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