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.SaveAlignment(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), false);\r
 562     }\r
 563 \r
 564     sg.setEndRes(viewport.alignment.getWidth());\r
 565     viewport.setSelectionGroup(sg);\r
 566     PaintRefresher.Refresh(null, viewport.alignment);\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     alignPanel.annotationPanel.activeRes=null;\r
 575     PaintRefresher.Refresh(null, viewport.alignment);\r
 576   }\r
 577 \r
 578   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 579   {\r
 580     SequenceGroup sg = viewport.getSelectionGroup();\r
 581     if(sg==null)\r
 582     {\r
 583       selectAllSequenceMenuItem_actionPerformed(null);\r
 584       return;\r
 585     }\r
 586 \r
 587     for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
 588          i++)\r
 589     {\r
 590       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
 591     }\r
 592 \r
 593     PaintRefresher.Refresh(null, viewport.alignment);\r
 594   }\r
 595 \r
 596   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 597   {\r
 598     ColumnSelection colSel = viewport.getColumnSelection();\r
 599 \r
 600     if (colSel.size() > 0)\r
 601     {\r
 602       addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
 603                                      HistoryItem.HIDE));\r
 604 \r
 605       int min = colSel.getMin();\r
 606       viewport.getAlignment().trimLeft(min);\r
 607       colSel.compensateForEdit(0, min);\r
 608 \r
 609       if (viewport.getSelectionGroup() != null)\r
 610       {\r
 611         viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 612       }\r
 613 \r
 614       Vector groups = viewport.alignment.getGroups();\r
 615 \r
 616       for (int i = 0; i < groups.size(); i++)\r
 617       {\r
 618         SequenceGroup sg = (SequenceGroup) groups.get(i);\r
 619 \r
 620         if (!sg.adjustForRemoveLeft(min))\r
 621         {\r
 622           viewport.alignment.deleteGroup(sg);\r
 623         }\r
 624       }\r
 625 \r
 626       alignPanel.repaint();\r
 627     }\r
 628   }\r
 629 \r
 630   public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 631   {\r
 632     ColumnSelection colSel = viewport.getColumnSelection();\r
 633 \r
 634     if (colSel.size() > 0)\r
 635     {\r
 636       addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
 637                                      HistoryItem.HIDE));\r
 638 \r
 639       int max = colSel.getMax();\r
 640       viewport.getAlignment().trimRight(max);\r
 641 \r
 642       if (viewport.getSelectionGroup() != null)\r
 643       {\r
 644         viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 645       }\r
 646 \r
 647       Vector groups = viewport.alignment.getGroups();\r
 648 \r
 649       for (int i = 0; i < groups.size(); i++)\r
 650       {\r
 651         SequenceGroup sg = (SequenceGroup) groups.get(i);\r
 652 \r
 653         if (!sg.adjustForRemoveRight(max))\r
 654         {\r
 655           viewport.alignment.deleteGroup(sg);\r
 656         }\r
 657       }\r
 658 \r
 659       alignPanel.repaint();\r
 660     }\r
 661   }\r
 662 \r
 663   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 664   {\r
 665     addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
 666                                    viewport.alignment, HistoryItem.HIDE));\r
 667 \r
 668     viewport.getAlignment().removeGaps();\r
 669     viewport.updateConservation();\r
 670     viewport.updateConsensus();\r
 671     alignPanel.repaint();\r
 672   }\r
 673 \r
 674   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 675   {\r
 676     addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
 677                                    HistoryItem.HIDE));\r
 678 \r
 679     SequenceI current;\r
 680     int jSize;\r
 681 \r
 682     for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
 683          i++)\r
 684     {\r
 685       current = viewport.getAlignment().getSequenceAt(i);\r
 686       jSize = current.getLength();\r
 687 \r
 688       for (int j = 0; j < jSize; j++)\r
 689       {\r
 690         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 691         {\r
 692           current.deleteCharAt(j);\r
 693           j--;\r
 694           jSize--;\r
 695         }\r
 696       }\r
 697     }\r
 698 \r
 699     viewport.updateConservation();\r
 700     viewport.updateConsensus();\r
 701     alignPanel.repaint();\r
 702   }\r
 703 \r
 704   public void padGapsMenuitem_actionPerformed(ActionEvent e)\r
 705   {\r
 706     addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,\r
