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
2403     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2404     {
2405       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2406     }
2407
2408     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2409     viewport.setSelectionGroup(sg);
2410     viewport.sendSelection();
2411     // JAL-2034 - should delegate to
2412     // alignPanel to decide if overview needs
2413     // updating.
2414     alignPanel.paintAlignment(false, false);
2415     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2416   }
2417
2418   /**
2419    * DOCUMENT ME!
2420    *
2421    * @param e
2422    *          DOCUMENT ME!
2423    */
2424   @Override
2425   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2426   {
2427     if (viewport.cursorMode)
2428     {
2429       alignPanel.getSeqPanel().keyboardNo1 = null;
2430       alignPanel.getSeqPanel().keyboardNo2 = null;
2431     }
2432     viewport.setSelectionGroup(null);
2433     viewport.getColumnSelection().clear();
2434     viewport.setSelectionGroup(null);
2435     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2436     // JAL-2034 - should delegate to
2437     // alignPanel to decide if overview needs
2438     // updating.
2439     alignPanel.paintAlignment(false, false);
2440     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2441     viewport.sendSelection();
2442   }
2443
2444   /**
2445    * DOCUMENT ME!
2446    *
2447    * @param e
2448    *          DOCUMENT ME!
2449    */
2450   @Override
2451   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2452   {
2453     SequenceGroup sg = viewport.getSelectionGroup();
2454
2455     if (sg == null)
2456     {
2457       selectAllSequenceMenuItem_actionPerformed(null);
2458
2459       return;
2460     }
2461
2462     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2463     {
2464       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2465     }
2466     // JAL-2034 - should delegate to
2467     // alignPanel to decide if overview needs
2468     // updating.
2469
2470     alignPanel.paintAlignment(true, false);
2471     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2472     viewport.sendSelection();
2473   }
2474
2475   @Override
2476   public void invertColSel_actionPerformed(ActionEvent e)
2477   {
2478     viewport.invertColumnSelection();
2479     alignPanel.paintAlignment(true, false);
2480     viewport.sendSelection();
2481   }
2482
2483   /**
2484    * DOCUMENT ME!
2485    *
2486    * @param e
2487    *          DOCUMENT ME!
2488    */
2489   @Override
2490   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2491   {
2492     trimAlignment(true);
2493   }
2494
2495   /**
2496    * DOCUMENT ME!
2497    *
2498    * @param e
2499    *          DOCUMENT ME!
2500    */
2501   @Override
2502   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2503   {
2504     trimAlignment(false);
2505   }
2506
2507   void trimAlignment(boolean trimLeft)
2508   {
2509     ColumnSelection colSel = viewport.getColumnSelection();
2510     int column;
2511
2512     if (!colSel.isEmpty())
2513     {
2514       if (trimLeft)
2515       {
2516         column = colSel.getMin();
2517       }
2518       else
2519       {
2520         column = colSel.getMax();
2521       }
2522
2523       SequenceI[] seqs;
2524       if (viewport.getSelectionGroup() != null)
2525       {
2526         seqs = viewport.getSelectionGroup()
2527                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2528       }
2529       else
2530       {
2531         seqs = viewport.getAlignment().getSequencesArray();
2532       }
2533
2534       TrimRegionCommand trimRegion;
2535       if (trimLeft)
2536       {
2537         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2538                 column, viewport.getAlignment());
2539         viewport.getRanges().setStartRes(0);
2540       }
2541       else
2542       {
2543         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2544                 column, viewport.getAlignment());
2545       }
2546
2547       statusBar.setText(MessageManager
2548               .formatMessage("label.removed_columns", new String[]
2549               { Integer.valueOf(trimRegion.getSize()).toString() }));
2550
2551       addHistoryItem(trimRegion);
2552
2553       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2554       {
2555         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2556                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2557         {
2558           viewport.getAlignment().deleteGroup(sg);
2559         }
2560       }
2561
2562       viewport.firePropertyChange("alignment", null,
2563               viewport.getAlignment().getSequences());
2564     }
2565   }
2566
2567   /**
2568    * DOCUMENT ME!
2569    *
2570    * @param e
2571    *          DOCUMENT ME!
2572    */
2573   @Override
2574   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2575   {
2576     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2577
2578     SequenceI[] seqs;
2579     if (viewport.getSelectionGroup() != null)
2580     {
2581       seqs = viewport.getSelectionGroup()
2582               .getSequencesAsArray(viewport.getHiddenRepSequences());
2583       start = viewport.getSelectionGroup().getStartRes();
2584       end = viewport.getSelectionGroup().getEndRes();
2585     }
2586     else
2587     {
2588       seqs = viewport.getAlignment().getSequencesArray();
2589     }
2590
2591     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2592             "Remove Gapped Columns", seqs, start, end,
2593             viewport.getAlignment());
2594
2595     addHistoryItem(removeGapCols);
2596
2597     statusBar.setText(MessageManager
2598             .formatMessage("label.removed_empty_columns", new Object[]
2599             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2600
2601     // This is to maintain viewport position on first residue
2602     // of first sequence
2603     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2604     ViewportRanges ranges = viewport.getRanges();
2605     int startRes = seq.findPosition(ranges.getStartRes());
2606     // ShiftList shifts;
2607     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2608     // edit.alColumnChanges=shifts.getInverse();
2609     // if (viewport.hasHiddenColumns)
2610     // viewport.getColumnSelection().compensateForEdits(shifts);
2611     ranges.setStartRes(seq.findIndex(startRes) - 1);
2612     viewport.firePropertyChange("alignment", null,
2613             viewport.getAlignment().getSequences());
2614
2615   }
2616
2617   /**
2618    * DOCUMENT ME!
