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.jbappletgui.GAlignFrame;\r
  23 import jalview.schemes.*;\r
  24 import jalview.datamodel.*;\r
  25 import jalview.analysis.*;\r
  26 import jalview.io.*;\r
  27 import java.awt.*;\r
  28 import java.awt.event.*;\r
  29 import java.util.*;\r
  30 \r
  31 public class AlignFrame\r
  32     extends GAlignFrame\r
  33 {\r
  34   final AlignmentPanel alignPanel;\r
  35   final AlignViewport viewport;\r
  36   public static final int NEW_WINDOW_WIDTH = 700;\r
  37   public static final int NEW_WINDOW_HEIGHT = 500;\r
  38   jalview.bin.JalviewLite applet;\r
  39 \r
  40   public AlignFrame(AlignmentI al)\r
  41   {\r
  42     this.applet = null;\r
  43     viewport = new AlignViewport(al, null);\r
  44     alignPanel = new AlignmentPanel(this, viewport);\r
  45     add(alignPanel);\r
  46     alignPanel.validate();\r
  47   }\r
  48 \r
  49   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)\r
  50   {\r
  51     this.applet = applet;\r
  52     viewport = new AlignViewport(al, applet);\r
  53     alignPanel = new AlignmentPanel(this, viewport);\r
  54     add(alignPanel);\r
  55     alignPanel.validate();\r
  56 \r
  57     String treeFile = applet.getParameter("treeFile");\r
  58     TreePanel treepanel = null;\r
  59     if (treeFile != null)\r
  60     {\r
  61       try\r
  62       {\r
  63         treeFile = treeFile;\r
  64         jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
  65             getCodeBase() + treeFile, "URL");\r
  66         fin.parse();\r
  67 \r
  68         if (fin.getTree() != null)\r
  69         {\r
  70           TreePanel tp = null;\r
  71           tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
  72                              fin, "FromFile", applet.getCodeBase() + treeFile);\r
  73           jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
  74           addTreeMenuItem(tp, treeFile);\r
  75         }\r
  76       }\r
  77       catch (Exception ex)\r
  78       {\r
  79         ex.printStackTrace();\r
  80       }\r
  81     }\r
  82 \r
  83 \r
  84       if( applet.getParameter("servletAllowed") !=null)\r
  85      {\r
  86        ServletGUI plug = new ServletGUI(this, fileMenu, calculateMenu);\r
  87      }\r
  88 \r
  89 \r
  90 \r
  91   }\r
  92 \r
  93   public void inputText_actionPerformed(ActionEvent e)\r
  94   {\r
  95     CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
  96     Frame frame = new Frame();\r
  97     frame.add(cap);\r
  98     jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
  99   }\r
 100 \r
 101   protected void outputText_actionPerformed(ActionEvent e)\r
 102   {\r
 103     CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
 104     Frame frame = new Frame();\r
 105     frame.add(cap);\r
 106     jalview.bin.JalviewLite.addFrame(frame,\r
 107                                      "Alignment output - " + e.getActionCommand(),\r
 108                                      600, 500);\r
 109     cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),\r
 110                                               viewport.getAlignment().\r
 111                                               getSequences()));\r
 112   }\r
 113 \r
 114   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 115   {\r
 116     dispose();\r
 117   }\r
 118 \r
 119   Stack historyList = new Stack();\r
 120   Stack redoList = new Stack();\r
 121 \r
 122   void updateEditMenuBar()\r
 123   {\r
 124     if (historyList.size() > 0)\r
 125     {\r
 126       undoMenuItem.setEnabled(true);\r
 127       HistoryItem hi = (HistoryItem) historyList.peek();\r
 128       undoMenuItem.setLabel("Undo " + hi.getDescription());\r
 129     }\r
 130     else\r
 131     {\r
 132       undoMenuItem.setEnabled(false);\r
 133       undoMenuItem.setLabel("Undo");\r
 134     }\r
 135 \r
 136     if (redoList.size() > 0)\r
 137     {\r
 138       redoMenuItem.setEnabled(true);\r
 139       HistoryItem hi = (HistoryItem) redoList.peek();\r
 140       redoMenuItem.setLabel("Redo " + hi.getDescription());\r
 141     }\r
 142     else\r
 143     {\r
 144       redoMenuItem.setEnabled(false);\r
 145       redoMenuItem.setLabel("Redo");\r
 146     }\r
 147   }\r
 148 \r
 149   public void addHistoryItem(HistoryItem hi)\r
 150   {\r
 151     historyList.push(hi);\r
 152     updateEditMenuBar();\r
 153   }\r
 154 \r
 155   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 156   {\r
 157     HistoryItem hi = (HistoryItem) historyList.pop();\r
 158     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
 159                                   HistoryItem.HIDE));\r
 160     restoreHistoryItem(hi);\r
 161   }\r
 162 \r
 163   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 164   {\r
 165     HistoryItem hi = (HistoryItem) redoList.pop();\r
 166     restoreHistoryItem(hi);\r
 167     updateEditMenuBar();\r
