 816     else\r
 817       copiedHiddenColumns = null;\r
 818 \r
 819 \r
 820     for (int i = 0; i < sg.getSize(false); i++)\r
 821     {\r
 822         SequenceI seq = null;\r
 823 \r
 824         while (seq == null)\r
 825         {\r
 826             if (orderedSeqs.containsKey(index + ""))\r
 827             {\r
 828                 seq = (SequenceI) orderedSeqs.get(index + "");\r
 829                 index++;\r
 830 \r
 831                 break;\r
 832             }\r
 833             else\r
 834             {\r
 835                 index++;\r
 836             }\r
 837         }\r
 838 \r
 839         //FIND START RES\r
 840         //Returns residue following index if gap\r
 841         startRes = seq.findPosition(sg.getStartRes());\r
 842 \r
 843         //FIND END RES\r
 844         //Need to find the residue preceeding index if gap\r
 845         endRes = 0;\r
 846 \r
 847         for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
 848         {\r
 849           ch = seq.getCharAt(j);\r
 850           if (!jalview.util.Comparison.isGap( (ch)))\r
 851           {\r
 852             endRes++;\r
 853           }\r
 854         }\r
 855 \r
 856         if(endRes>0)\r
 857         {\r
 858           endRes += seq.getStart() -1;\r
 859         }\r
 860 \r
 861         copiedSequences.append(seq.getName() + "\t" +\r
 862             startRes + "\t" +\r
 863             endRes + "\t" +\r
 864             seq.getSequence(sg.getStartRes(),\r
 865                 sg.getEndRes() + 1) + "\n");\r
 866     }\r
 867 \r
 868   }\r
 869 \r
 870   protected void pasteNew_actionPerformed()\r
 871   {\r
 872     paste(true);\r
 873   }\r
 874 \r
 875   protected void pasteThis_actionPerformed()\r
 876   {\r
 877     paste(false);\r
 878   }\r
 879 \r
 880   void paste(boolean newAlignment)\r
 881   {\r
 882     try\r
 883     {\r
 884       if (copiedSequences == null)\r
 885       {\r
 886         return;\r
 887       }\r
 888 \r
 889       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 890       Vector seqs = new Vector();\r
 891       while (st.hasMoreElements())\r
 892       {\r
 893         String name = st.nextToken();\r
 894         int start = Integer.parseInt(st.nextToken());\r
 895         int end = Integer.parseInt(st.nextToken());\r
 896         seqs.addElement(new Sequence(name, st.nextToken(), start, end));\r
 897       }\r
 898       SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 899       for (int i = 0; i < seqs.size(); i++)\r
 900       {\r
 901         newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
 902       }\r
 903 \r
 904       if (newAlignment)\r
 905       {\r
 906         String newtitle = new String("Copied sequences");\r
 907         if (getTitle().startsWith("Copied sequences"))\r
 908         {\r
 909           newtitle = getTitle();\r
 910         }\r
 911         else\r
 912         {\r
 913           newtitle = newtitle.concat("- from " + getTitle());\r
 914         }\r
 915         AlignFrame af = new AlignFrame(new Alignment(newSeqs),\r
 916                                        viewport.applet,\r
 917                                        newtitle,\r
 918                                        false);\r
 919         if (copiedHiddenColumns != null)\r
 920         {\r
 921           for (int i = 0; i < copiedHiddenColumns.size(); i++)\r
 922           {\r
 923             int[] region = (int[]) copiedHiddenColumns.elementAt(i);\r
 924             af.viewport.hideColumns(region[0], region[1]);\r
 925           }\r
 926         }\r
 927 \r
 928 \r
 929         jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,\r
 930                                          DEFAULT_HEIGHT);\r
 931       }\r
 932       else\r
 933       {\r
 934         //!newAlignment\r
 935         addHistoryItem(new EditCommand(\r
 936             "Add sequences",\r
 937             EditCommand.PASTE,\r
 938             newSeqs,\r
 939             0,\r
 940             viewport.alignment.getWidth(),\r
 941             viewport.alignment)\r
 942             );\r
 943 \r
 944         viewport.setEndSeq(viewport.alignment.getHeight());\r
 945         viewport.alignment.getWidth();\r
 946         viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 947       }\r
 948 \r
 949     }\r
 950     catch (Exception ex)\r
 951     {} // could be anything being pasted in here\r
 952 \r
 953   }\r
 954 \r
 955   protected void cut_actionPerformed()\r
 956   {\r
 957     copy_actionPerformed();\r
 958     delete_actionPerformed();\r
 959   }\r
 960 \r
 961   protected void delete_actionPerformed()\r
 962   {\r
 963 \r
 964     SequenceGroup sg = viewport.getSelectionGroup();\r
 965     if (sg == null)\r
 966     {\r
 967       return;\r
 968     }\r
 969 \r
 970     Vector seqs = new Vector();\r
 971     SequenceI seq;\r
 972     for (int i = 0; i < sg.getSize(false); i++)\r
 973     {\r
 974       seq = sg.getSequenceAt(i);\r
 975       seqs.addElement(seq);\r
 976     }\r
 977 \r
 978 \r
 979    // If the cut affects all sequences, remove highlighted columns\r
 980    if (sg.getSize(false) == viewport.alignment.getHeight())\r
 981    {\r
 982      viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
 983          sg.getEndRes() + 1);\r
 984    }\r
 985 \r
 986 \r
 987     SequenceI [] cut = new SequenceI[seqs.size()];\r
 988     for(int i=0; i<seqs.size(); i++)\r
 989       cut[i] = (SequenceI)seqs.elementAt(i);\r
 990 \r
 991 \r
 992     /*\r
 993     //ADD HISTORY ITEM\r
 994     */\r
 995     addHistoryItem(new EditCommand("Cut Sequences",\r
 996                                       EditCommand.CUT,\r
 997                                       cut,\r
 998                                       sg.getStartRes(),\r
 999                                       sg.getEndRes()-sg.getStartRes()+1,\r
1000                                       viewport.alignment));\r
1001 \r
1002 \r
1003     viewport.setSelectionGroup(null);\r
1004     viewport.alignment.deleteGroup(sg);\r
1005 \r
1006     viewport.firePropertyChange("alignment", null,\r
1007                                   viewport.getAlignment().getSequences());\r
1008 \r
1009     if (viewport.getAlignment().getHeight() < 1)\r
1010     {\r
1011         this.setVisible(false);\r
1012     }\r
1013   }\r
1014 \r
1015   protected void deleteGroups_actionPerformed()\r
1016   {\r
1017     viewport.alignment.deleteAllGroups();\r
1018     viewport.sequenceColours=null;\r
1019     viewport.setSelectionGroup(null);\r
1020 \r
1021     alignPanel.repaint();\r
1022   }\r
1023 \r
1024   public void selectAllSequenceMenuItem_actionPerformed()\r
1025   {\r
1026     SequenceGroup sg = new SequenceGroup();\r
1027     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
1028     {\r
1029       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
1030     }\r
1031     sg.setEndRes(viewport.alignment.getWidth()-1);\r
1032     viewport.setSelectionGroup(sg);\r
1033     alignPanel.repaint();\r
1034     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
1035   }\r
1036 \r
1037   public void deselectAllSequenceMenuItem_actionPerformed()\r
1038   {\r
1039     if(viewport.cursorMode)\r
1040     {\r
1041       alignPanel.seqPanel.keyboardNo1=null;\r
1042       alignPanel.seqPanel.keyboardNo2=null;\r
