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