src/jalview/appletgui/AlignFrame.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 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 java.awt.*;\r
  27 import java.awt.event.*;\r
  28 import java.util.*;\r
  29 import java.io.InputStreamReader;\r
  30 import java.io.BufferedReader;\r
  31 import java.net.URL;\r
  32 \r
  33 \r
  34 public class AlignFrame extends Frame implements ActionListener,\r
  35     ItemListener, KeyListener, MouseListener\r
  36 {\r
  37   public AlignmentPanel alignPanel;\r
  38   public AlignViewport viewport;\r
  39   int NEW_WINDOW_WIDTH = 700;\r
  40   int NEW_WINDOW_HEIGHT = 500;\r
  41 \r
  42   String jalviewServletURL;\r
  43 \r
  44 \r
  45    public AlignFrame(AlignmentI al,\r
  46                      jalview.bin.JalviewLite applet,\r
  47                      String title,\r
  48                      boolean embedded)\r
  49   {\r
  50 \r
  51     jalviewServletURL = applet.getParameter("APPLICATION_URL");\r
  52 \r
  53     try{\r
  54       jbInit();\r
  55     }catch(Exception ex)\r
  56     {\r
  57       ex.printStackTrace();\r
  58     }\r
  59 \r
  60     viewport = new AlignViewport(al, applet);\r
  61     alignPanel = new AlignmentPanel(this, viewport);\r
  62 \r
  63     annotationPanelMenuItem.setState(viewport.showAnnotation);\r
  64 \r
  65     seqLimits.setState(viewport.showJVSuffix);\r
  66 \r
  67     if(applet!=null)\r
  68     {\r
  69       String param = applet.getParameter("sortBy");\r
  70       if (param != null)\r
  71       {\r
  72         if (param.equalsIgnoreCase("Id"))\r
  73           sortIDMenuItem_actionPerformed();\r
  74         else if (param.equalsIgnoreCase("Pairwise Identity"))\r
  75           sortPairwiseMenuItem_actionPerformed();\r
  76       }\r
  77 \r
  78       param = applet.getParameter("wrap");\r
  79       if (param != null)\r
  80       {\r
  81         if (param.equalsIgnoreCase("true"))\r
  82         {\r
  83           wrapMenuItem.setState(true);\r
  84           wrapMenuItem_actionPerformed();\r
  85         }\r
  86       }\r
  87 \r
  88       try\r
  89       {\r
  90         param = applet.getParameter("windowWidth");\r
  91         if (param != null)\r
  92         {\r
  93           int width = Integer.parseInt(param);\r
  94           NEW_WINDOW_WIDTH = width;\r
  95         }\r
  96         param = applet.getParameter("windowHeight");\r
  97         if (param != null)\r
  98         {\r
  99           int height = Integer.parseInt(param);\r
 100           NEW_WINDOW_HEIGHT = height;\r
 101         }\r
 102       }\r
 103       catch (Exception ex)\r
 104       {}\r
 105 \r
 106     }\r
 107 \r
 108    //Some JVMS send keyevents to Top frame or lowest panel,\r
 109    //Havent worked out why yet. So add to both this frame and seqCanvas for now\r
 110    this.addKeyListener(this);\r
 111    alignPanel.seqPanel.seqCanvas.addKeyListener(this);\r
 112    alignPanel.idPanel.idCanvas.addKeyListener(this);\r
 113 \r
 114     viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
 115     {\r
 116      public void propertyChange(java.beans.PropertyChangeEvent evt)\r
 117      {\r
 118        if (evt.getPropertyName().equals("alignment"))\r
 119        {\r
 120          alignmentChanged();\r
 121        }\r
 122      }\r
 123    });\r
 124 \r
 125 \r
 126    if(embedded)\r
 127    {\r
 128      setEmbedded();\r
 129    }\r
 130    else\r
 131    {\r
 132      add(alignPanel, BorderLayout.CENTER);\r
 133      jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH,\r
 134                                       NEW_WINDOW_HEIGHT);\r
 135    }\r
 136    alignPanel.validate();\r
 137    alignPanel.repaint();\r
 138   }\r
 139   public AlignViewport getAlignViewport()\r
 140   {\r
 141     return viewport;\r
 142   }\r
 143 \r
 144   public SeqCanvas getSeqcanvas()\r
 145   {\r
 146     return alignPanel.seqPanel.seqCanvas;\r
 147   }\r
 148 \r
 149 \r
 150   /**\r
 151    * DOCUMENT ME!\r
 152    *\r
 153    * @param String DOCUMENT ME!\r
 154    */\r
 155 \r
 156   public void parseFeaturesFile(String file, String type)\r
 157   {\r
 158     Hashtable featureLinks = new Hashtable();\r
 159     boolean featuresFile = false;\r
 160     try{\r
 161       featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,\r
 162                                          alignPanel.seqPanel.seqCanvas.\r
 163                                          getFeatureRenderer().featureColours,\r
 164                                          featureLinks,\r
 165                                          true);\r
 166     }\r
 167     catch(Exception ex)\r
 168     {\r
 169       ex.printStackTrace();\r
 170     }\r
 171 \r
 172     if(featuresFile)\r
 173     {\r
 174       if(featureLinks.size()>0)\r
 175         alignPanel.seqPanel.seqCanvas\r
 176             .getFeatureRenderer().featureLinks = featureLinks;\r
 177       viewport.showSequenceFeatures = true;\r
 178       sequenceFeatures.setState(true);\r
 179       alignPanel.repaint();\r
 180     }\r
 181 \r
 182   }\r
 183 \r
 184 \r
 185   public void keyPressed(KeyEvent evt)\r
 186   {\r
 187     if (viewport.cursorMode\r
 188         && evt.getKeyCode() >= KeyEvent.VK_0\r
 189         && evt.getKeyCode() <= KeyEvent.VK_9)\r
 190     {\r
 191       alignPanel.seqPanel.numberPressed(evt.getKeyChar());\r
 192     }\r
 193 \r
 194     switch (evt.getKeyCode())\r
 195     {\r
 196       case 27: // escape key\r
 197         deselectAllSequenceMenuItem_actionPerformed();\r
 198         break;\r
 199       case KeyEvent.VK_X:\r
 200         if (evt.isControlDown() || evt.isMetaDown())\r
 201         {\r
 202           cut_actionPerformed();\r
 203         }\r
 204         break;\r
 205       case KeyEvent.VK_C:\r
 206         if (viewport.cursorMode && !evt.isControlDown())\r
 207         {\r
 208           alignPanel.seqPanel.setCursorColumn();\r
 209         }\r
 210         if (evt.isControlDown() || evt.isMetaDown())\r
 211         {\r
 212           copy_actionPerformed();\r
 213         }\r
 214         break;\r
 215       case KeyEvent.VK_V:\r
 216         if (evt.isControlDown() || evt.isMetaDown())\r
 217         {\r
 218           paste(true);\r
 219         }\r
 220         break;\r
 221       case KeyEvent.VK_A:\r
 222         if (evt.isControlDown() || evt.isMetaDown())\r
 223         {\r
 224           selectAllSequenceMenuItem_actionPerformed();\r
 225         }\r
 226         break;\r
 227       case KeyEvent.VK_DOWN:\r
 228         if(viewport.cursorMode)\r
 229         {\r
 230           alignPanel.seqPanel.moveCursor(0,1);\r
 231         }\r
 232         else\r
 233           moveSelectedSequences(false);\r
 234         break;\r
 235 \r
 236       case KeyEvent.VK_UP:\r
 237         if (viewport.cursorMode)\r
 238         {\r
 239           alignPanel.seqPanel.moveCursor(0,-1);\r
 240         }\r
 241         else\r
 242           moveSelectedSequences(true);\r
 243         break;\r
 244 \r
 245       case KeyEvent.VK_LEFT:\r
 246         if(viewport.cursorMode)\r
 247         {\r
 248           alignPanel.seqPanel.moveCursor(-1,0);\r
 249         }\r
 250         break;\r
 251 \r
 252       case KeyEvent.VK_RIGHT:\r
 253         if (viewport.cursorMode)\r
 254         {\r
 255           alignPanel.seqPanel.moveCursor(1,0);\r
 256         }\r
 257         break;\r
 258       case KeyEvent.VK_SPACE:\r
 259         if(viewport.cursorMode)\r
 260         {\r
 261           alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown());\r
 262         }\r
 263         break;\r
 264 \r
 265       case KeyEvent.VK_DELETE:\r
 266       case KeyEvent.VK_BACK_SPACE:\r
 267         if(viewport.cursorMode)\r
 268         {\r
 269           alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown());\r
 270         }\r
 271        else\r
 272         {\r
 273           cut_actionPerformed();\r
 274           alignPanel.seqPanel.seqCanvas.repaint();\r
 275         }\r
 276         break;\r
 277 \r
 278       case KeyEvent.VK_S:\r
 279         if(viewport.cursorMode)\r
 280         {\r
 281           alignPanel.seqPanel.setCursorRow();\r
 282         }\r
 283         break;\r
 284       case KeyEvent.VK_P:\r
 285         if(viewport.cursorMode)\r
 286         {\r
 287           alignPanel.seqPanel.setCursorPosition();\r
 288         }\r
 289         break;\r
 290 \r
 291       case KeyEvent.VK_ENTER:\r
 292       case KeyEvent.VK_COMMA:\r
 293         if(viewport.cursorMode)\r
 294         {\r
 295           alignPanel.seqPanel.setCursorRowAndColumn();\r
 296         }\r
 297         break;\r
 298 \r
 299       case KeyEvent.VK_Q:\r
 300         if(viewport.cursorMode)\r
 301         {\r
 302           alignPanel.seqPanel.setSelectionAreaAtCursor(true);\r
 303         }\r
 304         break;\r
 305       case KeyEvent.VK_M:\r
 306         if(viewport.cursorMode)\r
 307         {\r
 308           alignPanel.seqPanel.setSelectionAreaAtCursor(false);\r
 309         }\r
 310         break;\r
 311 \r
 312      case KeyEvent.VK_F2:\r
 313        viewport.cursorMode = ! viewport.cursorMode;\r
 314        statusBar.setText("Keyboard editing mode is "+\r
 315            (viewport.cursorMode ? "on" : "off"));\r
 316        if(viewport.cursorMode)\r
 317        {\r
 318          alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;\r
 319          alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;\r
 320        }\r
 321        alignPanel.seqPanel.seqCanvas.repaint();\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   }\r
 332   public void keyReleased(KeyEvent evt)\r
 333   {}\r
 334   public void keyTyped(KeyEvent evt)\r
 335   {}\r
 336 \r
 337 public void itemStateChanged(ItemEvent evt)\r
 338   {\r
 339     if(evt.getSource()==colourTextMenuItem)\r
 340             colourTextMenuItem_actionPerformed();\r
 341     else if(evt.getSource()==wrapMenuItem)\r
 342             wrapMenuItem_actionPerformed();\r
 343     else if(evt.getSource()==scaleAbove)\r
 344             scaleAbove_actionPerformed();\r
 345     else if(evt.getSource()==scaleLeft)\r
 346             scaleLeft_actionPerformed();\r
 347     else if(evt.getSource()==scaleRight)\r
 348             scaleRight_actionPerformed();\r
 349      else if(evt.getSource()==seqLimits)\r
 350       seqLimits_itemStateChanged();\r
 351     else if(evt.getSource()==viewBoxesMenuItem)\r
 352             viewBoxesMenuItem_actionPerformed();\r
 353     else if(evt.getSource()==viewTextMenuItem)\r
 354             viewTextMenuItem_actionPerformed();\r
 355     else if(evt.getSource()==renderGapsMenuItem)\r
 356             renderGapsMenuItem_actionPerformed();\r
 357     else if(evt.getSource()==annotationPanelMenuItem)\r
 358             annotationPanelMenuItem_actionPerformed();\r
