src/jalview/gui/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 package jalview.gui;\r
  20 \r
  21 import java.beans.*;\r
  22 import java.util.*;\r
  23 \r
  24 import java.awt.*;\r
  25 import java.awt.datatransfer.*;\r
  26 import java.awt.event.*;\r
  27 import java.awt.print.*;\r
  28 import javax.swing.*;\r
  29 import javax.swing.event.*;\r
  30 \r
  31 import jalview.analysis.*;\r
  32 import jalview.datamodel.*;\r
  33 import jalview.io.*;\r
  34 import jalview.jbgui.*;\r
  35 import jalview.schemes.*;\r
  36 import jalview.ws.*;\r
  37 \r
  38 public class AlignFrame\r
  39     extends GAlignFrame\r
  40 {\r
  41   public static final int NEW_WINDOW_WIDTH = 700;\r
  42   public static final int NEW_WINDOW_HEIGHT = 500;\r
  43   final AlignmentPanel alignPanel;\r
  44   final AlignViewport viewport;\r
  45   public String currentFileFormat = "Jalview";\r
  46   Stack historyList = new Stack();\r
  47   Stack redoList = new Stack();\r
  48   private int treeCount = 0;\r
  49 \r
  50   public AlignFrame(AlignmentI al)\r
  51   {\r
  52     viewport = new AlignViewport(al);\r
  53 \r
  54     alignPanel = new AlignmentPanel(this, viewport);\r
  55     alignPanel.annotationPanel.adjustPanelHeight();\r
  56     alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.\r
  57         annotationPanel.getPreferredSize());\r
  58     alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.\r
  59         getPreferredSize());\r
  60     alignPanel.setAnnotationVisible(viewport.getShowAnnotation());\r
  61 \r
  62     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
  63 \r
  64     addInternalFrameListener(new InternalFrameAdapter()\r
  65     {\r
  66       public void internalFrameActivated(InternalFrameEvent evt)\r
  67       {\r
  68         javax.swing.SwingUtilities.invokeLater(new Runnable()\r
  69         {\r
  70           public void run()\r
  71           {\r
  72             alignPanel.requestFocus();\r
  73           }\r
  74         });\r
  75       }\r
  76     });\r
  77   }\r
  78 \r
  79   public void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
  80   {\r
  81     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
  82         getProperty(\r
  83             "LAST_DIRECTORY"),\r
  84         new String[]\r
  85         {\r
  86         "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
  87         "jar"\r
  88     },\r
  89         new String[]\r
  90         {\r
  91         "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
  92     }, currentFileFormat);\r
  93 \r
  94     chooser.setAcceptAllFileFilterUsed(false);\r
  95     chooser.setFileView(new JalviewFileView());\r
  96     chooser.setDialogTitle("Save Alignment to file");\r
  97     chooser.setToolTipText("Save");\r
  98 \r
  99     int value = chooser.showSaveDialog(this);\r
 100 \r
 101     if (value == JalviewFileChooser.APPROVE_OPTION)\r
 102     {\r
 103       currentFileFormat = chooser.getSelectedFormat();\r
 104       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",\r
 105                                     currentFileFormat);\r
 106 \r
 107       if (currentFileFormat.equals("Jalview"))\r
 108       {\r
 109         String shortName = title;\r
 110 \r
 111         if (shortName.indexOf(java.io.File.separatorChar) > -1)\r
 112         {\r
 113           shortName = shortName.substring(shortName.lastIndexOf(\r
 114               java.io.File.separatorChar) + 1);\r
 115         }\r
 116 \r
 117         String choice = chooser.getSelectedFile().getPath();\r
 118         Jalview2XML.SaveState(this, choice, shortName);\r
 119 \r
 120         // USE Jalview2XML to save this file\r
 121         return;\r
 122       }\r
 123 \r
 124       String choice = chooser.getSelectedFile().getPath();\r
 125       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
 126 \r
 127       String output = FormatAdapter.formatSequences(currentFileFormat,\r
 128           viewport.getAlignment().getSequences());\r
 129 \r
 130       try\r
 131       {\r
 132         java.io.PrintWriter out = new java.io.PrintWriter(new java.io.\r
 133             FileWriter(\r
 134                 choice));\r
 135         out.println(output);\r
 136         out.close();\r
 137       }\r
 138       catch (Exception ex)\r
 139       {\r
 140       }\r
 141     }\r
 142   }\r
 143 \r
 144   protected void outputText_actionPerformed(ActionEvent e)\r
 145   {\r
 146     CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 147     Desktop.addInternalFrame(cap,\r
 148                              "Alignment output - " + e.getActionCommand(), 600,\r
 149                              500);\r
 150     cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),\r
 151                                               viewport.getAlignment().\r
 152                                               getSequences()));\r
 153   }\r
 154 \r
 155   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 156   {\r
 157     new HTMLOutput(viewport);\r
 158   }\r
 159 \r
 160   protected void createPNG_actionPerformed(ActionEvent e)\r
 161   {\r
 162     alignPanel.makePNG();\r
 163   }\r
 164 \r
 165   protected void epsFile_actionPerformed(ActionEvent e)\r
 166   {\r
 167     alignPanel.makeEPS();\r
 168   }\r
 169 \r
 170   public void printMenuItem_actionPerformed(ActionEvent e)\r
 171   {\r
 172     //Putting in a thread avoids Swing painting problems\r
 173     PrintThread thread = new PrintThread();\r
 174     thread.start();\r
 175   }\r
 176 \r
 177   public void closeMenuItem_actionPerformed(ActionEvent e)\r
 178   {\r
 179     try\r
 180     {\r
 181       this.setClosed(true);\r
 182     }\r
 183     catch (Exception ex)\r
 184     {\r
 185     }\r
 186   }\r
 187 \r
 188   void updateEditMenuBar()\r
 189   {\r
 190     if (historyList.size() > 0)\r
 191     {\r
 192       undoMenuItem.setEnabled(true);\r
 193 \r
 194       HistoryItem hi = (HistoryItem) historyList.peek();\r
 195       undoMenuItem.setText("Undo " + hi.getDescription());\r
 196     }\r
 197     else\r
 198     {\r
 199       undoMenuItem.setEnabled(false);\r
 200       undoMenuItem.setText("Undo");\r
 201     }\r
 202 \r
 203     if (redoList.size() > 0)\r
 204     {\r
 205       redoMenuItem.setEnabled(true);\r
 206 \r
 207       HistoryItem hi = (HistoryItem) redoList.peek();\r
 208       redoMenuItem.setText("Redo " + hi.getDescription());\r
 209     }\r
 210     else\r
 211     {\r
 212       redoMenuItem.setEnabled(false);\r
 213       redoMenuItem.setText("Redo");\r
 214     }\r
 215   }\r
 216 \r
 217   public void addHistoryItem(HistoryItem hi)\r
 218   {\r
 219     historyList.push(hi);\r
 220     updateEditMenuBar();\r
 221   }\r
 222 \r
