src/jalview/appletgui/AlignFrame.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 \r
  20 package jalview.appletgui;\r
  21 \r
  22 import jalview.schemes.*;\r
  23 import jalview.datamodel.*;\r
  24 import jalview.analysis.*;\r
  25 import jalview.io.*;\r
  26 import java.awt.*;\r
  27 import java.awt.event.*;\r
  28 import java.util.*;\r
  29 import java.io.InputStreamReader;\r
  30 import java.io.BufferedReader;\r
  31 import java.net.URL;\r
  32 \r
  33 \r
  34 public class AlignFrame extends Frame implements ActionListener,\r
  35     ItemListener, KeyListener, MouseListener\r
  36 {\r
  37   public AlignmentPanel alignPanel;\r
  38   public AlignViewport viewport;\r
  39   int NEW_WINDOW_WIDTH = 700;\r
  40   int NEW_WINDOW_HEIGHT = 500;\r
  41   jalview.bin.JalviewLite applet;\r
  42 \r
  43 \r
  44    public AlignFrame(AlignmentI al,\r
  45                      jalview.bin.JalviewLite applet,\r
  46                      String title,\r
  47                      boolean embedded)\r
  48   {\r
  49     try{\r
  50       jbInit();\r
  51     }catch(Exception ex)\r
  52     {\r
  53       ex.printStackTrace();\r
  54     }\r
  55 \r
  56     this.applet = applet;\r
  57     viewport = new AlignViewport(al, applet);\r
  58     alignPanel = new AlignmentPanel(this, viewport);\r
  59 \r
  60     annotationPanelMenuItem.setState(viewport.showAnnotation);\r
  61 \r
  62     if(applet!=null)\r
  63     {\r
  64       String param = applet.getParameter("sortBy");\r
  65       if (param != null)\r
  66       {\r
  67         if (param.equalsIgnoreCase("Id"))\r
  68           sortIDMenuItem_actionPerformed();\r
  69         else if (param.equalsIgnoreCase("Pairwise Identity"))\r
  70           sortPairwiseMenuItem_actionPerformed();\r
  71       }\r
  72 \r
  73       param = applet.getParameter("wrap");\r
  74       if (param != null)\r
  75       {\r
  76         if (param.equalsIgnoreCase("true"))\r
  77         {\r
  78           wrapMenuItem.setState(true);\r
  79           wrapMenuItem_actionPerformed();\r
  80         }\r
  81       }\r
  82 \r
  83       try\r
  84       {\r
  85         param = applet.getParameter("windowWidth");\r
  86         if (param != null)\r
  87         {\r
  88           int width = Integer.parseInt(param);\r
  89           NEW_WINDOW_WIDTH = width;\r
  90         }\r
  91         param = applet.getParameter("windowHeight");\r
  92         if (param != null)\r
  93         {\r
  94           int height = Integer.parseInt(param);\r
  95           NEW_WINDOW_HEIGHT = height;\r
  96         }\r
  97       }\r
  98       catch (Exception ex)\r
  99       {}\r
 100 \r
 101     }\r
 102 \r
 103    //Some JVMS send keyevents to Top frame or lowest panel,\r
 104    //Havent worked out why yet. So add to both this frame and seqCanvas for now\r
 105    this.addKeyListener(this);\r
 106    alignPanel.seqPanel.seqCanvas.addKeyListener(this);\r
 107    alignPanel.idPanel.idCanvas.addKeyListener(this);\r
 108 \r
 109     viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
 110     {\r
 111      public void propertyChange(java.beans.PropertyChangeEvent evt)\r
 112      {\r
 113        if (evt.getPropertyName().equals("alignment"))\r
 114        {\r
 115          alignmentChanged();\r
 116        }\r
 117      }\r
 118    });\r
 119 \r
 120 \r
 121    if(embedded)\r
 122    {\r
 123      setEmbedded();\r
 124    }\r
 125    else\r
 126    {\r
 127      add(alignPanel, BorderLayout.CENTER);\r
 128      jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH,\r
 129                                       NEW_WINDOW_HEIGHT);\r
 130    }\r
 131    alignPanel.validate();\r
 132    alignPanel.repaint();\r
 133   }\r
 134   public AlignViewport getAlignViewport()\r
 135   {\r
 136     return viewport;\r
 137   }\r
 138 \r
 139   public SeqCanvas getSeqcanvas()\r
 140   {\r
 141     return alignPanel.seqPanel.seqCanvas;\r
 142   }\r
 143 \r
 144 \r
 145   /**\r
 146    * DOCUMENT ME!\r
 147    *\r
 148    * @param String DOCUMENT ME!\r
 149    */\r
 150 \r
 151   public void parseFeaturesFile(String file)\r
 152   {\r
 153     String line = null;\r
 154     try\r
 155     {\r
 156       BufferedReader in = null;\r
 157       java.io.InputStream is = getClass().getResourceAsStream("/" + file);\r
 158       if (is != null)\r
 159       {\r
 160         in = new BufferedReader(new java.io.InputStreamReader(is));\r
 161       }\r
 162       else\r
 163       {\r
 164         URL url = new URL(file);\r
 165         in = new BufferedReader(new InputStreamReader(url.openStream()));\r
 166       }\r
 167 \r
 168       SequenceI seq = null;\r
 169       String type, desc, token;\r
 170 \r
 171       int index, start, end;\r
 172       StringTokenizer st;\r
 173       SequenceFeature sf;\r
 174       FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
 175       int lineNo = 0;\r
 176       String featureGroup = null;\r
 177       while ( (line = in.readLine()) != null)\r
 178       {\r
 179         lineNo++;\r
 180         st = new StringTokenizer(line, "\t");\r
 181         if (st.countTokens() == 2)\r
 182         {\r
 183           type = st.nextToken();\r
 184           if(type.equalsIgnoreCase("startgroup"))\r
 185           {\r
 186             featureGroup = st.nextToken();\r
 187           }\r
 188           else if(type.equalsIgnoreCase("endgroup"))\r
 189           {\r
 190             //We should check whether this is the current group,\r
 191             //but at present theres no way of showing more than 1 group\r
 192             st.nextToken();\r
 193             featureGroup = null;\r
 194           }\r
 195           else\r
 196           {\r
 197             UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
 198             fr.setColour(type, ucs.findColour("A"));\r
 199           }\r
 200           continue;\r
 201         }\r
 202 \r
 203         while (st.hasMoreElements())\r
 204         {\r
 205           desc = st.nextToken();\r
 206           token = st.nextToken();\r
 207           if (!token.equals("ID_NOT_SPECIFIED"))\r
 208           {\r
 209             index = viewport.alignment.findIndex(viewport.alignment.findName(\r
 210                 token));\r
 211             st.nextToken();\r
 212           }\r
 213           else\r
 214           {\r
 215             index = Integer.parseInt(st.nextToken());\r
 216           }\r
 217 \r
 218           start = Integer.parseInt(st.nextToken());\r
 219           end = Integer.parseInt(st.nextToken());\r
 220 \r
 221           seq = viewport.alignment.getSequenceAt(index);\r
 222 \r
 223           type = st.nextToken();\r
 224 \r
 225           if(fr.getColour(type)==null)\r
 226           {\r
 227             // Probably the old style groups file\r
 228             UserColourScheme ucs = new UserColourScheme(type);\r
 229             fr.setColour(type, ucs.findColour("A"));\r
 230           }\r
 231 \r
 232           sf = new SequenceFeature(type, desc, "", start, end, featureGroup);\r
 233 \r
 234           seq.addSequenceFeature(sf);\r
 235         }\r
 236       }\r
 237 \r
 238       viewport.showSequenceFeatures = true;\r
 239       sequenceFeatures.setState(true);\r
 240 \r
 241       alignPanel.repaint();\r
 242 \r
 243     }\r
 244     catch (Exception ex)\r
 245     {\r
 246       ex.printStackTrace();\r
 247       System.out.println("Error parsing groups file: " + ex +"\n"+line);\r
 248     }\r
 249   }\r
 250 \r
 251   public void keyPressed(KeyEvent evt)\r
 252   {\r
 253     switch (evt.getKeyCode())\r
 254     {\r
 255       case 27: // escape key\r
 256         deselectAllSequenceMenuItem_actionPerformed();\r
 257         break;\r
 258       case KeyEvent.VK_X:\r
 259         if (evt.isControlDown() || evt.isMetaDown())\r
 260         {\r
 261           cut_actionPerformed();\r
 262         }\r
 263         break;\r
 264       case KeyEvent.VK_C:\r
 265         if (evt.isControlDown() || evt.isMetaDown())\r
 266         {\r
 267           copy_actionPerformed();\r
 268         }\r
 269         break;\r
 270       case KeyEvent.VK_V:\r
 271         if (evt.isControlDown() || evt.isMetaDown())\r
 272         {\r
 273           paste(true);\r
 274         }\r
 275         break;\r
 276       case KeyEvent.VK_A:\r
 277         if (evt.isControlDown() || evt.isMetaDown())\r
 278         {\r
 279           selectAllSequenceMenuItem_actionPerformed();\r
 280         }\r
 281         break;\r
 282       case KeyEvent.VK_DOWN:\r
 283         moveSelectedSequences(false);\r
 284         break;\r
 285       case KeyEvent.VK_UP:\r
 286         moveSelectedSequences(true);\r
 287         break;\r
 288       case KeyEvent.VK_F:\r
 289         if (evt.isControlDown())\r
 290         {\r
 291           findMenuItem_actionPerformed();\r
 292         }\r
 293         break;\r
 294       case KeyEvent.VK_BACK_SPACE:\r
 295       case KeyEvent.VK_DELETE:\r
 296         cut_actionPerformed();\r
 297         break;\r
 298     }\r
 299   }\r
 300   public void keyReleased(KeyEvent evt)\r
 301   {}\r
 302   public void keyTyped(KeyEvent evt)\r
 303   {}\r
 304 \r
 305 public void itemStateChanged(ItemEvent evt)\r
 306   {\r
 307     if(evt.getSource()==colourTextMenuItem)\r
 308             colourTextMenuItem_actionPerformed();\r
 309     else if(evt.getSource()==wrapMenuItem)\r
 310             wrapMenuItem_actionPerformed();\r
 311     else if(evt.getSource()==scaleAbove)\r
 312             scaleAbove_actionPerformed();\r
 313     else if(evt.getSource()==scaleLeft)\r
 314             scaleLeft_actionPerformed();\r
 315     else if(evt.getSource()==scaleRight)\r
 316             scaleRight_actionPerformed();\r
 317      else if(evt.getSource()==seqLimits)\r
 318       seqLimits_itemStateChanged();\r
 319     else if(evt.getSource()==viewBoxesMenuItem)\r
 320             viewBoxesMenuItem_actionPerformed();\r
 321     else if(evt.getSource()==viewTextMenuItem)\r
 322             viewTextMenuItem_actionPerformed();\r
 323     else if(evt.getSource()==renderGapsMenuItem)\r