2619    *
2620    * @param e
2621    *          DOCUMENT ME!
2622    */
2623   @Override
2624   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2625   {
2626     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2627
2628     SequenceI[] seqs;
2629     if (viewport.getSelectionGroup() != null)
2630     {
2631       seqs = viewport.getSelectionGroup()
2632               .getSequencesAsArray(viewport.getHiddenRepSequences());
2633       start = viewport.getSelectionGroup().getStartRes();
2634       end = viewport.getSelectionGroup().getEndRes();
2635     }
2636     else
2637     {
2638       seqs = viewport.getAlignment().getSequencesArray();
2639     }
2640
2641     // This is to maintain viewport position on first residue
2642     // of first sequence
2643     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2644     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2645
2646     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2647             viewport.getAlignment()));
2648
2649     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2650
2651     viewport.firePropertyChange("alignment", null,
2652             viewport.getAlignment().getSequences());
2653
2654   }
2655
2656   /**
2657    * DOCUMENT ME!
2658    *
2659    * @param e
2660    *          DOCUMENT ME!
2661    */
2662   @Override
2663   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2664   {
2665     viewport.setPadGaps(padGapsMenuitem.isSelected());
2666     viewport.firePropertyChange("alignment", null,
2667             viewport.getAlignment().getSequences());
2668   }
2669
2670   /**
2671    * DOCUMENT ME!
2672    *
2673    * @param e
2674    *          DOCUMENT ME!
2675    */
2676   @Override
2677   public void findMenuItem_actionPerformed(ActionEvent e)
2678   {
2679     new Finder();
2680   }
2681
2682   /**
2683    * Create a new view of the current alignment.
2684    */
2685   @Override
2686   public void newView_actionPerformed(ActionEvent e)
2687   {
2688     newView(null, true);
2689   }
2690
2691   /**
2692    * Creates and shows a new view of the current alignment.
2693    *
2694    * @param viewTitle
2695    *          title of newly created view; if null, one will be generated
2696    * @param copyAnnotation
2697    *          if true then duplicate all annnotation, groups and settings
2698    * @return new alignment panel, already displayed.
2699    */
2700   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2701   {
2702     /*
2703      * Create a new AlignmentPanel (with its own, new Viewport)
2704      */
2705     AlignmentPanel newap = new jalview.project.Jalview2XML()
2706             .copyAlignPanel(alignPanel);
2707     if (!copyAnnotation)
2708     {
2709       /*
2710        * remove all groups and annotation except for the automatic stuff
2711        */
2712       newap.av.getAlignment().deleteAllGroups();
2713       newap.av.getAlignment().deleteAllAnnotations(false);
2714     }
2715
2716     newap.av.setGatherViewsHere(false);
2717
2718     if (viewport.getViewName() == null)
2719     {
2720       viewport.setViewName(MessageManager
2721               .getString("label.view_name_original"));
2722     }
2723
2724     /*
2725      * Views share the same edits undo and redo stacks
2726      */
2727     newap.av.setHistoryList(viewport.getHistoryList());
2728     newap.av.setRedoList(viewport.getRedoList());
2729
2730     /*
2731      * Views share the same mappings; need to deregister any new mappings
2732      * created by copyAlignPanel, and register the new reference to the shared
2733      * mappings
2734      */
2735     newap.av.replaceMappings(viewport.getAlignment());
2736
2737     /*
2738      * start up cDNA consensus (if applicable) now mappings are in place
2739      */
2740     if (newap.av.initComplementConsensus())
2741     {
2742       newap.refresh(true); // adjust layout of annotations
2743     }
2744
2745     newap.av.setViewName(getNewViewName(viewTitle));
2746
2747     addAlignmentPanel(newap, true);
2748     newap.alignmentChanged();
2749
2750     if (alignPanels.size() == 2)
2751     {
2752       viewport.setGatherViewsHere(true);
2753     }
2754     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2755     return newap;
2756   }
2757
2758   /**
2759    * Make a new name for the view, ensuring it is unique within the current
2760    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2761    * these now use viewId. Unique view names are still desirable for usability.)
