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     Vector seqs=null;\r
 683 \r
 684     int start=0, end = viewport.alignment.getWidth();\r
 685 \r
 686     if(viewport.getSelectionGroup()!=null)\r
 687     {\r
 688       seqs = viewport.getSelectionGroup().sequences;\r
 689       start = viewport.getSelectionGroup().getStartRes();\r
 690       end = viewport.getSelectionGroup().getEndRes();\r
 691     }\r
 692     else\r
 693       seqs = viewport.alignment.getSequences();\r
 694 \r
 695     for (int i = 0; i <seqs.size(); i++)\r
 696     {\r
 697       current = (SequenceI)seqs.elementAt(i);\r
 698       jSize = current.getLength();\r
 699 \r
 700       int j = start;\r
 701       do\r
 702       {\r
 703         if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 704         {\r
 705           current.deleteCharAt(j);\r
 706           j--;\r
 707           jSize--;\r
 708         }\r
 709         j++;\r
 710       }\r
 711       while(j < end);\r
 712     }\r
 713 \r
 714     viewport.updateConservation();\r
 715     viewport.updateConsensus();\r
 716     alignPanel.repaint();\r
 717   }\r
 718 \r
 719   public void padGapsMenuitem_actionPerformed(ActionEvent e)\r
 720   {\r
 721     addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,\r
 722                                    HistoryItem.HIDE));\r
 723 \r
 724     SequenceI current;\r
 725     int Width = viewport.getAlignment().getWidth();\r
 726 \r
 727     for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
 728          i++)\r
 729     {\r
 730       current = viewport.getAlignment().getSequenceAt(i);\r
 731 \r
 732       if (current.getLength() < Width)\r
 733       {\r
 734         current.insertCharAt(Width-1, viewport.getGapCharacter());\r
 735       }\r
 736     }\r
 737 \r
 738     viewport.updateConservation();\r
 739     viewport.updateConsensus();\r
 740     alignPanel.repaint();\r
 741   }\r
 742 \r
 743   public void findMenuItem_actionPerformed(ActionEvent e)\r
 744   {\r
 745     JInternalFrame frame = new JInternalFrame();\r
 746     Finder finder = new Finder(viewport, alignPanel, frame);\r
 747     frame.setContentPane(finder);\r
 748     Desktop.addInternalFrame(frame, "Find", 340, 110);\r
 749     frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
 750   }\r
 751 \r
 752   public void font_actionPerformed(ActionEvent e)\r
 753   {\r
 754     FontChooser fc = new FontChooser(alignPanel);\r
 755   }\r
 756 \r
 757   protected void fullSeqId_actionPerformed(ActionEvent e)\r
 758   {\r
 759     viewport.setShowFullId(fullSeqId.isSelected());\r
 760 \r
 761     alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());\r
 762     alignPanel.repaint();\r
 763   }\r
 764 \r
 765   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
 766   {\r
 767     viewport.setColourText(colourTextMenuItem.isSelected());\r
 768     alignPanel.repaint();\r
 769   }\r
 770 \r
 771   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
 772   {\r
 773     viewport.setWrapAlignment(wrapMenuItem.isSelected());\r
 774     alignPanel.setWrapAlignment(wrapMenuItem.isSelected());\r
 775     scaleAbove.setVisible(wrapMenuItem.isSelected());\r
 776     scaleLeft.setVisible(wrapMenuItem.isSelected());\r
 777     scaleRight.setVisible(wrapMenuItem.isSelected());\r
 778     alignPanel.repaint();\r
 779   }\r
 780 \r
 781   protected void scaleAbove_actionPerformed(ActionEvent e)\r
 782   {\r
 783     viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
 784     alignPanel.repaint();\r
 785   }\r
 786 \r
 787   protected void scaleLeft_actionPerformed(ActionEvent e)\r
 788   {\r
 789     viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
 790     alignPanel.repaint();\r
 791   }\r
 792 \r
 793   protected void scaleRight_actionPerformed(ActionEvent e)\r
 794   {\r
 795     viewport.setScaleRightWrapped(scaleRight.isSelected());\r
 796     alignPanel.repaint();\r
 797   }\r
 798 \r
 799   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
 800   {\r
 801     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());\r
 802     alignPanel.repaint();\r
 803   }\r
 804 \r
 805   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
 806   {\r
