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 jalview.analysis.*;\r
  22 \r
  23 import jalview.datamodel.*;\r
  24 \r
  25 import jalview.io.*;\r
  26 \r
  27 import jalview.jbgui.*;\r
  28 \r
  29 import jalview.schemes.*;\r
  30 \r
  31 import jalview.ws.*;\r
  32 \r
  33 import java.awt.*;\r
  34 import java.awt.datatransfer.*;\r
  35 import java.awt.event.*;\r
  36 import java.awt.print.*;\r
  37 \r
  38 import java.io.*;\r
  39 \r
  40 import java.beans.*;\r
  41 \r
  42 import java.util.*;\r
  43 \r
  44 import javax.swing.*;\r
  45 import javax.swing.event.*;\r
  46 \r
  47 \r
  48 /**\r
  49  * DOCUMENT ME!\r
  50  *\r
  51  * @author $author$\r
  52  * @version $Revision$\r
  53  */\r
  54 public class AlignFrame extends GAlignFrame\r
  55 {\r
  56     /** DOCUMENT ME!! */\r
  57     public static final int NEW_WINDOW_WIDTH = 700;\r
  58 \r
  59     /** DOCUMENT ME!! */\r
  60     public static final int NEW_WINDOW_HEIGHT = 500;\r
  61     final AlignmentPanel alignPanel;\r
  62     final AlignViewport viewport;\r
  63 \r
  64     /** DOCUMENT ME!! */\r
  65     public String currentFileFormat = null;\r
  66     Stack historyList = new Stack();\r
  67     Stack redoList = new Stack();\r
  68     private int treeCount = 0;\r
  69 \r
  70     /**\r
  71      * Creates a new AlignFrame object.\r
  72      *\r
  73      * @param al DOCUMENT ME!\r
  74      */\r
  75     public AlignFrame(AlignmentI al)\r
  76     {\r
  77         viewport = new AlignViewport(al);\r
  78 \r
  79         alignPanel = new AlignmentPanel(this, viewport);\r
  80         alignPanel.annotationPanel.adjustPanelHeight();\r
  81         alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
  82         alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
  83         alignPanel.setAnnotationVisible(viewport.getShowAnnotation());\r
  84 \r
  85         getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
  86 \r
  87         addInternalFrameListener(new InternalFrameAdapter()\r
  88             {\r
  89                 public void internalFrameActivated(InternalFrameEvent evt)\r
  90                 {\r
  91                     javax.swing.SwingUtilities.invokeLater(new Runnable()\r
  92                         {\r
  93                             public void run()\r
  94                             {\r
  95                                 alignPanel.requestFocus();\r
  96                             }\r
  97                         });\r
  98                 }\r
  99             });\r
 100     }\r
 101 \r
 102 \r
 103     /**\r
 104      * DOCUMENT ME!\r
 105      *\r
 106      * @param e DOCUMENT ME!\r
 107      */\r
 108     public void parseGroupsFile(String file)\r
 109     {\r
 110       try{\r
 111         BufferedReader in = new BufferedReader(new FileReader(file));\r
 112         SequenceI seq=null;\r
 113         String line, text, token;\r
 114         UserColourScheme ucs;\r
 115         int index, start, end;\r
 116         StringTokenizer st;\r
 117         SequenceGroup sg;\r
 118         while( (line = in.readLine())!=null)\r
 119         {\r
 120           st = new StringTokenizer(line, "\t");\r
 121           if(st.countTokens()!=6)\r
 122           {\r
 123             System.out.println("Groups file "+file+" is invalid. Read help file.");\r
 124             System.exit(1);\r
 125           }\r
 126 \r
 127           while(st.hasMoreElements())\r
 128           {\r
 129             text = st.nextToken();\r
 130             token = st.nextToken();\r
 131             if(!token.equals("ID_NOT_SPECIFIED"))\r
 132             {\r
 133               index = viewport.alignment.findIndex(viewport.alignment.findName(\r
 134                   token));\r
 135               st.nextToken();\r
 136             }\r
 137             else\r
 138               index = Integer.parseInt( st.nextToken() );\r
 139 \r
 140             start=Integer.parseInt( st.nextToken() );\r
 141             end = Integer.parseInt( st.nextToken() );\r
 142             ucs = new UserColourScheme(st.nextToken());\r
 143 \r
 144             seq = viewport.alignment.getSequenceAt(index);\r
 145             start = seq.findIndex(start)-1;\r
 146             end = seq.findIndex(end)-1;\r
 147 \r
 148             sg = new SequenceGroup(text,ucs,true,true,false,start,end);\r
 149             sg.addSequence( seq,true);\r
 150 \r
 151             viewport.alignment.addGroup(sg);\r
 152           }\r
 153         }\r
 154 \r
 155       }catch(Exception ex){System.out.println("Error parsing groups file: "+ex);}\r
 156     }\r
 157 \r
 158     /**\r
 159      * DOCUMENT ME!\r
 160      *\r
 161      * @param e DOCUMENT ME!\r
 162      */\r
 163     public void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
 164     {\r
 165         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 166                     "LAST_DIRECTORY"),\r
 167                 new String[]\r
 168                 {\r
 169                     "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
 170                     "jar"\r
 171                 },\r
 172                 new String[]\r
 173                 {\r
 174                     "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
 175                 }, currentFileFormat);\r
 176 \r
 177         chooser.setAcceptAllFileFilterUsed(false);\r
 178         chooser.setFileView(new JalviewFileView());\r
 179         chooser.setDialogTitle("Save Alignment to file");\r
 180         chooser.setToolTipText("Save");\r
 181 \r
 182         int value = chooser.showSaveDialog(this);\r
 183 \r
 184         if (value == JalviewFileChooser.APPROVE_OPTION)\r
 185         {\r
 186             currentFileFormat = chooser.getSelectedFormat();\r
 187             jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",\r
 188                 currentFileFormat);\r
 189 \r
 190             String choice = chooser.getSelectedFile().getPath();\r
 191             jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
 192 \r
 193             saveAlignment(choice, currentFileFormat);\r
 194         }\r
 195     }\r
 196 \r
 197     public boolean saveAlignment(String file, String format)\r
 198     {\r
 199       if (format.equalsIgnoreCase("Jalview"))\r
 200       {\r
 201         String shortName = title;\r
 202 \r
 203         if (shortName.indexOf(java.io.File.separatorChar) > -1)\r
 204         {\r
 205           shortName = shortName.substring(shortName.lastIndexOf(\r
 206               java.io.File.separatorChar) + 1);\r
 207         }\r
 208 \r
 209         Jalview2XML.SaveAlignment(this, file, shortName);\r
 210 \r
 211         // USE Jalview2XML to save this file\r
 212         return true;\r
 213       }\r
 214       else\r
 215       {\r
 216         String output = FormatAdapter.formatSequences(format,\r
 217             viewport.getAlignment().\r
 218             getSequences());\r
 219         if(output==null)\r
 220           return false;\r
 221 \r
 222         try\r
 223         {\r
 224           java.io.PrintWriter out = new java.io.PrintWriter(\r
 225               new java.io.FileWriter(file));\r
 226           out.println(output);\r
 227           out.close();\r
 228           return true;\r
 229         }\r
 230         catch (Exception ex)\r
 231         {\r
 232           ex.printStackTrace();\r
 233         }\r
 234       }\r
 235       return false;\r
 236     }\r
 237 \r
 238 \r
 239     /**\r
 240      * DOCUMENT ME!\r
 241      *\r
 242      * @param e DOCUMENT ME!\r
 243      */\r
 244     protected void outputText_actionPerformed(ActionEvent e)\r
 245     {\r
 246         CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
 247         Desktop.addInternalFrame(cap,\r
 248             "Alignment output - " + e.getActionCommand(), 600, 500);\r
 249         cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),\r
 250                 viewport.getAlignment().getSequences()));\r
 251     }\r
 252 \r
 253     /**\r
 254      * DOCUMENT ME!\r
 255      *\r
 256      * @param e DOCUMENT ME!\r
 257      */\r
 258     protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
 259     {\r
 260         new HTMLOutput(viewport);\r
 261     }\r
 262 \r
 263     public void createImageMap(File file, String image)\r
 264     {\r
 265       alignPanel.makePNGImageMap(file, image);\r
 266     }\r
 267 \r
 268     /**\r
 269      * DOCUMENT ME!\r
 270      *\r
 271      * @param e DOCUMENT ME!\r
 272      */\r
 273     public void createPNG(File f)\r
 274     {\r
 275         alignPanel.makePNG(f);\r
 276     }\r
 277 \r
 278     /**\r
 279      * DOCUMENT ME!\r
 280      *\r
 281      * @param e DOCUMENT ME!\r
 282      */\r
 283     public void createEPS(File f)\r
 284     {\r
 285         alignPanel.makeEPS(f);\r
 286     }\r
 287 \r
 288     /**\r
 289      * DOCUMENT ME!\r
 290      *\r
 291      * @param e DOCUMENT ME!\r
 292      */\r
 293     public void printMenuItem_actionPerformed(ActionEvent e)\r