 324             renderGapsMenuItem_actionPerformed();\r
 325     else if(evt.getSource()==annotationPanelMenuItem)\r
 326             annotationPanelMenuItem_actionPerformed();\r
 327       else if(evt.getSource()==sequenceFeatures)\r
 328       {\r
 329            viewport.showSequenceFeatures(sequenceFeatures.getState());\r
 330             alignPanel.seqPanel.seqCanvas.repaint();\r
 331       }\r
 332       else if(evt.getSource()==conservationMenuItem)\r
 333             conservationMenuItem_actionPerformed();\r
 334       else if(evt.getSource()==abovePIDThreshold)\r
 335             abovePIDThreshold_actionPerformed();\r
 336           else if(evt.getSource()==applyToAllGroups)\r
 337             applyToAllGroups_actionPerformed();\r
 338   }\r
 339  public void actionPerformed(ActionEvent evt)\r
 340  {\r
 341     if(evt.getSource()==inputText)\r
 342       inputText_actionPerformed();\r
 343     else if(evt.getSource()==loadTree)\r
 344       loadTree_actionPerformed();\r
 345     else if(evt.getSource()==closeMenuItem)\r
 346       closeMenuItem_actionPerformed();\r
 347     else if(evt.getSource()==copy)\r
 348       copy_actionPerformed();\r
 349     else if(evt.getSource()==undoMenuItem)\r
 350       undoMenuItem_actionPerformed();\r
 351     else if(evt.getSource()==redoMenuItem)\r
 352       redoMenuItem_actionPerformed();\r
 353     else if(evt.getSource()==inputText)\r
 354             inputText_actionPerformed();\r
 355     else if(evt.getSource()==closeMenuItem)\r
 356             closeMenuItem_actionPerformed();\r
 357     else if(evt.getSource()==undoMenuItem)\r
 358             undoMenuItem_actionPerformed();\r
 359     else if(evt.getSource()==redoMenuItem)\r
 360             redoMenuItem_actionPerformed();\r
 361     else if(evt.getSource()==copy)\r
 362             copy_actionPerformed();\r
 363     else if(evt.getSource()==pasteNew)\r
 364             pasteNew_actionPerformed();\r
 365     else if(evt.getSource()==pasteThis)\r
 366             pasteThis_actionPerformed();\r
 367     else if(evt.getSource()==cut)\r
 368             cut_actionPerformed();\r
 369     else if(evt.getSource()==delete)\r
 370             delete_actionPerformed();\r
 371     else if(evt.getSource()==deleteGroups)\r
 372             deleteGroups_actionPerformed();\r
 373     else if(evt.getSource()==selectAllSequenceMenuItem)\r
 374             selectAllSequenceMenuItem_actionPerformed();\r
 375     else if(evt.getSource()==deselectAllSequenceMenuItem)\r
 376             deselectAllSequenceMenuItem_actionPerformed();\r
 377     else if(evt.getSource()==invertSequenceMenuItem)\r
 378             invertSequenceMenuItem_actionPerformed();\r
 379     else if(evt.getSource()==remove2LeftMenuItem)\r
 380             remove2LeftMenuItem_actionPerformed();\r
 381     else if(evt.getSource()==remove2RightMenuItem)\r
 382             remove2RightMenuItem_actionPerformed();\r
 383     else if(evt.getSource()==removeGappedColumnMenuItem)\r
 384             removeGappedColumnMenuItem_actionPerformed();\r
 385     else if(evt.getSource()==removeAllGapsMenuItem)\r
 386             removeAllGapsMenuItem_actionPerformed();\r
 387     else if(evt.getSource()==findMenuItem)\r
 388             findMenuItem_actionPerformed();\r
 389     else if(evt.getSource()==font)\r
 390             font_actionPerformed();\r
 391     else if(evt.getSource()==featureSettings)\r
 392             featureSettings_actionPerformed();\r
 393     else if(evt.getSource()==overviewMenuItem)\r
 394             overviewMenuItem_actionPerformed();\r
 395     else if(evt.getSource()==noColourmenuItem)\r
 396             noColourmenuItem_actionPerformed();\r
 397     else if(evt.getSource()==clustalColour)\r
 398             clustalColour_actionPerformed();\r
 399     else if(evt.getSource()==zappoColour)\r
 400             zappoColour_actionPerformed();\r
 401     else if(evt.getSource()==taylorColour)\r
 402             taylorColour_actionPerformed();\r
 403     else if(evt.getSource()==hydrophobicityColour)\r
 404             hydrophobicityColour_actionPerformed();\r
 405     else if(evt.getSource()==helixColour)\r
 406             helixColour_actionPerformed();\r
 407     else if(evt.getSource()==strandColour)\r
 408             strandColour_actionPerformed();\r
 409     else if(evt.getSource()==turnColour)\r
 410             turnColour_actionPerformed();\r
 411     else if(evt.getSource()==buriedColour)\r
 412             buriedColour_actionPerformed();\r
 413     else if(evt.getSource()==nucleotideColour)\r
 414             nucleotideColour_actionPerformed();\r
 415     else if(evt.getSource()==modifyPID)\r
 416             modifyPID_actionPerformed();\r
 417     else if(evt.getSource()==modifyConservation)\r
 418             modifyConservation_actionPerformed();\r
 419     else if(evt.getSource()==userDefinedColour)\r
 420             userDefinedColour_actionPerformed();\r
 421     else if(evt.getSource()==PIDColour)\r
 422             PIDColour_actionPerformed();\r
 423     else if(evt.getSource()==BLOSUM62Colour)\r
 424             BLOSUM62Colour_actionPerformed();\r
 425     else if(evt.getSource()==annotationColour)\r
 426            new AnnotationColourChooser(viewport, alignPanel);\r
 427     else if(evt.getSource()==sortPairwiseMenuItem)\r
 428             sortPairwiseMenuItem_actionPerformed();\r
 429     else if(evt.getSource()==sortIDMenuItem)\r
 430             sortIDMenuItem_actionPerformed();\r
 431     else if(evt.getSource()==sortGroupMenuItem)\r
 432             sortGroupMenuItem_actionPerformed();\r
 433     else if(evt.getSource()==removeRedundancyMenuItem)\r
 434             removeRedundancyMenuItem_actionPerformed();\r
 435     else if(evt.getSource()==pairwiseAlignmentMenuItem)\r
 436             pairwiseAlignmentMenuItem_actionPerformed();\r
 437     else if(evt.getSource()==PCAMenuItem)\r
 438             PCAMenuItem_actionPerformed();\r
 439     else if(evt.getSource()==averageDistanceTreeMenuItem)\r
 440             averageDistanceTreeMenuItem_actionPerformed();\r
 441     else if(evt.getSource()==neighbourTreeMenuItem)\r
 442             neighbourTreeMenuItem_actionPerformed();\r
 443     else if(evt.getSource()==njTreeBlosumMenuItem)\r
 444             njTreeBlosumMenuItem_actionPerformed();\r
 445     else if(evt.getSource()==avDistanceTreeBlosumMenuItem)\r
 446             avTreeBlosumMenuItem_actionPerformed();\r
 447     else if(evt.getSource()==documentation)\r
 448             documentation_actionPerformed();\r
 449     else if(evt.getSource()==about)\r
 450             about_actionPerformed();\r
 451 \r
 452  }\r
 453 \r
 454   public void inputText_actionPerformed()\r
 455   {\r
 456     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
 457     Frame frame = new Frame();\r
 458     frame.add(cap);\r
 459     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
 460   }\r
 461 \r
 462   protected void outputText_actionPerformed(ActionEvent e)\r
 463   {\r
 464     CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
 465     Frame frame = new Frame();\r
 466     frame.add(cap);\r
 467     jalview.bin.JalviewLite.addFrame(frame,\r
 468                                      "Alignment output - " + e.getActionCommand(),\r
 469                                      600, 500);\r
 470     cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
 471                                               viewport.getAlignment().getSequences(),\r
 472                                                       viewport.showJVSuffix));\r
 473   }\r
 474 \r
 475   public void closeMenuItem_actionPerformed()\r
 476   {\r
 477     PaintRefresher.components.remove(viewport.alignment);\r
 478     if(PaintRefresher.components.size()==0 && applet==null)\r
 479       System.exit(0);\r
 480 \r
 481     this.dispose();\r
 482   }\r
 483 \r
 484   Stack historyList = new Stack();\r
 485   Stack redoList = new Stack();\r
 486 \r
 487   void updateEditMenuBar()\r
 488   {\r
 489     if (historyList.size() > 0)\r
 490     {\r
 491       undoMenuItem.setEnabled(true);\r
 492       HistoryItem hi = (HistoryItem) historyList.peek();\r
 493       undoMenuItem.setLabel("Undo " + hi.getDescription());\r
 494     }\r
 495     else\r
 496     {\r
 497       undoMenuItem.setEnabled(false);\r
 498       undoMenuItem.setLabel("Undo");\r
 499     }\r
 500 \r
 501     if (redoList.size() > 0)\r
 502     {\r
 503       redoMenuItem.setEnabled(true);\r
 504       HistoryItem hi = (HistoryItem) redoList.peek();\r
 505       redoMenuItem.setLabel("Redo " + hi.getDescription());\r
 506     }\r
 507     else\r
 508     {\r
 509       redoMenuItem.setEnabled(false);\r
 510       redoMenuItem.setLabel("Redo");\r
 511     }\r
 512   }\r
 513 \r
 514   public void addHistoryItem(HistoryItem hi)\r
 515   {\r
 516     historyList.push(hi);\r
 517     updateEditMenuBar();\r
 518   }\r
 519 \r
 520   protected void undoMenuItem_actionPerformed()\r
 521   {\r
 522     HistoryItem hi = (HistoryItem) historyList.pop();\r
 523     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
 524                                   HistoryItem.HIDE));\r
 525     restoreHistoryItem(hi);\r
 526     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 527   }\r
 528 \r
 529   protected void redoMenuItem_actionPerformed()\r
 530   {\r
 531     HistoryItem hi = (HistoryItem) redoList.pop();\r
 532     restoreHistoryItem(hi);\r
 533     updateEditMenuBar();\r
 534     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 535   }\r
 536 \r
 537   // used by undo and redo\r
 538   void restoreHistoryItem(HistoryItem hi)\r
 539   {\r
 540     hi.restore();\r
 541 \r
 542     updateEditMenuBar();\r
 543 \r
 544     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 545   }\r
 546 \r
 547   public void moveSelectedSequences(boolean up)\r
 548   {\r
 549     SequenceGroup sg = viewport.getSelectionGroup();\r
 550     if (sg == null)\r
 551     {\r
 552       return;\r
 553     }\r
