src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.ScoreModelI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignedCodonFrame;
  49 import jalview.datamodel.Alignment;
  50 import jalview.datamodel.AlignmentAnnotation;
  51 import jalview.datamodel.AlignmentExportData;
  52 import jalview.datamodel.AlignmentI;
  53 import jalview.datamodel.AlignmentOrder;
  54 import jalview.datamodel.AlignmentView;
  55 import jalview.datamodel.ColumnSelection;
  56 import jalview.datamodel.HiddenSequences;
  57 import jalview.datamodel.PDBEntry;
  58 import jalview.datamodel.SeqCigar;
  59 import jalview.datamodel.Sequence;
  60 import jalview.datamodel.SequenceGroup;
  61 import jalview.datamodel.SequenceI;
  62 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  63 import jalview.io.AlignmentProperties;
  64 import jalview.io.AnnotationFile;
  65 import jalview.io.BioJsHTMLOutput;
  66 import jalview.io.DataSourceType;
  67 import jalview.io.FileFormat;
  68 import jalview.io.FileFormatI;
  69 import jalview.io.FileFormats;
  70 import jalview.io.FileLoader;
  71 import jalview.io.FormatAdapter;
  72 import jalview.io.HtmlSvgOutput;
  73 import jalview.io.IdentifyFile;
  74 import jalview.io.JPredFile;
  75 import jalview.io.JalviewFileChooser;
  76 import jalview.io.JalviewFileView;
  77 import jalview.io.JnetAnnotationMaker;
  78 import jalview.io.NewickFile;
  79 import jalview.io.TCoffeeScoreFile;
  80 import jalview.jbgui.GAlignFrame;
  81 import jalview.schemes.Blosum62ColourScheme;
  82 import jalview.schemes.BuriedColourScheme;
  83 import jalview.schemes.ClustalxColourScheme;
  84 import jalview.schemes.ColourSchemeI;
  85 import jalview.schemes.ColourSchemeProperty;
  86 import jalview.schemes.HelixColourScheme;
  87 import jalview.schemes.HydrophobicColourScheme;
  88 import jalview.schemes.NucleotideColourScheme;
  89 import jalview.schemes.PIDColourScheme;
  90 import jalview.schemes.PurinePyrimidineColourScheme;
  91 import jalview.schemes.RNAHelicesColourChooser;
  92 import jalview.schemes.ResidueProperties;
  93 import jalview.schemes.StrandColourScheme;
  94 import jalview.schemes.TCoffeeColourScheme;
  95 import jalview.schemes.TaylorColourScheme;
  96 import jalview.schemes.TurnColourScheme;
  97 import jalview.schemes.UserColourScheme;
  98 import jalview.schemes.ZappoColourScheme;
  99 import jalview.util.MessageManager;
 100 import jalview.viewmodel.AlignmentViewport;
 101 import jalview.ws.DBRefFetcher;
 102 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 103 import jalview.ws.jws1.Discoverer;
 104 import jalview.ws.jws2.Jws2Discoverer;
 105 import jalview.ws.jws2.jabaws2.Jws2Instance;
 106 import jalview.ws.seqfetcher.DbSourceProxy;
 107
 108 import java.awt.BorderLayout;
 109 import java.awt.Component;
 110 import java.awt.Rectangle;
 111 import java.awt.Toolkit;
 112 import java.awt.datatransfer.Clipboard;
 113 import java.awt.datatransfer.DataFlavor;
 114 import java.awt.datatransfer.StringSelection;
 115 import java.awt.datatransfer.Transferable;
 116 import java.awt.dnd.DnDConstants;
 117 import java.awt.dnd.DropTargetDragEvent;
 118 import java.awt.dnd.DropTargetDropEvent;
 119 import java.awt.dnd.DropTargetEvent;
 120 import java.awt.dnd.DropTargetListener;
 121 import java.awt.event.ActionEvent;
 122 import java.awt.event.ActionListener;
 123 import java.awt.event.FocusAdapter;
 124 import java.awt.event.FocusEvent;
 125 import java.awt.event.ItemEvent;
 126 import java.awt.event.ItemListener;
 127 import java.awt.event.KeyAdapter;
 128 import java.awt.event.KeyEvent;
 129 import java.awt.event.MouseAdapter;
 130 import java.awt.event.MouseEvent;
 131 import java.awt.print.PageFormat;
 132 import java.awt.print.PrinterJob;
 133 import java.beans.PropertyChangeEvent;
 134 import java.io.File;
 135 import java.io.FileWriter;
 136 import java.io.PrintWriter;
 137 import java.net.URL;
 138 import java.util.ArrayList;
 139 import java.util.Arrays;
 140 import java.util.Deque;
 141 import java.util.Enumeration;
 142 import java.util.Hashtable;
 143 import java.util.List;
 144 import java.util.Vector;
 145
 146 import javax.swing.JCheckBoxMenuItem;
 147 import javax.swing.JEditorPane;
 148 import javax.swing.JInternalFrame;
 149 import javax.swing.JLayeredPane;
 150 import javax.swing.JMenu;
 151 import javax.swing.JMenuItem;
 152 import javax.swing.JRadioButtonMenuItem;
 153 import javax.swing.JScrollPane;
 154 import javax.swing.SwingUtilities;
 155
 156 /**
 157  * DOCUMENT ME!
 158  *
 159  * @author $author$
 160  * @version $Revision$
 161  */
 162 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 163         IProgressIndicator, AlignViewControllerGuiI
 164 {
 165
 166   public static final int DEFAULT_WIDTH = 700;
 167
 168   public static final int DEFAULT_HEIGHT = 500;
 169
 170   /*
 171    * The currently displayed panel (selected tabbed view if more than one)
 172    */
 173   public AlignmentPanel alignPanel;
 174
 175   AlignViewport viewport;
 176
 177   public AlignViewControllerI avc;
 178
 179   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 180
 181   /**
 182    * Last format used to load or save alignments in this window
 183    */
 184   FileFormatI currentFileFormat = null;
 185
 186   /**
 187    * Current filename for this alignment
 188    */
 189   String fileName = null;
 190
 191   /**
 192    * Creates a new AlignFrame object with specific width and height.
 193    *
 194    * @param al
 195    * @param width
 196    * @param height
 197    */
 198   public AlignFrame(AlignmentI al, int width, int height)
 199   {
 200     this(al, null, width, height);
 201   }
 202
 203   /**
 204    * Creates a new AlignFrame object with specific width, height and
 205    * sequenceSetId
 206    *
 207    * @param al
 208    * @param width
 209    * @param height
 210    * @param sequenceSetId
 211    */
 212   public AlignFrame(AlignmentI al, int width, int height,
 213           String sequenceSetId)
 214   {
 215     this(al, null, width, height, sequenceSetId);
 216   }
 217
 218   /**
 219    * Creates a new AlignFrame object with specific width, height and
 220    * sequenceSetId
 221    *
 222    * @param al
 223    * @param width
 224    * @param height
 225    * @param sequenceSetId
 226    * @param viewId
 227    */
 228   public AlignFrame(AlignmentI al, int width, int height,
 229           String sequenceSetId, String viewId)
 230   {
 231     this(al, null, width, height, sequenceSetId, viewId);
 232   }
 233
 234   /**
 235    * new alignment window with hidden columns
 236    *
 237    * @param al
 238    *          AlignmentI
 239    * @param hiddenColumns
 240    *          ColumnSelection or null
 241    * @param width
 242    *          Width of alignment frame
 243    * @param height
 244    *          height of frame.
 245    */
 246   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 247           int width, int height)
 248   {
 249     this(al, hiddenColumns, width, height, null);
 250   }
 251
 252   /**
 253    * Create alignment frame for al with hiddenColumns, a specific width and
 254    * height, and specific sequenceId
 255    *
 256    * @param al
 257    * @param hiddenColumns
 258    * @param width
 259    * @param height
 260    * @param sequenceSetId
 261    *          (may be null)
 262    */
 263   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 264           int width, int height, String sequenceSetId)
 265   {
 266     this(al, hiddenColumns, width, height, sequenceSetId, null);
 267   }
 268
 269   /**
 270    * Create alignment frame for al with hiddenColumns, a specific width and
 271    * height, and specific sequenceId
 272    *
 273    * @param al
 274    * @param hiddenColumns
 275    * @param width
 276    * @param height
 277    * @param sequenceSetId
 278    *          (may be null)
 279    * @param viewId
 280    *          (may be null)
 281    */
 282   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 283           int width, int height, String sequenceSetId, String viewId)
 284   {
 285     setSize(width, height);
 286
 287     if (al.getDataset() == null)
 288     {
 289       al.setDataset(null);
 290     }
 291
 292     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 293
 294     alignPanel = new AlignmentPanel(this, viewport);
 295
 296     addAlignmentPanel(alignPanel, true);
 297     init();
 298   }
 299
 300   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 301           ColumnSelection hiddenColumns, int width, int height)
 302   {
 303     setSize(width, height);
 304
 305     if (al.getDataset() == null)
 306     {
 307       al.setDataset(null);
 308     }
 309
 310     viewport = new AlignViewport(al, hiddenColumns);
 311
 312     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 313     {
 314       viewport.hideSequence(hiddenSeqs);
 315     }
 316     alignPanel = new AlignmentPanel(this, viewport);
 317     addAlignmentPanel(alignPanel, true);
 318     init();
 319   }
 320
 321   /**
 322    * Make a new AlignFrame from existing alignmentPanels
 323    *
 324    * @param ap
 325    *          AlignmentPanel
 326    * @param av
 327    *          AlignViewport
 328    */
 329   public AlignFrame(AlignmentPanel ap)
 330   {
 331     viewport = ap.av;
 332     alignPanel = ap;
 333     addAlignmentPanel(ap, false);
 334     init();
 335   }
 336
 337   /**
 338    * initalise the alignframe from the underlying viewport data and the
 339    * configurations
 340    */
 341   void init()
 342   {
 343     if (!Jalview.isHeadlessMode())
 344     {
 345       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 346     }
 347
 348     avc = new jalview.controller.AlignViewController(this, viewport,
 349             alignPanel);
 350     if (viewport.getAlignmentConservationAnnotation() == null)
 351     {
 352       BLOSUM62Colour.setEnabled(false);
 353       conservationMenuItem.setEnabled(false);
 354       modifyConservation.setEnabled(false);
 355       // PIDColour.setEnabled(false);
 356       // abovePIDThreshold.setEnabled(false);
 357       // modifyPID.setEnabled(false);
 358     }
 359
 360     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 361             "No sort");
 362
 363     if (sortby.equals("Id"))
 364     {
 365       sortIDMenuItem_actionPerformed(null);
 366     }
 367     else if (sortby.equals("Pairwise Identity"))
 368     {
 369       sortPairwiseMenuItem_actionPerformed(null);
 370     }
 371
 372     if (Desktop.desktop != null)
 373     {
 374       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 375       addServiceListeners();
 376       setGUINucleotide(viewport.getAlignment().isNucleotide());
 377     }
 378
 379     this.alignPanel.av
 380             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 381
 382     setMenusFromViewport(viewport);
 383     buildSortByAnnotationScoresMenu();
 384     buildTreeMenu();
 385
 386     if (viewport.getWrapAlignment())
 387     {
 388       wrapMenuItem_actionPerformed(null);
 389     }
 390
 391     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 392     {
 393       this.overviewMenuItem_actionPerformed(null);
 394     }
 395
 396     addKeyListener();
 397
 398     final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
 399     final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
 400     final String menuLabel = MessageManager
 401             .getString("label.copy_format_from");
 402     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 403             new ViewSetProvider()
 404             {
 405
 406               @Override
 407               public AlignmentPanel[] getAllAlignmentPanels()
 408               {
 409                 origview.clear();
 410                 origview.add(alignPanel);
 411                 // make an array of all alignment panels except for this one
 412                 List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
 413                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 414                 aps.remove(AlignFrame.this.alignPanel);
 415                 return aps.toArray(new AlignmentPanel[aps.size()]);
 416               }
 417             }, selviews, new ItemListener()
 418             {
 419
 420               @Override
 421               public void itemStateChanged(ItemEvent e)
 422               {
 423                 if (origview.size() > 0)
 424                 {
 425                   final AlignmentPanel ap = origview.get(0);
 426
 427                   /*
 428                    * Copy the ViewStyle of the selected panel to 'this one'.
 429                    * Don't change value of 'scaleProteinAsCdna' unless copying
 430                    * from a SplitFrame.
 431                    */
 432                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 433                           .getViewStyle();
 434                   boolean fromSplitFrame = selviews.get(0)
 435                           .getAlignViewport().getCodingComplement() != null;
 436                   if (!fromSplitFrame)
 437                   {
 438                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 439                             .getViewStyle().isScaleProteinAsCdna());
 440                   }
 441                   ap.getAlignViewport().setViewStyle(vs);
 442
 443                   /*
 444                    * Also rescale ViewStyle of SplitFrame complement if there is
 445                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 446                    * the whole ViewStyle (allow cDNA protein to have different
 447                    * fonts)
 448                    */
 449                   AlignViewportI complement = ap.getAlignViewport()
 450                           .getCodingComplement();
 451                   if (complement != null && vs.isScaleProteinAsCdna())
 452                   {
 453                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 454                     ((SplitFrame) af.getSplitViewContainer())
 455                             .adjustLayout();
 456                     af.setMenusForViewport();
 457                   }
 458
 459                   ap.updateLayout();
 460                   ap.setSelected(true);
 461                   ap.alignFrame.setMenusForViewport();
 462
 463                 }
 464               }
 465             });
 466     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 467             .indexOf("devel") > -1
 468             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 469                     .indexOf("test") > -1)
 470     {
 471       formatMenu.add(vsel);
 472     }
 473     addFocusListener(new FocusAdapter()
 474     {
 475       @Override
 476       public void focusGained(FocusEvent e)
 477       {
 478         Jalview.setCurrentAlignFrame(AlignFrame.this);
 479       }
 480     });
 481
 482   }
 483
 484   /**
 485    * Change the filename and format for the alignment, and enable the 'reload'
 486    * button functionality.
 487    *
 488    * @param file
 489    *          valid filename
 490    * @param format
 491    *          format of file
 492    */
 493   public void setFileName(String file, FileFormatI format)
 494   {
 495     fileName = file;
 496     setFileFormat(format);
 497     reload.setEnabled(true);
 498   }
 499
 500   /**
 501    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 502    * events
 503    */
 504   void addKeyListener()
 505   {
 506     addKeyListener(new KeyAdapter()
 507     {
 508       @Override
 509       public void keyPressed(KeyEvent evt)
 510       {
 511         if (viewport.cursorMode
 512                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 513                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 514                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 515                 && Character.isDigit(evt.getKeyChar()))
 516         {
 517           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 518         }
 519
 520         switch (evt.getKeyCode())
 521         {
 522
 523         case 27: // escape key
 524           deselectAllSequenceMenuItem_actionPerformed(null);
 525
 526           break;
 527
 528         case KeyEvent.VK_DOWN:
 529           if (evt.isAltDown() || !viewport.cursorMode)
 530           {
 531             moveSelectedSequences(false);
 532           }
 533           if (viewport.cursorMode)
 534           {
 535             alignPanel.getSeqPanel().moveCursor(0, 1);
 536           }
 537           break;
 538
 539         case KeyEvent.VK_UP:
 540           if (evt.isAltDown() || !viewport.cursorMode)
 541           {
 542             moveSelectedSequences(true);
 543           }
 544           if (viewport.cursorMode)
 545           {
 546             alignPanel.getSeqPanel().moveCursor(0, -1);
 547           }
 548
 549           break;
 550
 551         case KeyEvent.VK_LEFT:
 552           if (evt.isAltDown() || !viewport.cursorMode)
 553           {
 554             slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
 555           }
 556           else
 557           {
 558             alignPanel.getSeqPanel().moveCursor(-1, 0);
 559           }
 560
 561           break;
 562
 563         case KeyEvent.VK_RIGHT:
 564           if (evt.isAltDown() || !viewport.cursorMode)
 565           {
 566             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 567           }
 568           else
 569           {
 570             alignPanel.getSeqPanel().moveCursor(1, 0);
 571           }
 572           break;
 573
 574         case KeyEvent.VK_SPACE:
 575           if (viewport.cursorMode)
 576           {
 577             alignPanel.getSeqPanel().insertGapAtCursor(
 578                     evt.isControlDown() || evt.isShiftDown()
 579                             || evt.isAltDown());
 580           }
 581           break;
 582
 583         // case KeyEvent.VK_A:
 584         // if (viewport.cursorMode)
 585         // {
 586         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 587         // //System.out.println("A");
 588         // }
 589         // break;
 590         /*
 591          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 592          * System.out.println("closing bracket"); } break;
 593          */
 594         case KeyEvent.VK_DELETE:
 595         case KeyEvent.VK_BACK_SPACE:
 596           if (!viewport.cursorMode)
 597           {
 598             cut_actionPerformed(null);
 599           }
 600           else
 601           {
 602             alignPanel.getSeqPanel().deleteGapAtCursor(
 603                     evt.isControlDown() || evt.isShiftDown()
 604                             || evt.isAltDown());
 605           }
 606
 607           break;
 608
 609         case KeyEvent.VK_S:
 610           if (viewport.cursorMode)
 611           {
 612             alignPanel.getSeqPanel().setCursorRow();
 613           }
 614           break;
 615         case KeyEvent.VK_C:
 616           if (viewport.cursorMode && !evt.isControlDown())
 617           {
 618             alignPanel.getSeqPanel().setCursorColumn();
 619           }
 620           break;
 621         case KeyEvent.VK_P:
 622           if (viewport.cursorMode)
 623           {
 624             alignPanel.getSeqPanel().setCursorPosition();
 625           }
 626           break;
 627
 628         case KeyEvent.VK_ENTER:
 629         case KeyEvent.VK_COMMA:
 630           if (viewport.cursorMode)
 631           {
 632             alignPanel.getSeqPanel().setCursorRowAndColumn();
 633           }
 634           break;
 635
 636         case KeyEvent.VK_Q:
 637           if (viewport.cursorMode)
 638           {
 639             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 640           }
 641           break;
 642         case KeyEvent.VK_M:
 643           if (viewport.cursorMode)
 644           {
 645             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 646           }
 647           break;
 648
 649         case KeyEvent.VK_F2:
 650           viewport.cursorMode = !viewport.cursorMode;
 651           statusBar.setText(MessageManager.formatMessage(
 652                   "label.keyboard_editing_mode",
 653                   new String[] { (viewport.cursorMode ? "on" : "off") }));
 654           if (viewport.cursorMode)
 655           {
 656             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
 657             alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
 658           }
 659           alignPanel.getSeqPanel().seqCanvas.repaint();
 660           break;
 661
 662         case KeyEvent.VK_F1:
 663           try
 664           {
 665             Help.showHelpWindow();
 666           } catch (Exception ex)
 667           {
 668             ex.printStackTrace();
 669           }
 670           break;
 671         case KeyEvent.VK_H:
 672         {
 673           boolean toggleSeqs = !evt.isControlDown();
 674           boolean toggleCols = !evt.isShiftDown();
 675           toggleHiddenRegions(toggleSeqs, toggleCols);
 676           break;
 677         }
 678         case KeyEvent.VK_B:
 679         {
 680           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 681           boolean modifyExisting = true; // always modify, don't clear
 682                                          // evt.isShiftDown();
 683           boolean invertHighlighted = evt.isAltDown();
 684           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 685                   toggleSel);
 686           break;
 687         }
 688         case KeyEvent.VK_PAGE_UP:
 689           if (viewport.getWrapAlignment())
 690           {
 691             alignPanel.scrollUp(true);
 692           }
 693           else
 694           {
 695             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 696                     - viewport.endSeq + viewport.startSeq);
 697           }
 698           break;
 699         case KeyEvent.VK_PAGE_DOWN:
 700           if (viewport.getWrapAlignment())
 701           {
 702             alignPanel.scrollUp(false);
 703           }
 704           else
 705           {
 706             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 707                     + viewport.endSeq - viewport.startSeq);
 708           }
 709           break;
 710         }
 711       }
 712
 713       @Override
 714       public void keyReleased(KeyEvent evt)
 715       {
 716         switch (evt.getKeyCode())
 717         {
 718         case KeyEvent.VK_LEFT:
 719           if (evt.isAltDown() || !viewport.cursorMode)
 720           {
 721             viewport.firePropertyChange("alignment", null, viewport
 722                     .getAlignment().getSequences());
 723           }
 724           break;
 725
 726         case KeyEvent.VK_RIGHT:
 727           if (evt.isAltDown() || !viewport.cursorMode)
 728           {
 729             viewport.firePropertyChange("alignment", null, viewport
 730                     .getAlignment().getSequences());
 731           }
 732           break;
 733         }
 734       }
 735     });
 736   }
 737
 738   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 739   {
 740     ap.alignFrame = this;
 741     avc = new jalview.controller.AlignViewController(this, viewport,
 742             alignPanel);
 743
 744     alignPanels.add(ap);
 745
 746     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 747
 748     int aSize = alignPanels.size();
 749
 750     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 751
 752     if (aSize == 1 && ap.av.viewName == null)
 753     {
 754       this.getContentPane().add(ap, BorderLayout.CENTER);
 755     }
 756     else
 757     {
 758       if (aSize == 2)
 759       {
 760         setInitialTabVisible();
 761       }
 762
 763       expandViews.setEnabled(true);
 764       gatherViews.setEnabled(true);
 765       tabbedPane.addTab(ap.av.viewName, ap);
 766
 767       ap.setVisible(false);
 768     }
 769
 770     if (newPanel)
 771     {
 772       if (ap.av.isPadGaps())
 773       {
 774         ap.av.getAlignment().padGaps();
 775       }
 776       ap.av.updateConservation(ap);
 777       ap.av.updateConsensus(ap);
 778       ap.av.updateStrucConsensus(ap);
 779     }
 780   }
 781
 782   public void setInitialTabVisible()
 783   {
 784     expandViews.setEnabled(true);
 785     gatherViews.setEnabled(true);
 786     tabbedPane.setVisible(true);
 787     AlignmentPanel first = alignPanels.get(0);
 788     tabbedPane.addTab(first.av.viewName, first);
 789     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 790   }
 791
 792   public AlignViewport getViewport()
 793   {
 794     return viewport;
 795   }
 796
 797   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 798   private void addServiceListeners()
 799   {
 800     final java.beans.PropertyChangeListener thisListener;
 801     Desktop.instance.addJalviewPropertyChangeListener("services",
 802             thisListener = new java.beans.PropertyChangeListener()
 803             {
 804               @Override
 805               public void propertyChange(PropertyChangeEvent evt)
 806               {
 807                 // // System.out.println("Discoverer property change.");
 808                 // if (evt.getPropertyName().equals("services"))
 809                 {
 810                   SwingUtilities.invokeLater(new Runnable()
 811                   {
 812
 813                     @Override
 814                     public void run()
 815                     {
 816                       System.err
 817                               .println("Rebuild WS Menu for service change");
 818                       BuildWebServiceMenu();
 819                     }
 820
 821                   });
 822                 }
 823               }
 824             });
 825     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 826     {
 827       @Override
 828       public void internalFrameClosed(
 829               javax.swing.event.InternalFrameEvent evt)
 830       {
 831         // System.out.println("deregistering discoverer listener");
 832         Desktop.instance.removeJalviewPropertyChangeListener("services",
 833                 thisListener);
 834         closeMenuItem_actionPerformed(true);
 835       };
 836     });
 837     // Finally, build the menu once to get current service state
 838     new Thread(new Runnable()
 839     {
 840       @Override
 841       public void run()
 842       {
 843         BuildWebServiceMenu();
 844       }
 845     }).start();
 846   }
 847
 848   /**
 849    * Configure menu items that vary according to whether the alignment is
 850    * nucleotide or protein
 851    *
 852    * @param nucleotide
 853    */
 854   public void setGUINucleotide(boolean nucleotide)
 855   {
 856     showTranslation.setVisible(nucleotide);
 857     showReverse.setVisible(nucleotide);
 858     showReverseComplement.setVisible(nucleotide);
 859     conservationMenuItem.setEnabled(!nucleotide);
 860     modifyConservation.setEnabled(!nucleotide);
 861     showGroupConservation.setEnabled(!nucleotide);
 862     rnahelicesColour.setEnabled(nucleotide);
 863     nucleotideColour.setEnabled(nucleotide);
 864     purinePyrimidineColour.setEnabled(nucleotide);
 865     RNAInteractionColour.setEnabled(nucleotide);
 866     showComplementMenuItem.setText(nucleotide ? MessageManager
 867             .getString("label.protein") : MessageManager
 868             .getString("label.nucleotide"));
 869     setColourSelected(jalview.bin.Cache.getDefault(
 870             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
 871                     : Preferences.DEFAULT_COLOUR_PROT, "None"));
 872   }
 873
 874   /**
 875    * set up menus for the current viewport. This may be called after any
 876    * operation that affects the data in the current view (selection changed,
 877    * etc) to update the menus to reflect the new state.
