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