 707                                    HistoryItem.HIDE));\r
 708 \r
 709     SequenceI current;\r
 710     int Width = viewport.getAlignment().getWidth();\r
 711 \r
 712     for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
 713          i++)\r
 714     {\r
 715       current = viewport.getAlignment().getSequenceAt(i);\r
 716 \r
 717       if (current.getLength() < Width)\r
 718       {\r
 719         current.insertCharAt(Width-1, viewport.getGapCharacter());\r
 720       }\r
 721     }\r
 722 \r
 723     viewport.updateConservation();\r
 724     viewport.updateConsensus();\r
 725     alignPanel.repaint();\r
 726   }\r
 727 \r
 728   public void findMenuItem_actionPerformed(ActionEvent e)\r
 729   {\r
 730     JInternalFrame frame = new JInternalFrame();\r
 731     Finder finder = new Finder(viewport, alignPanel, frame);\r
 732     frame.setContentPane(finder);\r
 733     Desktop.addInternalFrame(frame, "Find", 340, 110);\r
 734     frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
 735   }\r
 736 \r
 737   public void font_actionPerformed(ActionEvent e)\r
 738   {\r
 739     FontChooser fc = new FontChooser(alignPanel);\r
 740   }\r
 741 \r
 742   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 743   {\r
 744     viewport.setShowFullId(fullSeqId.isSelected());\r
 745 \r
 746     alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());\r
 747     alignPanel.repaint();\r
 748   }\r
 749 \r
 750   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 751   {\r
 752     viewport.setColourText(colourTextMenuItem.isSelected());\r
 753     alignPanel.repaint();\r
 754   }\r
 755 \r
 756   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 757   {\r
 758     viewport.setWrapAlignment(wrapMenuItem.isSelected());\r
 759     alignPanel.setWrapAlignment(wrapMenuItem.isSelected());\r
 760     scaleAbove.setVisible(wrapMenuItem.isSelected());\r
 761     scaleLeft.setVisible(wrapMenuItem.isSelected());\r
 762     scaleRight.setVisible(wrapMenuItem.isSelected());\r
 763     alignPanel.repaint();\r
 764   }\r
 765 \r
 766   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 767   {\r
 768     viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
 769     alignPanel.repaint();\r
 770   }\r
 771 \r
 772   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 773   {\r
 774     viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
 775     alignPanel.repaint();\r
 776   }\r
 777 \r
 778   protected void scaleRight_actionPerformed(ActionEvent e)\r
 779   {\r
 780     viewport.setScaleRightWrapped(scaleRight.isSelected());\r
 781     alignPanel.repaint();\r
 782   }\r
 783 \r
 784   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 785   {\r
 786     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());\r
 787     alignPanel.repaint();\r
 788   }\r
 789 \r
 790   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 791   {\r
 792     viewport.setShowText(viewTextMenuItem.isSelected());\r
 793     alignPanel.repaint();\r
 794   }\r
 795 \r
 796   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 797   {\r
 798     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 799     alignPanel.repaint();\r
 800   }\r
 801 \r
 802   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 803   {\r
 804     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 805 \r
 806     if (viewport.showSequenceFeatures &&\r
 807         ! ( (Alignment) viewport.alignment).featuresAdded)\r
 808     {\r
 809       SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.\r
 810           alignment,\r
 811           alignPanel);\r
 812       ( (Alignment) viewport.alignment).featuresAdded = true;\r
 813     }\r
 814 \r
 815     alignPanel.repaint();\r
 816   }\r
 817 \r
 818   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 819   {\r
 820     if (annotationPanelMenuItem.isSelected() &&\r
 821         viewport.getWrapAlignment())\r
 822     {\r
 823       annotationPanelMenuItem.setSelected(false);\r
 824 \r
 825       return;\r
 826     }\r
 827 \r
 828     viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());\r
 829     alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());\r
 830   }\r
 831 \r
 832   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 833   {\r
 834     if (alignPanel.overviewPanel != null)\r
 835     {\r
 836       return;\r
 837     }\r
 838 \r
 839     JInternalFrame frame = new JInternalFrame();\r
 840     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 841     frame.setContentPane(overview);\r