 878    */
 879   @Override
 880   public void setMenusForViewport()
 881   {
 882     setMenusFromViewport(viewport);
 883   }
 884
 885   /**
 886    * Need to call this method when tabs are selected for multiple views, or when
 887    * loading from Jalview2XML.java
 888    *
 889    * @param av
 890    *          AlignViewport
 891    */
 892   void setMenusFromViewport(AlignViewport av)
 893   {
 894     padGapsMenuitem.setSelected(av.isPadGaps());
 895     colourTextMenuItem.setSelected(av.isShowColourText());
 896     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 897     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 898     conservationMenuItem.setSelected(av.getConservationSelected());
 899     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 900     seqLimits.setSelected(av.getShowJVSuffix());
 901     idRightAlign.setSelected(av.isRightAlignIds());
 902     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 903     renderGapsMenuItem.setSelected(av.isRenderGaps());
 904     wrapMenuItem.setSelected(av.getWrapAlignment());
 905     scaleAbove.setVisible(av.getWrapAlignment());
 906     scaleLeft.setVisible(av.getWrapAlignment());
 907     scaleRight.setVisible(av.getWrapAlignment());
 908     annotationPanelMenuItem.setState(av.isShowAnnotation());
 909     /*
 910      * Show/hide annotations only enabled if annotation panel is shown
 911      */
 912     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 913     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 914     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 915     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 916     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 917     viewTextMenuItem.setSelected(av.getShowText());
 918     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 919     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 920     showGroupConservation.setSelected(av.isShowGroupConservation());
 921     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 922     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 923     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 924
 925     setColourSelected(ColourSchemeProperty.getColourName(av
 926             .getGlobalColourScheme()));
 927
 928     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 929     hiddenMarkers.setState(av.getShowHiddenMarkers());
 930     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 931     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 932     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 933     autoCalculate.setSelected(av.autoCalculateConsensus);
 934     sortByTree.setSelected(av.sortByTree);
 935     listenToViewSelections.setSelected(av.followSelection);
 936     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 937     rnahelicesColour
 938             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 939
 940     showProducts.setEnabled(canShowProducts());
 941     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 942
 943     updateEditMenuBar();
 944   }
 945
 946   /**
 947    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 948    *
 949    * @param b
 950    */
 951   public void setGroovyEnabled(boolean b)
 952   {
 953     runGroovy.setEnabled(b);
 954   }
 955
 956   private IProgressIndicator progressBar;
 957
 958   /*
 959    * (non-Javadoc)
 960    *
 961    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 962    */
 963   @Override
 964   public void setProgressBar(String message, long id)
 965   {
 966     progressBar.setProgressBar(message, id);
 967   }
 968
 969   @Override
 970   public void registerHandler(final long id,
 971           final IProgressIndicatorHandler handler)
 972   {
 973     progressBar.registerHandler(id, handler);
 974   }
 975
 976   /**
 977    *
 978    * @return true if any progress bars are still active
 979    */
 980   @Override
 981   public boolean operationInProgress()
 982   {
 983     return progressBar.operationInProgress();
 984   }
 985
 986   @Override
 987   public void setStatus(String text)
 988   {
 989     statusBar.setText(text);
 990   }
 991
 992   /*
 993    * Added so Castor Mapping file can obtain Jalview Version
 994    */
 995   public String getVersion()
 996   {
 997     return jalview.bin.Cache.getProperty("VERSION");
 998   }
 999
1000   public FeatureRenderer getFeatureRenderer()
1001   {
1002     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1003   }
1004
1005   @Override
1006   public void fetchSequence_actionPerformed(ActionEvent e)
1007   {
1008     new jalview.gui.SequenceFetcher(this);
1009   }
1010
1011   @Override
1012   public void addFromFile_actionPerformed(ActionEvent e)
1013   {
1014     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1015   }
1016
1017   @Override
1018   public void reload_actionPerformed(ActionEvent e)
1019   {
1020     if (fileName != null)
1021     {
1022       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1023       // originating file's format
1024       // TODO: work out how to recover feature settings for correct view(s) when
1025       // file is reloaded.
1026       if (FileFormat.Jalview.equals(currentFileFormat))
1027       {
1028         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1029         for (int i = 0; i < frames.length; i++)
1030         {
1031           if (frames[i] instanceof AlignFrame && frames[i] != this
1032                   && ((AlignFrame) frames[i]).fileName != null
1033                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1034           {
1035             try
1036             {
1037               frames[i].setSelected(true);
1038               Desktop.instance.closeAssociatedWindows();
1039             } catch (java.beans.PropertyVetoException ex)
1040             {
1041             }
1042           }
1043
1044         }
1045         Desktop.instance.closeAssociatedWindows();
1046
1047         FileLoader loader = new FileLoader();
1048         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1049                 : DataSourceType.FILE;
1050         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1051       }
1052       else
1053       {
1054         Rectangle bounds = this.getBounds();
1055
1056         FileLoader loader = new FileLoader();
1057         DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
1058                 : DataSourceType.FILE;
1059         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1060                 protocol, currentFileFormat);
1061
1062         newframe.setBounds(bounds);
1063         if (featureSettings != null && featureSettings.isShowing())
1064         {
1065           final Rectangle fspos = featureSettings.frame.getBounds();
1066           // TODO: need a 'show feature settings' function that takes bounds -
1067           // need to refactor Desktop.addFrame
1068           newframe.featureSettings_actionPerformed(null);
1069           final FeatureSettings nfs = newframe.featureSettings;
1070           SwingUtilities.invokeLater(new Runnable()
1071           {
1072             @Override
1073             public void run()
1074             {
1075               nfs.frame.setBounds(fspos);
1076             }
1077           });
1078           this.featureSettings.close();
1079           this.featureSettings = null;
1080         }
1081         this.closeMenuItem_actionPerformed(true);
1082       }
1083     }
1084   }
1085
1086   @Override
1087   public void addFromText_actionPerformed(ActionEvent e)
1088   {
1089     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
1090             .getAlignPanel());
1091   }
1092
1093   @Override
1094   public void addFromURL_actionPerformed(ActionEvent e)
1095   {
1096     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1097   }
1098
1099   @Override
1100   public void save_actionPerformed(ActionEvent e)
1101   {
1102     if (fileName == null || (currentFileFormat == null)
1103             || fileName.startsWith("http"))
1104     {
1105       saveAs_actionPerformed(null);
1106     }
1107     else
1108     {
1109       saveAlignment(fileName, currentFileFormat);
1110     }
1111   }
1112
1113   /**
1114    * DOCUMENT ME!
1115    *
1116    * @param e
1117    *          DOCUMENT ME!
1118    */
1119   @Override
1120   public void saveAs_actionPerformed(ActionEvent e)
1121   {
1122     String format = currentFileFormat == null ? null : currentFileFormat
1123             .getName();
1124     JalviewFileChooser chooser = JalviewFileChooser.forWrite(
1125             Cache.getProperty("LAST_DIRECTORY"), format);
1126
1127     chooser.setFileView(new JalviewFileView());
1128     chooser.setDialogTitle(MessageManager
1129             .getString("label.save_alignment_to_file"));
1130     chooser.setToolTipText(MessageManager.getString("action.save"));
1131
1132     int value = chooser.showSaveDialog(this);
1133
1134     if (value == JalviewFileChooser.APPROVE_OPTION)
1135     {
1136       currentFileFormat = chooser.getSelectedFormat();
1137       while (currentFileFormat == null)
1138       {
1139         JvOptionPane
1140                 .showInternalMessageDialog(
1141                         Desktop.desktop,
1142                         MessageManager
1143                                 .getString("label.select_file_format_before_saving"),
1144                         MessageManager
1145                                 .getString("label.file_format_not_specified"),
1146                         JvOptionPane.WARNING_MESSAGE);
1147         currentFileFormat = chooser.getSelectedFormat();
1148         value = chooser.showSaveDialog(this);
1149         if (value != JalviewFileChooser.APPROVE_OPTION)
1150         {
1151           return;
1152         }
1153       }
1154
1155       fileName = chooser.getSelectedFile().getPath();
1156
1157       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1158
1159       Cache.setProperty("LAST_DIRECTORY", fileName);
1160       saveAlignment(fileName, currentFileFormat);
1161     }
1162   }
1163
1164   public boolean saveAlignment(String file, FileFormatI format)
1165   {
1166     boolean success = true;
1167
1168     if (FileFormat.Jalview.equals(format))
1169     {
1170       String shortName = title;
1171
1172       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1173       {
1174         shortName = shortName.substring(shortName
1175                 .lastIndexOf(java.io.File.separatorChar) + 1);
1176       }
1177
1178       success = new Jalview2XML().saveAlignment(this, file, shortName);
1179
1180       statusBar.setText(MessageManager.formatMessage(
1181               "label.successfully_saved_to_file_in_format", new Object[] {
1182                   fileName, format }));
1183
1184     }
1185     else
1186     {
1187       AlignmentExportData exportData = getAlignmentForExport(format,
1188               viewport, null);
1189       if (exportData.getSettings().isCancelled())
1190       {
1191         return false;
1192       }
1193       FormatAdapter f = new FormatAdapter(alignPanel,
1194               exportData.getSettings());
1195       String output = f.formatSequences(
1196               format,
1197               exportData.getAlignment(), // class cast exceptions will
1198               // occur in the distant future
1199               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1200               f.getCacheSuffixDefault(format),
1201               viewport.getColumnSelection());
1202
1203       if (output == null)
1204       {
1205         success = false;
1206       }
1207       else
1208       {
1209         try
1210         {
1211           PrintWriter out = new PrintWriter(new FileWriter(file));
1212
1213           out.print(output);
1214           out.close();
1215           this.setTitle(file);
1216           statusBar.setText(MessageManager.formatMessage(
1217                   "label.successfully_saved_to_file_in_format",
1218                   new Object[] { fileName, format.getName() }));
1219         } catch (Exception ex)
1220         {
1221           success = false;
1222           ex.printStackTrace();
1223         }
1224       }
1225     }
1226
1227     if (!success)
1228     {
1229       JvOptionPane.showInternalMessageDialog(this, MessageManager
1230               .formatMessage("label.couldnt_save_file",
1231                       new Object[] { fileName }), MessageManager
1232               .getString("label.error_saving_file"),
1233               JvOptionPane.WARNING_MESSAGE);
1234     }
1235
1236     return success;
1237   }
1238
1239   private void warningMessage(String warning, String title)
1240   {
1241     if (new jalview.util.Platform().isHeadless())
1242     {
1243       System.err.println("Warning: " + title + "\nWarning: " + warning);
1244
1245     }
1246     else
1247     {
1248       JvOptionPane.showInternalMessageDialog(this, warning, title,
1249               JvOptionPane.WARNING_MESSAGE);
1250     }
1251     return;
1252   }
1253
1254   /**
1255    * DOCUMENT ME!
1256    *
1257    * @param e
1258    *          DOCUMENT ME!
1259    */
1260   @Override
1261   protected void outputText_actionPerformed(ActionEvent e)
1262   {
1263     FileFormatI fileFormat = FileFormats.getInstance().forName(
1264             e.getActionCommand());
1265     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1266             viewport, null);
1267     if (exportData.getSettings().isCancelled())
1268     {
1269       return;
1270     }
1271     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1272     cap.setForInput(null);
1273     try
1274     {
1275       FileFormatI format = fileFormat;
1276       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1277               .formatSequences(format,
1278                       exportData.getAlignment(),
1279                       exportData.getOmitHidden(),
1280                       exportData.getStartEndPostions(),
1281                       viewport.getColumnSelection()));
1282       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1283               "label.alignment_output_command",
1284               new Object[] { e.getActionCommand() }), 600, 500);
1285     } catch (OutOfMemoryError oom)
1286     {
1287       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1288       cap.dispose();
1289     }
1290
1291   }
1292
1293   public static AlignmentExportData getAlignmentForExport(
1294           FileFormatI format, AlignViewportI viewport,
1295           AlignExportSettingI exportSettings)
1296   {
1297     AlignmentI alignmentToExport = null;
1298     AlignExportSettingI settings = exportSettings;
1299     String[] omitHidden = null;
1300
1301     HiddenSequences hiddenSeqs = viewport.getAlignment()
1302             .getHiddenSequences();
1303
1304     alignmentToExport = viewport.getAlignment();
1305
1306     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1307     if (settings == null)
1308     {
1309       settings = new AlignExportSettings(hasHiddenSeqs,
1310               viewport.hasHiddenColumns(), format);
1311     }
1312     // settings.isExportAnnotations();
1313
1314     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1315     {
1316       omitHidden = viewport.getViewAsString(false,
1317               settings.isExportHiddenSequences());
1318     }
1319
1320     int[] alignmentStartEnd = new int[2];
1321     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1322     {
1323       alignmentToExport = hiddenSeqs.getFullAlignment();
1324     }
1325     else
1326     {
1327       alignmentToExport = viewport.getAlignment();
1328     }
1329     alignmentStartEnd = alignmentToExport
1330             .getVisibleStartAndEndIndex(viewport.getColumnSelection()
1331                     .getHiddenColumns());
1332     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1333             omitHidden, alignmentStartEnd, settings);
1334     return ed;
1335   }
1336
1337   /**
1338    * DOCUMENT ME!
1339    *
1340    * @param e
1341    *          DOCUMENT ME!
1342    */
1343   @Override
1344   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1345   {
1346     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1347     htmlSVG.exportHTML(null);
1348   }
1349
1350   @Override
1351   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1352   {
1353     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1354     bjs.exportHTML(null);
1355   }
1356
1357   public void createImageMap(File file, String image)
1358   {
1359     alignPanel.makePNGImageMap(file, image);
1360   }
1361
1362   /**
1363    * DOCUMENT ME!
1364    *
1365    * @param e
1366    *          DOCUMENT ME!
1367    */
1368   @Override
1369   public void createPNG(File f)
1370   {
1371     alignPanel.makePNG(f);
1372   }
1373
1374   /**
1375    * DOCUMENT ME!
1376    *
1377    * @param e
1378    *          DOCUMENT ME!
1379    */
1380   @Override
1381   public void createEPS(File f)
1382   {
1383     alignPanel.makeEPS(f);
1384   }
1385
1386   @Override
1387   public void createSVG(File f)
1388   {
1389     alignPanel.makeSVG(f);
1390   }
1391
1392   @Override
1393   public void pageSetup_actionPerformed(ActionEvent e)
1394   {
1395     PrinterJob printJob = PrinterJob.getPrinterJob();
1396     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1397   }
1398
1399   /**
1400    * DOCUMENT ME!
1401    *
1402    * @param e
1403    *          DOCUMENT ME!
1404    */
1405   @Override
1406   public void printMenuItem_actionPerformed(ActionEvent e)
1407   {
1408     // Putting in a thread avoids Swing painting problems
1409     PrintThread thread = new PrintThread(alignPanel);
1410     thread.start();
1411   }
1412
1413   @Override
1414   public void exportFeatures_actionPerformed(ActionEvent e)
1415   {
1416     new AnnotationExporter().exportFeatures(alignPanel);
1417   }
1418
1419   @Override
1420   public void exportAnnotations_actionPerformed(ActionEvent e)
1421   {
1422     new AnnotationExporter().exportAnnotations(alignPanel);
1423   }
1424
1425   @Override
1426   public void associatedData_actionPerformed(ActionEvent e)
1427   {
1428     // Pick the tree file
1429     JalviewFileChooser chooser = new JalviewFileChooser(
1430             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1431     chooser.setFileView(new JalviewFileView());
1432     chooser.setDialogTitle(MessageManager
1433             .getString("label.load_jalview_annotations"));
1434     chooser.setToolTipText(MessageManager
1435             .getString("label.load_jalview_annotations"));
1436
1437     int value = chooser.showOpenDialog(null);
1438
1439     if (value == JalviewFileChooser.APPROVE_OPTION)
1440     {
1441       String choice = chooser.getSelectedFile().getPath();
1442       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1443       loadJalviewDataFile(choice, null, null, null);
1444     }
1445
1446   }
1447
1448   /**
1449    * Close the current view or all views in the alignment frame. If the frame
1450    * only contains one view then the alignment will be removed from memory.
