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