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             || viewport.getSelectionGroup().sequences.size()<1)\r
 922         {\r
 923             seqs = viewport.getSelectionGroup().sequences;\r
 924             start = viewport.getSelectionGroup().getStartRes();\r
 925             end = viewport.getSelectionGroup().getEndRes();\r
 926         }\r
 927         else\r
 928         {\r
 929             seqs = viewport.alignment.getSequences();\r
 930         }\r
 931 \r
 932         for (int i = 0; i < seqs.size(); i++)\r
 933         {\r
 934             current = (SequenceI) seqs.elementAt(i);\r
 935             jSize = current.getLength();\r
 936 \r
 937             int j = start;\r
 938 \r
 939             do\r
 940             {\r
 941                 if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
 942                 {\r
 943                     current.deleteCharAt(j);\r
 944                     j--;\r
 945                     jSize--;\r
 946                 }\r
 947 \r
 948                 j++;\r
 949             }\r
 950             while (j < end && j < jSize);\r
 951         }\r
 952 \r
 953         viewport.updateConservation();\r
 954         viewport.updateConsensus();\r
 955         alignPanel.repaint();\r
 956     }\r
 957 \r
 958     /**\r
 959      * DOCUMENT ME!\r
 960      *\r
 961      * @param e DOCUMENT ME!\r
 962      */\r
 963     public void padGapsMenuitem_actionPerformed(ActionEvent e)\r
 964     {\r
 965         addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,\r
 966                 HistoryItem.HIDE));\r
 967 \r
 968         SequenceI current;\r
 969         int Width = viewport.getAlignment().getWidth();\r
 970 \r
 971         for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
 972                 i++)\r
 973         {\r
 974             current = viewport.getAlignment().getSequenceAt(i);\r
 975 \r
 976             if (current.getLength() < Width)\r
 977             {\r
 978                 current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
 979             }\r
 980         }\r
 981 \r
 982         viewport.updateConservation();\r
 983         viewport.updateConsensus();\r
 984         alignPanel.repaint();\r
 985     }\r
 986 \r
 987     /**\r
 988      * DOCUMENT ME!\r
 989      *\r
 990      * @param e DOCUMENT ME!\r
 991      */\r
 992     public void findMenuItem_actionPerformed(ActionEvent e)\r
 993     {\r
 994         JInternalFrame frame = new JInternalFrame();\r
 995         Finder finder = new Finder(viewport, alignPanel, frame);\r
 996         frame.setContentPane(finder);\r
 997         Desktop.addInternalFrame(frame, "Find", 340, 110);\r
 998         frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
 999     }\r
1000 \r
1001     /**\r
1002      * DOCUMENT ME!\r
1003      *\r
1004      * @param e DOCUMENT ME!\r
1005      */\r
1006     public void font_actionPerformed(ActionEvent e)\r
1007     {\r
1008         FontChooser fc = new FontChooser(alignPanel);\r
1009     }\r
1010 \r
1011     /**\r
1012      * DOCUMENT ME!\r
1013      *\r
1014      * @param e DOCUMENT ME!\r
1015      */\r
1016     protected void fullSeqId_actionPerformed(ActionEvent e)\r
1017     {\r
1018         viewport.setShowFullId(fullSeqId.isSelected());\r
1019 \r
1020         alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());\r
1021         alignPanel.repaint();\r
1022     }\r
1023 \r
1024     /**\r
1025      * DOCUMENT ME!\r
1026      *\r
1027      * @param e DOCUMENT ME!\r
1028      */\r
1029     protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
1030     {\r
1031         viewport.setColourText(colourTextMenuItem.isSelected());\r
1032         alignPanel.repaint();\r
1033     }\r
1034 \r
1035     /**\r
1036      * DOCUMENT ME!\r
1037      *\r
1038      * @param e DOCUMENT ME!\r
1039      */\r
1040     protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
1041     {\r
1042         viewport.setWrapAlignment(wrapMenuItem.isSelected());\r
1043         alignPanel.setWrapAlignment(wrapMenuItem.isSelected());\r
1044         scaleAbove.setVisible(wrapMenuItem.isSelected());\r
1045         scaleLeft.setVisible(wrapMenuItem.isSelected());\r
1046         scaleRight.setVisible(wrapMenuItem.isSelected());\r
1047         alignPanel.repaint();\r
1048     }\r
1049 \r
1050     /**\r
1051      * DOCUMENT ME!\r
1052      *\r
1053      * @param e DOCUMENT ME!\r
1054      */\r
1055     protected void scaleAbove_actionPerformed(ActionEvent e)\r
1056     {\r
1057         viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
1058         alignPanel.repaint();\r
1059     }\r
1060 \r
1061     /**\r
1062      * DOCUMENT ME!\r
1063      *\r
1064      * @param e DOCUMENT ME!\r
1065      */\r
1066     protected void scaleLeft_actionPerformed(ActionEvent e)\r
1067     {\r
1068         viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
1069         alignPanel.repaint();\r
1070     }\r
1071 \r
1072     /**\r
1073      * DOCUMENT ME!\r
1074      *\r
1075      * @param e DOCUMENT ME!\r
1076      */\r
1077     protected void scaleRight_actionPerformed(ActionEvent e)\r
1078     {\r
1079         viewport.setScaleRightWrapped(scaleRight.isSelected());\r
1080         alignPanel.repaint();\r
1081     }\r
1082 \r
1083     /**\r