1451    *
1452    * @param closeAllTabs
1453    */
1454   @Override
1455   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1456   {
1457     if (alignPanels != null && alignPanels.size() < 2)
1458     {
1459       closeAllTabs = true;
1460     }
1461
1462     try
1463     {
1464       if (alignPanels != null)
1465       {
1466         if (closeAllTabs)
1467         {
1468           if (this.isClosed())
1469           {
1470             // really close all the windows - otherwise wait till
1471             // setClosed(true) is called
1472             for (int i = 0; i < alignPanels.size(); i++)
1473             {
1474               AlignmentPanel ap = alignPanels.get(i);
1475               ap.closePanel();
1476             }
1477           }
1478         }
1479         else
1480         {
1481           closeView(alignPanel);
1482         }
1483       }
1484
1485       if (closeAllTabs)
1486       {
1487         /*
1488          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1489          * be called recursively, with the frame now in 'closed' state
1490          */
1491         this.setClosed(true);
1492       }
1493     } catch (Exception ex)
1494     {
1495       ex.printStackTrace();
1496     }
1497   }
1498
1499   /**
1500    * Close the specified panel and close up tabs appropriately.
1501    *
1502    * @param panelToClose
1503    */
1504   public void closeView(AlignmentPanel panelToClose)
1505   {
1506     int index = tabbedPane.getSelectedIndex();
1507     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1508     alignPanels.remove(panelToClose);
1509     panelToClose.closePanel();
1510     panelToClose = null;
1511
1512     tabbedPane.removeTabAt(closedindex);
1513     tabbedPane.validate();
1514
1515     if (index > closedindex || index == tabbedPane.getTabCount())
1516     {
1517       // modify currently selected tab index if necessary.
1518       index--;
1519     }
1520
1521     this.tabSelectionChanged(index);
1522   }
1523
1524   /**
1525    * DOCUMENT ME!
1526    */
1527   void updateEditMenuBar()
1528   {
1529
1530     if (viewport.getHistoryList().size() > 0)
1531     {
1532       undoMenuItem.setEnabled(true);
1533       CommandI command = viewport.getHistoryList().peek();
1534       undoMenuItem.setText(MessageManager.formatMessage(
1535               "label.undo_command",
1536               new Object[] { command.getDescription() }));
1537     }
1538     else
1539     {
1540       undoMenuItem.setEnabled(false);
1541       undoMenuItem.setText(MessageManager.getString("action.undo"));
1542     }
1543
1544     if (viewport.getRedoList().size() > 0)
1545     {
1546       redoMenuItem.setEnabled(true);
1547
1548       CommandI command = viewport.getRedoList().peek();
1549       redoMenuItem.setText(MessageManager.formatMessage(
1550               "label.redo_command",
1551               new Object[] { command.getDescription() }));
1552     }
1553     else
1554     {
1555       redoMenuItem.setEnabled(false);
1556       redoMenuItem.setText(MessageManager.getString("action.redo"));
1557     }
1558   }
1559
1560   @Override
1561   public void addHistoryItem(CommandI command)
1562   {
1563     if (command.getSize() > 0)
1564     {
1565       viewport.addToHistoryList(command);
1566       viewport.clearRedoList();
1567       updateEditMenuBar();
1568       viewport.updateHiddenColumns();
1569       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1570       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1571       // viewport.getColumnSelection()
1572       // .getHiddenColumns().size() > 0);
1573     }
1574   }
1575
1576   /**
1577    *
1578    * @return alignment objects for all views
1579    */
1580   AlignmentI[] getViewAlignments()
1581   {
1582     if (alignPanels != null)
1583     {
1584       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1585       int i = 0;
1586       for (AlignmentPanel ap : alignPanels)
1587       {
1588         als[i++] = ap.av.getAlignment();
1589       }
1590       return als;
1591     }
1592     if (viewport != null)
1593     {
1594       return new AlignmentI[] { viewport.getAlignment() };
1595     }
1596     return null;
1597   }
1598
1599   /**
1600    * DOCUMENT ME!
1601    *
1602    * @param e
1603    *          DOCUMENT ME!
1604    */
1605   @Override
1606   protected void undoMenuItem_actionPerformed(ActionEvent e)
1607   {
1608     if (viewport.getHistoryList().isEmpty())
1609     {
1610       return;
1611     }
1612     CommandI command = viewport.getHistoryList().pop();
1613     viewport.addToRedoList(command);
1614     command.undoCommand(getViewAlignments());
1615
1616     AlignmentViewport originalSource = getOriginatingSource(command);
1617     updateEditMenuBar();
1618
1619     if (originalSource != null)
1620     {
1621       if (originalSource != viewport)
1622       {
1623         Cache.log
1624                 .warn("Implementation worry: mismatch of viewport origin for undo");
1625       }
1626       originalSource.updateHiddenColumns();
1627       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1628       // null
1629       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1630       // viewport.getColumnSelection()
1631       // .getHiddenColumns().size() > 0);
1632       originalSource.firePropertyChange("alignment", null, originalSource
1633               .getAlignment().getSequences());
1634     }
1635   }
1636
1637   /**
1638    * DOCUMENT ME!
1639    *
1640    * @param e
1641    *          DOCUMENT ME!
1642    */
1643   @Override
1644   protected void redoMenuItem_actionPerformed(ActionEvent e)
1645   {
1646     if (viewport.getRedoList().size() < 1)
1647     {
1648       return;
1649     }
1650
1651     CommandI command = viewport.getRedoList().pop();
1652     viewport.addToHistoryList(command);
1653     command.doCommand(getViewAlignments());
1654
1655     AlignmentViewport originalSource = getOriginatingSource(command);
1656     updateEditMenuBar();
1657
1658     if (originalSource != null)
1659     {
1660
1661       if (originalSource != viewport)
1662       {
1663         Cache.log
1664                 .warn("Implementation worry: mismatch of viewport origin for redo");
1665       }
1666       originalSource.updateHiddenColumns();
1667       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1668       // null
1669       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1670       // viewport.getColumnSelection()
1671       // .getHiddenColumns().size() > 0);
1672       originalSource.firePropertyChange("alignment", null, originalSource
1673               .getAlignment().getSequences());
1674     }
1675   }
1676
1677   AlignmentViewport getOriginatingSource(CommandI command)
1678   {
1679     AlignmentViewport originalSource = null;
1680     // For sequence removal and addition, we need to fire
1681     // the property change event FROM the viewport where the
1682     // original alignment was altered
1683     AlignmentI al = null;
1684     if (command instanceof EditCommand)
1685     {
1686       EditCommand editCommand = (EditCommand) command;
1687       al = editCommand.getAlignment();
1688       List<Component> comps = PaintRefresher.components.get(viewport
1689               .getSequenceSetId());
1690
1691       for (Component comp : comps)
1692       {
1693         if (comp instanceof AlignmentPanel)
1694         {
1695           if (al == ((AlignmentPanel) comp).av.getAlignment())
1696           {
1697             originalSource = ((AlignmentPanel) comp).av;
1698             break;
1699           }
1700         }
1701       }
1702     }
1703
1704     if (originalSource == null)
1705     {
1706       // The original view is closed, we must validate
1707       // the current view against the closed view first
1708       if (al != null)
1709       {
1710         PaintRefresher.validateSequences(al, viewport.getAlignment());
1711       }
1712
1713       originalSource = viewport;
1714     }
1715
1716     return originalSource;
1717   }
1718
1719   /**
1720    * DOCUMENT ME!
1721    *
1722    * @param up
1723    *          DOCUMENT ME!
1724    */
1725   public void moveSelectedSequences(boolean up)
1726   {
1727     SequenceGroup sg = viewport.getSelectionGroup();
1728
1729     if (sg == null)
1730     {
1731       return;
1732     }
1733     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1734             viewport.getHiddenRepSequences(), up);
1735     alignPanel.paintAlignment(true);
1736   }
1737
1738   synchronized void slideSequences(boolean right, int size)
1739   {
1740     List<SequenceI> sg = new ArrayList<SequenceI>();
1741     if (viewport.cursorMode)
1742     {
1743       sg.add(viewport.getAlignment().getSequenceAt(
1744               alignPanel.getSeqPanel().seqCanvas.cursorY));
1745     }
1746     else if (viewport.getSelectionGroup() != null
1747             && viewport.getSelectionGroup().getSize() != viewport
1748                     .getAlignment().getHeight())
1749     {
1750       sg = viewport.getSelectionGroup().getSequences(
1751               viewport.getHiddenRepSequences());
1752     }
1753
1754     if (sg.size() < 1)
1755     {
1756       return;
1757     }
1758
1759     List<SequenceI> invertGroup = new ArrayList<SequenceI>();
1760
1761     for (SequenceI seq : viewport.getAlignment().getSequences())
1762     {
1763       if (!sg.contains(seq))
1764       {
1765         invertGroup.add(seq);
1766       }
1767     }
1768
1769     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1770
1771     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1772     for (int i = 0; i < invertGroup.size(); i++)
1773     {
1774       seqs2[i] = invertGroup.get(i);
1775     }
1776
1777     SlideSequencesCommand ssc;
1778     if (right)
1779     {
1780       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1781               size, viewport.getGapCharacter());
1782     }
1783     else
1784     {
1785       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1786               size, viewport.getGapCharacter());
1787     }
1788
1789     int groupAdjustment = 0;
1790     if (ssc.getGapsInsertedBegin() && right)
1791     {
1792       if (viewport.cursorMode)
1793       {
1794         alignPanel.getSeqPanel().moveCursor(size, 0);
1795       }
1796       else
1797       {
1798         groupAdjustment = size;
1799       }
1800     }
1801     else if (!ssc.getGapsInsertedBegin() && !right)
1802     {
1803       if (viewport.cursorMode)
1804       {
1805         alignPanel.getSeqPanel().moveCursor(-size, 0);
1806       }
1807       else
1808       {
1809         groupAdjustment = -size;
1810       }
1811     }
1812
1813     if (groupAdjustment != 0)
1814     {
1815       viewport.getSelectionGroup().setStartRes(
1816               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1817       viewport.getSelectionGroup().setEndRes(
1818               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1819     }
1820
1821     /*
1822      * just extend the last slide command if compatible; but not if in
1823      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1824      */
1825     boolean appendHistoryItem = false;
1826     Deque<CommandI> historyList = viewport.getHistoryList();
1827     boolean inSplitFrame = getSplitViewContainer() != null;
1828     if (!inSplitFrame && historyList != null && historyList.size() > 0
1829             && historyList.peek() instanceof SlideSequencesCommand)
1830     {
1831       appendHistoryItem = ssc
1832               .appendSlideCommand((SlideSequencesCommand) historyList
1833                       .peek());
1834     }
1835
1836     if (!appendHistoryItem)
1837     {
1838       addHistoryItem(ssc);
1839     }
1840
1841     repaint();
1842   }
1843
1844   /**
1845    * DOCUMENT ME!
1846    *
1847    * @param e
1848    *          DOCUMENT ME!
1849    */
1850   @Override
1851   protected void copy_actionPerformed(ActionEvent e)
1852   {
1853     System.gc();
1854     if (viewport.getSelectionGroup() == null)
1855     {
1856       return;
1857     }
1858     // TODO: preserve the ordering of displayed alignment annotation in any
1859     // internal paste (particularly sequence associated annotation)
1860     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1861     String[] omitHidden = null;
1862
1863     if (viewport.hasHiddenColumns())
1864     {
1865       omitHidden = viewport.getViewAsString(true);
1866     }
1867
1868     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1869             seqs,
1870             omitHidden, null);
1871
1872     StringSelection ss = new StringSelection(output);
1873
1874     try
1875     {
1876       jalview.gui.Desktop.internalCopy = true;
1877       // Its really worth setting the clipboard contents
1878       // to empty before setting the large StringSelection!!
1879       Toolkit.getDefaultToolkit().getSystemClipboard()
1880               .setContents(new StringSelection(""), null);
1881
1882       Toolkit.getDefaultToolkit().getSystemClipboard()
1883               .setContents(ss, Desktop.instance);
1884     } catch (OutOfMemoryError er)
1885     {
1886       new OOMWarning("copying region", er);
1887       return;
1888     }
1889
1890     ArrayList<int[]> hiddenColumns = null;
1891     if (viewport.hasHiddenColumns())
1892     {
1893       hiddenColumns = new ArrayList<int[]>();
1894       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1895               .getSelectionGroup().getEndRes();
1896       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1897       {
1898         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1899         {
1900           hiddenColumns.add(new int[] { region[0] - hiddenOffset,
1901               region[1] - hiddenOffset });
1902         }
1903       }
1904     }
1905
1906     Desktop.jalviewClipboard = new Object[] { seqs,
1907         viewport.getAlignment().getDataset(), hiddenColumns };
1908     statusBar.setText(MessageManager.formatMessage(
1909             "label.copied_sequences_to_clipboard", new Object[] { Integer
1910                     .valueOf(seqs.length).toString() }));
1911   }
1912
1913   /**
1914    * DOCUMENT ME!
1915    *
1916    * @param e
1917    *          DOCUMENT ME!
1918    */
1919   @Override
1920   protected void pasteNew_actionPerformed(ActionEvent e)
1921   {
1922     paste(true);
1923   }
1924
1925   /**
1926    * DOCUMENT ME!
1927    *
1928    * @param e
1929    *          DOCUMENT ME!
1930    */
1931   @Override
1932   protected void pasteThis_actionPerformed(ActionEvent e)
1933   {
1934     paste(false);
1935   }
1936
1937   /**
1938    * Paste contents of Jalview clipboard
1939    *
1940    * @param newAlignment
1941    *          true to paste to a new alignment, otherwise add to this.
1942    */
1943   void paste(boolean newAlignment)
1944   {
1945     boolean externalPaste = true;
1946     try
1947     {
1948       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1949       Transferable contents = c.getContents(this);
1950
1951       if (contents == null)
1952       {
1953         return;
1954       }
1955
1956       String str;
1957       FileFormatI format;
1958       try
1959       {
1960         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1961         if (str.length() < 1)
1962         {
1963           return;
1964         }
1965
1966         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1967
1968       } catch (OutOfMemoryError er)
1969       {
1970         new OOMWarning("Out of memory pasting sequences!!", er);
1971         return;
1972       }
1973
1974       SequenceI[] sequences;
1975       boolean annotationAdded = false;
1976       AlignmentI alignment = null;
1977
1978       if (Desktop.jalviewClipboard != null)
1979       {
1980         // The clipboard was filled from within Jalview, we must use the
1981         // sequences
1982         // And dataset from the copied alignment
1983         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1984         // be doubly sure that we create *new* sequence objects.
1985         sequences = new SequenceI[newseq.length];
1986         for (int i = 0; i < newseq.length; i++)
1987         {
1988           sequences[i] = new Sequence(newseq[i]);
1989         }
1990         alignment = new Alignment(sequences);
1991         externalPaste = false;
1992       }
1993       else
1994       {
1995         // parse the clipboard as an alignment.
1996         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1997                 format);
1998         sequences = alignment.getSequencesArray();
1999       }
2000
2001       int alwidth = 0;
2002       ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
2003       int fgroup = -1;
2004
2005       if (newAlignment)
2006       {
2007
2008         if (Desktop.jalviewClipboard != null)
2009         {
2010           // dataset is inherited
2011           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2012         }
2013         else
2014         {
2015           // new dataset is constructed
2016           alignment.setDataset(null);
2017         }
2018         alwidth = alignment.getWidth() + 1;
2019       }
2020       else
2021       {
2022         AlignmentI pastedal = alignment; // preserve pasted alignment object
2023         // Add pasted sequences and dataset into existing alignment.
2024         alignment = viewport.getAlignment();
2025         alwidth = alignment.getWidth() + 1;
2026         // decide if we need to import sequences from an existing dataset
2027         boolean importDs = Desktop.jalviewClipboard != null
2028                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2029         // importDs==true instructs us to copy over new dataset sequences from
2030         // an existing alignment
2031         Vector newDs = (importDs) ? new Vector() : null; // used to create
2032         // minimum dataset set
2033
2034         for (int i = 0; i < sequences.length; i++)
2035         {
2036           if (importDs)
2037           {
2038             newDs.addElement(null);
2039           }
2040           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2041           // paste
2042           if (importDs && ds != null)
2043           {
2044             if (!newDs.contains(ds))
2045             {
2046               newDs.setElementAt(ds, i);
2047               ds = new Sequence(ds);
2048               // update with new dataset sequence
2049               sequences[i].setDatasetSequence(ds);
2050             }
2051             else
2052             {
2053               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2054             }
2055           }
2056           else
2057           {
2058             // copy and derive new dataset sequence
2059             sequences[i] = sequences[i].deriveSequence();
2060             alignment.getDataset().addSequence(
2061                     sequences[i].getDatasetSequence());
2062             // TODO: avoid creation of duplicate dataset sequences with a
2063             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2064           }
2065           alignment.addSequence(sequences[i]); // merges dataset
2066         }
2067         if (newDs != null)
2068         {
2069           newDs.clear(); // tidy up
2070         }
2071         if (alignment.getAlignmentAnnotation() != null)
2072         {
2073           for (AlignmentAnnotation alan : alignment
2074                   .getAlignmentAnnotation())
2075           {
2076             if (alan.graphGroup > fgroup)
2077             {
2078               fgroup = alan.graphGroup;
2079             }
2080           }
2081         }
2082         if (pastedal.getAlignmentAnnotation() != null)
2083         {
2084           // Add any annotation attached to alignment.
2085           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2086           for (int i = 0; i < alann.length; i++)
2087           {
2088             annotationAdded = true;
2089             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2090             {
2091               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
2092               if (newann.graphGroup > -1)
2093               {
2094                 if (newGraphGroups.size() <= newann.graphGroup
2095                         || newGraphGroups.get(newann.graphGroup) == null)
2096                 {
2097                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2098                   {
2099                     newGraphGroups.add(q, null);
2100                   }
2101                   newGraphGroups.set(newann.graphGroup, new Integer(
2102                           ++fgroup));
2103                 }
2104                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2105                         .intValue();
2106               }
2107
2108               newann.padAnnotation(alwidth);
2109               alignment.addAnnotation(newann);
2110             }
2111           }
2112         }
2113       }
2114       if (!newAlignment)
2115       {
2116         // /////
2117         // ADD HISTORY ITEM
2118         //
2119         addHistoryItem(new EditCommand(
2120                 MessageManager.getString("label.add_sequences"),
2121                 Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
2122       }
2123       // Add any annotations attached to sequences
2124       for (int i = 0; i < sequences.length; i++)
2125       {
2126         if (sequences[i].getAnnotation() != null)
2127         {
2128           AlignmentAnnotation newann;
2129           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2130           {
2131             annotationAdded = true;
2132             newann = sequences[i].getAnnotation()[a];
2133             newann.adjustForAlignment();
2134             newann.padAnnotation(alwidth);
2135             if (newann.graphGroup > -1)
2136             {
2137               if (newann.graphGroup > -1)
2138               {
2139                 if (newGraphGroups.size() <= newann.graphGroup
2140                         || newGraphGroups.get(newann.graphGroup) == null)
2141                 {
2142                   for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
2143                   {
2144                     newGraphGroups.add(q, null);
2145                   }
2146                   newGraphGroups.set(newann.graphGroup, new Integer(
2147                           ++fgroup));
2148                 }
2149                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2150                         .intValue();
2151               }
2152             }
2153             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2154             // was
2155             // duplicated
2156             // earlier
2157             alignment
2158                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
2159           }
2160         }
2161       }
2162       if (!newAlignment)
2163       {
2164
2165         // propagate alignment changed.
2166         viewport.setEndSeq(alignment.getHeight());
2167         if (annotationAdded)
2168         {
2169           // Duplicate sequence annotation in all views.
2170           AlignmentI[] alview = this.getViewAlignments();
2171           for (int i = 0; i < sequences.length; i++)
2172           {
2173             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2174             if (sann == null)
2175             {
2176               continue;
2177             }
2178             for (int avnum = 0; avnum < alview.length; avnum++)
2179             {
2180               if (alview[avnum] != alignment)
2181               {
2182                 // duplicate in a view other than the one with input focus
2183                 int avwidth = alview[avnum].getWidth() + 1;
2184                 // this relies on sann being preserved after we
2185                 // modify the sequence's annotation array for each duplication
2186                 for (int a = 0; a < sann.length; a++)
2187                 {
2188                   AlignmentAnnotation newann = new AlignmentAnnotation(
2189                           sann[a]);
2190                   sequences[i].addAlignmentAnnotation(newann);
2191                   newann.padAnnotation(avwidth);
2192                   alview[avnum].addAnnotation(newann); // annotation was
2193                   // duplicated earlier
2194                   // TODO JAL-1145 graphGroups are not updated for sequence
2195                   // annotation added to several views. This may cause
2196                   // strangeness
2197                   alview[avnum].setAnnotationIndex(newann, a);
2198                 }
2199               }
2200             }
2201           }
2202           buildSortByAnnotationScoresMenu();
2203         }
2204         viewport.firePropertyChange("alignment", null,
2205                 alignment.getSequences());
2206         if (alignPanels != null)
2207         {
2208           for (AlignmentPanel ap : alignPanels)
2209           {
2210             ap.validateAnnotationDimensions(false);
2211           }
2212         }
2213         else
2214         {
2215           alignPanel.validateAnnotationDimensions(false);
2216         }
2217
2218       }
2219       else
2220       {
2221         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2222                 DEFAULT_HEIGHT);
2223         String newtitle = new String("Copied sequences");
2224
2225         if (Desktop.jalviewClipboard != null
2226                 && Desktop.jalviewClipboard[2] != null)
2227         {
2228           List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2229           for (int[] region : hc)
2230           {
2231             af.viewport.hideColumns(region[0], region[1]);
2232           }
2233         }
2234
2235         // >>>This is a fix for the moment, until a better solution is
2236         // found!!<<<
2237         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2238                 .transferSettings(
2239                         alignPanel.getSeqPanel().seqCanvas
2240                                 .getFeatureRenderer());
2241
2242         // TODO: maintain provenance of an alignment, rather than just make the
2243         // title a concatenation of operations.