 359       else if(evt.getSource()==sequenceFeatures)\r
 360       {\r
 361            viewport.showSequenceFeatures(sequenceFeatures.getState());\r
 362             alignPanel.seqPanel.seqCanvas.repaint();\r
 363       }\r
 364       else if(evt.getSource()==conservationMenuItem)\r
 365             conservationMenuItem_actionPerformed();\r
 366       else if(evt.getSource()==abovePIDThreshold)\r
 367             abovePIDThreshold_actionPerformed();\r
 368           else if(evt.getSource()==applyToAllGroups)\r
 369             applyToAllGroups_actionPerformed();\r
 370       else if(evt.getSource()==autoCalculate)\r
 371           viewport.autocalculateConsensus = autoCalculate.getState();\r
 372   }\r
 373  public void actionPerformed(ActionEvent evt)\r
 374  {\r
 375     Object source = evt.getSource();\r
 376 \r
 377     if(source==inputText)\r
 378       inputText_actionPerformed();\r
 379     else if(source==loadTree)\r
 380       loadTree_actionPerformed();\r
 381     else if(source==loadApplication)\r
 382       launchFullApplication();\r
 383     else if(source==closeMenuItem)\r
 384       closeMenuItem_actionPerformed();\r
 385     else if(source==copy)\r
 386       copy_actionPerformed();\r
 387     else if(source==undoMenuItem)\r
 388       undoMenuItem_actionPerformed();\r
 389     else if(source==redoMenuItem)\r
 390       redoMenuItem_actionPerformed();\r
 391     else if(source==inputText)\r
 392             inputText_actionPerformed();\r
 393     else if(source==closeMenuItem)\r
 394             closeMenuItem_actionPerformed();\r
 395     else if(source==undoMenuItem)\r
 396             undoMenuItem_actionPerformed();\r
 397     else if(source==redoMenuItem)\r
 398             redoMenuItem_actionPerformed();\r
 399     else if(source==copy)\r
 400             copy_actionPerformed();\r
 401     else if(source==pasteNew)\r
 402             pasteNew_actionPerformed();\r
 403     else if(source==pasteThis)\r
 404             pasteThis_actionPerformed();\r
 405     else if(source==cut)\r
 406             cut_actionPerformed();\r
 407     else if(source==delete)\r
 408             delete_actionPerformed();\r
 409     else if(source==deleteGroups)\r
 410             deleteGroups_actionPerformed();\r
 411     else if(source==selectAllSequenceMenuItem)\r
 412             selectAllSequenceMenuItem_actionPerformed();\r
 413     else if(source==deselectAllSequenceMenuItem)\r
 414             deselectAllSequenceMenuItem_actionPerformed();\r
 415     else if(source==invertSequenceMenuItem)\r
 416             invertSequenceMenuItem_actionPerformed();\r
 417     else if(source==invertColSel)\r
 418     { viewport.invertColumnSelection(); repaint(); }\r
 419     else if(source==remove2LeftMenuItem)\r
 420             remove2LeftMenuItem_actionPerformed();\r
 421     else if(source==remove2RightMenuItem)\r
 422             remove2RightMenuItem_actionPerformed();\r
 423     else if(source==removeGappedColumnMenuItem)\r
 424             removeGappedColumnMenuItem_actionPerformed();\r
 425     else if(source==removeAllGapsMenuItem)\r
 426             removeAllGapsMenuItem_actionPerformed();\r
 427     else if(source==findMenuItem)\r
 428             findMenuItem_actionPerformed();\r
 429     else if(source==font)\r
 430             font_actionPerformed();\r
 431     else if(source==showColumns)\r
 432     {\r
 433       viewport.showAllHiddenColumns(); repaint();\r
 434     }\r
 435     else if(source==showSeqs)\r
 436     {\r
 437       viewport.showAllHiddenSeqs(); repaint();\r
 438     }\r
 439     else if(source == hideColumns)\r
 440     {\r
 441       viewport.hideSelectedColumns(); repaint();\r
 442     }\r
 443     else if(source == hideSequences && viewport.getSelectionGroup()!=null)\r
 444     {\r
 445       SequenceI[] seqs = viewport.getSelectionGroup().getSequencesInOrder(\r
 446           viewport.alignment\r
 447           );\r
 448 \r
 449       for (int i = 0; i < seqs.length; i++)\r
 450       {\r
 451         viewport.hideSequence(seqs[i]);\r
 452       }\r
 453 \r
 454       alignPanel.repaint();\r
 455     }\r
 456     else if(source==featureSettings)\r
 457             featureSettings_actionPerformed();\r
 458     else if(source==overviewMenuItem)\r
 459             overviewMenuItem_actionPerformed();\r
 460     else if(source==noColourmenuItem)\r
 461             noColourmenuItem_actionPerformed();\r
 462     else if(source==clustalColour)\r
 463             clustalColour_actionPerformed();\r
 464     else if(source==zappoColour)\r
 465             zappoColour_actionPerformed();\r
 466     else if(source==taylorColour)\r
 467             taylorColour_actionPerformed();\r
 468     else if(source==hydrophobicityColour)\r
 469             hydrophobicityColour_actionPerformed();\r
 470     else if(source==helixColour)\r
 471             helixColour_actionPerformed();\r
 472     else if(source==strandColour)\r
 473             strandColour_actionPerformed();\r
 474     else if(source==turnColour)\r
 475             turnColour_actionPerformed();\r
 476     else if(source==buriedColour)\r
 477             buriedColour_actionPerformed();\r
 478     else if(source==nucleotideColour)\r
 479             nucleotideColour_actionPerformed();\r
 480     else if(source==modifyPID)\r
 481             modifyPID_actionPerformed();\r
 482     else if(source==modifyConservation)\r
 483             modifyConservation_actionPerformed();\r
 484     else if(source==userDefinedColour)\r
 485             userDefinedColour_actionPerformed();\r
 486     else if(source==PIDColour)\r
 487             PIDColour_actionPerformed();\r
 488     else if(source==BLOSUM62Colour)\r
 489             BLOSUM62Colour_actionPerformed();\r
 490     else if(source==annotationColour)\r
 491            new AnnotationColourChooser(viewport, alignPanel);\r
 492     else if(source==sortPairwiseMenuItem)\r
 493             sortPairwiseMenuItem_actionPerformed();\r
 494     else if(source==sortIDMenuItem)\r
 495             sortIDMenuItem_actionPerformed();\r
 496     else if(source==sortGroupMenuItem)\r
 497             sortGroupMenuItem_actionPerformed();\r
 498     else if(source==removeRedundancyMenuItem)\r
 499             removeRedundancyMenuItem_actionPerformed();\r
 500     else if(source==pairwiseAlignmentMenuItem)\r
 501             pairwiseAlignmentMenuItem_actionPerformed();\r
 502     else if(source==PCAMenuItem)\r
 503             PCAMenuItem_actionPerformed();\r
 504     else if(source==averageDistanceTreeMenuItem)\r
 505             averageDistanceTreeMenuItem_actionPerformed();\r
 506     else if(source==neighbourTreeMenuItem)\r
 507             neighbourTreeMenuItem_actionPerformed();\r
 508     else if(source==njTreeBlosumMenuItem)\r
 509             njTreeBlosumMenuItem_actionPerformed();\r
 510     else if(source==avDistanceTreeBlosumMenuItem)\r
 511             avTreeBlosumMenuItem_actionPerformed();\r
 512     else if(source==documentation)\r
 513             documentation_actionPerformed();\r
 514     else if(source==about)\r
 515             about_actionPerformed();\r
 516 \r
 517  }\r
 518 \r
 519   public void inputText_actionPerformed()\r
 520   {\r
 521     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
 522     Frame frame = new Frame();\r
 523     frame.add(cap);\r
 524     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
 525   }\r
 526 \r
 527   protected void outputText_actionPerformed(ActionEvent e)\r
 528   {\r
 529     CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
 530     Frame frame = new Frame();\r
 531     frame.add(cap);\r
 532     jalview.bin.JalviewLite.addFrame(frame,\r
 533                                      "Alignment output - " + e.getActionCommand(),\r
 534                                      600, 500);\r
 535     cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
 536                                               viewport.getAlignment().getSequences(),\r
 537                                                       viewport.showJVSuffix));\r
 538   }\r
 539 \r
 540   void launchFullApplication()\r
 541   {\r
 542     StringBuffer url = new StringBuffer(jalviewServletURL);\r
 543 \r
 544     url.append("?open="+\r
 545                appendProtocol( viewport.applet.getParameter("file") ) );\r
 546 \r
 547     if(viewport.applet.getParameter("features")!=null)\r
 548     {\r
 549       url.append( "&features=" );\r
 550       url.append( appendProtocol( viewport.applet.getParameter("features") ) );\r
 551     }\r
 552 \r
 553     if(viewport.applet.getParameter("annotations")!=null)\r
 554     {\r
 555       url.append( "&annotations=" );\r
 556       url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );\r
 557     }\r
 558 \r
 559     if(viewport.applet.getParameter("defaultColour")!=null)\r
 560     {\r
 561       url.append("&colour=" +\r
 562                  removeWhiteSpace(viewport.applet.getParameter("defaultColour"))\r
 563           );\r
 564     }\r
 565 \r
 566     if(viewport.applet.getParameter("userDefinedColour")!=null)\r
 567     {\r
 568       url.append( "&colour=" +\r
 569                  removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )\r
 570          );\r
 571     }\r
 572 \r
 573     showURL(url.toString(), "FULL_APP");\r
 574   }\r
 575 \r
 576 \r
 577   String removeWhiteSpace(String colour)\r
 578   {\r
 579     StringBuffer sb = new StringBuffer();\r
 580     for (int i = 0; i < colour.length(); i++)\r
 581     {\r
 582       if (Character.isWhitespace(colour.charAt(i)))\r
 583         sb.append("%20");\r
 584       else\r
 585         sb.append(colour.charAt(i));\r
 586     }\r
 587 \r
 588     return sb.toString();\r
 589   }\r
 590 \r
 591 \r
 592   String appendProtocol(String url)\r
 593   {\r
 594     try{\r
 595        new URL(url);\r
 596     }catch(java.net.MalformedURLException ex)\r
 597     {\r
 598       url = viewport.applet.getCodeBase()+url;\r
 599     }\r
 600     return url;\r
 601   }\r
 602 \r
 603   public void closeMenuItem_actionPerformed()\r
 604   {\r
 605     PaintRefresher.components.remove(viewport.alignment);\r
 606     if(PaintRefresher.components.size()==0 && viewport.applet==null)\r
 607       System.exit(0);\r
 608 \r
 609     this.dispose();\r
 610   }\r
 611 \r
 612   Stack historyList = new Stack();\r
 613   Stack redoList = new Stack();\r
 614 \r
 615   void updateEditMenuBar()\r
 616   {\r
 617     if (historyList.size() > 0)\r
 618     {\r
 619       undoMenuItem.setEnabled(true);\r
 620       HistoryItem hi = (HistoryItem) historyList.peek();\r
 621       undoMenuItem.setLabel("Undo " + hi.getDescription());\r
 622     }\r
 623     else\r
 624     {\r
 625       undoMenuItem.setEnabled(false);\r