 168     viewport.updateConsensus();\r
 169     alignPanel.repaint();\r
 170     alignPanel.repaint();\r
 171   }\r
 172 \r
 173   // used by undo and redo\r
 174   void restoreHistoryItem(HistoryItem hi)\r
 175   {\r
 176     if (hi.getType() == HistoryItem.SORT)\r
 177     {\r
 178       for (int i = 0; i < hi.getSequences().size(); i++)\r
 179       {\r
 180         viewport.alignment.getSequences().setElementAt(hi.getSequences().\r
 181             elementAt(i), i);\r
 182       }\r
 183     }\r
 184     else\r
 185     {\r
 186       for (int i = 0; i < hi.getSequences().size(); i++)\r
 187       {\r
 188         SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
 189         if (restore.getLength() == 0)\r
 190         {\r
 191           // log.System.out.println(hi.getHidden().elementAt(i));\r
 192           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 193           viewport.alignment.getSequences().insertElementAt(\r
 194               restore,\r
 195               hi.getAlignIndex(i));\r
 196         }\r
 197         else\r
 198         {\r
 199           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 200         }\r
 201       }\r
 202       if (hi.getType() == HistoryItem.PASTE)\r
 203       {\r
 204         for (int i = viewport.alignment.getHeight() - 1;\r
 205              i > hi.getSequences().size() - 1; i--)\r
 206         {\r
 207           viewport.alignment.deleteSequence(i);\r
 208         }\r
 209       }\r
 210     }\r
 211 \r
 212     updateEditMenuBar();\r
 213 \r
 214     viewport.updateConsensus();\r
 215     viewport.updateConservation();\r
 216     alignPanel.repaint();\r
 217   }\r
 218 \r
 219   public void moveSelectedSequences(boolean up)\r
 220   {\r
 221     SequenceGroup sg = viewport.getSelectionGroup();\r
 222     if (sg == null)\r
 223     {\r
 224       return;\r
 225     }\r
 226 \r
 227     if (up)\r
 228     {\r
 229       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 230       {\r
 231         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 232         if (!sg.sequences.contains(seq))\r
 233         {\r
 234           continue;\r
 235         }\r
 236 \r
 237         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 238         if (sg.sequences.contains(temp))\r
 239         {\r
 240           continue;\r
 241         }\r
 242 \r
 243         viewport.alignment.getSequences().setElementAt(temp, i);\r
 244         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 245       }\r
 246     }\r
 247     else\r
 248     {\r
 249       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 250       {\r
 251         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 252         if (!sg.sequences.contains(seq))\r
 253         {\r
 254           continue;\r
 255         }\r
 256 \r
 257         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 258         if (sg.sequences.contains(temp))\r
 259         {\r
 260           continue;\r
 261         }\r
 262 \r
 263         viewport.alignment.getSequences().setElementAt(temp, i);\r
 264         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 265       }\r
 266     }\r
 267 \r
 268     alignPanel.repaint();\r
 269   }\r
 270 \r
 271   StringBuffer copiedSequences;\r
 272   protected void copy_actionPerformed(ActionEvent e)\r
 273   {\r
 274     if (viewport.getSelectionGroup() == null)\r
 275     {\r
 276       return;\r
 277     }\r
 278 \r
 279     SequenceGroup sg = viewport.getSelectionGroup();\r
 280     copiedSequences = new StringBuffer();\r
 281     Hashtable orderedSeqs = new Hashtable();\r
 282     for (int i = 0; i < sg.getSize(); i++)\r
 283     {\r
 284       SequenceI seq = sg.getSequenceAt(i);\r
 285       int index = viewport.alignment.findIndex(seq);\r
 286       orderedSeqs.put(index + "", seq);\r
 287     }\r
 288 \r
 289     int index = 0, startRes, endRes;\r
 290     char ch;\r
 291 \r
 292     for (int i = 0; i < sg.getSize(); i++)\r
 293     {\r
 294         SequenceI seq = null;\r
 295 \r
 296         while (seq == null)\r
 297         {\r
 298             if (orderedSeqs.containsKey(index + ""))\r
 299             {\r
 300                 seq = (SequenceI) orderedSeqs.get(index + "");\r
 301                 index++;\r
 302 \r
 303                 break;\r
 304             }\r
 305             else\r
 306             {\r
 307                 index++;\r
 308             }\r
 309         }\r
 310 \r
 311         //FIND START RES\r
 312         //Returns residue following index if gap\r
 313         startRes = seq.findPosition(sg.getStartRes());\r
 314 \r
 315         //FIND END RES\r
 316         //Need to find the residue preceeding index if gap\r
 317         endRes = 0;\r
 318 \r
 319         for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
 320         {\r
 321           ch = seq.getCharAt(j);\r
 322           if (!jalview.util.Comparison.isGap( (ch)))\r