2244         if (!externalPaste)
2245         {
2246           if (title.startsWith("Copied sequences"))
2247           {
2248             newtitle = title;
2249           }
2250           else
2251           {
2252             newtitle = newtitle.concat("- from " + title);
2253           }
2254         }
2255         else
2256         {
2257           newtitle = new String("Pasted sequences");
2258         }
2259
2260         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2261                 DEFAULT_HEIGHT);
2262
2263       }
2264
2265     } catch (Exception ex)
2266     {
2267       ex.printStackTrace();
2268       System.out.println("Exception whilst pasting: " + ex);
2269       // could be anything being pasted in here
2270     }
2271
2272   }
2273
2274   @Override
2275   protected void expand_newalign(ActionEvent e)
2276   {
2277     try
2278     {
2279       AlignmentI alignment = AlignmentUtils.expandContext(getViewport()
2280               .getAlignment(), -1);
2281       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2282               DEFAULT_HEIGHT);
2283       String newtitle = new String("Flanking alignment");
2284
2285       if (Desktop.jalviewClipboard != null
2286               && Desktop.jalviewClipboard[2] != null)
2287       {
2288         List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
2289         for (int region[] : hc)
2290         {
2291           af.viewport.hideColumns(region[0], region[1]);
2292         }
2293       }
2294
2295       // >>>This is a fix for the moment, until a better solution is
2296       // found!!<<<
2297       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2298               .transferSettings(
2299                       alignPanel.getSeqPanel().seqCanvas
2300                               .getFeatureRenderer());
2301
2302       // TODO: maintain provenance of an alignment, rather than just make the
2303       // title a concatenation of operations.
2304       {
2305         if (title.startsWith("Copied sequences"))
2306         {
2307           newtitle = title;
2308         }
2309         else
2310         {
2311           newtitle = newtitle.concat("- from " + title);
2312         }
2313       }
2314
2315       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2316
2317     } catch (Exception ex)
2318     {
2319       ex.printStackTrace();
2320       System.out.println("Exception whilst pasting: " + ex);
2321       // could be anything being pasted in here
2322     } catch (OutOfMemoryError oom)
2323     {
2324       new OOMWarning("Viewing flanking region of alignment", oom);
2325     }
2326   }
2327
2328   /**
2329    * DOCUMENT ME!
2330    *
2331    * @param e
2332    *          DOCUMENT ME!
2333    */
2334   @Override
2335   protected void cut_actionPerformed(ActionEvent e)
2336   {
2337     copy_actionPerformed(null);
2338     delete_actionPerformed(null);
2339   }
2340
2341   /**
2342    * DOCUMENT ME!
2343    *
2344    * @param e
2345    *          DOCUMENT ME!
2346    */
2347   @Override
2348   protected void delete_actionPerformed(ActionEvent evt)
2349   {
2350
2351     SequenceGroup sg = viewport.getSelectionGroup();
2352     if (sg == null)
2353     {
2354       return;
2355     }
2356
2357     /*
2358      * If the cut affects all sequences, warn, remove highlighted columns
2359      */
2360     if (sg.getSize() == viewport.getAlignment().getHeight())
2361     {
2362       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2363               .getAlignment().getWidth()) ? true : false;
2364       if (isEntireAlignWidth)
2365       {
2366         int confirm = JvOptionPane.showConfirmDialog(this,
2367                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2368                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2369                 JvOptionPane.OK_CANCEL_OPTION);
2370
2371         if (confirm == JvOptionPane.CANCEL_OPTION
2372                 || confirm == JvOptionPane.CLOSED_OPTION)
2373         {
2374           return;
2375         }
2376       }
2377       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2378               sg.getEndRes() + 1);
2379     }
2380     SequenceI[] cut = sg.getSequences()
2381             .toArray(new SequenceI[sg.getSize()]);
2382
2383     addHistoryItem(new EditCommand(
2384             MessageManager.getString("label.cut_sequences"), Action.CUT,
2385             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2386             viewport.getAlignment()));
2387
2388     viewport.setSelectionGroup(null);
2389     viewport.sendSelection();
2390     viewport.getAlignment().deleteGroup(sg);
2391
2392     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2393             .getSequences());
2394     if (viewport.getAlignment().getHeight() < 1)
2395     {
2396       try
2397       {
2398         this.setClosed(true);
2399       } catch (Exception ex)
2400       {
2401       }
2402     }
2403   }
2404
2405   /**
2406    * DOCUMENT ME!
2407    *
2408    * @param e
2409    *          DOCUMENT ME!
2410    */
2411   @Override
2412   protected void deleteGroups_actionPerformed(ActionEvent e)
2413   {
2414     if (avc.deleteGroups())
2415     {
2416       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2417       alignPanel.updateAnnotation();
2418       alignPanel.paintAlignment(true);
2419     }
2420   }
2421
2422   /**
2423    * DOCUMENT ME!
2424    *
2425    * @param e
2426    *          DOCUMENT ME!
2427    */
2428   @Override
2429   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2430   {
2431     SequenceGroup sg = new SequenceGroup();
2432
2433     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2434     {
2435       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2436     }
2437
2438     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2439     viewport.setSelectionGroup(sg);
2440     viewport.sendSelection();
2441     // JAL-2034 - should delegate to
2442     // alignPanel to decide if overview needs
2443     // updating.
2444     alignPanel.paintAlignment(false);
2445     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2446   }
2447
2448   /**
2449    * DOCUMENT ME!
2450    *
2451    * @param e
2452    *          DOCUMENT ME!
2453    */
2454   @Override
2455   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2456   {
2457     if (viewport.cursorMode)
2458     {
2459       alignPanel.getSeqPanel().keyboardNo1 = null;
2460       alignPanel.getSeqPanel().keyboardNo2 = null;
2461     }
2462     viewport.setSelectionGroup(null);
2463     viewport.getColumnSelection().clear();
2464     viewport.setSelectionGroup(null);
2465     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
2466     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2467     // JAL-2034 - should delegate to
2468     // alignPanel to decide if overview needs
2469     // updating.
2470     alignPanel.paintAlignment(false);
2471     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2472     viewport.sendSelection();
2473   }
2474
2475   /**
2476    * DOCUMENT ME!
2477    *
2478    * @param e
2479    *          DOCUMENT ME!
2480    */
2481   @Override
2482   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2483   {
2484     SequenceGroup sg = viewport.getSelectionGroup();
2485
2486     if (sg == null)
2487     {
2488       selectAllSequenceMenuItem_actionPerformed(null);
2489
2490       return;
2491     }
2492
2493     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2494     {
2495       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2496     }
2497     // JAL-2034 - should delegate to
2498     // alignPanel to decide if overview needs
2499     // updating.
2500
2501     alignPanel.paintAlignment(true);
2502     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2503     viewport.sendSelection();
2504   }
2505
2506   @Override
2507   public void invertColSel_actionPerformed(ActionEvent e)
2508   {
2509     viewport.invertColumnSelection();
2510     alignPanel.paintAlignment(true);
2511     viewport.sendSelection();
2512   }
2513
2514   /**
2515    * DOCUMENT ME!
2516    *
2517    * @param e
2518    *          DOCUMENT ME!
2519    */
2520   @Override
2521   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2522   {
2523     trimAlignment(true);
2524   }
2525
2526   /**
2527    * DOCUMENT ME!
2528    *
2529    * @param e
2530    *          DOCUMENT ME!
2531    */
2532   @Override
2533   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2534   {
2535     trimAlignment(false);
2536   }
2537
2538   void trimAlignment(boolean trimLeft)
2539   {
2540     ColumnSelection colSel = viewport.getColumnSelection();
2541     int column;
2542
2543     if (!colSel.isEmpty())
2544     {
2545       if (trimLeft)
2546       {
2547         column = colSel.getMin();
2548       }
2549       else
2550       {
2551         column = colSel.getMax();
2552       }
2553
2554       SequenceI[] seqs;
2555       if (viewport.getSelectionGroup() != null)
2556       {
2557         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2558                 viewport.getHiddenRepSequences());
2559       }
2560       else
2561       {
2562         seqs = viewport.getAlignment().getSequencesArray();
2563       }
2564
2565       TrimRegionCommand trimRegion;
2566       if (trimLeft)
2567       {
2568         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2569                 column, viewport.getAlignment());
2570         viewport.setStartRes(0);
2571       }
2572       else
2573       {
2574         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2575                 column, viewport.getAlignment());
2576       }
2577
2578       statusBar.setText(MessageManager.formatMessage(
2579               "label.removed_columns",
2580               new String[] { Integer.valueOf(trimRegion.getSize())
2581                       .toString() }));
2582
2583       addHistoryItem(trimRegion);
2584
2585       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2586       {
2587         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2588                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2589         {
2590           viewport.getAlignment().deleteGroup(sg);
2591         }
2592       }
2593
2594       viewport.firePropertyChange("alignment", null, viewport
2595               .getAlignment().getSequences());
2596     }
2597   }
2598
2599   /**
2600    * DOCUMENT ME!
2601    *
2602    * @param e
2603    *          DOCUMENT ME!
2604    */
2605   @Override
2606   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2607   {
2608     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2609
2610     SequenceI[] seqs;
2611     if (viewport.getSelectionGroup() != null)
2612     {
2613       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2614               viewport.getHiddenRepSequences());
2615       start = viewport.getSelectionGroup().getStartRes();
2616       end = viewport.getSelectionGroup().getEndRes();
2617     }
2618     else
2619     {
2620       seqs = viewport.getAlignment().getSequencesArray();
2621     }
2622
2623     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2624             "Remove Gapped Columns", seqs, start, end,
2625             viewport.getAlignment());
2626
2627     addHistoryItem(removeGapCols);
2628
2629     statusBar.setText(MessageManager.formatMessage(
2630             "label.removed_empty_columns",
2631             new Object[] { Integer.valueOf(removeGapCols.getSize())
2632                     .toString() }));
2633
2634     // This is to maintain viewport position on first residue
2635     // of first sequence
2636     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2637     int startRes = seq.findPosition(viewport.startRes);
2638     // ShiftList shifts;
2639     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2640     // edit.alColumnChanges=shifts.getInverse();
2641     // if (viewport.hasHiddenColumns)
2642     // viewport.getColumnSelection().compensateForEdits(shifts);
2643     viewport.setStartRes(seq.findIndex(startRes) - 1);
2644     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2645             .getSequences());
2646
2647   }
2648
2649   /**
2650    * DOCUMENT ME!
2651    *
2652    * @param e
2653    *          DOCUMENT ME!
2654    */
2655   @Override
2656   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2657   {
2658     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2659
2660     SequenceI[] seqs;
2661     if (viewport.getSelectionGroup() != null)
2662     {
2663       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2664               viewport.getHiddenRepSequences());
2665       start = viewport.getSelectionGroup().getStartRes();
2666       end = viewport.getSelectionGroup().getEndRes();
2667     }
2668     else
2669     {
2670       seqs = viewport.getAlignment().getSequencesArray();
2671     }
2672
2673     // This is to maintain viewport position on first residue
2674     // of first sequence
2675     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2676     int startRes = seq.findPosition(viewport.startRes);
2677
2678     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2679             viewport.getAlignment()));
2680
2681     viewport.setStartRes(seq.findIndex(startRes) - 1);
2682
2683     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2684             .getSequences());
2685
2686   }
2687
2688   /**
2689    * DOCUMENT ME!
2690    *
2691    * @param e
2692    *          DOCUMENT ME!
2693    */
2694   @Override
2695   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2696   {
2697     viewport.setPadGaps(padGapsMenuitem.isSelected());
2698     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2699             .getSequences());
2700   }
2701
2702   /**
2703    * DOCUMENT ME!
2704    *
2705    * @param e
2706    *          DOCUMENT ME!
2707    */
2708   @Override
2709   public void findMenuItem_actionPerformed(ActionEvent e)
2710   {
2711     new Finder();
2712   }
2713
2714   /**
2715    * Create a new view of the current alignment.
2716    */
2717   @Override
2718   public void newView_actionPerformed(ActionEvent e)
2719   {
2720     newView(null, true);
2721   }
2722
2723   /**
2724    * Creates and shows a new view of the current alignment.
2725    *
2726    * @param viewTitle
2727    *          title of newly created view; if null, one will be generated
2728    * @param copyAnnotation
2729    *          if true then duplicate all annnotation, groups and settings
2730    * @return new alignment panel, already displayed.
2731    */
2732   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2733   {
2734     /*
2735      * Create a new AlignmentPanel (with its own, new Viewport)
2736      */
2737     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2738             true);
2739     if (!copyAnnotation)
2740     {
2741       /*
2742        * remove all groups and annotation except for the automatic stuff
2743        */
2744       newap.av.getAlignment().deleteAllGroups();
2745       newap.av.getAlignment().deleteAllAnnotations(false);
2746     }
2747
2748     newap.av.setGatherViewsHere(false);
2749
2750     if (viewport.viewName == null)
2751     {
2752       viewport.viewName = MessageManager
2753               .getString("label.view_name_original");
2754     }
2755
2756     /*
2757      * Views share the same edits undo and redo stacks
2758      */
2759     newap.av.setHistoryList(viewport.getHistoryList());
2760     newap.av.setRedoList(viewport.getRedoList());
2761
2762     /*
2763      * Views share the same mappings; need to deregister any new mappings
2764      * created by copyAlignPanel, and register the new reference to the shared
2765      * mappings
2766      */
2767     newap.av.replaceMappings(viewport.getAlignment());
2768
2769     newap.av.viewName = getNewViewName(viewTitle);
2770
2771     addAlignmentPanel(newap, true);
2772     newap.alignmentChanged();
2773
2774     if (alignPanels.size() == 2)
2775     {
2776       viewport.setGatherViewsHere(true);
2777     }
2778     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2779     return newap;
2780   }
2781
2782   /**
2783    * Make a new name for the view, ensuring it is unique within the current
2784    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2785    * these now use viewId. Unique view names are still desirable for usability.)
2786    *
2787    * @param viewTitle
2788    * @return
2789    */
2790   protected String getNewViewName(String viewTitle)
2791   {
2792     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2793     boolean addFirstIndex = false;
2794     if (viewTitle == null || viewTitle.trim().length() == 0)
2795     {
2796       viewTitle = MessageManager.getString("action.view");
2797       addFirstIndex = true;
2798     }
2799     else
2800     {
2801       index = 1;// we count from 1 if given a specific name
2802     }
2803     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2804
2805     List<Component> comps = PaintRefresher.components.get(viewport
2806             .getSequenceSetId());
2807
2808     List<String> existingNames = getExistingViewNames(comps);
2809
2810     while (existingNames.contains(newViewName))
2811     {
2812       newViewName = viewTitle + " " + (++index);
2813     }
2814     return newViewName;
2815   }
2816
2817   /**
2818    * Returns a list of distinct view names found in the given list of
2819    * components. View names are held on the viewport of an AlignmentPanel.
2820    *
2821    * @param comps
2822    * @return
2823    */
2824   protected List<String> getExistingViewNames(List<Component> comps)
2825   {
2826     List<String> existingNames = new ArrayList<String>();
2827     for (Component comp : comps)
2828     {
2829       if (comp instanceof AlignmentPanel)
2830       {
2831         AlignmentPanel ap = (AlignmentPanel) comp;
2832         if (!existingNames.contains(ap.av.viewName))
2833         {
2834           existingNames.add(ap.av.viewName);
2835         }
2836       }
2837     }
2838     return existingNames;
2839   }
2840
2841   /**
2842    * Explode tabbed views into separate windows.
2843    */
2844   @Override
2845   public void expandViews_actionPerformed(ActionEvent e)
2846   {
2847     Desktop.explodeViews(this);
2848   }
2849
2850   /**
2851    * Gather views in separate windows back into a tabbed presentation.
2852    */
2853   @Override
2854   public void gatherViews_actionPerformed(ActionEvent e)
2855   {
2856     Desktop.instance.gatherViews(this);
2857   }
2858
2859   /**
2860    * DOCUMENT ME!
2861    *
2862    * @param e
2863    *          DOCUMENT ME!
2864    */
2865   @Override
2866   public void font_actionPerformed(ActionEvent e)
2867   {
2868     new FontChooser(alignPanel);
2869   }
2870
2871   /**
2872    * DOCUMENT ME!
2873    *
2874    * @param e
2875    *          DOCUMENT ME!
2876    */
2877   @Override
2878   protected void seqLimit_actionPerformed(ActionEvent e)
2879   {
2880     viewport.setShowJVSuffix(seqLimits.isSelected());
2881
2882     alignPanel.getIdPanel().getIdCanvas()
2883             .setPreferredSize(alignPanel.calculateIdWidth());
2884     alignPanel.paintAlignment(true);
2885   }
2886
2887   @Override
2888   public void idRightAlign_actionPerformed(ActionEvent e)
2889   {
2890     viewport.setRightAlignIds(idRightAlign.isSelected());
2891     alignPanel.paintAlignment(true);
2892   }
2893
2894   @Override
2895   public void centreColumnLabels_actionPerformed(ActionEvent e)
2896   {
2897     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2898     alignPanel.paintAlignment(true);
2899   }
2900
2901   /*
2902    * (non-Javadoc)
2903    *
2904    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2905    */
2906   @Override
2907   protected void followHighlight_actionPerformed()
2908   {
2909     /*
2910      * Set the 'follow' flag on the Viewport (and scroll to position if now
2911      * true).
2912      */
2913     final boolean state = this.followHighlightMenuItem.getState();
2914     viewport.setFollowHighlight(state);
2915     if (state)
2916     {
2917       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2918     }
2919   }
2920
2921   /**
2922    * DOCUMENT ME!
2923    *
2924    * @param e
2925    *          DOCUMENT ME!
2926    */
2927   @Override
2928   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2929   {
2930     viewport.setColourText(colourTextMenuItem.isSelected());
2931     alignPanel.paintAlignment(true);
2932   }
2933
2934   /**
2935    * DOCUMENT ME!
2936    *
2937    * @param e
2938    *          DOCUMENT ME!
2939    */
2940   @Override
2941   public void wrapMenuItem_actionPerformed(ActionEvent e)
2942   {
2943     scaleAbove.setVisible(wrapMenuItem.isSelected());
2944     scaleLeft.setVisible(wrapMenuItem.isSelected());
2945     scaleRight.setVisible(wrapMenuItem.isSelected());
2946     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2947     alignPanel.updateLayout();
2948   }
2949
2950   @Override
2951   public void showAllSeqs_actionPerformed(ActionEvent e)
2952   {
2953     viewport.showAllHiddenSeqs();
2954   }
2955
2956   @Override
2957   public void showAllColumns_actionPerformed(ActionEvent e)
2958   {
2959     viewport.showAllHiddenColumns();
2960     repaint();
2961     viewport.sendSelection();
2962   }
2963
2964   @Override
2965   public void hideSelSequences_actionPerformed(ActionEvent e)
2966   {
2967     viewport.hideAllSelectedSeqs();
2968     // alignPanel.paintAlignment(true);
2969   }
2970
2971   /**
2972    * called by key handler and the hide all/show all menu items
2973    *
2974    * @param toggleSeqs
2975    * @param toggleCols
2976    */
2977   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2978   {
2979
2980     boolean hide = false;
2981     SequenceGroup sg = viewport.getSelectionGroup();
2982     if (!toggleSeqs && !toggleCols)
2983     {
2984       // Hide everything by the current selection - this is a hack - we do the
2985       // invert and then hide
2986       // first check that there will be visible columns after the invert.
2987       if (viewport.hasSelectedColumns()
2988               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2989                       .getEndRes()))
2990       {
2991         // now invert the sequence set, if required - empty selection implies
2992         // that no hiding is required.
2993         if (sg != null)
2994         {
2995           invertSequenceMenuItem_actionPerformed(null);
2996           sg = viewport.getSelectionGroup();
2997           toggleSeqs = true;
2998
2999         }
3000         viewport.expandColSelection(sg, true);
3001         // finally invert the column selection and get the new sequence
3002         // selection.