 294     {\r
 295         //Putting in a thread avoids Swing painting problems\r
 296         PrintThread thread = new PrintThread();\r
 297         thread.start();\r
 298     }\r
 299 \r
 300     /**\r
 301      * DOCUMENT ME!\r
 302      *\r
 303      * @param e DOCUMENT ME!\r
 304      */\r
 305     public void closeMenuItem_actionPerformed(ActionEvent e)\r
 306     {\r
 307         try\r
 308         {\r
 309             this.setClosed(true);\r
 310         }\r
 311         catch (Exception ex)\r
 312         {\r
 313         }\r
 314     }\r
 315 \r
 316     /**\r
 317      * DOCUMENT ME!\r
 318      */\r
 319     void updateEditMenuBar()\r
 320     {\r
 321         if (historyList.size() > 0)\r
 322         {\r
 323             undoMenuItem.setEnabled(true);\r
 324 \r
 325             HistoryItem hi = (HistoryItem) historyList.peek();\r
 326             undoMenuItem.setText("Undo " + hi.getDescription());\r
 327         }\r
 328         else\r
 329         {\r
 330             undoMenuItem.setEnabled(false);\r
 331             undoMenuItem.setText("Undo");\r
 332         }\r
 333 \r
 334         if (redoList.size() > 0)\r
 335         {\r
 336             redoMenuItem.setEnabled(true);\r
 337 \r
 338             HistoryItem hi = (HistoryItem) redoList.peek();\r
 339             redoMenuItem.setText("Redo " + hi.getDescription());\r
 340         }\r
 341         else\r
 342         {\r
 343             redoMenuItem.setEnabled(false);\r
 344             redoMenuItem.setText("Redo");\r
 345         }\r
 346     }\r
 347 \r
 348     /**\r
 349      * DOCUMENT ME!\r
 350      *\r
 351      * @param hi DOCUMENT ME!\r
 352      */\r
 353     public void addHistoryItem(HistoryItem hi)\r
 354     {\r
 355         historyList.push(hi);\r
 356         updateEditMenuBar();\r
 357     }\r
 358 \r
 359     /**\r
 360      * DOCUMENT ME!\r
 361      *\r
 362      * @param e DOCUMENT ME!\r
 363      */\r
 364     protected void undoMenuItem_actionPerformed(ActionEvent e)\r
 365     {\r
 366         HistoryItem hi = (HistoryItem) historyList.pop();\r
 367         redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
 368                 HistoryItem.HIDE));\r
 369         restoreHistoryItem(hi);\r
 370     }\r
 371 \r
 372     /**\r
 373      * DOCUMENT ME!\r
 374      *\r
 375      * @param e DOCUMENT ME!\r
 376      */\r
 377     protected void redoMenuItem_actionPerformed(ActionEvent e)\r
 378     {\r
 379         HistoryItem hi = (HistoryItem) redoList.pop();\r
 380         restoreHistoryItem(hi);\r
 381         updateEditMenuBar();\r
 382         viewport.updateConsensus();\r
 383         alignPanel.repaint();\r
 384         alignPanel.repaint();\r
 385     }\r
 386 \r
 387     // used by undo and redo\r
 388     void restoreHistoryItem(HistoryItem hi)\r
 389     {\r
 390         if (hi.getType() == HistoryItem.SORT)\r
 391         {\r
 392             for (int i = 0; i < hi.getSequences().size(); i++)\r
 393             {\r
 394                 viewport.alignment.getSequences().setElementAt(hi.getSequences()\r
 395                                                                  .elementAt(i),\r
 396                     i);\r
 397             }\r
 398         }\r
 399         else\r
 400         {\r
 401             for (int i = 0; i < hi.getSequences().size(); i++)\r
 402             {\r
 403                 SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
 404 \r
 405                 if (restore.getLength() == 0)\r
 406                 {\r
 407                     restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 408                     viewport.alignment.getSequences().insertElementAt(restore,\r
 409                         hi.getAlignIndex(i));\r
 410                 }\r
 411                 else\r
 412                 {\r
 413                     restore.setSequence(hi.getHidden().elementAt(i).toString());\r
 414                 }\r
 415             }\r
 416 \r
 417             if (hi.getType() == HistoryItem.PASTE)\r
 418             {\r
 419                 for (int i = viewport.alignment.getHeight() - 1;\r
 420                         i > (hi.getSequences().size() - 1); i--)\r
 421                 {\r
 422                     viewport.alignment.deleteSequence(i);\r
 423                 }\r
 424             }\r
 425         }\r
 426 \r
 427         updateEditMenuBar();\r
 428 \r
 429         viewport.updateConsensus();\r
 430         viewport.updateConservation();\r
 431         alignPanel.repaint();\r
 432         viewport.firePropertyChange("alignment", null,\r
 433             viewport.getAlignment().getSequences());\r
 434     }\r
 435 \r
 436     /**\r
 437      * DOCUMENT ME!\r
 438      *\r
 439      * @param up DOCUMENT ME!\r
 440      */\r
 441     public void moveSelectedSequences(boolean up)\r
 442     {\r
 443         SequenceGroup sg = viewport.getSelectionGroup();\r
 444 \r
 445         if (sg == null)\r
 446         {\r
 447             return;\r
 448         }\r
 449 \r
 450         if (up)\r
 451         {\r
 452             for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
 453             {\r
 454                 SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 455 \r
 456                 if (!sg.sequences.contains(seq))\r
 457                 {\r
 458                     continue;\r
 459                 }\r
 460 \r
 461                 SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
 462 \r
 463                 if (sg.sequences.contains(temp))\r
 464                 {\r
 465                     continue;\r
 466                 }\r
 467 \r
 468                 viewport.alignment.getSequences().setElementAt(temp, i);\r
 469                 viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
 470             }\r
 471         }\r
 472         else\r
 473         {\r
 474             for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
 475             {\r
 476                 SequenceI seq = viewport.alignment.getSequenceAt(i);\r
 477 \r
 478                 if (!sg.sequences.contains(seq))\r
 479                 {\r
 480                     continue;\r
 481                 }\r
 482 \r
 483                 SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
 484 \r
 485                 if (sg.sequences.contains(temp))\r
 486                 {\r
 487                     continue;\r
 488                 }\r
 489 \r
 490                 viewport.alignment.getSequences().setElementAt(temp, i);\r
 491                 viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
 492             }\r
 493         }\r
 494 \r
 495         alignPanel.repaint();\r
 496     }\r
 497 \r
 498     /**\r
 499      * DOCUMENT ME!\r
 500      *\r
 501      * @param e DOCUMENT ME!\r
 502      */\r
 503     protected void copy_actionPerformed(ActionEvent e)\r
 504     {\r
 505         if (viewport.getSelectionGroup() == null)\r
 506         {\r
 507             return;\r
 508         }\r
 509 \r
 510         SequenceGroup sg = viewport.getSelectionGroup();\r
 511 \r
 512         Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 513         StringBuffer buffer = new StringBuffer();\r
 514 \r
 515         Hashtable orderedSeqs = new Hashtable();\r
 516 \r
 517         for (int i = 0; i < sg.getSize(); i++)\r
 518         {\r
 519             SequenceI seq = sg.getSequenceAt(i);\r
 520             int index = viewport.alignment.findIndex(seq);\r
 521             orderedSeqs.put(index + "", seq);\r
 522         }\r
 523 \r
 524         int index = 0;\r
 525 \r
 526         for (int i = 0; i < sg.getSize(); i++)\r
 527         {\r
 528             SequenceI seq = null;\r
 529 \r
 530             while (seq == null)\r
 531             {\r
 532                 if (orderedSeqs.containsKey(index + ""))\r
 533                 {\r
 534                     seq = (SequenceI) orderedSeqs.get(index + "");\r
 535                     index++;\r
 536 \r
 537                     break;\r
 538                 }\r
 539                 else\r
 540                 {\r
 541                     index++;\r
 542                 }\r
 543             }\r
 544 \r
 545             buffer.append(seq.getName() + "\t" +\r
 546                 seq.findPosition(sg.getStartRes()) + "\t" +\r
 547                 seq.findPosition(sg.getEndRes()) + "\t" +\r
 548                 sg.getSequenceAt(i).getSequence(sg.getStartRes(),\r
 549                     sg.getEndRes() + 1) + "\n");\r
 550         }\r
 551 \r
 552         c.setContents(new StringSelection(buffer.toString()), null);\r
 553     }\r
 554 \r
 555     /**\r
 556      * DOCUMENT ME!\r
 557      *\r
 558      * @param e DOCUMENT ME!\r
 559      */\r
 560     protected void pasteNew_actionPerformed(ActionEvent e)\r
 561     {\r
 562         paste(true);\r
 563     }\r
 564 \r
 565     /**\r
 566      * DOCUMENT ME!\r
 567      *\r
 568      * @param e DOCUMENT ME!\r
 569      */\r