 807     viewport.setShowText(viewTextMenuItem.isSelected());\r
 808     alignPanel.repaint();\r
 809   }\r
 810 \r
 811   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
 812   {\r
 813     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
 814     alignPanel.repaint();\r
 815   }\r
 816 \r
 817   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
 818   {\r
 819     viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
 820 \r
 821     if (viewport.showSequenceFeatures &&\r
 822         ! ( (Alignment) viewport.alignment).featuresAdded)\r
 823     {\r
 824       SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.\r
 825           alignment,\r
 826           alignPanel);\r
 827       ( (Alignment) viewport.alignment).featuresAdded = true;\r
 828     }\r
 829 \r
 830     alignPanel.repaint();\r
 831   }\r
 832 \r
 833   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
 834   {\r
 835     if (annotationPanelMenuItem.isSelected() &&\r
 836         viewport.getWrapAlignment())\r
 837     {\r
 838       annotationPanelMenuItem.setSelected(false);\r
 839 \r
 840       return;\r
 841     }\r
 842 \r
 843     viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());\r
 844     alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());\r
 845   }\r
 846 \r
 847   public void overviewMenuItem_actionPerformed(ActionEvent e)\r
 848   {\r
 849     if (alignPanel.overviewPanel != null)\r
 850     {\r
 851       return;\r
 852     }\r
 853 \r
 854     JInternalFrame frame = new JInternalFrame();\r
 855     OverviewPanel overview = new OverviewPanel(alignPanel);\r
 856     frame.setContentPane(overview);\r
 857     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
 858                              frame.getWidth(), frame.getHeight());\r
 859     frame.pack();\r
 860     frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
 861     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 862     {\r
 863       public void internalFrameClosed(\r
 864           javax.swing.event.InternalFrameEvent evt)\r
 865       {\r
 866         alignPanel.setOverviewPanel(null);\r
 867       }\r
 868       ;\r
 869     });\r
 870 \r
 871     alignPanel.setOverviewPanel(overview);\r
 872   }\r
 873 \r
 874   protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
 875   {\r
 876     changeColour(null);\r
 877   }\r
 878 \r
 879   public void clustalColour_actionPerformed(ActionEvent e)\r
 880   {\r
 881     changeColour(new ClustalxColourScheme(\r
 882         viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
 883   }\r
 884 \r
 885   public void zappoColour_actionPerformed(ActionEvent e)\r
 886   {\r
 887     changeColour(new ZappoColourScheme());\r
 888   }\r
 889 \r
 890   public void taylorColour_actionPerformed(ActionEvent e)\r
 891   {\r
 892     changeColour(new TaylorColourScheme());\r
 893   }\r
 894 \r
 895   public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
 896   {\r
 897     changeColour(new HydrophobicColourScheme());\r
 898   }\r
 899 \r
 900   public void helixColour_actionPerformed(ActionEvent e)\r
 901   {\r
 902     changeColour(new HelixColourScheme());\r
 903   }\r
 904 \r
 905   public void strandColour_actionPerformed(ActionEvent e)\r
 906   {\r
 907     changeColour(new StrandColourScheme());\r
 908   }\r
 909 \r
 910   public void turnColour_actionPerformed(ActionEvent e)\r
 911   {\r
 912     changeColour(new TurnColourScheme());\r
 913   }\r
 914 \r
 915   public void buriedColour_actionPerformed(ActionEvent e)\r
 916   {\r
 917     changeColour(new BuriedColourScheme());\r
 918   }\r
 919 \r
 920   public void nucleotideColour_actionPerformed(ActionEvent e)\r
 921   {\r
 922     changeColour(new NucleotideColourScheme());\r
 923   }\r
 924 \r
 925   protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
 926   {\r
 927     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
 928   }\r
 929 \r
 930   void changeColour(ColourSchemeI cs)\r
 931   {\r
 932     int threshold = 0;\r
 933 \r
 934     if (viewport.getAbovePIDThreshold())\r
 935     {\r
 936       threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,\r
 937                                                  "Background");\r