3003         invertColSel_actionPerformed(null);
3004         toggleCols = true;
3005       }
3006     }
3007
3008     if (toggleSeqs)
3009     {
3010       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3011       {
3012         hideSelSequences_actionPerformed(null);
3013         hide = true;
3014       }
3015       else if (!(toggleCols && viewport.hasSelectedColumns()))
3016       {
3017         showAllSeqs_actionPerformed(null);
3018       }
3019     }
3020
3021     if (toggleCols)
3022     {
3023       if (viewport.hasSelectedColumns())
3024       {
3025         hideSelColumns_actionPerformed(null);
3026         if (!toggleSeqs)
3027         {
3028           viewport.setSelectionGroup(sg);
3029         }
3030       }
3031       else if (!hide)
3032       {
3033         showAllColumns_actionPerformed(null);
3034       }
3035     }
3036   }
3037
3038   /*
3039    * (non-Javadoc)
3040    *
3041    * @see
3042    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3043    * event.ActionEvent)
3044    */
3045   @Override
3046   public void hideAllButSelection_actionPerformed(ActionEvent e)
3047   {
3048     toggleHiddenRegions(false, false);
3049     viewport.sendSelection();
3050   }
3051
3052   /*
3053    * (non-Javadoc)
3054    *
3055    * @see
3056    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3057    * .ActionEvent)
3058    */
3059   @Override
3060   public void hideAllSelection_actionPerformed(ActionEvent e)
3061   {
3062     SequenceGroup sg = viewport.getSelectionGroup();
3063     viewport.expandColSelection(sg, false);
3064     viewport.hideAllSelectedSeqs();
3065     viewport.hideSelectedColumns();
3066     alignPanel.paintAlignment(true);
3067     viewport.sendSelection();
3068   }
3069
3070   /*
3071    * (non-Javadoc)
3072    *
3073    * @see
3074    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3075    * ActionEvent)
3076    */
3077   @Override
3078   public void showAllhidden_actionPerformed(ActionEvent e)
3079   {
3080     viewport.showAllHiddenColumns();
3081     viewport.showAllHiddenSeqs();
3082     alignPanel.paintAlignment(true);
3083     viewport.sendSelection();
3084   }
3085
3086   @Override
3087   public void hideSelColumns_actionPerformed(ActionEvent e)
3088   {
3089     viewport.hideSelectedColumns();
3090     alignPanel.paintAlignment(true);
3091     viewport.sendSelection();
3092   }
3093
3094   @Override
3095   public void hiddenMarkers_actionPerformed(ActionEvent e)
3096   {
3097     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3098     repaint();
3099   }
3100
3101   /**
3102    * DOCUMENT ME!
3103    *
3104    * @param e
3105    *          DOCUMENT ME!
3106    */
3107   @Override
3108   protected void scaleAbove_actionPerformed(ActionEvent e)
3109   {
3110     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3111     alignPanel.paintAlignment(true);
3112   }
3113
3114   /**
3115    * DOCUMENT ME!
3116    *
3117    * @param e
3118    *          DOCUMENT ME!
3119    */
3120   @Override
3121   protected void scaleLeft_actionPerformed(ActionEvent e)
3122   {
3123     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3124     alignPanel.paintAlignment(true);
3125   }
3126
3127   /**
3128    * DOCUMENT ME!
3129    *
3130    * @param e
3131    *          DOCUMENT ME!
3132    */
3133   @Override
3134   protected void scaleRight_actionPerformed(ActionEvent e)
3135   {
3136     viewport.setScaleRightWrapped(scaleRight.isSelected());
3137     alignPanel.paintAlignment(true);
3138   }
3139
3140   /**
3141    * DOCUMENT ME!
3142    *
3143    * @param e
3144    *          DOCUMENT ME!
3145    */
3146   @Override
3147   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3148   {
3149     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3150     alignPanel.paintAlignment(true);
3151   }
3152
3153   /**
3154    * DOCUMENT ME!
3155    *
3156    * @param e
3157    *          DOCUMENT ME!
3158    */
3159   @Override
3160   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3161   {
3162     viewport.setShowText(viewTextMenuItem.isSelected());
3163     alignPanel.paintAlignment(true);
3164   }
3165
3166   /**
3167    * DOCUMENT ME!
3168    *
3169    * @param e
3170    *          DOCUMENT ME!
3171    */
3172   @Override
3173   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3174   {
3175     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3176     alignPanel.paintAlignment(true);
3177   }
3178
3179   public FeatureSettings featureSettings;
3180
3181   @Override
3182   public FeatureSettingsControllerI getFeatureSettingsUI()
3183   {
3184     return featureSettings;
3185   }
3186
3187   @Override
3188   public void featureSettings_actionPerformed(ActionEvent e)
3189   {
3190     if (featureSettings != null)
3191     {
3192       featureSettings.close();
3193       featureSettings = null;
3194     }
3195     if (!showSeqFeatures.isSelected())
3196     {
3197       // make sure features are actually displayed
3198       showSeqFeatures.setSelected(true);
3199       showSeqFeatures_actionPerformed(null);
3200     }
3201     featureSettings = new FeatureSettings(this);
3202   }
3203
3204   /**
3205    * Set or clear 'Show Sequence Features'
3206    *
3207    * @param evt
3208    *          DOCUMENT ME!
3209    */
3210   @Override
3211   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3212   {
3213     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3214     alignPanel.paintAlignment(true);
3215     if (alignPanel.getOverviewPanel() != null)
3216     {
3217       alignPanel.getOverviewPanel().updateOverviewImage();
3218     }
3219   }
3220
3221   /**
3222    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3223    * the annotations panel as a whole.
3224    *
3225    * The options to show/hide all annotations should be enabled when the panel
3226    * is shown, and disabled when the panel is hidden.
3227    *
3228    * @param e
3229    */
3230   @Override
3231   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3232   {
3233     final boolean setVisible = annotationPanelMenuItem.isSelected();
3234     viewport.setShowAnnotation(setVisible);
3235     this.showAllSeqAnnotations.setEnabled(setVisible);
3236     this.hideAllSeqAnnotations.setEnabled(setVisible);
3237     this.showAllAlAnnotations.setEnabled(setVisible);
3238     this.hideAllAlAnnotations.setEnabled(setVisible);
3239     alignPanel.updateLayout();
3240   }
3241
3242   @Override
3243   public void alignmentProperties()
3244   {
3245     JEditorPane editPane = new JEditorPane("text/html", "");
3246     editPane.setEditable(false);
3247     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3248             .formatAsHtml();
3249     editPane.setText(MessageManager.formatMessage("label.html_content",
3250             new Object[] { contents.toString() }));
3251     JInternalFrame frame = new JInternalFrame();
3252     frame.getContentPane().add(new JScrollPane(editPane));
3253
3254     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3255             "label.alignment_properties", new Object[] { getTitle() }),
3256             500, 400);
3257   }
3258
3259   /**
3260    * DOCUMENT ME!
3261    *
3262    * @param e
3263    *          DOCUMENT ME!
3264    */
3265   @Override
3266   public void overviewMenuItem_actionPerformed(ActionEvent e)
3267   {
3268     if (alignPanel.overviewPanel != null)
3269     {
3270       return;
3271     }
3272
3273     JInternalFrame frame = new JInternalFrame();
3274     OverviewPanel overview = new OverviewPanel(alignPanel);
3275     frame.setContentPane(overview);
3276     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
3277             "label.overview_params", new Object[] { this.getTitle() }),
3278             frame.getWidth(), frame.getHeight());
3279     frame.pack();
3280     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3281     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
3282     {
3283       @Override
3284       public void internalFrameClosed(
3285               javax.swing.event.InternalFrameEvent evt)
3286       {
3287         alignPanel.setOverviewPanel(null);
3288       };
3289     });
3290
3291     alignPanel.setOverviewPanel(overview);
3292   }
3293
3294   @Override
3295   public void textColour_actionPerformed(ActionEvent e)
3296   {
3297     new TextColourChooser().chooseColour(alignPanel, null);
3298   }
3299
3300   /**
3301    * DOCUMENT ME!
3302    *
3303    * @param e
3304    *          DOCUMENT ME!
3305    */
3306   @Override
3307   protected void noColourmenuItem_actionPerformed(ActionEvent e)
3308   {
3309     changeColour(null);
3310   }
3311
3312   /**
3313    * DOCUMENT ME!
3314    *
3315    * @param e
3316    *          DOCUMENT ME!
3317    */
3318   @Override
3319   public void clustalColour_actionPerformed(ActionEvent e)
3320   {
3321     changeColour(new ClustalxColourScheme(viewport.getAlignment(),
3322             viewport.getHiddenRepSequences()));
3323   }
3324
3325   /**
3326    * DOCUMENT ME!
3327    *
3328    * @param e
3329    *          DOCUMENT ME!
3330    */
3331   @Override
3332   public void zappoColour_actionPerformed(ActionEvent e)
3333   {
3334     changeColour(new ZappoColourScheme());
3335   }
3336
3337   /**
3338    * DOCUMENT ME!
3339    *
3340    * @param e
3341    *          DOCUMENT ME!
3342    */
3343   @Override
3344   public void taylorColour_actionPerformed(ActionEvent e)
3345   {
3346     changeColour(new TaylorColourScheme());
3347   }
3348
3349   /**
3350    * DOCUMENT ME!
3351    *
3352    * @param e
3353    *          DOCUMENT ME!
3354    */
3355   @Override
3356   public void hydrophobicityColour_actionPerformed(ActionEvent e)
3357   {
3358     changeColour(new HydrophobicColourScheme());
3359   }
3360
3361   /**
3362    * DOCUMENT ME!
3363    *
3364    * @param e
3365    *          DOCUMENT ME!
3366    */
3367   @Override
3368   public void helixColour_actionPerformed(ActionEvent e)
3369   {
3370     changeColour(new HelixColourScheme());
3371   }
3372
3373   /**
3374    * DOCUMENT ME!
3375    *
3376    * @param e
3377    *          DOCUMENT ME!
3378    */
3379   @Override
3380   public void strandColour_actionPerformed(ActionEvent e)
3381   {
3382     changeColour(new StrandColourScheme());
3383   }
3384
3385   /**
3386    * DOCUMENT ME!
3387    *
3388    * @param e
3389    *          DOCUMENT ME!
3390    */
3391   @Override
3392   public void turnColour_actionPerformed(ActionEvent e)
3393   {
3394     changeColour(new TurnColourScheme());
3395   }
3396
3397   /**
3398    * DOCUMENT ME!
3399    *
3400    * @param e
3401    *          DOCUMENT ME!
3402    */
3403   @Override
3404   public void buriedColour_actionPerformed(ActionEvent e)
3405   {
3406     changeColour(new BuriedColourScheme());
3407   }
3408
3409   /**
3410    * DOCUMENT ME!
3411    *
3412    * @param e
3413    *          DOCUMENT ME!
3414    */
3415   @Override
3416   public void nucleotideColour_actionPerformed(ActionEvent e)
3417   {
3418     changeColour(new NucleotideColourScheme());
3419   }
3420
3421   @Override
3422   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3423   {
3424     changeColour(new PurinePyrimidineColourScheme());
3425   }
3426
3427   /*
3428    * public void covariationColour_actionPerformed(ActionEvent e) {
3429    * changeColour(new
3430    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3431    * ()[0])); }
3432    */
3433   @Override
3434   public void annotationColour_actionPerformed(ActionEvent e)
3435   {
3436     new AnnotationColourChooser(viewport, alignPanel);
3437   }
3438
3439   @Override
3440   public void annotationColumn_actionPerformed(ActionEvent e)
3441   {
3442     new AnnotationColumnChooser(viewport, alignPanel);
3443   }
3444
3445   @Override
3446   public void rnahelicesColour_actionPerformed(ActionEvent e)
3447   {
3448     new RNAHelicesColourChooser(viewport, alignPanel);
3449   }
3450
3451   /**
3452    * DOCUMENT ME!
3453    *
3454    * @param e
3455    *          DOCUMENT ME!
3456    */
3457   @Override
3458   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3459   {
3460     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3461   }
3462
3463   /**
3464    * DOCUMENT ME!
3465    *
3466    * @param cs
3467    *          DOCUMENT ME!
3468    */
3469   @Override
3470   public void changeColour(ColourSchemeI cs)
3471   {
3472     // TODO: pull up to controller method
3473
3474     if (cs != null)
3475     {
3476       // Make sure viewport is up to date w.r.t. any sliders
3477       if (viewport.getAbovePIDThreshold())
3478       {
3479         int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3480                 "Background");
3481         viewport.setThreshold(threshold);
3482       }
3483
3484       if (viewport.getConservationSelected())
3485       {
3486         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3487                 cs, "Background"));
3488       }
3489       if (cs instanceof TCoffeeColourScheme)
3490       {
3491         tcoffeeColour.setEnabled(true);
3492         tcoffeeColour.setSelected(true);
3493       }
3494     }
3495
3496     viewport.setGlobalColourScheme(cs);
3497
3498     alignPanel.paintAlignment(true);
3499   }
3500
3501   /**
3502    * DOCUMENT ME!
3503    */
3504   @Override
3505   protected void modifyPID_actionPerformed()
3506   {
3507     if (viewport.getAbovePIDThreshold()
3508             && viewport.getGlobalColourScheme() != null)
3509     {
3510       SliderPanel.setPIDSliderSource(alignPanel,
3511               viewport.getGlobalColourScheme(), "Background");
3512       SliderPanel.showPIDSlider();
3513     }
3514   }
3515
3516   /**
3517    * DOCUMENT ME!
3518    */
3519   @Override
3520   protected void modifyConservation_actionPerformed()
3521   {
3522     if (viewport.getConservationSelected()
3523             && viewport.getGlobalColourScheme() != null)
3524     {
3525       SliderPanel.setConservationSlider(alignPanel,
3526               viewport.getGlobalColourScheme(), "Background");
3527       SliderPanel.showConservationSlider();
3528     }
3529   }
3530
3531   /**
3532    * Action on selecting or deselecting (Colour) By Conservation
3533    */
3534   @Override
3535   protected void conservationMenuItem_actionPerformed()
3536   {
3537     boolean selected = conservationMenuItem.isSelected();
3538     modifyConservation.setEnabled(selected);
3539     viewport.setConservationSelected(selected);
3540
3541     changeColour(viewport.getGlobalColourScheme());
3542     if (selected)
3543     {
3544       modifyConservation_actionPerformed();
3545     }
3546     else
3547     {
3548       SliderPanel.hideConservationSlider();
3549     }
3550   }
3551
3552   /**
3553    * Action on selecting or deselecting (Colour) Above PID Threshold
3554    */
3555   @Override
3556   public void abovePIDThreshold_actionPerformed()
3557   {
3558     boolean selected = abovePIDThreshold.isSelected();
3559     modifyPID.setEnabled(selected);
3560     viewport.setAbovePIDThreshold(selected);
3561
3562     changeColour(viewport.getGlobalColourScheme());
3563     if (selected)
3564     {
3565       modifyPID_actionPerformed();
3566     }
3567     else
3568     {
3569       SliderPanel.hidePIDSlider();
3570     }
3571   }
3572
3573   /**
3574    * DOCUMENT ME!
3575    *
3576    * @param e
3577    *          DOCUMENT ME!
3578    */
3579   @Override
3580   public void userDefinedColour_actionPerformed(ActionEvent e)
3581   {
3582     if (e.getActionCommand().equals(
3583             MessageManager.getString("action.user_defined")))
3584     {
3585       new UserDefinedColours(alignPanel, null);
3586     }
3587     else
3588     {
3589       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3590               .getUserColourSchemes().get(e.getActionCommand());
3591
3592       changeColour(udc);
3593     }
3594   }
3595
3596   public void updateUserColourMenu()
3597   {
3598
3599     Component[] menuItems = colourMenu.getMenuComponents();
3600     int iSize = menuItems.length;
3601     for (int i = 0; i < iSize; i++)
3602     {
3603       if (menuItems[i].getName() != null
3604               && menuItems[i].getName().equals("USER_DEFINED"))
3605       {
3606         colourMenu.remove(menuItems[i]);
3607         iSize--;
3608       }
3609     }
3610     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3611     {
3612       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3613               .getUserColourSchemes().keys();
3614
3615       while (userColours.hasMoreElements())
3616       {
3617         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3618                 userColours.nextElement().toString());
3619         radioItem.setName("USER_DEFINED");
3620         radioItem.addMouseListener(new MouseAdapter()
3621         {
3622           @Override
3623           public void mousePressed(MouseEvent evt)
3624           {
3625             if (evt.isPopupTrigger()) // Mac
3626             {
3627               offerRemoval(radioItem);
3628             }
3629           }
3630
3631           @Override
3632           public void mouseReleased(MouseEvent evt)
3633           {
3634             if (evt.isPopupTrigger()) // Windows
3635             {
3636               offerRemoval(radioItem);
3637             }
3638           }
3639
3640           /**
3641            * @param radioItem
3642            */
3643           void offerRemoval(final JRadioButtonMenuItem radioItem)
3644           {
3645             radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3646
3647             int option = JvOptionPane.showInternalConfirmDialog(
3648                     jalview.gui.Desktop.desktop, MessageManager
3649                             .getString("label.remove_from_default_list"),
3650                     MessageManager
3651                             .getString("label.remove_user_defined_colour"),
3652                     JvOptionPane.YES_NO_OPTION);
3653             if (option == JvOptionPane.YES_OPTION)
3654             {
3655               jalview.gui.UserDefinedColours
3656                       .removeColourFromDefaults(radioItem.getText());
3657               colourMenu.remove(radioItem);
3658             }
3659             else
3660             {
3661               radioItem.addActionListener(new ActionListener()
3662               {
3663                 @Override
3664                 public void actionPerformed(ActionEvent evt)
3665                 {
3666                   userDefinedColour_actionPerformed(evt);
3667                 }
3668               });
3669             }
3670           }
3671         });
3672         radioItem.addActionListener(new ActionListener()
3673         {
3674           @Override
3675           public void actionPerformed(ActionEvent evt)
3676           {
3677             userDefinedColour_actionPerformed(evt);
3678           }
3679         });
3680
3681         colourMenu.insert(radioItem, 15);
3682         colours.add(radioItem);
3683       }
3684     }
3685   }
3686
3687   /**
3688    * DOCUMENT ME!
3689    *
3690    * @param e
3691    *          DOCUMENT ME!
3692    */
3693   @Override
3694   public void PIDColour_actionPerformed(ActionEvent e)
3695   {
3696     changeColour(new PIDColourScheme());
3697   }
3698
3699   /**
3700    * DOCUMENT ME!
3701    *
3702    * @param e
3703    *          DOCUMENT ME!
3704    */
3705   @Override
3706   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3707   {
3708     changeColour(new Blosum62ColourScheme());
3709   }
3710
3711   /**
3712    * DOCUMENT ME!
3713    *
3714    * @param e
3715    *          DOCUMENT ME!
3716    */
3717   @Override
3718   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3719   {
3720     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3721     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3722             .getAlignment().getSequenceAt(0), null);
3723     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3724             viewport.getAlignment()));
3725     alignPanel.paintAlignment(true);
3726   }
3727
3728   /**
3729    * DOCUMENT ME!
3730    *
3731    * @param e
3732    *          DOCUMENT ME!
3733    */
3734   @Override
3735   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3736   {
3737     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3738     AlignmentSorter.sortByID(viewport.getAlignment());
3739     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3740             viewport.getAlignment()));
3741     alignPanel.paintAlignment(true);
3742   }
3743
3744   /**
3745    * DOCUMENT ME!
3746    *
3747    * @param e
3748    *          DOCUMENT ME!
3749    */
3750   @Override
3751   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3752   {
3753     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3754     AlignmentSorter.sortByLength(viewport.getAlignment());
3755     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3756             viewport.getAlignment()));
3757     alignPanel.paintAlignment(true);
3758   }
3759
3760   /**
3761    * DOCUMENT ME!
3762    *
3763    * @param e
3764    *          DOCUMENT ME!
3765    */
3766   @Override
3767   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3768   {
3769     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3770     AlignmentSorter.sortByGroup(viewport.getAlignment());
3771     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3772             viewport.getAlignment()));
3773
3774     alignPanel.paintAlignment(true);
3775   }
3776
3777   /**
3778    * DOCUMENT ME!
3779    *
3780    * @param e
3781    *          DOCUMENT ME!
3782    */
3783   @Override
3784   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3785   {
3786     new RedundancyPanel(alignPanel, this);
3787   }
3788
3789   /**
3790    * DOCUMENT ME!
3791    *
3792    * @param e
3793    *          DOCUMENT ME!