1043     }\r
1044     viewport.setSelectionGroup(null);\r
1045     viewport.getColumnSelection().clear();\r
1046     viewport.setSelectionGroup(null);\r
1047     alignPanel.idPanel.idCanvas.searchResults = null;\r
1048     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
1049     alignPanel.repaint();\r
1050     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
1051   }\r
1052 \r
1053   public void invertSequenceMenuItem_actionPerformed()\r
1054   {\r
1055     SequenceGroup sg = viewport.getSelectionGroup();\r
1056     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
1057     {\r
1058       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
1059     }\r
1060 \r
1061     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
1062   }\r
1063 \r
1064   void trimAlignment(boolean trimLeft)\r
1065   {\r
1066     ColumnSelection colSel = viewport.getColumnSelection();\r
1067     int column;\r
1068 \r
1069     if (colSel.size() > 0)\r
1070     {\r
1071       if(trimLeft)\r
1072         column = colSel.getMin();\r
1073       else\r
1074         column = colSel.getMax();\r
1075 \r
1076       SequenceI [] seqs;\r
1077       if(viewport.getSelectionGroup()!=null)\r
1078         seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
1079       else\r
1080         seqs = viewport.alignment.getSequencesArray();\r
1081 \r
1082 \r
1083       TrimRegionCommand trimRegion;\r
1084       if(trimLeft)\r
1085       {\r
1086         trimRegion = new TrimRegionCommand("Remove Left",\r
1087                                     TrimRegionCommand.TRIM_LEFT,\r
1088                                     seqs,\r
1089                                     column,\r
1090                                     viewport.alignment,\r
1091                                     viewport.colSel,\r
1092                                     viewport.selectionGroup);\r
1093         viewport.setStartRes(0);\r
1094       }\r
1095      else\r
1096      {\r
1097        trimRegion = new TrimRegionCommand("Remove Right",\r
1098                                    TrimRegionCommand.TRIM_RIGHT,\r
1099                                    seqs,\r
1100                                    column,\r
1101                                    viewport.alignment,\r
1102                                    viewport.colSel,\r
1103                                    viewport.selectionGroup);\r
1104      }\r
1105 \r
1106      statusBar.setText("Removed "+trimRegion.getSize()+" columns.");\r
1107 \r
1108 \r
1109       addHistoryItem(trimRegion);\r
1110 \r
1111       Vector groups = viewport.alignment.getGroups();\r
1112 \r
1113       for (int i = 0; i < groups.size(); i++)\r
1114       {\r
1115         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1116 \r
1117         if ( (trimLeft && !sg.adjustForRemoveLeft(column))\r
1118             || (!trimLeft && !sg.adjustForRemoveRight(column)))\r
1119         {\r
1120           viewport.alignment.deleteGroup(sg);\r
1121         }\r
1122       }\r
1123 \r
1124       viewport.firePropertyChange("alignment", null,\r
1125                                   viewport.getAlignment().getSequences());\r
1126     }\r
1127   }\r
1128 \r
1129 \r
1130   public void removeGappedColumnMenuItem_actionPerformed()\r
1131   {\r
1132     int start = 0, end = viewport.alignment.getWidth()-1;\r
1133 \r
1134     SequenceI[] seqs;\r
1135     if (viewport.getSelectionGroup() != null)\r
1136     {\r
1137       seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
1138       start = viewport.getSelectionGroup().getStartRes();\r
1139       end = viewport.getSelectionGroup().getEndRes();\r
1140     }\r
1141     else\r
1142       seqs = viewport.alignment.getSequencesArray();\r
1143 \r
1144 \r
1145     RemoveGapColCommand removeGapCols =\r
1146         new RemoveGapColCommand("Remove Gapped Columns",\r
1147                                 seqs,\r
1148                                 start, end,\r
1149                                 viewport.getGapCharacter());\r
1150 \r
1151     addHistoryItem(removeGapCols);\r
1152 \r
1153     statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns.");\r
1154 \r
1155     //This is to maintain viewport position on first residue\r
1156     //of first sequence\r
1157     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
1158     int startRes = seq.findPosition(viewport.startRes);\r
1159    // ShiftList shifts;\r
1160    // viewport.getAlignment().removeGaps(shifts=new ShiftList());\r
1161    // edit.alColumnChanges=shifts.getInverse();\r
1162    // if (viewport.hasHiddenColumns)\r
1163    //   viewport.getColumnSelection().compensateForEdits(shifts);\r
1164    viewport.setStartRes(seq.findIndex(startRes)-1);\r
1165    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1166 \r
1167   }\r
1168 \r
1169   public void removeAllGapsMenuItem_actionPerformed()\r
1170   {\r
1171     int start = 0, end = viewport.alignment.getWidth()-1;\r
1172 \r
1173     SequenceI[] seqs;\r
1174     if (viewport.getSelectionGroup() != null)\r
1175     {\r
1176       seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
1177       start = viewport.getSelectionGroup().getStartRes();\r
1178       end = viewport.getSelectionGroup().getEndRes();\r
1179     }\r
1180     else\r
1181       seqs = viewport.alignment.getSequencesArray();\r
1182 \r
1183     //This is to maintain viewport position on first residue\r
1184     //of first sequence\r
1185     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
1186     int startRes = seq.findPosition(viewport.startRes);\r
1187 \r
1188     addHistoryItem(new RemoveGapsCommand("Remove Gaps",\r
1189                                            seqs,\r
1190                                            start, end,\r
1191                      viewport.getGapCharacter()));\r
1192 \r
1193     viewport.setStartRes(seq.findIndex(startRes)-1);\r
1194 \r
1195     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1196 \r
1197   }\r
1198 \r
1199   public void findMenuItem_actionPerformed()\r
1200   {\r
1201     new Finder(alignPanel);\r
1202   }\r
1203 \r
1204   public void font_actionPerformed()\r
1205   {\r
1206     new FontChooser(alignPanel);\r
1207   }\r
1208 \r
1209 \r
1210   public void seqLimits_itemStateChanged()\r
1211   {\r
1212     viewport.setShowJVSuffix(seqLimits.getState());\r
1213     alignPanel.fontChanged();\r
1214     alignPanel.repaint();\r
1215   }\r
1216 \r
1217 \r
1218   protected void colourTextMenuItem_actionPerformed()\r
1219   {\r
1220     viewport.setColourText(colourTextMenuItem.getState());\r
1221     alignPanel.repaint();\r
1222   }\r
1223 \r
1224   protected void wrapMenuItem_actionPerformed()\r
1225   {\r
1226     viewport.setWrapAlignment(wrapMenuItem.getState());\r
1227     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
1228     scaleAbove.setEnabled(wrapMenuItem.getState());\r
1229     scaleLeft.setEnabled(wrapMenuItem.getState());\r
1230     scaleRight.setEnabled(wrapMenuItem.getState());\r
1231     alignPanel.repaint();\r
1232   }\r
1233 \r
1234 \r
1235   protected void scaleAbove_actionPerformed()\r
1236   {\r
1237     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
1238     alignPanel.repaint();\r
1239   }\r
1240 \r
1241   protected void scaleLeft_actionPerformed()\r