 842     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 843                              frame.getWidth(), frame.getHeight());\r
 844     frame.pack();\r
 845     frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
 846     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 847     {\r
 848       public void internalFrameClosed(\r
 849           javax.swing.event.InternalFrameEvent evt)\r
 850       {\r
 851         alignPanel.setOverviewPanel(null);\r
 852       }\r
 853       ;\r
 854     });\r
 855 \r
 856     alignPanel.setOverviewPanel(overview);\r
 857   }\r
 858 \r
 859   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 860   {\r
 861     changeColour(null);\r
 862   }\r
 863 \r
 864   public void clustalColour_actionPerformed(ActionEvent e)\r
 865   {\r
 866     changeColour(new ClustalxColourScheme(\r
 867         viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 868   }\r
 869 \r
 870   public void zappoColour_actionPerformed(ActionEvent e)\r
 871   {\r
 872     changeColour(new ZappoColourScheme());\r
 873   }\r
 874 \r
 875   public void taylorColour_actionPerformed(ActionEvent e)\r
 876   {\r
 877     changeColour(new TaylorColourScheme());\r
 878   }\r
 879 \r
 880   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 881   {\r
 882     changeColour(new HydrophobicColourScheme());\r
 883   }\r
 884 \r
 885   public void helixColour_actionPerformed(ActionEvent e)\r
 886   {\r
 887     changeColour(new HelixColourScheme());\r
 888   }\r
 889 \r
 890   public void strandColour_actionPerformed(ActionEvent e)\r
 891   {\r
 892     changeColour(new StrandColourScheme());\r
 893   }\r
 894 \r
 895   public void turnColour_actionPerformed(ActionEvent e)\r
 896   {\r
 897     changeColour(new TurnColourScheme());\r
 898   }\r
 899 \r
 900   public void buriedColour_actionPerformed(ActionEvent e)\r
 901   {\r
 902     changeColour(new BuriedColourScheme());\r
 903   }\r
 904 \r
 905   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 906   {\r
 907     changeColour(new NucleotideColourScheme());\r
 908   }\r
 909 \r
 910   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 911   {\r
 912     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
 913   }\r
 914 \r
 915   void changeColour(ColourSchemeI cs)\r
 916   {\r
 917     int threshold = 0;\r
 918 \r
 919     if (viewport.getAbovePIDThreshold())\r
 920     {\r
 921       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,\r
 922                                                  "Background");\r
 923 \r
 924       if (cs instanceof ResidueColourScheme)\r
 925       {\r
 926         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 927       }\r
 928       else if (cs instanceof ScoreColourScheme)\r
 929       {\r
 930         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 931       }\r
 932 \r
 933       viewport.setGlobalColourScheme(cs);\r
 934     }\r
 935     else if (cs instanceof ResidueColourScheme)\r
 936     {\r
 937       ( (ResidueColourScheme) cs).setThreshold(0);\r
 938     }\r
 939     else if (cs instanceof ScoreColourScheme)\r
 940     {\r
 941       ( (ScoreColourScheme) cs).setThreshold(0);\r
 942     }\r
 943 \r
 944     if (viewport.getConservationSelected())\r
 945     {\r
 946       ConservationColourScheme ccs = null;\r
 947 \r
 948       Alignment al = (Alignment) viewport.alignment;\r
 949       Conservation c = new Conservation("All",\r
 950                                         ResidueProperties.propHash, 3,\r
 951                                         al.getSequences(), 0,\r
 952                                         al.getWidth() - 1);\r
 953 \r
 954       c.calculate();\r
 955       c.verdict(false, viewport.ConsPercGaps);\r
 956 \r
 957       ccs = new ConservationColourScheme(c, cs);\r
 958 \r
 959       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 960       ccs.setConsensus(viewport.vconsensus);\r
 961       viewport.setGlobalColourScheme(ccs);\r
 962 \r
 963       ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,\r
 964                                                   "Background");\r
 965     }\r
 966     else\r
 967     {\r
 968       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 969       if (cs != null)\r
 970       {\r
 971         cs.setConsensus(viewport.vconsensus);\r
 972       }\r
 973 \r
 974       viewport.setGlobalColourScheme(cs);\r
 975     }\r
 976 \r
 977     if (viewport.getColourAppliesToAllGroups())\r
 978     {\r
 979       Vector groups = viewport.alignment.getGroups();\r
 980 \r
 981       for (int i = 0; i < groups.size(); i++)\r
 982       {\r