 938 \r
 939       if (cs instanceof ResidueColourScheme)\r
 940       {\r
 941         ( (ResidueColourScheme) cs).setThreshold(threshold);\r
 942       }\r
 943       else if (cs instanceof ScoreColourScheme)\r
 944       {\r
 945         ( (ScoreColourScheme) cs).setThreshold(threshold);\r
 946       }\r
 947 \r
 948       viewport.setGlobalColourScheme(cs);\r
 949     }\r
 950     else if (cs instanceof ResidueColourScheme)\r
 951     {\r
 952       ( (ResidueColourScheme) cs).setThreshold(0);\r
 953     }\r
 954     else if (cs instanceof ScoreColourScheme)\r
 955     {\r
 956       ( (ScoreColourScheme) cs).setThreshold(0);\r
 957     }\r
 958 \r
 959     if (viewport.getConservationSelected())\r
 960     {\r
 961       ConservationColourScheme ccs = null;\r
 962 \r
 963       Alignment al = (Alignment) viewport.alignment;\r
 964       Conservation c = new Conservation("All",\r
 965                                         ResidueProperties.propHash, 3,\r
 966                                         al.getSequences(), 0,\r
 967                                         al.getWidth() - 1);\r
 968 \r
 969       c.calculate();\r
 970       c.verdict(false, viewport.ConsPercGaps);\r
 971 \r
 972       ccs = new ConservationColourScheme(c, cs);\r
 973 \r
 974       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 975       ccs.setConsensus(viewport.vconsensus);\r
 976       viewport.setGlobalColourScheme(ccs);\r
 977 \r
 978       ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,\r
 979                                                   "Background");\r
 980     }\r
 981     else\r
 982     {\r
 983       // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
 984       if (cs != null)\r
 985       {\r
 986         cs.setConsensus(viewport.vconsensus);\r
 987       }\r
 988 \r
 989       viewport.setGlobalColourScheme(cs);\r
 990     }\r
 991 \r
 992     if (viewport.getColourAppliesToAllGroups())\r
 993     {\r
 994       Vector groups = viewport.alignment.getGroups();\r
 995 \r
 996       for (int i = 0; i < groups.size(); i++)\r
 997       {\r
 998         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 999 \r
1000         if (cs == null)\r
1001         {\r
1002           sg.cs = null;\r
1003         }\r
1004         else if (cs instanceof ClustalxColourScheme)\r
1005         {\r
1006           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
1007         }\r
1008         else if (cs instanceof UserColourScheme)\r
1009         {\r
1010           sg.cs = new UserColourScheme( ( (UserColourScheme) cs).getColours());\r
1011         }\r
1012         else\r
1013         {\r
1014           try\r
1015           {\r
1016             sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
1017           }\r
1018           catch (Exception ex)\r
1019           {\r
1020           }\r
1021         }\r
1022 \r
1023         if (viewport.getAbovePIDThreshold())\r
1024         {\r
1025           if (sg.cs instanceof ResidueColourScheme)\r
1026           {\r
1027             ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
1028           }\r
1029           else if (sg.cs instanceof ScoreColourScheme)\r
1030           {\r
1031             ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
1032           }\r
1033 \r
1034           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
1035               sg.getWidth()));\r
1036         }\r
1037 \r
1038         if (viewport.getConservationSelected())\r
1039         {\r
1040           Conservation c = new Conservation("Group",\r
1041                                             ResidueProperties.propHash, 3,\r
1042                                             sg.sequences, 0,\r
1043                                             viewport.alignment.getWidth() - 1);\r
1044           c.calculate();\r
1045           c.verdict(false, viewport.ConsPercGaps);\r
1046 \r
1047           ConservationColourScheme ccs = new ConservationColourScheme(c,\r
1048               sg.cs);\r
1049 \r
1050           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
1051           ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
1052                                                  sg.getWidth()));\r
