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