 983         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 984 \r
 985         if (cs == null)\r
 986         {\r
 987           sg.cs = null;\r
 988         }\r
 989         else if (cs instanceof ClustalxColourScheme)\r
 990         {\r
 991           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
 992         }\r
 993         else if (cs instanceof UserColourScheme)\r
 994         {\r
 995           sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());\r
 996         }\r
 997         else\r
 998         {\r
 999           try\r
1000           {\r
1001             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
1002           }\r
1003           catch (Exception ex)\r
1004           {\r
1005           }\r
1006         }\r
1007 \r
1008         if (viewport.getAbovePIDThreshold())\r
1009         {\r
1010           if (sg.cs instanceof ResidueColourScheme)\r
1011           {\r
1012             ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
1013           }\r
1014           else if (sg.cs instanceof ScoreColourScheme)\r
1015           {\r
1016             ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
1017           }\r
1018 \r
1019           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
1020               sg.getWidth()));\r
1021         }\r
1022 \r
1023         if (viewport.getConservationSelected())\r
1024         {\r
1025           Conservation c = new Conservation("Group",\r
1026                                             ResidueProperties.propHash, 3,\r
1027                                             sg.sequences, 0,\r
1028                                             viewport.alignment.getWidth() - 1);\r
1029           c.calculate();\r
1030           c.verdict(false, viewport.ConsPercGaps);\r
1031 \r
1032           ConservationColourScheme ccs = new ConservationColourScheme(c,\r
1033               sg.cs);\r
1034 \r
1035           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
1036           ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
1037                                                  sg.getWidth()));\r
1038           sg.cs = ccs;\r
1039         }\r
1040         else if (cs != null)\r
1041         {\r
1042           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
1043           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
1044               sg.getWidth()));\r
1045         }\r
1046       }\r
1047     }\r
1048 \r
1049     if (alignPanel.getOverviewPanel() != null)\r
1050     {\r
1051       alignPanel.getOverviewPanel().updateOverviewImage();\r
1052     }\r
1053 \r
1054     alignPanel.repaint();\r
1055   }\r
1056 \r
1057   protected void modifyPID_actionPerformed(ActionEvent e)\r
1058   {\r
1059     if (viewport.getAbovePIDThreshold())\r
1060     {\r
1061       SliderPanel.setPIDSliderSource(alignPanel,\r
1062                                      viewport.getGlobalColourScheme(),\r
1063                                      "Background");\r
1064       SliderPanel.showPIDSlider();\r
1065     }\r
1066   }\r
1067 \r
1068   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1069   {\r
1070     if (viewport.getConservationSelected())\r
1071     {\r
1072       SliderPanel.setConservationSlider(alignPanel,\r
1073                                         viewport.globalColourScheme,\r
1074                                         "Background");\r
1075       SliderPanel.showConservationSlider();\r
1076     }\r
1077   }\r
1078 \r
1079   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1080   {\r
1081     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
1082 \r
1083     viewport.setAbovePIDThreshold(false);\r
1084     abovePIDThreshold.setSelected(false);\r
1085 \r
1086     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
1087 \r
1088     if (cs instanceof ConservationColourScheme)\r
1089     {\r
1090       changeColour( ( (ConservationColourScheme) cs).cs);\r
1091     }\r
1092     else\r
1093     {\r
1094       changeColour(cs);\r
1095     }\r
1096 \r
1097     modifyConservation_actionPerformed(null);\r
1098   }\r
1099 \r
1100   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1101   {\r
1102     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
1103 \r
1104     conservationMenuItem.setSelected(false);\r
1105     viewport.setConservationSelected(false);\r
1106 \r
1107     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
1108 \r
1109     if (cs instanceof ConservationColourScheme)\r
1110     {\r
1111       changeColour( ( (ConservationColourScheme) cs).cs);\r
1112     }\r
1113     else\r
1114     {\r
1115       changeColour(cs);\r
1116     }\r