 323           {\r
 324             endRes++;\r
 325           }\r
 326         }\r
 327 \r
 328         if(endRes>0)\r
 329         {\r
 330           endRes += seq.getStart() -1;\r
 331         }\r
 332 \r
 333         copiedSequences.append(seq.getName() + "\t" +\r
 334             startRes + "\t" +\r
 335             endRes + "\t" +\r
 336             seq.getSequence(sg.getStartRes(),\r
 337                 sg.getEndRes() + 1) + "\n");\r
 338     }\r
 339 \r
 340   }\r
 341 \r
 342   protected void pasteNew_actionPerformed(ActionEvent e)\r
 343   {\r
 344     paste(true);\r
 345   }\r
 346 \r
 347   protected void pasteThis_actionPerformed(ActionEvent e)\r
 348   {\r
 349     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
 350                                    HistoryItem.PASTE));\r
 351     paste(false);\r
 352   }\r
 353 \r
 354   void paste(boolean newAlignment)\r
 355   {\r
 356     try\r
 357     {\r
 358       if (copiedSequences == null)\r
 359       {\r
 360         return;\r
 361       }\r
 362 \r
 363       StringTokenizer st = new StringTokenizer(copiedSequences.toString());\r
 364       Vector seqs = new Vector();\r
 365       while (st.hasMoreElements())\r
 366       {\r
 367         String name = st.nextToken();\r
 368         int start = Integer.parseInt(st.nextToken());\r
 369         int end = Integer.parseInt(st.nextToken());\r
 370         Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
 371 \r
 372         if (!newAlignment)\r
 373         {\r
 374           viewport.alignment.addSequence(sequence);\r
 375         }\r
 376         else\r
 377         {\r
 378           seqs.addElement(sequence);\r
 379         }\r
 380       }\r
 381 \r
 382       if (newAlignment)\r
 383       {\r
 384         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 385         for (int i = 0; i < seqs.size(); i++)\r
 386         {\r
 387           newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
 388         }\r
 389 \r
 390         AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);\r
 391         String newtitle = new String("Copied sequences");\r
 392         if (getTitle().startsWith("Copied sequences"))\r
 393         {\r
 394           newtitle = getTitle();\r
 395         }\r
 396         else\r
 397         {\r
 398           newtitle = newtitle.concat("- from " + getTitle());\r
 399         }\r
 400         jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
 401                                          NEW_WINDOW_HEIGHT);\r
 402       }\r
 403       else\r
 404       {\r
 405         viewport.setEndSeq(viewport.alignment.getHeight());\r
 406         viewport.alignment.getWidth();\r
 407         viewport.updateConservation();\r
 408         viewport.updateConsensus();\r
 409         alignPanel.repaint();\r
 410       }\r
 411 \r
 412     }\r
 413     catch (Exception ex)\r
 414     {} // could be anything being pasted in here\r
 415 \r
 416   }\r
 417 \r
 418   protected void cut_actionPerformed(ActionEvent e)\r
 419   {\r
 420     copy_actionPerformed(null);\r
 421     delete_actionPerformed(null);\r
 422   }\r
 423 \r
 424   protected void delete_actionPerformed(ActionEvent e)\r
 425   {\r
 426     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
 427                                    HistoryItem.HIDE));\r
 428     if (viewport.getSelectionGroup() == null)\r
 429     {\r
 430       return;\r
 431     }\r
 432 \r
 433 \r
 434     SequenceGroup sg = viewport.getSelectionGroup();\r
 435     boolean allSequences = false;\r
 436     if(sg.sequences.size()==viewport.alignment.getHeight())\r
 437           allSequences = true;\r
 438 \r
 439     for (int i = 0; i < sg.sequences.size(); i++)\r
 440     {\r
 441       SequenceI seq = sg.getSequenceAt(i);\r
 442       int index = viewport.getAlignment().findIndex(seq);\r
 443       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 444 \r
 445       // If the cut affects all sequences, remove highlighted columns\r
 446       if (allSequences)\r
 447       {\r
 448         viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
 449                                                      sg.getEndRes() + 1);\r
 450       }\r
 451 \r
 452 \r
 453       if (seq.getSequence().length() < 1)\r
 454       {\r
 455         viewport.getAlignment().deleteSequence(seq);\r
 456       }\r
 457       else\r
 458       {\r
 459         viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 460       }\r
 461     }\r
 462 \r
 463     viewport.setSelectionGroup(null);\r
 464     viewport.alignment.deleteGroup(sg);\r
 465     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
 466     if (viewport.getAlignment().getHeight() < 1)\r
 467     {\r
 468       try\r
 469       {\r
 470         this.setVisible(false);\r
 471       }\r
 472       catch (Exception ex)\r
 473       {}\r
 474     }\r
 475     viewport.updateConservation();\r
