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    alignPanel.scalePanel.addKeyListener(this);\r
 114    alignPanel.annotationPanel.addKeyListener(this);\r
 115 \r
 116     viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
 117     {\r
 118      public void propertyChange(java.beans.PropertyChangeEvent evt)\r
 119      {\r
 120        if (evt.getPropertyName().equals("alignment"))\r
 121        {\r
 122          alignmentChanged();\r
 123        }\r
 124      }\r
 125    });\r
 126 \r
 127 \r
 128    if(embedded)\r
 129    {\r
 130      setEmbedded();\r
 131    }\r
 132    else\r
 133    {\r
 134      add(alignPanel, BorderLayout.CENTER);\r
 135      jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH,\r
 136                                       NEW_WINDOW_HEIGHT);\r
 137    }\r
 138    alignPanel.validate();\r
 139    alignPanel.repaint();\r
 140   }\r
 141   public AlignViewport getAlignViewport()\r
 142   {\r
 143     return viewport;\r
 144   }\r
 145 \r
 146   public SeqCanvas getSeqcanvas()\r
 147   {\r
 148     return alignPanel.seqPanel.seqCanvas;\r
 149   }\r
 150 \r
 151 \r
 152   /**\r
 153    * DOCUMENT ME!\r
 154    *\r
 155    * @param String DOCUMENT ME!\r
 156    */\r
 157 \r
 158   public void parseFeaturesFile(String file, String type)\r
 159   {\r
 160     Hashtable featureLinks = new Hashtable();\r
 161     boolean featuresFile = false;\r
 162     try{\r
 163       featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment,\r
 164                                          alignPanel.seqPanel.seqCanvas.\r
 165                                          getFeatureRenderer().featureColours,\r
 166                                          featureLinks,\r
 167                                          true);\r
 168     }\r
 169     catch(Exception ex)\r
 170     {\r
 171       ex.printStackTrace();\r
 172     }\r
 173 \r
 174     if(featuresFile)\r
 175     {\r
 176       if(featureLinks.size()>0)\r
 177         alignPanel.seqPanel.seqCanvas\r
 178             .getFeatureRenderer().featureLinks = featureLinks;\r
 179       viewport.showSequenceFeatures = true;\r
 180       sequenceFeatures.setState(true);\r
 181       alignPanel.repaint();\r
 182     }\r
 183 \r
 184   }\r
 185 \r
 186 \r
 187   public void keyPressed(KeyEvent evt)\r
 188   {\r
 189     if (viewport.cursorMode\r
 190         && evt.getKeyCode() >= KeyEvent.VK_0\r
 191         && evt.getKeyCode() <= KeyEvent.VK_9)\r
 192     {\r
 193       alignPanel.seqPanel.numberPressed(evt.getKeyChar());\r
 194     }\r
 195 \r
 196     switch (evt.getKeyCode())\r
 197     {\r
 198       case 27: // escape key\r
 199         deselectAllSequenceMenuItem_actionPerformed();\r
 200         break;\r
 201       case KeyEvent.VK_X:\r
 202         if (evt.isControlDown() || evt.isMetaDown())\r
 203         {\r
 204           cut_actionPerformed();\r
 205         }\r
 206         break;\r
 207       case KeyEvent.VK_C:\r
 208         if (viewport.cursorMode && !evt.isControlDown())\r
 209         {\r
 210           alignPanel.seqPanel.setCursorColumn();\r
 211         }\r
 212         if (evt.isControlDown() || evt.isMetaDown())\r
 213         {\r
 214           copy_actionPerformed();\r
 215         }\r
 216         break;\r
 217       case KeyEvent.VK_V:\r
 218         if (evt.isControlDown() || evt.isMetaDown())\r
 219         {\r
 220           paste(true);\r
 221         }\r
 222         break;\r
 223       case KeyEvent.VK_A:\r
 224         if (evt.isControlDown() || evt.isMetaDown())\r
 225         {\r
 226           selectAllSequenceMenuItem_actionPerformed();\r
 227         }\r
 228         break;\r
 229       case KeyEvent.VK_DOWN:\r
 230         if(viewport.cursorMode)\r
 231         {\r
 232           alignPanel.seqPanel.moveCursor(0,1);\r
 233         }\r
 234         else\r
 235           moveSelectedSequences(false);\r
 236         break;\r
 237 \r
 238       case KeyEvent.VK_UP:\r
 239         if (viewport.cursorMode)\r
 240         {\r
 241           alignPanel.seqPanel.moveCursor(0,-1);\r
 242         }\r
 243         else\r
 244           moveSelectedSequences(true);\r
 245         break;\r
 246 \r
 247       case KeyEvent.VK_LEFT:\r
 248         if(viewport.cursorMode)\r
 249         {\r
 250           alignPanel.seqPanel.moveCursor(-1,0);\r
 251         }\r
 252         break;\r
 253 \r
 254       case KeyEvent.VK_RIGHT:\r
 255         if (viewport.cursorMode)\r
 256         {\r
 257           alignPanel.seqPanel.moveCursor(1,0);\r
 258         }\r
 259         break;\r
 260       case KeyEvent.VK_SPACE:\r
 261         if(viewport.cursorMode)\r
 262         {\r
 263           alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown());\r
 264         }\r
 265         break;\r
 266 \r
 267       case KeyEvent.VK_DELETE:\r
 268       case KeyEvent.VK_BACK_SPACE:\r
 269         if(viewport.cursorMode)\r
 270         {\r
 271           alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown());\r
 272         }\r
 273        else\r
 274         {\r
 275           cut_actionPerformed();\r
 276           alignPanel.seqPanel.seqCanvas.repaint();\r
 277         }\r
 278         break;\r
 279 \r
 280       case KeyEvent.VK_S:\r
 281         if(viewport.cursorMode)\r
 282         {\r
 283           alignPanel.seqPanel.setCursorRow();\r
 284         }\r
 285         break;\r
 286       case KeyEvent.VK_P:\r
 287         if(viewport.cursorMode)\r
 288         {\r
 289           alignPanel.seqPanel.setCursorPosition();\r
 290         }\r
 291         break;\r
 292 \r
 293       case KeyEvent.VK_ENTER:\r
 294       case KeyEvent.VK_COMMA:\r
 295         if(viewport.cursorMode)\r
 296         {\r
 297           alignPanel.seqPanel.setCursorRowAndColumn();\r
 298         }\r
 299         break;\r
 300 \r
 301       case KeyEvent.VK_Q:\r
 302         if(viewport.cursorMode)\r
 303         {\r
 304           alignPanel.seqPanel.setSelectionAreaAtCursor(true);\r
 305         }\r
 306         break;\r
 307       case KeyEvent.VK_M:\r
 308         if(viewport.cursorMode)\r
 309         {\r
 310           alignPanel.seqPanel.setSelectionAreaAtCursor(false);\r
 311         }\r
 312         break;\r
 313 \r
 314      case KeyEvent.VK_F2:\r
 315        viewport.cursorMode = ! viewport.cursorMode;\r
 316        statusBar.setText("Keyboard editing mode is "+\r
 317            (viewport.cursorMode ? "on" : "off"));\r
 318        if(viewport.cursorMode)\r
 319        {\r
 320          alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;\r
 321          alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;\r
 322        }\r
 323        alignPanel.seqPanel.seqCanvas.repaint();\r
 324        break;\r
 325 \r
 326       case KeyEvent.VK_F:\r
 327         if (evt.isControlDown())\r
 328         {\r
 329           findMenuItem_actionPerformed();\r
 330         }\r
 331         break;\r
 332       case KeyEvent.VK_H:\r
 333       {\r
 334         boolean toggleSeqs = !evt.isControlDown();\r
 335         boolean toggleCols = !evt.isAltDown();\r
 336         boolean hide = false;\r
 337         SequenceGroup sg = viewport.getSelectionGroup();\r
 338 \r
 339         if(toggleSeqs)\r
 340         {\r
 341           if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())\r
 342           {\r
 343             hide = true;\r
 344             viewport.hideAllSelectedSeqs();\r
 345           }\r
 346           else\r
 347             viewport.showAllHiddenSeqs();\r
 348         }\r
 349 \r
 350         if(toggleCols)\r
 351         {\r
 352           if (viewport.colSel.getSelected().size() > 0)\r
 353             viewport.hideSelectedColumns();\r
 354           else if (!hide)\r
 355             viewport.showAllHiddenColumns();\r
 356         }\r
 357 \r
 358         alignPanel.repaint();\r
 359         break;\r
 360       }\r
 361 \r
 362     }\r
 363   }\r
 364   public void keyReleased(KeyEvent evt)\r
 365   {}\r
 366   public void keyTyped(KeyEvent evt)\r
 367   {}\r
 368 \r
 369 public void itemStateChanged(ItemEvent evt)\r
 370   {\r
 371     if(evt.getSource()==colourTextMenuItem)\r
 372             colourTextMenuItem_actionPerformed();\r
 373     else if(evt.getSource()==wrapMenuItem)\r
 374             wrapMenuItem_actionPerformed();\r
 375     else if(evt.getSource()==scaleAbove)\r
 376             scaleAbove_actionPerformed();\r
 377     else if(evt.getSource()==scaleLeft)\r
 378             scaleLeft_actionPerformed();\r
 379     else if(evt.getSource()==scaleRight)\r
 380             scaleRight_actionPerformed();\r
 381      else if(evt.getSource()==seqLimits)\r
 382       seqLimits_itemStateChanged();\r
 383     else if(evt.getSource()==viewBoxesMenuItem)\r
 384             viewBoxesMenuItem_actionPerformed();\r
 385     else if(evt.getSource()==viewTextMenuItem)\r
 386             viewTextMenuItem_actionPerformed();\r
 387     else if(evt.getSource()==renderGapsMenuItem)\r
 388             renderGapsMenuItem_actionPerformed();\r
 389     else if(evt.getSource()==annotationPanelMenuItem)\r
 390             annotationPanelMenuItem_actionPerformed();\r
 391       else if(evt.getSource()==sequenceFeatures)\r
 392       {\r
 393            viewport.showSequenceFeatures(sequenceFeatures.getState());\r
 394             alignPanel.seqPanel.seqCanvas.repaint();\r
 395       }\r
 396       else if(evt.getSource()==conservationMenuItem)\r
 397             conservationMenuItem_actionPerformed();\r
 398       else if(evt.getSource()==abovePIDThreshold)\r
 399             abovePIDThreshold_actionPerformed();\r
 400           else if(evt.getSource()==applyToAllGroups)\r
 401             applyToAllGroups_actionPerformed();\r
 402       else if(evt.getSource()==autoCalculate)\r
 403           viewport.autocalculateConsensus = autoCalculate.getState();\r
 404   }\r
 405  public void actionPerformed(ActionEvent evt)\r
 406  {\r
 407     Object source = evt.getSource();\r
 408 \r
 409     if(source==inputText)\r
 410       inputText_actionPerformed();\r
 411     else if(source==loadTree)\r
 412       loadTree_actionPerformed();\r
 413     else if(source==loadApplication)\r
 414       launchFullApplication();\r
 415     else if(source==closeMenuItem)\r
 416       closeMenuItem_actionPerformed();\r
 417     else if(source==copy)\r
 418       copy_actionPerformed();\r
 419     else if(source==undoMenuItem)\r
 420       undoMenuItem_actionPerformed();\r
 421     else if(source==redoMenuItem)\r
 422       redoMenuItem_actionPerformed();\r
 423     else if(source==inputText)\r