1117 \r
1118     modifyPID_actionPerformed(null);\r
1119   }\r
1120 \r
1121   public void userDefinedColour_actionPerformed(ActionEvent e)\r
1122   {\r
1123     new UserDefinedColours(alignPanel, null);\r
1124   }\r
1125 \r
1126   public void PIDColour_actionPerformed(ActionEvent e)\r
1127   {\r
1128     changeColour(new PIDColourScheme());\r
1129   }\r
1130 \r
1131   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1132   {\r
1133     changeColour(new Blosum62ColourScheme());\r
1134   }\r
1135 \r
1136   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1137   {\r
1138     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1139                                    HistoryItem.SORT));\r
1140     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1141                               viewport.getAlignment().getSequenceAt(0));\r
1142     alignPanel.repaint();\r
1143   }\r
1144 \r
1145   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1146   {\r
1147     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1148                                    HistoryItem.SORT));\r
1149     AlignmentSorter.sortByID(viewport.getAlignment());\r
1150     alignPanel.repaint();\r
1151   }\r
1152 \r
1153   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1154   {\r
1155     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1156                                    HistoryItem.SORT));\r
1157 \r
1158     //  AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1159     AlignmentSorter.sortGroups(viewport.getAlignment());\r
1160     alignPanel.repaint();\r
1161   }\r
1162 \r
1163   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1164   {\r
1165     RedundancyPanel sp = new RedundancyPanel(alignPanel, this);\r
1166     JInternalFrame frame = new JInternalFrame();\r
1167     frame.setContentPane(sp);\r
1168     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,\r
1169                              100, false);\r
1170   }\r
1171 \r
1172   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1173   {\r
1174     if ( (viewport.getSelectionGroup() == null) ||\r
1175         (viewport.getSelectionGroup().getSize() < 2))\r
1176     {\r
1177       JOptionPane.showInternalMessageDialog(this,\r
1178                                             "You must select at least 2 sequences.",\r
1179                                             "Invalid Selection",\r
1180                                             JOptionPane.WARNING_MESSAGE);\r
1181     }\r
1182     else\r
1183     {\r
1184       JInternalFrame frame = new JInternalFrame();\r
1185       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
1186       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
1187     }\r
1188   }\r
1189 \r
1190   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
1191   {\r
1192     if ( ( (viewport.getSelectionGroup() != null) &&\r
1193           (viewport.getSelectionGroup().getSize() < 4) &&\r
1194           (viewport.getSelectionGroup().getSize() > 0)) ||\r
1195         (viewport.getAlignment().getHeight() < 4))\r
1196     {\r
1197       JOptionPane.showInternalMessageDialog(this,\r
1198                                             "Principal component analysis must take\n" +\r
1199                                             "at least 4 input sequences.",\r
1200                                             "Sequence selection insufficient",\r
1201                                             JOptionPane.WARNING_MESSAGE);\r
1202 \r
1203       return;\r
1204     }\r
1205 \r
1206     try\r
1207     {\r
1208       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
1209       JInternalFrame frame = new JInternalFrame();\r
1210       frame.setContentPane(pcaPanel);\r
1211       Desktop.addInternalFrame(frame, "Principal component analysis",\r
1212                                400, 400);\r
1213     }\r
1214     catch (java.lang.OutOfMemoryError ex)\r
1215     {\r
1216       JOptionPane.showInternalMessageDialog(this,\r
1217                                             "Too many sequences selected\nfor Principal Component Analysis!!",\r
1218                                             "Out of memory",\r
1219                                             JOptionPane.WARNING_MESSAGE);\r
1220     }\r
1221   }\r
1222 \r
1223   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1224   {\r
1225     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1226   }\r
1227 \r
1228   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1229   {\r
1230     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1231   }\r
1232 \r