 223   protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 224   {\r
 225     HistoryItem hi = (HistoryItem) historyList.pop();\r
 226     redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
 227                                   HistoryItem.HIDE));\r
 228     restoreHistoryItem(hi);\r
 229   }\r
 230 \r
 231   protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 232   {\r
 233     HistoryItem hi = (HistoryItem) redoList.pop();\r
 234     restoreHistoryItem(hi);\r
 235     updateEditMenuBar();\r
 236     viewport.updateConsensus();\r
 237     alignPanel.repaint();\r
 238     alignPanel.repaint();\r
 239   }\r
 240 \r
 241   // used by undo and redo\r
 242   void restoreHistoryItem(HistoryItem hi)\r
 243   {\r
 244     if (hi.getType() == HistoryItem.SORT)\r
 245     {\r
 246       for (int i = 0; i < hi.getSequences().size(); i++)\r
 247       {\r
 248         viewport.alignment.getSequences().setElementAt(hi.getSequences()\r
 249             .elementAt(i),\r
 250             i);\r
 251       }\r
 252     }\r
 253     else\r
 254     {\r
 255       for (int i = 0; i < hi.getSequences().size(); i++)\r
 256       {\r
 257         SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
 258 \r
 259         if (restore.getLength() == 0)\r
 260         {\r
 261           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 262           viewport.alignment.getSequences().insertElementAt(restore,\r
 263               hi.getAlignIndex(i));\r
 264         }\r
 265         else\r
 266         {\r
 267           restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 268         }\r
 269       }\r
 270 \r
 271       if (hi.getType() == HistoryItem.PASTE)\r
 272       {\r
 273         for (int i = viewport.alignment.getHeight() - 1;\r
 274              i > (hi.getSequences().size() - 1); i--)\r
 275         {\r
 276           viewport.alignment.deleteSequence(i);\r
 277         }\r
 278       }\r
 279     }\r
 280 \r
 281     updateEditMenuBar();\r
 282 \r
 283     viewport.updateConsensus();\r
 284     viewport.updateConservation();\r
 285     alignPanel.repaint();\r
 286     viewport.firePropertyChange("alignment", null,\r
 287                                 viewport.getAlignment().getSequences());\r
 288   }\r
 289 \r
 290   public void moveSelectedSequences(boolean up)\r
 291   {\r
 292     SequenceGroup sg = viewport.getSelectionGroup();\r
 293 \r
 294     if (sg == null)\r
 295     {\r
 296       return;\r
 297     }\r
 298 \r
 299     if (up)\r
 300     {\r
 301       for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 302       {\r
 303         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 304 \r
 305         if (!sg.sequences.contains(seq))\r
 306         {\r
 307           continue;\r
 308         }\r
 309 \r
 310         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 311 \r
 312         if (sg.sequences.contains(temp))\r
 313         {\r
 314           continue;\r
 315         }\r
 316 \r
 317         viewport.alignment.getSequences().setElementAt(temp, i);\r
 318         viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 319       }\r
 320     }\r
 321     else\r
 322     {\r
 323       for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 324       {\r
 325         SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 326 \r
 327         if (!sg.sequences.contains(seq))\r
 328         {\r
 329           continue;\r
 330         }\r
 331 \r
 332         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 333 \r
 334         if (sg.sequences.contains(temp))\r
 335         {\r
 336           continue;\r
 337         }\r
 338 \r
 339         viewport.alignment.getSequences().setElementAt(temp, i);\r
 340         viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 341       }\r
 342     }\r
 343 \r
 344     alignPanel.repaint();\r
 345   }\r
 346 \r
 347   protected void copy_actionPerformed(ActionEvent e)\r
 348   {\r
 349     if (viewport.getSelectionGroup() == null)\r
 350     {\r
 351       return;\r
 352     }\r
 353 \r
 354     SequenceGroup sg = viewport.getSelectionGroup();\r
 355 \r
 356     Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 357     StringBuffer buffer = new StringBuffer();\r
 358 \r
 359     Hashtable orderedSeqs = new Hashtable();\r
 360 \r
 361     for (int i = 0; i < sg.getSize(); i++)\r
 362     {\r
 363       SequenceI seq = sg.getSequenceAt(i);\r
 364       int index = viewport.alignment.findIndex(seq);\r
 365       orderedSeqs.put(index + "", seq);\r
 366     }\r
 367 \r
 368     int index = 0;\r
 369 \r
 370     for (int i = 0; i < sg.getSize(); i++)\r
 371     {\r
 372       SequenceI seq = null;\r
 373 \r
 374       while (seq == null)\r
 375       {\r
 376         if (orderedSeqs.containsKey(index + ""))\r
 377         {\r
 378           seq = (SequenceI) orderedSeqs.get(index + "");\r
 379           index++;\r
 380 \r
 381           break;\r
 382         }\r
 383         else\r
 384         {\r
 385           index++;\r
 386         }\r
 387       }\r
 388 \r
 389       buffer.append(seq.getName() + "\t" +\r
 390                     seq.findPosition(sg.getStartRes()) + "\t" +\r
 391                     seq.findPosition(sg.getEndRes()) + "\t" +\r
 392                     sg.getSequenceAt(i).getSequence(sg.getStartRes(),\r
 393           sg.getEndRes() + 1) + "\n");\r
 394     }\r
 395 \r
 396     c.setContents(new StringSelection(buffer.toString()), null);\r
 397   }\r
 398 \r
 399   protected void pasteNew_actionPerformed(ActionEvent e)\r
 400   {\r
 401     paste(true);\r
 402   }\r
 403 \r
 404   protected void pasteThis_actionPerformed(ActionEvent e)\r
 405   {\r
 406     addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
 407                                    HistoryItem.PASTE));\r
 408     paste(false);\r
 409   }\r
 410 \r
 411   void paste(boolean newAlignment)\r
 412   {\r
 413     try\r
 414     {\r
 415       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 416       Transferable contents = c.getContents(this);\r
 417 \r
 418       if (contents == null)\r
 419       {\r
 420         return;\r
 421       }\r
 422 \r
 423       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
 424       StringTokenizer st = new StringTokenizer(str);\r
 425       ArrayList seqs = new ArrayList();\r
 426 \r
 427       while (st.hasMoreElements())\r
 428       {\r
 429         String name = st.nextToken();\r
 430         int start = Integer.parseInt(st.nextToken());\r
 431         int end = Integer.parseInt(st.nextToken());\r
 432         Sequence sequence = new Sequence(name, st.nextToken(), start,\r
 433                                          end);\r
 434 \r
 435         if (!newAlignment)\r
 436         {\r
 437           viewport.alignment.addSequence(sequence);\r