 476     viewport.updateConsensus();\r
 477     alignPanel.repaint();\r
 478 \r
 479   }\r
 480 \r
 481   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 482   {\r
 483     viewport.alignment.deleteAllGroups();\r
 484     viewport.setSelectionGroup(null);\r
 485 \r
 486     alignPanel.repaint();\r
 487   }\r
 488 \r
 489   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 490   {\r
 491     SequenceGroup sg = new SequenceGroup();\r
 492     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 493     {\r
 494       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
 495     }\r
 496     sg.setEndRes(viewport.alignment.getWidth());\r
 497     viewport.setSelectionGroup(sg);\r
 498     alignPanel.repaint();\r
 499     PaintRefresher.Refresh(null);\r
 500   }\r
 501 \r
 502   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 503   {\r
 504     viewport.setSelectionGroup(null);\r
 505     viewport.getColumnSelection().clear();\r
 506     viewport.setSelectionGroup(null);\r
 507     PaintRefresher.Refresh(null);\r
 508   }\r
 509 \r
 510   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 511   {\r
 512     SequenceGroup sg = viewport.getSelectionGroup();\r
 513     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
 514     {\r
 515       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
 516     }\r
 517 \r
 518     PaintRefresher.Refresh(null);\r
 519   }\r
 520 \r
 521   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 522   {\r
 523     ColumnSelection colSel = viewport.getColumnSelection();\r
 524     if (colSel.size() > 0)\r
 525     {\r
 526       addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
 527                                      HistoryItem.HIDE));\r
 528       int min = colSel.getMin();\r
 529       viewport.getAlignment().trimLeft(min);\r
 530       colSel.compensateForEdit(0, min);\r
 531 \r
 532       if (viewport.getSelectionGroup() != null)\r
 533       {\r
 534         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 535       }\r
 536 \r
 537       Vector groups = viewport.alignment.getGroups();\r
 538       for (int i = 0; i < groups.size(); i++)\r
 539       {\r
 540         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 541         if (!sg.adjustForRemoveLeft(min))\r
 542         {\r
 543           viewport.alignment.deleteGroup(sg);\r
 544         }\r
 545       }\r
 546 \r
 547       alignPanel.repaint();\r
 548     }\r
 549   }\r
 550 \r
 551   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 552   {\r
 553     ColumnSelection colSel = viewport.getColumnSelection();\r
 554     if (colSel.size() > 0)\r
 555     {\r
 556       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
 557                                      HistoryItem.HIDE));\r
 558       int max = colSel.getMax();\r
 559       viewport.getAlignment().trimRight(max);\r
 560       if (viewport.getSelectionGroup() != null)\r
 561       {\r
 562         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 563       }\r
 564 \r
 565       Vector groups = viewport.alignment.getGroups();\r
 566       for (int i = 0; i < groups.size(); i++)\r
 567       {\r
 568         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 569         if (!sg.adjustForRemoveRight(max))\r
 570         {\r
 571           viewport.alignment.deleteGroup(sg);\r
 572         }\r
 573       }\r
 574 \r
 575       alignPanel.repaint();\r
 576     }\r
 577 \r
 578   }\r
 579 \r
 580   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 581   {\r
 582     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
 583                                    viewport.alignment,\r
 584                                    HistoryItem.HIDE));\r
 585     viewport.getAlignment().removeGaps();\r
 586     viewport.updateConservation();\r
 587     viewport.updateConsensus();\r
 588     alignPanel.repaint();\r
 589   }\r
 590 \r
 591   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 592   {\r
 593     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
 594                                    HistoryItem.HIDE));\r
 595 \r
 596     SequenceI current;\r
 597     int jSize;\r
 598 \r
 599     Vector seqs=null;\r
 600 \r
 601     int start=0, end = viewport.alignment.getWidth();\r
 602 \r
 603     if (viewport.getSelectionGroup() != null\r
 604         && viewport.getSelectionGroup().sequences != null\r
 605         && viewport.getSelectionGroup().sequences.size()>0)\r
 606     {\r
 607       seqs = viewport.getSelectionGroup().sequences;\r
 608       start = viewport.getSelectionGroup().getStartRes();\r
 609       end = viewport.getSelectionGroup().getEndRes();\r
 610     }\r
 611     else\r
 612       seqs = viewport.alignment.getSequences();\r
 613 \r
 614     for (int i = 0; i <seqs.size(); i++)\r
 615     {\r
 616       current = (SequenceI)seqs.elementAt(i);\r
 617       jSize = current.getLength();\r
 618 \r