1084      * DOCUMENT ME!\r
1085      *\r
1086      * @param e DOCUMENT ME!\r
1087      */\r
1088     public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
1089     {\r
1090         viewport.setShowBoxes(viewBoxesMenuItem.isSelected());\r
1091         alignPanel.repaint();\r
1092     }\r
1093 \r
1094     /**\r
1095      * DOCUMENT ME!\r
1096      *\r
1097      * @param e DOCUMENT ME!\r
1098      */\r
1099     public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
1100     {\r
1101         viewport.setShowText(viewTextMenuItem.isSelected());\r
1102         alignPanel.repaint();\r
1103     }\r
1104 \r
1105     /**\r
1106      * DOCUMENT ME!\r
1107      *\r
1108      * @param e DOCUMENT ME!\r
1109      */\r
1110     protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
1111     {\r
1112         viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
1113         alignPanel.repaint();\r
1114     }\r
1115 \r
1116     /**\r
1117      * DOCUMENT ME!\r
1118      *\r
1119      * @param evt DOCUMENT ME!\r
1120      */\r
1121     public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
1122     {\r
1123         viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
1124 \r
1125         if (viewport.showSequenceFeatures &&\r
1126                 !((Alignment) viewport.alignment).featuresAdded)\r
1127         {\r
1128             SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment,\r
1129                     alignPanel);\r
1130             ((Alignment) viewport.alignment).featuresAdded = true;\r
1131         }\r
1132 \r
1133         alignPanel.repaint();\r
1134     }\r
1135 \r
1136     /**\r
1137      * DOCUMENT ME!\r
1138      *\r
1139      * @param e DOCUMENT ME!\r
1140      */\r
1141     public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
1142     {\r
1143         if (annotationPanelMenuItem.isSelected() &&\r
1144                 viewport.getWrapAlignment())\r
1145         {\r
1146             annotationPanelMenuItem.setSelected(false);\r
1147 \r
1148             return;\r
1149         }\r
1150 \r
1151         viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());\r
1152         alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());\r
1153     }\r
1154 \r
1155     /**\r
1156      * DOCUMENT ME!\r
1157      *\r
1158      * @param e DOCUMENT ME!\r
1159      */\r
1160     public void overviewMenuItem_actionPerformed(ActionEvent e)\r
1161     {\r
1162         if (alignPanel.overviewPanel != null)\r
1163         {\r
1164             return;\r
1165         }\r
1166 \r
1167         JInternalFrame frame = new JInternalFrame();\r
1168         OverviewPanel overview = new OverviewPanel(alignPanel);\r
1169         frame.setContentPane(overview);\r
1170         Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),\r
1171             frame.getWidth(), frame.getHeight());\r
1172         frame.pack();\r
1173         frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
1174         frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
1175             {\r
1176                 public void internalFrameClosed(\r
1177                     javax.swing.event.InternalFrameEvent evt)\r
1178                 {\r
1179                     alignPanel.setOverviewPanel(null);\r
1180                 }\r
1181                 ;\r
1182             });\r
1183 \r
1184         alignPanel.setOverviewPanel(overview);\r
1185     }\r
1186 \r
1187     /**\r
1188      * DOCUMENT ME!\r
1189      *\r
1190      * @param e DOCUMENT ME!\r
1191      */\r
1192     protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
1193     {\r
1194         changeColour(null);\r
1195     }\r
1196 \r
1197     /**\r
1198      * DOCUMENT ME!\r
1199      *\r
1200      * @param e DOCUMENT ME!\r
1201      */\r
1202     public void clustalColour_actionPerformed(ActionEvent e)\r
1203     {\r
1204         changeColour(new ClustalxColourScheme(\r
1205                 viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
1206     }\r
1207 \r
1208     /**\r
1209      * DOCUMENT ME!\r
1210      *\r
1211      * @param e DOCUMENT ME!\r
1212      */\r
1213     public void zappoColour_actionPerformed(ActionEvent e)\r
1214     {\r
1215         changeColour(new ZappoColourScheme());\r
1216     }\r
1217 \r
1218     /**\r
1219      * DOCUMENT ME!\r
1220      *\r
1221      * @param e DOCUMENT ME!\r
1222      */\r
1223     public void taylorColour_actionPerformed(ActionEvent e)\r
1224     {\r
1225         changeColour(new TaylorColourScheme());\r
1226     }\r
1227 \r
1228     /**\r
1229      * DOCUMENT ME!\r
1230      *\r
1231      * @param e DOCUMENT ME!\r
1232      */\r
1233     public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
1234     {\r
1235         changeColour(new HydrophobicColourScheme());\r
1236     }\r
1237 \r
1238     /**\r
1239      * DOCUMENT ME!\r
1240      *\r
1241      * @param e DOCUMENT ME!\r
1242      */\r
1243     public void helixColour_actionPerformed(ActionEvent e)\r
1244     {\r
1245         changeColour(new HelixColourScheme());\r
1246     }\r
1247 \r
1248     /**\r
1249      * DOCUMENT ME!\r
1250      *\r
1251      * @param e DOCUMENT ME!\r
1252      */\r
1253     public void strandColour_actionPerformed(ActionEvent e)\r
1254     {\r
1255         changeColour(new StrandColourScheme());\r