 424             inputText_actionPerformed();\r
 425     else if(source==closeMenuItem)\r
 426             closeMenuItem_actionPerformed();\r
 427     else if(source==undoMenuItem)\r
 428             undoMenuItem_actionPerformed();\r
 429     else if(source==redoMenuItem)\r
 430             redoMenuItem_actionPerformed();\r
 431     else if(source==copy)\r
 432             copy_actionPerformed();\r
 433     else if(source==pasteNew)\r
 434             pasteNew_actionPerformed();\r
 435     else if(source==pasteThis)\r
 436             pasteThis_actionPerformed();\r
 437     else if(source==cut)\r
 438             cut_actionPerformed();\r
 439     else if(source==delete)\r
 440             delete_actionPerformed();\r
 441     else if(source==deleteGroups)\r
 442             deleteGroups_actionPerformed();\r
 443     else if(source==selectAllSequenceMenuItem)\r
 444             selectAllSequenceMenuItem_actionPerformed();\r
 445     else if(source==deselectAllSequenceMenuItem)\r
 446             deselectAllSequenceMenuItem_actionPerformed();\r
 447     else if(source==invertSequenceMenuItem)\r
 448             invertSequenceMenuItem_actionPerformed();\r
 449     else if(source==invertColSel)\r
 450     { viewport.invertColumnSelection(); alignPanel.repaint(); }\r
 451     else if(source==remove2LeftMenuItem)\r
 452             remove2LeftMenuItem_actionPerformed();\r
 453     else if(source==remove2RightMenuItem)\r
 454             remove2RightMenuItem_actionPerformed();\r
 455     else if(source==removeGappedColumnMenuItem)\r
 456             removeGappedColumnMenuItem_actionPerformed();\r
 457     else if(source==removeAllGapsMenuItem)\r
 458             removeAllGapsMenuItem_actionPerformed();\r
 459     else if(source==findMenuItem)\r
 460             findMenuItem_actionPerformed();\r
 461     else if(source==font)\r
 462             font_actionPerformed();\r
 463     else if(source==showColumns)\r
 464     {\r
 465       viewport.showAllHiddenColumns(); alignPanel.repaint();\r
 466     }\r
 467     else if(source==showSeqs)\r
 468     {\r
 469       viewport.showAllHiddenSeqs();\r
 470     }\r
 471     else if(source == hideColumns)\r
 472     {\r
 473       viewport.hideSelectedColumns(); alignPanel.repaint();\r
 474     }\r
 475     else if(source == hideSequences && viewport.getSelectionGroup()!=null)\r
 476     {\r
 477       viewport.hideAllSelectedSeqs();\r
 478     }\r
 479     else if(source==featureSettings)\r
 480             featureSettings_actionPerformed();\r
 481     else if(source==overviewMenuItem)\r
 482             overviewMenuItem_actionPerformed();\r
 483     else if(source==noColourmenuItem)\r
 484             noColourmenuItem_actionPerformed();\r
 485     else if(source==clustalColour)\r
 486             clustalColour_actionPerformed();\r
 487     else if(source==zappoColour)\r
 488             zappoColour_actionPerformed();\r
 489     else if(source==taylorColour)\r
 490             taylorColour_actionPerformed();\r
 491     else if(source==hydrophobicityColour)\r
 492             hydrophobicityColour_actionPerformed();\r
 493     else if(source==helixColour)\r
 494             helixColour_actionPerformed();\r
 495     else if(source==strandColour)\r
 496             strandColour_actionPerformed();\r
 497     else if(source==turnColour)\r
 498             turnColour_actionPerformed();\r
 499     else if(source==buriedColour)\r
 500             buriedColour_actionPerformed();\r
 501     else if(source==nucleotideColour)\r
 502             nucleotideColour_actionPerformed();\r
 503     else if(source==modifyPID)\r
 504             modifyPID_actionPerformed();\r
 505     else if(source==modifyConservation)\r
 506             modifyConservation_actionPerformed();\r
 507     else if(source==userDefinedColour)\r
 508             userDefinedColour_actionPerformed();\r
 509     else if(source==PIDColour)\r
 510             PIDColour_actionPerformed();\r
 511     else if(source==BLOSUM62Colour)\r
 512             BLOSUM62Colour_actionPerformed();\r
 513     else if(source==annotationColour)\r
 514            new AnnotationColourChooser(viewport, alignPanel);\r
 515     else if(source==sortPairwiseMenuItem)\r
 516             sortPairwiseMenuItem_actionPerformed();\r
 517     else if(source==sortIDMenuItem)\r
 518             sortIDMenuItem_actionPerformed();\r
 519     else if(source==sortGroupMenuItem)\r
 520             sortGroupMenuItem_actionPerformed();\r
 521     else if(source==removeRedundancyMenuItem)\r
 522             removeRedundancyMenuItem_actionPerformed();\r
 523     else if(source==pairwiseAlignmentMenuItem)\r
 524             pairwiseAlignmentMenuItem_actionPerformed();\r
 525     else if(source==PCAMenuItem)\r
 526             PCAMenuItem_actionPerformed();\r
 527     else if(source==averageDistanceTreeMenuItem)\r
 528             averageDistanceTreeMenuItem_actionPerformed();\r
 529     else if(source==neighbourTreeMenuItem)\r
 530             neighbourTreeMenuItem_actionPerformed();\r
 531     else if(source==njTreeBlosumMenuItem)\r
 532             njTreeBlosumMenuItem_actionPerformed();\r
 533     else if(source==avDistanceTreeBlosumMenuItem)\r
 534             avTreeBlosumMenuItem_actionPerformed();\r
 535     else if(source==documentation)\r
 536             documentation_actionPerformed();\r
 537     else if(source==about)\r
 538             about_actionPerformed();\r
 539 \r
 540  }\r
 541 \r
 542   public void inputText_actionPerformed()\r
 543   {\r
 544     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
 545     Frame frame = new Frame();\r
 546     frame.add(cap);\r
 547     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
 548   }\r
 549 \r
 550   protected void outputText_actionPerformed(ActionEvent e)\r
 551   {\r
 552     CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
 553     Frame frame = new Frame();\r
 554     frame.add(cap);\r
 555     jalview.bin.JalviewLite.addFrame(frame,\r
 556                                      "Alignment output - " + e.getActionCommand(),\r
 557                                      600, 500);\r
 558     cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
 559                                               viewport.getAlignment().getSequences(),\r
 560                                                       viewport.showJVSuffix));\r
 561   }\r
 562 \r
 563   void launchFullApplication()\r
 564   {\r
 565     StringBuffer url = new StringBuffer(jalviewServletURL);\r
 566 \r
 567     url.append("?open="+\r
 568                appendProtocol( viewport.applet.getParameter("file") ) );\r
 569 \r
 570     if(viewport.applet.getParameter("features")!=null)\r
 571     {\r
 572       url.append( "&features=" );\r
 573       url.append( appendProtocol( viewport.applet.getParameter("features") ) );\r
 574     }\r
 575 \r
 576     if(viewport.applet.getParameter("annotations")!=null)\r
 577     {\r
 578       url.append( "&annotations=" );\r
 579       url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );\r
 580     }\r
 581 \r
 582     if(viewport.applet.getParameter("defaultColour")!=null)\r
 583     {\r
 584       url.append("&colour=" +\r
 585                  removeWhiteSpace(viewport.applet.getParameter("defaultColour"))\r
 586           );\r
 587     }\r
 588 \r
 589     if(viewport.applet.getParameter("userDefinedColour")!=null)\r
 590     {\r
 591       url.append( "&colour=" +\r
 592                  removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )\r
 593          );\r
 594     }\r
 595 \r
 596     showURL(url.toString(), "FULL_APP");\r
 597   }\r
 598 \r
 599 \r
 600   String removeWhiteSpace(String colour)\r
 601   {\r
 602     StringBuffer sb = new StringBuffer();\r
 603     for (int i = 0; i < colour.length(); i++)\r
 604     {\r
 605       if (Character.isWhitespace(colour.charAt(i)))\r
 606         sb.append("%20");\r
 607       else\r
 608         sb.append(colour.charAt(i));\r
 609     }\r
 610 \r
 611     return sb.toString();\r
 612   }\r
 613 \r
 614 \r
 615   String appendProtocol(String url)\r
 616   {\r
 617     try{\r
 618        new URL(url);\r
 619     }catch(java.net.MalformedURLException ex)\r
 620     {\r
 621       url = viewport.applet.getCodeBase()+url;\r
 622     }\r
 623     return url;\r
 624   }\r
 625 \r
 626   public void closeMenuItem_actionPerformed()\r
 627   {\r
 628     PaintRefresher.components.remove(viewport.alignment);\r
 629     if(PaintRefresher.components.size()==0 && viewport.applet==null)\r
 630       System.exit(0);\r
 631 \r
 632     this.dispose();\r
 633   }\r
 634 \r
 635   Stack historyList = new Stack();\r
 636   Stack redoList = new Stack();\r
 637 \r
 638   void updateEditMenuBar()\r
 639   {\r
 640     if (historyList.size() > 0)\r
 641     {\r
 642       undoMenuItem.setEnabled(true);\r
 643       HistoryItem hi = (HistoryItem) historyList.peek();\r
 644       undoMenuItem.setLabel("Undo " + hi.getDescription());\r
 645     }\r
 646     else\r
 647     {\r
 648       undoMenuItem.setEnabled(false);\r
 649       undoMenuItem.setLabel("Undo");\r
 650     }\r
 651 \r
 652     if (redoList.size() > 0)\r
 653     {\r
 654       redoMenuItem.setEnabled(true);\r
 655       HistoryItem hi = (HistoryItem) redoList.peek();\r
 656       redoMenuItem.setLabel("Redo " + hi.getDescription());\r
 657     }\r
 658     else\r
 659     {\r
 660       redoMenuItem.setEnabled(false);\r
 661       redoMenuItem.setLabel("Redo");\r
 662     }\r
 663   }\r
 664 \r
 665   public void addHistoryItem(HistoryItem hi)\r
 666   {\r
 667     historyList.push(hi);\r
 668     updateEditMenuBar();\r
 669   }\r
 670 \r
 671   protected void undoMenuItem_actionPerformed()\r
 672   {\r
 673     HistoryItem hi = (HistoryItem) historyList.pop();\r
 674     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
 675                                   HistoryItem.HIDE));\r
 676     restoreHistoryItem(hi);\r
 677     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 678   }\r
 679 \r
 680   protected void redoMenuItem_actionPerformed()\r
 681   {\r
 682     HistoryItem hi = (HistoryItem) redoList.pop();\r
 683     restoreHistoryItem(hi);\r
 684     updateEditMenuBar();\r
 685     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 686   }\r
 687 \r
 688   // used by undo and redo\r
 689   void restoreHistoryItem(HistoryItem hi)\r
 690   {\r
 691     hi.restore();\r
 692 \r
 693     updateEditMenuBar();\r
 694 \r
 695     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 696   }\r
 697 \r