1053           sg.cs = ccs;\r
1054         }\r
1055         else if (cs != null)\r
1056         {\r
1057           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
1058           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
1059               sg.getWidth()));\r
1060         }\r
1061       }\r
1062     }\r
1063 \r
1064     if (alignPanel.getOverviewPanel() != null)\r
1065     {\r
1066       alignPanel.getOverviewPanel().updateOverviewImage();\r
1067     }\r
1068 \r
1069     alignPanel.repaint();\r
1070   }\r
1071 \r
1072   protected void modifyPID_actionPerformed(ActionEvent e)\r
1073   {\r
1074     if (viewport.getAbovePIDThreshold())\r
1075     {\r
1076       SliderPanel.setPIDSliderSource(alignPanel,\r
1077                                      viewport.getGlobalColourScheme(),\r
1078                                      "Background");\r
1079       SliderPanel.showPIDSlider();\r
1080     }\r
1081   }\r
1082 \r
1083   protected void modifyConservation_actionPerformed(ActionEvent e)\r
1084   {\r
1085     if (viewport.getConservationSelected())\r
1086     {\r
1087       SliderPanel.setConservationSlider(alignPanel,\r
1088                                         viewport.globalColourScheme,\r
1089                                         "Background");\r
1090       SliderPanel.showConservationSlider();\r
1091     }\r
1092   }\r
1093 \r
1094   protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1095   {\r
1096     viewport.setConservationSelected(conservationMenuItem.isSelected());\r
1097 \r
1098     viewport.setAbovePIDThreshold(false);\r
1099     abovePIDThreshold.setSelected(false);\r
1100 \r
1101     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
1102 \r
1103     if (cs instanceof ConservationColourScheme)\r
1104     {\r
1105       changeColour( ( (ConservationColourScheme) cs).cs);\r
1106     }\r
1107     else\r
1108     {\r
1109       changeColour(cs);\r
1110     }\r
1111 \r
1112     modifyConservation_actionPerformed(null);\r
1113   }\r
1114 \r
1115   public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1116   {\r
1117     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
1118 \r
1119     conservationMenuItem.setSelected(false);\r
1120     viewport.setConservationSelected(false);\r
1121 \r
1122     ColourSchemeI cs = viewport.getGlobalColourScheme();\r
1123 \r
1124     if (cs instanceof ConservationColourScheme)\r
1125     {\r
1126       changeColour( ( (ConservationColourScheme) cs).cs);\r
1127     }\r
1128     else\r
1129     {\r
1130       changeColour(cs);\r
1131     }\r
1132 \r
1133     modifyPID_actionPerformed(null);\r
1134   }\r
1135 \r
1136   public void userDefinedColour_actionPerformed(ActionEvent e)\r
1137   {\r
1138     new UserDefinedColours(alignPanel, null);\r
1139   }\r
1140 \r
1141   public void PIDColour_actionPerformed(ActionEvent e)\r
1142   {\r
1143     changeColour(new PIDColourScheme());\r
1144   }\r
1145 \r
1146   public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1147   {\r
1148     changeColour(new Blosum62ColourScheme());\r
1149   }\r
1150 \r
1151   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1152   {\r
1153     addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1154                                    HistoryItem.SORT));\r
1155     AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1156                               viewport.getAlignment().getSequenceAt(0));\r
1157     alignPanel.repaint();\r
1158   }\r
1159 \r
1160   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1161   {\r
1162     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1163                                    HistoryItem.SORT));\r
1164     AlignmentSorter.sortByID(viewport.getAlignment());\r
1165     alignPanel.repaint();\r
1166   }\r
1167 \r
1168   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1169   {\r
1170     addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1171                                    HistoryItem.SORT));\r
1172 \r
1173     //  AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1174     AlignmentSorter.sortGroups(viewport.getAlignment());\r
1175     alignPanel.repaint();\r
1176   }\r
1177 \r