 619       int j = start;\r
 620       do\r
 621       {\r
 622         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 623         {\r
 624           current.deleteCharAt(j);\r
 625           j--;\r
 626           jSize--;\r
 627         }\r
 628         j++;\r
 629       }\r
 630       while(j < end && j < jSize) ;\r
 631     }\r
 632 \r
 633     viewport.updateConservation();\r
 634     viewport.updateConsensus();\r
 635     alignPanel.repaint();\r
 636   }\r
 637 \r
 638 \r
 639   public void findMenuItem_actionPerformed(ActionEvent e)\r
 640   {\r
 641     Finder finder = new Finder(alignPanel);\r
 642   }\r
 643 \r
 644   public void font_actionPerformed(ActionEvent e)\r
 645   {\r
 646     Frame frame = new Frame();\r
 647     FontChooser fc = new FontChooser(alignPanel, frame);\r
 648     frame.add(fc);\r
 649     jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);\r
 650 \r
 651   }\r
 652 \r
 653   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 654   {\r
 655     viewport.setShowFullId(fullSeqId.getState());\r
 656     alignPanel.fontChanged();\r
 657     alignPanel.repaint();\r
 658   }\r
 659 \r
 660   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 661   {\r
 662     viewport.setColourText(colourTextMenuItem.getState());\r
 663     alignPanel.repaint();\r
 664   }\r
 665 \r
 666   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 667   {\r
 668     viewport.setWrapAlignment(wrapMenuItem.getState());\r
 669     alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
 670     scaleAbove.setEnabled(wrapMenuItem.getState());\r
 671     scaleLeft.setEnabled(wrapMenuItem.getState());\r
 672     scaleRight.setEnabled(wrapMenuItem.getState());\r
 673     alignPanel.repaint();\r
 674   }\r
 675 \r
 676   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 677   {\r
 678     viewport.setScaleAboveWrapped(scaleAbove.getState());\r
 679     alignPanel.repaint();\r
 680   }\r
 681 \r
 682   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 683   {\r
 684     viewport.setScaleLeftWrapped(scaleLeft.getState());\r
 685     alignPanel.repaint();\r
 686   }\r
 687 \r
 688   protected void scaleRight_actionPerformed(ActionEvent e)\r
 689   {\r
 690     viewport.setScaleRightWrapped(scaleRight.getState());\r
 691     alignPanel.repaint();\r
 692   }\r
 693 \r
 694   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 695   {\r
 696     viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
 697     alignPanel.repaint();\r
 698   }\r
 699 \r
 700   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 701   {\r
 702     viewport.setShowText(viewTextMenuItem.getState());\r
 703     alignPanel.repaint();\r
 704   }\r
 705 \r
 706   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 707   {\r
 708     viewport.setRenderGaps(renderGapsMenuItem.getState());\r
 709     alignPanel.repaint();\r
 710   }\r
 711 \r
 712   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 713   {\r
 714     if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
 715     {\r
 716       annotationPanelMenuItem.setState(false);\r
 717       return;\r
 718     }\r
 719     viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
 720     alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
 721   }\r
 722 \r
 723   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 724   {\r
 725     if (alignPanel.overviewPanel != null)\r
 726     {\r
 727       return;\r
 728     }\r
 729 \r
 730     Frame frame = new Frame();\r
 731     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 732     frame.add(overview);\r
 733     // +50 must allow for applet frame window\r
 734     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
 735                                      overview.preferredSize().width,\r
 736                                      overview.preferredSize().height + 50);\r
 737 \r
 738     frame.pack();\r
 739     frame.addWindowListener(new WindowAdapter()\r
 740     {\r
 741       public void windowClosing(WindowEvent e)\r
 742       {\r
 743         alignPanel.setOverviewPanel(null);\r
 744       };\r
 745     });\r
 746 \r
 747     alignPanel.setOverviewPanel(overview);\r
 748 \r
 749   }\r
 750 \r
 751   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 752   {\r
 753     changeColour(null);\r
 754   }\r
 755 \r
 756   public void clustalColour_actionPerformed(ActionEvent e)\r
 757   {\r
 758     abovePIDThreshold.setState(false);\r
 759     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
 760                                           viewport.alignment.getWidth()));\r
 761   }\r
 762 \r
 763   public void zappoColour_actionPerformed(ActionEvent e)\r
 764   {\r
 765     changeColour(new ZappoColourScheme());\r
 766   }\r
 767 \r
 768   public void taylorColour_actionPerformed(ActionEvent e)\r
 769   {\r
 770     changeColour(new TaylorColourScheme());\r
 771   }\r
 772 \r