1242   {\r
1243     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
1244     alignPanel.repaint();\r
1245   }\r
1246 \r
1247   protected void scaleRight_actionPerformed()\r
1248   {\r
1249     viewport.setScaleRightWrapped(scaleRight.getState());\r
1250     alignPanel.repaint();\r
1251   }\r
1252 \r
1253   public void viewBoxesMenuItem_actionPerformed()\r
1254   {\r
1255     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
1256     alignPanel.repaint();\r
1257   }\r
1258 \r
1259   public void viewTextMenuItem_actionPerformed()\r
1260   {\r
1261     viewport.setShowText(viewTextMenuItem.getState());\r
1262     alignPanel.repaint();\r
1263   }\r
1264 \r
1265   protected void renderGapsMenuItem_actionPerformed()\r
1266   {\r
1267     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
1268     alignPanel.repaint();\r
1269   }\r
1270 \r
1271   public void annotationPanelMenuItem_actionPerformed()\r
1272   {\r
1273     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
1274     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
1275   }\r
1276 \r
1277   public void featureSettings_actionPerformed()\r
1278   {\r
1279     new FeatureSettings(viewport, alignPanel);\r
1280   }\r
1281 \r
1282   public void overviewMenuItem_actionPerformed()\r
1283   {\r
1284     if (alignPanel.overviewPanel != null)\r
1285     {\r
1286       return;\r
1287     }\r
1288 \r
1289     Frame frame = new Frame();\r
1290     OverviewPanel overview = new OverviewPanel(alignPanel);\r
1291     frame.add(overview);\r
1292     // +50 must allow for applet frame window\r
1293     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
1294                                      overview.preferredSize().width,\r
1295                                      overview.preferredSize().height + 50);\r
1296 \r
1297     frame.pack();\r
1298     frame.addWindowListener(new WindowAdapter()\r
1299     {\r
1300       public void windowClosing(WindowEvent e)\r
1301       {\r
1302         alignPanel.setOverviewPanel(null);\r
1303       };\r
1304     });\r
1305 \r
1306     alignPanel.setOverviewPanel(overview);\r
1307 \r
1308   }\r
1309 \r
1310   protected void noColourmenuItem_actionPerformed()\r
1311   {\r
1312     changeColour(null);\r
1313   }\r
1314 \r
1315   public void clustalColour_actionPerformed()\r
1316   {\r
1317     abovePIDThreshold.setState(false);\r
1318     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
1319                                           viewport.alignment.getWidth()));\r
1320   }\r
1321 \r
1322   public void zappoColour_actionPerformed()\r
1323   {\r
1324     changeColour(new ZappoColourScheme());\r
1325   }\r
1326 \r
1327   public void taylorColour_actionPerformed()\r
1328   {\r
1329     changeColour(new TaylorColourScheme());\r
1330   }\r
1331 \r
1332   public void hydrophobicityColour_actionPerformed()\r
1333   {\r
1334     changeColour(new HydrophobicColourScheme());\r
1335   }\r
1336 \r
1337   public void helixColour_actionPerformed()\r
1338   {\r
1339     changeColour(new HelixColourScheme());\r
1340   }\r
1341 \r
1342   public void strandColour_actionPerformed()\r
1343   {\r
1344     changeColour(new StrandColourScheme());\r
1345   }\r
1346 \r
1347   public void turnColour_actionPerformed()\r
1348   {\r
1349     changeColour(new TurnColourScheme());\r
1350   }\r
1351 \r
1352   public void buriedColour_actionPerformed()\r
1353   {\r
1354     changeColour(new BuriedColourScheme());\r
1355   }\r
1356 \r
1357   public void nucleotideColour_actionPerformed()\r
1358   {\r
1359     changeColour(new NucleotideColourScheme());\r
1360   }\r
1361 \r
1362   protected void applyToAllGroups_actionPerformed()\r
1363   {\r
1364     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
1365   }\r
1366 \r
1367   void changeColour(ColourSchemeI cs)\r
1368   {\r
1369     int threshold = 0;\r
1370 \r
1371     if(cs!=null)\r
1372     {\r
1373       if (viewport.getAbovePIDThreshold())\r
1374       {\r
1375         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
1376 \r
1377         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1378 \r
1379         viewport.setGlobalColourScheme(cs);\r
1380       }\r
1381       else\r
1382       {\r
1383         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1384       }\r
1385 \r
1386       if (viewport.getConservationSelected())\r
1387       {\r
1388 \r
1389         Alignment al = (Alignment) viewport.alignment;\r
1390         Conservation c = new Conservation("All",\r
1391                                           ResidueProperties.propHash, 3,\r
1392                                           al.getSequences(), 0,\r
1393                                           al.getWidth() - 1);\r
1394 \r
1395         c.calculate();\r
1396         c.verdict(false, viewport.ConsPercGaps);\r
1397 \r
1398         cs.setConservation(c);\r
1399 \r
1400         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
1401             "Background"));\r
1402 \r
1403       }\r
1404       else\r
1405       {\r
1406         cs.setConservation(null);\r
1407       }\r
1408 \r
1409       cs.setConsensus(viewport.hconsensus);\r
1410 \r
1411     }\r
1412     viewport.setGlobalColourScheme(cs);\r
1413 \r
1414     if (viewport.getColourAppliesToAllGroups())\r
1415     {\r
1416       Vector groups = viewport.alignment.getGroups();\r
1417       for (int i = 0; i < groups.size(); i++)\r
1418       {\r
1419         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1420 \r
1421         if(cs==null)\r
1422         {\r
1423           sg.cs = null;\r
1424           continue;\r
1425         }\r
1426         if (cs instanceof ClustalxColourScheme)\r
1427         {\r
1428           sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());\r
1429         }\r
1430         else\r
1431         {\r
1432           try\r
1433           {\r
1434             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
1435           }\r
1436           catch (Exception ex)\r
1437           {\r
1438             ex.printStackTrace();\r
1439             sg.cs = cs;\r
1440           }\r
1441         }\r
1442 \r
1443         if (viewport.getAbovePIDThreshold()\r
1444             || cs instanceof PIDColourScheme\r
1445             || cs instanceof Blosum62ColourScheme)\r
1446         {\r
1447           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1448           sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));\r
1449         }\r
1450         else\r
1451           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1452 \r
1453         if (viewport.getConservationSelected())\r
1454         {\r
1455           Conservation c = new Conservation("Group",\r
1456                                             ResidueProperties.propHash, 3,\r
1457                                             sg.getSequences(true), 0,\r
1458                                             viewport.alignment.getWidth() - 1);\r
1459           c.calculate();\r
1460           c.verdict(false, viewport.ConsPercGaps);\r
1461           sg.cs.setConservation(c);\r
1462         }\r
1463         else\r
1464         {\r
1465           sg.cs.setConservation(null);\r
1466           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1467         }\r
1468 \r
1469       }\r
1470     }\r