 570     protected void pasteThis_actionPerformed(ActionEvent e)\r
 571     {\r
 572         addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
 573                 HistoryItem.PASTE));\r
 574         paste(false);\r
 575     }\r
 576 \r
 577     /**\r
 578      * DOCUMENT ME!\r
 579      *\r
 580      * @param newAlignment DOCUMENT ME!\r
 581      */\r
 582     void paste(boolean newAlignment)\r
 583     {\r
 584         try\r
 585         {\r
 586             Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
 587             Transferable contents = c.getContents(this);\r
 588 \r
 589             if (contents == null)\r
 590             {\r
 591                 return;\r
 592             }\r
 593 \r
 594             String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
 595             StringTokenizer st = new StringTokenizer(str);\r
 596             ArrayList seqs = new ArrayList();\r
 597 \r
 598             while (st.hasMoreElements())\r
 599             {\r
 600                 String name = st.nextToken();\r
 601                 int start = Integer.parseInt(st.nextToken());\r
 602                 int end = Integer.parseInt(st.nextToken());\r
 603                 Sequence sequence = new Sequence(name, st.nextToken(), start,\r
 604                         end);\r
 605 \r
 606                 if (!newAlignment)\r
 607                 {\r
 608                     viewport.alignment.addSequence(sequence);\r
 609                 }\r
 610                 else\r
 611                 {\r
 612                     seqs.add(sequence);\r
 613                 }\r
 614             }\r
 615 \r
 616             if (newAlignment)\r
 617             {\r
 618                 SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
 619                 seqs.toArray(newSeqs);\r
 620 \r
 621                 AlignFrame af = new AlignFrame(new Alignment(newSeqs));\r
 622                 String newtitle = new String("Copied sequences");\r
 623 \r
 624                 if (title.startsWith("Copied sequences"))\r
 625                 {\r
 626                     newtitle = title;\r
 627                 }\r
 628                 else\r
 629                 {\r
 630                     newtitle = newtitle.concat("- from " + title);\r
 631                 }\r
 632 \r
 633                 Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
 634                     NEW_WINDOW_HEIGHT);\r
 635             }\r
 636             else\r
 637             {\r
 638                 viewport.firePropertyChange("alignment", null,\r
 639                     viewport.getAlignment().getSequences());\r
 640                 viewport.setEndSeq(viewport.alignment.getHeight());\r
 641                 viewport.alignment.getWidth();\r
 642                 viewport.updateConservation();\r
 643                 viewport.updateConsensus();\r
 644                 alignPanel.repaint();\r
 645             }\r
 646         }\r
 647         catch (Exception ex)\r
 648         {\r
 649         }\r
 650 \r
 651         // could be anything being pasted in here\r
 652     }\r
 653 \r
 654     /**\r
 655      * DOCUMENT ME!\r
 656      *\r
 657      * @param e DOCUMENT ME!\r
 658      */\r
 659     protected void cut_actionPerformed(ActionEvent e)\r
 660     {\r
 661         copy_actionPerformed(null);\r
 662         delete_actionPerformed(null);\r
 663     }\r
 664 \r
 665     /**\r
 666      * DOCUMENT ME!\r
 667      *\r
 668      * @param e DOCUMENT ME!\r
 669      */\r
 670     protected void delete_actionPerformed(ActionEvent e)\r
 671     {\r
 672         boolean seqsdeleted = false;\r
 673 \r
 674         if (viewport.getSelectionGroup() == null)\r
 675         {\r
 676             return;\r
 677         }\r
 678 \r
 679         addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
 680                 HistoryItem.HIDE));\r
 681 \r
 682         SequenceGroup sg = viewport.getSelectionGroup();\r
 683         boolean allSequences = false;\r
 684         if(sg.sequences.size()==viewport.alignment.getHeight())\r
 685           allSequences = true;\r
 686 \r
 687         for (int i = 0; i < sg.sequences.size(); i++)\r
 688         {\r
 689             SequenceI seq = sg.getSequenceAt(i);\r
 690             int index = viewport.getAlignment().findIndex(seq);\r
 691             seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 692 \r
 693             // If the cut affects all sequences, remove highlighted columns\r
 694             if(allSequences)\r
 695             {\r
 696               viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes()+1);\r
 697             }\r
 698 \r
 699 \r
 700             if (seq.getSequence().length() < 1)\r
 701             {\r
 702                 seqsdeleted = true;\r
 703                 viewport.getAlignment().deleteSequence(seq);\r
 704             }\r
 705             else\r
 706             {\r
 707                 viewport.getAlignment().getSequences().setElementAt(seq, index);\r
 708             }\r
 709         }\r
 710 \r
 711         viewport.setSelectionGroup(null);\r
 712         viewport.alignment.deleteGroup(sg);\r
 713 \r
 714         if (seqsdeleted)\r
 715         {\r
 716             viewport.firePropertyChange("alignment", null,\r
 717                 viewport.getAlignment().getSequences());\r
 718         }\r
 719 \r
 720         viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());\r
 721 \r
 722         if (viewport.getAlignment().getHeight() < 1)\r
 723         {\r
 724             try\r
 725             {\r
 726                 this.setClosed(true);\r
 727             }\r
 728             catch (Exception ex)\r
 729             {\r
 730             }\r
 731         }\r
 732 \r
 733         viewport.updateConservation();\r
 734         viewport.updateConsensus();\r
 735         alignPanel.repaint();\r
 736     }\r
 737 \r
 738     /**\r
 739      * DOCUMENT ME!\r
 740      *\r
 741      * @param e DOCUMENT ME!\r
 742      */\r
 743     protected void deleteGroups_actionPerformed(ActionEvent e)\r
 744     {\r
 745         viewport.alignment.deleteAllGroups();\r
 746         viewport.setSelectionGroup(null);\r
 747         alignPanel.repaint();\r
 748     }\r
 749 \r
 750     /**\r
 751      * DOCUMENT ME!\r
 752      *\r
 753      * @param e DOCUMENT ME!\r
 754      */\r
 755     public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 756     {\r
 757         SequenceGroup sg = new SequenceGroup();\r
 758 \r
 759         for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
 760                 i++)\r
 761         {\r
 762             sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
 763         }\r
 764 \r
 765         sg.setEndRes(viewport.alignment.getWidth());\r
 766         viewport.setSelectionGroup(sg);\r
 767         PaintRefresher.Refresh(null, viewport.alignment);\r
 768     }\r
 769 \r
 770     /**\r
 771      * DOCUMENT ME!\r
 772      *\r
 773      * @param e DOCUMENT ME!\r
 774      */\r
 775     public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
 776     {\r
 777         viewport.setSelectionGroup(null);\r
 778         viewport.getColumnSelection().clear();\r
 779         viewport.setSelectionGroup(null);\r
 780         alignPanel.annotationPanel.activeRes = null;\r
 781         PaintRefresher.Refresh(null, viewport.alignment);\r
 782     }\r
 783 \r
 784     /**\r
 785      * DOCUMENT ME!\r
 786      *\r
 787      * @param e DOCUMENT ME!\r
 788      */\r
 789     public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
 790     {\r
 791         SequenceGroup sg = viewport.getSelectionGroup();\r
 792 \r
 793         if (sg == null)\r
 794         {\r
 795             selectAllSequenceMenuItem_actionPerformed(null);\r
 796 \r
 797             return;\r
 798         }\r
 799 \r
 800         for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
 801                 i++)\r
 802         {\r
 803             sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
 804         }\r
 805 \r
 806         PaintRefresher.Refresh(null, viewport.alignment);\r
 807     }\r
 808 \r
 809     /**\r
 810      * DOCUMENT ME!\r
 811      *\r
 812      * @param e DOCUMENT ME!\r
 813      */\r
 814     public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
 815     {\r
 816         ColumnSelection colSel = viewport.getColumnSelection();\r
 817 \r
 818         if (colSel.size() > 0)\r
 819         {\r
 820             addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
 821                     HistoryItem.HIDE));\r
 822 \r
 823             int min = colSel.getMin();\r
 824             viewport.getAlignment().trimLeft(min);\r
 825             colSel.compensateForEdit(0, min);\r
 826 \r
 827             if (viewport.getSelectionGroup() != null)\r
 828             {\r
 829                 viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
 830             }\r
 831 \r
 832             Vector groups = viewport.alignment.getGroups();\r