 626       undoMenuItem.setLabel("Undo");\r
 627     }\r
 628 \r
 629     if (redoList.size() > 0)\r
 630     {\r
 631       redoMenuItem.setEnabled(true);\r
 632       HistoryItem hi = (HistoryItem) redoList.peek();\r
 633       redoMenuItem.setLabel("Redo " + hi.getDescription());\r
 634     }\r
 635     else\r
 636     {\r
 637       redoMenuItem.setEnabled(false);\r
 638       redoMenuItem.setLabel("Redo");\r
 639     }\r
 640   }\r
 641 \r
 642   public void addHistoryItem(HistoryItem hi)\r
 643   {\r
 644     historyList.push(hi);\r
 645     updateEditMenuBar();\r
 646   }\r
 647 \r
 648   protected void undoMenuItem_actionPerformed()\r
 649   {\r
 650     HistoryItem hi = (HistoryItem) historyList.pop();\r
 651     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
 652                                   HistoryItem.HIDE));\r
 653     restoreHistoryItem(hi);\r
 654     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 655   }\r
 656 \r
 657   protected void redoMenuItem_actionPerformed()\r
 658   {\r
 659     HistoryItem hi = (HistoryItem) redoList.pop();\r
 660     restoreHistoryItem(hi);\r
 661     updateEditMenuBar();\r
 662     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 663   }\r
 664 \r
 665   // used by undo and redo\r
 666   void restoreHistoryItem(HistoryItem hi)\r
 667   {\r
 668     hi.restore();\r
 669 \r
 670     updateEditMenuBar();\r
 671 \r
 672     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 673   }\r
 674 \r
 675   public void moveSelectedSequences(boolean up)\r
 676   {\r
 677     SequenceGroup sg = viewport.getSelectionGroup();\r
 678     if (sg == null)\r
 679     {\r
 680       return;\r
 681     }\r
 682 \r
 683     if (up)\r
 684     {\r
 685       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 686       {\r
 687         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 688         if (!sg.getSequences(false).contains(seq))\r
 689         {\r
 690           continue;\r
 691         }\r
 692 \r
 693         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 694         if (sg.getSequences(false).contains(temp))\r
 695         {\r
 696           continue;\r
 697         }\r
 698 \r
 699         viewport.alignment.getSequences().setElementAt(temp, i);\r
 700         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 701       }\r
 702     }\r
 703     else\r
 704     {\r
 705       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 706       {\r
 707         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 708         if (!sg.getSequences(true).contains(seq))\r
 709         {\r
 710           continue;\r
 711         }\r
 712 \r
 713         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 714         if (sg.getSequences(true).contains(temp))\r
 715         {\r
 716           continue;\r
 717         }\r
 718 \r
 719         viewport.alignment.getSequences().setElementAt(temp, i);\r
 720         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 721       }\r
 722     }\r
 723 \r
 724     alignPanel.repaint();\r
 725   }\r
 726 \r
 727   static StringBuffer copiedSequences;\r
 728   static Vector copiedHiddenColumns;\r
 729   protected void copy_actionPerformed()\r
 730   {\r
 731     if (viewport.getSelectionGroup() == null)\r
 732     {\r
 733       return;\r
 734     }\r
 735 \r
 736     SequenceGroup sg = viewport.getSelectionGroup();\r
 737     copiedSequences = new StringBuffer();\r
 738     Hashtable orderedSeqs = new Hashtable();\r
 739     for (int i = 0; i < sg.getSize(false); i++)\r
 740     {\r
 741       SequenceI seq = sg.getSequenceAt(i);\r
 742       int index = viewport.alignment.findIndex(seq);\r
 743       orderedSeqs.put(index + "", seq);\r
 744     }\r
 745 \r
 746     int index = 0, startRes, endRes;\r
 747     char ch;\r
 748 \r
 749     if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)\r
 750     {\r
 751       copiedHiddenColumns = new Vector();\r
 752       int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
 753       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();\r
 754            i++)\r
 755       {\r
 756         int[] region = (int[])\r
 757             viewport.getColumnSelection().getHiddenColumns().elementAt(i);\r
 758 \r
 759         copiedHiddenColumns.addElement(new int[]\r
 760                                  {region[0] - hiddenOffset,\r
 761                                  region[1] - hiddenOffset});\r
 762       }\r
 763     }\r
 764     else\r
 765       copiedHiddenColumns = null;\r
 766 \r
 767 \r
 768     for (int i = 0; i < sg.getSize(false); i++)\r
 769     {\r
 770         SequenceI seq = null;\r
 771 \r
 772         while (seq == null)\r
 773         {\r
 774             if (orderedSeqs.containsKey(index + ""))\r
 775             {\r
 776                 seq = (SequenceI) orderedSeqs.get(index + "");\r
 777                 index++;\r
 778 \r
 779                 break;\r
 780             }\r
 781             else\r
 782             {\r
 783                 index++;\r
 784             }\r
 785         }\r
 786 \r
 787         //FIND START RES\r
 788         //Returns residue following index if gap\r
 789         startRes = seq.findPosition(sg.getStartRes());\r
 790 \r
 791         //FIND END RES\r
 792         //Need to find the residue preceeding index if gap\r
 793         endRes = 0;\r
 794 \r
 795         for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
 796         {\r
 797           ch = seq.getCharAt(j);\r
 798           if (!jalview.util.Comparison.isGap( (ch)))\r
 799           {\r
 800             endRes++;\r
 801           }\r
 802         }\r
 803 \r
 804         if(endRes>0)\r
 805         {\r
 806           endRes += seq.getStart() -1;\r
 807         }\r
 808 \r
 809         copiedSequences.append(seq.getName() + "\t" +\r
 810             startRes + "\t" +\r
 811             endRes + "\t" +\r
 812             seq.getSequence(sg.getStartRes(),\r
 813                 sg.getEndRes() + 1) + "\n");\r
 814     }\r
 815 \r
 816   }\r
 817 \r
 818   protected void pasteNew_actionPerformed()\r
 819   {\r
 820     paste(true);\r
 821   }\r
 822 \r
 823   protected void pasteThis_actionPerformed()\r
 824   {\r
 825     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
 826                                    HistoryItem.PASTE));\r
 827     paste(false);\r
 828   }\r
 829 \r
 830   void paste(boolean newAlignment)\r
 831   {\r
 832     try\r
 833     {\r
 834       if (copiedSequences == null)\r
 835       {\r
 836         return;\r
 837       }\r
 838 \r
 839       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 840       Vector seqs = new Vector();\r
 841       while (st.hasMoreElements())\r
 842       {\r
 843         String name = st.nextToken();\r
 844         int start = Integer.parseInt(st.nextToken());\r
 845         int end = Integer.parseInt(st.nextToken());\r
 846         Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
 847 \r
 848         if (!newAlignment)\r
 849         {\r
 850           viewport.alignment.addSequence(sequence);\r
 851         }\r
 852         else\r
 853         {\r
 854           seqs.addElement(sequence);\r
 855         }\r
 856       }\r
 857 \r
 858       if (newAlignment)\r
 859       {\r
 860         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 861         for (int i = 0; i < seqs.size(); i++)\r
 862         {\r
 863           newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
 864         }\r
 865 \r
 866         String newtitle = new String("Copied sequences");\r
 867         if (getTitle().startsWith("Copied sequences"))\r
 868         {\r
 869           newtitle = getTitle();\r
 870         }\r
 871         else\r
 872         {\r
 873           newtitle = newtitle.concat("- from " + getTitle());\r
 874         }\r
 875         AlignFrame af = new AlignFrame(new Alignment(newSeqs),\r
 876                                        viewport.applet,\r
 877                                        newtitle,\r
 878                                        false);\r
 879         if (copiedHiddenColumns != null)\r
 880         {\r
 881           for (int i = 0; i < copiedHiddenColumns.size(); i++)\r
 882           {\r
 883             int[] region = (int[]) copiedHiddenColumns.elementAt(i);\r
 884             af.viewport.hideColumns(region[0], region[1]);\r
 885           }\r
 886         }\r
 887 \r
 888 \r
 889         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
 890                                          NEW_WINDOW_HEIGHT);\r
 891       }\r
 892       else\r
 893       {\r
 894         viewport.setEndSeq(viewport.alignment.getHeight());\r
 895         viewport.alignment.getWidth();\r
 896         viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 897       }\r
 898 \r
 899     }\r
 900     catch (Exception ex)\r
 901     {} // could be anything being pasted in here\r
 902 \r
 903   }\r
 904 \r
 905   protected void cut_actionPerformed()\r
 906   {\r
 907     copy_actionPerformed();\r
 908     delete_actionPerformed();\r
 909   }\r
 910 \r
 911   protected void delete_actionPerformed()\r
 912   {\r
 913     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
 914                                    HistoryItem.HIDE));\r
 915     if (viewport.getSelectionGroup() == null)\r
 916     {\r
 917       return;\r
 918     }\r
 919 \r
 920 \r
 921     SequenceGroup sg = viewport.getSelectionGroup();\r
 922     boolean allSequences = false;\r
 923     if(sg.getSize(false)==viewport.alignment.getHeight())\r
 924           allSequences = true;\r
 925 \r
 926     for (int i = 0; i < sg.getSize(false); i++)\r
 927     {\r
 928       SequenceI seq = sg.getSequenceAt(i);\r
 929       int index = viewport.getAlignment().findIndex(seq);\r
 930       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 931 \r
 932       // If the cut affects all sequences, remove highlighted columns\r
 933       if (allSequences)\r
 934       {\r
 935         viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
 936                                                      sg.getEndRes() + 1);\r
 937       }\r
 938 \r
 939 \r
 940       if (seq.getSequence().length() < 1)\r
 941       {\r
 942         viewport.getAlignment().deleteSequence(seq);\r
 943       }\r
 944       else\r
 945       {\r
 946         viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 947       }\r
 948     }\r
 949 \r
 950     viewport.setSelectionGroup(null);\r
 951     viewport.alignment.deleteGroup(sg);\r
 952     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
 953     if (viewport.getAlignment().getHeight() < 1)\r
 954     {\r
 955       try\r
 956       {\r
 957         this.setVisible(false);\r
 958       }\r
 959       catch (Exception ex)\r