1256     }\r
1257 \r
1258     /**\r
1259      * DOCUMENT ME!\r
1260      *\r
1261      * @param e DOCUMENT ME!\r
1262      */\r
1263     public void turnColour_actionPerformed(ActionEvent e)\r
1264     {\r
1265         changeColour(new TurnColourScheme());\r
1266     }\r
1267 \r
1268     /**\r
1269      * DOCUMENT ME!\r
1270      *\r
1271      * @param e DOCUMENT ME!\r
1272      */\r
1273     public void buriedColour_actionPerformed(ActionEvent e)\r
1274     {\r
1275         changeColour(new BuriedColourScheme());\r
1276     }\r
1277 \r
1278     /**\r
1279      * DOCUMENT ME!\r
1280      *\r
1281      * @param e DOCUMENT ME!\r
1282      */\r
1283     public void nucleotideColour_actionPerformed(ActionEvent e)\r
1284     {\r
1285         changeColour(new NucleotideColourScheme());\r
1286     }\r
1287 \r
1288     /**\r
1289      * DOCUMENT ME!\r
1290      *\r
1291      * @param e DOCUMENT ME!\r
1292      */\r
1293     protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
1294     {\r
1295         viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
1296     }\r
1297 \r
1298     /**\r
1299      * DOCUMENT ME!\r
1300      *\r
1301      * @param cs DOCUMENT ME!\r
1302      */\r
1303     void changeColour(ColourSchemeI cs)\r
1304     {\r
1305         int threshold = 0;\r
1306 \r
1307         if (viewport.getAbovePIDThreshold())\r
1308         {\r
1309             threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,\r
1310                     "Background");\r
1311 \r
1312             if (cs instanceof ResidueColourScheme)\r
1313             {\r
1314                 ((ResidueColourScheme) cs).setThreshold(threshold);\r
1315             }\r
1316             else if (cs instanceof ScoreColourScheme)\r
1317             {\r
1318                 ((ScoreColourScheme) cs).setThreshold(threshold);\r
1319             }\r
1320 \r
1321             viewport.setGlobalColourScheme(cs);\r
1322         }\r
1323         else if (cs instanceof ResidueColourScheme)\r
1324         {\r
1325             ((ResidueColourScheme) cs).setThreshold(0);\r
1326         }\r
1327         else if (cs instanceof ScoreColourScheme)\r
1328         {\r
1329             ((ScoreColourScheme) cs).setThreshold(0);\r
1330         }\r
1331 \r
1332         if (viewport.getConservationSelected())\r
1333         {\r
1334             ConservationColourScheme ccs = null;\r
1335 \r
1336             Alignment al = (Alignment) viewport.alignment;\r
1337             Conservation c = new Conservation("All",\r
1338                     ResidueProperties.propHash, 3, al.getSequences(), 0,\r
1339                     al.getWidth() - 1);\r
1340 \r
1341             c.calculate();\r
1342             c.verdict(false, viewport.ConsPercGaps);\r
1343 \r
1344             ccs = new ConservationColourScheme(c, cs);\r
1345 \r
1346             // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
1347             ccs.setConsensus(viewport.vconsensus);\r
1348             viewport.setGlobalColourScheme(ccs);\r
1349 \r
1350             ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,\r
1351                     "Background");\r
1352         }\r
1353         else\r
1354         {\r
1355             // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
1356             if (cs != null)\r
1357             {\r
1358                 cs.setConsensus(viewport.vconsensus);\r
1359             }\r
1360 \r
1361             viewport.setGlobalColourScheme(cs);\r
1362         }\r
1363 \r
1364         if (viewport.getColourAppliesToAllGroups())\r
1365         {\r
1366             Vector groups = viewport.alignment.getGroups();\r
1367 \r
1368             for (int i = 0; i < groups.size(); i++)\r
1369             {\r
1370                 SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
1371 \r
1372                 if (cs == null)\r
1373                 {\r
1374                     sg.cs = null;\r
1375                 }\r
1376                 else if (cs instanceof ClustalxColourScheme)\r
1377                 {\r
1378                     sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
1379                 }\r
1380                 else if (cs instanceof UserColourScheme)\r
1381                 {\r
1382                     sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());\r
1383                 }\r
1384                 else\r
1385                 {\r
1386                     try\r
1387                     {\r
1388                         sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
1389                     }\r
1390                     catch (Exception ex)\r
1391                     {\r
1392                     }\r
1393                 }\r
1394 \r
1395                 if (viewport.getAbovePIDThreshold())\r
1396                 {\r
1397                     if (sg.cs instanceof ResidueColourScheme)\r
1398                     {\r
1399                         ((ResidueColourScheme) sg.cs).setThreshold(threshold);\r
1400                     }\r
1401                     else if (sg.cs instanceof ScoreColourScheme)\r
1402                     {\r
1403                         ((ScoreColourScheme) sg.cs).setThreshold(threshold);\r
1404                     }\r
1405 \r
1406                     sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
