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