 960       {}\r
 961     }\r
 962     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 963 \r
 964   }\r
 965 \r
 966   protected void deleteGroups_actionPerformed()\r
 967   {\r
 968     viewport.alignment.deleteAllGroups();\r
 969     viewport.setSelectionGroup(null);\r
 970 \r
 971     alignPanel.repaint();\r
 972   }\r
 973 \r
 974   public void selectAllSequenceMenuItem_actionPerformed()\r
 975   {\r
 976     SequenceGroup sg = new SequenceGroup();\r
 977     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 978     {\r
 979       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
 980     }\r
 981     sg.setEndRes(viewport.alignment.getWidth()-1);\r
 982     viewport.setSelectionGroup(sg);\r
 983     alignPanel.repaint();\r
 984     PaintRefresher.Refresh(null, viewport.alignment);\r
 985   }\r
 986 \r
 987   public void deselectAllSequenceMenuItem_actionPerformed()\r
 988   {\r
 989     if(viewport.cursorMode)\r
 990     {\r
 991       alignPanel.seqPanel.keyboardNo1=null;\r
 992       alignPanel.seqPanel.keyboardNo2=null;\r
 993     }\r
 994     viewport.setSelectionGroup(null);\r
 995     viewport.getColumnSelection().clear();\r
 996     viewport.setSelectionGroup(null);\r
 997     alignPanel.idPanel.idCanvas.searchResults = null;\r
 998     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
 999     alignPanel.repaint();\r
1000     PaintRefresher.Refresh(null, viewport.alignment);\r
1001   }\r
1002 \r
1003   public void invertSequenceMenuItem_actionPerformed()\r
1004   {\r
1005     SequenceGroup sg = viewport.getSelectionGroup();\r
1006     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
1007     {\r
1008       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
1009     }\r
1010 \r
1011     PaintRefresher.Refresh(null, viewport.alignment);\r
1012   }\r
1013 \r
1014   public void remove2LeftMenuItem_actionPerformed()\r
1015   {\r
1016     ColumnSelection colSel = viewport.getColumnSelection();\r
1017     if (colSel.size() > 0)\r
1018     {\r
1019       addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
1020                                      HistoryItem.HIDE));\r
1021       int min = colSel.getMin();\r
1022       viewport.getAlignment().trimLeft(min);\r
1023       colSel.compensateForEdit(0, min);\r
1024 \r
1025       if (viewport.getSelectionGroup() != null)\r
1026       {\r
1027         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
1028       }\r
1029 \r
1030       Vector groups = viewport.alignment.getGroups();\r
1031       for (int i = 0; i < groups.size(); i++)\r
1032       {\r
1033         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1034         if (!sg.adjustForRemoveLeft(min))\r
1035         {\r
1036           viewport.alignment.deleteGroup(sg);\r
1037         }\r
1038       }\r
1039       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1040     }\r
1041   }\r
1042 \r
1043   public void remove2RightMenuItem_actionPerformed()\r
1044   {\r
1045     ColumnSelection colSel = viewport.getColumnSelection();\r
1046     if (colSel.size() > 0)\r
1047     {\r
1048       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
1049                                      HistoryItem.HIDE));\r
1050       int max = colSel.getMax();\r
1051       viewport.getAlignment().trimRight(max);\r
1052       if (viewport.getSelectionGroup() != null)\r
1053       {\r
1054         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
1055       }\r
1056 \r
1057       Vector groups = viewport.alignment.getGroups();\r
1058       for (int i = 0; i < groups.size(); i++)\r
1059       {\r
1060         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1061         if (!sg.adjustForRemoveRight(max))\r
1062         {\r
1063           viewport.alignment.deleteGroup(sg);\r
1064         }\r
1065       }\r
1066       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1067     }\r
1068 \r
1069   }\r
1070 \r
1071   public void removeGappedColumnMenuItem_actionPerformed()\r
1072   {\r
1073     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
1074                                    viewport.alignment,\r
1075                                    HistoryItem.HIDE));\r
1076 \r
1077     //This is to maintain viewport position on first residue\r
1078     //of first sequence\r
1079     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
1080     int startRes = seq.findPosition(viewport.startRes);\r
1081 \r
1082     viewport.getAlignment().removeGaps();\r
1083 \r
1084     viewport.setStartRes(seq.findIndex(startRes)-1);\r
1085 \r
1086     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1087   }\r
1088 \r
1089   public void removeAllGapsMenuItem_actionPerformed()\r
1090   {\r
1091     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
1092                                    HistoryItem.HIDE));\r
1093 \r
1094     //This is to maintain viewport position on first residue\r
1095     //of first sequence\r
1096     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
1097     int startRes = seq.findPosition(viewport.startRes);\r
1098 \r
1099     SequenceI current;\r
1100     int jSize;\r
1101 \r
1102     Vector seqs=null;\r
1103 \r
1104     int start=0, end = viewport.alignment.getWidth();\r
1105 \r
1106     if (viewport.getSelectionGroup() != null\r
1107         && viewport.getSelectionGroup().getSequences(false) != null\r
1108         && viewport.getSelectionGroup().getSize(false)>0)\r
1109     {\r
1110       seqs = viewport.getSelectionGroup().getSequences(true);\r
1111       start = viewport.getSelectionGroup().getStartRes();\r
1112       end = viewport.getSelectionGroup().getEndRes()+1;\r
1113     }\r
1114     else\r
1115       seqs = viewport.alignment.getSequences();\r
1116 \r
1117     for (int i = 0; i < seqs.size(); i++)\r
1118     {\r
1119       current = (SequenceI) seqs.elementAt(i);\r
1120       jSize = current.getLength();\r
1121 \r
1122       // Removing a range is much quicker than removing gaps\r
1123       // one by one for long sequences\r
1124       int j = start;\r
1125       int rangeStart=-1, rangeEnd=-1;\r
1126 \r
1127       do\r
1128       {\r
1129         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
1130         {\r
1131           if(rangeStart==-1)\r
1132            {\r
1133              rangeStart = j;\r
1134              rangeEnd = j+1;\r
1135            }\r
1136            else\r
1137            {\r
1138              rangeEnd++;\r
1139            }\r
1140            j++;\r
1141         }\r
1142         else\r
1143         {\r
1144           if(rangeStart>-1)\r
1145           {\r
1146             current.deleteChars(rangeStart, rangeEnd);\r
1147             j-=rangeEnd-rangeStart;\r
1148             jSize-=rangeEnd-rangeStart;\r
1149             rangeStart = -1;\r
1150             rangeEnd = -1;\r
1151           }\r
1152           else\r
1153             j++;\r
1154         }\r
1155       }\r
1156       while (j < end && j < jSize);\r
1157       if(rangeStart>-1)\r
1158       {\r
1159        current.deleteChars(rangeStart, rangeEnd);\r
1160       }\r
1161     }\r
1162     viewport.setStartRes(seq.findIndex(startRes)-1);\r
1163     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1164   }\r
1165 \r
1166   public void alignmentChanged()\r
1167   {\r
1168     viewport.alignment.padGaps();\r
1169     if(viewport.autocalculateConsensus)\r
1170     {\r
1171       viewport.updateConsensus();\r
1172       viewport.updateConservation();\r
1173     }\r
1174 \r
1175     resetAllColourSchemes();\r
1176     if(alignPanel.overviewPanel!=null)\r
1177       alignPanel.overviewPanel.updateOverviewImage();\r
1178 \r
1179     viewport.alignment.adjustSequenceAnnotations();\r
1180     alignPanel.repaint();\r
1181   }\r
1182 \r
1183   void resetAllColourSchemes()\r
1184   {\r
1185     ColourSchemeI cs = viewport.globalColourScheme;\r
1186     if(cs!=null)\r
1187     {\r
1188       if (cs instanceof ClustalxColourScheme)\r
1189       {\r
1190         ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
1191             resetClustalX(viewport.alignment.getSequences(),\r
1192                           viewport.alignment.getWidth());\r
1193       }\r
1194 \r
1195       cs.setConsensus(viewport.vconsensus);\r
1196       if (cs.conservationApplied())\r
1197       {\r
1198         Alignment al = (Alignment) viewport.alignment;\r
1199         Conservation c = new Conservation("All",\r
1200                                           ResidueProperties.propHash, 3,\r
1201                                           al.getSequences(), 0,\r
1202                                           al.getWidth() - 1);\r
1203         c.calculate();\r
1204         c.verdict(false, viewport.ConsPercGaps);\r
1205 \r
1206         cs.setConservation(c);\r
1207       }\r
1208     }\r
1209 \r
1210     int s, sSize = viewport.alignment.getGroups().size();\r
1211     for(s=0; s<sSize; s++)\r
1212     {\r
1213       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
1214       if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
1215       {\r
1216         ((ClustalxColourScheme)sg.cs).resetClustalX(\r
1217             sg.getSequences(true), sg.getWidth());\r
1218       }\r
1219       sg.recalcConservation();\r
1220     }\r
1221   }\r
1222 \r
1223 \r
1224 \r
1225   public void findMenuItem_actionPerformed()\r
1226   {\r
1227     new Finder(alignPanel);\r
1228   }\r
1229 \r
1230   public void font_actionPerformed()\r
1231   {\r
1232     new FontChooser(alignPanel);\r
1233   }\r
1234 \r
1235 \r
1236   public void seqLimits_itemStateChanged()\r
1237   {\r
1238     viewport.setShowJVSuffix(seqLimits.getState());\r
1239     alignPanel.fontChanged();\r
1240     alignPanel.repaint();\r
1241   }\r
1242 \r
1243 \r
1244   protected void colourTextMenuItem_actionPerformed()\r
1245   {\r
1246     viewport.setColourText(colourTextMenuItem.getState());\r
1247     alignPanel.repaint();\r
1248   }\r
1249 \r
1250   protected void wrapMenuItem_actionPerformed()\r
1251   {\r
1252     viewport.setWrapAlignment(wrapMenuItem.getState());\r
1253     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
1254     scaleAbove.setEnabled(wrapMenuItem.getState());\r
1255     scaleLeft.setEnabled(wrapMenuItem.getState());\r
1256     scaleRight.setEnabled(wrapMenuItem.getState());\r
1257     alignPanel.repaint();\r
1258   }\r
1259 \r
1260   protected void scaleAbove_actionPerformed()\r
1261   {\r
1262     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
1263     alignPanel.repaint();\r
1264   }\r
1265 \r
1266   protected void scaleLeft_actionPerformed()\r
1267   {\r
1268     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
1269     alignPanel.repaint();\r
1270   }\r
1271 \r
1272   protected void scaleRight_actionPerformed()\r
1273   {\r