1407                             sg.getWidth()));\r
1408                 }\r
1409 \r
1410                 if (viewport.getConservationSelected())\r
1411                 {\r
1412                     Conservation c = new Conservation("Group",\r
1413                             ResidueProperties.propHash, 3, sg.sequences, 0,\r
1414                             viewport.alignment.getWidth() - 1);\r
1415                     c.calculate();\r
1416                     c.verdict(false, viewport.ConsPercGaps);\r
1417 \r
1418                     ConservationColourScheme ccs = new ConservationColourScheme(c,\r
1419                             sg.cs);\r
1420 \r
1421                     // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
1422                     ccs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
1423                             sg.getWidth()));\r
1424                     sg.cs = ccs;\r
1425                 }\r
1426                 else if (cs != null)\r
1427                 {\r
1428                     // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
1429                     sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
1430                             sg.getWidth()));\r
1431                 }\r
1432             }\r
1433         }\r
1434 \r
1435         if (alignPanel.getOverviewPanel() != null)\r
1436         {\r
1437             alignPanel.getOverviewPanel().updateOverviewImage();\r
1438         }\r
1439 \r
1440         alignPanel.repaint();\r
1441     }\r
1442 \r
1443     /**\r
1444      * DOCUMENT ME!\r
1445      *\r
1446      * @param e DOCUMENT ME!\r
1447      */\r
1448     protected void modifyPID_actionPerformed(ActionEvent e)\r
1449     {\r
1450         if (viewport.getAbovePIDThreshold())\r
1451         {\r
1452             SliderPanel.setPIDSliderSource(alignPanel,\r
1453                 viewport.getGlobalColourScheme(), "Background");\r
1454             SliderPanel.showPIDSlider();\r
1455         }\r
1456     }\r
1457 \r
1458     /**\r
1459      * DOCUMENT ME!\r
1460      *\r
1461      * @param e DOCUMENT ME!\r
1462      */\r
1463     protected void modifyConservation_actionPerformed(ActionEvent e)\r
1464     {\r
1465         if (viewport.getConservationSelected())\r
1466         {\r
1467             SliderPanel.setConservationSlider(alignPanel,\r
1468                 viewport.globalColourScheme, "Background");\r
1469             SliderPanel.showConservationSlider();\r
1470         }\r
1471     }\r
1472 \r
1473     /**\r
1474      * DOCUMENT ME!\r
1475      *\r
1476      * @param e DOCUMENT ME!\r
1477      */\r
1478     protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
1479     {\r
1480         viewport.setConservationSelected(conservationMenuItem.isSelected());\r
1481 \r
1482         viewport.setAbovePIDThreshold(false);\r
1483         abovePIDThreshold.setSelected(false);\r
1484 \r
1485         ColourSchemeI cs = viewport.getGlobalColourScheme();\r
1486 \r
1487         if (cs instanceof ConservationColourScheme)\r
1488         {\r
1489             changeColour(((ConservationColourScheme) cs).cs);\r
1490         }\r
1491         else\r
1492         {\r
1493             changeColour(cs);\r
1494         }\r
1495 \r
1496         modifyConservation_actionPerformed(null);\r
1497     }\r
1498 \r
1499     /**\r
1500      * DOCUMENT ME!\r
1501      *\r
1502      * @param e DOCUMENT ME!\r
1503      */\r
1504     public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
1505     {\r
1506         viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
1507 \r
1508         conservationMenuItem.setSelected(false);\r
1509         viewport.setConservationSelected(false);\r
1510 \r
1511         ColourSchemeI cs = viewport.getGlobalColourScheme();\r
1512 \r
1513         if (cs instanceof ConservationColourScheme)\r
1514         {\r
1515             changeColour(((ConservationColourScheme) cs).cs);\r
1516         }\r
1517         else\r
1518         {\r
1519             changeColour(cs);\r
1520         }\r
1521 \r
1522         modifyPID_actionPerformed(null);\r
1523     }\r
1524 \r
1525     /**\r
1526      * DOCUMENT ME!\r
1527      *\r
1528      * @param e DOCUMENT ME!\r
1529      */\r
1530     public void userDefinedColour_actionPerformed(ActionEvent e)\r
1531     {\r
1532         new UserDefinedColours(alignPanel, null);\r
1533     }\r
1534 \r
1535     /**\r
1536      * DOCUMENT ME!\r
1537      *\r
1538      * @param e DOCUMENT ME!\r
1539      */\r
1540     public void PIDColour_actionPerformed(ActionEvent e)\r
1541     {\r
1542         changeColour(new PIDColourScheme());\r
1543     }\r
1544 \r
1545     /**\r
1546      * DOCUMENT ME!\r
1547      *\r
1548      * @param e DOCUMENT ME!\r
1549      */\r
1550     public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
1551     {\r
1552         changeColour(new Blosum62ColourScheme());\r
1553     }\r
1554 \r
1555     /**\r
1556      * DOCUMENT ME!\r
1557      *\r
1558      * @param e DOCUMENT ME!\r
1559      */\r
1560     public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
1561     {\r
1562         addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
1563                 HistoryItem.SORT));\r
1564         AlignmentSorter.sortByPID(viewport.getAlignment(),\r