1471 \r
1472 \r
1473     if (alignPanel.getOverviewPanel() != null)\r
1474     {\r
1475       alignPanel.getOverviewPanel().updateOverviewImage();\r
1476     }\r
1477 \r
1478     alignPanel.repaint();\r
1479   }\r
1480 \r
1481 \r
1482 \r
1483   protected void modifyPID_actionPerformed()\r
1484   {\r
1485     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
1486     {\r
1487       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
1488                                      "Background");\r
1489       SliderPanel.showPIDSlider();\r
1490     }\r
1491   }\r
1492 \r
1493   protected void modifyConservation_actionPerformed()\r
1494   {\r
1495     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
1496     {\r
1497       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
1498                                         "Background");\r
1499       SliderPanel.showConservationSlider();\r
1500     }\r
1501   }\r
1502 \r
1503   protected void conservationMenuItem_actionPerformed()\r
1504   {\r
1505     viewport.setConservationSelected(conservationMenuItem.getState());\r
1506 \r
1507     viewport.setAbovePIDThreshold(false);\r
1508     abovePIDThreshold.setState(false);\r
1509 \r
1510     changeColour(viewport.getGlobalColourScheme());\r
1511 \r
1512     modifyConservation_actionPerformed();\r
1513   }\r
1514 \r
1515   public void abovePIDThreshold_actionPerformed()\r
1516   {\r
1517     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
1518 \r
1519     conservationMenuItem.setState(false);\r
1520     viewport.setConservationSelected(false);\r
1521 \r
1522     changeColour(viewport.getGlobalColourScheme());\r
1523 \r
1524     modifyPID_actionPerformed();\r
1525   }\r
1526 \r
1527   public void userDefinedColour_actionPerformed()\r
1528   {\r
1529     new UserDefinedColours(alignPanel, null);\r
1530   }\r
1531 \r
1532   public void PIDColour_actionPerformed()\r
1533   {\r
1534     changeColour(new PIDColourScheme());\r
1535   }\r
1536 \r
1537   public void BLOSUM62Colour_actionPerformed()\r
1538   {\r
1539     changeColour(new Blosum62ColourScheme());\r
1540   }\r
1541 \r
1542   public void sortPairwiseMenuItem_actionPerformed()\r
1543   {\r
1544     SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();\r
1545     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1546                               viewport.getAlignment().getSequenceAt(0));\r
1547     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment));\r
1548     alignPanel.repaint();\r
1549   }\r
1550 \r
1551   public void sortIDMenuItem_actionPerformed()\r
1552   {\r
1553   //  addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1554    //                                HistoryItem.SORT));\r
1555     AlignmentSorter.sortByID(viewport.getAlignment());\r
1556     alignPanel.repaint();\r
1557   }\r
1558 \r
1559   public void sortGroupMenuItem_actionPerformed()\r
1560   {\r
1561   //  addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1562   //                                 HistoryItem.SORT));\r
1563     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1564     alignPanel.repaint();\r
1565 \r
1566   }\r
1567 \r
1568   public void removeRedundancyMenuItem_actionPerformed()\r
1569   {\r
1570      new RedundancyPanel(alignPanel);\r
1571   }\r
1572 \r
1573   public void pairwiseAlignmentMenuItem_actionPerformed()\r
1574   {\r
1575     if (viewport.getSelectionGroup()!=null\r
1576         && viewport.getSelectionGroup().getSize(false) > 1)\r
1577     {\r
1578       Frame frame = new Frame();\r
1579       frame.add(new PairwiseAlignPanel(alignPanel));\r
1580       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1581     }\r
1582   }\r
1583 \r
1584   public void PCAMenuItem_actionPerformed()\r
1585   {\r
1586     //are the sequences aligned?\r
1587     if (!viewport.alignment.isAligned())\r
1588     {\r
1589       SequenceI current;\r
1590       int Width = viewport.getAlignment().getWidth();\r
1591 \r
1592       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1593            i++)\r
1594       {\r
1595         current = viewport.getAlignment().getSequenceAt(i);\r
1596 \r
1597         if (current.getLength() < Width)\r
1598         {\r
1599           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1600         }\r
1601       }\r
1602       alignPanel.repaint();\r
1603     }\r
1604 \r
1605     if ( (viewport.getSelectionGroup() != null &&\r
1606           viewport.getSelectionGroup().getSize(false) < 4 &&\r
1607           viewport.getSelectionGroup().getSize(false) > 0)\r
1608         || viewport.getAlignment().getHeight() < 4)\r
1609     {\r
1610       return;\r
1611     }\r
1612 \r
1613     try\r
1614     {\r
1615       new PCAPanel(viewport);\r
1616     }\r
1617     catch (java.lang.OutOfMemoryError ex)\r
1618     {\r
1619     }\r
1620 \r
1621   }\r
1622 \r
1623   public void averageDistanceTreeMenuItem_actionPerformed()\r
1624   {\r
1625     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1626   }\r
1627 \r
1628   public void neighbourTreeMenuItem_actionPerformed()\r
1629   {\r
1630     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1631   }\r
1632 \r
1633   protected void njTreeBlosumMenuItem_actionPerformed()\r
1634   {\r
1635     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1636   }\r
1637 \r
1638   protected void avTreeBlosumMenuItem_actionPerformed()\r
1639   {\r
1640     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1641   }\r
1642 \r
1643   void NewTreePanel(String type, String pwType, String title)\r
1644   {\r
1645     //are the sequences aligned?\r
1646     if (!viewport.alignment.isAligned())\r
1647     {\r
1648       SequenceI current;\r
1649       int Width = viewport.getAlignment().getWidth();\r
1650 \r
1651       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1652            i++)\r
1653       {\r
1654         current = viewport.getAlignment().getSequenceAt(i);\r
1655 \r
1656         if (current.getLength() < Width)\r
1657         {\r
1658           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1659         }\r
1660       }\r
1661       alignPanel.repaint();\r
1662 \r
1663     }\r
1664 \r
1665     if ( (viewport.getSelectionGroup() != null &&\r
1666           viewport.getSelectionGroup().getSize(false) > 1)\r
1667       || (viewport.getSelectionGroup() == null\r
1668           && viewport.alignment.getHeight() > 1))\r
1669     {\r
1670       final TreePanel tp = new TreePanel(viewport,\r
1671                                          type,\r
1672                                          pwType);\r
1673 \r
1674       addTreeMenuItem(tp, title);\r
1675 \r
1676       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1677     }\r
1678   }\r
1679 \r
1680   void loadTree_actionPerformed()\r
1681   {\r
1682       CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
1683       cap.setText("Paste your Newick tree file here.");\r
1684       cap.treeImport = true;\r
1685       Frame frame = new Frame();\r
1686       frame.add(cap);\r
1687       jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);\r
1688   }\r
1689 \r
1690   public void loadTree(jalview.io.NewickFile tree, String treeFile)\r
1691   {\r
1692     TreePanel tp = new TreePanel(viewport,\r
1693                                  treeFile,\r