 698   public void moveSelectedSequences(boolean up)\r
 699   {\r
 700     SequenceGroup sg = viewport.getSelectionGroup();\r
 701     if (sg == null)\r
 702     {\r
 703       return;\r
 704     }\r
 705 \r
 706     if (up)\r
 707     {\r
 708       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 709       {\r
 710         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 711         if (!sg.getSequences(false).contains(seq))\r
 712         {\r
 713           continue;\r
 714         }\r
 715 \r
 716         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 717         if (sg.getSequences(false).contains(temp))\r
 718         {\r
 719           continue;\r
 720         }\r
 721 \r
 722         viewport.alignment.getSequences().setElementAt(temp, i);\r
 723         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 724       }\r
 725     }\r
 726     else\r
 727     {\r
 728       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 729       {\r
 730         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 731         if (!sg.getSequences(true).contains(seq))\r
 732         {\r
 733           continue;\r
 734         }\r
 735 \r
 736         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 737         if (sg.getSequences(true).contains(temp))\r
 738         {\r
 739           continue;\r
 740         }\r
 741 \r
 742         viewport.alignment.getSequences().setElementAt(temp, i);\r
 743         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 744       }\r
 745     }\r
 746 \r
 747     alignPanel.repaint();\r
 748   }\r
 749 \r
 750   static StringBuffer copiedSequences;\r
 751   static Vector copiedHiddenColumns;\r
 752   protected void copy_actionPerformed()\r
 753   {\r
 754     if (viewport.getSelectionGroup() == null)\r
 755     {\r
 756       return;\r
 757     }\r
 758 \r
 759     SequenceGroup sg = viewport.getSelectionGroup();\r
 760     copiedSequences = new StringBuffer();\r
 761     Hashtable orderedSeqs = new Hashtable();\r
 762     for (int i = 0; i < sg.getSize(false); i++)\r
 763     {\r
 764       SequenceI seq = sg.getSequenceAt(i);\r
 765       int index = viewport.alignment.findIndex(seq);\r
 766       orderedSeqs.put(index + "", seq);\r
 767     }\r
 768 \r
 769     int index = 0, startRes, endRes;\r
 770     char ch;\r
 771 \r
 772     if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)\r
 773     {\r
 774       copiedHiddenColumns = new Vector();\r
 775       int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
 776       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();\r
 777            i++)\r
 778       {\r
 779         int[] region = (int[])\r
 780             viewport.getColumnSelection().getHiddenColumns().elementAt(i);\r
 781 \r
 782         copiedHiddenColumns.addElement(new int[]\r
 783                                  {region[0] - hiddenOffset,\r
 784                                  region[1] - hiddenOffset});\r
 785       }\r
 786     }\r
 787     else\r
 788       copiedHiddenColumns = null;\r
 789 \r
 790 \r
 791     for (int i = 0; i < sg.getSize(false); i++)\r
 792     {\r
 793         SequenceI seq = null;\r
 794 \r
 795         while (seq == null)\r
 796         {\r
 797             if (orderedSeqs.containsKey(index + ""))\r
 798             {\r
 799                 seq = (SequenceI) orderedSeqs.get(index + "");\r
 800                 index++;\r
 801 \r
 802                 break;\r
 803             }\r
 804             else\r
 805             {\r
 806                 index++;\r
 807             }\r
 808         }\r
 809 \r
 810         //FIND START RES\r
 811         //Returns residue following index if gap\r
 812         startRes = seq.findPosition(sg.getStartRes());\r
 813 \r
 814         //FIND END RES\r
 815         //Need to find the residue preceeding index if gap\r
 816         endRes = 0;\r
 817 \r
 818         for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
 819         {\r
 820           ch = seq.getCharAt(j);\r
 821           if (!jalview.util.Comparison.isGap( (ch)))\r
 822           {\r
 823             endRes++;\r
 824           }\r
 825         }\r
 826 \r
 827         if(endRes>0)\r
 828         {\r
 829           endRes += seq.getStart() -1;\r
 830         }\r
 831 \r
 832         copiedSequences.append(seq.getName() + "\t" +\r
 833             startRes + "\t" +\r
 834             endRes + "\t" +\r
 835             seq.getSequence(sg.getStartRes(),\r
 836                 sg.getEndRes() + 1) + "\n");\r
 837     }\r
 838 \r
 839   }\r
 840 \r
 841   protected void pasteNew_actionPerformed()\r
 842   {\r
 843     paste(true);\r
 844   }\r
 845 \r
 846   protected void pasteThis_actionPerformed()\r
 847   {\r
 848     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
 849                                    HistoryItem.PASTE));\r
 850     paste(false);\r
 851   }\r
 852 \r
 853   void paste(boolean newAlignment)\r
 854   {\r
 855     try\r
 856     {\r
 857       if (copiedSequences == null)\r
 858       {\r
 859         return;\r
 860       }\r
 861 \r
 862       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 863       Vector seqs = new Vector();\r
 864       while (st.hasMoreElements())\r
 865       {\r
 866         String name = st.nextToken();\r
 867         int start = Integer.parseInt(st.nextToken());\r
 868         int end = Integer.parseInt(st.nextToken());\r
 869         Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
 870 \r
 871         if (!newAlignment)\r
 872         {\r
 873           viewport.alignment.addSequence(sequence);\r
 874         }\r
 875         else\r
 876         {\r
 877           seqs.addElement(sequence);\r
 878         }\r
 879       }\r
 880 \r
 881       if (newAlignment)\r
 882       {\r
 883         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 884         for (int i = 0; i < seqs.size(); i++)\r
 885         {\r
 886           newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
 887         }\r
 888 \r
 889         String newtitle = new String("Copied sequences");\r
 890         if (getTitle().startsWith("Copied sequences"))\r
 891         {\r
 892           newtitle = getTitle();\r
 893         }\r
 894         else\r
 895         {\r
 896           newtitle = newtitle.concat("- from " + getTitle());\r
 897         }\r
 898         AlignFrame af = new AlignFrame(new Alignment(newSeqs),\r
 899                                        viewport.applet,\r
 900                                        newtitle,\r
 901                                        false);\r
 902         if (copiedHiddenColumns != null)\r
 903         {\r
 904           for (int i = 0; i < copiedHiddenColumns.size(); i++)\r
 905           {\r
 906             int[] region = (int[]) copiedHiddenColumns.elementAt(i);\r
 907             af.viewport.hideColumns(region[0], region[1]);\r
 908           }\r
 909         }\r
 910 \r
 911 \r
 912         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
 913                                          NEW_WINDOW_HEIGHT);\r
 914       }\r
 915       else\r
 916       {\r
 917         viewport.setEndSeq(viewport.alignment.getHeight());\r
 918         viewport.alignment.getWidth();\r
 919         viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 920       }\r
 921 \r
 922     }\r
 923     catch (Exception ex)\r
 924     {} // could be anything being pasted in here\r
 925 \r
 926   }\r
 927 \r
 928   protected void cut_actionPerformed()\r
 929   {\r
 930     copy_actionPerformed();\r
 931     delete_actionPerformed();\r
 932   }\r
 933 \r
 934   protected void delete_actionPerformed()\r
 935   {\r
 936     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
 937                                    HistoryItem.HIDE));\r
 938     if (viewport.getSelectionGroup() == null)\r
 939     {\r
 940       return;\r
 941     }\r
 942 \r
 943 \r
 944     SequenceGroup sg = viewport.getSelectionGroup();\r
 945     boolean allSequences = false;\r
 946     if(sg.getSize(false)==viewport.alignment.getHeight())\r
 947           allSequences = true;\r
 948 \r
 949     for (int i = 0; i < sg.getSize(false); i++)\r
 950     {\r
 951       SequenceI seq = sg.getSequenceAt(i);\r
 952       int index = viewport.getAlignment().findIndex(seq);\r
 953       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 954 \r
 955       // If the cut affects all sequences, remove highlighted columns\r
 956       if (allSequences)\r
 957       {\r
 958         viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
 959                                                      sg.getEndRes() + 1);\r
 960       }\r
 961 \r
 962 \r
 963       if (seq.getSequence().length() < 1)\r
 964       {\r
 965         viewport.getAlignment().deleteSequence(seq);\r
 966       }\r
 967       else\r
 968       {\r
 969         viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 970       }\r
 971     }\r
 972 \r
 973     viewport.setSelectionGroup(null);\r
 974     viewport.alignment.deleteGroup(sg);\r
 975     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
 976     if (viewport.getAlignment().getHeight() < 1)\r
 977     {\r
 978       try\r
 979       {\r
 980         this.setVisible(false);\r
 981       }\r
 982       catch (Exception ex)\r
 983       {}\r
 984     }\r
 985     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 986 \r
 987   }\r
 988 \r
 989   protected void deleteGroups_actionPerformed()\r
 990   {\r
 991     viewport.alignment.deleteAllGroups();\r
 992     viewport.setSelectionGroup(null);\r
 993 \r
 994     alignPanel.repaint();\r
 995   }\r
 996 \r
 997   public void selectAllSequenceMenuItem_actionPerformed()\r
 998   {\r
 999     SequenceGroup sg = new SequenceGroup();\r
1000     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
1001     {\r
1002       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
1003     }\r
1004     sg.setEndRes(viewport.alignment.getWidth()-1);\r
1005     viewport.setSelectionGroup(sg);\r
1006     alignPanel.repaint();\r
1007     PaintRefresher.Refresh(null, viewport.alignment);\r
1008   }\r
1009 \r
1010   public void deselectAllSequenceMenuItem_actionPerformed()\r
1011   {\r
1012     if(viewport.cursorMode)\r
1013     {\r
1014       alignPanel.seqPanel.keyboardNo1=null;\r
1015       alignPanel.seqPanel.keyboardNo2=null;\r
1016     }\r
1017     viewport.setSelectionGroup(null);\r
1018     viewport.getColumnSelection().clear();\r
1019     viewport.setSelectionGroup(null);\r
1020     alignPanel.idPanel.idCanvas.searchResults = null;\r