1565             viewport.getAlignment().getSequenceAt(0));\r
1566         alignPanel.repaint();\r
1567     }\r
1568 \r
1569     /**\r
1570      * DOCUMENT ME!\r
1571      *\r
1572      * @param e DOCUMENT ME!\r
1573      */\r
1574     public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
1575     {\r
1576         addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
1577                 HistoryItem.SORT));\r
1578         AlignmentSorter.sortByID(viewport.getAlignment());\r
1579         alignPanel.repaint();\r
1580     }\r
1581 \r
1582     /**\r
1583      * DOCUMENT ME!\r
1584      *\r
1585      * @param e DOCUMENT ME!\r
1586      */\r
1587     public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
1588     {\r
1589         addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
1590                 HistoryItem.SORT));\r
1591 \r
1592         AlignmentSorter.sortByGroup(viewport.getAlignment());\r
1593         alignPanel.repaint();\r
1594     }\r
1595 \r
1596     /**\r
1597      * DOCUMENT ME!\r
1598      *\r
1599      * @param e DOCUMENT ME!\r
1600      */\r
1601     public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
1602     {\r
1603         RedundancyPanel sp = new RedundancyPanel(alignPanel, this);\r
1604         JInternalFrame frame = new JInternalFrame();\r
1605         frame.setContentPane(sp);\r
1606         Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,\r
1607             100, false);\r
1608     }\r
1609 \r
1610     /**\r
1611      * DOCUMENT ME!\r
1612      *\r
1613      * @param e DOCUMENT ME!\r
1614      */\r
1615     public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
1616     {\r
1617         if ((viewport.getSelectionGroup() == null) ||\r
1618                 (viewport.getSelectionGroup().getSize() < 2))\r
1619         {\r
1620             JOptionPane.showInternalMessageDialog(this,\r
1621                 "You must select at least 2 sequences.", "Invalid Selection",\r
1622                 JOptionPane.WARNING_MESSAGE);\r
1623         }\r
1624         else\r
1625         {\r
1626             JInternalFrame frame = new JInternalFrame();\r
1627             frame.setContentPane(new PairwiseAlignPanel(viewport));\r
1628             Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);\r
1629         }\r
1630     }\r
1631 \r
1632     /**\r
1633      * DOCUMENT ME!\r
1634      *\r
1635      * @param e DOCUMENT ME!\r
1636      */\r
1637     public void PCAMenuItem_actionPerformed(ActionEvent e)\r
1638     {\r
1639         if (((viewport.getSelectionGroup() != null) &&\r
1640                 (viewport.getSelectionGroup().getSize() < 4) &&\r
1641                 (viewport.getSelectionGroup().getSize() > 0)) ||\r
1642                 (viewport.getAlignment().getHeight() < 4))\r
1643         {\r
1644             JOptionPane.showInternalMessageDialog(this,\r
1645                 "Principal component analysis must take\n" +\r
1646                 "at least 4 input sequences.",\r
1647                 "Sequence selection insufficient", JOptionPane.WARNING_MESSAGE);\r
1648 \r
1649             return;\r
1650         }\r
1651 \r
1652         try\r
1653         {\r
1654             PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
1655             JInternalFrame frame = new JInternalFrame();\r
1656             frame.setContentPane(pcaPanel);\r
1657             Desktop.addInternalFrame(frame, "Principal component analysis",\r
1658                 400, 400);\r
1659         }\r
1660         catch (java.lang.OutOfMemoryError ex)\r
1661         {\r
1662             JOptionPane.showInternalMessageDialog(this,\r
1663                 "Too many sequences selected\nfor Principal Component Analysis!!",\r
1664                 "Out of memory", JOptionPane.WARNING_MESSAGE);\r
1665         }\r
1666     }\r
1667 \r
1668     /**\r
1669      * DOCUMENT ME!\r
1670      *\r
1671      * @param e DOCUMENT ME!\r
1672      */\r
1673     public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
1674     {\r
1675         NewTreePanel("AV", "PID", "Average distance tree using PID");\r
1676     }\r
1677 \r
1678     /**\r
1679      * DOCUMENT ME!\r
1680      *\r
1681      * @param e DOCUMENT ME!\r
1682      */\r
1683     public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
1684     {\r
1685         NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
1686     }\r
1687 \r
1688     /**\r
1689      * DOCUMENT ME!\r
1690      *\r
1691      * @param e DOCUMENT ME!\r
1692      */\r
1693     protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1694     {\r
1695         NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
1696     }\r
1697 \r
1698     /**\r
1699      * DOCUMENT ME!\r
1700      *\r
1701      * @param e DOCUMENT ME!\r
1702      */\r
1703     protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
1704     {\r
1705         NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
1706     }\r
1707 \r
1708     /**\r
1709      * DOCUMENT ME!\r
1710      *\r
1711      * @param type DOCUMENT ME!\r
1712      * @param pwType DOCUMENT ME!\r
1713      * @param title DOCUMENT ME!\r
1714      */\r
1715     void NewTreePanel(String type, String pwType, String title)\r
1716     {\r
1717         final TreePanel tp;\r
1718 \r