1694                                  "From File - ",\r
1695                                  tree);\r
1696     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
1697     addTreeMenuItem(tp, treeFile);\r
1698   }\r
1699 \r
1700   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1701   {\r
1702     final MenuItem item = new MenuItem(title);\r
1703     sortByTreeMenu.add(item);\r
1704     item.addActionListener(new java.awt.event.ActionListener()\r
1705     {\r
1706       public void actionPerformed(ActionEvent evt)\r
1707       {\r
1708       //  addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1709       //                                 HistoryItem.SORT));\r
1710         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1711         alignPanel.repaint();\r
1712       }\r
1713     });\r
1714 \r
1715     treePanel.addWindowListener(new WindowAdapter()\r
1716     {\r
1717       public void windowClosing(WindowEvent e)\r
1718       {\r
1719         sortByTreeMenu.remove(item);\r
1720       };\r
1721     });\r
1722   }\r
1723 \r
1724   protected void documentation_actionPerformed()\r
1725   {\r
1726     showURL("http://www.jalview.org/help.html", "HELP");\r
1727   }\r
1728 \r
1729   protected void about_actionPerformed()\r
1730   {\r
1731 \r
1732     class AboutPanel extends Canvas\r
1733     {\r
1734       String version;\r
1735       public AboutPanel(String version)\r
1736       { this.version = version; }\r
1737 \r
1738       public void paint(Graphics g)\r
1739       {\r
1740         g.setColor(Color.white);\r
1741         g.fillRect(0, 0, getSize().width, getSize().height);\r
1742         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1743         FontMetrics fm = g.getFontMetrics();\r
1744         int fh = fm.getHeight();\r
1745         int y = 5, x = 7;\r
1746         g.setColor(Color.black);\r
1747         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1748         g.drawString("Jalview - Release "+version, 200, y += fh);\r
1749         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1750         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1751                      x, y += fh * 2);\r
1752         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1753                      x, y += fh);\r
1754         g.drawString(\r
1755             "For any issues relating to Jalview, email help@jalview.org", x,\r
1756             y += fh);\r
1757         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1758         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1759                      x, y += fh);\r
1760         g.drawString("Bioinformatics,  2004 20;426-7.", x, y += fh);\r
1761       }\r
1762     }\r
1763 \r
1764     String version = "test";\r
1765     java.net.URL url = getClass().getResource("/.build_properties");\r
1766     if (url != null)\r
1767     {\r
1768       try\r
1769       {\r
1770         BufferedReader reader = new BufferedReader(new InputStreamReader(\r
1771             url.openStream()));\r
1772         String line;\r
1773         while ( (line = reader.readLine()) != null)\r
1774         {\r
1775           if (line.indexOf("VERSION") > -1)\r
1776           {\r
1777             version = line.substring(line.indexOf("=") + 1);\r
1778           }\r
1779         }\r
1780       }\r
1781       catch (Exception ex)\r
1782       {\r
1783         ex.printStackTrace();\r
1784       }\r
1785     }\r
1786 \r
1787 \r
1788     Frame frame = new Frame();\r
1789     frame.add(new AboutPanel(version));\r
1790     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1791 \r
1792   }\r
1793 \r
1794   public void showURL(String url, String target)\r
1795   {\r
1796     if (viewport.applet == null)\r
1797     {\r
1798       System.out.println("Not running as applet - no browser available.");\r
1799     }\r
1800     else\r
1801     {\r
1802       try\r
1803       {\r
1804         System.out.println("Show url: "+url);\r
1805         viewport.applet.getAppletContext().showDocument(new java.net.URL(url),\r
1806                                                target);\r
1807       }\r
1808       catch (Exception ex)\r
1809       {\r
1810         ex.printStackTrace();\r
1811       }\r
1812     }\r
1813   }\r
1814 \r
1815 \r
1816   //////////////////////////////////////////////////////////////////////////////////\r
1817   //JBuilder Graphics here\r
1818 \r
1819     protected MenuBar alignFrameMenuBar = new MenuBar();\r
1820     protected Menu fileMenu = new Menu("File");\r
1821     protected MenuItem loadApplication = new MenuItem("View in Full Application");\r
1822     protected MenuItem loadTree = new MenuItem("Load Associated Tree");\r
1823     protected MenuItem closeMenuItem = new MenuItem("Close");\r
1824     protected Menu editMenu = new Menu("Edit");\r
1825     protected Menu viewMenu = new Menu("View");\r
1826     protected Menu colourMenu = new Menu("Colour");\r
1827     protected Menu calculateMenu = new Menu("Calculate");\r
1828     protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
1829     protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
1830     protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
1831     protected MenuItem remove2LeftMenuItem = new MenuItem();\r
1832     protected MenuItem remove2RightMenuItem = new MenuItem();\r
1833     protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
1834     protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
1835     protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
1836     protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
1837     protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
1838     protected MenuItem sortIDMenuItem = new MenuItem();\r
1839     protected MenuItem sortGroupMenuItem = new MenuItem();\r
1840     protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
1841     protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
1842     protected MenuItem PCAMenuItem = new MenuItem();\r
1843     protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
1844     protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
1845     BorderLayout borderLayout1 = new BorderLayout();\r
1846     public Label statusBar = new Label();\r
1847     protected Menu outputTextboxMenu = new Menu();\r
1848     protected MenuItem clustalColour = new MenuItem();\r
1849     protected MenuItem zappoColour = new MenuItem();\r
1850     protected MenuItem taylorColour = new MenuItem();\r
1851     protected MenuItem hydrophobicityColour = new MenuItem();\r
1852     protected MenuItem helixColour = new MenuItem();\r
1853     protected MenuItem strandColour = new MenuItem();\r
1854     protected MenuItem turnColour = new MenuItem();\r
1855     protected MenuItem buriedColour = new MenuItem();\r
1856     protected MenuItem userDefinedColour = new MenuItem();\r
1857     protected MenuItem PIDColour = new MenuItem();\r
1858     protected MenuItem BLOSUM62Colour = new MenuItem();\r
1859     MenuItem njTreeBlosumMenuItem = new MenuItem();\r
1860     MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
1861     protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
1862     protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
1863     MenuItem overviewMenuItem = new MenuItem();\r