1021     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
1022     alignPanel.repaint();\r
1023     PaintRefresher.Refresh(null, viewport.alignment);\r
1024   }\r
1025 \r
1026   public void invertSequenceMenuItem_actionPerformed()\r
1027   {\r
1028     SequenceGroup sg = viewport.getSelectionGroup();\r
1029     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
1030     {\r
1031       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
1032     }\r
1033 \r
1034     PaintRefresher.Refresh(null, viewport.alignment);\r
1035   }\r
1036 \r
1037   public void remove2LeftMenuItem_actionPerformed()\r
1038   {\r
1039     ColumnSelection colSel = viewport.getColumnSelection();\r
1040     if (colSel.size() > 0)\r
1041     {\r
1042       addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
1043                                      HistoryItem.HIDE));\r
1044       int min = colSel.getMin();\r
1045       viewport.getAlignment().trimLeft(min);\r
1046       colSel.compensateForEdit(0, min);\r
1047 \r
1048       if (viewport.getSelectionGroup() != null)\r
1049       {\r
1050         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
1051       }\r
1052 \r
1053       Vector groups = viewport.alignment.getGroups();\r
1054       for (int i = 0; i < groups.size(); i++)\r
1055       {\r
1056         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1057         if (!sg.adjustForRemoveLeft(min))\r
1058         {\r
1059           viewport.alignment.deleteGroup(sg);\r
1060         }\r
1061       }\r
1062       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1063     }\r
1064   }\r
1065 \r
1066   public void remove2RightMenuItem_actionPerformed()\r
1067   {\r
1068     ColumnSelection colSel = viewport.getColumnSelection();\r
1069     if (colSel.size() > 0)\r
1070     {\r
1071       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
1072                                      HistoryItem.HIDE));\r
1073       int max = colSel.getMax();\r
1074       viewport.getAlignment().trimRight(max);\r
1075       if (viewport.getSelectionGroup() != null)\r
1076       {\r
1077         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
1078       }\r
1079 \r
1080       Vector groups = viewport.alignment.getGroups();\r
1081       for (int i = 0; i < groups.size(); i++)\r
1082       {\r
1083         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1084         if (!sg.adjustForRemoveRight(max))\r
1085         {\r
1086           viewport.alignment.deleteGroup(sg);\r
1087         }\r
1088       }\r
1089       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1090     }\r
1091 \r
1092   }\r
1093 \r
1094   public void removeGappedColumnMenuItem_actionPerformed()\r
1095   {\r
1096     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
1097                                    viewport.alignment,\r
1098                                    HistoryItem.HIDE));\r
1099 \r
1100     //This is to maintain viewport position on first residue\r
1101     //of first sequence\r
1102     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
1103     int startRes = seq.findPosition(viewport.startRes);\r
1104 \r
1105     viewport.getAlignment().removeGaps();\r
1106 \r
1107     viewport.setStartRes(seq.findIndex(startRes)-1);\r
1108 \r
1109     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1110   }\r
1111 \r
1112   public void removeAllGapsMenuItem_actionPerformed()\r
1113   {\r
1114     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
1115                                    HistoryItem.HIDE));\r
1116 \r
1117     //This is to maintain viewport position on first residue\r
1118     //of first sequence\r
1119     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
1120     int startRes = seq.findPosition(viewport.startRes);\r
1121 \r
1122     SequenceI current;\r
1123     int jSize;\r
1124 \r
1125     Vector seqs=null;\r
1126 \r
1127     int start=0, end = viewport.alignment.getWidth();\r
1128 \r
1129     if (viewport.getSelectionGroup() != null\r
1130         && viewport.getSelectionGroup().getSequences(false) != null\r
1131         && viewport.getSelectionGroup().getSize(false)>0)\r
1132     {\r
1133       seqs = viewport.getSelectionGroup().getSequences(true);\r
1134       start = viewport.getSelectionGroup().getStartRes();\r
1135       end = viewport.getSelectionGroup().getEndRes()+1;\r
1136     }\r
1137     else\r
1138       seqs = viewport.alignment.getSequences();\r
1139 \r
1140     for (int i = 0; i < seqs.size(); i++)\r
1141     {\r
1142       current = (SequenceI) seqs.elementAt(i);\r
1143       jSize = current.getLength();\r
1144 \r
1145       // Removing a range is much quicker than removing gaps\r
1146       // one by one for long sequences\r
1147       int j = start;\r
1148       int rangeStart=-1, rangeEnd=-1;\r
1149 \r
1150       do\r
1151       {\r
1152         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
1153         {\r
1154           if(rangeStart==-1)\r
1155            {\r
1156              rangeStart = j;\r
1157              rangeEnd = j+1;\r
1158            }\r
1159            else\r
1160            {\r
1161              rangeEnd++;\r
1162            }\r
1163            j++;\r
1164         }\r
1165         else\r
1166         {\r
1167           if(rangeStart>-1)\r
1168           {\r
1169             current.deleteChars(rangeStart, rangeEnd);\r
1170             j-=rangeEnd-rangeStart;\r
1171             jSize-=rangeEnd-rangeStart;\r
1172             rangeStart = -1;\r
1173             rangeEnd = -1;\r
1174           }\r
1175           else\r
1176             j++;\r
1177         }\r
1178       }\r
1179       while (j < end && j < jSize);\r
1180       if(rangeStart>-1)\r
1181       {\r
1182        current.deleteChars(rangeStart, rangeEnd);\r
1183       }\r
1184     }\r
1185     viewport.setStartRes(seq.findIndex(startRes)-1);\r
1186     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1187   }\r
1188 \r
1189   public void alignmentChanged()\r
1190   {\r
1191     viewport.alignment.padGaps();\r
1192     if(viewport.autocalculateConsensus)\r
1193     {\r
1194       viewport.updateConsensus();\r
1195       viewport.updateConservation();\r
1196     }\r
1197 \r
1198     resetAllColourSchemes();\r
1199     if(alignPanel.overviewPanel!=null)\r
1200       alignPanel.overviewPanel.updateOverviewImage();\r
1201 \r
1202     viewport.alignment.adjustSequenceAnnotations();\r
1203     alignPanel.repaint();\r
1204   }\r
1205 \r
1206   void resetAllColourSchemes()\r
1207   {\r
1208     ColourSchemeI cs = viewport.globalColourScheme;\r
1209     if(cs!=null)\r
1210     {\r
1211       if (cs instanceof ClustalxColourScheme)\r
1212       {\r
1213         ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
1214             resetClustalX(viewport.alignment.getSequences(),\r
1215                           viewport.alignment.getWidth());\r
1216       }\r
1217 \r
1218       cs.setConsensus(viewport.vconsensus);\r
1219       if (cs.conservationApplied())\r
1220       {\r
1221         Alignment al = (Alignment) viewport.alignment;\r
1222         Conservation c = new Conservation("All",\r
1223                                           ResidueProperties.propHash, 3,\r
1224                                           al.getSequences(), 0,\r
1225                                           al.getWidth() - 1);\r
1226         c.calculate();\r
1227         c.verdict(false, viewport.ConsPercGaps);\r
1228 \r
1229         cs.setConservation(c);\r
1230       }\r
1231     }\r
1232 \r
1233     int s, sSize = viewport.alignment.getGroups().size();\r
1234     for(s=0; s<sSize; s++)\r
1235     {\r
1236       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
1237       if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
1238       {\r
1239         ((ClustalxColourScheme)sg.cs).resetClustalX(\r
1240             sg.getSequences(true), sg.getWidth());\r
1241       }\r
1242       sg.recalcConservation();\r
1243     }\r
1244   }\r
1245 \r
1246 \r
1247 \r
1248   public void findMenuItem_actionPerformed()\r
1249   {\r
1250     new Finder(alignPanel);\r
1251   }\r
1252 \r
1253   public void font_actionPerformed()\r
1254   {\r
1255     new FontChooser(alignPanel);\r
1256   }\r
1257 \r
1258 \r
1259   public void seqLimits_itemStateChanged()\r
1260   {\r
1261     viewport.setShowJVSuffix(seqLimits.getState());\r
1262     alignPanel.fontChanged();\r
1263     alignPanel.repaint();\r
1264   }\r
1265 \r
1266 \r
1267   protected void colourTextMenuItem_actionPerformed()\r
1268   {\r
1269     viewport.setColourText(colourTextMenuItem.getState());\r
1270     alignPanel.repaint();\r
1271   }\r
1272 \r
1273   protected void wrapMenuItem_actionPerformed()\r
1274   {\r
1275     viewport.setWrapAlignment(wrapMenuItem.getState());\r
1276     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
1277     scaleAbove.setEnabled(wrapMenuItem.getState());\r
1278     scaleLeft.setEnabled(wrapMenuItem.getState());\r
1279     scaleRight.setEnabled(wrapMenuItem.getState());\r
1280     alignPanel.repaint();\r
1281   }\r
1282 \r
1283 \r
1284   protected void scaleAbove_actionPerformed()\r
1285   {\r
1286     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
1287     alignPanel.repaint();\r
1288   }\r
1289 \r
1290   protected void scaleLeft_actionPerformed()\r
1291   {\r
1292     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
1293     alignPanel.repaint();\r
1294   }\r
1295 \r
1296   protected void scaleRight_actionPerformed()\r
1297   {\r
1298     viewport.setScaleRightWrapped(scaleRight.getState());\r
1299     alignPanel.repaint();\r
1300   }\r
1301 \r
1302   public void viewBoxesMenuItem_actionPerformed()\r
1303   {\r
1304     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
1305     alignPanel.repaint();\r
1306   }\r
1307 \r
1308   public void viewTextMenuItem_actionPerformed()\r
1309   {\r
1310     viewport.setShowText(viewTextMenuItem.getState());\r
1311     alignPanel.repaint();\r
1312   }\r
1313 \r
1314   protected void renderGapsMenuItem_actionPerformed()\r
1315   {\r
1316     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
1317     alignPanel.repaint();\r
1318   }\r
1319 \r
1320   public void annotationPanelMenuItem_actionPerformed()\r
1321   {\r
1322     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
1323     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
1324   }\r
1325 \r
1326   public void featureSettings_actionPerformed()\r
1327   {\r
1328     new FeatureSettings(viewport, alignPanel);\r
1329   }\r
1330 \r
1331   public void overviewMenuItem_actionPerformed()\r
1332   {\r