1719         if ((viewport.getSelectionGroup() != null) &&\r
1720                 (viewport.getSelectionGroup().getSize() > 3))\r
1721         {\r
1722             int s = 0;\r
1723             SequenceGroup sg = viewport.getSelectionGroup();\r
1724 \r
1725             /* Decide if the selection is a column region */\r
1726             while (s < sg.sequences.size())\r
1727             {\r
1728                 if (((SequenceI) sg.sequences.elementAt(s++)).getLength() < sg.getEndRes())\r
1729                 {\r
1730                     JOptionPane.showMessageDialog(Desktop.desktop,\r
1731                         "The selected region to create a tree may\nonly contain residues or gaps.\n" +\r
1732                         "Try using the Pad function in the edit menu,\n" +\r
1733                         "or one of the multiple sequence alignment web services.",\r
1734                         "Sequences in selection are not aligned",\r
1735                         JOptionPane.WARNING_MESSAGE);\r
1736 \r
1737                     return;\r
1738                 }\r
1739             }\r
1740 \r
1741             title = title + " on region";\r
1742             tp = new TreePanel(viewport,\r
1743                     viewport.getSelectionGroup().sequences, type, pwType,\r
1744                     sg.getStartRes(), sg.getEndRes());\r
1745         }\r
1746         else\r
1747         {\r
1748             //are the sequences aligned?\r
1749             if (!viewport.alignment.isAligned())\r
1750             {\r
1751                 JOptionPane.showMessageDialog(Desktop.desktop,\r
1752                     "The sequences must be aligned before creating a tree.\n" +\r
1753                     "Try using the Pad function in the edit menu,\n" +\r
1754                     "or one of the multiple sequence alignment web services.",\r
1755                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);\r
1756 \r
1757                 return;\r
1758             }\r
1759 \r
1760             tp = new TreePanel(viewport,\r
1761                     viewport.getAlignment().getSequences(), type, pwType, 0,\r
1762                     viewport.alignment.getWidth());\r
1763         }\r
1764 \r
1765         addTreeMenuItem(tp, title);\r
1766         viewport.setCurrentTree(tp.getTree());\r
1767 \r
1768         Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);\r
1769     }\r
1770 \r
1771     /**\r
1772      * DOCUMENT ME!\r
1773      *\r
1774      * @param title DOCUMENT ME!\r
1775      * @param order DOCUMENT ME!\r
1776      */\r
1777     public void addSortByOrderMenuItem(String title, final AlignmentOrder order)\r
1778     {\r
1779         final JMenuItem item = new JMenuItem("by " + title);\r
1780         sort.add(item);\r
1781         item.addActionListener(new java.awt.event.ActionListener()\r
1782             {\r
1783                 public void actionPerformed(ActionEvent e)\r
1784                 {\r
1785                     addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
1786                             HistoryItem.SORT));\r
1787 \r
1788                     // TODO: JBPNote - have to map order entries to curent SequenceI pointers\r
1789                     AlignmentSorter.sortBy(viewport.getAlignment(), order);\r
1790                     alignPanel.repaint();\r
1791                 }\r
1792             });\r
1793     }\r
1794 \r
1795     /**\r
1796      * DOCUMENT ME!\r
1797      *\r
1798      * @param treePanel DOCUMENT ME!\r
1799      * @param title DOCUMENT ME!\r
1800      */\r
1801     void addTreeMenuItem(final TreePanel treePanel, String title)\r
1802     {\r
1803         final JMenuItem item = new JMenuItem(title);\r
1804 \r
1805         treeCount++;\r
1806 \r
1807         if (treeCount == 1)\r
1808         {\r
1809             sort.add(sortByTreeMenu);\r
1810         }\r
1811 \r
1812         sortByTreeMenu.add(item);\r
1813         item.addActionListener(new java.awt.event.ActionListener()\r
1814             {\r
1815                 public void actionPerformed(ActionEvent e)\r
1816                 {\r
1817                     addHistoryItem(new HistoryItem("Tree Sort",\r
1818                             viewport.alignment, HistoryItem.SORT));\r
1819                     AlignmentSorter.sortByTree(viewport.getAlignment(),\r
1820                         treePanel.getTree());\r
1821                     alignPanel.repaint();\r
1822                 }\r
1823             });\r
1824 \r
1825         treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
1826             {\r
1827                 public void internalFrameClosed(\r
1828                     javax.swing.event.InternalFrameEvent evt)\r
1829                 {\r
1830                     treeCount--;\r
1831                     sortByTreeMenu.remove(item);\r
1832 \r
1833                     if (treeCount == 0)\r
1834                     {\r
1835                         sort.remove(sortByTreeMenu);\r
1836                     }\r
1837                 }\r
1838                 ;\r
1839             });\r
1840         viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
1841             {\r
1842                 public void propertyChange(PropertyChangeEvent evt)\r
1843                 {\r