1233   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1234   {\r
1235     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1236   }\r
1237 \r
1238   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1239   {\r
1240     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
1241   }\r
1242 \r
1243   void NewTreePanel(String type, String pwType, String title)\r
1244   {\r
1245     final TreePanel tp;\r
1246 \r
1247     if ( (viewport.getSelectionGroup() != null) &&\r
1248         (viewport.getSelectionGroup().getSize() > 3))\r
1249     {\r
1250       int s = 0;\r
1251       SequenceGroup sg = viewport.getSelectionGroup();\r
1252 \r
1253       /* Decide if the selection is a column region */\r
1254       while (s < sg.sequences.size())\r
1255       {\r
1256         if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <\r
1257             sg.getEndRes())\r
1258         {\r
1259           JOptionPane.showMessageDialog(Desktop.desktop,\r
1260                                         "The selected region to create a tree may\nonly contain residues or gaps.\n" +\r
1261                                         "Try using the Pad function in the edit menu,\n" +\r
1262                                         "or one of the multiple sequence alignment web services.",\r
1263                                         "Sequences in selection are not aligned",\r
1264                                         JOptionPane.WARNING_MESSAGE);\r
1265 \r
1266           return;\r
1267         }\r
1268       }\r
1269 \r
1270       title = title + " on region";\r
1271       tp = new TreePanel(viewport,\r
1272                          viewport.getSelectionGroup().sequences, type, pwType,\r
1273                          sg.getStartRes(), sg.getEndRes());\r
1274     }\r
1275     else\r
1276     {\r
1277       //are the sequences aligned?\r
1278       if (!viewport.alignment.isAligned())\r
1279       {\r
1280         JOptionPane.showMessageDialog(Desktop.desktop,\r
1281                                       "The sequences must be aligned before creating a tree.\n" +\r
1282                                       "Try using the Pad function in the edit menu,\n" +\r
1283                                       "or one of the multiple sequence alignment web services.",\r
1284                                       "Sequences not aligned",\r
1285                                       JOptionPane.WARNING_MESSAGE);\r
1286 \r
1287         return;\r
1288       }\r
1289 \r
1290       tp = new TreePanel(viewport,\r
1291                          viewport.getAlignment().getSequences(), type, pwType,\r
1292                          0,\r
1293                          viewport.alignment.getWidth());\r
1294     }\r
1295 \r
1296     addTreeMenuItem(tp, title);\r
1297     viewport.setCurrentTree(tp.getTree());\r
1298 \r
1299     Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);\r
1300   }\r
1301 \r
1302   public void addSortByOrderMenuItem(String title, final AlignmentOrder order)\r
1303   {\r
1304     final JMenuItem item = new JMenuItem("by " + title);\r
1305     sort.add(item);\r
1306     item.addActionListener(new java.awt.event.ActionListener()\r
1307     {\r
1308       public void actionPerformed(ActionEvent e)\r
1309       {\r
1310         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1311                                        HistoryItem.SORT));\r
1312 \r
1313         // TODO: JBPNote - have to map order entries to curent SequenceI pointers\r
1314         AlignmentSorter.sortBy(viewport.getAlignment(), order);\r
1315         alignPanel.repaint();\r
1316       }\r
1317     });\r
1318   }\r
1319 \r
1320   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1321   {\r
1322     final JMenuItem item = new JMenuItem(title);\r
1323 \r
1324     treeCount++;\r
1325 \r
1326     if (treeCount == 1)\r
1327     {\r
1328       sort.add(sortByTreeMenu);\r
1329     }\r
1330 \r
1331     sortByTreeMenu.add(item);\r
1332     item.addActionListener(new java.awt.event.ActionListener()\r
1333     {\r
1334       public void actionPerformed(ActionEvent e)\r
1335       {\r
1336         addHistoryItem(new HistoryItem("Tree Sort",\r
1337                                        viewport.alignment, HistoryItem.SORT));\r
1338         AlignmentSorter.sortByTree(viewport.getAlignment(),\r
1339                                    treePanel.getTree());\r
1340         alignPanel.repaint();\r
1341       }\r
1342     });\r
1343 \r
1344     treePanel.addInternalFrameListener(new javax.swing.event.\r
1345                                        InternalFrameAdapter()\r
1346     {\r