1333     if (alignPanel.overviewPanel != null)\r
1334     {\r
1335       return;\r
1336     }\r
1337 \r
1338     Frame frame = new Frame();\r
1339     OverviewPanel overview = new OverviewPanel(alignPanel);\r
1340     frame.add(overview);\r
1341     // +50 must allow for applet frame window\r
1342     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
1343                                      overview.preferredSize().width,\r
1344                                      overview.preferredSize().height + 50);\r
1345 \r
1346     frame.pack();\r
1347     frame.addWindowListener(new WindowAdapter()\r
1348     {\r
1349       public void windowClosing(WindowEvent e)\r
1350       {\r
1351         alignPanel.setOverviewPanel(null);\r
1352       };\r
1353     });\r
1354 \r
1355     alignPanel.setOverviewPanel(overview);\r
1356 \r
1357   }\r
1358 \r
1359   protected void noColourmenuItem_actionPerformed()\r
1360   {\r
1361     changeColour(null);\r
1362   }\r
1363 \r
1364   public void clustalColour_actionPerformed()\r
1365   {\r
1366     abovePIDThreshold.setState(false);\r
1367     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
1368                                           viewport.alignment.getWidth()));\r
1369   }\r
1370 \r
1371   public void zappoColour_actionPerformed()\r
1372   {\r
1373     changeColour(new ZappoColourScheme());\r
1374   }\r
1375 \r
1376   public void taylorColour_actionPerformed()\r
1377   {\r
1378     changeColour(new TaylorColourScheme());\r
1379   }\r
1380 \r
1381   public void hydrophobicityColour_actionPerformed()\r
1382   {\r
1383     changeColour(new HydrophobicColourScheme());\r
1384   }\r
1385 \r
1386   public void helixColour_actionPerformed()\r
1387   {\r
1388     changeColour(new HelixColourScheme());\r
1389   }\r
1390 \r
1391   public void strandColour_actionPerformed()\r
1392   {\r
1393     changeColour(new StrandColourScheme());\r
1394   }\r
1395 \r
1396   public void turnColour_actionPerformed()\r
1397   {\r
1398     changeColour(new TurnColourScheme());\r
1399   }\r
1400 \r
1401   public void buriedColour_actionPerformed()\r
1402   {\r
1403     changeColour(new BuriedColourScheme());\r
1404   }\r
1405 \r
1406   public void nucleotideColour_actionPerformed()\r
1407   {\r
1408     changeColour(new NucleotideColourScheme());\r
1409   }\r
1410 \r
1411   protected void applyToAllGroups_actionPerformed()\r
1412   {\r
1413     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
1414   }\r
1415 \r
1416   void changeColour(ColourSchemeI cs)\r
1417   {\r
1418     int threshold = 0;\r
1419 \r
1420     if(cs!=null)\r
1421     {\r
1422       if (viewport.getAbovePIDThreshold())\r
1423       {\r
1424         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
1425 \r
1426         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1427 \r
1428         viewport.setGlobalColourScheme(cs);\r
1429       }\r
1430       else\r
1431       {\r
1432         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1433       }\r
1434 \r
1435       if (viewport.getConservationSelected())\r
1436       {\r
1437 \r
1438         Alignment al = (Alignment) viewport.alignment;\r
1439         Conservation c = new Conservation("All",\r
1440                                           ResidueProperties.propHash, 3,\r
1441                                           al.getSequences(), 0,\r
1442                                           al.getWidth() - 1);\r
1443 \r
1444         c.calculate();\r
1445         c.verdict(false, viewport.ConsPercGaps);\r
1446 \r
1447         cs.setConservation(c);\r
1448 \r
1449         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
1450             "Background"));\r
1451 \r
1452       }\r
1453       else\r
1454       {\r
1455         cs.setConservation(null);\r
1456       }\r
1457 \r
1458       cs.setConsensus(viewport.vconsensus);\r
1459 \r
1460     }\r
1461     viewport.setGlobalColourScheme(cs);\r
1462 \r
1463     if (viewport.getColourAppliesToAllGroups())\r
1464     {\r
1465       Vector groups = viewport.alignment.getGroups();\r
1466       for (int i = 0; i < groups.size(); i++)\r
1467       {\r
1468         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1469 \r
1470         if(cs==null)\r
1471         {\r
1472           sg.cs = null;\r
1473           continue;\r
1474         }\r
1475         if (cs instanceof ClustalxColourScheme)\r
1476         {\r
1477           sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());\r
1478         }\r
1479         else\r
1480         {\r
1481           try\r
1482           {\r
1483             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
1484           }\r
1485           catch (Exception ex)\r
1486           {\r
1487             ex.printStackTrace();\r
1488             sg.cs = cs;\r
1489           }\r
1490         }\r
1491 \r
1492         if (viewport.getAbovePIDThreshold()\r
1493             || cs instanceof PIDColourScheme\r
1494             || cs instanceof Blosum62ColourScheme)\r
1495         {\r
1496           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1497           sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));\r
1498         }\r
1499         else\r
1500           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1501 \r
1502         if (viewport.getConservationSelected())\r
1503         {\r
1504           Conservation c = new Conservation("Group",\r
1505                                             ResidueProperties.propHash, 3,\r
1506                                             sg.getSequences(true), 0,\r
1507                                             viewport.alignment.getWidth() - 1);\r
1508           c.calculate();\r
1509           c.verdict(false, viewport.ConsPercGaps);\r
1510           sg.cs.setConservation(c);\r
1511         }\r
1512         else\r
1513         {\r
1514           sg.cs.setConservation(null);\r
1515           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1516         }\r
1517 \r
1518       }\r
1519     }\r
1520 \r
1521 \r
1522     if (alignPanel.getOverviewPanel() != null)\r
1523     {\r
1524       alignPanel.getOverviewPanel().updateOverviewImage();\r
1525     }\r
1526 \r
1527     alignPanel.repaint();\r
1528   }\r
1529 \r
1530 \r
1531 \r
1532   protected void modifyPID_actionPerformed()\r
1533   {\r
1534     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
1535     {\r
1536       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
1537                                      "Background");\r
1538       SliderPanel.showPIDSlider();\r
1539     }\r
1540   }\r
1541 \r
1542   protected void modifyConservation_actionPerformed()\r
1543   {\r
1544     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
1545     {\r
1546       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
1547                                         "Background");\r
1548       SliderPanel.showConservationSlider();\r
1549     }\r
1550   }\r
1551 \r
1552   protected void conservationMenuItem_actionPerformed()\r
1553   {\r
1554     viewport.setConservationSelected(conservationMenuItem.getState());\r
1555 \r
1556     viewport.setAbovePIDThreshold(false);\r
1557     abovePIDThreshold.setState(false);\r
1558 \r
1559     changeColour(viewport.getGlobalColourScheme());\r
1560 \r
1561     modifyConservation_actionPerformed();\r
1562   }\r
1563 \r
1564   public void abovePIDThreshold_actionPerformed()\r
1565   {\r
1566     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
1567 \r
1568     conservationMenuItem.setState(false);\r
1569     viewport.setConservationSelected(false);\r
1570 \r
1571     changeColour(viewport.getGlobalColourScheme());\r
1572 \r
1573     modifyPID_actionPerformed();\r
1574   }\r
1575 \r
1576   public void userDefinedColour_actionPerformed()\r
1577   {\r
1578     new UserDefinedColours(alignPanel, null);\r
1579   }\r
1580 \r
1581   public void PIDColour_actionPerformed()\r
1582   {\r
1583     changeColour(new PIDColourScheme());\r
1584   }\r
1585 \r
1586   public void BLOSUM62Colour_actionPerformed()\r
1587   {\r
1588     changeColour(new Blosum62ColourScheme());\r
1589   }\r
1590 \r
1591   public void sortPairwiseMenuItem_actionPerformed()\r
1592   {\r
1593     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1594                                    HistoryItem.SORT));\r
1595     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1596                               viewport.getAlignment().getSequenceAt(0));\r
1597     alignPanel.repaint();\r
1598   }\r
1599 \r
1600   public void sortIDMenuItem_actionPerformed()\r
1601   {\r
1602     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1603                                    HistoryItem.SORT));\r
1604     AlignmentSorter.sortByID(viewport.getAlignment());\r
1605     alignPanel.repaint();\r
1606   }\r
1607 \r
1608   public void sortGroupMenuItem_actionPerformed()\r
1609   {\r
1610     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1611                                    HistoryItem.SORT));\r
1612     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1613     alignPanel.repaint();\r
1614 \r
1615   }\r
1616 \r
1617   public void removeRedundancyMenuItem_actionPerformed()\r
1618   {\r
1619      new RedundancyPanel(alignPanel);\r
1620   }\r
1621 \r
1622   public void pairwiseAlignmentMenuItem_actionPerformed()\r
1623   {\r
1624     if (viewport.getSelectionGroup()!=null\r
1625         && viewport.getSelectionGroup().getSize(false) > 1)\r
1626     {\r
1627       Frame frame = new Frame();\r
1628       frame.add(new PairwiseAlignPanel(alignPanel));\r
1629       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1630     }\r
1631   }\r
1632 \r
1633   public void PCAMenuItem_actionPerformed()\r
1634   {\r
1635     //are the sequences aligned?\r
1636     if (!viewport.alignment.isAligned())\r
1637     {\r
1638       SequenceI current;\r
1639       int Width = viewport.getAlignment().getWidth();\r
1640 \r
1641       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1642            i++)\r
1643       {\r
1644         current = viewport.getAlignment().getSequenceAt(i);\r
1645 \r
1646         if (current.getLength() < Width)\r
1647         {\r
1648           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1649         }\r
1650       }\r
1651       alignPanel.repaint();\r
1652     }\r
1653 \r
1654     if ( (viewport.getSelectionGroup() != null &&\r
1655           viewport.getSelectionGroup().getSize(false) < 4 &&\r
1656           viewport.getSelectionGroup().getSize(false) > 0)\r
1657         || viewport.getAlignment().getHeight() < 4)\r
