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