1844                     if (evt.getPropertyName().equals("alignment"))\r
1845                     {\r
1846                         treePanel.getTree().UpdatePlaceHolders((Vector) evt.getNewValue());\r
1847                         treePanel.repaint();\r
1848                     }\r
1849                 }\r
1850             });\r
1851     }\r
1852 \r
1853     /**\r
1854      * DOCUMENT ME!\r
1855      *\r
1856      * @param e DOCUMENT ME!\r
1857      */\r
1858     public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
1859     {\r
1860         // TODO:resolve which menu item was actually selected\r
1861         // Now, check we have enough sequences\r
1862         SequenceI[] msa = null;\r
1863 \r
1864         if ((viewport.getSelectionGroup() != null) &&\r
1865                 (viewport.getSelectionGroup().getSize() > 1))\r
1866         {\r
1867             // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1868             SequenceGroup seqs = viewport.getSelectionGroup();\r
1869             int sz;\r
1870             msa = new SequenceI[sz = seqs.getSize()];\r
1871 \r
1872             for (int i = 0; i < sz; i++)\r
1873             {\r
1874                 msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1875             }\r
1876         }\r
1877         else\r
1878         {\r
1879             Vector seqs = viewport.getAlignment().getSequences();\r
1880 \r
1881             if (seqs.size() > 1)\r
1882             {\r
1883                 msa = new SequenceI[seqs.size()];\r
1884 \r
1885                 for (int i = 0; i < seqs.size(); i++)\r
1886                 {\r
1887                     msa[i] = (SequenceI) seqs.elementAt(i);\r
1888                 }\r
1889             }\r
1890         }\r
1891 \r
1892         if (msa != null)\r
1893         {\r
1894             jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",\r
1895                     title, msa, false, true);\r
1896         }\r
1897     }\r
1898 \r
1899     /**\r
1900      * DOCUMENT ME!\r
1901      *\r
1902      * @param e DOCUMENT ME!\r
1903      */\r
1904     public void ClustalRealign_actionPerformed(ActionEvent e)\r
1905     {\r
1906         // TODO:resolve which menu item was actually selected\r
1907         // Now, check we have enough sequences\r
1908         SequenceI[] msa = null;\r
1909 \r
1910         if ((viewport.getSelectionGroup() != null) &&\r
1911                 (viewport.getSelectionGroup().getSize() > 1))\r
1912         {\r
1913             // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1914             SequenceGroup seqs = viewport.getSelectionGroup();\r
1915             int sz;\r
1916             msa = new SequenceI[sz = seqs.getSize()];\r
1917 \r
1918             for (int i = 0; i < sz; i++)\r
1919             {\r
1920                 msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1921             }\r
1922         }\r
1923         else\r
1924         {\r
1925             Vector seqs = viewport.getAlignment().getSequences();\r
1926 \r
1927             if (seqs.size() > 1)\r
1928             {\r
1929                 msa = new SequenceI[seqs.size()];\r
1930 \r
1931                 for (int i = 0; i < seqs.size(); i++)\r
1932                 {\r
1933                     msa[i] = (SequenceI) seqs.elementAt(i);\r
1934                 }\r
1935             }\r
1936         }\r
1937 \r
1938         if (msa != null)\r
1939         {\r
1940             jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",\r
1941                     title, msa, true, true);\r
1942         }\r
1943     }\r
1944 \r
1945     /**\r
1946      * DOCUMENT ME!\r
1947      *\r
1948      * @param e DOCUMENT ME!\r
1949      */\r
1950     protected void jpred_actionPerformed(ActionEvent e)\r
1951     {\r
1952         SequenceI seq = null;\r
1953         SequenceI[] msa = null;\r
1954 \r
1955         if ((viewport.getSelectionGroup() != null) &&\r
1956                 (viewport.getSelectionGroup().getSize() > 0))\r
1957         {\r
1958             // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
1959             SequenceGroup seqs = viewport.getSelectionGroup();\r
1960 \r
1961             if ((seqs.getSize() == 1) || !viewport.alignment.isAligned())\r
1962             {\r
1963                 seq = (SequenceI) seqs.getSequenceAt(0);\r
1964             }\r
1965             else\r
1966             {\r
1967                 int sz;\r
1968                 msa = new SequenceI[sz = seqs.getSize()];\r
1969 \r
1970                 for (int i = 0; i < sz; i++)\r
1971                 {\r
1972                     msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
1973                 }\r
1974             }\r
1975         }\r
1976         else\r
1977         {\r
1978             Vector seqs = viewport.getAlignment().getSequences();\r
1979 \r
1980             if ((seqs.size() == 1) || !viewport.alignment.isAligned())\r
1981             {\r
1982                 seq = (SequenceI) seqs.elementAt(0);\r
1983             }\r
1984             else\r
1985             {\r
1986                 msa = new SequenceI[seqs.size()];\r
1987 \r
1988                 for (int i = 0; i < seqs.size(); i++)\r
1989                 {\r
1990                     msa[i] = (SequenceI) seqs.elementAt(i);\r
1991                 }\r