 438         }\r
 439         else\r
 440         {\r
 441           seqs.add(sequence);\r
 442         }\r
 443       }\r
 444 \r
 445       if (newAlignment)\r
 446       {\r
 447         SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 448         seqs.toArray(newSeqs);\r
 449 \r
 450         AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
 451         String newtitle = new String("Copied sequences");\r
 452 \r
 453         if (title.startsWith("Copied sequences"))\r
 454         {\r
 455           newtitle = title;\r
 456         }\r
 457         else\r
 458         {\r
 459           newtitle = newtitle.concat("- from " + title);\r
 460         }\r
 461 \r
 462         Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
 463                                  NEW_WINDOW_HEIGHT);\r
 464       }\r
 465       else\r
 466       {\r
 467         viewport.firePropertyChange("alignment", null,\r
 468                                     viewport.getAlignment().getSequences());\r
 469         viewport.setEndSeq(viewport.alignment.getHeight());\r
 470         viewport.alignment.getWidth();\r
 471         viewport.updateConservation();\r
 472         viewport.updateConsensus();\r
 473         alignPanel.repaint();\r
 474       }\r
 475     }\r
 476     catch (Exception ex)\r
 477     {\r
 478     }\r
 479 \r
 480     // could be anything being pasted in here\r
 481   }\r
 482 \r
 483   protected void cut_actionPerformed(ActionEvent e)\r
 484   {\r
 485     copy_actionPerformed(null);\r
 486     delete_actionPerformed(null);\r
 487   }\r
 488 \r
 489   protected void delete_actionPerformed(ActionEvent e)\r
 490   {\r
 491     boolean seqsdeleted = false;\r
 492 \r
 493     if (viewport.getSelectionGroup() == null)\r
 494     {\r
 495       return;\r
 496     }\r
 497 \r
 498     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
 499                                    HistoryItem.HIDE));\r
 500 \r
 501     SequenceGroup sg = viewport.getSelectionGroup();\r
 502 \r
 503     for (int i = 0; i < sg.sequences.size(); i++)\r
 504     {\r
 505       SequenceI seq = sg.getSequenceAt(i);\r
 506       int index = viewport.getAlignment().findIndex(seq);\r
 507       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 508 \r
 509       if (seq.getSequence().length() < 1)\r
 510       {\r
 511         seqsdeleted = true;\r
 512         viewport.getAlignment().deleteSequence(seq);\r
 513       }\r
 514       else\r
 515       {\r
 516         viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 517       }\r
 518     }\r
 519 \r
 520     viewport.setSelectionGroup(null);\r
 521     viewport.alignment.deleteGroup(sg);\r
 522 \r
 523     if (seqsdeleted)\r
 524     {\r
 525       viewport.firePropertyChange("alignment", null,\r
 526                                   viewport.getAlignment().getSequences());\r
 527     }\r
 528 \r
 529     viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());\r
 530 \r
 531     if (viewport.getAlignment().getHeight() < 1)\r
 532     {\r
 533       try\r
 534       {\r
 535         this.setClosed(true);\r
 536       }\r
 537       catch (Exception ex)\r
 538       {\r
 539       }\r
 540     }\r
 541 \r
 542     viewport.updateConservation();\r
 543     viewport.updateConsensus();\r
 544     alignPanel.repaint();\r
 545   }\r
 546 \r
 547   protected void deleteGroups_actionPerformed(ActionEvent e)\r
 548   {\r
 549     viewport.alignment.deleteAllGroups();\r
 550     viewport.setSelectionGroup(null);\r
 551     alignPanel.repaint();\r
 552   }\r
 553 \r
 554   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 555   {\r
 556     SequenceGroup sg = new SequenceGroup();\r
 557 \r
 558     for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
 559          i++)\r
 560     {\r
 561       sg.addSequence(viewport.getAlignment().getSequenceAt(i));\r
 562     }\r
 563 \r
 564     sg.setEndRes(viewport.alignment.getWidth());\r
 565     viewport.setSelectionGroup(sg);\r
 566     PaintRefresher.Refresh(null);\r
 567   }\r
 568 \r
 569   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 570   {\r
 571     viewport.setSelectionGroup(null);\r
 572     viewport.getColumnSelection().clear();\r
 573     viewport.setSelectionGroup(null);\r
 574     PaintRefresher.Refresh(null);\r
 575   }\r
 576 \r
 577   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 578   {\r
 579     SequenceGroup sg = viewport.getSelectionGroup();\r
 580 \r
 581     for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
 582          i++)\r
 583     {\r
 584       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i));\r
 585     }\r
 586 \r
 587     PaintRefresher.Refresh(null);\r
 588   }\r
 589 \r
 590   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 591   {\r
 592     ColumnSelection colSel = viewport.getColumnSelection();\r
 593 \r
 594     if (colSel.size() > 0)\r
 595     {\r
 596       addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
 597                                      HistoryItem.HIDE));\r
 598 \r
 599       int min = colSel.getMin();\r
 600       viewport.getAlignment().trimLeft(min);\r
 601       colSel.compensateForEdit(0, min);\r
 602 \r
 603       if (viewport.getSelectionGroup() != null)\r
 604       {\r
 605         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 606       }\r
 607 \r
 608       Vector groups = viewport.alignment.getGroups();\r
 609 \r
 610       for (int i = 0; i < groups.size(); i++)\r
 611       {\r
 612         SequenceGroup sg = (SequenceGroup) groups.get(i);\r
 613 \r
 614         if (!sg.adjustForRemoveLeft(min))\r
 615         {\r
 616           viewport.alignment.deleteGroup(sg);\r
 617         }\r
 618       }\r
 619 \r
 620       alignPanel.repaint();\r
 621     }\r
 622   }\r
 623 \r
 624   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 625   {\r
 626     ColumnSelection colSel = viewport.getColumnSelection();\r
 627 \r
 628     if (colSel.size() > 0)\r
 629     {\r
 630       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
 631                                      HistoryItem.HIDE));\r
 632 \r
 633       int max = colSel.getMax();\r
 634       viewport.getAlignment().trimRight(max);\r
 635 \r
 636       if (viewport.getSelectionGroup() != null)\r
 637       {\r
 638         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 639       }\r
 640 \r
 641       Vector groups = viewport.alignment.getGroups();\r
 642 \r
 643       for (int i = 0; i < groups.size(); i++)\r
 644       {\r
 645         SequenceGroup sg = (SequenceGroup) groups.get(i);\r
 646 \r
 647         if (!sg.adjustForRemoveRight(max))\r
 648         {\r
 649           viewport.alignment.deleteGroup(sg);\r
 650         }\r