 554 \r
 555     if (up)\r
 556     {\r
 557       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 558       {\r
 559         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 560         if (!sg.sequences.contains(seq))\r
 561         {\r
 562           continue;\r
 563         }\r
 564 \r
 565         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 566         if (sg.sequences.contains(temp))\r
 567         {\r
 568           continue;\r
 569         }\r
 570 \r
 571         viewport.alignment.getSequences().setElementAt(temp, i);\r
 572         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 573       }\r
 574     }\r
 575     else\r
 576     {\r
 577       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 578       {\r
 579         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 580         if (!sg.sequences.contains(seq))\r
 581         {\r
 582           continue;\r
 583         }\r
 584 \r
 585         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 586         if (sg.sequences.contains(temp))\r
 587         {\r
 588           continue;\r
 589         }\r
 590 \r
 591         viewport.alignment.getSequences().setElementAt(temp, i);\r
 592         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 593       }\r
 594     }\r
 595 \r
 596     alignPanel.repaint();\r
 597   }\r
 598 \r
 599   StringBuffer copiedSequences;\r
 600   protected void copy_actionPerformed()\r
 601   {\r
 602     if (viewport.getSelectionGroup() == null)\r
 603     {\r
 604       return;\r
 605     }\r
 606 \r
 607     SequenceGroup sg = viewport.getSelectionGroup();\r
 608     copiedSequences = new StringBuffer();\r
 609     Hashtable orderedSeqs = new Hashtable();\r
 610     for (int i = 0; i < sg.getSize(); i++)\r
 611     {\r
 612       SequenceI seq = sg.getSequenceAt(i);\r
 613       int index = viewport.alignment.findIndex(seq);\r
 614       orderedSeqs.put(index + "", seq);\r
 615     }\r
 616 \r
 617     int index = 0, startRes, endRes;\r
 618     char ch;\r
 619 \r
 620     for (int i = 0; i < sg.getSize(); i++)\r
 621     {\r
 622         SequenceI seq = null;\r
 623 \r
 624         while (seq == null)\r
 625         {\r
 626             if (orderedSeqs.containsKey(index + ""))\r
 627             {\r
 628                 seq = (SequenceI) orderedSeqs.get(index + "");\r
 629                 index++;\r
 630 \r
 631                 break;\r
 632             }\r
 633             else\r
 634             {\r
 635                 index++;\r
 636             }\r
 637         }\r
 638 \r
 639         //FIND START RES\r
 640         //Returns residue following index if gap\r
 641         startRes = seq.findPosition(sg.getStartRes());\r
 642 \r
 643         //FIND END RES\r
 644         //Need to find the residue preceeding index if gap\r
 645         endRes = 0;\r
 646 \r
 647         for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
 648         {\r
 649           ch = seq.getCharAt(j);\r
 650           if (!jalview.util.Comparison.isGap( (ch)))\r
 651           {\r
 652             endRes++;\r
 653           }\r
 654         }\r
 655 \r
 656         if(endRes>0)\r
 657         {\r
 658           endRes += seq.getStart() -1;\r
 659         }\r
 660 \r
 661         copiedSequences.append(seq.getName() + "\t" +\r
 662             startRes + "\t" +\r
 663             endRes + "\t" +\r
 664             seq.getSequence(sg.getStartRes(),\r
 665                 sg.getEndRes() + 1) + "\n");\r
 666     }\r
 667 \r
 668   }\r
 669 \r
 670   protected void pasteNew_actionPerformed()\r
 671   {\r
 672     paste(true);\r
 673   }\r
 674 \r
 675   protected void pasteThis_actionPerformed()\r
 676   {\r
 677     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
 678                                    HistoryItem.PASTE));\r
 679     paste(false);\r
 680   }\r
 681 \r
 682   void paste(boolean newAlignment)\r
 683   {\r
 684     try\r
 685     {\r
 686       if (copiedSequences == null)\r
 687       {\r
 688         return;\r
 689       }\r
 690 \r
 691       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 692       Vector seqs = new Vector();\r
 693       while (st.hasMoreElements())\r
 694       {\r
 695         String name = st.nextToken();\r
 696         int start = Integer.parseInt(st.nextToken());\r
 697         int end = Integer.parseInt(st.nextToken());\r
 698         Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
 699 \r
 700         if (!newAlignment)\r
 701         {\r
 702           viewport.alignment.addSequence(sequence);\r
 703         }\r
 704         else\r
 705         {\r
 706           seqs.addElement(sequence);\r
 707         }\r
 708       }\r
 709 \r
 710       if (newAlignment)\r
 711       {\r
 712         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 713         for (int i = 0; i < seqs.size(); i++)\r
 714         {\r
 715           newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
 716         }\r
 717 \r
 718         String newtitle = new String("Copied sequences");\r
 719         if (getTitle().startsWith("Copied sequences"))\r
 720         {\r
 721           newtitle = getTitle();\r
 722         }\r
 723         else\r
 724         {\r
 725           newtitle = newtitle.concat("- from " + getTitle());\r
 726         }\r
 727         AlignFrame af = new AlignFrame(new Alignment(newSeqs),\r
 728                                        applet,\r
 729                                        newtitle,\r
 730                                        false);\r
 731 \r
 732         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
 733                                          NEW_WINDOW_HEIGHT);\r
 734       }\r
 735       else\r
 736       {\r
 737         viewport.setEndSeq(viewport.alignment.getHeight());\r
 738         viewport.alignment.getWidth();\r
 739         viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 740       }\r
 741 \r
 742     }\r
 743     catch (Exception ex)\r
 744     {} // could be anything being pasted in here\r
 745 \r
 746   }\r
 747 \r
 748   protected void cut_actionPerformed()\r
 749   {\r
 750     copy_actionPerformed();\r
 751     delete_actionPerformed();\r
 752   }\r
 753 \r
 754   protected void delete_actionPerformed()\r
 755   {\r
 756     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
 757                                    HistoryItem.HIDE));\r
 758     if (viewport.getSelectionGroup() == null)\r
 759     {\r
 760       return;\r
 761     }\r
 762 \r
 763 \r
 764     SequenceGroup sg = viewport.getSelectionGroup();\r
 765     boolean allSequences = false;\r
 766     if(sg.sequences.size()==viewport.alignment.getHeight())\r
 767           allSequences = true;\r
 768 \r
 769     for (int i = 0; i < sg.sequences.size(); i++)\r
 770     {\r
 771       SequenceI seq = sg.getSequenceAt(i);\r
 772       int index = viewport.getAlignment().findIndex(seq);\r
 773       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 774 \r
 775       // If the cut affects all sequences, remove highlighted columns\r
 776       if (allSequences)\r
 777       {\r
 778         viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
 779                                                      sg.getEndRes() + 1);\r
 780       }\r
 781 \r
 782 \r
 783       if (seq.getSequence().length() < 1)\r
 784       {\r
 785         viewport.getAlignment().deleteSequence(seq);\r
 786       }\r
 787       else\r
 788       {\r
 789         viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 790       }\r
 791     }\r
 792 \r
 793     viewport.setSelectionGroup(null);\r
 794     viewport.alignment.deleteGroup(sg);\r
 795     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
 796     if (viewport.getAlignment().getHeight() < 1)\r
 797     {\r
 798       try\r
 799       {\r
 800         this.setVisible(false);\r
 801       }\r
 802       catch (Exception ex)\r
 803       {}\r
 804     }\r
 805     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 806 \r
 807   }\r
 808 \r
 809   protected void deleteGroups_actionPerformed()\r
 810   {\r
 811     viewport.alignment.deleteAllGroups();\r
 812     viewport.setSelectionGroup(null);\r
 813 \r
 814     alignPanel.repaint();\r
 815   }\r
 816 \r
 817   public void selectAllSequenceMenuItem_actionPerformed()\r
 818   {\r
 819     SequenceGroup sg = new SequenceGroup();\r
 820     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 821     {\r
 822       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
 823     }\r
 824     sg.setEndRes(viewport.alignment.getWidth()-1);\r
 825     viewport.setSelectionGroup(sg);\r
 826     alignPanel.repaint();\r
 827     PaintRefresher.Refresh(null, viewport.alignment);\r
 828   }\r
 829 \r
 830   public void deselectAllSequenceMenuItem_actionPerformed()\r
 831   {\r
 832     viewport.setSelectionGroup(null);\r
 833     viewport.getColumnSelection().clear();\r
 834     viewport.setSelectionGroup(null);\r
 835     alignPanel.idPanel.idCanvas.searchResults = null;\r
 836     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
 837     alignPanel.repaint();\r
 838     PaintRefresher.Refresh(null, viewport.alignment);\r
 839   }\r
 840 \r
 841   public void invertSequenceMenuItem_actionPerformed()\r
 842   {\r
 843     SequenceGroup sg = viewport.getSelectionGroup();\r
 844     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 845     {\r
 846       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
 847     }\r
 848 \r
 849     PaintRefresher.Refresh(null, viewport.alignment);\r
 850   }\r
 851 \r
 852   public void remove2LeftMenuItem_actionPerformed()\r
 853   {\r
 854     ColumnSelection colSel = viewport.getColumnSelection();\r
 855     if (colSel.size() > 0)\r
 856     {\r
 857       addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
 858                                      HistoryItem.HIDE));\r
 859       int min = colSel.getMin();\r
 860       viewport.getAlignment().trimLeft(min);\r
 861       colSel.compensateForEdit(0, min);\r