 833 \r
 834             for (int i = 0; i < groups.size(); i++)\r
 835             {\r
 836                 SequenceGroup sg = (SequenceGroup) groups.get(i);\r
 837 \r
 838                 if (!sg.adjustForRemoveLeft(min))\r
 839                 {\r
 840                     viewport.alignment.deleteGroup(sg);\r
 841                 }\r
 842             }\r
 843 \r
 844             alignPanel.repaint();\r
 845         }\r
 846     }\r
 847 \r
 848     /**\r
 849      * DOCUMENT ME!\r
 850      *\r
 851      * @param e DOCUMENT ME!\r
 852      */\r
 853     public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
 854     {\r
 855         ColumnSelection colSel = viewport.getColumnSelection();\r
 856 \r
 857         if (colSel.size() > 0)\r
 858         {\r
 859             addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
 860                     HistoryItem.HIDE));\r
 861 \r
 862             int max = colSel.getMax();\r
 863             viewport.getAlignment().trimRight(max);\r
 864 \r
 865             if (viewport.getSelectionGroup() != null)\r
 866             {\r
 867                 viewport.getSelectionGroup().adjustForRemoveRight(max);\r
 868             }\r
 869 \r
 870             Vector groups = viewport.alignment.getGroups();\r
 871 \r
 872             for (int i = 0; i < groups.size(); i++)\r
 873             {\r
 874                 SequenceGroup sg = (SequenceGroup) groups.get(i);\r
 875 \r
 876                 if (!sg.adjustForRemoveRight(max))\r
 877                 {\r
 878                     viewport.alignment.deleteGroup(sg);\r
 879                 }\r
 880             }\r
 881 \r
 882             alignPanel.repaint();\r
 883         }\r
 884     }\r
 885 \r
 886     /**\r
 887      * DOCUMENT ME!\r
 888      *\r
 889      * @param e DOCUMENT ME!\r
 890      */\r
 891     public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
 892     {\r
 893         addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
 894                 viewport.alignment, HistoryItem.HIDE));\r
 895 \r
 896         viewport.getAlignment().removeGaps();\r
 897         viewport.updateConservation();\r
 898         viewport.updateConsensus();\r
 899         alignPanel.repaint();\r
 900     }\r
 901 \r
 902     /**\r
 903      * DOCUMENT ME!\r
 904      *\r
 905      * @param e DOCUMENT ME!\r
 906      */\r
 907     public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
 908     {\r
 909         addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
 910                 HistoryItem.HIDE));\r
 911 \r
 912         SequenceI current;\r
 913         int jSize;\r
 914 \r
 915         Vector seqs = null;\r
 916 \r
 917         int start = 0;\r
 918         int end = viewport.alignment.getWidth();\r
 919 \r
 920         if (viewport.getSelectionGroup() != null)\r
 921         {\r
 922             seqs = viewport.getSelectionGroup().sequences;\r
 923             start = viewport.getSelectionGroup().getStartRes();\r
 924             end = viewport.getSelectionGroup().getEndRes();\r
 925         }\r
 926         else\r
 927         {\r
 928             seqs = viewport.alignment.getSequences();\r
 929         }\r
 930 \r
 931         for (int i = 0; i < seqs.size(); i++)\r
 932         {\r
 933             current = (SequenceI) seqs.elementAt(i);\r
 934             jSize = current.getLength();\r
 935 \r
 936             int j = start;\r
 937 \r
 938             do\r
 939             {\r
 940                 if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 941                 {\r
 942                     current.deleteCharAt(j);\r
 943                     j--;\r
 944                     jSize--;\r
 945                 }\r
 946 \r
 947                 j++;\r
 948             }\r
 949             while (j < end && j < jSize);\r
 950         }\r
 951 \r
 952         viewport.updateConservation();\r
 953         viewport.updateConsensus();\r
 954         alignPanel.repaint();\r
 955     }\r
 956 \r
 957     /**\r
 958      * DOCUMENT ME!\r
 959      *\r
 960      * @param e DOCUMENT ME!\r
 961      */\r
 962     public void padGapsMenuitem_actionPerformed(ActionEvent e)\r
 963     {\r
 964         addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,\r
 965                 HistoryItem.HIDE));\r
 966 \r
 967         SequenceI current;\r
 968         int Width = viewport.getAlignment().getWidth();\r
 969 \r
 970         for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
 971                 i++)\r
 972         {\r
 973             current = viewport.getAlignment().getSequenceAt(i);\r
 974 \r
 975             if (current.getLength() < Width)\r
 976             {\r
 977                 current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
 978             }\r
 979         }\r
 980 \r
 981         viewport.updateConservation();\r
 982         viewport.updateConsensus();\r
 983         alignPanel.repaint();\r
 984     }\r
 985 \r
 986     /**\r
 987      * DOCUMENT ME!\r
 988      *\r
 989      * @param e DOCUMENT ME!\r
 990      */\r
 991     public void findMenuItem_actionPerformed(ActionEvent e)\r
 992     {\r
 993         JInternalFrame frame = new JInternalFrame();\r
 994         Finder finder = new Finder(viewport, alignPanel, frame);\r
 995         frame.setContentPane(finder);\r
 996         Desktop.addInternalFrame(frame, "Find", 340, 110);\r
 997         frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
 998     }\r
 999 \r
1000     /**\r
1001      * DOCUMENT ME!\r
1002      *\r
1003      * @param e DOCUMENT ME!\r
1004      */\r
1005     public void font_actionPerformed(ActionEvent e)\r
1006     {\r
1007         FontChooser fc = new FontChooser(alignPanel);\r
1008     }\r
1009 \r
1010     /**\r
1011      * DOCUMENT ME!\r
1012      *\r
1013      * @param e DOCUMENT ME!\r
1014      */\r
1015     protected void fullSeqId_actionPerformed(ActionEvent e)\r
1016     {\r
1017         viewport.setShowFullId(fullSeqId.isSelected());\r
1018 \r
1019         alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());\r
1020         alignPanel.repaint();\r
1021     }\r
1022 \r
1023     /**\r
1024      * DOCUMENT ME!\r
1025      *\r
1026      * @param e DOCUMENT ME!\r
1027      */\r
1028     protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
1029     {\r
1030         viewport.setColourText(colourTextMenuItem.isSelected());\r
1031         alignPanel.repaint();\r
1032     }\r
1033 \r
1034     /**\r
1035      * DOCUMENT ME!\r
1036      *\r
1037      * @param e DOCUMENT ME!\r
1038      */\r
1039     protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
1040     {\r
1041         viewport.setWrapAlignment(wrapMenuItem.isSelected());\r
1042         alignPanel.setWrapAlignment(wrapMenuItem.isSelected());\r
1043         scaleAbove.setVisible(wrapMenuItem.isSelected());\r
1044         scaleLeft.setVisible(wrapMenuItem.isSelected());\r
1045         scaleRight.setVisible(wrapMenuItem.isSelected());\r
1046         alignPanel.repaint();\r
1047     }\r
1048 \r
1049     /**\r
1050      * DOCUMENT ME!\r
1051      *\r
1052      * @param e DOCUMENT ME!\r
1053      */\r
1054     protected void scaleAbove_actionPerformed(ActionEvent e)\r
1055     {\r
1056         viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
1057         alignPanel.repaint();\r
1058     }\r
1059 \r
1060     /**\r
1061      * DOCUMENT ME!\r
1062      *\r
1063      * @param e DOCUMENT ME!\r
1064      */\r
1065     protected void scaleLeft_actionPerformed(ActionEvent e)\r
1066     {\r
1067         viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
1068         alignPanel.repaint();\r
1069     }\r
1070 \r
1071     /**\r
1072      * DOCUMENT ME!\r
1073      *\r
1074      * @param e DOCUMENT ME!\r
1075      */\r
1076     protected void scaleRight_actionPerformed(ActionEvent e)\r
1077     {\r
1078         viewport.setScaleRightWrapped(scaleRight.isSelected());\r
1079         alignPanel.repaint();\r
1080     }\r
1081 \r
1082     /**\r
1083      * DOCUMENT ME!\r
1084      *\r
1085      * @param e DOCUMENT ME!\r
1086      */\r
1087     public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
1088     {\r
1089         viewport.setShowBoxes(viewBoxesMenuItem.isSelected());\r
1090         alignPanel.repaint();\r
1091     }\r
1092 \r
1093     /**\r
1094      * DOCUMENT ME!\r
1095      *\r
1096      * @param e DOCUMENT ME!\r
1097      */\r
1098     public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
1099     {\r
1100         viewport.setShowText(viewTextMenuItem.isSelected());\r
1101         alignPanel.repaint();\r
1102     }\r
1103 \r
1104     /**\r
1105      * DOCUMENT ME!\r
1106      *\r
1107      * @param e DOCUMENT ME!\r
1108      */\r
1109     protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1110     {\r
1111         viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
1112         alignPanel.repaint();\r
1113     }\r
1114 \r
1115     /**\r
1116      * DOCUMENT ME!\r
1117      *\r