 651       }\r
 652 \r
 653       alignPanel.repaint();\r
 654     }\r
 655   }\r
 656 \r
 657   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 658   {\r
 659     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
 660                                    viewport.alignment, HistoryItem.HIDE));\r
 661 \r
 662     viewport.getAlignment().removeGaps();\r
 663     viewport.updateConservation();\r
 664     viewport.updateConsensus();\r
 665     alignPanel.repaint();\r
 666   }\r
 667 \r
 668   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 669   {\r
 670     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
 671                                    HistoryItem.HIDE));\r
 672 \r
 673     SequenceI current;\r
 674     int jSize;\r
 675 \r
 676     for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
 677          i++)\r
 678     {\r
 679       current = viewport.getAlignment().getSequenceAt(i);\r
 680       jSize = current.getLength();\r
 681 \r
 682       for (int j = 0; j < jSize; j++)\r
 683       {\r
 684         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 685         {\r
 686           current.deleteCharAt(j);\r
 687           j--;\r
 688           jSize--;\r
 689         }\r
 690       }\r
 691     }\r
 692 \r
 693     viewport.updateConservation();\r
 694     viewport.updateConsensus();\r
 695     alignPanel.repaint();\r
 696   }\r
 697 \r
 698   public void padGapsMenuitem_actionPerformed(ActionEvent e)\r
 699   {\r
 700     addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,\r
 701                                    HistoryItem.HIDE));\r
 702 \r
 703     SequenceI current;\r
 704     int Width = viewport.getAlignment().getWidth() - 1;\r
 705 \r
 706     for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
 707          i++)\r
 708     {\r
 709       current = viewport.getAlignment().getSequenceAt(i);\r
 710 \r
 711       if (current.getLength() < Width)\r
 712       {\r
 713         current.insertCharAt(Width, viewport.getGapCharacter());\r
 714       }\r
 715     }\r
 716 \r
 717     viewport.updateConservation();\r
 718     viewport.updateConsensus();\r
 719     alignPanel.repaint();\r
 720   }\r
 721 \r
 722   public void findMenuItem_actionPerformed(ActionEvent e)\r
 723   {\r
 724     JInternalFrame frame = new JInternalFrame();\r
 725     Finder finder = new Finder(viewport, alignPanel, frame);\r
 726     frame.setContentPane(finder);\r
 727     Desktop.addInternalFrame(frame, "Find", 340, 110);\r
 728     frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
 729   }\r
 730 \r
 731   public void font_actionPerformed(ActionEvent e)\r
 732   {\r
 733     FontChooser fc = new FontChooser(alignPanel);\r
 734   }\r
 735 \r
 736   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 737   {\r
 738     viewport.setShowFullId(fullSeqId.isSelected());\r
 739 \r
 740     alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());\r
 741     alignPanel.repaint();\r
 742   }\r
 743 \r
 744   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 745   {\r
 746     viewport.setColourText(colourTextMenuItem.isSelected());\r
 747     alignPanel.repaint();\r
 748   }\r
 749 \r
 750   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 751   {\r
 752     viewport.setWrapAlignment(wrapMenuItem.isSelected());\r
 753     alignPanel.setWrapAlignment(wrapMenuItem.isSelected());\r
 754     scaleAbove.setVisible(wrapMenuItem.isSelected());\r
 755     scaleLeft.setVisible(wrapMenuItem.isSelected());\r
 756     scaleRight.setVisible(wrapMenuItem.isSelected());\r
 757     alignPanel.repaint();\r
 758   }\r
 759 \r
 760   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 761   {\r
 762     viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
 763     alignPanel.repaint();\r
 764   }\r
 765 \r
 766   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 767   {\r
 768     viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
 769     alignPanel.repaint();\r
 770   }\r
 771 \r
 772   protected void scaleRight_actionPerformed(ActionEvent e)\r
 773   {\r
 774     viewport.setScaleRightWrapped(scaleRight.isSelected());\r
 775     alignPanel.repaint();\r
 776   }\r
 777 \r
 778   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 779   {\r
 780     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());\r
 781     alignPanel.repaint();\r
 782   }\r
 783 \r
 784   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 785   {\r
 786     viewport.setShowText(viewTextMenuItem.isSelected());\r
 787     alignPanel.repaint();\r
 788   }\r
 789 \r
 790   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 791   {\r
 792     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 793     alignPanel.repaint();\r
 794   }\r
 795 \r
 796   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 797   {\r
 798     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 799 \r
 800     if (viewport.showSequenceFeatures &&\r
 801         ! ( (Alignment) viewport.alignment).featuresAdded)\r
 802     {\r
 803       SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.\r
 804           alignment,\r
 805           alignPanel);\r
 806       ( (Alignment) viewport.alignment).featuresAdded = true;\r
 807     }\r
 808 \r
 809     alignPanel.repaint();\r
 810   }\r
 811 \r
 812   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 813   {\r
 814     if (annotationPanelMenuItem.isSelected() &&\r
 815         viewport.getWrapAlignment())\r
 816     {\r
 817       annotationPanelMenuItem.setSelected(false);\r
 818 \r
 819       return;\r
 820     }\r
 821 \r
 822     viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());\r
 823     alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());\r
 824   }\r
 825 \r
 826   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 827   {\r
 828     if (alignPanel.overviewPanel != null)\r
 829     {\r
 830       return;\r
 831     }\r
 832 \r
 833     JInternalFrame frame = new JInternalFrame();\r
 834     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 835     frame.setContentPane(overview);\r
 836     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 837                              frame.getWidth(), frame.getHeight());\r
 838     frame.pack();\r
 839     frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
 840     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 841     {\r
 842       public void internalFrameClosed(\r
 843           javax.swing.event.InternalFrameEvent evt)\r
 844       {\r
 845         alignPanel.setOverviewPanel(null);\r
 846       }\r
 847       ;\r
 848     });\r
 849 \r
 850     alignPanel.setOverviewPanel(overview);\r
 851   }\r
 852 \r
 853   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 854   {\r