3794    */
3795   @Override
3796   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3797   {
3798     if ((viewport.getSelectionGroup() == null)
3799             || (viewport.getSelectionGroup().getSize() < 2))
3800     {
3801       JvOptionPane.showInternalMessageDialog(this, MessageManager
3802               .getString("label.you_must_select_least_two_sequences"),
3803               MessageManager.getString("label.invalid_selection"),
3804               JvOptionPane.WARNING_MESSAGE);
3805     }
3806     else
3807     {
3808       JInternalFrame frame = new JInternalFrame();
3809       frame.setContentPane(new PairwiseAlignPanel(viewport));
3810       Desktop.addInternalFrame(frame,
3811               MessageManager.getString("action.pairwise_alignment"), 600,
3812               500);
3813     }
3814   }
3815
3816   /**
3817    * DOCUMENT ME!
3818    *
3819    * @param e
3820    *          DOCUMENT ME!
3821    */
3822   @Override
3823   public void PCAMenuItem_actionPerformed(ActionEvent e)
3824   {
3825     if (((viewport.getSelectionGroup() != null)
3826             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3827             .getSelectionGroup().getSize() > 0))
3828             || (viewport.getAlignment().getHeight() < 4))
3829     {
3830       JvOptionPane
3831               .showInternalMessageDialog(
3832                       this,
3833                       MessageManager
3834                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
3835                       MessageManager
3836                               .getString("label.sequence_selection_insufficient"),
3837                       JvOptionPane.WARNING_MESSAGE);
3838
3839       return;
3840     }
3841
3842     new PCAPanel(alignPanel);
3843   }
3844
3845   @Override
3846   public void autoCalculate_actionPerformed(ActionEvent e)
3847   {
3848     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3849     if (viewport.autoCalculateConsensus)
3850     {
3851       viewport.firePropertyChange("alignment", null, viewport
3852               .getAlignment().getSequences());
3853     }
3854   }
3855
3856   @Override
3857   public void sortByTreeOption_actionPerformed(ActionEvent e)
3858   {
3859     viewport.sortByTree = sortByTree.isSelected();
3860   }
3861
3862   @Override
3863   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3864   {
3865     viewport.followSelection = listenToViewSelections.isSelected();
3866   }
3867
3868   /**
3869    * DOCUMENT ME!
3870    *
3871    * @param e
3872    *          DOCUMENT ME!
3873    */
3874   @Override
3875   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3876   {
3877     newTreePanel("AV", "PID", "Average distance tree using PID");
3878   }
3879
3880   /**
3881    * DOCUMENT ME!
3882    *
3883    * @param e
3884    *          DOCUMENT ME!
3885    */
3886   @Override
3887   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3888   {
3889     newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3890   }
3891
3892   /**
3893    * DOCUMENT ME!
3894    *
3895    * @param e
3896    *          DOCUMENT ME!
3897    */
3898   @Override
3899   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3900   {
3901     newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3902   }
3903
3904   /**
3905    * DOCUMENT ME!
3906    *
3907    * @param e
3908    *          DOCUMENT ME!
3909    */
3910   @Override
3911   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3912   {
3913     newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3914   }
3915
3916   /**
3917    * DOCUMENT ME!
3918    *
3919    * @param type
3920    *          DOCUMENT ME!
3921    * @param pwType
3922    *          DOCUMENT ME!
3923    * @param title
3924    *          DOCUMENT ME!
3925    */
3926   void newTreePanel(String type, String pwType, String title)
3927   {
3928     TreePanel tp;
3929
3930     if (viewport.getSelectionGroup() != null
3931             && viewport.getSelectionGroup().getSize() > 0)
3932     {
3933       if (viewport.getSelectionGroup().getSize() < 3)
3934       {
3935         JvOptionPane
3936                 .showMessageDialog(
3937                         Desktop.desktop,
3938                         MessageManager
3939                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
3940                         MessageManager
3941                                 .getString("label.not_enough_sequences"),
3942                         JvOptionPane.WARNING_MESSAGE);
3943         return;
3944       }
3945
3946       SequenceGroup sg = viewport.getSelectionGroup();
3947
3948       /* Decide if the selection is a column region */
3949       for (SequenceI _s : sg.getSequences())
3950       {
3951         if (_s.getLength() < sg.getEndRes())
3952         {
3953           JvOptionPane
3954                   .showMessageDialog(
3955                           Desktop.desktop,
3956                           MessageManager
3957                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3958                           MessageManager
3959                                   .getString("label.sequences_selection_not_aligned"),
3960                           JvOptionPane.WARNING_MESSAGE);
3961
3962           return;
3963         }
3964       }
3965
3966       title = title + " on region";
3967       tp = new TreePanel(alignPanel, type, pwType);
3968     }
3969     else
3970     {
3971       // are the visible sequences aligned?
3972       if (!viewport.getAlignment().isAligned(false))
3973       {
3974         JvOptionPane
3975                 .showMessageDialog(
3976                         Desktop.desktop,
3977                         MessageManager
3978                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
3979                         MessageManager
3980                                 .getString("label.sequences_not_aligned"),
3981                         JvOptionPane.WARNING_MESSAGE);
3982
3983         return;
3984       }
3985
3986       if (viewport.getAlignment().getHeight() < 2)
3987       {
3988         return;
3989       }
3990
3991       tp = new TreePanel(alignPanel, type, pwType);
3992     }
3993
3994     title += " from ";
3995
3996     if (viewport.viewName != null)
3997     {
3998       title += viewport.viewName + " of ";
3999     }
4000
4001     title += this.title;
4002
4003     Desktop.addInternalFrame(tp, title, 600, 500);
4004   }
4005
4006   /**
4007    * DOCUMENT ME!
4008    *
4009    * @param title
4010    *          DOCUMENT ME!
4011    * @param order
4012    *          DOCUMENT ME!
4013    */
4014   public void addSortByOrderMenuItem(String title,
4015           final AlignmentOrder order)
4016   {
4017     final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
4018             "action.by_title_param", new Object[] { title }));
4019     sort.add(item);
4020     item.addActionListener(new java.awt.event.ActionListener()
4021     {
4022       @Override
4023       public void actionPerformed(ActionEvent e)
4024       {
4025         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4026
4027         // TODO: JBPNote - have to map order entries to curent SequenceI
4028         // pointers
4029         AlignmentSorter.sortBy(viewport.getAlignment(), order);
4030
4031         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
4032                 .getAlignment()));
4033
4034         alignPanel.paintAlignment(true);
4035       }
4036     });
4037   }
4038
4039   /**
4040    * Add a new sort by annotation score menu item
4041    *
4042    * @param sort
4043    *          the menu to add the option to
4044    * @param scoreLabel
4045    *          the label used to retrieve scores for each sequence on the
4046    *          alignment
4047    */
4048   public void addSortByAnnotScoreMenuItem(JMenu sort,
4049           final String scoreLabel)
4050   {
4051     final JMenuItem item = new JMenuItem(scoreLabel);
4052     sort.add(item);
4053     item.addActionListener(new java.awt.event.ActionListener()
4054     {
4055       @Override
4056       public void actionPerformed(ActionEvent e)
4057       {
4058         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4059         AlignmentSorter.sortByAnnotationScore(scoreLabel,
4060                 viewport.getAlignment());// ,viewport.getSelectionGroup());
4061         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
4062                 viewport.getAlignment()));
4063         alignPanel.paintAlignment(true);
4064       }
4065     });
4066   }
4067
4068   /**
4069    * last hash for alignment's annotation array - used to minimise cost of
4070    * rebuild.
4071    */
4072   protected int _annotationScoreVectorHash;
4073
4074   /**
4075    * search the alignment and rebuild the sort by annotation score submenu the
4076    * last alignment annotation vector hash is stored to minimize cost of
4077    * rebuilding in subsequence calls.
4078    *
4079    */
4080   @Override
4081   public void buildSortByAnnotationScoresMenu()
4082   {
4083     if (viewport.getAlignment().getAlignmentAnnotation() == null)
4084     {
4085       return;
4086     }
4087
4088     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
4089     {
4090       sortByAnnotScore.removeAll();
4091       // almost certainly a quicker way to do this - but we keep it simple
4092       Hashtable scoreSorts = new Hashtable();
4093       AlignmentAnnotation aann[];
4094       for (SequenceI sqa : viewport.getAlignment().getSequences())
4095       {
4096         aann = sqa.getAnnotation();
4097         for (int i = 0; aann != null && i < aann.length; i++)
4098         {
4099           if (aann[i].hasScore() && aann[i].sequenceRef != null)
4100           {
4101             scoreSorts.put(aann[i].label, aann[i].label);
4102           }
4103         }
4104       }
4105       Enumeration labels = scoreSorts.keys();
4106       while (labels.hasMoreElements())
4107       {
4108         addSortByAnnotScoreMenuItem(sortByAnnotScore,
4109                 (String) labels.nextElement());
4110       }
4111       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
4112       scoreSorts.clear();
4113
4114       _annotationScoreVectorHash = viewport.getAlignment()
4115               .getAlignmentAnnotation().hashCode();
4116     }
4117   }
4118
4119   /**
4120    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
4121    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
4122    * call. Listeners are added to remove the menu item when the treePanel is
4123    * closed, and adjust the tree leaf to sequence mapping when the alignment is
4124    * modified.
4125    *
4126    * @param treePanel
4127    *          Displayed tree window.
4128    * @param title
4129    *          SortBy menu item title.
4130    */
4131   @Override
4132   public void buildTreeMenu()
4133   {
4134     calculateTree.removeAll();
4135     // build the calculate menu
4136
4137     for (final String type : new String[] { "NJ", "AV" })
4138     {
4139       String treecalcnm = MessageManager.getString("label.tree_calc_"
4140               + type.toLowerCase());
4141       for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
4142       {
4143         JMenuItem tm = new JMenuItem();
4144         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
4145         if (sm.isDNA() == viewport.getAlignment().isNucleotide()
4146                 || sm.isProtein() == !viewport.getAlignment()
4147                         .isNucleotide())
4148         {
4149           String smn = MessageManager.getStringOrReturn(
4150                   "label.score_model_", sm.getName());
4151           final String title = MessageManager.formatMessage(
4152                   "label.treecalc_title", treecalcnm, smn);
4153           tm.setText(title);//
4154           tm.addActionListener(new java.awt.event.ActionListener()
4155           {
4156             @Override
4157             public void actionPerformed(ActionEvent e)
4158             {
4159               newTreePanel(type, pwtype, title);
4160             }
4161           });
4162           calculateTree.add(tm);
4163         }
4164
4165       }
4166     }
4167     sortByTreeMenu.removeAll();
4168
4169     List<Component> comps = PaintRefresher.components.get(viewport
4170             .getSequenceSetId());
4171     List<TreePanel> treePanels = new ArrayList<TreePanel>();
4172     for (Component comp : comps)
4173     {
4174       if (comp instanceof TreePanel)
4175       {
4176         treePanels.add((TreePanel) comp);
4177       }
4178     }
4179
4180     if (treePanels.size() < 1)
4181     {
4182       sortByTreeMenu.setVisible(false);
4183       return;
4184     }
4185
4186     sortByTreeMenu.setVisible(true);
4187
4188     for (final TreePanel tp : treePanels)
4189     {
4190       final JMenuItem item = new JMenuItem(tp.getTitle());
4191       item.addActionListener(new java.awt.event.ActionListener()
4192       {
4193         @Override
4194         public void actionPerformed(ActionEvent e)
4195         {
4196           tp.sortByTree_actionPerformed();
4197           addHistoryItem(tp.sortAlignmentIn(alignPanel));
4198
4199         }
4200       });
4201
4202       sortByTreeMenu.add(item);
4203     }
4204   }
4205
4206   public boolean sortBy(AlignmentOrder alorder, String undoname)
4207   {
4208     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
4209     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
4210     if (undoname != null)
4211     {
4212       addHistoryItem(new OrderCommand(undoname, oldOrder,
4213               viewport.getAlignment()));
4214     }
4215     alignPanel.paintAlignment(true);
4216     return true;
4217   }
4218
4219   /**
4220    * Work out whether the whole set of sequences or just the selected set will
4221    * be submitted for multiple alignment.
4222    *
4223    */
4224   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
4225   {
4226     // Now, check we have enough sequences
4227     AlignmentView msa = null;
4228
4229     if ((viewport.getSelectionGroup() != null)
4230             && (viewport.getSelectionGroup().getSize() > 1))
4231     {
4232       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
4233       // some common interface!
4234       /*
4235        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4236        * SequenceI[sz = seqs.getSize(false)];
4237        *
4238        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4239        * seqs.getSequenceAt(i); }
4240        */
4241       msa = viewport.getAlignmentView(true);
4242     }
4243     else if (viewport.getSelectionGroup() != null
4244             && viewport.getSelectionGroup().getSize() == 1)
4245     {
4246       int option = JvOptionPane.showConfirmDialog(this,
4247               MessageManager.getString("warn.oneseq_msainput_selection"),
4248               MessageManager.getString("label.invalid_selection"),
4249               JvOptionPane.OK_CANCEL_OPTION);
4250       if (option == JvOptionPane.OK_OPTION)
4251       {
4252         msa = viewport.getAlignmentView(false);
4253       }
4254     }
4255     else
4256     {
4257       msa = viewport.getAlignmentView(false);
4258     }
4259     return msa;
4260   }
4261
4262   /**
4263    * Decides what is submitted to a secondary structure prediction service: the
4264    * first sequence in the alignment, or in the current selection, or, if the
4265    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4266    * region or the whole alignment. (where the first sequence in the set is the
4267    * one that the prediction will be for).
4268    */
4269   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4270   {
4271     AlignmentView seqs = null;
4272
4273     if ((viewport.getSelectionGroup() != null)
4274             && (viewport.getSelectionGroup().getSize() > 0))
4275     {
4276       seqs = viewport.getAlignmentView(true);
4277     }
4278     else
4279     {
4280       seqs = viewport.getAlignmentView(false);
4281     }
4282     // limit sequences - JBPNote in future - could spawn multiple prediction
4283     // jobs
4284     // TODO: viewport.getAlignment().isAligned is a global state - the local
4285     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4286     if (!viewport.getAlignment().isAligned(false))
4287     {
4288       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4289       // TODO: if seqs.getSequences().length>1 then should really have warned
4290       // user!
4291
4292     }
4293     return seqs;
4294   }
4295
4296   /**
4297    * DOCUMENT ME!
4298    *
4299    * @param e
4300    *          DOCUMENT ME!
4301    */
4302   @Override
4303   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4304   {
4305     // Pick the tree file
4306     JalviewFileChooser chooser = new JalviewFileChooser(
4307             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4308     chooser.setFileView(new JalviewFileView());
4309     chooser.setDialogTitle(MessageManager
4310             .getString("label.select_newick_like_tree_file"));
4311     chooser.setToolTipText(MessageManager.getString("label.load_tree_file"));
4312
4313     int value = chooser.showOpenDialog(null);
4314
4315     if (value == JalviewFileChooser.APPROVE_OPTION)
4316     {
4317       String choice = chooser.getSelectedFile().getPath();
4318       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
4319       jalview.io.NewickFile fin = null;
4320       try
4321       {
4322         fin = new NewickFile(choice, DataSourceType.FILE);
4323         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
4324       } catch (Exception ex)
4325       {
4326         JvOptionPane
4327                 .showMessageDialog(
4328                         Desktop.desktop,
4329                         ex.getMessage(),
4330                         MessageManager
4331                                 .getString("label.problem_reading_tree_file"),
4332                         JvOptionPane.WARNING_MESSAGE);
4333         ex.printStackTrace();
4334       }
4335       if (fin != null && fin.hasWarningMessage())
4336       {
4337         JvOptionPane.showMessageDialog(Desktop.desktop, fin
4338                 .getWarningMessage(), MessageManager
4339                 .getString("label.possible_problem_with_tree_file"),
4340                 JvOptionPane.WARNING_MESSAGE);
4341       }
4342     }
4343   }
4344
4345   @Override
4346   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
4347   {
4348     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4349   }
4350
4351   public TreePanel ShowNewickTree(NewickFile nf, String title)
4352   {
4353     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4354   }
4355
4356   public TreePanel ShowNewickTree(NewickFile nf, String title,
4357           AlignmentView input)
4358   {
4359     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4360   }
4361
4362   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4363           int h, int x, int y)
4364   {
4365     return ShowNewickTree(nf, title, null, w, h, x, y);
4366   }
4367
4368   /**
4369    * Add a treeviewer for the tree extracted from a newick file object to the
4370    * current alignment view
4371    *
4372    * @param nf
4373    *          the tree
4374    * @param title
4375    *          tree viewer title
4376    * @param input
4377    *          Associated alignment input data (or null)
4378    * @param w
4379    *          width
4380    * @param h
4381    *          height
4382    * @param x
4383    *          position
4384    * @param y
4385    *          position
4386    * @return TreePanel handle
4387    */
4388   public TreePanel ShowNewickTree(NewickFile nf, String title,
4389           AlignmentView input, int w, int h, int x, int y)
4390   {
4391     TreePanel tp = null;
4392
4393     try
4394     {
4395       nf.parse();
4396
4397       if (nf.getTree() != null)
4398       {
4399         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4400
4401         tp.setSize(w, h);
4402
4403         if (x > 0 && y > 0)
4404         {
4405           tp.setLocation(x, y);
4406         }
4407
4408         Desktop.addInternalFrame(tp, title, w, h);
4409       }
4410     } catch (Exception ex)
4411     {
4412       ex.printStackTrace();
4413     }
4414
4415     return tp;
4416   }
4417
4418   private boolean buildingMenu = false;
4419
4420   /**
4421    * Generates menu items and listener event actions for web service clients
4422    *
4423    */
4424   public void BuildWebServiceMenu()
4425   {
4426     while (buildingMenu)
4427     {
4428       try
4429       {
4430         System.err.println("Waiting for building menu to finish.");
4431         Thread.sleep(10);
4432       } catch (Exception e)
4433       {
4434       }
4435     }
4436     final AlignFrame me = this;
4437     buildingMenu = true;
4438     new Thread(new Runnable()
4439     {
4440       @Override
4441       public void run()
4442       {
4443         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
4444         try
4445         {
4446           // System.err.println("Building ws menu again "
4447           // + Thread.currentThread());
4448           // TODO: add support for context dependent disabling of services based
4449           // on
4450           // alignment and current selection
4451           // TODO: add additional serviceHandle parameter to specify abstract
4452           // handler
4453           // class independently of AbstractName
4454           // TODO: add in rediscovery GUI function to restart discoverer
4455           // TODO: group services by location as well as function and/or
4456           // introduce
4457           // object broker mechanism.
4458           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4459           final IProgressIndicator af = me;
4460
4461           /*
4462            * do not i18n these strings - they are hard-coded in class
4463            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4464            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4465            */
4466           final JMenu msawsmenu = new JMenu("Alignment");
4467           final JMenu secstrmenu = new JMenu(
4468                   "Secondary Structure Prediction");
4469           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4470           final JMenu analymenu = new JMenu("Analysis");
4471           final JMenu dismenu = new JMenu("Protein Disorder");
4472           // JAL-940 - only show secondary structure prediction services from
4473           // the legacy server
4474           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4475               // &&
4476           Discoverer.services != null && (Discoverer.services.size() > 0))
4477           {
4478             // TODO: refactor to allow list of AbstractName/Handler bindings to
4479             // be
4480             // stored or retrieved from elsewhere
4481             // No MSAWS used any more:
4482             // Vector msaws = null; // (Vector)
4483             // Discoverer.services.get("MsaWS");
4484             Vector secstrpr = (Vector) Discoverer.services
4485                     .get("SecStrPred");
4486             if (secstrpr != null)
4487             {
4488               // Add any secondary structure prediction services
4489               for (int i = 0, j = secstrpr.size(); i < j; i++)
4490               {
4491                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4492                         .get(i);
4493                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4494                         .getServiceClient(sh);
4495                 int p = secstrmenu.getItemCount();
4496                 impl.attachWSMenuEntry(secstrmenu, me);
4497                 int q = secstrmenu.getItemCount();
4498                 for (int litm = p; litm < q; litm++)
4499                 {
4500                   legacyItems.add(secstrmenu.getItem(litm));
4501                 }
4502               }
4503             }
4504           }
4505
4506           // Add all submenus in the order they should appear on the web
4507           // services menu
4508           wsmenu.add(msawsmenu);
4509           wsmenu.add(secstrmenu);
4510           wsmenu.add(dismenu);
4511           wsmenu.add(analymenu);
4512           // No search services yet
4513           // wsmenu.add(seqsrchmenu);
4514
4515           javax.swing.SwingUtilities.invokeLater(new Runnable()
4516           {
4517             @Override
4518             public void run()
4519             {
4520               try
4521               {
4522                 webService.removeAll();
4523                 // first, add discovered services onto the webservices menu
4524                 if (wsmenu.size() > 0)
4525                 {
4526                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4527                   {
4528                     webService.add(wsmenu.get(i));
4529                   }
4530                 }
4531                 else
4532                 {
4533                   webService.add(me.webServiceNoServices);
4534                 }
4535                 // TODO: move into separate menu builder class.