1658     {\r
1659       return;\r
1660     }\r
1661 \r
1662     try\r
1663     {\r
1664       new PCAPanel(viewport);\r
1665     }\r
1666     catch (java.lang.OutOfMemoryError ex)\r
1667     {\r
1668     }\r
1669 \r
1670   }\r
1671 \r
1672   public void averageDistanceTreeMenuItem_actionPerformed()\r
1673   {\r
1674     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1675   }\r
1676 \r
1677   public void neighbourTreeMenuItem_actionPerformed()\r
1678   {\r
1679     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1680   }\r
1681 \r
1682   protected void njTreeBlosumMenuItem_actionPerformed()\r
1683   {\r
1684     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1685   }\r
1686 \r
1687   protected void avTreeBlosumMenuItem_actionPerformed()\r
1688   {\r
1689     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1690   }\r
1691 \r
1692   void NewTreePanel(String type, String pwType, String title)\r
1693   {\r
1694     //are the sequences aligned?\r
1695     if (!viewport.alignment.isAligned())\r
1696     {\r
1697       SequenceI current;\r
1698       int Width = viewport.getAlignment().getWidth();\r
1699 \r
1700       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1701            i++)\r
1702       {\r
1703         current = viewport.getAlignment().getSequenceAt(i);\r
1704 \r
1705         if (current.getLength() < Width)\r
1706         {\r
1707           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1708         }\r
1709       }\r
1710       alignPanel.repaint();\r
1711 \r
1712     }\r
1713 \r
1714     if ( (viewport.getSelectionGroup() != null &&\r
1715           viewport.getSelectionGroup().getSize(false) > 1)\r
1716       || (viewport.getSelectionGroup() == null\r
1717           && viewport.alignment.getHeight() > 1))\r
1718     {\r
1719       final TreePanel tp = new TreePanel(viewport,\r
1720                                          type,\r
1721                                          pwType);\r
1722 \r
1723       addTreeMenuItem(tp, title);\r
1724 \r
1725       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1726     }\r
1727   }\r
1728 \r
1729   void loadTree_actionPerformed()\r
1730   {\r
1731       CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
1732       cap.setText("Paste your Newick tree file here.");\r
1733       cap.treeImport = true;\r
1734       Frame frame = new Frame();\r
1735       frame.add(cap);\r
1736       jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);\r
1737   }\r
1738 \r
1739   public void loadTree(jalview.io.NewickFile tree, String treeFile)\r
1740   {\r
1741     TreePanel tp = new TreePanel(viewport,\r
1742                                  treeFile,\r
1743                                  "From File - ",\r
1744                                  tree);\r
1745     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
1746     addTreeMenuItem(tp, treeFile);\r
1747   }\r
1748 \r
1749   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1750   {\r
1751     final MenuItem item = new MenuItem(title);\r
1752     sortByTreeMenu.add(item);\r
1753     item.addActionListener(new java.awt.event.ActionListener()\r
1754     {\r
1755       public void actionPerformed(ActionEvent evt)\r
1756       {\r
1757         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1758                                        HistoryItem.SORT));\r
1759         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1760         alignPanel.repaint();\r
1761       }\r
1762     });\r
1763 \r
1764     treePanel.addWindowListener(new WindowAdapter()\r
1765     {\r
1766       public void windowClosing(WindowEvent e)\r
1767       {\r
1768         sortByTreeMenu.remove(item);\r
1769       };\r
1770     });\r
1771   }\r
1772 \r
1773   protected void documentation_actionPerformed()\r
1774   {\r
1775     showURL("http://www.jalview.org/help.html", "HELP");\r
1776   }\r
1777 \r
1778   protected void about_actionPerformed()\r
1779   {\r
1780 \r
1781     class AboutPanel extends Canvas\r
1782     {\r
1783       String version;\r
1784       public AboutPanel(String version)\r
1785       { this.version = version; }\r
1786 \r
1787       public void paint(Graphics g)\r
1788       {\r
1789         g.setColor(Color.white);\r
1790         g.fillRect(0, 0, getSize().width, getSize().height);\r
1791         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1792         FontMetrics fm = g.getFontMetrics();\r
1793         int fh = fm.getHeight();\r
1794         int y = 5, x = 7;\r
1795         g.setColor(Color.black);\r
1796         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1797         g.drawString("Jalview - Release "+version, 200, y += fh);\r
1798         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1799         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1800                      x, y += fh * 2);\r
1801         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1802                      x, y += fh);\r
1803         g.drawString(\r
1804             "For any issues relating to Jalview, email help@jalview.org", x,\r
1805             y += fh);\r
1806         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1807         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1808                      x, y += fh);\r
1809         g.drawString("Bioinformatics,  2004 20;426-7.", x, y += fh);\r
1810       }\r
1811     }\r
1812 \r
1813     String version = "test";\r
1814     java.net.URL url = getClass().getResource("/.build_properties");\r
1815     if (url != null)\r
1816     {\r
1817       try\r
1818       {\r
1819         BufferedReader reader = new BufferedReader(new InputStreamReader(\r
1820             url.openStream()));\r
1821         String line;\r
1822         while ( (line = reader.readLine()) != null)\r
1823         {\r
1824           if (line.indexOf("VERSION") > -1)\r
1825           {\r
1826             version = line.substring(line.indexOf("=") + 1);\r
1827           }\r
1828         }\r
1829       }\r
1830       catch (Exception ex)\r
1831       {\r
1832         ex.printStackTrace();\r
1833       }\r
1834     }\r
1835 \r
1836 \r
1837     Frame frame = new Frame();\r
1838     frame.add(new AboutPanel(version));\r
1839     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1840 \r
1841   }\r
1842 \r
1843   public void showURL(String url, String target)\r
1844   {\r
1845     if (viewport.applet == null)\r
1846     {\r
1847       System.out.println("Not running as applet - no browser available.");\r
1848     }\r
1849     else\r
1850     {\r
1851       try\r
1852       {\r
1853         System.out.println("Show url: "+url);\r
1854         viewport.applet.getAppletContext().showDocument(new java.net.URL(url),\r
1855                                                target);\r
1856       }\r
1857       catch (Exception ex)\r
1858       {\r
1859         ex.printStackTrace();\r
1860       }\r
1861     }\r
1862   }\r
1863 \r
1864 \r
1865   //////////////////////////////////////////////////////////////////////////////////\r
1866   //JBuilder Graphics here\r
1867 \r
1868     protected MenuBar alignFrameMenuBar = new MenuBar();\r
1869     protected Menu fileMenu = new Menu("File");\r
1870     protected MenuItem loadApplication = new MenuItem("View in Full Application");\r
1871     protected MenuItem loadTree = new MenuItem("Load Associated Tree");\r
1872     protected MenuItem closeMenuItem = new MenuItem("Close");\r
1873     protected Menu editMenu = new Menu("Edit");\r
1874     protected Menu viewMenu = new Menu("View");\r
1875     protected Menu colourMenu = new Menu("Colour");\r
1876     protected Menu calculateMenu = new Menu("Calculate");\r
1877     protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
1878     protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
1879     protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
1880     protected MenuItem remove2LeftMenuItem = new MenuItem();\r
1881     protected MenuItem remove2RightMenuItem = new MenuItem();\r
1882     protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
1883     protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
1884     protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
1885     protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
1886     protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
1887     protected MenuItem sortIDMenuItem = new MenuItem();\r
1888     protected MenuItem sortGroupMenuItem = new MenuItem();\r
1889     protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
1890     protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
1891     protected MenuItem PCAMenuItem = new MenuItem();\r
1892     protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
1893     protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
1894     BorderLayout borderLayout1 = new BorderLayout();\r
1895     public Label statusBar = new Label();\r
1896     protected Menu outputTextboxMenu = new Menu();\r
1897     protected MenuItem clustalColour = new MenuItem();\r
1898     protected MenuItem zappoColour = new MenuItem();\r
1899     protected MenuItem taylorColour = new MenuItem();\r
1900     protected MenuItem hydrophobicityColour = new MenuItem();\r
1901     protected MenuItem helixColour = new MenuItem();\r
1902     protected MenuItem strandColour = new MenuItem();\r
1903     protected MenuItem turnColour = new MenuItem();\r
1904     protected MenuItem buriedColour = new MenuItem();\r
1905     protected MenuItem userDefinedColour = new MenuItem();\r
1906     protected MenuItem PIDColour = new MenuItem();\r
1907     protected MenuItem BLOSUM62Colour = new MenuItem();\r
1908     MenuItem njTreeBlosumMenuItem = new MenuItem();\r
1909     MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
1910     protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
1911     protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
1912     MenuItem overviewMenuItem = new MenuItem();\r
1913     protected MenuItem undoMenuItem = new MenuItem();\r
1914     protected MenuItem redoMenuItem = new MenuItem();\r
1915     protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
1916     MenuItem noColourmenuItem = new MenuItem();\r
1917     protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
1918     protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
1919     MenuItem findMenuItem = new MenuItem();\r
1920     Menu searchMenu = new Menu();\r
1921     protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
1922     protected MenuItem nucleotideColour = new MenuItem();\r