1274     viewport.setScaleRightWrapped(scaleRight.getState());\r
1275     alignPanel.repaint();\r
1276   }\r
1277 \r
1278   public void viewBoxesMenuItem_actionPerformed()\r
1279   {\r
1280     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
1281     alignPanel.repaint();\r
1282   }\r
1283 \r
1284   public void viewTextMenuItem_actionPerformed()\r
1285   {\r
1286     viewport.setShowText(viewTextMenuItem.getState());\r
1287     alignPanel.repaint();\r
1288   }\r
1289 \r
1290   protected void renderGapsMenuItem_actionPerformed()\r
1291   {\r
1292     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
1293     alignPanel.repaint();\r
1294   }\r
1295 \r
1296   public void annotationPanelMenuItem_actionPerformed()\r
1297   {\r
1298     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
1299     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
1300   }\r
1301 \r
1302   public void featureSettings_actionPerformed()\r
1303   {\r
1304     new FeatureSettings(viewport, alignPanel);\r
1305   }\r
1306 \r
1307   public void overviewMenuItem_actionPerformed()\r
1308   {\r
1309     if (alignPanel.overviewPanel != null)\r
1310     {\r
1311       return;\r
1312     }\r
1313 \r
1314     Frame frame = new Frame();\r
1315     OverviewPanel overview = new OverviewPanel(alignPanel);\r
1316     frame.add(overview);\r
1317     // +50 must allow for applet frame window\r
1318     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
1319                                      overview.preferredSize().width,\r
1320                                      overview.preferredSize().height + 50);\r
1321 \r
1322     frame.pack();\r
1323     frame.addWindowListener(new WindowAdapter()\r
1324     {\r
1325       public void windowClosing(WindowEvent e)\r
1326       {\r
1327         alignPanel.setOverviewPanel(null);\r
1328       };\r
1329     });\r
1330 \r
1331     alignPanel.setOverviewPanel(overview);\r
1332 \r
1333   }\r
1334 \r
1335   protected void noColourmenuItem_actionPerformed()\r
1336   {\r
1337     changeColour(null);\r
1338   }\r
1339 \r
1340   public void clustalColour_actionPerformed()\r
1341   {\r
1342     abovePIDThreshold.setState(false);\r
1343     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
1344                                           viewport.alignment.getWidth()));\r
1345   }\r
1346 \r
1347   public void zappoColour_actionPerformed()\r
1348   {\r
1349     changeColour(new ZappoColourScheme());\r
1350   }\r
1351 \r
1352   public void taylorColour_actionPerformed()\r
1353   {\r
1354     changeColour(new TaylorColourScheme());\r
1355   }\r
1356 \r
1357   public void hydrophobicityColour_actionPerformed()\r
1358   {\r
1359     changeColour(new HydrophobicColourScheme());\r
1360   }\r
1361 \r
1362   public void helixColour_actionPerformed()\r
1363   {\r
1364     changeColour(new HelixColourScheme());\r
1365   }\r
1366 \r
1367   public void strandColour_actionPerformed()\r
1368   {\r
1369     changeColour(new StrandColourScheme());\r
1370   }\r
1371 \r
1372   public void turnColour_actionPerformed()\r
1373   {\r
1374     changeColour(new TurnColourScheme());\r
1375   }\r
1376 \r
1377   public void buriedColour_actionPerformed()\r
1378   {\r
1379     changeColour(new BuriedColourScheme());\r
1380   }\r
1381 \r
1382   public void nucleotideColour_actionPerformed()\r
1383   {\r
1384     changeColour(new NucleotideColourScheme());\r
1385   }\r
1386 \r
1387   protected void applyToAllGroups_actionPerformed()\r
1388   {\r
1389     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
1390   }\r
1391 \r
1392   void changeColour(ColourSchemeI cs)\r
1393   {\r
1394     int threshold = 0;\r
1395 \r
1396     if(cs!=null)\r
1397     {\r
1398       if (viewport.getAbovePIDThreshold())\r
1399       {\r
1400         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
1401 \r
1402         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1403 \r
1404         viewport.setGlobalColourScheme(cs);\r
1405       }\r
1406       else\r
1407       {\r
1408         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1409       }\r
1410 \r
1411       if (viewport.getConservationSelected())\r
1412       {\r
1413 \r
1414         Alignment al = (Alignment) viewport.alignment;\r
1415         Conservation c = new Conservation("All",\r
1416                                           ResidueProperties.propHash, 3,\r
1417                                           al.getSequences(), 0,\r
1418                                           al.getWidth() - 1);\r
1419 \r
1420         c.calculate();\r
1421         c.verdict(false, viewport.ConsPercGaps);\r
1422 \r
1423         cs.setConservation(c);\r
1424 \r
1425         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
1426             "Background"));\r
1427 \r
1428       }\r
1429       else\r
1430       {\r
1431         cs.setConservation(null);\r
1432       }\r
1433 \r
1434       cs.setConsensus(viewport.vconsensus);\r
1435 \r
1436     }\r
1437     viewport.setGlobalColourScheme(cs);\r
1438 \r
1439     if (viewport.getColourAppliesToAllGroups())\r
1440     {\r
1441       Vector groups = viewport.alignment.getGroups();\r
1442       for (int i = 0; i < groups.size(); i++)\r
1443       {\r
1444         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1445 \r
1446         if(cs==null)\r
1447         {\r
1448           sg.cs = null;\r
1449           continue;\r
1450         }\r
1451         if (cs instanceof ClustalxColourScheme)\r
1452         {\r
1453           sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());\r
1454         }\r
1455         else\r
1456         {\r
1457           try\r
1458           {\r
1459             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
1460           }\r
1461           catch (Exception ex)\r
1462           {\r
1463             ex.printStackTrace();\r
1464             sg.cs = cs;\r
1465           }\r
1466         }\r
1467 \r
1468         if (viewport.getAbovePIDThreshold()\r
1469             || cs instanceof PIDColourScheme\r
1470             || cs instanceof Blosum62ColourScheme)\r
1471         {\r
1472           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1473           sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));\r
1474         }\r
1475         else\r
1476           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1477 \r
1478         if (viewport.getConservationSelected())\r
1479         {\r
1480           Conservation c = new Conservation("Group",\r
1481                                             ResidueProperties.propHash, 3,\r
1482                                             sg.getSequences(true), 0,\r
1483                                             viewport.alignment.getWidth() - 1);\r
1484           c.calculate();\r
1485           c.verdict(false, viewport.ConsPercGaps);\r
1486           sg.cs.setConservation(c);\r
1487         }\r
1488         else\r
1489         {\r
1490           sg.cs.setConservation(null);\r
1491           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1492         }\r
1493 \r
1494       }\r
1495     }\r
1496 \r
1497 \r
1498     if (alignPanel.getOverviewPanel() != null)\r
1499     {\r
1500       alignPanel.getOverviewPanel().updateOverviewImage();\r
1501     }\r
1502 \r
1503     alignPanel.repaint();\r
1504   }\r
1505 \r
1506 \r
1507 \r
1508   protected void modifyPID_actionPerformed()\r
1509   {\r
1510     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
1511     {\r
1512       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
1513                                      "Background");\r
1514       SliderPanel.showPIDSlider();\r
1515     }\r
1516   }\r
1517 \r
1518   protected void modifyConservation_actionPerformed()\r
1519   {\r
1520     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
1521     {\r
1522       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
1523                                         "Background");\r
1524       SliderPanel.showConservationSlider();\r
1525     }\r
1526   }\r
1527 \r
1528   protected void conservationMenuItem_actionPerformed()\r
1529   {\r
1530     viewport.setConservationSelected(conservationMenuItem.getState());\r
1531 \r
1532     viewport.setAbovePIDThreshold(false);\r
1533     abovePIDThreshold.setState(false);\r
1534 \r
1535     changeColour(viewport.getGlobalColourScheme());\r
1536 \r
1537     modifyConservation_actionPerformed();\r
1538   }\r
1539 \r
1540   public void abovePIDThreshold_actionPerformed()\r
1541   {\r
1542     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
1543 \r
1544     conservationMenuItem.setState(false);\r
1545     viewport.setConservationSelected(false);\r
1546 \r
1547     changeColour(viewport.getGlobalColourScheme());\r
1548 \r
1549     modifyPID_actionPerformed();\r
1550   }\r
1551 \r
1552   public void userDefinedColour_actionPerformed()\r
1553   {\r
1554     new UserDefinedColours(alignPanel, null);\r
1555   }\r
1556 \r
1557   public void PIDColour_actionPerformed()\r
1558   {\r
1559     changeColour(new PIDColourScheme());\r
1560   }\r
1561 \r
1562   public void BLOSUM62Colour_actionPerformed()\r
1563   {\r
1564     changeColour(new Blosum62ColourScheme());\r
1565   }\r
1566 \r
1567   public void sortPairwiseMenuItem_actionPerformed()\r
1568   {\r
1569     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1570                                    HistoryItem.SORT));\r
1571     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1572                               viewport.getAlignment().getSequenceAt(0));\r
1573     alignPanel.repaint();\r
1574   }\r
1575 \r
1576   public void sortIDMenuItem_actionPerformed()\r
1577   {\r
1578     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1579                                    HistoryItem.SORT));\r
1580     AlignmentSorter.sortByID(viewport.getAlignment());\r
1581     alignPanel.repaint();\r
1582   }\r
1583 \r
1584   public void sortGroupMenuItem_actionPerformed()\r
1585   {\r
1586     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1587                                    HistoryItem.SORT));\r
1588     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1589     alignPanel.repaint();\r
1590 \r
1591   }\r
1592 \r
1593   public void removeRedundancyMenuItem_actionPerformed()\r
1594   {\r
1595      new RedundancyPanel(alignPanel);\r
1596   }\r
1597 \r
1598   public void pairwiseAlignmentMenuItem_actionPerformed()\r
1599   {\r
1600     if (viewport.getSelectionGroup().getSize(false) > 1)\r
1601     {\r
1602       Frame frame = new Frame();\r
1603       frame.add(new PairwiseAlignPanel(alignPanel));\r
1604       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1605     }\r
1606   }\r
1607 \r
1608   public void PCAMenuItem_actionPerformed()\r
1609   {\r
1610     //are the sequences aligned?\r