1864     protected MenuItem undoMenuItem = new MenuItem();\r
1865     protected MenuItem redoMenuItem = new MenuItem();\r
1866     protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
1867     MenuItem noColourmenuItem = new MenuItem();\r
1868     protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
1869     protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
1870     MenuItem findMenuItem = new MenuItem();\r
1871   protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
1872     protected MenuItem nucleotideColour = new MenuItem();\r
1873     MenuItem deleteGroups = new MenuItem();\r
1874     MenuItem delete = new MenuItem();\r
1875     MenuItem copy = new MenuItem();\r
1876     MenuItem cut = new MenuItem();\r
1877     Menu pasteMenu = new Menu();\r
1878     MenuItem pasteNew = new MenuItem();\r
1879     MenuItem pasteThis = new MenuItem();\r
1880     protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
1881     protected MenuItem font = new MenuItem();\r
1882     protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
1883     protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
1884     protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
1885     MenuItem modifyPID = new MenuItem();\r
1886     MenuItem modifyConservation = new MenuItem();\r
1887     protected CheckboxMenuItem autoCalculate\r
1888         = new CheckboxMenuItem("Autocalculate Consensus", true);\r
1889     protected Menu sortByTreeMenu = new Menu();\r
1890     Menu sort = new Menu();\r
1891     Menu calculate = new Menu();\r
1892     MenuItem inputText = new MenuItem();\r
1893     Menu helpMenu = new Menu();\r
1894     MenuItem documentation = new MenuItem();\r
1895     MenuItem about = new MenuItem();\r
1896     protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
1897   Panel embeddedMenu;\r
1898   Label embeddedEdit;\r
1899   Label embeddedSelect;\r
1900   Label embeddedView;\r
1901   Label embeddedFormat;\r
1902   Label embeddedColour;\r
1903   Label embeddedFile;\r
1904   Label embeddedHelp;\r
1905   Label embeddedCalculate;\r
1906   FlowLayout flowLayout1;\r
1907 \r
1908   private void jbInit() throws Exception {\r
1909 \r
1910       setMenuBar(alignFrameMenuBar);\r
1911 \r
1912       MenuItem item;\r
1913 \r
1914       // dynamically fill save as menu with available formats\r
1915       for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
1916       {\r
1917 \r
1918         item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);\r
1919 \r
1920         item.addActionListener(new java.awt.event.ActionListener()\r
1921         {\r
1922           public void actionPerformed(ActionEvent e)\r
1923           {\r
1924             outputText_actionPerformed(e);\r
1925           }\r
1926         });\r
1927 \r
1928         outputTextboxMenu.add(item);\r
1929       }\r
1930         closeMenuItem.addActionListener(this);\r
1931         loadApplication.addActionListener(this);\r
1932 \r
1933         loadTree.addActionListener(this);\r
1934         selectAllSequenceMenuItem.addActionListener(this);\r
1935         deselectAllSequenceMenuItem.addActionListener(this);\r
1936         invertSequenceMenuItem.addActionListener(this);\r
1937         remove2LeftMenuItem.setLabel("Remove Left");\r
1938         remove2LeftMenuItem.addActionListener(this);\r
1939         remove2RightMenuItem.setLabel("Remove Right");\r
1940         remove2RightMenuItem.addActionListener(this);\r
1941         removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
1942         removeGappedColumnMenuItem.addActionListener(this);\r
1943         removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
1944         removeAllGapsMenuItem.addActionListener(this);\r
1945         viewBoxesMenuItem.setLabel("Boxes");\r
1946         viewBoxesMenuItem.setState(true);\r
1947         viewBoxesMenuItem.addItemListener(this);\r
1948         viewTextMenuItem.setLabel("Text");\r
1949         viewTextMenuItem.setState(true);\r
1950         viewTextMenuItem.addItemListener(this);\r
1951         sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
1952         sortPairwiseMenuItem.addActionListener(this);\r
1953         sortIDMenuItem.setLabel("by ID");\r
1954         sortIDMenuItem.addActionListener(this);\r
1955         sortGroupMenuItem.setLabel("by Group");\r
1956         sortGroupMenuItem.addActionListener(this);\r
1957         removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
1958         removeRedundancyMenuItem.addActionListener(this);\r
1959         pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
1960         pairwiseAlignmentMenuItem.addActionListener(this);\r
1961         PCAMenuItem.setLabel("Principal Component Analysis");\r
1962         PCAMenuItem.addActionListener(this);\r
1963         averageDistanceTreeMenuItem.setLabel(\r
1964             "Average Distance Using % Identity");\r
1965         averageDistanceTreeMenuItem.addActionListener(this);\r
1966         neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
1967         neighbourTreeMenuItem.addActionListener(this);\r
1968         alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
1969         statusBar.setBackground(Color.white);\r
1970         statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
1971         statusBar.setText("Status bar");\r
1972         outputTextboxMenu.setLabel("Output to Textbox");\r
1973         clustalColour.setLabel("Clustalx");\r
1974 \r
1975         clustalColour.addActionListener(this);\r
1976         zappoColour.setLabel("Zappo");\r
1977         zappoColour.addActionListener(this);\r
1978         taylorColour.setLabel("Taylor");\r
1979         taylorColour.addActionListener(this);\r
1980         hydrophobicityColour.setLabel("Hydrophobicity");\r
1981         hydrophobicityColour.addActionListener(this);\r
1982         helixColour.setLabel("Helix Propensity");\r
1983         helixColour.addActionListener(this);\r
1984         strandColour.setLabel("Strand Propensity");\r
1985         strandColour.addActionListener(this);\r
1986         turnColour.setLabel("Turn Propensity");\r
1987         turnColour.addActionListener(this);\r
1988         buriedColour.setLabel("Buried Index");\r
1989         buriedColour.addActionListener(this);\r
1990         userDefinedColour.setLabel("User Defined...");\r
1991         userDefinedColour.addActionListener(this);\r
1992         PIDColour.setLabel("Percentage Identity");\r
1993         PIDColour.addActionListener(this);\r
1994         BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
1995         BLOSUM62Colour.addActionListener(this);\r
1996         avDistanceTreeBlosumMenuItem.setLabel(\r
1997             "Average Distance Using BLOSUM62");\r
1998         avDistanceTreeBlosumMenuItem.addActionListener(this);\r
1999         njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
2000         njTreeBlosumMenuItem.addActionListener(this);\r
2001         annotationPanelMenuItem.setLabel("Show Annotations");\r
2002         annotationPanelMenuItem.addItemListener(this);\r
2003         colourTextMenuItem.setLabel("Colour Text");\r
2004         colourTextMenuItem.addItemListener(this);\r
2005         overviewMenuItem.setLabel("Overview Window");\r
2006         overviewMenuItem.addActionListener(this);\r