1923     MenuItem deleteGroups = new MenuItem();\r
1924     MenuItem delete = new MenuItem();\r
1925     MenuItem copy = new MenuItem();\r
1926     MenuItem cut = new MenuItem();\r
1927     Menu pasteMenu = new Menu();\r
1928     MenuItem pasteNew = new MenuItem();\r
1929     MenuItem pasteThis = new MenuItem();\r
1930     protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
1931     protected MenuItem font = new MenuItem();\r
1932     protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
1933     protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
1934     protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
1935     MenuItem modifyPID = new MenuItem();\r
1936     MenuItem modifyConservation = new MenuItem();\r
1937     protected CheckboxMenuItem autoCalculate\r
1938         = new CheckboxMenuItem("Autocalculate Consensus", true);\r
1939     protected Menu sortByTreeMenu = new Menu();\r
1940     Menu sort = new Menu();\r
1941     Menu calculate = new Menu();\r
1942     MenuItem inputText = new MenuItem();\r
1943     Menu helpMenu = new Menu();\r
1944     MenuItem documentation = new MenuItem();\r
1945     MenuItem about = new MenuItem();\r
1946     protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
1947   Panel embeddedMenu;\r
1948   Label embeddedEdit;\r
1949   Label embeddedSearch;\r
1950   Label embeddedView;\r
1951   Label embeddedColour;\r
1952   Label embeddedFile;\r
1953   Label embeddedHelp;\r
1954   Label embeddedCalculate;\r
1955   FlowLayout flowLayout1;\r
1956 \r
1957   private void jbInit() throws Exception {\r
1958 \r
1959       setMenuBar(alignFrameMenuBar);\r
1960 \r
1961       MenuItem item;\r
1962 \r
1963       // dynamically fill save as menu with available formats\r
1964       for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
1965       {\r
1966 \r
1967         item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);\r
1968 \r
1969         item.addActionListener(new java.awt.event.ActionListener()\r
1970         {\r
1971           public void actionPerformed(ActionEvent e)\r
1972           {\r
1973             outputText_actionPerformed(e);\r
1974           }\r
1975         });\r
1976 \r
1977         outputTextboxMenu.add(item);\r
1978       }\r
1979         closeMenuItem.addActionListener(this);\r
1980         loadApplication.addActionListener(this);\r
1981 \r
1982         loadTree.addActionListener(this);\r
1983         selectAllSequenceMenuItem.addActionListener(this);\r
1984         deselectAllSequenceMenuItem.addActionListener(this);\r
1985         invertSequenceMenuItem.addActionListener(this);\r
1986         remove2LeftMenuItem.setLabel("Remove Left");\r
1987         remove2LeftMenuItem.addActionListener(this);\r
1988         remove2RightMenuItem.setLabel("Remove Right");\r
1989         remove2RightMenuItem.addActionListener(this);\r
1990         removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
1991         removeGappedColumnMenuItem.addActionListener(this);\r
1992         removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
1993         removeAllGapsMenuItem.addActionListener(this);\r
1994         viewBoxesMenuItem.setLabel("Boxes");\r
1995         viewBoxesMenuItem.setState(true);\r
1996         viewBoxesMenuItem.addItemListener(this);\r
1997         viewTextMenuItem.setLabel("Text");\r
1998         viewTextMenuItem.setState(true);\r
1999         viewTextMenuItem.addItemListener(this);\r
2000         sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
2001         sortPairwiseMenuItem.addActionListener(this);\r
2002         sortIDMenuItem.setLabel("by ID");\r
2003         sortIDMenuItem.addActionListener(this);\r
2004         sortGroupMenuItem.setLabel("by Group");\r
2005         sortGroupMenuItem.addActionListener(this);\r
2006         removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
2007         removeRedundancyMenuItem.addActionListener(this);\r
2008         pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
2009         pairwiseAlignmentMenuItem.addActionListener(this);\r
2010         PCAMenuItem.setLabel("Principal Component Analysis");\r
2011         PCAMenuItem.addActionListener(this);\r
2012         averageDistanceTreeMenuItem.setLabel(\r
2013             "Average Distance Using % Identity");\r
2014         averageDistanceTreeMenuItem.addActionListener(this);\r
2015         neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
2016         neighbourTreeMenuItem.addActionListener(this);\r
2017         alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
2018         statusBar.setBackground(Color.white);\r
2019         statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
2020         statusBar.setText("Status bar");\r
2021         outputTextboxMenu.setLabel("Output to Textbox");\r
2022         clustalColour.setLabel("Clustalx");\r
2023 \r
2024         clustalColour.addActionListener(this);\r
2025         zappoColour.setLabel("Zappo");\r
2026         zappoColour.addActionListener(this);\r
2027         taylorColour.setLabel("Taylor");\r
2028         taylorColour.addActionListener(this);\r
2029         hydrophobicityColour.setLabel("Hydrophobicity");\r
2030         hydrophobicityColour.addActionListener(this);\r
2031         helixColour.setLabel("Helix Propensity");\r
2032         helixColour.addActionListener(this);\r
2033         strandColour.setLabel("Strand Propensity");\r
2034         strandColour.addActionListener(this);\r
2035         turnColour.setLabel("Turn Propensity");\r
2036         turnColour.addActionListener(this);\r
2037         buriedColour.setLabel("Buried Index");\r
2038         buriedColour.addActionListener(this);\r
2039         userDefinedColour.setLabel("User Defined...");\r
2040         userDefinedColour.addActionListener(this);\r
2041         PIDColour.setLabel("Percentage Identity");\r
2042         PIDColour.addActionListener(this);\r
2043         BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
2044         BLOSUM62Colour.addActionListener(this);\r
2045         avDistanceTreeBlosumMenuItem.setLabel(\r
2046             "Average Distance Using BLOSUM62");\r
2047         avDistanceTreeBlosumMenuItem.addActionListener(this);\r
2048         njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
2049         njTreeBlosumMenuItem.addActionListener(this);\r
2050         annotationPanelMenuItem.setLabel("Show Annotations");\r
2051         annotationPanelMenuItem.addItemListener(this);\r
2052         colourTextMenuItem.setLabel("Colour Text");\r
2053         colourTextMenuItem.addItemListener(this);\r
2054         overviewMenuItem.setLabel("Overview Window");\r
2055         overviewMenuItem.addActionListener(this);\r
2056         undoMenuItem.setEnabled(false);\r
2057         undoMenuItem.setLabel("Undo");\r
2058         undoMenuItem.addActionListener(this);\r
2059         redoMenuItem.setEnabled(false);\r
2060         redoMenuItem.setLabel("Redo");\r
2061         redoMenuItem.addActionListener(this);\r
2062         conservationMenuItem.setLabel("by Conservation");\r
2063         conservationMenuItem.addItemListener(this);\r
2064         noColourmenuItem.setLabel("None");\r
2065         noColourmenuItem.addActionListener(this);\r
2066         wrapMenuItem.setLabel("Wrap");\r
2067         wrapMenuItem.addItemListener(this);\r
2068         renderGapsMenuItem.setLabel("Show Gaps");\r
2069         renderGapsMenuItem.setState(true);\r
2070         renderGapsMenuItem.addItemListener(this);\r
2071         findMenuItem.setLabel("Find...");\r
2072         findMenuItem.addActionListener(this);\r
2073         searchMenu.setLabel("Search");\r
2074 \r
2075         abovePIDThreshold.setLabel("Above Identity Threshold");\r
2076         abovePIDThreshold.addItemListener(this);\r
2077         nucleotideColour.setLabel("Nucleotide");\r
2078         nucleotideColour.addActionListener(this);\r
2079         deleteGroups.setLabel("Undefine Groups");\r
2080         deleteGroups.addActionListener(this);\r
2081         copy.setLabel("Copy");\r
2082         copy.addActionListener(this);\r
2083         cut.setLabel("Cut");\r
2084         cut.addActionListener(this);\r
2085         delete.setLabel("Delete");\r
2086         delete.addActionListener(this);\r
2087         pasteMenu.setLabel("Paste");\r
2088         pasteNew.setLabel("To New Alignment");\r
2089         pasteNew.addActionListener(this);\r
2090         pasteThis.setLabel("Add To This Alignment");\r
2091         pasteThis.addActionListener(this);\r
2092         applyToAllGroups.setLabel("Apply Colour To All Groups");\r
2093         applyToAllGroups.setState(true);\r
2094         applyToAllGroups.addItemListener(this);\r
2095         font.setLabel("Font...");\r
2096         font.addActionListener(this);\r
2097         scaleAbove.setLabel("Scale Above");\r
2098         scaleAbove.setState(true);\r
2099         scaleAbove.setEnabled(false);\r
2100         scaleAbove.addItemListener(this);\r
2101         scaleLeft.setEnabled(false);\r
2102         scaleLeft.setState(true);\r
2103         scaleLeft.setLabel("Scale Left");\r
2104         scaleLeft.addItemListener(this);\r
2105         scaleRight.setEnabled(false);\r
2106         scaleRight.setState(true);\r
2107         scaleRight.setLabel("Scale Right");\r
2108         scaleRight.addItemListener(this);\r
2109         modifyPID.setLabel("Modify Identity Threshold...");\r
2110         modifyPID.addActionListener(this);\r
2111         modifyConservation.setLabel("Modify Conservation Threshold...");\r
2112         modifyConservation.addActionListener(this);\r
2113         sortByTreeMenu.setLabel("By Tree Order");\r
2114         sort.setLabel("Sort");\r
2115         calculate.setLabel("Calculate Tree");\r
2116         autoCalculate.addItemListener(this);\r
2117         inputText.setLabel("Input from textbox");\r
2118         inputText.addActionListener(this);\r
2119 \r
2120         helpMenu.setLabel("Help");\r
2121         documentation.setLabel("Documentation");\r
2122         documentation.addActionListener(this);\r
2123 \r
2124         about.setLabel("About...");\r
2125         about.addActionListener(this);\r
2126           seqLimits.setState(true);\r
2127     seqLimits.setLabel("Show Sequence Limits");\r
2128     seqLimits.addItemListener(this);\r
2129     featureSettings.setLabel("Feature Settings...");\r
2130     featureSettings.addActionListener(this);\r
2131     sequenceFeatures.setLabel("Sequence Features");\r
2132     sequenceFeatures.addItemListener(this);\r
2133     sequenceFeatures.setState(false);\r
2134     annotationColour.setLabel("by Annotation...");\r