 855     changeColour(null);\r
 856   }\r
 857 \r
 858   public void clustalColour_actionPerformed(ActionEvent e)\r
 859   {\r
 860     changeColour(new ClustalxColourScheme(\r
 861         viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 862   }\r
 863 \r
 864   public void zappoColour_actionPerformed(ActionEvent e)\r
 865   {\r
 866     changeColour(new ZappoColourScheme());\r
 867   }\r
 868 \r
 869   public void taylorColour_actionPerformed(ActionEvent e)\r
 870   {\r
 871     changeColour(new TaylorColourScheme());\r
 872   }\r
 873 \r
 874   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 875   {\r
 876     changeColour(new HydrophobicColourScheme());\r
 877   }\r
 878 \r
 879   public void helixColour_actionPerformed(ActionEvent e)\r
 880   {\r
 881     changeColour(new HelixColourScheme());\r
 882   }\r
 883 \r
 884   public void strandColour_actionPerformed(ActionEvent e)\r
 885   {\r
 886     changeColour(new StrandColourScheme());\r
 887   }\r
 888 \r
 889   public void turnColour_actionPerformed(ActionEvent e)\r
 890   {\r
 891     changeColour(new TurnColourScheme());\r
 892   }\r
 893 \r
 894   public void buriedColour_actionPerformed(ActionEvent e)\r
 895   {\r
 896     changeColour(new BuriedColourScheme());\r
 897   }\r
 898 \r
 899   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 900   {\r
 901     changeColour(new NucleotideColourScheme());\r
 902   }\r
 903 \r
 904   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 905   {\r
 906     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
 907   }\r
 908 \r
 909   void changeColour(ColourSchemeI cs)\r
 910   {\r
 911     int threshold = 0;\r
 912 \r
 913     if (viewport.getAbovePIDThreshold())\r
 914     {\r
 915       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,\r
 916                                                  "Background");\r
 917 \r
 918       if (cs instanceof ResidueColourScheme)\r
 919       {\r
 920         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 921       }\r
 922       else if (cs instanceof ScoreColourScheme)\r
 923       {\r
 924         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 925       }\r
 926 \r
 927       viewport.setGlobalColourScheme(cs);\r
 928     }\r
 929     else if (cs instanceof ResidueColourScheme)\r
 930     {\r
 931       ( (ResidueColourScheme) cs).setThreshold(0);\r
 932     }\r
 933     else if (cs instanceof ScoreColourScheme)\r
 934     {\r
 935       ( (ScoreColourScheme) cs).setThreshold(0);\r
 936     }\r
 937 \r
 938     if (viewport.getConservationSelected())\r
 939     {\r
 940       ConservationColourScheme ccs = null;\r
 941 \r
 942       Alignment al = (Alignment) viewport.alignment;\r
 943       Conservation c = new Conservation("All",\r
 944                                         ResidueProperties.propHash, 3,\r
 945                                         al.getSequences(), 0,\r
 946                                         al.getWidth() - 1);\r
 947 \r
 948       c.calculate();\r
 949       c.verdict(false, viewport.ConsPercGaps);\r
 950 \r
 951       ccs = new ConservationColourScheme(c, cs);\r
 952 \r
 953       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 954       ccs.setConsensus(viewport.vconsensus);\r
 955       viewport.setGlobalColourScheme(ccs);\r
 956 \r
 957       ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,\r
 958                                                   "Background");\r
 959     }\r
 960     else\r
 961     {\r
 962       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 963       if (cs != null)\r
 964       {\r
 965         cs.setConsensus(viewport.vconsensus);\r
 966       }\r
 967 \r
 968       viewport.setGlobalColourScheme(cs);\r
 969     }\r
 970 \r
 971     if (viewport.getColourAppliesToAllGroups())\r
 972     {\r
 973       Vector groups = viewport.alignment.getGroups();\r
 974 \r
 975       for (int i = 0; i < groups.size(); i++)\r
 976       {\r
 977         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 978 \r
 979         if (cs == null)\r
 980         {\r
 981           sg.cs = null;\r
 982         }\r
 983         else if (cs instanceof ClustalxColourScheme)\r
 984         {\r
 985           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
 986         }\r
 987         else if (cs instanceof UserColourScheme)\r
 988         {\r
 989           sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());\r
 990         }\r
 991         else\r
 992         {\r
 993           try\r
 994           {\r
 995             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
 996           }\r
 997           catch (Exception ex)\r
 998           {\r
 999           }\r
1000         }\r
1001 \r
1002         if (viewport.getAbovePIDThreshold())\r
1003         {\r
1004           if (sg.cs instanceof ResidueColourScheme)\r
1005           {\r
1006             ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
1007           }\r
1008           else if (sg.cs instanceof ScoreColourScheme)\r
1009           {\r
1010             ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
1011           }\r
1012 \r
1013           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
1014               sg.getWidth()));\r
1015         }\r
1016 \r
1017         if (viewport.getConservationSelected())\r
1018         {\r
1019           Conservation c = new Conservation("Group",\r
1020                                             ResidueProperties.propHash, 3,\r
1021                                             sg.sequences, 0,\r
1022                                             viewport.alignment.getWidth() - 1);\r
1023           c.calculate();\r
1024           c.verdict(false, viewport.ConsPercGaps);\r
1025 \r
1026           ConservationColourScheme ccs = new ConservationColourScheme(c,\r
1027               sg.cs);\r
1028 \r
1029           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
1030           ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
1031                                                  sg.getWidth()));\r
1032           sg.cs = ccs;\r
1033         }\r
1034         else if (cs != null)\r
1035         {\r
1036           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
1037           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
1038               sg.getWidth()));\r
1039         }\r
1040       }\r
1041     }\r
1042 \r
1043     if (alignPanel.getOverviewPanel() != null)\r
1044     {\r
1045       alignPanel.getOverviewPanel().updateOverviewImage();\r
1046     }\r
1047 \r
1048     alignPanel.repaint();\r
1049   }\r
1050 \r
1051   protected void modifyPID_actionPerformed(ActionEvent e)\r
1052   {\r
1053     if (viewport.getAbovePIDThreshold())\r
1054     {\r