1118      * @param evt DOCUMENT ME!\r
1119      */\r
1120     public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
1121     {\r
1122         viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
1123 \r
1124         if (viewport.showSequenceFeatures &&\r
1125                 !((Alignment) viewport.alignment).featuresAdded)\r
1126         {\r
1127             SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment,\r
1128                     alignPanel);\r
1129             ((Alignment) viewport.alignment).featuresAdded = true;\r
1130         }\r
1131 \r
1132         alignPanel.repaint();\r
1133     }\r
1134 \r
1135     /**\r
1136      * DOCUMENT ME!\r
1137      *\r
1138      * @param e DOCUMENT ME!\r
1139      */\r
1140     public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
1141     {\r
1142         if (annotationPanelMenuItem.isSelected() &&\r
1143                 viewport.getWrapAlignment())\r
1144         {\r
1145             annotationPanelMenuItem.setSelected(false);\r
1146 \r
1147             return;\r
1148         }\r
1149 \r
1150         viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());\r
1151         alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());\r
1152     }\r
1153 \r
1154     /**\r
1155      * DOCUMENT ME!\r
1156      *\r
1157      * @param e DOCUMENT ME!\r
1158      */\r
1159     public void overviewMenuItem_actionPerformed(ActionEvent e)\r
1160     {\r
1161         if (alignPanel.overviewPanel != null)\r
1162         {\r
1163             return;\r
1164         }\r
1165 \r
1166         JInternalFrame frame = new JInternalFrame();\r
1167         OverviewPanel overview = new OverviewPanel(alignPanel);\r
1168         frame.setContentPane(overview);\r
1169         Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
1170             frame.getWidth(), frame.getHeight());\r
1171         frame.pack();\r
1172         frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
1173         frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
1174             {\r
1175                 public void internalFrameClosed(\r
1176                     javax.swing.event.InternalFrameEvent evt)\r
1177                 {\r
1178                     alignPanel.setOverviewPanel(null);\r
1179                 }\r
1180                 ;\r
1181             });\r
1182 \r
1183         alignPanel.setOverviewPanel(overview);\r
1184     }\r
1185 \r
1186     /**\r
1187      * DOCUMENT ME!\r
1188      *\r
1189      * @param e DOCUMENT ME!\r
1190      */\r
1191     protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1192     {\r
1193         changeColour(null);\r
1194     }\r
1195 \r
1196     /**\r
1197      * DOCUMENT ME!\r
1198      *\r
1199      * @param e DOCUMENT ME!\r
1200      */\r
1201     public void clustalColour_actionPerformed(ActionEvent e)\r
1202     {\r
1203         changeColour(new ClustalxColourScheme(\r
1204                 viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
1205     }\r
1206 \r
1207     /**\r
1208      * DOCUMENT ME!\r
1209      *\r
1210      * @param e DOCUMENT ME!\r
1211      */\r
1212     public void zappoColour_actionPerformed(ActionEvent e)\r
1213     {\r
1214         changeColour(new ZappoColourScheme());\r
1215     }\r
1216 \r
1217     /**\r
1218      * DOCUMENT ME!\r
1219      *\r
1220      * @param e DOCUMENT ME!\r
1221      */\r
1222     public void taylorColour_actionPerformed(ActionEvent e)\r
1223     {\r
1224         changeColour(new TaylorColourScheme());\r
1225     }\r
1226 \r
1227     /**\r
1228      * DOCUMENT ME!\r
1229      *\r
1230      * @param e DOCUMENT ME!\r
1231      */\r
1232     public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1233     {\r
1234         changeColour(new HydrophobicColourScheme());\r
1235     }\r
1236 \r
1237     /**\r
1238      * DOCUMENT ME!\r
1239      *\r
1240      * @param e DOCUMENT ME!\r
1241      */\r
1242     public void helixColour_actionPerformed(ActionEvent e)\r
1243     {\r
1244         changeColour(new HelixColourScheme());\r
1245     }\r
1246 \r
1247     /**\r
1248      * DOCUMENT ME!\r
1249      *\r
1250      * @param e DOCUMENT ME!\r
1251      */\r
1252     public void strandColour_actionPerformed(ActionEvent e)\r
1253     {\r
1254         changeColour(new StrandColourScheme());\r
1255     }\r
1256 \r
1257     /**\r
1258      * DOCUMENT ME!\r
1259      *\r
1260      * @param e DOCUMENT ME!\r
1261      */\r
1262     public void turnColour_actionPerformed(ActionEvent e)\r
1263     {\r
1264         changeColour(new TurnColourScheme());\r
1265     }\r
1266 \r
1267     /**\r
1268      * DOCUMENT ME!\r
1269      *\r
1270      * @param e DOCUMENT ME!\r
1271      */\r
1272     public void buriedColour_actionPerformed(ActionEvent e)\r
1273     {\r
1274         changeColour(new BuriedColourScheme());\r
1275     }\r
1276 \r
1277     /**\r
1278      * DOCUMENT ME!\r
1279      *\r
1280      * @param e DOCUMENT ME!\r
1281      */\r
1282     public void nucleotideColour_actionPerformed(ActionEvent e)\r
1283     {\r
1284         changeColour(new NucleotideColourScheme());\r
1285     }\r
1286 \r
1287     /**\r
1288      * DOCUMENT ME!\r
1289      *\r
1290      * @param e DOCUMENT ME!\r
1291      */\r
1292     protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1293     {\r
1294         viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
1295     }\r
1296 \r
1297     /**\r
1298      * DOCUMENT ME!\r
1299      *\r
1300      * @param cs DOCUMENT ME!\r
1301      */\r
1302     void changeColour(ColourSchemeI cs)\r
1303     {\r
1304         int threshold = 0;\r
1305 \r
1306         if (viewport.getAbovePIDThreshold())\r
1307         {\r
1308             threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,\r
1309                     "Background");\r
1310 \r
1311             if (cs instanceof ResidueColourScheme)\r
1312             {\r
1313                 ((ResidueColourScheme) cs).setThreshold(threshold);\r
1314             }\r
1315             else if (cs instanceof ScoreColourScheme)\r
1316             {\r
1317                 ((ScoreColourScheme) cs).setThreshold(threshold);\r
1318             }\r
1319 \r
1320             viewport.setGlobalColourScheme(cs);\r
1321         }\r
1322         else if (cs instanceof ResidueColourScheme)\r
1323         {\r
1324             ((ResidueColourScheme) cs).setThreshold(0);\r
1325         }\r
1326         else if (cs instanceof ScoreColourScheme)\r
1327         {\r
1328             ((ScoreColourScheme) cs).setThreshold(0);\r
1329         }\r
1330 \r
1331         if (viewport.getConservationSelected())\r
1332         {\r
1333             ConservationColourScheme ccs = null;\r
1334 \r
1335             Alignment al = (Alignment) viewport.alignment;\r
1336             Conservation c = new Conservation("All",\r
1337                     ResidueProperties.propHash, 3, al.getSequences(), 0,\r
1338                     al.getWidth() - 1);\r
1339 \r
1340             c.calculate();\r
1341             c.verdict(false, viewport.ConsPercGaps);\r
1342 \r
1343             ccs = new ConservationColourScheme(c, cs);\r
1344 \r
1345             // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
1346             ccs.setConsensus(viewport.vconsensus);\r
1347             viewport.setGlobalColourScheme(ccs);\r
1348 \r
1349             ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,\r
1350                     "Background");\r
1351         }\r
1352         else\r
1353         {\r
1354             // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
1355             if (cs != null)\r
1356             {\r
1357                 cs.setConsensus(viewport.vconsensus);\r
1358             }\r
1359 \r
1360             viewport.setGlobalColourScheme(cs);\r
1361         }\r
1362 \r
1363         if (viewport.getColourAppliesToAllGroups())\r
1364         {\r
1365             Vector groups = viewport.alignment.getGroups();\r
1366 \r
1367             for (int i = 0; i < groups.size(); i++)\r
1368             {\r
1369                 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1370 \r
1371                 if (cs == null)\r
1372                 {\r
1373                     sg.cs = null;\r
1374                 }\r
1375                 else if (cs instanceof ClustalxColourScheme)\r
1376                 {\r
1377                     sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
1378                 }\r
1379                 else if (cs instanceof UserColourScheme)\r
1380                 {\r
1381                     sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());\r
1382                 }\r
1383                 else\r
1384                 {\r
1385                     try\r
1386                     {\r
1387                         sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
1388                     }\r
1389                     catch (Exception ex)\r
1390                     {\r
1391                     }\r
1392                 }\r