2135     annotationColour.addActionListener(this);\r
2136     invertSequenceMenuItem.setLabel("Invert Sequence Selection");\r
2137     invertColSel.setLabel("Invert Column Selection");\r
2138     menu1.setLabel("Show");\r
2139     showColumns.setLabel("All Columns ");\r
2140     showSeqs.setLabel("All Sequences");\r
2141     menu2.setLabel("Hide");\r
2142     hideColumns.setLabel("Selected Columns");\r
2143     hideSequences.setLabel("Selected Sequences");\r
2144     invertColSel.addActionListener(this);\r
2145     showColumns.addActionListener(this);\r
2146     showSeqs.addActionListener(this);\r
2147     hideColumns.addActionListener(this);\r
2148     hideSequences.addActionListener(this);\r
2149 \r
2150 \r
2151     alignFrameMenuBar.add(fileMenu);\r
2152         alignFrameMenuBar.add(editMenu);\r
2153         alignFrameMenuBar.add(searchMenu);\r
2154         alignFrameMenuBar.add(viewMenu);\r
2155         alignFrameMenuBar.add(colourMenu);\r
2156         alignFrameMenuBar.add(calculateMenu);\r
2157         alignFrameMenuBar.add(helpMenu);\r
2158         fileMenu.add(inputText);\r
2159         fileMenu.add(outputTextboxMenu);\r
2160         if(jalviewServletURL!=null)\r
2161           fileMenu.add(loadApplication);\r
2162         fileMenu.addSeparator();\r
2163         fileMenu.add(loadTree);\r
2164         fileMenu.add(closeMenuItem);\r
2165         editMenu.add(undoMenuItem);\r
2166         editMenu.add(redoMenuItem);\r
2167         editMenu.add(cut);\r
2168         editMenu.add(copy);\r
2169         editMenu.add(pasteMenu);\r
2170         editMenu.add(delete);\r
2171         editMenu.addSeparator();\r
2172         editMenu.add(selectAllSequenceMenuItem);\r
2173         editMenu.add(deselectAllSequenceMenuItem);\r
2174         editMenu.add(invertSequenceMenuItem);\r
2175     editMenu.add(invertColSel);\r
2176     editMenu.add(deleteGroups);\r
2177         editMenu.addSeparator();\r
2178         editMenu.add(remove2LeftMenuItem);\r
2179         editMenu.add(remove2RightMenuItem);\r
2180         editMenu.add(removeGappedColumnMenuItem);\r
2181         editMenu.add(removeAllGapsMenuItem);\r
2182         editMenu.add(removeRedundancyMenuItem);\r
2183         searchMenu.add(findMenuItem);\r
2184         viewMenu.add(font);\r
2185         viewMenu.addSeparator();\r
2186     viewMenu.add(menu1);\r
2187     viewMenu.add(menu2);\r
2188     viewMenu.addSeparator();\r
2189     viewMenu.add(wrapMenuItem);\r
2190         viewMenu.add(scaleAbove);\r
2191         viewMenu.add(scaleLeft);\r
2192         viewMenu.add(scaleRight);\r
2193         viewMenu.addSeparator();\r
2194     viewMenu.add(seqLimits);\r
2195     viewMenu.add(viewBoxesMenuItem);\r
2196         viewMenu.add(viewTextMenuItem);\r
2197         viewMenu.add(colourTextMenuItem);\r
2198         viewMenu.add(renderGapsMenuItem);\r
2199         viewMenu.add(annotationPanelMenuItem);\r
2200     viewMenu.addSeparator();\r
2201         viewMenu.add(sequenceFeatures);\r
2202         viewMenu.add(featureSettings);\r
2203     viewMenu.addSeparator();\r
2204         viewMenu.add(overviewMenuItem);\r
2205         colourMenu.add(applyToAllGroups);\r
2206         colourMenu.addSeparator();\r
2207         colourMenu.add(noColourmenuItem);\r
2208         colourMenu.add(clustalColour);\r
2209         colourMenu.add(BLOSUM62Colour);\r
2210         colourMenu.add(PIDColour);\r
2211         colourMenu.add(zappoColour);\r
2212         colourMenu.add(taylorColour);\r
2213         colourMenu.add(hydrophobicityColour);\r
2214         colourMenu.add(helixColour);\r
2215         colourMenu.add(strandColour);\r
2216         colourMenu.add(turnColour);\r
2217         colourMenu.add(buriedColour);\r
2218         colourMenu.add(nucleotideColour);\r
2219         colourMenu.add(userDefinedColour);\r
2220         colourMenu.addSeparator();\r
2221         colourMenu.add(conservationMenuItem);\r
2222         colourMenu.add(modifyConservation);\r
2223         colourMenu.add(abovePIDThreshold);\r
2224         colourMenu.add(modifyPID);\r
2225     colourMenu.add(annotationColour);\r
2226     calculateMenu.add(sort);\r
2227         calculateMenu.add(calculate);\r
2228         calculateMenu.addSeparator();\r
2229         calculateMenu.add(pairwiseAlignmentMenuItem);\r
2230         calculateMenu.add(PCAMenuItem);\r
2231         calculateMenu.add(autoCalculate);\r
2232         this.add(statusBar, BorderLayout.SOUTH);\r
2233         pasteMenu.add(pasteNew);\r
2234         pasteMenu.add(pasteThis);\r
2235         sort.add(sortIDMenuItem);\r
2236         sort.add(sortByTreeMenu);\r
2237         sort.add(sortGroupMenuItem);\r
2238         sort.add(sortPairwiseMenuItem);\r
2239         calculate.add(averageDistanceTreeMenuItem);\r
2240         calculate.add(neighbourTreeMenuItem);\r
2241         calculate.add(avDistanceTreeBlosumMenuItem);\r
2242         calculate.add(njTreeBlosumMenuItem);\r
2243         helpMenu.add(documentation);\r
2244         helpMenu.add(about);\r
2245     menu1.add(showColumns);\r
2246     menu1.add(showSeqs);\r
2247     menu2.add(hideColumns);\r
2248     menu2.add(hideSequences);\r
2249   }\r
2250 \r
2251   public void setEmbedded()\r
2252   {\r
2253 \r
2254     embeddedMenu = new Panel();\r
2255     embeddedEdit = new Label();\r
2256     embeddedSearch = new Label();\r
2257     embeddedView = new Label();\r
2258     embeddedColour = new Label();\r
2259     embeddedFile = new Label();\r
2260     embeddedHelp = new Label();\r
2261     embeddedCalculate = new Label();\r
2262     flowLayout1 = new FlowLayout();\r
2263     embeddedMenu.setBackground(Color.lightGray);\r
2264     embeddedMenu.setLayout(flowLayout1);\r
2265     embeddedEdit.setText("Edit");\r
2266     embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2267     embeddedSearch.setText("Search");\r
2268     embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2269     embeddedView.setText("View");\r
2270     embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2271     embeddedColour.setText("Colour");\r
2272     embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2273     embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2274     embeddedFile.setText("File");\r
2275     embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2276     embeddedHelp.setText("Help");\r
2277     embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2278     embeddedCalculate.setText("Calculate");\r
2279     embeddedMenu.add(embeddedFile);\r
2280     embeddedMenu.add(embeddedEdit);\r
2281     embeddedMenu.add(embeddedSearch);\r
2282     embeddedMenu.add(embeddedView);\r
2283     embeddedMenu.add(embeddedColour);\r
2284     embeddedMenu.add(embeddedCalculate);\r
2285     embeddedMenu.add(embeddedHelp);\r
2286     flowLayout1.setAlignment(FlowLayout.LEFT);\r
2287     flowLayout1.setHgap(2);\r
2288     flowLayout1.setVgap(0);\r
2289     embeddedFile.addMouseListener(this);\r
2290     embeddedEdit.addMouseListener(this);\r
2291     embeddedSearch.addMouseListener(this);\r
2292     embeddedView.addMouseListener(this);\r
2293     embeddedColour.addMouseListener(this);\r
2294     embeddedCalculate.addMouseListener(this);\r
2295     embeddedHelp.addMouseListener(this);\r
2296 \r
2297    // setVisible(false);\r
2298     fileMenu.remove(closeMenuItem);\r
2299     fileMenu.remove(3); // Seperator\r
2300 \r
2301     viewport.applet.setLayout(new BorderLayout());\r
2302     viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
2303     viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
2304    // viewport.applet.validate();\r
2305 \r
2306     alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height\r
2307                        - embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
2308 \r
2309      viewport.applet.add(alignPanel, BorderLayout.CENTER);\r
2310      viewport.applet.validate();\r
2311 \r
2312   }\r
2313 \r
2314 \r
2315 \r
2316   PopupMenu filePopup, editPopup, searchPopup,\r
2317       viewPopup, colourPopup, calculatePopup, helpPopup;\r
2318   MenuItem featureSettings = new MenuItem();\r
2319   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
2320   MenuItem annotationColour = new MenuItem();\r
2321   MenuItem invertColSel = new MenuItem();\r
2322   Menu menu1 = new Menu();\r
2323   MenuItem showColumns = new MenuItem();\r
2324   MenuItem showSeqs = new MenuItem();\r
2325   Menu menu2 = new Menu();\r
2326   MenuItem hideColumns = new MenuItem();\r
2327   MenuItem hideSequences = new MenuItem();\r
2328 \r
2329   public void mousePressed(MouseEvent evt)\r
2330   {\r
2331     PopupMenu popup = null;\r
2332     Label source = (Label)evt.getSource();\r
2333     if(source==embeddedFile)\r
2334     {\r
2335       popup = filePopup = genPopupMenu(filePopup, fileMenu);\r
2336     }\r
2337     else if(source==embeddedEdit)\r
2338     {\r
2339       popup = editPopup = genPopupMenu(editPopup, editMenu);\r
2340     }\r
2341     else if(source==embeddedSearch)\r
2342     {\r
2343       popup = searchPopup = genPopupMenu(searchPopup, searchMenu);\r
2344     }\r
2345     else if(source==embeddedView)\r
2346     {\r
2347       popup = viewPopup = genPopupMenu(viewPopup, viewMenu);\r
2348     }\r
2349     else if(source==embeddedColour)\r
2350     {\r
2351       popup = colourPopup = genPopupMenu(colourPopup, colourMenu);\r
2352     }\r
2353     else if(source==embeddedCalculate)\r
2354     {\r
2355       popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);\r
2356     }\r
2357     else if(source==embeddedHelp)\r
2358     {\r
2359       popup = helpPopup = genPopupMenu(helpPopup, helpMenu);\r
2360     }\r
2361 \r
2362     embeddedMenu.add(popup);\r
2363     popup.show(embeddedMenu,\r
2364                source.getBounds().x,\r
2365                source.getBounds().y + source.getBounds().getSize().height);\r
2366   }\r
2367 \r
2368   PopupMenu genPopupMenu(PopupMenu popup, Menu original)\r
2369   {\r
2370     if(popup!=null)\r
2371     {\r
2372       return popup;\r
2373     }\r
2374     popup = new PopupMenu();\r
2375     int m, mSize = original.getItemCount();\r
2376     for(m=0; m<mSize; m++)\r
2377     {\r
2378       popup.add(original.getItem(m));\r
2379       mSize--;\r
2380       m--;\r
2381     }\r
2382 \r
2383     return popup;\r
2384   }\r
2385   public void mouseClicked(MouseEvent evt)\r
2386   {}\r
2387   public void mouseReleased(MouseEvent evt)\r
2388   {}\r
2389   public void mouseEntered(MouseEvent evt)\r
2390   {}\r
2391   public void mouseExited(MouseEvent evt)\r
2392   {}\r
2393 \r
2394 }\r
2395 \r