1055       SliderPanel.setPIDSliderSource(alignPanel,\r
1056                                      viewport.getGlobalColourScheme(),\r
1057                                      "Background");\r
1058       SliderPanel.showPIDSlider();\r
1059     }\r
1060   }\r
1061 \r
1062   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1063   {\r
1064     if (viewport.getConservationSelected())\r
1065     {\r
1066       SliderPanel.setConservationSlider(alignPanel,\r
1067                                         viewport.globalColourScheme,\r
1068                                         "Background");\r
1069       SliderPanel.showConservationSlider();\r
1070     }\r
1071   }\r
1072 \r
1073   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1074   {\r
1075     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
1076 \r
1077     viewport.setAbovePIDThreshold(false);\r
1078     abovePIDThreshold.setSelected(false);\r
1079 \r
1080     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
1081 \r
1082     if (cs instanceof ConservationColourScheme)\r
1083     {\r
1084       changeColour( ( (ConservationColourScheme) cs).cs);\r
1085     }\r
1086     else\r
1087     {\r
1088       changeColour(cs);\r
1089     }\r
1090 \r
1091     modifyConservation_actionPerformed(null);\r
1092   }\r
1093 \r
1094   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1095   {\r
1096     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
1097 \r
1098     conservationMenuItem.setSelected(false);\r
1099     viewport.setConservationSelected(false);\r
1100 \r
1101     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
1102 \r
1103     if (cs instanceof ConservationColourScheme)\r
1104     {\r
1105       changeColour( ( (ConservationColourScheme) cs).cs);\r
1106     }\r
1107     else\r
1108     {\r
1109       changeColour(cs);\r
1110     }\r
1111 \r
1112     modifyPID_actionPerformed(null);\r
1113   }\r
1114 \r
1115   public void userDefinedColour_actionPerformed(ActionEvent e)\r
1116   {\r
1117     new UserDefinedColours(alignPanel, null);\r
1118   }\r
1119 \r
1120   public void PIDColour_actionPerformed(ActionEvent e)\r
1121   {\r
1122     changeColour(new PIDColourScheme());\r
1123   }\r
1124 \r
1125   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1126   {\r
1127     changeColour(new Blosum62ColourScheme());\r
1128   }\r
1129 \r
1130   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1131   {\r
1132     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1133                                    HistoryItem.SORT));\r
1134     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1135                               viewport.getAlignment().getSequenceAt(0));\r
1136     alignPanel.repaint();\r
1137   }\r
1138 \r
1139   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1140   {\r
1141     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1142                                    HistoryItem.SORT));\r
1143     AlignmentSorter.sortByID(viewport.getAlignment());\r
1144     alignPanel.repaint();\r
1145   }\r
1146 \r
1147   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1148   {\r
1149     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1150                                    HistoryItem.SORT));\r
1151 \r
1152     //  AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1153     AlignmentSorter.sortGroups(viewport.getAlignment());\r
1154     alignPanel.repaint();\r
1155   }\r
1156 \r
1157   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1158   {\r
1159     RedundancyPanel sp = new RedundancyPanel(alignPanel, this);\r
1160     JInternalFrame frame = new JInternalFrame();\r
1161     frame.setContentPane(sp);\r
1162     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,\r
1163                              100, false);\r
1164   }\r
1165 \r
1166   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1167   {\r
1168     if ( (viewport.getSelectionGroup() == null) ||\r
1169         (viewport.getSelectionGroup().getSize() < 2))\r
1170     {\r
1171       JOptionPane.showInternalMessageDialog(this,\r
1172                                             "You must select at least 2 sequences.",\r
1173                                             "Invalid Selection",\r
1174                                             JOptionPane.WARNING_MESSAGE);\r
1175     }\r
1176     else\r
1177     {\r
1178       JInternalFrame frame = new JInternalFrame();\r
1179       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
1180       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
1181     }\r
1182   }\r
1183 \r
1184   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
1185   {\r
1186     if ( ( (viewport.getSelectionGroup() != null) &&\r
1187           (viewport.getSelectionGroup().getSize() < 4) &&\r
1188           (viewport.getSelectionGroup().getSize() > 0)) ||\r
1189         (viewport.getAlignment().getHeight() < 4))\r
1190     {\r
1191       JOptionPane.showInternalMessageDialog(this,\r
1192                                             "Principal component analysis must take\n" +\r
1193                                             "at least 4 input sequences.",\r
1194                                             "Sequence selection insufficient",\r
1195                                             JOptionPane.WARNING_MESSAGE);\r
1196 \r
1197       return;\r
1198     }\r
1199 \r
1200     try\r
1201     {\r
1202       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
1203       JInternalFrame frame = new JInternalFrame();\r
1204       frame.setContentPane(pcaPanel);\r
1205       Desktop.addInternalFrame(frame, "Principal component analysis",\r
1206                                400, 400);\r
1207     }\r
1208     catch (java.lang.OutOfMemoryError ex)\r
1209     {\r
1210       JOptionPane.showInternalMessageDialog(this,\r
1211                                             "Too many sequences selected\nfor Principal Component Analysis!!",\r
1212                                             "Out of memory",\r
1213                                             JOptionPane.WARNING_MESSAGE);\r
1214     }\r
1215   }\r
1216 \r
1217   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1218   {\r
1219     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1220   }\r
1221 \r
1222   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1223   {\r
1224     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1225   }\r
1226 \r
1227   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1228   {\r
1229     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1230   }\r
1231 \r
1232   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1233   {\r
1234     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
1235   }\r
1236 \r