 862 \r
 863       if (viewport.getSelectionGroup() != null)\r
 864       {\r
 865         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 866       }\r
 867 \r
 868       Vector groups = viewport.alignment.getGroups();\r
 869       for (int i = 0; i < groups.size(); i++)\r
 870       {\r
 871         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 872         if (!sg.adjustForRemoveLeft(min))\r
 873         {\r
 874           viewport.alignment.deleteGroup(sg);\r
 875         }\r
 876       }\r
 877       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 878     }\r
 879   }\r
 880 \r
 881   public void remove2RightMenuItem_actionPerformed()\r
 882   {\r
 883     ColumnSelection colSel = viewport.getColumnSelection();\r
 884     if (colSel.size() > 0)\r
 885     {\r
 886       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
 887                                      HistoryItem.HIDE));\r
 888       int max = colSel.getMax();\r
 889       viewport.getAlignment().trimRight(max);\r
 890       if (viewport.getSelectionGroup() != null)\r
 891       {\r
 892         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 893       }\r
 894 \r
 895       Vector groups = viewport.alignment.getGroups();\r
 896       for (int i = 0; i < groups.size(); i++)\r
 897       {\r
 898         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 899         if (!sg.adjustForRemoveRight(max))\r
 900         {\r
 901           viewport.alignment.deleteGroup(sg);\r
 902         }\r
 903       }\r
 904       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 905     }\r
 906 \r
 907   }\r
 908 \r
 909   public void removeGappedColumnMenuItem_actionPerformed()\r
 910   {\r
 911     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
 912                                    viewport.alignment,\r
 913                                    HistoryItem.HIDE));\r
 914 \r
 915     //This is to maintain viewport position on first residue\r
 916     //of first sequence\r
 917     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 918     int startRes = seq.findPosition(viewport.startRes);\r
 919 \r
 920     viewport.getAlignment().removeGaps();\r
 921 \r
 922     viewport.setStartRes(seq.findIndex(startRes)-1);\r
 923 \r
 924     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
 925   }\r
 926 \r
 927   public void removeAllGapsMenuItem_actionPerformed()\r
 928   {\r
 929     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
 930                                    HistoryItem.HIDE));\r
 931 \r
 932     //This is to maintain viewport position on first residue\r
 933     //of first sequence\r
 934     SequenceI seq = viewport.alignment.getSequenceAt(0);\r
 935     int startRes = seq.findPosition(viewport.startRes);\r
 936 \r
 937     SequenceI current;\r
 938     int jSize;\r
 939 \r
 940     Vector seqs=null;\r
 941 \r
 942     int start=0, end = viewport.alignment.getWidth();\r
 943 \r
 944     if (viewport.getSelectionGroup() != null\r
 945         && viewport.getSelectionGroup().sequences != null\r
 946         && viewport.getSelectionGroup().sequences.size()>0)\r
 947     {\r
 948       seqs = viewport.getSelectionGroup().sequences;\r
 949       start = viewport.getSelectionGroup().getStartRes();\r
 950       end = viewport.getSelectionGroup().getEndRes()+1;\r
 951     }\r
 952     else\r
 953       seqs = viewport.alignment.getSequences();\r
 954 \r
 955     for (int i = 0; i < seqs.size(); i++)\r
 956     {\r
 957       current = (SequenceI) seqs.elementAt(i);\r
 958       jSize = current.getLength();\r
 959 \r
 960       // Removing a range is much quicker than removing gaps\r
 961       // one by one for long sequences\r
 962       int j = start;\r
 963       int rangeStart=-1, rangeEnd=-1;\r
 964 \r
 965       do\r
 966       {\r
 967         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 968         {\r
 969           if(rangeStart==-1)\r
 970            {\r
 971              rangeStart = j;\r
 972              rangeEnd = j+1;\r
 973            }\r
 974            else\r
 975            {\r
 976              rangeEnd++;\r
 977            }\r
 978            j++;\r
 979         }\r
 980         else\r
 981         {\r
 982           if(rangeStart>-1)\r
 983           {\r
 984             current.deleteChars(rangeStart, rangeEnd);\r
 985             j-=rangeEnd-rangeStart;\r
 986             jSize-=rangeEnd-rangeStart;\r
 987             rangeStart = -1;\r
 988             rangeEnd = -1;\r
 989           }\r
 990           else\r
 991             j++;\r
 992         }\r
 993       }\r
 994       while (j < end && j < jSize);\r
 995       if(rangeStart>-1)\r
 996       {\r
 997        current.deleteChars(rangeStart, rangeEnd);\r
 998       }\r
 999     }\r
1000     viewport.setStartRes(seq.findIndex(startRes)-1);\r
1001     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
1002   }\r
1003 \r
1004   public void alignmentChanged()\r
1005   {\r
1006     viewport.updateConsensus();\r
1007     viewport.updateConservation ();\r
1008     resetAllColourSchemes();\r
1009     if(alignPanel.overviewPanel!=null)\r
1010       alignPanel.overviewPanel.updateOverviewImage();\r
1011 \r
1012     viewport.alignment.adjustSequenceAnnotations();\r
1013     alignPanel.repaint();\r
1014   }\r
1015 \r
1016   void resetAllColourSchemes()\r
1017   {\r
1018     ColourSchemeI cs = viewport.globalColourScheme;\r
1019     if(cs!=null)\r
1020     {\r
1021       if (cs instanceof ClustalxColourScheme)\r
1022       {\r
1023         ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
1024             resetClustalX(viewport.alignment.getSequences(),\r
1025                           viewport.alignment.getWidth());\r
1026       }\r
1027 \r
1028       cs.setConsensus(viewport.vconsensus);\r
1029       if (cs.conservationApplied())\r
1030       {\r
1031         Alignment al = (Alignment) viewport.alignment;\r
1032         Conservation c = new Conservation("All",\r
1033                                           ResidueProperties.propHash, 3,\r
1034                                           al.getSequences(), 0,\r
1035                                           al.getWidth() - 1);\r
1036         c.calculate();\r
1037         c.verdict(false, viewport.ConsPercGaps);\r
1038 \r
1039         cs.setConservation(c);\r
1040       }\r
1041     }\r
1042 \r
1043     int s, sSize = viewport.alignment.getGroups().size();\r
1044     for(s=0; s<sSize; s++)\r
1045     {\r
1046       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
1047       if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
1048       {\r
1049         ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
1050       }\r
1051       sg.recalcConservation();\r
1052     }\r
1053   }\r
1054 \r
1055 \r
1056 \r
1057   public void findMenuItem_actionPerformed()\r
1058   {\r
1059     new Finder(alignPanel);\r
1060   }\r
1061 \r
1062   public void font_actionPerformed()\r
1063   {\r
1064     new FontChooser(alignPanel);\r
1065   }\r
1066 \r
1067 \r
1068   public void seqLimits_itemStateChanged()\r
1069   {\r
1070     viewport.setShowJVSuffix(seqLimits.getState());\r
1071     alignPanel.fontChanged();\r
1072     alignPanel.repaint();\r
1073   }\r
1074 \r
1075 \r
1076   protected void colourTextMenuItem_actionPerformed()\r
1077   {\r
1078     viewport.setColourText(colourTextMenuItem.getState());\r
1079     alignPanel.repaint();\r
1080   }\r
1081 \r
1082   protected void wrapMenuItem_actionPerformed()\r
1083   {\r
1084     viewport.setWrapAlignment(wrapMenuItem.getState());\r
1085     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
1086     scaleAbove.setEnabled(wrapMenuItem.getState());\r
1087     scaleLeft.setEnabled(wrapMenuItem.getState());\r
1088     scaleRight.setEnabled(wrapMenuItem.getState());\r
1089     alignPanel.repaint();\r
1090   }\r
1091 \r
1092   protected void scaleAbove_actionPerformed()\r
1093   {\r
1094     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
1095     alignPanel.repaint();\r
1096   }\r
1097 \r
1098   protected void scaleLeft_actionPerformed()\r
1099   {\r
1100     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
1101     alignPanel.repaint();\r
1102   }\r
1103 \r
1104   protected void scaleRight_actionPerformed()\r
1105   {\r
1106     viewport.setScaleRightWrapped(scaleRight.getState());\r
1107     alignPanel.repaint();\r
1108   }\r
1109 \r
1110   public void viewBoxesMenuItem_actionPerformed()\r
1111   {\r
1112     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
1113     alignPanel.repaint();\r
1114   }\r
1115 \r
1116   public void viewTextMenuItem_actionPerformed()\r
1117   {\r
1118     viewport.setShowText(viewTextMenuItem.getState());\r
1119     alignPanel.repaint();\r
1120   }\r
1121 \r
1122   protected void renderGapsMenuItem_actionPerformed()\r
1123   {\r
1124     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
1125     alignPanel.repaint();\r
1126   }\r
1127 \r
1128   public void annotationPanelMenuItem_actionPerformed()\r
1129   {\r
1130     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
1131     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
1132   }\r
1133 \r
1134   public void featureSettings_actionPerformed()\r
1135   {\r
1136     new FeatureSettings(viewport, alignPanel);\r
1137   }\r
1138 \r
1139   public void overviewMenuItem_actionPerformed()\r
1140   {\r
1141     if (alignPanel.overviewPanel != null)\r
1142     {\r
1143       return;\r
1144     }\r
1145 \r
1146     Frame frame = new Frame();\r
1147     OverviewPanel overview = new OverviewPanel(alignPanel);\r
1148     frame.add(overview);\r
1149     // +50 must allow for applet frame window\r
1150     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
1151                                      overview.preferredSize().width,\r
1152                                      overview.preferredSize().height + 50);\r
1153 \r
1154     frame.pack();\r
1155     frame.addWindowListener(new WindowAdapter()\r
1156     {\r
1157       public void windowClosing(WindowEvent e)\r