1178   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1179   {\r
1180     RedundancyPanel sp = new RedundancyPanel(alignPanel, this);\r
1181     JInternalFrame frame = new JInternalFrame();\r
1182     frame.setContentPane(sp);\r
1183     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,\r
1184                              100, false);\r
1185   }\r
1186 \r
1187   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1188   {\r
1189     if ( (viewport.getSelectionGroup() == null) ||\r
1190         (viewport.getSelectionGroup().getSize() < 2))\r
1191     {\r
1192       JOptionPane.showInternalMessageDialog(this,\r
1193                                             "You must select at least 2 sequences.",\r
1194                                             "Invalid Selection",\r
1195                                             JOptionPane.WARNING_MESSAGE);\r
1196     }\r
1197     else\r
1198     {\r
1199       JInternalFrame frame = new JInternalFrame();\r
1200       frame.setContentPane(new PairwiseAlignPanel(viewport));\r
1201       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
1202     }\r
1203   }\r
1204 \r
1205   public void PCAMenuItem_actionPerformed(ActionEvent e)\r
1206   {\r
1207     if ( ( (viewport.getSelectionGroup() != null) &&\r
1208           (viewport.getSelectionGroup().getSize() < 4) &&\r
1209           (viewport.getSelectionGroup().getSize() > 0)) ||\r
1210         (viewport.getAlignment().getHeight() < 4))\r
1211     {\r
1212       JOptionPane.showInternalMessageDialog(this,\r
1213                                             "Principal component analysis must take\n" +\r
1214                                             "at least 4 input sequences.",\r
1215                                             "Sequence selection insufficient",\r
1216                                             JOptionPane.WARNING_MESSAGE);\r
1217 \r
1218       return;\r
1219     }\r
1220 \r
1221     try\r
1222     {\r
1223       PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
1224       JInternalFrame frame = new JInternalFrame();\r
1225       frame.setContentPane(pcaPanel);\r
1226       Desktop.addInternalFrame(frame, "Principal component analysis",\r
1227                                400, 400);\r
1228     }\r
1229     catch (java.lang.OutOfMemoryError ex)\r
1230     {\r
1231       JOptionPane.showInternalMessageDialog(this,\r
1232                                             "Too many sequences selected\nfor Principal Component Analysis!!",\r
1233                                             "Out of memory",\r
1234                                             JOptionPane.WARNING_MESSAGE);\r
1235     }\r
1236   }\r
1237 \r
1238   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1239   {\r
1240     NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1241   }\r
1242 \r
1243   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1244   {\r
1245     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1246   }\r
1247 \r
1248   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1249   {\r
1250     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1251   }\r
1252 \r
1253   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1254   {\r
1255     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
1256   }\r
1257 \r
1258   void NewTreePanel(String type, String pwType, String title)\r
1259   {\r
1260     final TreePanel tp;\r
1261 \r
1262     if ( (viewport.getSelectionGroup() != null) &&\r
1263         (viewport.getSelectionGroup().getSize() > 3))\r
1264     {\r
1265       int s = 0;\r
1266       SequenceGroup sg = viewport.getSelectionGroup();\r
1267 \r
1268       /* Decide if the selection is a column region */\r
1269       while (s < sg.sequences.size())\r
1270       {\r
1271         if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <\r
1272             sg.getEndRes())\r
1273         {\r
1274           JOptionPane.showMessageDialog(Desktop.desktop,\r
1275                                         "The selected region to create a tree may\nonly contain residues or gaps.\n" +\r
1276                                         "Try using the Pad function in the edit menu,\n" +\r