2007         undoMenuItem.setEnabled(false);\r
2008         undoMenuItem.setLabel("Undo");\r
2009         undoMenuItem.addActionListener(this);\r
2010         redoMenuItem.setEnabled(false);\r
2011         redoMenuItem.setLabel("Redo");\r
2012         redoMenuItem.addActionListener(this);\r
2013         conservationMenuItem.setLabel("by Conservation");\r
2014         conservationMenuItem.addItemListener(this);\r
2015         noColourmenuItem.setLabel("None");\r
2016         noColourmenuItem.addActionListener(this);\r
2017         wrapMenuItem.setLabel("Wrap");\r
2018         wrapMenuItem.addItemListener(this);\r
2019         renderGapsMenuItem.setLabel("Show Gaps");\r
2020         renderGapsMenuItem.setState(true);\r
2021         renderGapsMenuItem.addItemListener(this);\r
2022         findMenuItem.setLabel("Find...");\r
2023         findMenuItem.addActionListener(this);\r
2024     abovePIDThreshold.setLabel("Above Identity Threshold");\r
2025         abovePIDThreshold.addItemListener(this);\r
2026         nucleotideColour.setLabel("Nucleotide");\r
2027         nucleotideColour.addActionListener(this);\r
2028         deleteGroups.setLabel("Undefine Groups");\r
2029         deleteGroups.addActionListener(this);\r
2030         copy.setLabel("Copy");\r
2031         copy.addActionListener(this);\r
2032         cut.setLabel("Cut");\r
2033         cut.addActionListener(this);\r
2034         delete.setLabel("Delete");\r
2035         delete.addActionListener(this);\r
2036         pasteMenu.setLabel("Paste");\r
2037         pasteNew.setLabel("To New Alignment");\r
2038         pasteNew.addActionListener(this);\r
2039         pasteThis.setLabel("Add To This Alignment");\r
2040         pasteThis.addActionListener(this);\r
2041         applyToAllGroups.setLabel("Apply Colour To All Groups");\r
2042         applyToAllGroups.setState(true);\r
2043         applyToAllGroups.addItemListener(this);\r
2044         font.setLabel("Font...");\r
2045         font.addActionListener(this);\r
2046         scaleAbove.setLabel("Scale Above");\r
2047         scaleAbove.setState(true);\r
2048         scaleAbove.setEnabled(false);\r
2049         scaleAbove.addItemListener(this);\r
2050         scaleLeft.setEnabled(false);\r
2051         scaleLeft.setState(true);\r
2052         scaleLeft.setLabel("Scale Left");\r
2053         scaleLeft.addItemListener(this);\r
2054         scaleRight.setEnabled(false);\r
2055         scaleRight.setState(true);\r
2056         scaleRight.setLabel("Scale Right");\r
2057         scaleRight.addItemListener(this);\r
2058         modifyPID.setLabel("Modify Identity Threshold...");\r
2059         modifyPID.addActionListener(this);\r
2060         modifyConservation.setLabel("Modify Conservation Threshold...");\r
2061         modifyConservation.addActionListener(this);\r
2062         sortByTreeMenu.setLabel("By Tree Order");\r
2063         sort.setLabel("Sort");\r
2064         calculate.setLabel("Calculate Tree");\r
2065         autoCalculate.addItemListener(this);\r
2066         inputText.setLabel("Input from textbox");\r
2067         inputText.addActionListener(this);\r
2068 \r
2069         helpMenu.setLabel("Help");\r
2070         documentation.setLabel("Documentation");\r
2071         documentation.addActionListener(this);\r
2072 \r
2073         about.setLabel("About...");\r
2074         about.addActionListener(this);\r
2075           seqLimits.setState(true);\r
2076     seqLimits.setLabel("Show Sequence Limits");\r
2077     seqLimits.addItemListener(this);\r
2078     featureSettings.setLabel("Feature Settings...");\r
2079     featureSettings.addActionListener(this);\r
2080     sequenceFeatures.setLabel("Sequence Features");\r
2081     sequenceFeatures.addItemListener(this);\r
2082     sequenceFeatures.setState(false);\r
2083     annotationColour.setLabel("by Annotation...");\r
2084     annotationColour.addActionListener(this);\r
2085     invertSequenceMenuItem.setLabel("Invert Sequence Selection");\r
2086     invertColSel.setLabel("Invert Column Selection");\r
2087     menu1.setLabel("Show");\r
2088     showColumns.setLabel("All Columns ");\r
2089     showSeqs.setLabel("All Sequences");\r
2090     menu2.setLabel("Hide");\r
2091     hideColumns.setLabel("Selected Columns");\r
2092     hideSequences.setLabel("Selected Sequences");\r
2093     invertColSel.addActionListener(this);\r
2094     showColumns.addActionListener(this);\r
2095     showSeqs.addActionListener(this);\r
2096     hideColumns.addActionListener(this);\r
2097     hideSequences.addActionListener(this);\r
2098     formatMenu.setLabel("Format");\r
2099     selectMenu.setLabel("Select");\r
2100     alignFrameMenuBar.add(fileMenu);\r
2101         alignFrameMenuBar.add(editMenu);\r
2102     alignFrameMenuBar.add(selectMenu);\r
2103     alignFrameMenuBar.add(viewMenu);\r
2104     alignFrameMenuBar.add(formatMenu);\r
2105     alignFrameMenuBar.add(colourMenu);\r
2106         alignFrameMenuBar.add(calculateMenu);\r
2107         alignFrameMenuBar.add(helpMenu);\r
2108         fileMenu.add(inputText);\r
2109         fileMenu.add(outputTextboxMenu);\r
2110         if(jalviewServletURL!=null)\r
2111           fileMenu.add(loadApplication);\r
2112         fileMenu.addSeparator();\r
2113         fileMenu.add(loadTree);\r
2114         fileMenu.add(closeMenuItem);\r
2115         editMenu.add(undoMenuItem);\r
2116         editMenu.add(redoMenuItem);\r
2117         editMenu.add(cut);\r
2118         editMenu.add(copy);\r
2119         editMenu.add(pasteMenu);\r
2120         editMenu.add(delete);\r
2121     editMenu.addSeparator();\r
2122         editMenu.add(remove2LeftMenuItem);\r
2123         editMenu.add(remove2RightMenuItem);\r
2124         editMenu.add(removeGappedColumnMenuItem);\r
2125         editMenu.add(removeAllGapsMenuItem);\r
2126         editMenu.add(removeRedundancyMenuItem);\r
2127     viewMenu.add(menu1);\r
2128     viewMenu.add(menu2);\r
2129     viewMenu.addSeparator();\r
2130     viewMenu.add(annotationPanelMenuItem);\r
2131     viewMenu.addSeparator();\r
2132         viewMenu.add(sequenceFeatures);\r
2133         viewMenu.add(featureSettings);\r
2134     viewMenu.addSeparator();\r
2135         viewMenu.add(overviewMenuItem);\r
2136         colourMenu.add(applyToAllGroups);\r
2137         colourMenu.addSeparator();\r
2138         colourMenu.add(noColourmenuItem);\r
2139         colourMenu.add(clustalColour);\r
2140         colourMenu.add(BLOSUM62Colour);\r
2141         colourMenu.add(PIDColour);\r
2142         colourMenu.add(zappoColour);\r
2143         colourMenu.add(taylorColour);\r
2144         colourMenu.add(hydrophobicityColour);\r
2145         colourMenu.add(helixColour);\r
2146         colourMenu.add(strandColour);\r
2147         colourMenu.add(turnColour);\r
2148         colourMenu.add(buriedColour);\r
2149         colourMenu.add(nucleotideColour);\r
2150         colourMenu.add(userDefinedColour);\r
2151         colourMenu.addSeparator();\r
2152         colourMenu.add(conservationMenuItem);\r
2153         colourMenu.add(modifyConservation);\r
2154         colourMenu.add(abovePIDThreshold);\r
2155         colourMenu.add(modifyPID);\r
2156     colourMenu.add(annotationColour);\r
2157     calculateMenu.add(sort);\r
2158         calculateMenu.add(calculate);\r