1611     if (!viewport.alignment.isAligned())\r
1612     {\r
1613       SequenceI current;\r
1614       int Width = viewport.getAlignment().getWidth();\r
1615 \r
1616       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1617            i++)\r
1618       {\r
1619         current = viewport.getAlignment().getSequenceAt(i);\r
1620 \r
1621         if (current.getLength() < Width)\r
1622         {\r
1623           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1624         }\r
1625       }\r
1626       alignPanel.repaint();\r
1627     }\r
1628 \r
1629     if ( (viewport.getSelectionGroup() != null &&\r
1630           viewport.getSelectionGroup().getSize(false) < 4 &&\r
1631           viewport.getSelectionGroup().getSize(false) > 0)\r
1632         || viewport.getAlignment().getHeight() < 4)\r
1633     {\r
1634       return;\r
1635     }\r
1636 \r
1637     try\r
1638     {\r
1639       new PCAPanel(viewport);\r
1640     }\r
1641     catch (java.lang.OutOfMemoryError ex)\r
1642     {\r
1643     }\r
1644 \r
1645   }\r
1646 \r
1647   public void averageDistanceTreeMenuItem_actionPerformed()\r
1648   {\r
1649     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1650   }\r
1651 \r
1652   public void neighbourTreeMenuItem_actionPerformed()\r
1653   {\r
1654     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1655   }\r
1656 \r
1657   protected void njTreeBlosumMenuItem_actionPerformed()\r
1658   {\r
1659     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1660   }\r
1661 \r
1662   protected void avTreeBlosumMenuItem_actionPerformed()\r
1663   {\r
1664     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1665   }\r
1666 \r
1667   void NewTreePanel(String type, String pwType, String title)\r
1668   {\r
1669     //are the sequences aligned?\r
1670     if (!viewport.alignment.isAligned())\r
1671     {\r
1672       SequenceI current;\r
1673       int Width = viewport.getAlignment().getWidth();\r
1674 \r
1675       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1676            i++)\r
1677       {\r
1678         current = viewport.getAlignment().getSequenceAt(i);\r
1679 \r
1680         if (current.getLength() < Width)\r
1681         {\r
1682           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1683         }\r
1684       }\r
1685       alignPanel.repaint();\r
1686 \r
1687     }\r
1688 \r
1689     final TreePanel tp = new TreePanel(viewport,\r
1690                          type,\r
1691                          pwType);\r
1692 \r
1693     addTreeMenuItem(tp, title);\r
1694 \r
1695     jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1696   }\r
1697 \r
1698   void loadTree_actionPerformed()\r
1699   {\r
1700       CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
1701       cap.setText("Paste your Newick tree file here.");\r
1702       cap.treeImport = true;\r
1703       Frame frame = new Frame();\r
1704       frame.add(cap);\r
1705       jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);\r
1706   }\r
1707 \r
1708   public void loadTree(jalview.io.NewickFile tree, String treeFile)\r
1709   {\r
1710     TreePanel tp = new TreePanel(viewport,\r
1711                                  treeFile,\r
1712                                  "From File - ",\r
1713                                  tree);\r
1714     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
1715     addTreeMenuItem(tp, treeFile);\r
1716   }\r
1717 \r
1718   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1719   {\r
1720     final MenuItem item = new MenuItem(title);\r
1721     sortByTreeMenu.add(item);\r
1722     item.addActionListener(new java.awt.event.ActionListener()\r
1723     {\r
1724       public void actionPerformed(ActionEvent evt)\r
1725       {\r
1726         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1727                                        HistoryItem.SORT));\r
1728         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1729         alignPanel.repaint();\r
1730       }\r
1731     });\r
1732 \r
1733     treePanel.addWindowListener(new WindowAdapter()\r
1734     {\r
1735       public void windowClosing(WindowEvent e)\r
1736       {\r
1737         sortByTreeMenu.remove(item);\r
1738       };\r
1739     });\r
1740   }\r
1741 \r
1742   protected void documentation_actionPerformed()\r
1743   {\r
1744     showURL("http://www.jalview.org/help.html", "HELP");\r
1745   }\r
1746 \r
1747   protected void about_actionPerformed()\r
1748   {\r
1749 \r
1750     class AboutPanel extends Canvas\r
1751     {\r
1752       String version;\r
1753       public AboutPanel(String version)\r
1754       { this.version = version; }\r
1755 \r
1756       public void paint(Graphics g)\r
1757       {\r
1758         g.setColor(Color.white);\r
1759         g.fillRect(0, 0, getSize().width, getSize().height);\r
1760         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1761         FontMetrics fm = g.getFontMetrics();\r
1762         int fh = fm.getHeight();\r
1763         int y = 5, x = 7;\r
1764         g.setColor(Color.black);\r
1765         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1766         g.drawString("Jalview - Release "+version, 200, y += fh);\r
1767         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1768         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1769                      x, y += fh * 2);\r
1770         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1771                      x, y += fh);\r
1772         g.drawString(\r
1773             "For any issues relating to Jalview, email help@jalview.org", x,\r
1774             y += fh);\r
1775         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1776         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1777                      x, y += fh);\r
1778         g.drawString("Bioinformatics,  2004 20;426-7.", x, y += fh);\r
1779       }\r
1780     }\r
1781 \r
1782     String version = "test";\r
1783     java.net.URL url = getClass().getResource("/.build_properties");\r
1784     if (url != null)\r
1785     {\r
1786       try\r
1787       {\r
1788         BufferedReader reader = new BufferedReader(new InputStreamReader(\r
1789             url.openStream()));\r
1790         String line;\r
1791         while ( (line = reader.readLine()) != null)\r
1792         {\r
1793           if (line.indexOf("VERSION") > -1)\r
1794           {\r
1795             version = line.substring(line.indexOf("=") + 1);\r
1796           }\r
1797         }\r
1798       }\r
1799       catch (Exception ex)\r
1800       {\r
1801         ex.printStackTrace();\r
1802       }\r
1803     }\r
1804 \r
1805 \r
1806     Frame frame = new Frame();\r
1807     frame.add(new AboutPanel(version));\r
1808     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1809 \r
1810   }\r
1811 \r
1812   public void showURL(String url, String target)\r
1813   {\r
1814     if (viewport.applet == null)\r
1815     {\r
1816       System.out.println("Not running as applet - no browser available.");\r
1817     }\r
1818     else\r
1819     {\r
1820       try\r
1821       {\r
1822         System.out.println("Show url: "+url);\r
1823         viewport.applet.getAppletContext().showDocument(new java.net.URL(url),\r
1824                                                target);\r
1825       }\r
1826       catch (Exception ex)\r
1827       {\r
1828         ex.printStackTrace();\r
1829       }\r
1830     }\r
1831   }\r
1832 \r
1833 \r
1834   //////////////////////////////////////////////////////////////////////////////////\r
1835   //JBuilder Graphics here\r
1836 \r
1837     protected MenuBar alignFrameMenuBar = new MenuBar();\r
1838     protected Menu fileMenu = new Menu("File");\r
1839     protected MenuItem loadApplication = new MenuItem("View in Full Application");\r
1840     protected MenuItem loadTree = new MenuItem("Load Associated Tree");\r
1841     protected MenuItem closeMenuItem = new MenuItem("Close");\r
1842     protected Menu editMenu = new Menu("Edit");\r
1843     protected Menu viewMenu = new Menu("View");\r
1844     protected Menu colourMenu = new Menu("Colour");\r
1845     protected Menu calculateMenu = new Menu("Calculate");\r
1846     protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
1847     protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
1848     protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
1849     protected MenuItem remove2LeftMenuItem = new MenuItem();\r
1850     protected MenuItem remove2RightMenuItem = new MenuItem();\r
1851     protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
1852     protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
1853     protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
1854     protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
1855     protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
1856     protected MenuItem sortIDMenuItem = new MenuItem();\r
1857     protected MenuItem sortGroupMenuItem = new MenuItem();\r
1858     protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
1859     protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
1860     protected MenuItem PCAMenuItem = new MenuItem();\r
1861     protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
1862     protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
1863     BorderLayout borderLayout1 = new BorderLayout();\r
1864     public Label statusBar = new Label();\r
1865     protected Menu outputTextboxMenu = new Menu();\r
1866     protected MenuItem clustalColour = new MenuItem();\r
1867     protected MenuItem zappoColour = new MenuItem();\r
1868     protected MenuItem taylorColour = new MenuItem();\r
1869     protected MenuItem hydrophobicityColour = new MenuItem();\r
1870     protected MenuItem helixColour = new MenuItem();\r
1871     protected MenuItem strandColour = new MenuItem();\r
1872     protected MenuItem turnColour = new MenuItem();\r
1873     protected MenuItem buriedColour = new MenuItem();\r
1874     protected MenuItem userDefinedColour = new MenuItem();\r
1875     protected MenuItem PIDColour = new MenuItem();\r
1876     protected MenuItem BLOSUM62Colour = new MenuItem();\r
1877     MenuItem njTreeBlosumMenuItem = new MenuItem();\r
1878     MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
1879     protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
1880     protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
1881     MenuItem overviewMenuItem = new MenuItem();\r
1882     protected MenuItem undoMenuItem = new MenuItem();\r
1883     protected MenuItem redoMenuItem = new MenuItem();\r
1884     protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
1885     MenuItem noColourmenuItem = new MenuItem();\r
1886     protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