1158       {\r
1159         alignPanel.setOverviewPanel(null);\r
1160       };\r
1161     });\r
1162 \r
1163     alignPanel.setOverviewPanel(overview);\r
1164 \r
1165   }\r
1166 \r
1167   protected void noColourmenuItem_actionPerformed()\r
1168   {\r
1169     changeColour(null);\r
1170   }\r
1171 \r
1172   public void clustalColour_actionPerformed()\r
1173   {\r
1174     abovePIDThreshold.setState(false);\r
1175     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
1176                                           viewport.alignment.getWidth()));\r
1177   }\r
1178 \r
1179   public void zappoColour_actionPerformed()\r
1180   {\r
1181     changeColour(new ZappoColourScheme());\r
1182   }\r
1183 \r
1184   public void taylorColour_actionPerformed()\r
1185   {\r
1186     changeColour(new TaylorColourScheme());\r
1187   }\r
1188 \r
1189   public void hydrophobicityColour_actionPerformed()\r
1190   {\r
1191     changeColour(new HydrophobicColourScheme());\r
1192   }\r
1193 \r
1194   public void helixColour_actionPerformed()\r
1195   {\r
1196     changeColour(new HelixColourScheme());\r
1197   }\r
1198 \r
1199   public void strandColour_actionPerformed()\r
1200   {\r
1201     changeColour(new StrandColourScheme());\r
1202   }\r
1203 \r
1204   public void turnColour_actionPerformed()\r
1205   {\r
1206     changeColour(new TurnColourScheme());\r
1207   }\r
1208 \r
1209   public void buriedColour_actionPerformed()\r
1210   {\r
1211     changeColour(new BuriedColourScheme());\r
1212   }\r
1213 \r
1214   public void nucleotideColour_actionPerformed()\r
1215   {\r
1216     changeColour(new NucleotideColourScheme());\r
1217   }\r
1218 \r
1219   protected void applyToAllGroups_actionPerformed()\r
1220   {\r
1221     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
1222   }\r
1223 \r
1224   void changeColour(ColourSchemeI cs)\r
1225   {\r
1226     int threshold = 0;\r
1227 \r
1228     if(cs!=null)\r
1229     {\r
1230       if (viewport.getAbovePIDThreshold())\r
1231       {\r
1232         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
1233 \r
1234         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1235 \r
1236         viewport.setGlobalColourScheme(cs);\r
1237       }\r
1238       else\r
1239       {\r
1240         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1241       }\r
1242 \r
1243       if (viewport.getConservationSelected())\r
1244       {\r
1245 \r
1246         Alignment al = (Alignment) viewport.alignment;\r
1247         Conservation c = new Conservation("All",\r
1248                                           ResidueProperties.propHash, 3,\r
1249                                           al.getSequences(), 0,\r
1250                                           al.getWidth() - 1);\r
1251 \r
1252         c.calculate();\r
1253         c.verdict(false, viewport.ConsPercGaps);\r
1254 \r
1255         cs.setConservation(c);\r
1256 \r
1257         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
1258             "Background"));\r
1259 \r
1260       }\r
1261       else\r
1262       {\r
1263         cs.setConservation(null);\r
1264       }\r
1265 \r
1266       cs.setConsensus(viewport.vconsensus);\r
1267 \r
1268     }\r
1269     viewport.setGlobalColourScheme(cs);\r
1270 \r
1271     if (viewport.getColourAppliesToAllGroups())\r
1272     {\r
1273       Vector groups = viewport.alignment.getGroups();\r
1274       for (int i = 0; i < groups.size(); i++)\r
1275       {\r
1276         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1277 \r
1278         if(cs==null)\r
1279         {\r
1280           sg.cs = null;\r
1281           continue;\r
1282         }\r
1283         if (cs instanceof ClustalxColourScheme)\r
1284         {\r
1285           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
1286         }\r
1287         else\r
1288         {\r
1289           try\r
1290           {\r
1291             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
1292           }\r
1293           catch (Exception ex)\r
1294           {\r
1295             ex.printStackTrace();\r
1296             sg.cs = cs;\r
1297           }\r
1298         }\r
1299 \r
1300         if (viewport.getAbovePIDThreshold()\r
1301             || cs instanceof PIDColourScheme\r
1302             || cs instanceof Blosum62ColourScheme)\r
1303         {\r
1304           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
1305           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
1306         }\r
1307         else\r
1308           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1309 \r
1310         if (viewport.getConservationSelected())\r
1311         {\r
1312           Conservation c = new Conservation("Group",\r
1313                                             ResidueProperties.propHash, 3,\r
1314                                             sg.sequences, 0,\r
1315                                             viewport.alignment.getWidth() - 1);\r
1316           c.calculate();\r
1317           c.verdict(false, viewport.ConsPercGaps);\r
1318           sg.cs.setConservation(c);\r
1319         }\r
1320         else\r
1321         {\r
1322           sg.cs.setConservation(null);\r
1323           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
1324         }\r
1325 \r
1326       }\r
1327     }\r
1328 \r
1329 \r
1330     if (alignPanel.getOverviewPanel() != null)\r
1331     {\r
1332       alignPanel.getOverviewPanel().updateOverviewImage();\r
1333     }\r
1334 \r
1335     alignPanel.repaint();\r
1336   }\r
1337 \r
1338 \r
1339 \r
1340   protected void modifyPID_actionPerformed()\r
1341   {\r
1342     if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
1343     {\r
1344       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
1345                                      "Background");\r
1346       SliderPanel.showPIDSlider();\r
1347     }\r
1348   }\r
1349 \r
1350   protected void modifyConservation_actionPerformed()\r
1351   {\r
1352     if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
1353     {\r
1354       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
1355                                         "Background");\r
1356       SliderPanel.showConservationSlider();\r
1357     }\r
1358   }\r
1359 \r
1360   protected void conservationMenuItem_actionPerformed()\r
1361   {\r
1362     viewport.setConservationSelected(conservationMenuItem.getState());\r
1363 \r
1364     viewport.setAbovePIDThreshold(false);\r
1365     abovePIDThreshold.setState(false);\r
1366 \r
1367     changeColour(viewport.getGlobalColourScheme());\r
1368 \r
1369     modifyConservation_actionPerformed();\r
1370   }\r
1371 \r
1372   public void abovePIDThreshold_actionPerformed()\r
1373   {\r
1374     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
1375 \r
1376     conservationMenuItem.setState(false);\r
1377     viewport.setConservationSelected(false);\r
1378 \r
1379     changeColour(viewport.getGlobalColourScheme());\r
1380 \r
1381     modifyPID_actionPerformed();\r
1382   }\r
1383 \r
1384   public void userDefinedColour_actionPerformed()\r
1385   {\r
1386     new UserDefinedColours(alignPanel, null);\r
1387   }\r
1388 \r
1389   public void PIDColour_actionPerformed()\r
1390   {\r
1391     changeColour(new PIDColourScheme());\r
1392   }\r
1393 \r
1394   public void BLOSUM62Colour_actionPerformed()\r
1395   {\r
1396     changeColour(new Blosum62ColourScheme());\r
1397   }\r
1398 \r
1399   public void sortPairwiseMenuItem_actionPerformed()\r
1400   {\r
1401     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1402                                    HistoryItem.SORT));\r
1403     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1404                               viewport.getAlignment().getSequenceAt(0));\r
1405     alignPanel.repaint();\r
1406   }\r
1407 \r
1408   public void sortIDMenuItem_actionPerformed()\r
1409   {\r
1410     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1411                                    HistoryItem.SORT));\r
1412     AlignmentSorter.sortByID(viewport.getAlignment());\r
1413     alignPanel.repaint();\r
1414   }\r
1415 \r
1416   public void sortGroupMenuItem_actionPerformed()\r
1417   {\r
1418     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1419                                    HistoryItem.SORT));\r
1420     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1421     alignPanel.repaint();\r
1422 \r
1423   }\r
1424 \r
1425   public void removeRedundancyMenuItem_actionPerformed()\r
1426   {\r
1427     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
1428     Frame frame = new Frame();\r
1429     frame.add(sp);\r
1430     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
1431                                      400, 120);\r
1432 \r
1433   }\r
1434 \r
1435   public void pairwiseAlignmentMenuItem_actionPerformed()\r
1436   {\r
1437     if (viewport.getSelectionGroup().getSize() > 1)\r
1438     {\r
1439       Frame frame = new Frame();\r
1440       frame.add(new PairwiseAlignPanel(alignPanel));\r
1441       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1442     }\r
1443   }\r
1444 \r
1445   public void PCAMenuItem_actionPerformed()\r
1446   {\r
1447     //are the sequences aligned?\r
1448     if (!viewport.alignment.isAligned())\r
1449     {\r
1450       SequenceI current;\r
1451       int Width = viewport.getAlignment().getWidth();\r
1452 \r
1453       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1454            i++)\r
1455       {\r
1456         current = viewport.getAlignment().getSequenceAt(i);\r
1457 \r
1458         if (current.getLength() < Width)\r
1459         {\r
1460           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1461         }\r
1462       }\r
1463       alignPanel.repaint();\r
1464     }\r
1465 \r
1466     if ( (viewport.getSelectionGroup() != null &&\r
1467           viewport.getSelectionGroup().getSize() < 4 &&\r
1468           viewport.getSelectionGroup().getSize() > 0)\r
1469         || viewport.getAlignment().getHeight() < 4)\r