1277                                         "or one of the multiple sequence alignment web services.",\r
1278                                         "Sequences in selection are not aligned",\r
1279                                         JOptionPane.WARNING_MESSAGE);\r
1280 \r
1281           return;\r
1282         }\r
1283       }\r
1284 \r
1285       title = title + " on region";\r
1286       tp = new TreePanel(viewport,\r
1287                          viewport.getSelectionGroup().sequences, type, pwType,\r
1288                          sg.getStartRes(), sg.getEndRes());\r
1289     }\r
1290     else\r
1291     {\r
1292       //are the sequences aligned?\r
1293       if (!viewport.alignment.isAligned())\r
1294       {\r
1295         JOptionPane.showMessageDialog(Desktop.desktop,\r
1296                                       "The sequences must be aligned before creating a tree.\n" +\r
1297                                       "Try using the Pad function in the edit menu,\n" +\r
1298                                       "or one of the multiple sequence alignment web services.",\r
1299                                       "Sequences not aligned",\r
1300                                       JOptionPane.WARNING_MESSAGE);\r
1301 \r
1302         return;\r
1303       }\r
1304 \r
1305       tp = new TreePanel(viewport,\r
1306                          viewport.getAlignment().getSequences(), type, pwType,\r
1307                          0,\r
1308                          viewport.alignment.getWidth());\r
1309     }\r
1310 \r
1311     addTreeMenuItem(tp, title);\r
1312     viewport.setCurrentTree(tp.getTree());\r
1313 \r
1314     Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);\r
1315   }\r
1316 \r
1317   public void addSortByOrderMenuItem(String title, final AlignmentOrder order)\r
1318   {\r
1319     final JMenuItem item = new JMenuItem("by " + title);\r
1320     sort.add(item);\r
1321     item.addActionListener(new java.awt.event.ActionListener()\r
1322     {\r
1323       public void actionPerformed(ActionEvent e)\r
1324       {\r
1325         addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1326                                        HistoryItem.SORT));\r
1327 \r
1328         // TODO: JBPNote - have to map order entries to curent SequenceI pointers\r
1329         AlignmentSorter.sortBy(viewport.getAlignment(), order);\r
1330         alignPanel.repaint();\r
1331       }\r
1332     });\r
1333   }\r
1334 \r
1335   void addTreeMenuItem(final TreePanel treePanel, String title)\r
1336   {\r
1337     final JMenuItem item = new JMenuItem(title);\r
1338 \r
1339     treeCount++;\r
1340 \r
1341     if (treeCount == 1)\r
1342     {\r
1343       sort.add(sortByTreeMenu);\r
1344     }\r
1345 \r
1346     sortByTreeMenu.add(item);\r
1347     item.addActionListener(new java.awt.event.ActionListener()\r
1348     {\r
1349       public void actionPerformed(ActionEvent e)\r
1350       {\r
1351         addHistoryItem(new HistoryItem("Tree Sort",\r
1352                                        viewport.alignment, HistoryItem.SORT));\r
1353         AlignmentSorter.sortByTree(viewport.getAlignment(),\r
1354                                    treePanel.getTree());\r
1355         alignPanel.repaint();\r
1356       }\r
1357     });\r
1358 \r
1359     treePanel.addInternalFrameListener(new javax.swing.event.\r
1360                                        InternalFrameAdapter()\r
1361     {\r
1362       public void internalFrameClosed(\r
1363           javax.swing.event.InternalFrameEvent evt)\r
1364       {\r
1365         treeCount--;\r
1366         sortByTreeMenu.remove(item);\r
1367 \r
1368         if (treeCount == 0)\r
1369         {\r
1370           sort.remove(sortByTreeMenu);\r
1371         }\r
1372       }\r
1373       ;\r
1374     });\r
1375     viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
1376     {\r
1377       public void propertyChange(PropertyChangeEvent evt)\r
1378       {\r
1379         if (evt.getPropertyName().equals("alignment"))\r
1380         {\r
1381           treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());\r
1382           treePanel.repaint();\r
1383         }\r
1384       }\r
1385     });\r
1386   }\r
1387 \r