1887     protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
1888     MenuItem findMenuItem = new MenuItem();\r
1889     Menu searchMenu = new Menu();\r
1890     protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
1891     protected MenuItem nucleotideColour = new MenuItem();\r
1892     MenuItem deleteGroups = new MenuItem();\r
1893     MenuItem delete = new MenuItem();\r
1894     MenuItem copy = new MenuItem();\r
1895     MenuItem cut = new MenuItem();\r
1896     Menu pasteMenu = new Menu();\r
1897     MenuItem pasteNew = new MenuItem();\r
1898     MenuItem pasteThis = new MenuItem();\r
1899     protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
1900     protected MenuItem font = new MenuItem();\r
1901     protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
1902     protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
1903     protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
1904     MenuItem modifyPID = new MenuItem();\r
1905     MenuItem modifyConservation = new MenuItem();\r
1906     protected CheckboxMenuItem autoCalculate\r
1907         = new CheckboxMenuItem("Autocalculate Consensus", true);\r
1908     protected Menu sortByTreeMenu = new Menu();\r
1909     Menu sort = new Menu();\r
1910     Menu calculate = new Menu();\r
1911     MenuItem inputText = new MenuItem();\r
1912     Menu helpMenu = new Menu();\r
1913     MenuItem documentation = new MenuItem();\r
1914     MenuItem about = new MenuItem();\r
1915     protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
1916   Panel embeddedMenu;\r
1917   Label embeddedEdit;\r
1918   Label embeddedSearch;\r
1919   Label embeddedView;\r
1920   Label embeddedColour;\r
1921   Label embeddedFile;\r
1922   Label embeddedHelp;\r
1923   Label embeddedCalculate;\r
1924   FlowLayout flowLayout1;\r
1925 \r
1926   private void jbInit() throws Exception {\r
1927 \r
1928       setMenuBar(alignFrameMenuBar);\r
1929 \r
1930       MenuItem item;\r
1931 \r
1932       // dynamically fill save as menu with available formats\r
1933       for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)\r
1934       {\r
1935 \r
1936         item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.\r
1937                             elementAt(\r
1938                                 i));\r
1939         item.addActionListener(new java.awt.event.ActionListener()\r
1940         {\r
1941           public void actionPerformed(ActionEvent e)\r
1942           {\r
1943             outputText_actionPerformed(e);\r
1944           }\r
1945         });\r
1946 \r
1947         outputTextboxMenu.add(item);\r
1948       }\r
1949         closeMenuItem.addActionListener(this);\r
1950         loadApplication.addActionListener(this);\r
1951 \r
1952         loadTree.addActionListener(this);\r
1953         selectAllSequenceMenuItem.addActionListener(this);\r
1954         deselectAllSequenceMenuItem.addActionListener(this);\r
1955         invertSequenceMenuItem.addActionListener(this);\r
1956         remove2LeftMenuItem.setLabel("Remove Left");\r
1957         remove2LeftMenuItem.addActionListener(this);\r
1958         remove2RightMenuItem.setLabel("Remove Right");\r
1959         remove2RightMenuItem.addActionListener(this);\r
1960         removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
1961         removeGappedColumnMenuItem.addActionListener(this);\r
1962         removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
1963         removeAllGapsMenuItem.addActionListener(this);\r
1964         viewBoxesMenuItem.setLabel("Boxes");\r
1965         viewBoxesMenuItem.setState(true);\r
1966         viewBoxesMenuItem.addItemListener(this);\r
1967         viewTextMenuItem.setLabel("Text");\r
1968         viewTextMenuItem.setState(true);\r
1969         viewTextMenuItem.addItemListener(this);\r
1970         sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
1971         sortPairwiseMenuItem.addActionListener(this);\r
1972         sortIDMenuItem.setLabel("by ID");\r
1973         sortIDMenuItem.addActionListener(this);\r
1974         sortGroupMenuItem.setLabel("by Group");\r
1975         sortGroupMenuItem.addActionListener(this);\r
1976         removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
1977         removeRedundancyMenuItem.addActionListener(this);\r
1978         pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
1979         pairwiseAlignmentMenuItem.addActionListener(this);\r
1980         PCAMenuItem.setLabel("Principal Component Analysis");\r
1981         PCAMenuItem.addActionListener(this);\r
1982         averageDistanceTreeMenuItem.setLabel(\r
1983             "Average Distance Using % Identity");\r
1984         averageDistanceTreeMenuItem.addActionListener(this);\r
1985         neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
1986         neighbourTreeMenuItem.addActionListener(this);\r
1987         alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
1988         statusBar.setBackground(Color.white);\r
1989         statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
1990         statusBar.setText("Status bar");\r
1991         outputTextboxMenu.setLabel("Output to Textbox");\r
1992         clustalColour.setLabel("Clustalx");\r
1993 \r
1994         clustalColour.addActionListener(this);\r
1995         zappoColour.setLabel("Zappo");\r
1996         zappoColour.addActionListener(this);\r
1997         taylorColour.setLabel("Taylor");\r
1998         taylorColour.addActionListener(this);\r
1999         hydrophobicityColour.setLabel("Hydrophobicity");\r
2000         hydrophobicityColour.addActionListener(this);\r
2001         helixColour.setLabel("Helix Propensity");\r
2002         helixColour.addActionListener(this);\r
2003         strandColour.setLabel("Strand Propensity");\r
2004         strandColour.addActionListener(this);\r
2005         turnColour.setLabel("Turn Propensity");\r
2006         turnColour.addActionListener(this);\r
2007         buriedColour.setLabel("Buried Index");\r
2008         buriedColour.addActionListener(this);\r
2009         userDefinedColour.setLabel("User Defined...");\r
2010         userDefinedColour.addActionListener(this);\r
2011         PIDColour.setLabel("Percentage Identity");\r
2012         PIDColour.addActionListener(this);\r
2013         BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
2014         BLOSUM62Colour.addActionListener(this);\r
2015         avDistanceTreeBlosumMenuItem.setLabel(\r
2016             "Average Distance Using BLOSUM62");\r
2017         avDistanceTreeBlosumMenuItem.addActionListener(this);\r
2018         njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
2019         njTreeBlosumMenuItem.addActionListener(this);\r
2020         annotationPanelMenuItem.setLabel("Show Annotations");\r
2021         annotationPanelMenuItem.addItemListener(this);\r
2022         colourTextMenuItem.setLabel("Colour Text");\r
2023         colourTextMenuItem.addItemListener(this);\r
2024         overviewMenuItem.setLabel("Overview Window");\r
2025         overviewMenuItem.addActionListener(this);\r
2026         undoMenuItem.setEnabled(false);\r
2027         undoMenuItem.setLabel("Undo");\r
2028         undoMenuItem.addActionListener(this);\r
2029         redoMenuItem.setEnabled(false);\r
2030         redoMenuItem.setLabel("Redo");\r
2031         redoMenuItem.addActionListener(this);\r
2032         conservationMenuItem.setLabel("by Conservation");\r
2033         conservationMenuItem.addItemListener(this);\r
2034         noColourmenuItem.setLabel("None");\r
2035         noColourmenuItem.addActionListener(this);\r
2036         wrapMenuItem.setLabel("Wrap");\r
2037         wrapMenuItem.addItemListener(this);\r
2038         renderGapsMenuItem.setLabel("Show Gaps");\r
2039         renderGapsMenuItem.setState(true);\r
2040         renderGapsMenuItem.addItemListener(this);\r
2041         findMenuItem.setLabel("Find...");\r
2042         findMenuItem.addActionListener(this);\r
2043         searchMenu.setLabel("Search");\r
2044 \r
2045         abovePIDThreshold.setLabel("Above Identity Threshold");\r
2046         abovePIDThreshold.addItemListener(this);\r
2047         nucleotideColour.setLabel("Nucleotide");\r
2048         nucleotideColour.addActionListener(this);\r
2049         deleteGroups.setLabel("Undefine Groups");\r
2050         deleteGroups.addActionListener(this);\r
2051         copy.setLabel("Copy");\r
2052         copy.addActionListener(this);\r
2053         cut.setLabel("Cut");\r
2054         cut.addActionListener(this);\r
2055         delete.setLabel("Delete");\r
2056         delete.addActionListener(this);\r
2057         pasteMenu.setLabel("Paste");\r
2058         pasteNew.setLabel("To New Alignment");\r
2059         pasteNew.addActionListener(this);\r
2060         pasteThis.setLabel("Add To This Alignment");\r
2061         pasteThis.addActionListener(this);\r
2062         applyToAllGroups.setLabel("Apply Colour To All Groups");\r
2063         applyToAllGroups.setState(true);\r
2064         applyToAllGroups.addItemListener(this);\r
2065         font.setLabel("Font...");\r
2066         font.addActionListener(this);\r
2067         scaleAbove.setLabel("Scale Above");\r
2068         scaleAbove.setState(true);\r
2069         scaleAbove.setEnabled(false);\r
2070         scaleAbove.addItemListener(this);\r
2071         scaleLeft.setEnabled(false);\r
2072         scaleLeft.setState(true);\r
2073         scaleLeft.setLabel("Scale Left");\r
2074         scaleLeft.addItemListener(this);\r
2075         scaleRight.setEnabled(false);\r
2076         scaleRight.setState(true);\r
2077         scaleRight.setLabel("Scale Right");\r
2078         scaleRight.addItemListener(this);\r
2079         modifyPID.setLabel("Modify Identity Threshold...");\r
2080         modifyPID.addActionListener(this);\r
2081         modifyConservation.setLabel("Modify Conservation Threshold...");\r
2082         modifyConservation.addActionListener(this);\r
2083         sortByTreeMenu.setLabel("By Tree Order");\r
2084         sort.setLabel("Sort");\r
2085         calculate.setLabel("Calculate Tree");\r
2086         autoCalculate.addItemListener(this);\r
2087         inputText.setLabel("Input from textbox");\r
2088         inputText.addActionListener(this);\r
2089 \r
2090         helpMenu.setLabel("Help");\r
2091         documentation.setLabel("Documentation");\r
2092         documentation.addActionListener(this);\r
2093 \r
2094         about.setLabel("About...");\r
2095         about.addActionListener(this);\r
2096           seqLimits.setState(true);\r
2097     seqLimits.setLabel("Show Sequence Limits");\r
2098     seqLimits.addItemListener(this);\r
2099     featureSettings.setLabel("Feature Settings...");\r
2100     featureSettings.addActionListener(this);\r