1470     {\r
1471       return;\r
1472     }\r
1473 \r
1474     try\r
1475     {\r
1476       new PCAPanel(viewport);\r
1477     }\r
1478     catch (java.lang.OutOfMemoryError ex)\r
1479     {\r
1480     }\r
1481 \r
1482   }\r
1483 \r
1484   public void averageDistanceTreeMenuItem_actionPerformed()\r
1485   {\r
1486     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1487   }\r
1488 \r
1489   public void neighbourTreeMenuItem_actionPerformed()\r
1490   {\r
1491     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1492   }\r
1493 \r
1494   protected void njTreeBlosumMenuItem_actionPerformed()\r
1495   {\r
1496     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1497   }\r
1498 \r
1499   protected void avTreeBlosumMenuItem_actionPerformed()\r
1500   {\r
1501     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1502   }\r
1503 \r
1504   void NewTreePanel(String type, String pwType, String title)\r
1505   {\r
1506     //are the sequences aligned?\r
1507     if (!viewport.alignment.isAligned())\r
1508     {\r
1509       SequenceI current;\r
1510       int Width = viewport.getAlignment().getWidth();\r
1511 \r
1512       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1513            i++)\r
1514       {\r
1515         current = viewport.getAlignment().getSequenceAt(i);\r
1516 \r
1517         if (current.getLength() < Width)\r
1518         {\r
1519           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1520         }\r
1521       }\r
1522       alignPanel.repaint();\r
1523 \r
1524     }\r
1525 \r
1526     final TreePanel tp;\r
1527     if (viewport.getSelectionGroup() != null &&\r
1528         viewport.getSelectionGroup().getSize() > 3)\r
1529     {\r
1530       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1531                          pwType,\r
1532                          0, viewport.alignment.getWidth());\r
1533     }\r
1534     else\r
1535     {\r
1536       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1537                          type, pwType, 0, viewport.alignment.getWidth());\r
1538     }\r
1539 \r
1540     addTreeMenuItem(tp, title);\r
1541 \r
1542     jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1543   }\r
1544 \r
1545   void loadTree_actionPerformed()\r
1546   {\r
1547     TreePanel tp = null;\r
1548 \r
1549       CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
1550       cap.setText("Paste your Newick tree file here.");\r
1551       cap.treeImport = true;\r
1552       Frame frame = new Frame();\r
1553       frame.add(cap);\r
1554       jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);\r
1555   }\r
1556 \r
1557   public void loadTree(jalview.io.NewickFile tree, String treeFile)\r
1558   {\r
1559     TreePanel tp = new TreePanel(viewport,\r
1560                       viewport.getAlignment().getSequences(),\r
1561                       tree, "From File - ", treeFile);\r
1562     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
1563     addTreeMenuItem(tp, treeFile);\r
1564   }\r
1565 \r
1566   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1567   {\r
1568     final MenuItem item = new MenuItem(title);\r
1569     sortByTreeMenu.add(item);\r
1570     item.addActionListener(new java.awt.event.ActionListener()\r
1571     {\r
1572       public void actionPerformed(ActionEvent evt)\r
1573       {\r
1574         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1575                                        HistoryItem.SORT));\r
1576         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1577         alignPanel.repaint();\r
1578       }\r
1579     });\r
1580 \r
1581     treePanel.addWindowListener(new WindowAdapter()\r
1582     {\r
1583       public void windowClosing(WindowEvent e)\r
1584       {\r
1585         sortByTreeMenu.remove(item);\r
1586       };\r
1587     });\r
1588   }\r
1589 \r
1590   protected void documentation_actionPerformed()\r
1591   {\r
1592     showURL("http://www.jalview.org/help.html", "HELP");\r
1593   }\r
1594 \r
1595   protected void about_actionPerformed()\r
1596   {\r
1597 \r
1598     class AboutPanel extends Canvas\r
1599     {\r
1600       String version;\r
1601       public AboutPanel(String version)\r
1602       { this.version = version; }\r
1603 \r
1604       public void paint(Graphics g)\r
1605       {\r
1606         g.setColor(Color.white);\r
1607         g.fillRect(0, 0, getSize().width, getSize().height);\r
1608         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1609         FontMetrics fm = g.getFontMetrics();\r
1610         int fh = fm.getHeight();\r
1611         int y = 5, x = 7;\r
1612         g.setColor(Color.black);\r
1613         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1614         g.drawString("Jalview - Release "+version, 200, y += fh);\r
1615         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1616         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1617                      x, y += fh * 2);\r
1618         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1619                      x, y += fh);\r
1620         g.drawString(\r
1621             "For any issues relating to Jalview, email help@jalview.org", x,\r
1622             y += fh);\r
1623         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1624         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1625                      x, y += fh);\r
1626         g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);\r
1627       }\r
1628     }\r
1629 \r
1630     String version = "test";\r
1631     java.net.URL url = getClass().getResource("/.build_properties");\r
1632     if (url != null)\r
1633     {\r
1634       try\r
1635       {\r
1636         BufferedReader reader = new BufferedReader(new InputStreamReader(\r
1637             url.openStream()));\r
1638         String line;\r
1639         while ( (line = reader.readLine()) != null)\r
1640         {\r
1641           if (line.indexOf("VERSION") > -1)\r
1642           {\r
1643             version = line.substring(line.indexOf("=") + 1);\r
1644           }\r
1645         }\r
1646       }\r
1647       catch (Exception ex)\r
1648       {\r
1649         ex.printStackTrace();\r
1650       }\r
1651     }\r
1652 \r
1653 \r
1654     Frame frame = new Frame();\r
1655     frame.add(new AboutPanel(version));\r
1656     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1657 \r
1658   }\r
1659 \r
1660   public void showURL(String url, String target)\r
1661   {\r
1662     if (applet == null)\r
1663     {\r
1664       System.out.println("Not running as applet - no browser available.");\r
1665     }\r
1666     else\r
1667     {\r
1668       try\r
1669       {\r
1670         applet.getAppletContext().showDocument(new java.net.URL(url),\r
1671                                                target);\r
1672       }\r
1673       catch (Exception ex)\r
1674       {\r
1675         ex.printStackTrace();\r
1676       }\r
1677     }\r
1678   }\r
1679 \r
1680 \r
1681   //////////////////////////////////////////////////////////////////////////////////\r
1682   //JBuilder Graphics here\r
1683 \r
1684     protected MenuBar alignFrameMenuBar = new MenuBar();\r
1685     protected Menu fileMenu = new Menu("File");\r
1686     protected MenuItem loadTree = new MenuItem("Load Associated Tree");\r
1687     protected MenuItem closeMenuItem = new MenuItem("Close");\r
1688     protected Menu editMenu = new Menu("Edit");\r
1689     protected Menu viewMenu = new Menu("View");\r
1690     protected Menu colourMenu = new Menu("Colour");\r
1691     protected Menu calculateMenu = new Menu("Calculate");\r
1692     protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
1693     protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
1694     protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
1695     protected MenuItem remove2LeftMenuItem = new MenuItem();\r
1696     protected MenuItem remove2RightMenuItem = new MenuItem();\r
1697     protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
1698     protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
1699     protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
1700     protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
1701     protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
1702     protected MenuItem sortIDMenuItem = new MenuItem();\r
1703     protected MenuItem sortGroupMenuItem = new MenuItem();\r
1704     protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
1705     protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
1706     protected MenuItem PCAMenuItem = new MenuItem();\r
1707     protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
1708     protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
1709     BorderLayout borderLayout1 = new BorderLayout();\r
1710     public Label statusBar = new Label();\r
1711     protected Menu outputTextboxMenu = new Menu();\r
1712     protected MenuItem clustalColour = new MenuItem();\r
1713     protected MenuItem zappoColour = new MenuItem();\r
1714     protected MenuItem taylorColour = new MenuItem();\r
1715     protected MenuItem hydrophobicityColour = new MenuItem();\r
1716     protected MenuItem helixColour = new MenuItem();\r
1717     protected MenuItem strandColour = new MenuItem();\r
1718     protected MenuItem turnColour = new MenuItem();\r
1719     protected MenuItem buriedColour = new MenuItem();\r
1720     protected MenuItem userDefinedColour = new MenuItem();\r
1721     protected MenuItem PIDColour = new MenuItem();\r
1722     protected MenuItem BLOSUM62Colour = new MenuItem();\r
1723     MenuItem njTreeBlosumMenuItem = new MenuItem();\r
1724     MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
1725     protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
1726     protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
1727     MenuItem overviewMenuItem = new MenuItem();\r
1728     protected MenuItem undoMenuItem = new MenuItem();\r
1729     protected MenuItem redoMenuItem = new MenuItem();\r