1237   void NewTreePanel(String type, String pwType, String title)\r
1238   {\r
1239     String ltitle;\r
1240     final TreePanel tp;\r
1241 \r
1242     if ( (viewport.getSelectionGroup() != null) &&\r
1243         (viewport.getSelectionGroup().getSize() > 3))\r
1244     {\r
1245       int s = 0;\r
1246       SequenceGroup sg = viewport.getSelectionGroup();\r
1247 \r
1248       /* Decide if the selection is a column region */\r
1249       while (s < sg.sequences.size())\r
1250       {\r
1251         if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <\r
1252             sg.getEndRes())\r
1253         {\r
1254           JOptionPane.showMessageDialog(Desktop.desktop,\r
1255                                         "The selected region to create a tree may\nonly contain residues or gaps.\n" +\r
1256                                         "Try using the Pad function in the edit menu,\n" +\r
1257                                         "or one of the multiple sequence alignment web services.",\r
1258                                         "Sequences in selection are not aligned",\r
1259                                         JOptionPane.WARNING_MESSAGE);\r
1260 \r
1261           return;\r
1262         }\r
1263       }\r
1264 \r
1265       title = title + " on region";\r
1266       tp = new TreePanel(viewport,\r
1267                          viewport.getSelectionGroup().sequences, type, pwType,\r
1268                          sg.getStartRes(), sg.getEndRes());\r
1269     }\r
1270     else\r
1271     {\r
1272       //are the sequences aligned?\r
1273       if (!viewport.alignment.isAligned())\r
1274       {\r
1275         JOptionPane.showMessageDialog(Desktop.desktop,\r
1276                                       "The sequences must be aligned before creating a tree.\n" +\r
1277                                       "Try using the Pad function in the edit menu,\n" +\r
1278                                       "or one of the multiple sequence alignment web services.",\r
1279                                       "Sequences not aligned",\r
1280                                       JOptionPane.WARNING_MESSAGE);\r
1281 \r
1282         return;\r
1283       }\r
1284 \r
1285       tp = new TreePanel(viewport,\r
1286                          viewport.getAlignment().getSequences(), type, pwType,\r
1287                          0,\r
1288                          viewport.alignment.getWidth());\r
1289     }\r
1290 \r
1291     addTreeMenuItem(tp, title);\r
1292     viewport.setCurrentTree(tp.getTree());\r
1293 \r
1294     Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);\r
1295   }\r
1296 \r
1297   public void addSortByOrderMenuItem(String title, final AlignmentOrder order)\r
1298   {\r
1299     final JMenuItem item = new JMenuItem("by " + title);\r
1300     sort.add(item);\r
1301     item.addActionListener(new java.awt.event.ActionListener()\r
1302     {\r
1303       public void actionPerformed(ActionEvent e)\r
1304       {\r
1305         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1306                                        HistoryItem.SORT));\r
1307 \r
1308         // TODO: JBPNote - have to map order entries to curent SequenceI pointers\r
1309         AlignmentSorter.sortBy(viewport.getAlignment(), order);\r
1310         alignPanel.repaint();\r
1311       }\r
1312     });\r
1313   }\r
1314 \r
1315   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1316   {\r
1317     final JMenuItem item = new JMenuItem(title);\r
1318 \r
1319     treeCount++;\r
1320 \r
1321     if (treeCount == 1)\r
1322     {\r
1323       sort.add(sortByTreeMenu);\r
1324     }\r
1325 \r
1326     sortByTreeMenu.add(item);\r
1327     item.addActionListener(new java.awt.event.ActionListener()\r
1328     {\r
1329       public void actionPerformed(ActionEvent e)\r
1330       {\r
1331         addHistoryItem(new HistoryItem("Tree Sort",\r
1332                                        viewport.alignment, HistoryItem.SORT));\r
1333         AlignmentSorter.sortByTree(viewport.getAlignment(),\r
1334                                    treePanel.getTree());\r
1335         alignPanel.repaint();\r
1336       }\r
1337     });\r
1338 \r
1339     treePanel.addInternalFrameListener(new javax.swing.event.\r
1340                                        InternalFrameAdapter()\r
1341     {\r
1342       public void internalFrameClosed(\r
1343           javax.swing.event.InternalFrameEvent evt)\r
1344       {\r
1345         treeCount--;\r
1346         sortByTreeMenu.remove(item);\r
1347 \r
1348         if (treeCount == 0)\r
1349         {\r
1350           sort.remove(sortByTreeMenu);\r
1351         }\r
1352       }\r
1353       ;\r
1354     });\r
1355     viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
1356     {\r
1357       public void propertyChange(PropertyChangeEvent evt)\r
1358       {\r
1359         if (evt.getPropertyName().equals("alignment"))\r
1360         {\r
1361           treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());\r
1362           treePanel.repaint();\r
1363         }\r
1364       }\r
1365     });\r
1366   }\r
1367 \r
1368   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
1369   {\r
1370     // TODO:resolve which menu item was actually selected\r
1371     // Now, check we have enough sequences\r
1372     SequenceI[] msa = null;\r
1373 \r
1374     if ( (viewport.getSelectionGroup() != null) &&\r
1375         (viewport.getSelectionGroup().getSize() > 1))\r
1376     {\r
1377       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1378       SequenceGroup seqs = viewport.getSelectionGroup();\r
1379       int sz;\r
1380       msa = new SequenceI[sz = seqs.getSize()];\r
1381 \r
1382       for (int i = 0; i < sz; i++)\r
1383       {\r
1384         msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1385       }\r
1386     }\r
1387     else\r
1388     {\r
1389       Vector seqs = viewport.getAlignment().getSequences();\r
1390 \r
1391       if (seqs.size() > 1)\r
1392       {\r
1393         msa = new SequenceI[seqs.size()];\r
1394 \r
1395         for (int i = 0; i < seqs.size(); i++)\r
1396         {\r
1397           msa[i] = (SequenceI) seqs.elementAt(i);\r
1398         }\r
1399       }\r
1400     }\r
1401 \r
1402     if (msa != null)\r
1403     {\r
1404       jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",\r
1405           title, msa, false, true);\r
1406     }\r
1407   }\r
1408 \r
1409   public void ClustalRealign_actionPerformed(ActionEvent e)\r
1410   {\r
1411     // TODO:resolve which menu item was actually selected\r
1412     // Now, check we have enough sequences\r
1413     SequenceI[] msa = null;\r
1414 \r
1415     if ( (viewport.getSelectionGroup() != null) &&\r
1416         (viewport.getSelectionGroup().getSize() > 1))\r