1393 \r
1394                 if (viewport.getAbovePIDThreshold())\r
1395                 {\r
1396                     if (sg.cs instanceof ResidueColourScheme)\r
1397                     {\r
1398                         ((ResidueColourScheme) sg.cs).setThreshold(threshold);\r
1399                     }\r
1400                     else if (sg.cs instanceof ScoreColourScheme)\r
1401                     {\r
1402                         ((ScoreColourScheme) sg.cs).setThreshold(threshold);\r
1403                     }\r
1404 \r
1405                     sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
1406                             sg.getWidth()));\r
1407                 }\r
1408 \r
1409                 if (viewport.getConservationSelected())\r
1410                 {\r
1411                     Conservation c = new Conservation("Group",\r
1412                             ResidueProperties.propHash, 3, sg.sequences, 0,\r
1413                             viewport.alignment.getWidth() - 1);\r
1414                     c.calculate();\r
1415                     c.verdict(false, viewport.ConsPercGaps);\r
1416 \r
1417                     ConservationColourScheme ccs = new ConservationColourScheme(c,\r
1418                             sg.cs);\r
1419 \r
1420                     // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
1421                     ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
1422                             sg.getWidth()));\r
1423                     sg.cs = ccs;\r
1424                 }\r
1425                 else if (cs != null)\r
1426                 {\r
1427                     // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
1428                     sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
1429                             sg.getWidth()));\r
1430                 }\r
1431             }\r
1432         }\r
1433 \r
1434         if (alignPanel.getOverviewPanel() != null)\r
1435         {\r
1436             alignPanel.getOverviewPanel().updateOverviewImage();\r
1437         }\r
1438 \r
1439         alignPanel.repaint();\r
1440     }\r
1441 \r
1442     /**\r
1443      * DOCUMENT ME!\r
1444      *\r
1445      * @param e DOCUMENT ME!\r
1446      */\r
1447     protected void modifyPID_actionPerformed(ActionEvent e)\r
1448     {\r
1449         if (viewport.getAbovePIDThreshold())\r
1450         {\r
1451             SliderPanel.setPIDSliderSource(alignPanel,\r
1452                 viewport.getGlobalColourScheme(), "Background");\r
1453             SliderPanel.showPIDSlider();\r
1454         }\r
1455     }\r
1456 \r
1457     /**\r
1458      * DOCUMENT ME!\r
1459      *\r
1460      * @param e DOCUMENT ME!\r
1461      */\r
1462     protected void modifyConservation_actionPerformed(ActionEvent e)\r
1463     {\r
1464         if (viewport.getConservationSelected())\r
1465         {\r
1466             SliderPanel.setConservationSlider(alignPanel,\r
1467                 viewport.globalColourScheme, "Background");\r
1468             SliderPanel.showConservationSlider();\r
1469         }\r
1470     }\r
1471 \r
1472     /**\r
1473      * DOCUMENT ME!\r
1474      *\r
1475      * @param e DOCUMENT ME!\r
1476      */\r
1477     protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1478     {\r
1479         viewport.setConservationSelected(conservationMenuItem.isSelected());\r
1480 \r
1481         viewport.setAbovePIDThreshold(false);\r
1482         abovePIDThreshold.setSelected(false);\r
1483 \r
1484         ColourSchemeI cs = viewport.getGlobalColourScheme();\r
1485 \r
1486         if (cs instanceof ConservationColourScheme)\r
1487         {\r
1488             changeColour(((ConservationColourScheme) cs).cs);\r
1489         }\r
1490         else\r
1491         {\r
1492             changeColour(cs);\r
1493         }\r
1494 \r
1495         modifyConservation_actionPerformed(null);\r
1496     }\r
1497 \r
1498     /**\r
1499      * DOCUMENT ME!\r
1500      *\r
1501      * @param e DOCUMENT ME!\r
1502      */\r
1503     public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1504     {\r
1505         viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
1506 \r
1507         conservationMenuItem.setSelected(false);\r
1508         viewport.setConservationSelected(false);\r
1509 \r
1510         ColourSchemeI cs = viewport.getGlobalColourScheme();\r
1511 \r
1512         if (cs instanceof ConservationColourScheme)\r
1513         {\r
1514             changeColour(((ConservationColourScheme) cs).cs);\r
1515         }\r
1516         else\r
1517         {\r
1518             changeColour(cs);\r
1519         }\r
1520 \r
1521         modifyPID_actionPerformed(null);\r
1522     }\r
1523 \r
1524     /**\r
1525      * DOCUMENT ME!\r
1526      *\r
1527      * @param e DOCUMENT ME!\r
1528      */\r
1529     public void userDefinedColour_actionPerformed(ActionEvent e)\r
1530     {\r
1531         new UserDefinedColours(alignPanel, null);\r
1532     }\r
1533 \r
1534     /**\r
1535      * DOCUMENT ME!\r
1536      *\r
1537      * @param e DOCUMENT ME!\r
1538      */\r
1539     public void PIDColour_actionPerformed(ActionEvent e)\r
1540     {\r
1541         changeColour(new PIDColourScheme());\r
1542     }\r
1543 \r
1544     /**\r
1545      * DOCUMENT ME!\r
1546      *\r
1547      * @param e DOCUMENT ME!\r
1548      */\r
1549     public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1550     {\r
1551         changeColour(new Blosum62ColourScheme());\r
1552     }\r
1553 \r
1554     /**\r
1555      * DOCUMENT ME!\r
1556      *\r
1557      * @param e DOCUMENT ME!\r
1558      */\r
1559     public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1560     {\r
1561         addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1562                 HistoryItem.SORT));\r
1563         AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1564             viewport.getAlignment().getSequenceAt(0));\r
1565         alignPanel.repaint();\r
1566     }\r
1567 \r
1568     /**\r
1569      * DOCUMENT ME!\r
1570      *\r
1571      * @param e DOCUMENT ME!\r
1572      */\r
1573     public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1574     {\r
1575         addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1576                 HistoryItem.SORT));\r
1577         AlignmentSorter.sortByID(viewport.getAlignment());\r
1578         alignPanel.repaint();\r
1579     }\r
1580 \r
1581     /**\r
1582      * DOCUMENT ME!\r
1583      *\r
1584      * @param e DOCUMENT ME!\r
1585      */\r
1586     public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1587     {\r
1588         addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1589                 HistoryItem.SORT));\r
1590 \r
1591         AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1592         alignPanel.repaint();\r
1593     }\r
1594 \r
1595     /**\r
1596      * DOCUMENT ME!\r
1597      *\r
1598      * @param e DOCUMENT ME!\r
1599      */\r
1600     public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1601     {\r
1602         RedundancyPanel sp = new RedundancyPanel(alignPanel, this);\r
1603         JInternalFrame frame = new JInternalFrame();\r
1604         frame.setContentPane(sp);\r
1605         Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,\r
1606             100, false);\r
1607     }\r
1608 \r
1609     /**\r
1610      * DOCUMENT ME!\r
1611      *\r
1612      * @param e DOCUMENT ME!\r
1613      */\r
1614     public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1615     {\r
1616         if ((viewport.getSelectionGroup() == null) ||\r
1617                 (viewport.getSelectionGroup().getSize() < 2))\r
1618         {\r
1619             JOptionPane.showInternalMessageDialog(this,\r
1620                 "You must select at least 2 sequences.", "Invalid Selection",\r
1621                 JOptionPane.WARNING_MESSAGE);\r
1622         }\r
1623         else\r
1624         {\r
1625             JInternalFrame frame = new JInternalFrame();\r
1626             frame.setContentPane(new PairwiseAlignPanel(viewport));\r
1627             Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
1628         }\r
1629     }\r
1630 \r
1631     /**\r
1632      * DOCUMENT ME!\r
1633      *\r
1634      * @param e DOCUMENT ME!\r
1635      */\r
1636     public void PCAMenuItem_actionPerformed(ActionEvent e)\r
1637     {\r
1638         if (((viewport.getSelectionGroup() != null) &&\r
1639                 (viewport.getSelectionGroup().getSize() < 4) &&\r
1640                 (viewport.getSelectionGroup().getSize() > 0)) ||\r
1641                 (viewport.getAlignment().getHeight() < 4))\r
1642         {\r
1643             JOptionPane.showInternalMessageDialog(this,\r
1644                 "Principal component analysis must take\n" +\r
1645                 "at least 4 input sequences.",\r
1646                 "Sequence selection insufficient", JOptionPane.WARNING_MESSAGE);\r
1647 \r
1648             return;\r