 773   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 774   {\r
 775     changeColour(new HydrophobicColourScheme());\r
 776   }\r
 777 \r
 778   public void helixColour_actionPerformed(ActionEvent e)\r
 779   {\r
 780     changeColour(new HelixColourScheme());\r
 781   }\r
 782 \r
 783   public void strandColour_actionPerformed(ActionEvent e)\r
 784   {\r
 785     changeColour(new StrandColourScheme());\r
 786   }\r
 787 \r
 788   public void turnColour_actionPerformed(ActionEvent e)\r
 789   {\r
 790     changeColour(new TurnColourScheme());\r
 791   }\r
 792 \r
 793   public void buriedColour_actionPerformed(ActionEvent e)\r
 794   {\r
 795     changeColour(new BuriedColourScheme());\r
 796   }\r
 797 \r
 798   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 799   {\r
 800     changeColour(new NucleotideColourScheme());\r
 801   }\r
 802 \r
 803   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 804   {\r
 805     viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
 806   }\r
 807 \r
 808   void changeColour(ColourSchemeI cs)\r
 809   {\r
 810     int threshold = 0;\r
 811 \r
 812     if (viewport.getAbovePIDThreshold())\r
 813     {\r
 814       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
 815 \r
 816       if (cs instanceof ResidueColourScheme)\r
 817       {\r
 818         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 819       }\r
 820 \r
 821       viewport.setGlobalColourScheme(cs);\r
 822     }\r
 823     else if (cs instanceof ResidueColourScheme)\r
 824     {\r
 825       ( (ResidueColourScheme) cs).setThreshold(0);\r
 826     }\r
 827 \r
 828     if (viewport.getConservationSelected())\r
 829     {\r
 830       ConservationColourScheme ccs = null;\r
 831 \r
 832       Alignment al = (Alignment) viewport.alignment;\r
 833       Conservation c = new Conservation("All",\r
 834                                         ResidueProperties.propHash, 3,\r
 835                                         al.getSequences(), 0,\r
 836                                         al.getWidth() - 1);\r
 837 \r
 838       c.calculate();\r
 839       c.verdict(false, viewport.ConsPercGaps);\r
 840 \r
 841       ccs = new ConservationColourScheme(c, cs);\r
 842 \r
 843       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 844       ccs.setConsensus(viewport.vconsensus);\r
 845       viewport.setGlobalColourScheme(ccs);\r
 846 \r
 847       SliderPanel.setConservationSlider(alignPanel, ccs, "Background");\r
 848 \r
 849     }\r
 850     else\r
 851     {\r
 852       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 853       if (cs != null)\r
 854       {\r
 855         cs.setConsensus(viewport.vconsensus);\r
 856       }\r
 857       viewport.setGlobalColourScheme(cs);\r
 858     }\r
 859 \r
 860     if (viewport.getColourAppliesToAllGroups())\r
 861     {\r
 862       Vector groups = viewport.alignment.getGroups();\r
 863       for (int i = 0; i < groups.size(); i++)\r
 864       {\r
 865         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 866 \r
 867         if(cs==null)\r
 868         {\r
 869           sg.cs = null;\r
 870           continue;\r
 871         }\r
 872         if (cs instanceof ClustalxColourScheme)\r
 873         {\r
 874           ClustalxColourScheme cxs = (ClustalxColourScheme) cs;\r
 875           cxs.resetClustalX(viewport.alignment.getSequences(), viewport.alignment.getWidth());\r
 876           sg.cs = cxs;\r
 877         }\r
 878         else\r
 879         {\r
 880           try\r
 881           {\r
 882             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
 883           }\r
 884           catch (Exception ex)\r
 885           {\r
 886             ex.printStackTrace();\r
 887             sg.cs = cs;\r
 888           }\r
 889         }\r
 890 \r
 891         if (viewport.getAbovePIDThreshold())\r
 892         {\r
 893           if (sg.cs instanceof ResidueColourScheme)\r
 894           {\r
 895             ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
 896           }\r
 897 \r
 898           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 899         }\r
 900 \r
 901         if (viewport.getConservationSelected())\r
 902         {\r
 903           Conservation c = new Conservation("Group",\r
 904                                             ResidueProperties.propHash, 3,\r
 905                                             sg.sequences, 0,\r
 906                                             viewport.alignment.getWidth() - 1);\r
 907           c.calculate();\r
 908           c.verdict(false, viewport.ConsPercGaps);\r
 909           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
 910 \r
 911           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 912           ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 913           sg.cs = ccs;\r
 914         }\r
 915         else\r
 916         {\r