1992             }\r
1993         }\r
1994 \r
1995         if (msa != null)\r
1996         {\r
1997             JPredClient ct = new JPredClient(title, msa);\r
1998         }\r
1999         else if (seq != null)\r
2000         {\r
2001             JPredClient ct = new JPredClient(title, seq);\r
2002         }\r
2003         else\r
2004         {\r
2005             System.err.print(\r
2006                 "JALVIEW ERROR! - Unexpected JPred selection state!\n");\r
2007         }\r
2008     }\r
2009 \r
2010     /**\r
2011      * DOCUMENT ME!\r
2012      *\r
2013      * @param e DOCUMENT ME!\r
2014      */\r
2015     protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
2016     {\r
2017         // TODO:resolve which menu item was actually selected\r
2018         // Now, check we have enough sequences\r
2019         SequenceI[] msa = null;\r
2020 \r
2021         if ((viewport.getSelectionGroup() != null) &&\r
2022                 (viewport.getSelectionGroup().getSize() > 1))\r
2023         {\r
2024             // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
2025             SequenceGroup seqs = viewport.getSelectionGroup();\r
2026             int sz;\r
2027             msa = new SequenceI[sz = seqs.getSize()];\r
2028 \r
2029             for (int i = 0; i < sz; i++)\r
2030             {\r
2031                 msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
2032             }\r
2033         }\r
2034         else\r
2035         {\r
2036             Vector seqs = viewport.getAlignment().getSequences();\r
2037 \r
2038             if (seqs.size() > 1)\r
2039             {\r
2040                 msa = new SequenceI[seqs.size()];\r
2041 \r
2042                 for (int i = 0; i < seqs.size(); i++)\r
2043                 {\r
2044                     msa[i] = (SequenceI) seqs.elementAt(i);\r
2045                 }\r
2046             }\r
2047         }\r
2048 \r
2049         if (msa != null)\r
2050         {\r
2051             MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa,\r
2052                     false, true);\r
2053         }\r
2054     }\r
2055 \r
2056     /**\r
2057      * DOCUMENT ME!\r
2058      *\r
2059      * @param e DOCUMENT ME!\r
2060      */\r
2061     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
2062     {\r
2063         // Pick the tree file\r
2064         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
2065                     "LAST_DIRECTORY"));\r
2066         chooser.setFileView(new JalviewFileView());\r
2067         chooser.setDialogTitle("Select a newick-like tree file");\r
2068         chooser.setToolTipText("Load a tree file");\r
2069 \r
2070         int value = chooser.showOpenDialog(null);\r
2071 \r
2072         if (value == JalviewFileChooser.APPROVE_OPTION)\r
2073         {\r
2074             String choice = chooser.getSelectedFile().getPath();\r
2075             jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
2076 \r
2077             try\r
2078             {\r
2079                 jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,\r
2080                         "File");\r
2081                 viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());\r
2082             }\r
2083             catch (Exception ex)\r
2084             {\r
2085                 JOptionPane.showMessageDialog(Desktop.desktop,\r
2086                     "Problem reading tree file", ex.getMessage(),\r
2087                     JOptionPane.WARNING_MESSAGE);\r
2088                 ex.printStackTrace();\r
2089             }\r
2090         }\r
2091     }\r
2092 \r
2093     /**\r
2094      * DOCUMENT ME!\r
2095      *\r
2096      * @param nf DOCUMENT ME!\r
2097      * @param title DOCUMENT ME!\r
2098      *\r
2099      * @return DOCUMENT ME!\r
2100      */\r
2101     public TreePanel ShowNewickTree(NewickFile nf, String title)\r
2102     {\r
2103         TreePanel tp = null;\r
2104 \r
2105         try\r
2106         {\r
2107             nf.parse();\r
2108 \r
2109             if (nf.getTree() != null)\r
2110             {\r
2111                 tp = new TreePanel(viewport,\r
2112                         viewport.getAlignment().getSequences(), nf, "FromFile",\r
2113                         title);\r
2114                 Desktop.addInternalFrame(tp, title, 600, 500);\r
2115                 addTreeMenuItem(tp, title);\r
2116             }\r
2117         }\r
2118         catch (Exception ex)\r
2119         {\r
2120             ex.printStackTrace();\r
2121         }\r
2122 \r
2123         return tp;\r
2124     }\r
2125 \r
2126     class PrintThread extends Thread\r
2127     {\r
2128         public void run()\r
2129         {\r
2130             PrinterJob printJob = PrinterJob.getPrinterJob();\r
2131             PageFormat pf = printJob.pageDialog(printJob.defaultPage());\r
2132             printJob.setPrintable(alignPanel, pf);\r
2133 \r
2134             if (printJob.printDialog())\r
2135             {\r
2136                 try\r
2137                 {\r
2138                     printJob.print();\r
2139                 }\r
2140                 catch (Exception PrintException)\r
2141                 {\r
2142                     PrintException.printStackTrace();\r
2143                 }\r
2144             }\r
2145         }\r
2146     }\r
2147 }\r