1730     protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
1731     MenuItem noColourmenuItem = new MenuItem();\r
1732     protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
1733     protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
1734     MenuItem findMenuItem = new MenuItem();\r
1735     Menu searchMenu = new Menu();\r
1736     protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
1737     protected MenuItem nucleotideColour = new MenuItem();\r
1738     MenuItem deleteGroups = new MenuItem();\r
1739     MenuItem delete = new MenuItem();\r
1740     MenuItem copy = new MenuItem();\r
1741     MenuItem cut = new MenuItem();\r
1742     Menu pasteMenu = new Menu();\r
1743     MenuItem pasteNew = new MenuItem();\r
1744     MenuItem pasteThis = new MenuItem();\r
1745     protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
1746     protected MenuItem font = new MenuItem();\r
1747     protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
1748     protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
1749     protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
1750     MenuItem modifyPID = new MenuItem();\r
1751     MenuItem modifyConservation = new MenuItem();\r
1752     protected Menu sortByTreeMenu = new Menu();\r
1753     Menu sort = new Menu();\r
1754     Menu calculate = new Menu();\r
1755     MenuItem inputText = new MenuItem();\r
1756     Menu helpMenu = new Menu();\r
1757     MenuItem documentation = new MenuItem();\r
1758     MenuItem about = new MenuItem();\r
1759     protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
1760   Panel embeddedMenu;\r
1761   Label embeddedEdit;\r
1762   Label embeddedSearch;\r
1763   Label embeddedView;\r
1764   Label embeddedColour;\r
1765   Label embeddedFile;\r
1766   Label embeddedHelp;\r
1767   Label embeddedCalculate;\r
1768   FlowLayout flowLayout1;\r
1769 \r
1770   private void jbInit() throws Exception {\r
1771 \r
1772       setMenuBar(alignFrameMenuBar);\r
1773 \r
1774       MenuItem item;\r
1775 \r
1776       // dynamically fill save as menu with available formats\r
1777       for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)\r
1778       {\r
1779 \r
1780         item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.\r
1781                             elementAt(\r
1782                                 i));\r
1783         item.addActionListener(new java.awt.event.ActionListener()\r
1784         {\r
1785           public void actionPerformed(ActionEvent e)\r
1786           {\r
1787             outputText_actionPerformed(e);\r
1788           }\r
1789         });\r
1790 \r
1791         outputTextboxMenu.add(item);\r
1792       }\r
1793         closeMenuItem.addActionListener(this);\r
1794 \r
1795         loadTree.addActionListener(this);\r
1796         selectAllSequenceMenuItem.addActionListener(this);\r
1797         deselectAllSequenceMenuItem.addActionListener(this);\r
1798         invertSequenceMenuItem.addActionListener(this);\r
1799         remove2LeftMenuItem.setLabel("Remove Left");\r
1800         remove2LeftMenuItem.addActionListener(this);\r
1801         remove2RightMenuItem.setLabel("Remove Right");\r
1802         remove2RightMenuItem.addActionListener(this);\r
1803         removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
1804         removeGappedColumnMenuItem.addActionListener(this);\r
1805         removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
1806         removeAllGapsMenuItem.addActionListener(this);\r
1807         viewBoxesMenuItem.setLabel("Boxes");\r
1808         viewBoxesMenuItem.setState(true);\r
1809         viewBoxesMenuItem.addItemListener(this);\r
1810         viewTextMenuItem.setLabel("Text");\r
1811         viewTextMenuItem.setState(true);\r
1812         viewTextMenuItem.addItemListener(this);\r
1813         sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
1814         sortPairwiseMenuItem.addActionListener(this);\r
1815         sortIDMenuItem.setLabel("by ID");\r
1816         sortIDMenuItem.addActionListener(this);\r
1817         sortGroupMenuItem.setLabel("by Group");\r
1818         sortGroupMenuItem.addActionListener(this);\r
1819         removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
1820         removeRedundancyMenuItem.addActionListener(this);\r
1821         pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
1822         pairwiseAlignmentMenuItem.addActionListener(this);\r
1823         PCAMenuItem.setLabel("Principal Component Analysis");\r
1824         PCAMenuItem.addActionListener(this);\r
1825         averageDistanceTreeMenuItem.setLabel(\r
1826             "Average Distance Using % Identity");\r
1827         averageDistanceTreeMenuItem.addActionListener(this);\r
1828         neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
1829         neighbourTreeMenuItem.addActionListener(this);\r
1830         alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
1831         statusBar.setBackground(Color.white);\r
1832         statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
1833         statusBar.setText("Status bar");\r
1834         outputTextboxMenu.setLabel("Output to Textbox");\r
1835         clustalColour.setLabel("Clustalx");\r
1836 \r
1837         clustalColour.addActionListener(this);\r
1838         zappoColour.setLabel("Zappo");\r
1839         zappoColour.addActionListener(this);\r
1840         taylorColour.setLabel("Taylor");\r
1841         taylorColour.addActionListener(this);\r
1842         hydrophobicityColour.setLabel("Hydrophobicity");\r
1843         hydrophobicityColour.addActionListener(this);\r
1844         helixColour.setLabel("Helix Propensity");\r
1845         helixColour.addActionListener(this);\r
1846         strandColour.setLabel("Strand Propensity");\r
1847         strandColour.addActionListener(this);\r
1848         turnColour.setLabel("Turn Propensity");\r
1849         turnColour.addActionListener(this);\r
1850         buriedColour.setLabel("Buried Index");\r
1851         buriedColour.addActionListener(this);\r
1852         userDefinedColour.setLabel("User Defined...");\r
1853         userDefinedColour.addActionListener(this);\r
1854         PIDColour.setLabel("Percentage Identity");\r
1855         PIDColour.addActionListener(this);\r
1856         BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
1857         BLOSUM62Colour.addActionListener(this);\r
1858         avDistanceTreeBlosumMenuItem.setLabel(\r
1859             "Average Distance Using BLOSUM62");\r
1860         avDistanceTreeBlosumMenuItem.addActionListener(this);\r
1861         njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
1862         njTreeBlosumMenuItem.addActionListener(this);\r
1863         annotationPanelMenuItem.setLabel("Show Annotations");\r
1864         annotationPanelMenuItem.addItemListener(this);\r
1865         colourTextMenuItem.setLabel("Colour Text");\r
1866         colourTextMenuItem.addItemListener(this);\r
1867         overviewMenuItem.setLabel("Overview Window");\r
1868         overviewMenuItem.addActionListener(this);\r
1869         undoMenuItem.setEnabled(false);\r
1870         undoMenuItem.setLabel("Undo");\r
1871         undoMenuItem.addActionListener(this);\r
1872         redoMenuItem.setEnabled(false);\r
1873         redoMenuItem.setLabel("Redo");\r
1874         redoMenuItem.addActionListener(this);\r
1875         conservationMenuItem.setLabel("by Conservation");\r
1876         conservationMenuItem.addItemListener(this);\r
1877         noColourmenuItem.setLabel("None");\r
1878         noColourmenuItem.addActionListener(this);\r
1879         wrapMenuItem.setLabel("Wrap");\r
1880         wrapMenuItem.addItemListener(this);\r
1881         renderGapsMenuItem.setLabel("Show Gaps");\r
1882         renderGapsMenuItem.setState(true);\r
1883         renderGapsMenuItem.addItemListener(this);\r
1884         findMenuItem.setLabel("Find...");\r
1885         findMenuItem.addActionListener(this);\r
1886         searchMenu.setLabel("Search");\r
1887 \r
1888         abovePIDThreshold.setLabel("Above Identity Threshold");\r
1889         abovePIDThreshold.addItemListener(this);\r
1890         nucleotideColour.setLabel("Nucleotide");\r
1891         nucleotideColour.addActionListener(this);\r
1892         deleteGroups.setLabel("Undefine Groups");\r
1893         deleteGroups.addActionListener(this);\r
1894         copy.setLabel("Copy");\r
1895         copy.addActionListener(this);\r
1896         cut.setLabel("Cut");\r
1897         cut.addActionListener(this);\r
1898         delete.setLabel("Delete");\r
1899         delete.addActionListener(this);\r
1900         pasteMenu.setLabel("Paste");\r
1901         pasteNew.setLabel("To New Alignment");\r
1902         pasteNew.addActionListener(this);\r
1903         pasteThis.setLabel("Add To This Alignment");\r
1904         pasteThis.addActionListener(this);\r
1905         applyToAllGroups.setLabel("Apply Colour To All Groups");\r
1906         applyToAllGroups.setState(true);\r
1907         applyToAllGroups.addItemListener(this);\r
1908         font.setLabel("Font...");\r
1909         font.addActionListener(this);\r
1910         scaleAbove.setLabel("Scale Above");\r
1911         scaleAbove.setState(true);\r
1912         scaleAbove.setEnabled(false);\r
1913         scaleAbove.addItemListener(this);\r
1914         scaleLeft.setEnabled(false);\r
1915         scaleLeft.setState(true);\r
1916         scaleLeft.setLabel("Scale Left");\r
1917         scaleLeft.addItemListener(this);\r
1918         scaleRight.setEnabled(false);\r
1919         scaleRight.setState(true);\r
1920         scaleRight.setLabel("Scale Right");\r
1921         scaleRight.addItemListener(this);\r
1922         modifyPID.setLabel("Modify Identity Threshold...");\r
1923         modifyPID.addActionListener(this);\r
1924         modifyConservation.setLabel("Modify Conservation Threshold...");\r
1925         modifyConservation.addActionListener(this);\r
1926         sortByTreeMenu.setLabel("By Tree Order");\r
1927         sort.setLabel("Sort");\r