 917           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 918           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
 919         }\r
 920 \r
 921       }\r
 922     }\r
 923 \r
 924     if (alignPanel.getOverviewPanel() != null)\r
 925     {\r
 926       alignPanel.getOverviewPanel().updateOverviewImage();\r
 927     }\r
 928 \r
 929     alignPanel.repaint();\r
 930   }\r
 931 \r
 932   protected void modifyPID_actionPerformed(ActionEvent e)\r
 933   {\r
 934     if (viewport.getAbovePIDThreshold())\r
 935     {\r
 936       SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
 937                                      "Background");\r
 938       SliderPanel.showPIDSlider();\r
 939     }\r
 940   }\r
 941 \r
 942   protected void modifyConservation_actionPerformed(ActionEvent e)\r
 943   {\r
 944     if (viewport.getConservationSelected())\r
 945     {\r
 946       SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
 947                                         "Background");\r
 948       SliderPanel.showConservationSlider();\r
 949     }\r
 950   }\r
 951 \r
 952   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
 953   {\r
 954     viewport.setConservationSelected(conservationMenuItem.getState());\r
 955 \r
 956     viewport.setAbovePIDThreshold(false);\r
 957     abovePIDThreshold.setState(false);\r
 958 \r
 959     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 960     if (cs instanceof ConservationColourScheme)\r
 961     {\r
 962       changeColour( ( (ConservationColourScheme) cs).cs);\r
 963     }\r
 964     else\r
 965     {\r
 966       changeColour(cs);\r
 967     }\r
 968 \r
 969     modifyConservation_actionPerformed(null);\r
 970   }\r
 971 \r
 972   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
 973   {\r
 974     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
 975 \r
 976     conservationMenuItem.setState(false);\r
 977     viewport.setConservationSelected(false);\r
 978 \r
 979     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
 980 \r
 981     if (cs instanceof ConservationColourScheme)\r
 982     {\r
 983       changeColour( ( (ConservationColourScheme) cs).cs);\r
 984     }\r
 985     else\r
 986     {\r
 987       changeColour(cs);\r
 988     }\r
 989 \r
 990     modifyPID_actionPerformed(null);\r
 991   }\r
 992 \r
 993   public void userDefinedColour_actionPerformed(ActionEvent e)\r
 994   {\r
 995     UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);\r
 996   }\r
 997 \r
 998   public void PIDColour_actionPerformed(ActionEvent e)\r
 999   {\r
1000     changeColour(new PIDColourScheme());\r
1001   }\r
1002 \r
1003   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1004   {\r
1005     changeColour(new Blosum62ColourScheme());\r
1006   }\r
1007 \r
1008   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1009   {\r
1010     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1011                                    HistoryItem.SORT));\r
1012     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1013                               viewport.getAlignment().getSequenceAt(0));\r
1014     alignPanel.repaint();\r
1015   }\r
1016 \r
1017   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1018   {\r
1019     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1020                                    HistoryItem.SORT));\r
1021     AlignmentSorter.sortByID(viewport.getAlignment());\r
1022     alignPanel.repaint();\r
1023   }\r
1024 \r
1025   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1026   {\r
1027     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1028                                    HistoryItem.SORT));\r
1029     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1030     alignPanel.repaint();\r
1031 \r
1032   }\r
1033 \r
1034   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1035   {\r
1036     RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
1037     Frame frame = new Frame();\r
1038     frame.add(sp);\r
1039     jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
1040                                      400, 120);\r
1041 \r
1042   }\r
1043 \r
1044   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1045   {\r
1046     if (viewport.getSelectionGroup().getSize() > 1)\r
1047     {\r
1048       Frame frame = new Frame();\r
1049       frame.add(new PairwiseAlignPanel(viewport));\r
1050       jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
1051     }\r
1052   }\r
1053 \r
1054   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
1055   {\r
1056 \r
1057     if ( (viewport.getSelectionGroup() != null &&\r
1058           viewport.getSelectionGroup().getSize() < 4 &&\r
1059           viewport.getSelectionGroup().getSize() > 0)\r
1060         || viewport.getAlignment().getHeight() < 4)\r
1061     {\r
1062       return;\r
1063     }\r
1064 \r
1065     try\r
1066     {\r