1347       public void internalFrameClosed(\r
1348           javax.swing.event.InternalFrameEvent evt)\r
1349       {\r
1350         treeCount--;\r
1351         sortByTreeMenu.remove(item);\r
1352 \r
1353         if (treeCount == 0)\r
1354         {\r
1355           sort.remove(sortByTreeMenu);\r
1356         }\r
1357       }\r
1358       ;\r
1359     });\r
1360     viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
1361     {\r
1362       public void propertyChange(PropertyChangeEvent evt)\r
1363       {\r
1364         if (evt.getPropertyName().equals("alignment"))\r
1365         {\r
1366           treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());\r
1367           treePanel.repaint();\r
1368         }\r
1369       }\r
1370     });\r
1371   }\r
1372 \r
1373   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
1374   {\r
1375     // TODO:resolve which menu item was actually selected\r
1376     // Now, check we have enough sequences\r
1377     SequenceI[] msa = null;\r
1378 \r
1379     if ( (viewport.getSelectionGroup() != null) &&\r
1380         (viewport.getSelectionGroup().getSize() > 1))\r
1381     {\r
1382       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1383       SequenceGroup seqs = viewport.getSelectionGroup();\r
1384       int sz;\r
1385       msa = new SequenceI[sz = seqs.getSize()];\r
1386 \r
1387       for (int i = 0; i < sz; i++)\r
1388       {\r
1389         msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1390       }\r
1391     }\r
1392     else\r
1393     {\r
1394       Vector seqs = viewport.getAlignment().getSequences();\r
1395 \r
1396       if (seqs.size() > 1)\r
1397       {\r
1398         msa = new SequenceI[seqs.size()];\r
1399 \r
1400         for (int i = 0; i < seqs.size(); i++)\r
1401         {\r
1402           msa[i] = (SequenceI) seqs.elementAt(i);\r
1403         }\r
1404       }\r
1405     }\r
1406 \r
1407     if (msa != null)\r
1408     {\r
1409       jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",\r
1410           title, msa, false, true);\r
1411     }\r
1412   }\r
1413 \r
1414   public void ClustalRealign_actionPerformed(ActionEvent e)\r
1415   {\r
1416     // TODO:resolve which menu item was actually selected\r
1417     // Now, check we have enough sequences\r
1418     SequenceI[] msa = null;\r
1419 \r
1420     if ( (viewport.getSelectionGroup() != null) &&\r
1421         (viewport.getSelectionGroup().getSize() > 1))\r
1422     {\r
1423       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1424       SequenceGroup seqs = viewport.getSelectionGroup();\r
1425       int sz;\r
1426       msa = new SequenceI[sz = seqs.getSize()];\r
1427 \r
1428       for (int i = 0; i < sz; i++)\r
1429       {\r
1430         msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1431       }\r
1432     }\r
1433     else\r
1434     {\r
1435       Vector seqs = viewport.getAlignment().getSequences();\r
1436 \r
1437       if (seqs.size() > 1)\r
1438       {\r
1439         msa = new SequenceI[seqs.size()];\r
1440 \r
1441         for (int i = 0; i < seqs.size(); i++)\r
1442         {\r
1443           msa[i] = (SequenceI) seqs.elementAt(i);\r
1444         }\r
1445       }\r
1446     }\r
1447 \r
1448     if (msa != null)\r
1449     {\r
1450       jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",\r
1451           title, msa, true, true);\r
1452     }\r
1453   }\r
1454 \r
1455   protected void jpred_actionPerformed(ActionEvent e)\r
1456   {\r
1457     SequenceI seq = null;\r
1458     SequenceI[] msa = null;\r
1459 \r
1460     if ( (viewport.getSelectionGroup() != null) &&\r
1461         (viewport.getSelectionGroup().getSize() > 0))\r
1462     {\r
1463       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1464       SequenceGroup seqs = viewport.getSelectionGroup();\r
1465 \r
1466       if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())\r
1467       {\r
1468         seq = (SequenceI) seqs.getSequenceAt(0);\r
1469       }\r
1470       else\r
1471       {\r
1472         int sz;\r
1473         msa = new SequenceI[sz = seqs.getSize()];\r
1474 \r
1475         for (int i = 0; i < sz; i++)\r
1476         {\r
1477           msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1478         }\r
1479       }\r
1480     }\r
1481     else\r
1482     {\r
1483       Vector seqs = viewport.getAlignment().getSequences();\r
1484 \r
1485       if ( (seqs.size() == 1) || !viewport.alignment.isAligned())\r
1486       {\r
1487         seq = (SequenceI) seqs.elementAt(0);\r
1488       }\r
1489       else\r
1490       {\r
1491         msa = new SequenceI[seqs.size()];\r