1388   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
1389   {\r
1390     // TODO:resolve which menu item was actually selected\r
1391     // Now, check we have enough sequences\r
1392     SequenceI[] msa = null;\r
1393 \r
1394     if ( (viewport.getSelectionGroup() != null) &&\r
1395         (viewport.getSelectionGroup().getSize() > 1))\r
1396     {\r
1397       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1398       SequenceGroup seqs = viewport.getSelectionGroup();\r
1399       int sz;\r
1400       msa = new SequenceI[sz = seqs.getSize()];\r
1401 \r
1402       for (int i = 0; i < sz; i++)\r
1403       {\r
1404         msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1405       }\r
1406     }\r
1407     else\r
1408     {\r
1409       Vector seqs = viewport.getAlignment().getSequences();\r
1410 \r
1411       if (seqs.size() > 1)\r
1412       {\r
1413         msa = new SequenceI[seqs.size()];\r
1414 \r
1415         for (int i = 0; i < seqs.size(); i++)\r
1416         {\r
1417           msa[i] = (SequenceI) seqs.elementAt(i);\r
1418         }\r
1419       }\r
1420     }\r
1421 \r
1422     if (msa != null)\r
1423     {\r
1424       jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",\r
1425           title, msa, false, true);\r
1426     }\r
1427   }\r
1428 \r
1429   public void ClustalRealign_actionPerformed(ActionEvent e)\r
1430   {\r
1431     // TODO:resolve which menu item was actually selected\r
1432     // Now, check we have enough sequences\r
1433     SequenceI[] msa = null;\r
1434 \r
1435     if ( (viewport.getSelectionGroup() != null) &&\r
1436         (viewport.getSelectionGroup().getSize() > 1))\r
1437     {\r
1438       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1439       SequenceGroup seqs = viewport.getSelectionGroup();\r
1440       int sz;\r
1441       msa = new SequenceI[sz = seqs.getSize()];\r
1442 \r
1443       for (int i = 0; i < sz; i++)\r
1444       {\r
1445         msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1446       }\r
1447     }\r
1448     else\r
1449     {\r
1450       Vector seqs = viewport.getAlignment().getSequences();\r
1451 \r
1452       if (seqs.size() > 1)\r
1453       {\r
1454         msa = new SequenceI[seqs.size()];\r
1455 \r
1456         for (int i = 0; i < seqs.size(); i++)\r
1457         {\r
1458           msa[i] = (SequenceI) seqs.elementAt(i);\r
1459         }\r
1460       }\r
1461     }\r
1462 \r
1463     if (msa != null)\r
1464     {\r
1465       jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",\r
1466           title, msa, true, true);\r
1467     }\r
1468   }\r
1469 \r
1470   protected void jpred_actionPerformed(ActionEvent e)\r
1471   {\r
1472     SequenceI seq = null;\r
1473     SequenceI[] msa = null;\r
1474 \r
1475     if ( (viewport.getSelectionGroup() != null) &&\r
1476         (viewport.getSelectionGroup().getSize() > 0))\r
1477     {\r
1478       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1479       SequenceGroup seqs = viewport.getSelectionGroup();\r
1480 \r
1481       if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())\r
1482       {\r
1483         seq = (SequenceI) seqs.getSequenceAt(0);\r
1484       }\r
1485       else\r
1486       {\r
1487         int sz;\r
1488         msa = new SequenceI[sz = seqs.getSize()];\r
1489 \r
1490         for (int i = 0; i < sz; i++)\r
1491         {\r
1492           msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1493         }\r
1494       }\r
1495     }\r
1496     else\r
1497     {\r
1498       Vector seqs = viewport.getAlignment().getSequences();\r
1499 \r
1500       if ( (seqs.size() == 1) || !viewport.alignment.isAligned())\r
1501       {\r
1502         seq = (SequenceI) seqs.elementAt(0);\r
1503       }\r
1504       else\r
1505       {\r
1506         msa = new SequenceI[seqs.size()];\r
1507 \r
1508         for (int i = 0; i < seqs.size(); i++)\r
1509         {\r
1510           msa[i] = (SequenceI) seqs.elementAt(i);\r
1511         }\r
1512       }\r
1513     }\r
1514 \r
1515     if (msa != null)\r
1516     {\r
1517       JPredClient ct = new JPredClient(title, msa);\r
1518     }\r
1519     else if (seq != null)\r
1520     {\r
1521       JPredClient ct = new JPredClient(title, seq);\r