1067       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
1068       Frame frame = new Frame();\r
1069       frame.add(pcaPanel);\r
1070       jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",\r
1071                                        400, 400);\r
1072     }\r
1073     catch (java.lang.OutOfMemoryError ex)\r
1074     {\r
1075     }\r
1076 \r
1077   }\r
1078 \r
1079   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1080   {\r
1081     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1082   }\r
1083 \r
1084   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1085   {\r
1086     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1087   }\r
1088 \r
1089   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1090   {\r
1091     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1092   }\r
1093 \r
1094   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1095   {\r
1096     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
1097   }\r
1098 \r
1099   void NewTreePanel(String type, String pwType, String title)\r
1100   {\r
1101     //are the sequences aligned?\r
1102     if (!viewport.alignment.isAligned())\r
1103     {\r
1104       SequenceI current;\r
1105       int Width = viewport.getAlignment().getWidth();\r
1106 \r
1107       for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
1108            i++)\r
1109       {\r
1110         current = viewport.getAlignment().getSequenceAt(i);\r
1111 \r
1112         if (current.getLength() < Width)\r
1113         {\r
1114           current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
1115         }\r
1116       }\r
1117       alignPanel.repaint();\r
1118 \r
1119     }\r
1120 \r
1121     final TreePanel tp;\r
1122     if (viewport.getSelectionGroup() != null &&\r
1123         viewport.getSelectionGroup().getSize() > 3)\r
1124     {\r
1125       tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
1126                          pwType,\r
1127                          0, viewport.alignment.getWidth());\r
1128     }\r
1129     else\r
1130     {\r
1131       tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
1132                          type, pwType, 0, viewport.alignment.getWidth());\r
1133     }\r
1134 \r
1135     addTreeMenuItem(tp, title);\r
1136 \r
1137     jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
1138   }\r
1139 \r
1140   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1141   {\r
1142     final MenuItem item = new MenuItem(title);\r
1143     sortByTreeMenu.add(item);\r
1144     item.addActionListener(new java.awt.event.ActionListener()\r
1145     {\r
1146       public void actionPerformed(ActionEvent e)\r
1147       {\r
1148         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1149                                        HistoryItem.SORT));\r
1150         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
1151         alignPanel.repaint();\r
1152       }\r
1153     });\r
1154 \r
1155     treePanel.addWindowListener(new WindowAdapter()\r
1156     {\r
1157       public void windowClosing(WindowEvent e)\r
1158       {\r
1159         sortByTreeMenu.remove(item);\r
1160       };\r
1161     });\r
1162   }\r
1163 \r
1164   protected void documentation_actionPerformed(ActionEvent e)\r
1165   {\r
1166     jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");\r
1167   }\r
1168 \r
1169   protected void about_actionPerformed(ActionEvent e)\r
1170   {\r
1171     class AboutPanel\r
1172         extends Canvas\r
1173     {\r
1174       public void paint(Graphics g)\r
1175       {\r
1176         g.setColor(Color.white);\r
1177         g.fillRect(0, 0, getSize().width, getSize().height);\r
1178         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1179         FontMetrics fm = g.getFontMetrics();\r
1180         int fh = fm.getHeight();\r
1181         int y = 5, x = 7;\r
1182         g.setColor(Color.black);\r
1183         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
1184         g.drawString("JalView - Release 2.01", 200, y += fh);\r
1185         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
1186         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
1187                      x, y += fh * 2);\r
1188         g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
1189                      x, y += fh);\r
1190         g.drawString(\r
1191             "For any issues relating to Jalview, email help@jalview.org", x,\r
1192             y += fh);\r
1193         g.drawString("If  you use JalView, please cite:", x, y += fh + 8);\r
1194         g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
1195                      x, y += fh);\r
1196         g.drawString("Bioinformatics,  2004 12;426-7.", x, y += fh);\r
1197       }\r
1198     }\r
1199 \r
1200     Frame frame = new Frame();\r
1201     frame.add(new AboutPanel());\r
1202     jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
1203 \r
1204   }\r
1205 }\r