1649         }\r
1650 \r
1651         try\r
1652         {\r
1653             PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
1654             JInternalFrame frame = new JInternalFrame();\r
1655             frame.setContentPane(pcaPanel);\r
1656             Desktop.addInternalFrame(frame, "Principal component analysis",\r
1657                 400, 400);\r
1658         }\r
1659         catch (java.lang.OutOfMemoryError ex)\r
1660         {\r
1661             JOptionPane.showInternalMessageDialog(this,\r
1662                 "Too many sequences selected\nfor Principal Component Analysis!!",\r
1663                 "Out of memory", JOptionPane.WARNING_MESSAGE);\r
1664         }\r
1665     }\r
1666 \r
1667     /**\r
1668      * DOCUMENT ME!\r
1669      *\r
1670      * @param e DOCUMENT ME!\r
1671      */\r
1672     public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1673     {\r
1674         NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1675     }\r
1676 \r
1677     /**\r
1678      * DOCUMENT ME!\r
1679      *\r
1680      * @param e DOCUMENT ME!\r
1681      */\r
1682     public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1683     {\r
1684         NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1685     }\r
1686 \r
1687     /**\r
1688      * DOCUMENT ME!\r
1689      *\r
1690      * @param e DOCUMENT ME!\r
1691      */\r
1692     protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1693     {\r
1694         NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1695     }\r
1696 \r
1697     /**\r
1698      * DOCUMENT ME!\r
1699      *\r
1700      * @param e DOCUMENT ME!\r
1701      */\r
1702     protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1703     {\r
1704         NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
1705     }\r
1706 \r
1707     /**\r
1708      * DOCUMENT ME!\r
1709      *\r
1710      * @param type DOCUMENT ME!\r
1711      * @param pwType DOCUMENT ME!\r
1712      * @param title DOCUMENT ME!\r
1713      */\r
1714     void NewTreePanel(String type, String pwType, String title)\r
1715     {\r
1716         final TreePanel tp;\r
1717 \r
1718         if ((viewport.getSelectionGroup() != null) &&\r
1719                 (viewport.getSelectionGroup().getSize() > 3))\r
1720         {\r
1721             int s = 0;\r
1722             SequenceGroup sg = viewport.getSelectionGroup();\r
1723 \r
1724             /* Decide if the selection is a column region */\r
1725             while (s < sg.sequences.size())\r
1726             {\r
1727                 if (((SequenceI) sg.sequences.elementAt(s++)).getLength() < sg.getEndRes())\r
1728                 {\r
1729                     JOptionPane.showMessageDialog(Desktop.desktop,\r
1730                         "The selected region to create a tree may\nonly contain residues or gaps.\n" +\r
1731                         "Try using the Pad function in the edit menu,\n" +\r
1732                         "or one of the multiple sequence alignment web services.",\r
1733                         "Sequences in selection are not aligned",\r
1734                         JOptionPane.WARNING_MESSAGE);\r
1735 \r
1736                     return;\r
1737                 }\r
1738             }\r
1739 \r
1740             title = title + " on region";\r
1741             tp = new TreePanel(viewport,\r
1742                     viewport.getSelectionGroup().sequences, type, pwType,\r
1743                     sg.getStartRes(), sg.getEndRes());\r
1744         }\r
1745         else\r
1746         {\r
1747             //are the sequences aligned?\r
1748             if (!viewport.alignment.isAligned())\r
1749             {\r
1750                 JOptionPane.showMessageDialog(Desktop.desktop,\r
1751                     "The sequences must be aligned before creating a tree.\n" +\r
1752                     "Try using the Pad function in the edit menu,\n" +\r
1753                     "or one of the multiple sequence alignment web services.",\r
1754                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
1755 \r
1756                 return;\r
1757             }\r
1758 \r
1759             tp = new TreePanel(viewport,\r
1760                     viewport.getAlignment().getSequences(), type, pwType, 0,\r
1761                     viewport.alignment.getWidth());\r
1762         }\r
1763 \r
1764         addTreeMenuItem(tp, title);\r
1765         viewport.setCurrentTree(tp.getTree());\r
1766 \r
1767         Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);\r
1768     }\r
1769 \r
1770     /**\r
1771      * DOCUMENT ME!\r
1772      *\r
1773      * @param title DOCUMENT ME!\r
1774      * @param order DOCUMENT ME!\r
1775      */\r
1776     public void addSortByOrderMenuItem(String title, final AlignmentOrder order)\r
1777     {\r
1778         final JMenuItem item = new JMenuItem("by " + title);\r
1779         sort.add(item);\r
1780         item.addActionListener(new java.awt.event.ActionListener()\r
1781             {\r
1782                 public void actionPerformed(ActionEvent e)\r
1783                 {\r
1784                     addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1785                             HistoryItem.SORT));\r
1786 \r
1787                     // TODO: JBPNote - have to map order entries to curent SequenceI pointers\r
1788                     AlignmentSorter.sortBy(viewport.getAlignment(), order);\r
1789                     alignPanel.repaint();\r
1790                 }\r
1791             });\r
1792     }\r
1793 \r
1794     /**\r
1795      * DOCUMENT ME!\r
1796      *\r
1797      * @param treePanel DOCUMENT ME!\r
1798      * @param title DOCUMENT ME!\r
1799      */\r
1800     void addTreeMenuItem(final TreePanel treePanel, String title)\r
1801     {\r
1802         final JMenuItem item = new JMenuItem(title);\r
1803 \r
1804         treeCount++;\r
1805 \r
1806         if (treeCount == 1)\r
1807         {\r
1808             sort.add(sortByTreeMenu);\r
1809         }\r
1810 \r
1811         sortByTreeMenu.add(item);\r
1812         item.addActionListener(new java.awt.event.ActionListener()\r
1813             {\r
1814                 public void actionPerformed(ActionEvent e)\r
1815                 {\r
1816                     addHistoryItem(new HistoryItem("Tree Sort",\r
1817                             viewport.alignment, HistoryItem.SORT));\r
1818                     AlignmentSorter.sortByTree(viewport.getAlignment(),\r
1819                         treePanel.getTree());\r
1820                     alignPanel.repaint();\r
1821                 }\r
1822             });\r
1823 \r
1824         treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
1825             {\r
1826                 public void internalFrameClosed(\r
1827                     javax.swing.event.InternalFrameEvent evt)\r
1828                 {\r
1829                     treeCount--;\r
1830                     sortByTreeMenu.remove(item);\r
1831 \r
1832                     if (treeCount == 0)\r
1833                     {\r
1834                         sort.remove(sortByTreeMenu);\r
1835                     }\r
1836                 }\r
1837                 ;\r
1838             });\r
1839         viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
1840             {\r
1841                 public void propertyChange(PropertyChangeEvent evt)\r
1842                 {\r
1843                     if (evt.getPropertyName().equals("alignment"))\r
1844                     {\r
1845                         treePanel.getTree().UpdatePlaceHolders((Vector) evt.getNewValue());\r
1846                         treePanel.repaint();\r
1847                     }\r
1848                 }\r
1849             });\r
1850     }\r
1851 \r
1852     /**\r
1853      * DOCUMENT ME!\r
1854      *\r
1855      * @param e DOCUMENT ME!\r
1856      */\r
1857     public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
1858     {\r
1859         // TODO:resolve which menu item was actually selected\r
1860         // Now, check we have enough sequences\r
1861         SequenceI[] msa = null;\r
1862 \r
1863         if ((viewport.getSelectionGroup() != null) &&\r
1864                 (viewport.getSelectionGroup().getSize() > 1))\r
1865         {\r
1866             // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1867             SequenceGroup seqs = viewport.getSelectionGroup();\r
1868             int sz;\r
1869             msa = new SequenceI[sz = seqs.getSize()];\r
1870 \r
1871             for (int i = 0; i < sz; i++)\r
1872             {\r
1873                 msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1874             }\r
1875         }\r
1876         else\r
1877         {\r
1878             Vector seqs = viewport.getAlignment().getSequences();\r
1879 \r
1880             if (seqs.size() > 1)\r
1881             {\r
1882                 msa = new SequenceI[seqs.size()];\r
1883 \r
1884                 for (int i = 0; i < seqs.size(); i++)\r