4536                 boolean new_sspred = false;
4537                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4538                 {
4539                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4540                   if (jws2servs != null)
4541                   {
4542                     if (jws2servs.hasServices())
4543                     {
4544                       jws2servs.attachWSMenuEntry(webService, me);
4545                       for (Jws2Instance sv : jws2servs.getServices())
4546                       {
4547                         if (sv.description.toLowerCase().contains("jpred"))
4548                         {
4549                           for (JMenuItem jmi : legacyItems)
4550                           {
4551                             jmi.setVisible(false);
4552                           }
4553                         }
4554                       }
4555
4556                     }
4557                     if (jws2servs.isRunning())
4558                     {
4559                       JMenuItem tm = new JMenuItem(
4560                               "Still discovering JABA Services");
4561                       tm.setEnabled(false);
4562                       webService.add(tm);
4563                     }
4564                   }
4565                 }
4566                 build_urlServiceMenu(me.webService);
4567                 build_fetchdbmenu(webService);
4568                 for (JMenu item : wsmenu)
4569                 {
4570                   if (item.getItemCount() == 0)
4571                   {
4572                     item.setEnabled(false);
4573                   }
4574                   else
4575                   {
4576                     item.setEnabled(true);
4577                   }
4578                 }
4579               } catch (Exception e)
4580               {
4581                 Cache.log
4582                         .debug("Exception during web service menu building process.",
4583                                 e);
4584               }
4585             }
4586           });
4587         } catch (Exception e)
4588         {
4589         }
4590         buildingMenu = false;
4591       }
4592     }).start();
4593
4594   }
4595
4596   /**
4597    * construct any groupURL type service menu entries.
4598    *
4599    * @param webService
4600    */
4601   private void build_urlServiceMenu(JMenu webService)
4602   {
4603     // TODO: remove this code when 2.7 is released
4604     // DEBUG - alignmentView
4605     /*
4606      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4607      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4608      *
4609      * @Override public void actionPerformed(ActionEvent e) {
4610      * jalview.datamodel.AlignmentView
4611      * .testSelectionViews(af.viewport.getAlignment(),
4612      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4613      *
4614      * }); webService.add(testAlView);
4615      */
4616     // TODO: refactor to RestClient discoverer and merge menu entries for
4617     // rest-style services with other types of analysis/calculation service
4618     // SHmmr test client - still being implemented.
4619     // DEBUG - alignmentView
4620
4621     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4622             .getRestClients())
4623     {
4624       client.attachWSMenuEntry(
4625               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4626               this);
4627     }
4628   }
4629
4630   /**
4631    * Searches the alignment sequences for xRefs and builds the Show
4632    * Cross-References menu (formerly called Show Products), with database
4633    * sources for which cross-references are found (protein sources for a
4634    * nucleotide alignment and vice versa)
4635    *
4636    * @return true if Show Cross-references menu should be enabled
4637    */
4638   public boolean canShowProducts()
4639   {
4640     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4641     AlignmentI dataset = viewport.getAlignment().getDataset();
4642
4643     showProducts.removeAll();
4644     final boolean dna = viewport.getAlignment().isNucleotide();
4645
4646     if (seqs == null || seqs.length == 0)
4647     {
4648       // nothing to see here.
4649       return false;
4650     }
4651
4652     boolean showp = false;
4653     try
4654     {
4655       List<String> ptypes = new CrossRef(seqs, dataset)
4656               .findXrefSourcesForSequences(dna);
4657
4658       for (final String source : ptypes)
4659       {
4660         showp = true;
4661         final AlignFrame af = this;
4662         JMenuItem xtype = new JMenuItem(source);
4663         xtype.addActionListener(new ActionListener()
4664         {
4665           @Override
4666           public void actionPerformed(ActionEvent e)
4667           {
4668             showProductsFor(af.viewport.getSequenceSelection(), dna, source);
4669           }
4670         });
4671         showProducts.add(xtype);
4672       }
4673       showProducts.setVisible(showp);
4674       showProducts.setEnabled(showp);
4675     } catch (Exception e)
4676     {
4677       Cache.log
4678               .warn("canShowProducts threw an exception - please report to help@jalview.org",
4679                       e);
4680       return false;
4681     }
4682     return showp;
4683   }
4684
4685   /**
4686    * Finds and displays cross-references for the selected sequences (protein
4687    * products for nucleotide sequences, dna coding sequences for peptides).
4688    *
4689    * @param sel
4690    *          the sequences to show cross-references for
4691    * @param dna
4692    *          true if from a nucleotide alignment (so showing proteins)
4693    * @param source
4694    *          the database to show cross-references for
4695    */
4696   protected void showProductsFor(final SequenceI[] sel,
4697           final boolean _odna, final String source)
4698   {
4699     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4700             .start();
4701   }
4702
4703   /**
4704    * Construct and display a new frame containing the translation of this
4705    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4706    */
4707   @Override
4708   public void showTranslation_actionPerformed(ActionEvent e)
4709   {
4710     AlignmentI al = null;
4711     try
4712     {
4713       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4714
4715       al = dna.translateCdna();
4716     } catch (Exception ex)
4717     {
4718       jalview.bin.Cache.log.error(
4719               "Exception during translation. Please report this !", ex);
4720       final String msg = MessageManager
4721               .getString("label.error_when_translating_sequences_submit_bug_report");
4722       final String errorTitle = MessageManager
4723               .getString("label.implementation_error")
4724               + MessageManager.getString("label.translation_failed");
4725       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4726               JvOptionPane.ERROR_MESSAGE);
4727       return;
4728     }
4729     if (al == null || al.getHeight() == 0)
4730     {
4731       final String msg = MessageManager
4732               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4733       final String errorTitle = MessageManager
4734               .getString("label.translation_failed");
4735       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4736               JvOptionPane.WARNING_MESSAGE);
4737     }
4738     else
4739     {
4740       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4741       af.setFileFormat(this.currentFileFormat);
4742       final String newTitle = MessageManager.formatMessage(
4743               "label.translation_of_params",
4744               new Object[] { this.getTitle() });
4745       af.setTitle(newTitle);
4746       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4747       {
4748         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4749         viewport.openSplitFrame(af, new Alignment(seqs));
4750       }
4751       else
4752       {
4753         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4754                 DEFAULT_HEIGHT);
4755       }
4756     }
4757   }
4758
4759   /**
4760    * Set the file format
4761    *
4762    * @param format
4763    */
4764   public void setFileFormat(FileFormatI format)
4765   {
4766     this.currentFileFormat = format;
4767   }
4768
4769   /**
4770    * Try to load a features file onto the alignment.
4771    *
4772    * @param file
4773    *          contents or path to retrieve file
4774    * @param sourceType
4775    *          access mode of file (see jalview.io.AlignFile)
4776    * @return true if features file was parsed correctly.
4777    */
4778   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4779   {
4780     return avc.parseFeaturesFile(file, sourceType,
4781             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4782
4783   }
4784
4785   @Override
4786   public void refreshFeatureUI(boolean enableIfNecessary)
4787   {
4788     // note - currently this is only still here rather than in the controller
4789     // because of the featureSettings hard reference that is yet to be
4790     // abstracted
4791     if (enableIfNecessary)
4792     {
4793       viewport.setShowSequenceFeatures(true);
4794       showSeqFeatures.setSelected(true);
4795     }
4796
4797   }
4798
4799   @Override
4800   public void dragEnter(DropTargetDragEvent evt)
4801   {
4802   }
4803
4804   @Override
4805   public void dragExit(DropTargetEvent evt)
4806   {
4807   }
4808
4809   @Override
4810   public void dragOver(DropTargetDragEvent evt)
4811   {
4812   }
4813
4814   @Override
4815   public void dropActionChanged(DropTargetDragEvent evt)
4816   {
4817   }
4818
4819   @Override
4820   public void drop(DropTargetDropEvent evt)
4821   {
4822     // JAL-1552 - acceptDrop required before getTransferable call for
4823     // Java's Transferable for native dnd
4824     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4825     Transferable t = evt.getTransferable();
4826     List<String> files = new ArrayList<String>();
4827     List<DataSourceType> protocols = new ArrayList<DataSourceType>();
4828
4829     try
4830     {
4831       Desktop.transferFromDropTarget(files, protocols, evt, t);
4832     } catch (Exception e)
4833     {
4834       e.printStackTrace();
4835     }
4836     if (files != null)
4837     {
4838       try
4839       {
4840         // check to see if any of these files have names matching sequences in
4841         // the alignment
4842         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4843                 .getAlignment().getSequencesArray());
4844         /**
4845          * Object[] { String,SequenceI}
4846          */
4847         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4848         ArrayList<String> filesnotmatched = new ArrayList<String>();
4849         for (int i = 0; i < files.size(); i++)
4850         {
4851           String file = files.get(i).toString();
4852           String pdbfn = "";
4853           DataSourceType protocol = FormatAdapter.checkProtocol(file);
4854           if (protocol == DataSourceType.FILE)
4855           {
4856             File fl = new File(file);
4857             pdbfn = fl.getName();
4858           }
4859           else if (protocol == DataSourceType.URL)
4860           {
4861             URL url = new URL(file);
4862             pdbfn = url.getFile();
4863           }
4864           if (pdbfn.length() > 0)
4865           {
4866             // attempt to find a match in the alignment
4867             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4868             int l = 0, c = pdbfn.indexOf(".");
4869             while (mtch == null && c != -1)
4870             {
4871               do
4872               {
4873                 l = c;
4874               } while ((c = pdbfn.indexOf(".", l)) > l);
4875               if (l > -1)
4876               {
4877                 pdbfn = pdbfn.substring(0, l);
4878               }
4879               mtch = idm.findAllIdMatches(pdbfn);
4880             }
4881             if (mtch != null)
4882             {
4883               FileFormatI type = null;
4884               try
4885               {
4886                 type = new IdentifyFile().identify(file, protocol);
4887               } catch (Exception ex)
4888               {
4889                 type = null;
4890               }
4891               if (type != null && type.isStructureFile())
4892               {
4893                 filesmatched.add(new Object[] { file, protocol, mtch });
4894                 continue;
4895               }
4896             }
4897             // File wasn't named like one of the sequences or wasn't a PDB file.
4898             filesnotmatched.add(file);
4899           }
4900         }
4901         int assocfiles = 0;
4902         if (filesmatched.size() > 0)
4903         {
4904           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4905                   || JvOptionPane
4906                           .showConfirmDialog(
4907                                   this,
4908                                   MessageManager
4909                                           .formatMessage(
4910                                                   "label.automatically_associate_structure_files_with_sequences_same_name",
4911                                                   new Object[] { Integer
4912                                                           .valueOf(
4913                                                                   filesmatched
4914                                                                           .size())
4915                                                           .toString() }),
4916                                   MessageManager
4917                                           .getString("label.automatically_associate_structure_files_by_name"),
4918                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
4919
4920           {
4921             for (Object[] fm : filesmatched)
4922             {
4923               // try and associate
4924               // TODO: may want to set a standard ID naming formalism for
4925               // associating PDB files which have no IDs.
4926               for (SequenceI toassoc : (SequenceI[]) fm[2])
4927               {
4928                 PDBEntry pe = new AssociatePdbFileWithSeq()
4929                         .associatePdbWithSeq((String) fm[0],
4930                                 (DataSourceType) fm[1], toassoc, false,
4931                                 Desktop.instance);
4932                 if (pe != null)
4933                 {
4934                   System.err.println("Associated file : "
4935                           + ((String) fm[0]) + " with "
4936                           + toassoc.getDisplayId(true));
4937                   assocfiles++;
4938                 }
4939               }
4940               alignPanel.paintAlignment(true);
4941             }
4942           }
4943         }
4944         if (filesnotmatched.size() > 0)
4945         {
4946           if (assocfiles > 0
4947                   && (Cache.getDefault(
4948                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
4949                           .showConfirmDialog(
4950                                   this,
4951                                   "<html>"
4952                                           + MessageManager
4953                                                   .formatMessage(
4954                                                           "label.ignore_unmatched_dropped_files_info",
4955                                                           new Object[] { Integer
4956                                                                   .valueOf(
4957                                                                           filesnotmatched
4958                                                                                   .size())
4959                                                                   .toString() })
4960                                           + "</html>",
4961                                   MessageManager
4962                                           .getString("label.ignore_unmatched_dropped_files"),
4963                                   JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4964           {
4965             return;
4966           }
4967           for (String fn : filesnotmatched)
4968           {
4969             loadJalviewDataFile(fn, null, null, null);
4970           }
4971
4972         }
4973       } catch (Exception ex)
4974       {
4975         ex.printStackTrace();
4976       }
4977     }
4978   }
4979
4980   /**
4981    * Attempt to load a "dropped" file or URL string: First by testing whether
4982    * it's an Annotation file, then a JNet file, and finally a features file. If
4983    * all are false then the user may have dropped an alignment file onto this
4984    * AlignFrame.
4985    *
4986    * @param file
4987    *          either a filename or a URL string.
4988    */
4989   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4990           FileFormatI format, SequenceI assocSeq)
4991   {
4992     try
4993     {
4994       if (sourceType == null)
4995       {
4996         sourceType = FormatAdapter.checkProtocol(file);
4997       }
4998       // if the file isn't identified, or not positively identified as some
4999       // other filetype (PFAM is default unidentified alignment file type) then
5000       // try to parse as annotation.
5001       boolean isAnnotation = (format == null || FileFormat.Pfam
5002               .equals(format)) ? new AnnotationFile()
5003               .annotateAlignmentView(viewport, file, sourceType) : false;
5004
5005       if (!isAnnotation)
5006       {
5007         // first see if its a T-COFFEE score file
5008         TCoffeeScoreFile tcf = null;
5009         try
5010         {
5011           tcf = new TCoffeeScoreFile(file, sourceType);
5012           if (tcf.isValid())
5013           {
5014             if (tcf.annotateAlignment(viewport.getAlignment(), true))
5015             {
5016               tcoffeeColour.setEnabled(true);
5017               tcoffeeColour.setSelected(true);
5018               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
5019               isAnnotation = true;
5020               statusBar
5021                       .setText(MessageManager
5022                               .getString("label.successfully_pasted_tcoffee_scores_to_alignment"));
5023             }
5024             else
5025             {
5026               // some problem - if no warning its probable that the ID matching
5027               // process didn't work
5028               JvOptionPane
5029                       .showMessageDialog(
5030                               Desktop.desktop,
5031                               tcf.getWarningMessage() == null ? MessageManager
5032                                       .getString("label.check_file_matches_sequence_ids_alignment")
5033                                       : tcf.getWarningMessage(),
5034                               MessageManager
5035                                       .getString("label.problem_reading_tcoffee_score_file"),
5036                               JvOptionPane.WARNING_MESSAGE);
5037             }
5038           }
5039           else
5040           {
5041             tcf = null;
5042           }
5043         } catch (Exception x)
5044         {
5045           Cache.log
5046                   .debug("Exception when processing data source as T-COFFEE score file",
5047                           x);
5048           tcf = null;
5049         }
5050         if (tcf == null)
5051         {
5052           // try to see if its a JNet 'concise' style annotation file *before*
5053           // we
5054           // try to parse it as a features file
5055           if (format == null)
5056           {
5057             format = new IdentifyFile().identify(file, sourceType);
5058           }
5059           if (FileFormat.Jnet.equals(format))
5060           {
5061             JPredFile predictions = new JPredFile(
5062                     file, sourceType);
5063             new JnetAnnotationMaker();
5064             JnetAnnotationMaker.add_annotation(predictions,
5065                     viewport.getAlignment(), 0, false);
5066             SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
5067             viewport.getAlignment().setSeqrep(repseq);
5068             ColumnSelection cs = new ColumnSelection();
5069             cs.hideInsertionsFor(repseq);
5070             viewport.setColumnSelection(cs);
5071             isAnnotation = true;
5072           }
5073           // else if (IdentifyFile.FeaturesFile.equals(format))
5074           else if (FileFormat.Features.equals(format))
5075           {
5076             if (parseFeaturesFile(file, sourceType))
5077             {
5078               alignPanel.paintAlignment(true);
5079             }
5080           }
5081           else
5082           {
5083             new FileLoader().LoadFile(viewport, file, sourceType, format);
5084           }
5085         }
5086       }
5087       if (isAnnotation)
5088       {
5089
5090         alignPanel.adjustAnnotationHeight();
5091         viewport.updateSequenceIdColours();
5092         buildSortByAnnotationScoresMenu();
5093         alignPanel.paintAlignment(true);
5094       }
5095     } catch (Exception ex)
5096     {
5097       ex.printStackTrace();
5098     } catch (OutOfMemoryError oom)
5099     {
5100       try
5101       {
5102         System.gc();
5103       } catch (Exception x)
5104       {
5105       }
5106       new OOMWarning(
5107               "loading data "
5108                       + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
5109                               : "using " + sourceType + " from " + file)
5110                               : ".")
5111                       + (format != null ? "(parsing as '" + format
5112                               + "' file)" : ""), oom, Desktop.desktop);
5113     }
5114   }
5115
5116   /**
5117    * Method invoked by the ChangeListener on the tabbed pane, in other words
5118    * when a different tabbed pane is selected by the user or programmatically.
5119    */
5120   @Override
5121   public void tabSelectionChanged(int index)
5122   {
5123     if (index > -1)
5124     {
5125       alignPanel = alignPanels.get(index);
5126       viewport = alignPanel.av;
5127       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
5128       setMenusFromViewport(viewport);
5129     }
5130
5131     /*
5132      * If there is a frame linked to this one in a SplitPane, switch it to the
5133      * same view tab index. No infinite recursion of calls should happen, since
5134      * tabSelectionChanged() should not get invoked on setting the selected
5135      * index to an unchanged value. Guard against setting an invalid index
5136      * before the new view peer tab has been created.
5137      */
5138     final AlignViewportI peer = viewport.getCodingComplement();
5139     if (peer != null)
5140     {
5141       AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
5142       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5143       {
5144         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5145       }
5146     }
5147   }
5148
5149   /**
5150    * On right mouse click on view tab, prompt for and set new view name.
5151    */
5152   @Override
5153   public void tabbedPane_mousePressed(MouseEvent e)
5154   {
5155     if (e.isPopupTrigger())
5156     {
5157       String msg = MessageManager.getString("label.enter_view_name");
5158       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
5159               JvOptionPane.QUESTION_MESSAGE);
5160
5161       if (reply != null)
5162       {
5163         viewport.viewName = reply;
5164         // TODO warn if reply is in getExistingViewNames()?
5165         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5166       }
5167     }
5168   }
5169
5170   public AlignViewport getCurrentView()
5171   {
5172     return viewport;
5173   }
5174
5175   /**
5176    * Open the dialog for regex description parsing.
5177    */
5178   @Override
5179   protected void extractScores_actionPerformed(ActionEvent e)
5180   {
5181     ParseProperties pp = new jalview.analysis.ParseProperties(
5182             viewport.getAlignment());
5183     // TODO: verify regex and introduce GUI dialog for version 2.5
5184     // if (pp.getScoresFromDescription("col", "score column ",
5185     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5186     // true)>0)
5187     if (pp.getScoresFromDescription("description column",
5188             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5189     {
5190       buildSortByAnnotationScoresMenu();
5191     }
5192   }
5193
5194   /*
5195    * (non-Javadoc)
5196    *
5197    * @see
5198    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5199    * )
5200    */
5201   @Override
5202   protected void showDbRefs_actionPerformed(ActionEvent e)
5203   {
5204     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5205   }
5206
5207   /*
5208    * (non-Javadoc)
5209    *
5210    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5211    * ActionEvent)
5212    */
5213   @Override
5214   protected void showNpFeats_actionPerformed(ActionEvent e)
5215   {
5216     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5217   }
5218
5219   /**
5220    * find the viewport amongst the tabs in this alignment frame and close that
5221    * tab
5222    *
5223    * @param av
5224    */
5225   public boolean closeView(AlignViewportI av)
5226   {
5227     if (viewport == av)
5228     {
5229       this.closeMenuItem_actionPerformed(false);
5230       return true;
5231     }
5232     Component[] comp = tabbedPane.getComponents();
5233     for (int i = 0; comp != null && i < comp.length; i++)
5234     {
5235       if (comp[i] instanceof AlignmentPanel)
5236       {
5237         if (((AlignmentPanel) comp[i]).av == av)
5238         {
5239           // close the view.
