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