1885                 {\r
1886                     msa[i] = (SequenceI) seqs.elementAt(i);\r
1887                 }\r
1888             }\r
1889         }\r
1890 \r
1891         if (msa != null)\r
1892         {\r
1893             jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",\r
1894                     title, msa, false, true);\r
1895         }\r
1896     }\r
1897 \r
1898     /**\r
1899      * DOCUMENT ME!\r
1900      *\r
1901      * @param e DOCUMENT ME!\r
1902      */\r
1903     public void ClustalRealign_actionPerformed(ActionEvent e)\r
1904     {\r
1905         // TODO:resolve which menu item was actually selected\r
1906         // Now, check we have enough sequences\r
1907         SequenceI[] msa = null;\r
1908 \r
1909         if ((viewport.getSelectionGroup() != null) &&\r
1910                 (viewport.getSelectionGroup().getSize() > 1))\r
1911         {\r
1912             // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1913             SequenceGroup seqs = viewport.getSelectionGroup();\r
1914             int sz;\r
1915             msa = new SequenceI[sz = seqs.getSize()];\r
1916 \r
1917             for (int i = 0; i < sz; i++)\r
1918             {\r
1919                 msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1920             }\r
1921         }\r
1922         else\r
1923         {\r
1924             Vector seqs = viewport.getAlignment().getSequences();\r
1925 \r
1926             if (seqs.size() > 1)\r
1927             {\r
1928                 msa = new SequenceI[seqs.size()];\r
1929 \r
1930                 for (int i = 0; i < seqs.size(); i++)\r
1931                 {\r
1932                     msa[i] = (SequenceI) seqs.elementAt(i);\r
1933                 }\r
1934             }\r
1935         }\r
1936 \r
1937         if (msa != null)\r
1938         {\r
1939             jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",\r
1940                     title, msa, true, true);\r
1941         }\r
1942     }\r
1943 \r
1944     /**\r
1945      * DOCUMENT ME!\r
1946      *\r
1947      * @param e DOCUMENT ME!\r
1948      */\r
1949     protected void jpred_actionPerformed(ActionEvent e)\r
1950     {\r
1951         SequenceI seq = null;\r
1952         SequenceI[] msa = null;\r
1953 \r
1954         if ((viewport.getSelectionGroup() != null) &&\r
1955                 (viewport.getSelectionGroup().getSize() > 0))\r
1956         {\r
1957             // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1958             SequenceGroup seqs = viewport.getSelectionGroup();\r
1959 \r
1960             if ((seqs.getSize() == 1) || !viewport.alignment.isAligned())\r
1961             {\r
1962                 seq = (SequenceI) seqs.getSequenceAt(0);\r
1963             }\r
1964             else\r
1965             {\r
1966                 int sz;\r
1967                 msa = new SequenceI[sz = seqs.getSize()];\r
1968 \r
1969                 for (int i = 0; i < sz; i++)\r
1970                 {\r
1971                     msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1972                 }\r
1973             }\r
1974         }\r
1975         else\r
1976         {\r
1977             Vector seqs = viewport.getAlignment().getSequences();\r
1978 \r
1979             if ((seqs.size() == 1) || !viewport.alignment.isAligned())\r
1980             {\r
1981                 seq = (SequenceI) seqs.elementAt(0);\r
1982             }\r
1983             else\r
1984             {\r
1985                 msa = new SequenceI[seqs.size()];\r
1986 \r
1987                 for (int i = 0; i < seqs.size(); i++)\r
1988                 {\r
1989                     msa[i] = (SequenceI) seqs.elementAt(i);\r
1990                 }\r
1991             }\r
1992         }\r
1993 \r
1994         if (msa != null)\r
1995         {\r
1996             JPredClient ct = new JPredClient(title, msa);\r
1997         }\r
1998         else if (seq != null)\r
1999         {\r
2000             JPredClient ct = new JPredClient(title, seq);\r
2001         }\r
2002         else\r
2003         {\r
2004             System.err.print(\r
2005                 "JALVIEW ERROR! - Unexpected JPred selection state!\n");\r
2006         }\r
2007     }\r
2008 \r
2009     /**\r
2010      * DOCUMENT ME!\r
2011      *\r
2012      * @param e DOCUMENT ME!\r
2013      */\r
2014     protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
2015     {\r
2016         // TODO:resolve which menu item was actually selected\r
2017         // Now, check we have enough sequences\r
2018         SequenceI[] msa = null;\r
2019 \r
2020         if ((viewport.getSelectionGroup() != null) &&\r
2021                 (viewport.getSelectionGroup().getSize() > 1))\r
2022         {\r
2023             // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
2024             SequenceGroup seqs = viewport.getSelectionGroup();\r
2025             int sz;\r
2026             msa = new SequenceI[sz = seqs.getSize()];\r
2027 \r
2028             for (int i = 0; i < sz; i++)\r
2029             {\r
2030                 msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
2031             }\r
2032         }\r
2033         else\r
2034         {\r
2035             Vector seqs = viewport.getAlignment().getSequences();\r
2036 \r
2037             if (seqs.size() > 1)\r
2038             {\r
2039                 msa = new SequenceI[seqs.size()];\r
2040 \r
2041                 for (int i = 0; i < seqs.size(); i++)\r
2042                 {\r
2043                     msa[i] = (SequenceI) seqs.elementAt(i);\r
2044                 }\r
2045             }\r
2046         }\r
2047 \r
2048         if (msa != null)\r
2049         {\r
2050             MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa,\r
2051                     false, true);\r
2052         }\r
2053     }\r
2054 \r
2055     /**\r
2056      * DOCUMENT ME!\r
2057      *\r
2058      * @param e DOCUMENT ME!\r
2059      */\r
2060     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
2061     {\r
2062         // Pick the tree file\r
2063         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
2064                     "LAST_DIRECTORY"));\r
2065         chooser.setFileView(new JalviewFileView());\r
2066         chooser.setDialogTitle("Select a newick-like tree file");\r
2067         chooser.setToolTipText("Load a tree file");\r
2068 \r
2069         int value = chooser.showOpenDialog(null);\r
2070 \r
2071         if (value == JalviewFileChooser.APPROVE_OPTION)\r
2072         {\r
2073             String choice = chooser.getSelectedFile().getPath();\r
2074             jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
2075 \r
2076             try\r
2077             {\r
2078                 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,\r
2079                         "File");\r
2080                 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());\r
2081             }\r
2082             catch (Exception ex)\r
2083             {\r
2084                 JOptionPane.showMessageDialog(Desktop.desktop,\r
2085                     "Problem reading tree file", ex.getMessage(),\r
2086                     JOptionPane.WARNING_MESSAGE);\r
2087                 ex.printStackTrace();\r
2088             }\r
2089         }\r
2090     }\r
2091 \r
2092     /**\r
2093      * DOCUMENT ME!\r
2094      *\r
2095      * @param nf DOCUMENT ME!\r
2096      * @param title DOCUMENT ME!\r
2097      *\r
2098      * @return DOCUMENT ME!\r
2099      */\r
2100     public TreePanel ShowNewickTree(NewickFile nf, String title)\r
2101     {\r
2102         TreePanel tp = null;\r
2103 \r
2104         try\r
2105         {\r
2106             nf.parse();\r
2107 \r
2108             if (nf.getTree() != null)\r
2109             {\r
2110                 tp = new TreePanel(viewport,\r
2111                         viewport.getAlignment().getSequences(), nf, "FromFile",\r
2112                         title);\r
2113                 Desktop.addInternalFrame(tp, title, 600, 500);\r
2114                 addTreeMenuItem(tp, title);\r
2115             }\r
2116         }\r
2117         catch (Exception ex)\r
2118         {\r
2119             ex.printStackTrace();\r
2120         }\r
2121 \r
2122         return tp;\r
2123     }\r
2124 \r
2125     class PrintThread extends Thread\r
2126     {\r
2127         public void run()\r
2128         {\r
2129             PrinterJob printJob = PrinterJob.getPrinterJob();\r
2130             PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
2131             printJob.setPrintable(alignPanel, pf);\r
2132 \r
2133             if (printJob.printDialog())\r
2134             {\r
2135                 try\r
2136                 {\r
2137                     printJob.print();\r
2138                 }\r
2139                 catch (Exception PrintException)\r
2140                 {\r
2141                     PrintException.printStackTrace();\r
2142                 }\r
2143             }\r
2144         }\r
2145     }\r
2146 }\r