2101     sequenceFeatures.setLabel("Sequence Features");\r
2102     sequenceFeatures.addItemListener(this);\r
2103     sequenceFeatures.setState(false);\r
2104     annotationColour.setLabel("by Annotation...");\r
2105     annotationColour.addActionListener(this);\r
2106     invertSequenceMenuItem.setLabel("Invert Sequence Selection");\r
2107     invertColSel.setLabel("Invert Column Selection");\r
2108     menu1.setLabel("Show");\r
2109     showColumns.setLabel("All Columns ");\r
2110     showSeqs.setLabel("All Sequences");\r
2111     menu2.setLabel("Hide");\r
2112     hideColumns.setLabel("Selected Columns");\r
2113     hideSequences.setLabel("Selected Sequences");\r
2114     invertColSel.addActionListener(this);\r
2115     showColumns.addActionListener(this);\r
2116     showSeqs.addActionListener(this);\r
2117     hideColumns.addActionListener(this);\r
2118     hideSequences.addActionListener(this);\r
2119 \r
2120 \r
2121     alignFrameMenuBar.add(fileMenu);\r
2122         alignFrameMenuBar.add(editMenu);\r
2123         alignFrameMenuBar.add(searchMenu);\r
2124         alignFrameMenuBar.add(viewMenu);\r
2125         alignFrameMenuBar.add(colourMenu);\r
2126         alignFrameMenuBar.add(calculateMenu);\r
2127         alignFrameMenuBar.add(helpMenu);\r
2128         fileMenu.add(inputText);\r
2129         fileMenu.add(outputTextboxMenu);\r
2130         if(jalviewServletURL!=null)\r
2131           fileMenu.add(loadApplication);\r
2132         fileMenu.addSeparator();\r
2133         fileMenu.add(loadTree);\r
2134         fileMenu.add(closeMenuItem);\r
2135         editMenu.add(undoMenuItem);\r
2136         editMenu.add(redoMenuItem);\r
2137         editMenu.add(cut);\r
2138         editMenu.add(copy);\r
2139         editMenu.add(pasteMenu);\r
2140         editMenu.add(delete);\r
2141         editMenu.addSeparator();\r
2142         editMenu.add(selectAllSequenceMenuItem);\r
2143         editMenu.add(deselectAllSequenceMenuItem);\r
2144         editMenu.add(invertSequenceMenuItem);\r
2145     editMenu.add(invertColSel);\r
2146     editMenu.add(deleteGroups);\r
2147         editMenu.addSeparator();\r
2148         editMenu.add(remove2LeftMenuItem);\r
2149         editMenu.add(remove2RightMenuItem);\r
2150         editMenu.add(removeGappedColumnMenuItem);\r
2151         editMenu.add(removeAllGapsMenuItem);\r
2152         editMenu.add(removeRedundancyMenuItem);\r
2153         searchMenu.add(findMenuItem);\r
2154         viewMenu.add(font);\r
2155         viewMenu.addSeparator();\r
2156     viewMenu.add(menu1);\r
2157     viewMenu.add(menu2);\r
2158     viewMenu.addSeparator();\r
2159     viewMenu.add(wrapMenuItem);\r
2160         viewMenu.add(scaleAbove);\r
2161         viewMenu.add(scaleLeft);\r
2162         viewMenu.add(scaleRight);\r
2163         viewMenu.addSeparator();\r
2164     viewMenu.add(seqLimits);\r
2165     viewMenu.add(viewBoxesMenuItem);\r
2166         viewMenu.add(viewTextMenuItem);\r
2167         viewMenu.add(colourTextMenuItem);\r
2168         viewMenu.add(renderGapsMenuItem);\r
2169         viewMenu.add(annotationPanelMenuItem);\r
2170     viewMenu.addSeparator();\r
2171         viewMenu.add(sequenceFeatures);\r
2172         viewMenu.add(featureSettings);\r
2173     viewMenu.addSeparator();\r
2174         viewMenu.add(overviewMenuItem);\r
2175         colourMenu.add(applyToAllGroups);\r
2176         colourMenu.addSeparator();\r
2177         colourMenu.add(noColourmenuItem);\r
2178         colourMenu.add(clustalColour);\r
2179         colourMenu.add(BLOSUM62Colour);\r
2180         colourMenu.add(PIDColour);\r
2181         colourMenu.add(zappoColour);\r
2182         colourMenu.add(taylorColour);\r
2183         colourMenu.add(hydrophobicityColour);\r
2184         colourMenu.add(helixColour);\r
2185         colourMenu.add(strandColour);\r
2186         colourMenu.add(turnColour);\r
2187         colourMenu.add(buriedColour);\r
2188         colourMenu.add(nucleotideColour);\r
2189         colourMenu.add(userDefinedColour);\r
2190         colourMenu.addSeparator();\r
2191         colourMenu.add(conservationMenuItem);\r
2192         colourMenu.add(modifyConservation);\r
2193         colourMenu.add(abovePIDThreshold);\r
2194         colourMenu.add(modifyPID);\r
2195     colourMenu.add(annotationColour);\r
2196     calculateMenu.add(sort);\r
2197         calculateMenu.add(calculate);\r
2198         calculateMenu.addSeparator();\r
2199         calculateMenu.add(pairwiseAlignmentMenuItem);\r
2200         calculateMenu.add(PCAMenuItem);\r
2201         calculateMenu.add(autoCalculate);\r
2202         this.add(statusBar, BorderLayout.SOUTH);\r
2203         pasteMenu.add(pasteNew);\r
2204         pasteMenu.add(pasteThis);\r
2205         sort.add(sortIDMenuItem);\r
2206         sort.add(sortByTreeMenu);\r
2207         sort.add(sortGroupMenuItem);\r
2208         sort.add(sortPairwiseMenuItem);\r
2209         calculate.add(averageDistanceTreeMenuItem);\r
2210         calculate.add(neighbourTreeMenuItem);\r
2211         calculate.add(avDistanceTreeBlosumMenuItem);\r
2212         calculate.add(njTreeBlosumMenuItem);\r
2213         helpMenu.add(documentation);\r
2214         helpMenu.add(about);\r
2215     menu1.add(showColumns);\r
2216     menu1.add(showSeqs);\r
2217     menu2.add(hideColumns);\r
2218     menu2.add(hideSequences);\r
2219   }\r
2220 \r
2221   public void setEmbedded()\r
2222   {\r
2223 \r
2224     embeddedMenu = new Panel();\r
2225     embeddedEdit = new Label();\r
2226     embeddedSearch = new Label();\r
2227     embeddedView = new Label();\r
2228     embeddedColour = new Label();\r
2229     embeddedFile = new Label();\r
2230     embeddedHelp = new Label();\r
2231     embeddedCalculate = new Label();\r
2232     flowLayout1 = new FlowLayout();\r
2233     embeddedMenu.setBackground(Color.lightGray);\r
2234     embeddedMenu.setLayout(flowLayout1);\r
2235     embeddedEdit.setText("Edit");\r
2236     embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2237     embeddedSearch.setText("Search");\r
2238     embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2239     embeddedView.setText("View");\r
2240     embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2241     embeddedColour.setText("Colour");\r
2242     embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2243     embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2244     embeddedFile.setText("File");\r
2245     embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2246     embeddedHelp.setText("Help");\r
2247     embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2248     embeddedCalculate.setText("Calculate");\r
2249     embeddedMenu.add(embeddedFile);\r
2250     embeddedMenu.add(embeddedEdit);\r
2251     embeddedMenu.add(embeddedSearch);\r
2252     embeddedMenu.add(embeddedView);\r
2253     embeddedMenu.add(embeddedColour);\r
2254     embeddedMenu.add(embeddedCalculate);\r
2255     embeddedMenu.add(embeddedHelp);\r
2256     flowLayout1.setAlignment(FlowLayout.LEFT);\r
2257     flowLayout1.setHgap(2);\r
2258     flowLayout1.setVgap(0);\r
2259     embeddedFile.addMouseListener(this);\r
2260     embeddedEdit.addMouseListener(this);\r
2261     embeddedSearch.addMouseListener(this);\r
2262     embeddedView.addMouseListener(this);\r
2263     embeddedColour.addMouseListener(this);\r
2264     embeddedCalculate.addMouseListener(this);\r
2265     embeddedHelp.addMouseListener(this);\r
2266 \r
2267    // setVisible(false);\r
2268     fileMenu.remove(closeMenuItem);\r
2269     fileMenu.remove(3); // Seperator\r
2270 \r
2271     viewport.applet.setLayout(new BorderLayout());\r
2272     viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
2273     viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
2274    // viewport.applet.validate();\r
2275 \r
2276     alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height\r
2277                        - embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
2278 \r
2279      viewport.applet.add(alignPanel, BorderLayout.CENTER);\r
2280      viewport.applet.validate();\r
2281 \r
2282   }\r
2283 \r
2284 \r
2285 \r
2286   PopupMenu filePopup, editPopup, searchPopup,\r
2287       viewPopup, colourPopup, calculatePopup, helpPopup;\r
2288   MenuItem featureSettings = new MenuItem();\r
2289   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
2290   MenuItem annotationColour = new MenuItem();\r
2291   MenuItem invertColSel = new MenuItem();\r
2292   Menu menu1 = new Menu();\r
2293   MenuItem showColumns = new MenuItem();\r
2294   MenuItem showSeqs = new MenuItem();\r
2295   Menu menu2 = new Menu();\r
2296   MenuItem hideColumns = new MenuItem();\r
2297   MenuItem hideSequences = new MenuItem();\r
2298 \r
2299   public void mousePressed(MouseEvent evt)\r
2300   {\r
2301     PopupMenu popup = null;\r
2302     Label source = (Label)evt.getSource();\r
2303     if(source==embeddedFile)\r
2304     {\r
2305       popup = filePopup = genPopupMenu(filePopup, fileMenu);\r
2306     }\r
2307     else if(source==embeddedEdit)\r
2308     {\r
2309       popup = editPopup = genPopupMenu(editPopup, editMenu);\r
2310     }\r
2311     else if(source==embeddedSearch)\r
2312     {\r
2313       popup = searchPopup = genPopupMenu(searchPopup, searchMenu);\r
2314     }\r
2315     else if(source==embeddedView)\r
2316     {\r
2317       popup = viewPopup = genPopupMenu(viewPopup, viewMenu);\r
2318     }\r
2319     else if(source==embeddedColour)\r
2320     {\r
2321       popup = colourPopup = genPopupMenu(colourPopup, colourMenu);\r
2322     }\r
2323     else if(source==embeddedCalculate)\r
2324     {\r
2325       popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);\r
2326     }\r
2327     else if(source==embeddedHelp)\r
2328     {\r
2329       popup = helpPopup = genPopupMenu(helpPopup, helpMenu);\r
2330     }\r
2331 \r
2332     embeddedMenu.add(popup);\r
2333     popup.show(embeddedMenu,\r
2334                source.getBounds().x,\r
2335                source.getBounds().y + source.getBounds().getSize().height);\r
2336   }\r
2337 \r
2338   PopupMenu genPopupMenu(PopupMenu popup, Menu original)\r
2339   {\r
2340     if(popup!=null)\r
2341     {\r
2342       return popup;\r
2343     }\r
2344     popup = new PopupMenu();\r
2345     int m, mSize = original.getItemCount();\r
2346     for(m=0; m<mSize; m++)\r
2347     {\r
2348       popup.add(original.getItem(m));\r
2349       mSize--;\r
2350       m--;\r
2351     }\r
2352 \r
2353     return popup;\r
2354   }\r
2355   public void mouseClicked(MouseEvent evt)\r
2356   {}\r
2357   public void mouseReleased(MouseEvent evt)\r
2358   {}\r
2359   public void mouseEntered(MouseEvent evt)\r
2360   {}\r
2361   public void mouseExited(MouseEvent evt)\r
2362   {}\r
2363 \r
2364 }\r
2365 \r