1417     {\r
1418       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1419       SequenceGroup seqs = viewport.getSelectionGroup();\r
1420       int sz;\r
1421       msa = new SequenceI[sz = seqs.getSize()];\r
1422 \r
1423       for (int i = 0; i < sz; i++)\r
1424       {\r
1425         msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1426       }\r
1427     }\r
1428     else\r
1429     {\r
1430       Vector seqs = viewport.getAlignment().getSequences();\r
1431 \r
1432       if (seqs.size() > 1)\r
1433       {\r
1434         msa = new SequenceI[seqs.size()];\r
1435 \r
1436         for (int i = 0; i < seqs.size(); i++)\r
1437         {\r
1438           msa[i] = (SequenceI) seqs.elementAt(i);\r
1439         }\r
1440       }\r
1441     }\r
1442 \r
1443     if (msa != null)\r
1444     {\r
1445       jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",\r
1446           title, msa, true, true);\r
1447     }\r
1448   }\r
1449 \r
1450   protected void jpred_actionPerformed(ActionEvent e)\r
1451   {\r
1452     SequenceI seq = null;\r
1453     SequenceI[] msa = null;\r
1454 \r
1455     if ( (viewport.getSelectionGroup() != null) &&\r
1456         (viewport.getSelectionGroup().getSize() > 0))\r
1457     {\r
1458       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1459       SequenceGroup seqs = viewport.getSelectionGroup();\r
1460 \r
1461       if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())\r
1462       {\r
1463         seq = (SequenceI) seqs.getSequenceAt(0);\r
1464       }\r
1465       else\r
1466       {\r
1467         int sz;\r
1468         msa = new SequenceI[sz = seqs.getSize()];\r
1469 \r
1470         for (int i = 0; i < sz; i++)\r
1471         {\r
1472           msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1473         }\r
1474       }\r
1475     }\r
1476     else\r
1477     {\r
1478       Vector seqs = viewport.getAlignment().getSequences();\r
1479 \r
1480       if ( (seqs.size() == 1) || !viewport.alignment.isAligned())\r
1481       {\r
1482         seq = (SequenceI) seqs.elementAt(0);\r
1483       }\r
1484       else\r
1485       {\r
1486         msa = new SequenceI[seqs.size()];\r
1487 \r
1488         for (int i = 0; i < seqs.size(); i++)\r
1489         {\r
1490           msa[i] = (SequenceI) seqs.elementAt(i);\r
1491         }\r
1492       }\r
1493     }\r
1494 \r
1495     if (msa != null)\r
1496     {\r
1497       JPredClient ct = new JPredClient(title, msa);\r
1498     }\r
1499     else if (seq != null)\r
1500     {\r
1501       JPredClient ct = new JPredClient(title, seq);\r
1502     }\r
1503     else\r
1504     {\r
1505       System.err.print(\r
1506           "JALVIEW ERROR! - Unexpected JPred selection state!\n");\r
1507     }\r
1508   }\r
1509 \r
1510   protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
1511   {\r
1512     // TODO:resolve which menu item was actually selected\r
1513     // Now, check we have enough sequences\r
1514     SequenceI[] msa = null;\r
1515 \r
1516     if ( (viewport.getSelectionGroup() != null) &&\r
1517         (viewport.getSelectionGroup().getSize() > 1))\r
1518     {\r
1519       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1520       SequenceGroup seqs = viewport.getSelectionGroup();\r
1521       int sz;\r
1522       msa = new SequenceI[sz = seqs.getSize()];\r
1523 \r
1524       for (int i = 0; i < sz; i++)\r
1525       {\r
1526         msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1527       }\r
1528     }\r
1529     else\r
1530     {\r
1531       Vector seqs = viewport.getAlignment().getSequences();\r
1532 \r
1533       if (seqs.size() > 1)\r
1534       {\r
1535         msa = new SequenceI[seqs.size()];\r
1536 \r
1537         for (int i = 0; i < seqs.size(); i++)\r
1538         {\r
1539           msa[i] = (SequenceI) seqs.elementAt(i);\r
1540         }\r
1541       }\r
1542     }\r
1543 \r
1544     if (msa != null)\r
1545     {\r
1546       MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa,\r
1547                                                   false, true);\r
1548     }\r
1549   }\r
1550 \r
1551   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1552   {\r
1553     // Pick the tree file\r
1554     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
1555         getProperty(\r
1556             "LAST_DIRECTORY"));\r
1557     chooser.setFileView(new JalviewFileView());\r
1558     chooser.setDialogTitle("Select a newick-like tree file");\r
1559     chooser.setToolTipText("Load a tree file");\r
1560 \r
1561     int value = chooser.showOpenDialog(null);\r
1562 \r
1563     if (value == JalviewFileChooser.APPROVE_OPTION)\r
1564     {\r
1565       String choice = chooser.getSelectedFile().getPath();\r
1566       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1567 \r
1568       try\r
1569       {\r
1570         jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,\r
1571             "File");\r
1572         ShowNewickTree(fin, choice);\r
1573       }\r
1574       catch (Exception ex)\r
1575       {\r
1576         JOptionPane.showMessageDialog(Desktop.desktop,\r
1577                                       "Problem reading tree file",\r
1578                                       ex.getMessage(),\r
1579                                       JOptionPane.WARNING_MESSAGE);\r
1580         ex.printStackTrace();\r
1581       }\r
1582     }\r
1583   }\r
1584 \r
1585   public void ShowNewickTree(NewickFile nf, String title)\r
1586   {\r
1587     try\r
1588     {\r
1589       nf.parse();\r
1590 \r
1591       if (nf.getTree() != null)\r
1592       {\r
1593         TreePanel tp = new TreePanel(viewport,\r
1594                                      viewport.getAlignment().getSequences(), nf,\r
1595                                      "FromFile",\r
1596                                      title);\r
1597         Desktop.addInternalFrame(tp, title, 600, 500);\r
1598         addTreeMenuItem(tp, title);\r
1599         viewport.setCurrentTree(tp.getTree());\r
1600       }\r
1601     }\r
1602     catch (Exception ex)\r
1603     {\r
1604       ex.printStackTrace();\r
1605     }\r
1606   }\r
1607 \r
1608   class PrintThread\r
1609       extends Thread\r
1610   {\r
1611     public void run()\r
1612     {\r
1613       PrinterJob printJob = PrinterJob.getPrinterJob();\r
1614       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
1615       printJob.setPrintable(alignPanel, pf);\r
1616 \r
1617       if (printJob.printDialog())\r
1618       {\r
1619         try\r
1620         {\r
1621           printJob.print();\r
1622         }\r
1623         catch (Exception PrintException)\r
1624         {\r
1625           PrintException.printStackTrace();\r
1626         }\r
1627       }\r
1628     }\r
1629   }\r
1630 }\r