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