2159         calculateMenu.addSeparator();\r
2160         calculateMenu.add(pairwiseAlignmentMenuItem);\r
2161         calculateMenu.add(PCAMenuItem);\r
2162         calculateMenu.add(autoCalculate);\r
2163         this.add(statusBar, BorderLayout.SOUTH);\r
2164         pasteMenu.add(pasteNew);\r
2165         pasteMenu.add(pasteThis);\r
2166         sort.add(sortIDMenuItem);\r
2167         sort.add(sortByTreeMenu);\r
2168         sort.add(sortGroupMenuItem);\r
2169         sort.add(sortPairwiseMenuItem);\r
2170         calculate.add(averageDistanceTreeMenuItem);\r
2171         calculate.add(neighbourTreeMenuItem);\r
2172         calculate.add(avDistanceTreeBlosumMenuItem);\r
2173         calculate.add(njTreeBlosumMenuItem);\r
2174         helpMenu.add(documentation);\r
2175         helpMenu.add(about);\r
2176     menu1.add(showColumns);\r
2177     menu1.add(showSeqs);\r
2178     menu2.add(hideColumns);\r
2179     menu2.add(hideSequences);\r
2180     formatMenu.add(font);\r
2181     formatMenu.add(seqLimits);\r
2182     formatMenu.add(wrapMenuItem);\r
2183     formatMenu.add(scaleAbove);\r
2184     formatMenu.add(scaleLeft);\r
2185     formatMenu.add(scaleRight);\r
2186     formatMenu.add(viewBoxesMenuItem);\r
2187     formatMenu.add(viewTextMenuItem);\r
2188     formatMenu.add(colourTextMenuItem);\r
2189     formatMenu.add(renderGapsMenuItem);\r
2190     selectMenu.add(findMenuItem);\r
2191     selectMenu.addSeparator();\r
2192     selectMenu.add(selectAllSequenceMenuItem);\r
2193     selectMenu.add(deselectAllSequenceMenuItem);\r
2194     selectMenu.add(invertSequenceMenuItem);\r
2195     selectMenu.add(invertColSel);\r
2196     selectMenu.add(deleteGroups);\r
2197   }\r
2198 \r
2199   public void setEmbedded()\r
2200   {\r
2201 \r
2202     embeddedMenu = new Panel();\r
2203     embeddedEdit = new Label("Edit");\r
2204     embeddedSelect = new Label("Select");\r
2205     embeddedView = new Label("View");\r
2206     embeddedFormat = new Label("Label");\r
2207     embeddedColour = new Label("Colour");\r
2208     embeddedFile = new Label("File");\r
2209     embeddedHelp = new Label("Help");\r
2210     embeddedCalculate = new Label("Calculate");\r
2211     flowLayout1 = new FlowLayout();\r
2212     embeddedMenu.setBackground(Color.lightGray);\r
2213     embeddedMenu.setLayout(flowLayout1);\r
2214     embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2215     embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2216     embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2217     embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2218     embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2219     embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2220     embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2221     embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2222     embeddedMenu.add(embeddedFile);\r
2223     embeddedMenu.add(embeddedEdit);\r
2224     embeddedMenu.add(embeddedSelect);\r
2225     embeddedMenu.add(embeddedView);\r
2226     embeddedMenu.add(embeddedFormat);\r
2227     embeddedMenu.add(embeddedColour);\r
2228     embeddedMenu.add(embeddedCalculate);\r
2229     embeddedMenu.add(embeddedHelp);\r
2230     flowLayout1.setAlignment(FlowLayout.LEFT);\r
2231     flowLayout1.setHgap(2);\r
2232     flowLayout1.setVgap(0);\r
2233     embeddedFile.addMouseListener(this);\r
2234     embeddedEdit.addMouseListener(this);\r
2235     embeddedSelect.addMouseListener(this);\r
2236     embeddedView.addMouseListener(this);\r
2237     embeddedFormat.addMouseListener(this);\r
2238     embeddedColour.addMouseListener(this);\r
2239     embeddedCalculate.addMouseListener(this);\r
2240     embeddedHelp.addMouseListener(this);\r
2241 \r
2242    // setVisible(false);\r
2243     fileMenu.remove(closeMenuItem);\r
2244     fileMenu.remove(3); // Seperator\r
2245 \r
2246     viewport.applet.setLayout(new BorderLayout());\r
2247     viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
2248     viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
2249    // viewport.applet.validate();\r
2250 \r
2251     alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height\r
2252                        - embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
2253 \r
2254      viewport.applet.add(alignPanel, BorderLayout.CENTER);\r
2255      viewport.applet.validate();\r
2256 \r
2257   }\r
2258 \r
2259 \r
2260 \r
2261   PopupMenu filePopup, editPopup, searchPopup,\r
2262       viewPopup, colourPopup, calculatePopup, helpPopup;\r
2263   MenuItem featureSettings = new MenuItem();\r
2264   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
2265   MenuItem annotationColour = new MenuItem();\r
2266   MenuItem invertColSel = new MenuItem();\r
2267   Menu menu1 = new Menu();\r
2268   MenuItem showColumns = new MenuItem();\r
2269   MenuItem showSeqs = new MenuItem();\r
2270   Menu menu2 = new Menu();\r
2271   MenuItem hideColumns = new MenuItem();\r
2272   MenuItem hideSequences = new MenuItem();\r
2273   Menu formatMenu = new Menu();\r
2274   Menu selectMenu = new Menu();\r
2275 \r
2276   public void mousePressed(MouseEvent evt)\r
2277   {\r
2278     PopupMenu popup = null;\r
2279     Label source = (Label)evt.getSource();\r
2280     if(source==embeddedFile)\r
2281     {\r
2282       popup = filePopup = genPopupMenu(filePopup, fileMenu);\r
2283     }\r
2284     else if(source==embeddedEdit)\r
2285     {\r
2286       popup = editPopup = genPopupMenu(editPopup, editMenu);\r
2287     }\r
2288     else if(source==embeddedSelect)\r
2289     {\r
2290       popup = searchPopup = genPopupMenu(searchPopup, selectMenu);\r
2291     }\r
2292     else if(source==embeddedView)\r
2293     {\r
2294       popup = viewPopup = genPopupMenu(viewPopup, viewMenu);\r
2295     }\r
2296     else if (source ==embeddedFormat)\r
2297     {\r
2298       popup = viewPopup = genPopupMenu(viewPopup, formatMenu);\r
2299     }\r
2300     else if(source==embeddedColour)\r
2301     {\r
2302       popup = colourPopup = genPopupMenu(colourPopup, colourMenu);\r
2303     }\r
2304     else if(source==embeddedCalculate)\r
2305     {\r
2306       popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);\r
2307     }\r
2308     else if(source==embeddedHelp)\r
2309     {\r
2310       popup = helpPopup = genPopupMenu(helpPopup, helpMenu);\r
2311     }\r
2312 \r
2313     embeddedMenu.add(popup);\r
2314     popup.show(embeddedMenu,\r
2315                source.getBounds().x,\r
2316                source.getBounds().y + source.getBounds().getSize().height);\r
2317   }\r
2318 \r
2319   PopupMenu genPopupMenu(PopupMenu popup, Menu original)\r
2320   {\r
2321     if(popup!=null)\r
2322     {\r
2323       return popup;\r
2324     }\r
2325     popup = new PopupMenu();\r
2326     int m, mSize = original.getItemCount();\r
2327     for(m=0; m<mSize; m++)\r
2328     {\r
2329       popup.add(original.getItem(m));\r
2330       mSize--;\r
2331       m--;\r
2332     }\r
2333 \r
2334     return popup;\r
2335   }\r
2336   public void mouseClicked(MouseEvent evt)\r
2337   {}\r
2338   public void mouseReleased(MouseEvent evt)\r
2339   {}\r
2340   public void mouseEntered(MouseEvent evt)\r
2341   {}\r
2342   public void mouseExited(MouseEvent evt)\r
2343   {}\r
2344 \r
2345 }\r
2346 \r