1928         calculate.setLabel("Calculate Tree");\r
1929         inputText.setLabel("Input from textbox");\r
1930         inputText.addActionListener(this);\r
1931 \r
1932         helpMenu.setLabel("Help");\r
1933         documentation.setLabel("Documentation");\r
1934         documentation.addActionListener(this);\r
1935 \r
1936         about.setLabel("About...");\r
1937         about.addActionListener(this);\r
1938           seqLimits.setState(true);\r
1939     seqLimits.setLabel("Show Sequence Limits");\r
1940     seqLimits.addItemListener(this);\r
1941     featureSettings.setLabel("Feature Settings...");\r
1942     featureSettings.addActionListener(this);\r
1943     sequenceFeatures.setLabel("Sequence Features");\r
1944     sequenceFeatures.addItemListener(this);\r
1945     sequenceFeatures.setState(false);\r
1946     annotationColour.setLabel("by Annotation...");\r
1947     annotationColour.addActionListener(this);\r
1948 \r
1949     alignFrameMenuBar.add(fileMenu);\r
1950         alignFrameMenuBar.add(editMenu);\r
1951         alignFrameMenuBar.add(searchMenu);\r
1952         alignFrameMenuBar.add(viewMenu);\r
1953         alignFrameMenuBar.add(colourMenu);\r
1954         alignFrameMenuBar.add(calculateMenu);\r
1955         alignFrameMenuBar.add(helpMenu);\r
1956         fileMenu.add(inputText);\r
1957         fileMenu.add(outputTextboxMenu);\r
1958         fileMenu.addSeparator();\r
1959         fileMenu.add(loadTree);\r
1960         fileMenu.add(closeMenuItem);\r
1961         editMenu.add(undoMenuItem);\r
1962         editMenu.add(redoMenuItem);\r
1963         editMenu.add(cut);\r
1964         editMenu.add(copy);\r
1965         editMenu.add(pasteMenu);\r
1966         editMenu.add(delete);\r
1967         editMenu.addSeparator();\r
1968         editMenu.add(selectAllSequenceMenuItem);\r
1969         editMenu.add(deselectAllSequenceMenuItem);\r
1970         editMenu.add(invertSequenceMenuItem);\r
1971         editMenu.add(deleteGroups);\r
1972         editMenu.addSeparator();\r
1973         editMenu.add(remove2LeftMenuItem);\r
1974         editMenu.add(remove2RightMenuItem);\r
1975         editMenu.add(removeGappedColumnMenuItem);\r
1976         editMenu.add(removeAllGapsMenuItem);\r
1977         editMenu.add(removeRedundancyMenuItem);\r
1978         searchMenu.add(findMenuItem);\r
1979         viewMenu.add(font);\r
1980         viewMenu.addSeparator();\r
1981     viewMenu.add(seqLimits);\r
1982         viewMenu.addSeparator();\r
1983     viewMenu.add(wrapMenuItem);\r
1984         viewMenu.add(scaleAbove);\r
1985         viewMenu.add(scaleLeft);\r
1986         viewMenu.add(scaleRight);\r
1987         viewMenu.addSeparator();\r
1988     viewMenu.add(viewBoxesMenuItem);\r
1989         viewMenu.add(viewTextMenuItem);\r
1990         viewMenu.add(colourTextMenuItem);\r
1991         viewMenu.add(renderGapsMenuItem);\r
1992         viewMenu.add(annotationPanelMenuItem);\r
1993     viewMenu.addSeparator();\r
1994         viewMenu.add(sequenceFeatures);\r
1995         viewMenu.add(featureSettings);\r
1996     viewMenu.addSeparator();\r
1997         viewMenu.add(overviewMenuItem);\r
1998         colourMenu.add(applyToAllGroups);\r
1999         colourMenu.addSeparator();\r
2000         colourMenu.add(noColourmenuItem);\r
2001         colourMenu.add(clustalColour);\r
2002         colourMenu.add(BLOSUM62Colour);\r
2003         colourMenu.add(PIDColour);\r
2004         colourMenu.add(zappoColour);\r
2005         colourMenu.add(taylorColour);\r
2006         colourMenu.add(hydrophobicityColour);\r
2007         colourMenu.add(helixColour);\r
2008         colourMenu.add(strandColour);\r
2009         colourMenu.add(turnColour);\r
2010         colourMenu.add(buriedColour);\r
2011         colourMenu.add(nucleotideColour);\r
2012         colourMenu.add(userDefinedColour);\r
2013         colourMenu.addSeparator();\r
2014         colourMenu.add(conservationMenuItem);\r
2015         colourMenu.add(modifyConservation);\r
2016         colourMenu.add(abovePIDThreshold);\r
2017         colourMenu.add(modifyPID);\r
2018     colourMenu.add(annotationColour);\r
2019     calculateMenu.add(sort);\r
2020         calculateMenu.add(calculate);\r
2021         calculateMenu.addSeparator();\r
2022         calculateMenu.add(pairwiseAlignmentMenuItem);\r
2023         calculateMenu.add(PCAMenuItem);\r
2024         this.add(statusBar, BorderLayout.SOUTH);\r
2025         pasteMenu.add(pasteNew);\r
2026         pasteMenu.add(pasteThis);\r
2027         sort.add(sortIDMenuItem);\r
2028         sort.add(sortByTreeMenu);\r
2029         sort.add(sortGroupMenuItem);\r
2030         sort.add(sortPairwiseMenuItem);\r
2031         calculate.add(averageDistanceTreeMenuItem);\r
2032         calculate.add(neighbourTreeMenuItem);\r
2033         calculate.add(avDistanceTreeBlosumMenuItem);\r
2034         calculate.add(njTreeBlosumMenuItem);\r
2035         helpMenu.add(documentation);\r
2036         helpMenu.add(about);\r
2037   }\r
2038 \r
2039   public void setEmbedded()\r
2040   {\r
2041 \r
2042     embeddedMenu = new Panel();\r
2043     embeddedEdit = new Label();\r
2044     embeddedSearch = new Label();\r
2045     embeddedView = new Label();\r
2046     embeddedColour = new Label();\r
2047     embeddedFile = new Label();\r
2048     embeddedHelp = new Label();\r
2049     embeddedCalculate = new Label();\r
2050     flowLayout1 = new FlowLayout();\r
2051     embeddedMenu.setBackground(Color.lightGray);\r
2052     embeddedMenu.setLayout(flowLayout1);\r
2053     embeddedEdit.setText("Edit");\r
2054     embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2055     embeddedSearch.setText("Search");\r
2056     embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2057     embeddedView.setText("View");\r
2058     embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2059     embeddedColour.setText("Colour");\r
2060     embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2061     embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2062     embeddedFile.setText("File");\r
2063     embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2064     embeddedHelp.setText("Help");\r
2065     embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
2066     embeddedCalculate.setText("Calculate");\r
2067     embeddedMenu.add(embeddedFile);\r
2068     embeddedMenu.add(embeddedEdit);\r
2069     embeddedMenu.add(embeddedSearch);\r
2070     embeddedMenu.add(embeddedView);\r
2071     embeddedMenu.add(embeddedColour);\r
2072     embeddedMenu.add(embeddedCalculate);\r
2073     embeddedMenu.add(embeddedHelp);\r
2074     flowLayout1.setAlignment(FlowLayout.LEFT);\r
2075     flowLayout1.setHgap(2);\r
2076     flowLayout1.setVgap(0);\r
2077     embeddedFile.addMouseListener(this);\r
2078     embeddedEdit.addMouseListener(this);\r
2079     embeddedSearch.addMouseListener(this);\r
2080     embeddedView.addMouseListener(this);\r
2081     embeddedColour.addMouseListener(this);\r
2082     embeddedCalculate.addMouseListener(this);\r
2083     embeddedHelp.addMouseListener(this);\r
2084 \r
2085    // setVisible(false);\r
2086     fileMenu.remove(closeMenuItem);\r
2087     fileMenu.remove(2); // Seperator\r
2088 \r
2089     applet.setLayout(new BorderLayout());\r
2090     applet.add(embeddedMenu, BorderLayout.NORTH);\r
2091     applet.add(statusBar, BorderLayout.SOUTH);\r
2092    // applet.validate();\r
2093 \r
2094     alignPanel.setSize(applet.size().width, applet.size().height\r
2095                        - embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
2096 \r
2097      applet.add(alignPanel, BorderLayout.CENTER);\r
2098      applet.validate();\r
2099 \r
2100   }\r
2101 \r
2102 \r
2103 \r
2104   PopupMenu filePopup, editPopup, searchPopup,\r
2105       viewPopup, colourPopup, calculatePopup, helpPopup;\r
2106   MenuItem featureSettings = new MenuItem();\r
2107   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
2108   MenuItem annotationColour = new MenuItem();\r
2109 \r
2110   public void mousePressed(MouseEvent evt)\r
2111   {\r
2112     PopupMenu popup = null;\r
2113     Label source = (Label)evt.getSource();\r
2114     if(source==embeddedFile)\r
2115     {\r
2116       popup = filePopup = genPopupMenu(filePopup, fileMenu);\r
2117     }\r
2118     else if(source==embeddedEdit)\r
2119     {\r
2120       popup = editPopup = genPopupMenu(editPopup, editMenu);\r
2121     }\r
2122     else if(source==embeddedSearch)\r
2123     {\r
2124       popup = searchPopup = genPopupMenu(searchPopup, searchMenu);\r
2125     }\r
2126     else if(source==embeddedView)\r
2127     {\r
2128       popup = viewPopup = genPopupMenu(viewPopup, viewMenu);\r
2129     }\r
2130     else if(source==embeddedColour)\r
2131     {\r
2132       popup = colourPopup = genPopupMenu(colourPopup, colourMenu);\r
2133     }\r
2134     else if(source==embeddedCalculate)\r
2135     {\r
2136       popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);\r
2137     }\r
2138     else if(source==embeddedHelp)\r
2139     {\r
2140       popup = helpPopup = genPopupMenu(helpPopup, helpMenu);\r
2141     }\r
2142 \r
2143     embeddedMenu.add(popup);\r
2144     popup.show(embeddedMenu,\r
2145                source.getBounds().x,\r
2146                source.getBounds().y + source.getBounds().getSize().height);\r
2147   }\r
2148 \r
2149   PopupMenu genPopupMenu(PopupMenu popup, Menu original)\r
2150   {\r
2151     if(popup!=null)\r
2152     {\r
2153       return popup;\r
2154     }\r
2155     popup = new PopupMenu();\r
2156     int m, mSize = original.getItemCount();\r
2157     for(m=0; m<mSize; m++)\r
2158     {\r
2159       popup.add(original.getItem(m));\r
2160       mSize--;\r
2161       m--;\r
2162     }\r
2163 \r
2164     return popup;\r
2165   }\r
2166   public void mouseClicked(MouseEvent evt)\r
2167   {}\r
2168   public void mouseReleased(MouseEvent evt)\r
2169   {}\r
2170   public void mouseEntered(MouseEvent evt)\r
2171   {}\r
2172   public void mouseExited(MouseEvent evt)\r
2173   {}\r
2174 \r
2175 }\r
2176 \r