5240           closeView((AlignmentPanel) comp[i]);
5241           return true;
5242         }
5243       }
5244     }
5245     return false;
5246   }
5247
5248   protected void build_fetchdbmenu(JMenu webService)
5249   {
5250     // Temporary hack - DBRef Fetcher always top level ws entry.
5251     // TODO We probably want to store a sequence database checklist in
5252     // preferences and have checkboxes.. rather than individual sources selected
5253     // here
5254     final JMenu rfetch = new JMenu(
5255             MessageManager.getString("action.fetch_db_references"));
5256     rfetch.setToolTipText(MessageManager
5257             .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5258     webService.add(rfetch);
5259
5260     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5261             MessageManager.getString("option.trim_retrieved_seqs"));
5262     trimrs.setToolTipText(MessageManager
5263             .getString("label.trim_retrieved_sequences"));
5264     trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
5265     trimrs.addActionListener(new ActionListener()
5266     {
5267       @Override
5268       public void actionPerformed(ActionEvent e)
5269       {
5270         trimrs.setSelected(trimrs.isSelected());
5271         Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
5272                 Boolean.valueOf(trimrs.isSelected()).toString());
5273       };
5274     });
5275     rfetch.add(trimrs);
5276     JMenuItem fetchr = new JMenuItem(
5277             MessageManager.getString("label.standard_databases"));
5278     fetchr.setToolTipText(MessageManager
5279             .getString("label.fetch_embl_uniprot"));
5280     fetchr.addActionListener(new ActionListener()
5281     {
5282
5283       @Override
5284       public void actionPerformed(ActionEvent e)
5285       {
5286         new Thread(new Runnable()
5287         {
5288           @Override
5289           public void run()
5290           {
5291             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5292                     .getAlignment().isNucleotide();
5293             DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
5294                     .getSequenceSelection(), alignPanel.alignFrame, null,
5295                     alignPanel.alignFrame.featureSettings, isNucleotide);
5296             dbRefFetcher.addListener(new FetchFinishedListenerI()
5297             {
5298               @Override
5299               public void finished()
5300               {
5301                 AlignFrame.this.setMenusForViewport();
5302               }
5303             });
5304             dbRefFetcher.fetchDBRefs(false);
5305           }
5306         }).start();
5307
5308       }
5309
5310     });
5311     rfetch.add(fetchr);
5312     final AlignFrame me = this;
5313     new Thread(new Runnable()
5314     {
5315       @Override
5316       public void run()
5317       {
5318         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5319                 .getSequenceFetcherSingleton(me);
5320         javax.swing.SwingUtilities.invokeLater(new Runnable()
5321         {
5322           @Override
5323           public void run()
5324           {
5325             String[] dbclasses = sf.getOrderedSupportedSources();
5326             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5327             // jalview.util.QuickSort.sort(otherdb, otherdb);
5328             List<DbSourceProxy> otherdb;
5329             JMenu dfetch = new JMenu();
5330             JMenu ifetch = new JMenu();
5331             JMenuItem fetchr = null;
5332             int comp = 0, icomp = 0, mcomp = 15;
5333             String mname = null;
5334             int dbi = 0;
5335             for (String dbclass : dbclasses)
5336             {
5337               otherdb = sf.getSourceProxy(dbclass);
5338               // add a single entry for this class, or submenu allowing 'fetch
5339               // all' or pick one
5340               if (otherdb == null || otherdb.size() < 1)
5341               {
5342                 continue;
5343               }
5344               // List<DbSourceProxy> dbs=otherdb;
5345               // otherdb=new ArrayList<DbSourceProxy>();
5346               // for (DbSourceProxy db:dbs)
5347               // {
5348               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5349               // }
5350               if (mname == null)
5351               {
5352                 mname = "From " + dbclass;
5353               }
5354               if (otherdb.size() == 1)
5355               {
5356                 final DbSourceProxy[] dassource = otherdb
5357                         .toArray(new DbSourceProxy[0]);
5358                 DbSourceProxy src = otherdb.get(0);
5359                 fetchr = new JMenuItem(src.getDbSource());
5360                 fetchr.addActionListener(new ActionListener()
5361                 {
5362
5363                   @Override
5364                   public void actionPerformed(ActionEvent e)
5365                   {
5366                     new Thread(new Runnable()
5367                     {
5368
5369                       @Override
5370                       public void run()
5371                       {
5372                         boolean isNucleotide = alignPanel.alignFrame
5373                                 .getViewport().getAlignment()
5374                                 .isNucleotide();
5375                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5376                                 alignPanel.av.getSequenceSelection(),
5377                                 alignPanel.alignFrame, dassource,
5378                                 alignPanel.alignFrame.featureSettings,
5379                                 isNucleotide);
5380                         dbRefFetcher
5381                                 .addListener(new FetchFinishedListenerI()
5382                                 {
5383                                   @Override
5384                                   public void finished()
5385                                   {
5386                                     AlignFrame.this.setMenusForViewport();
5387                                   }
5388                                 });
5389                         dbRefFetcher.fetchDBRefs(false);
5390                       }
5391                     }).start();
5392                   }
5393
5394                 });
5395                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5396                         MessageManager.formatMessage(
5397                                 "label.fetch_retrieve_from",
5398                                 new Object[] { src.getDbName() })));
5399                 dfetch.add(fetchr);
5400                 comp++;
5401               }
5402               else
5403               {
5404                 final DbSourceProxy[] dassource = otherdb
5405                         .toArray(new DbSourceProxy[0]);
5406                 // fetch all entry
5407                 DbSourceProxy src = otherdb.get(0);
5408                 fetchr = new JMenuItem(MessageManager.formatMessage(
5409                         "label.fetch_all_param",
5410                         new Object[] { src.getDbSource() }));
5411                 fetchr.addActionListener(new ActionListener()
5412                 {
5413                   @Override
5414                   public void actionPerformed(ActionEvent e)
5415                   {
5416                     new Thread(new Runnable()
5417                     {
5418
5419                       @Override
5420                       public void run()
5421                       {
5422                         boolean isNucleotide = alignPanel.alignFrame
5423                                 .getViewport().getAlignment()
5424                                 .isNucleotide();
5425                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5426                                 alignPanel.av.getSequenceSelection(),
5427                                 alignPanel.alignFrame, dassource,
5428                                 alignPanel.alignFrame.featureSettings,
5429                                 isNucleotide);
5430                         dbRefFetcher
5431                                 .addListener(new FetchFinishedListenerI()
5432                                 {
5433                                   @Override
5434                                   public void finished()
5435                                   {
5436                                     AlignFrame.this.setMenusForViewport();
5437                                   }
5438                                 });
5439                         dbRefFetcher.fetchDBRefs(false);
5440                       }
5441                     }).start();
5442                   }
5443                 });
5444
5445                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5446                         MessageManager.formatMessage(
5447                                 "label.fetch_retrieve_from_all_sources",
5448                                 new Object[] {
5449                                     Integer.valueOf(otherdb.size())
5450                                             .toString(), src.getDbSource(),
5451                                     src.getDbName() })));
5452                 dfetch.add(fetchr);
5453                 comp++;
5454                 // and then build the rest of the individual menus
5455                 ifetch = new JMenu(MessageManager.formatMessage(
5456                         "label.source_from_db_source",
5457                         new Object[] { src.getDbSource() }));
5458                 icomp = 0;
5459                 String imname = null;
5460                 int i = 0;
5461                 for (DbSourceProxy sproxy : otherdb)
5462                 {
5463                   String dbname = sproxy.getDbName();
5464                   String sname = dbname.length() > 5 ? dbname.substring(0,
5465                           5) + "..." : dbname;
5466                   String msname = dbname.length() > 10 ? dbname.substring(
5467                           0, 10) + "..." : dbname;
5468                   if (imname == null)
5469                   {
5470                     imname = MessageManager.formatMessage(
5471                             "label.from_msname", new Object[] { sname });
5472                   }
5473                   fetchr = new JMenuItem(msname);
5474                   final DbSourceProxy[] dassrc = { sproxy };
5475                   fetchr.addActionListener(new ActionListener()
5476                   {
5477
5478                     @Override
5479                     public void actionPerformed(ActionEvent e)
5480                     {
5481                       new Thread(new Runnable()
5482                       {
5483
5484                         @Override
5485                         public void run()
5486                         {
5487                           boolean isNucleotide = alignPanel.alignFrame
5488                                   .getViewport().getAlignment()
5489                                   .isNucleotide();
5490                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5491                                   alignPanel.av.getSequenceSelection(),
5492                                   alignPanel.alignFrame, dassrc,
5493                                   alignPanel.alignFrame.featureSettings,
5494                                   isNucleotide);
5495                           dbRefFetcher
5496                                   .addListener(new FetchFinishedListenerI()
5497                                   {
5498                                     @Override
5499                                     public void finished()
5500                                     {
5501                                       AlignFrame.this.setMenusForViewport();
5502                                     }
5503                                   });
5504                           dbRefFetcher.fetchDBRefs(false);
5505                         }
5506                       }).start();
5507                     }
5508
5509                   });
5510                   fetchr.setToolTipText("<html>"
5511                           + MessageManager.formatMessage(
5512                                   "label.fetch_retrieve_from", new Object[]
5513                                   { dbname }));
5514                   ifetch.add(fetchr);
5515                   ++i;
5516                   if (++icomp >= mcomp || i == (otherdb.size()))
5517                   {
5518                     ifetch.setText(MessageManager.formatMessage(
5519                             "label.source_to_target", imname, sname));
5520                     dfetch.add(ifetch);
5521                     ifetch = new JMenu();
5522                     imname = null;
5523                     icomp = 0;
5524                     comp++;
5525                   }
5526                 }
5527               }
5528               ++dbi;
5529               if (comp >= mcomp || dbi >= (dbclasses.length))
5530               {
5531                 dfetch.setText(MessageManager.formatMessage(
5532                         "label.source_to_target", mname, dbclass));
5533                 rfetch.add(dfetch);
5534                 dfetch = new JMenu();
5535                 mname = null;
5536                 comp = 0;
5537               }
5538             }
5539           }
5540         });
5541       }
5542     }).start();
5543
5544   }
5545
5546   /**
5547    * Left justify the whole alignment.
5548    */
5549   @Override
5550   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5551   {
5552     AlignmentI al = viewport.getAlignment();
5553     al.justify(false);
5554     viewport.firePropertyChange("alignment", null, al);
5555   }
5556
5557   /**
5558    * Right justify the whole alignment.
5559    */
5560   @Override
5561   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5562   {
5563     AlignmentI al = viewport.getAlignment();
5564     al.justify(true);
5565     viewport.firePropertyChange("alignment", null, al);
5566   }
5567
5568   @Override
5569   public void setShowSeqFeatures(boolean b)
5570   {
5571     showSeqFeatures.setSelected(b);
5572     viewport.setShowSequenceFeatures(b);
5573   }
5574
5575   /*
5576    * (non-Javadoc)
5577    *
5578    * @see
5579    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5580    * awt.event.ActionEvent)
5581    */
5582   @Override
5583   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5584   {
5585     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5586     alignPanel.paintAlignment(true);
5587   }
5588
5589   /*
5590    * (non-Javadoc)
5591    *
5592    * @see
5593    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5594    * .ActionEvent)
5595    */
5596   @Override
5597   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5598   {
5599     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5600     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5601
5602   }
5603
5604   /*
5605    * (non-Javadoc)
5606    *
5607    * @see
5608    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5609    * .event.ActionEvent)
5610    */
5611   @Override
5612   protected void showGroupConservation_actionPerformed(ActionEvent e)
5613   {
5614     viewport.setShowGroupConservation(showGroupConservation.getState());
5615     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5616   }
5617
5618   /*
5619    * (non-Javadoc)
5620    *
5621    * @see
5622    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5623    * .event.ActionEvent)
5624    */
5625   @Override
5626   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5627   {
5628     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5629     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5630   }
5631
5632   /*
5633    * (non-Javadoc)
5634    *
5635    * @see
5636    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5637    * .event.ActionEvent)
5638    */
5639   @Override
5640   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5641   {
5642     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5643     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5644   }
5645
5646   @Override
5647   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5648   {
5649     showSequenceLogo.setState(true);
5650     viewport.setShowSequenceLogo(true);
5651     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5652     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5653   }
5654
5655   @Override
5656   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5657   {
5658     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5659   }
5660
5661   /*
5662    * (non-Javadoc)
5663    *
5664    * @see
5665    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5666    * .event.ActionEvent)
5667    */
5668   @Override
5669   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5670   {
5671     if (avc.makeGroupsFromSelection())
5672     {
5673       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5674       alignPanel.updateAnnotation();
5675       alignPanel.paintAlignment(true);
5676     }
5677   }
5678
5679   public void clearAlignmentSeqRep()
5680   {
5681     // TODO refactor alignmentseqrep to controller
5682     if (viewport.getAlignment().hasSeqrep())
5683     {
5684       viewport.getAlignment().setSeqrep(null);
5685       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5686       alignPanel.updateAnnotation();
5687       alignPanel.paintAlignment(true);
5688     }
5689   }
5690
5691   @Override
5692   protected void createGroup_actionPerformed(ActionEvent e)
5693   {
5694     if (avc.createGroup())
5695     {
5696       alignPanel.alignmentChanged();
5697     }
5698   }
5699
5700   @Override
5701   protected void unGroup_actionPerformed(ActionEvent e)
5702   {
5703     if (avc.unGroup())
5704     {
5705       alignPanel.alignmentChanged();
5706     }
5707   }
5708
5709   /**
5710    * make the given alignmentPanel the currently selected tab
5711    *
5712    * @param alignmentPanel
5713    */
5714   public void setDisplayedView(AlignmentPanel alignmentPanel)
5715   {
5716     if (!viewport.getSequenceSetId().equals(
5717             alignmentPanel.av.getSequenceSetId()))
5718     {
5719       throw new Error(
5720               MessageManager
5721                       .getString("error.implementation_error_cannot_show_view_alignment_frame"));
5722     }
5723     if (tabbedPane != null
5724             && tabbedPane.getTabCount() > 0
5725             && alignPanels.indexOf(alignmentPanel) != tabbedPane
5726                     .getSelectedIndex())
5727     {
5728       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5729     }
5730   }
5731
5732   /**
5733    * Action on selection of menu options to Show or Hide annotations.
5734    *
5735    * @param visible
5736    * @param forSequences
5737    *          update sequence-related annotations
5738    * @param forAlignment
5739    *          update non-sequence-related annotations
5740    */
5741   @Override
5742   protected void setAnnotationsVisibility(boolean visible,
5743           boolean forSequences, boolean forAlignment)
5744   {
5745     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5746             .getAlignmentAnnotation();
5747     if (anns == null)
5748     {
5749       return;
5750     }
5751     for (AlignmentAnnotation aa : anns)
5752     {
5753       /*
5754        * don't display non-positional annotations on an alignment
5755        */
5756       if (aa.annotations == null)
5757       {
5758         continue;
5759       }
5760       boolean apply = (aa.sequenceRef == null && forAlignment)
5761               || (aa.sequenceRef != null && forSequences);
5762       if (apply)
5763       {
5764         aa.visible = visible;
5765       }
5766     }
5767     alignPanel.validateAnnotationDimensions(true);
5768     alignPanel.alignmentChanged();
5769   }
5770
5771   /**
5772    * Store selected annotation sort order for the view and repaint.
5773    */
5774   @Override
5775   protected void sortAnnotations_actionPerformed()
5776   {
5777     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5778     this.alignPanel.av
5779             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5780     alignPanel.paintAlignment(true);
5781   }
5782
5783   /**
5784    *
5785    * @return alignment panels in this alignment frame
5786    */
5787   public List<? extends AlignmentViewPanel> getAlignPanels()
5788   {
5789     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5790   }
5791
5792   /**
5793    * Open a new alignment window, with the cDNA associated with this (protein)
5794    * alignment, aligned as is the protein.
5795    */
5796   protected void viewAsCdna_actionPerformed()
5797   {
5798     // TODO no longer a menu action - refactor as required
5799     final AlignmentI alignment = getViewport().getAlignment();
5800     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5801     if (mappings == null)
5802     {
5803       return;
5804     }
5805     List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
5806     for (SequenceI aaSeq : alignment.getSequences())
5807     {
5808       for (AlignedCodonFrame acf : mappings)
5809       {
5810         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5811         if (dnaSeq != null)
5812         {
5813           /*
5814            * There is a cDNA mapping for this protein sequence - add to new
5815            * alignment. It will share the same dataset sequence as other mapped
5816            * cDNA (no new mappings need to be created).
5817            */
5818           final Sequence newSeq = new Sequence(dnaSeq);
5819           newSeq.setDatasetSequence(dnaSeq);
5820           cdnaSeqs.add(newSeq);
5821         }
5822       }
5823     }
5824     if (cdnaSeqs.size() == 0)
5825     {
5826       // show a warning dialog no mapped cDNA
5827       return;
5828     }
5829     AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
5830             .size()]));
5831     AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5832             AlignFrame.DEFAULT_HEIGHT);
5833     cdna.alignAs(alignment);
5834     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5835             + this.title;
5836     Desktop.addInternalFrame(alignFrame, newtitle,
5837             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
5838   }
5839
5840   /**
5841    * Set visibility of dna/protein complement view (available when shown in a
5842    * split frame).
5843    *
5844    * @param show
5845    */
5846   @Override
5847   protected void showComplement_actionPerformed(boolean show)
5848   {
5849     SplitContainerI sf = getSplitViewContainer();
5850     if (sf != null)
5851     {
5852       sf.setComplementVisible(this, show);
5853     }
5854   }
5855
5856   /**
5857    * Generate the reverse (optionally complemented) of the selected sequences,
5858    * and add them to the alignment
5859    */
5860   @Override
5861   protected void showReverse_actionPerformed(boolean complement)
5862   {
5863     AlignmentI al = null;
5864     try
5865     {
5866       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5867       al = dna.reverseCdna(complement);
5868       viewport.addAlignment(al, "");
5869       addHistoryItem(new EditCommand(
5870               MessageManager.getString("label.add_sequences"),
5871               Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
5872               viewport.getAlignment()));
5873     } catch (Exception ex)
5874     {
5875       System.err.println(ex.getMessage());
5876       return;
5877     }
5878   }
5879
5880   /**
5881    * Try to run a script in the Groovy console, having first ensured that this
5882    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5883    * be targeted at this alignment.
5884    */
5885   @Override
5886   protected void runGroovy_actionPerformed()
5887   {
5888     Jalview.setCurrentAlignFrame(this);
5889     groovy.ui.Console console = Desktop.getGroovyConsole();
5890     if (console != null)
5891     {
5892       try
5893       {
5894         console.runScript();
5895       } catch (Exception ex)
5896       {
5897         System.err.println((ex.toString()));
5898         JvOptionPane
5899                 .showInternalMessageDialog(Desktop.desktop, MessageManager
5900                         .getString("label.couldnt_run_groovy_script"),
5901                         MessageManager
5902                                 .getString("label.groovy_support_failed"),
5903                         JvOptionPane.ERROR_MESSAGE);
5904       }
5905     }
5906     else
5907     {
5908       System.err.println("Can't run Groovy script as console not found");
5909     }
5910   }
5911
5912   /**
5913    * Hides columns containing (or not containing) a specified feature, provided
5914    * that would not leave all columns hidden
5915    *
5916    * @param featureType
5917    * @param columnsContaining
5918    * @return
5919    */
5920   public boolean hideFeatureColumns(String featureType,
5921           boolean columnsContaining)
5922   {
5923     boolean notForHiding = avc.markColumnsContainingFeatures(
5924             columnsContaining, false, false, featureType);
5925     if (notForHiding)
5926     {
5927       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5928               false, featureType))
5929       {
5930         getViewport().hideSelectedColumns();
5931         return true;
5932       }
5933     }
5934     return false;
5935   }
5936
5937   @Override
5938   protected void selectHighlightedColumns_actionPerformed(
5939           ActionEvent actionEvent)
5940   {
5941     // include key modifier check in case user selects from menu
5942     avc.markHighlightedColumns(
5943             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
5944             true,
5945             (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
5946   }
5947 }
5948
5949 class PrintThread extends Thread
5950 {
5951   AlignmentPanel ap;
5952
5953   public PrintThread(AlignmentPanel ap)
5954   {
5955     this.ap = ap;
5956   }
5957
5958   static PageFormat pf;
5959
5960   @Override
5961   public void run()
5962   {
5963     PrinterJob printJob = PrinterJob.getPrinterJob();
5964
5965     if (pf != null)
5966     {
5967       printJob.setPrintable(ap, pf);
5968     }
5969     else
5970     {
5971       printJob.setPrintable(ap);
5972     }
5973
5974     if (printJob.printDialog())
5975     {
5976       try
5977       {
5978         printJob.print();
5979       } catch (Exception PrintException)
5980       {
5981         PrintException.printStackTrace();
5982       }
5983     }
5984   }
5985 }