1522     }\r
1523     else\r
1524     {\r
1525       System.err.print(\r
1526           "JALVIEW ERROR! - Unexpected JPred selection state!\n");\r
1527     }\r
1528   }\r
1529 \r
1530   protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
1531   {\r
1532     // TODO:resolve which menu item was actually selected\r
1533     // Now, check we have enough sequences\r
1534     SequenceI[] msa = null;\r
1535 \r
1536     if ( (viewport.getSelectionGroup() != null) &&\r
1537         (viewport.getSelectionGroup().getSize() > 1))\r
1538     {\r
1539       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1540       SequenceGroup seqs = viewport.getSelectionGroup();\r
1541       int sz;\r
1542       msa = new SequenceI[sz = seqs.getSize()];\r
1543 \r
1544       for (int i = 0; i < sz; i++)\r
1545       {\r
1546         msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1547       }\r
1548     }\r
1549     else\r
1550     {\r
1551       Vector seqs = viewport.getAlignment().getSequences();\r
1552 \r
1553       if (seqs.size() > 1)\r
1554       {\r
1555         msa = new SequenceI[seqs.size()];\r
1556 \r
1557         for (int i = 0; i < seqs.size(); i++)\r
1558         {\r
1559           msa[i] = (SequenceI) seqs.elementAt(i);\r
1560         }\r
1561       }\r
1562     }\r
1563 \r
1564     if (msa != null)\r
1565     {\r
1566       MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa,\r
1567                                                   false, true);\r
1568     }\r
1569   }\r
1570 \r
1571   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
1572   {\r
1573     // Pick the tree file\r
1574     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
1575         getProperty(\r
1576             "LAST_DIRECTORY"));\r
1577     chooser.setFileView(new JalviewFileView());\r
1578     chooser.setDialogTitle("Select a newick-like tree file");\r
1579     chooser.setToolTipText("Load a tree file");\r
1580 \r
1581     int value = chooser.showOpenDialog(null);\r
1582 \r
1583     if (value == JalviewFileChooser.APPROVE_OPTION)\r
1584     {\r
1585       String choice = chooser.getSelectedFile().getPath();\r
1586       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1587 \r
1588       try\r
1589       {\r
1590         jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,\r
1591             "File");\r
1592         viewport.setCurrentTree( ShowNewickTree(fin, choice).getTree() );\r
1593       }\r
1594       catch (Exception ex)\r
1595       {\r
1596         JOptionPane.showMessageDialog(Desktop.desktop,\r
1597                                       "Problem reading tree file",\r
1598                                       ex.getMessage(),\r
1599                                       JOptionPane.WARNING_MESSAGE);\r
1600         ex.printStackTrace();\r
1601       }\r
1602     }\r
1603   }\r
1604 \r
1605   public TreePanel ShowNewickTree(NewickFile nf, String title)\r
1606   {\r
1607     TreePanel tp = null;\r
1608     try\r
1609     {\r
1610       nf.parse();\r
1611       if (nf.getTree() != null)\r
1612       {\r
1613         tp = new TreePanel(viewport,\r
1614                                      viewport.getAlignment().getSequences(), nf,\r
1615                                      "FromFile",\r
1616                                      title);\r
1617         Desktop.addInternalFrame(tp, title, 600, 500);\r
1618         addTreeMenuItem(tp, title);\r
1619       }\r
1620     }\r
1621     catch (Exception ex)\r
1622     {\r
1623       ex.printStackTrace();\r
1624     }\r
1625     return tp;\r
1626   }\r
1627 \r
1628   class PrintThread\r
1629       extends Thread\r
1630   {\r
1631     public void run()\r
1632     {\r
1633       PrinterJob printJob = PrinterJob.getPrinterJob();\r
1634       PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
1635       printJob.setPrintable(alignPanel, pf);\r
1636 \r
1637       if (printJob.printDialog())\r
1638       {\r
1639         try\r
1640         {\r
1641           printJob.print();\r
1642         }\r
1643         catch (Exception PrintException)\r
1644         {\r
1645           PrintException.printStackTrace();\r
1646         }\r
1647       }\r
1648     }\r
1649   }\r
1650 }\r