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