1492 \r
1493         for (int i = 0; i < seqs.size(); i++)\r
1494         {\r
1495           msa[i] = (SequenceI) seqs.elementAt(i);\r
1496         }\r
1497       }\r
1498     }\r
1499 \r
1500     if (msa != null)\r
1501     {\r
1502       JPredClient ct = new JPredClient(title, msa);\r
1503     }\r
1504     else if (seq != null)\r
1505     {\r
1506       JPredClient ct = new JPredClient(title, seq);\r
1507     }\r
1508     else\r
1509     {\r
1510       System.err.print(\r
1511           "JALVIEW ERROR! - Unexpected JPred selection state!\n");\r
1512     }\r
1513   }\r
1514 \r
1515   protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
1516   {\r
1517     // TODO:resolve which menu item was actually selected\r
1518     // Now, check we have enough sequences\r
1519     SequenceI[] msa = null;\r
1520 \r
1521     if ( (viewport.getSelectionGroup() != null) &&\r
1522         (viewport.getSelectionGroup().getSize() > 1))\r
1523     {\r
1524       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1525       SequenceGroup seqs = viewport.getSelectionGroup();\r
1526       int sz;\r
1527       msa = new SequenceI[sz = seqs.getSize()];\r
1528 \r
1529       for (int i = 0; i < sz; i++)\r
1530       {\r
1531         msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1532       }\r
1533     }\r
1534     else\r
1535     {\r
1536       Vector seqs = viewport.getAlignment().getSequences();\r
1537 \r
1538       if (seqs.size() > 1)\r
1539       {\r
1540         msa = new SequenceI[seqs.size()];\r
1541 \r
1542         for (int i = 0; i < seqs.size(); i++)\r
1543         {\r
1544           msa[i] = (SequenceI) seqs.elementAt(i);\r
1545         }\r
1546       }\r
1547     }\r
1548 \r
1549     if (msa != null)\r
1550     {\r
1551       MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa,\r
1552                                                   false, true);\r
1553     }\r
1554   }\r
1555 \r
1556   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1557   {\r
1558     // Pick the tree file\r
1559     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
1560         getProperty(\r
1561             "LAST_DIRECTORY"));\r
1562     chooser.setFileView(new JalviewFileView());\r
1563     chooser.setDialogTitle("Select a newick-like tree file");\r
1564     chooser.setToolTipText("Load a tree file");\r
1565 \r
1566     int value = chooser.showOpenDialog(null);\r
1567 \r
1568     if (value == JalviewFileChooser.APPROVE_OPTION)\r
1569     {\r
1570       String choice = chooser.getSelectedFile().getPath();\r
1571       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1572 \r
1573       try\r
1574       {\r
1575         jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,\r
1576             "File");\r
1577         viewport.setCurrentTree( ShowNewickTree(fin, choice).getTree() );\r
1578       }\r
1579       catch (Exception ex)\r
1580       {\r
1581         JOptionPane.showMessageDialog(Desktop.desktop,\r
1582                                       "Problem reading tree file",\r
1583                                       ex.getMessage(),\r
1584                                       JOptionPane.WARNING_MESSAGE);\r
1585         ex.printStackTrace();\r
1586       }\r
1587     }\r
1588   }\r
1589 \r
1590   public TreePanel ShowNewickTree(NewickFile nf, String title)\r
1591   {\r
1592     TreePanel tp = null;\r
1593     try\r
1594     {\r
1595       nf.parse();\r
1596       if (nf.getTree() != null)\r
1597       {\r
1598         tp = new TreePanel(viewport,\r
1599                                      viewport.getAlignment().getSequences(), nf,\r
1600                                      "FromFile",\r
1601                                      title);\r
1602         Desktop.addInternalFrame(tp, title, 600, 500);\r
1603         addTreeMenuItem(tp, title);\r
1604       }\r
1605     }\r
1606     catch (Exception ex)\r
1607     {\r
1608       ex.printStackTrace();\r
1609     }\r
1610     return tp;\r
1611   }\r
1612 \r
1613   class PrintThread\r
1614       extends Thread\r
1615   {\r
1616     public void run()\r
1617     {\r
1618       PrinterJob printJob = PrinterJob.getPrinterJob();\r
1619       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
1620       printJob.setPrintable(alignPanel, pf);\r
1621 \r
1622       if (printJob.printDialog())\r
1623       {\r
1624         try\r
1625         {\r
1626           printJob.print();\r
1627         }\r
1628         catch (Exception PrintException)\r
1629         {\r
1630           PrintException.printStackTrace();\r
1631         }\r
1632       }\r
1633     }\r
1634   }\r
1635 }\r