2762    *
2763    * @param viewTitle
2764    * @return
2765    */
2766   protected String getNewViewName(String viewTitle)
2767   {
2768     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2769     boolean addFirstIndex = false;
2770     if (viewTitle == null || viewTitle.trim().length() == 0)
2771     {
2772       viewTitle = MessageManager.getString("action.view");
2773       addFirstIndex = true;
2774     }
2775     else
2776     {
2777       index = 1;// we count from 1 if given a specific name
2778     }
2779     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2780
2781     List<Component> comps = PaintRefresher.components
2782             .get(viewport.getSequenceSetId());
2783
2784     List<String> existingNames = getExistingViewNames(comps);
2785
2786     while (existingNames.contains(newViewName))
2787     {
2788       newViewName = viewTitle + " " + (++index);
2789     }
2790     return newViewName;
2791   }
2792
2793   /**
2794    * Returns a list of distinct view names found in the given list of
2795    * components. View names are held on the viewport of an AlignmentPanel.
2796    *
2797    * @param comps
2798    * @return
2799    */
2800   protected List<String> getExistingViewNames(List<Component> comps)
2801   {
2802     List<String> existingNames = new ArrayList<>();
2803     for (Component comp : comps)
2804     {
2805       if (comp instanceof AlignmentPanel)
2806       {
2807         AlignmentPanel ap = (AlignmentPanel) comp;
2808         if (!existingNames.contains(ap.av.getViewName()))
2809         {
2810           existingNames.add(ap.av.getViewName());
2811         }
2812       }
2813     }
2814     return existingNames;
2815   }
2816
2817   /**
2818    * Explode tabbed views into separate windows.
2819    */
2820   @Override
2821   public void expandViews_actionPerformed(ActionEvent e)
2822   {
2823     Desktop.explodeViews(this);
2824   }
2825
2826   /**
2827    * Gather views in separate windows back into a tabbed presentation.
2828    */
2829   @Override
2830   public void gatherViews_actionPerformed(ActionEvent e)
2831   {
2832     Desktop.instance.gatherViews(this);
2833   }
2834
2835   /**
2836    * DOCUMENT ME!
2837    *
2838    * @param e
2839    *          DOCUMENT ME!
2840    */
2841   @Override
2842   public void font_actionPerformed(ActionEvent e)
2843   {
2844     new FontChooser(alignPanel);
2845   }
2846
2847   /**
2848    * DOCUMENT ME!
2849    *
2850    * @param e
2851    *          DOCUMENT ME!
2852    */
2853   @Override
2854   protected void seqLimit_actionPerformed(ActionEvent e)
2855   {
2856     viewport.setShowJVSuffix(seqLimits.isSelected());
2857
2858     alignPanel.getIdPanel().getIdCanvas()
2859             .setPreferredSize(alignPanel.calculateIdWidth());
2860     alignPanel.paintAlignment(true, false);
2861   }
2862
2863   @Override
2864   public void idRightAlign_actionPerformed(ActionEvent e)
2865   {
2866     viewport.setRightAlignIds(idRightAlign.isSelected());
2867     alignPanel.paintAlignment(false, false);
2868   }
2869
2870   @Override
2871   public void centreColumnLabels_actionPerformed(ActionEvent e)
2872   {
2873     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2874     alignPanel.paintAlignment(false, false);
2875   }
2876
2877   /*
2878    * (non-Javadoc)
2879    *
2880    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2881    */
2882   @Override
2883   protected void followHighlight_actionPerformed()
2884   {
2885     /*
2886      * Set the 'follow' flag on the Viewport (and scroll to position if now
2887      * true).
2888      */
2889     final boolean state = this.followHighlightMenuItem.getState();
2890     viewport.setFollowHighlight(state);
2891     if (state)
2892     {
2893       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2894     }
2895   }
2896
2897   /**
2898    * DOCUMENT ME!
2899    *
2900    * @param e
2901    *          DOCUMENT ME!
2902    */
2903   @Override
2904   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2905   {
2906     viewport.setColourText(colourTextMenuItem.isSelected());
2907     alignPanel.paintAlignment(false, false);
2908   }
2909
2910   /**
2911    * DOCUMENT ME!
2912    *
2913    * @param e
2914    *          DOCUMENT ME!
2915    */
2916   @Override
2917   public void wrapMenuItem_actionPerformed(ActionEvent e)
2918   {
2919     scaleAbove.setVisible(wrapMenuItem.isSelected());
2920     scaleLeft.setVisible(wrapMenuItem.isSelected());
2921     scaleRight.setVisible(wrapMenuItem.isSelected());
2922     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2923     alignPanel.updateLayout();
2924   }
2925
2926   @Override
2927   public void showAllSeqs_actionPerformed(ActionEvent e)
2928   {
2929     viewport.showAllHiddenSeqs();
2930   }
2931
2932   @Override
2933   public void showAllColumns_actionPerformed(ActionEvent e)
2934   {
2935     viewport.showAllHiddenColumns();
2936     alignPanel.paintAlignment(true, true);
2937     viewport.sendSelection();
2938   }
2939
2940   @Override
2941   public void hideSelSequences_actionPerformed(ActionEvent e)
2942   {
2943     viewport.hideAllSelectedSeqs();
2944   }
2945
2946   /**
2947    * called by key handler and the hide all/show all menu items
2948    *
2949    * @param toggleSeqs
2950    * @param toggleCols
2951    */
2952   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2953   {
2954
2955     boolean hide = false;
2956     SequenceGroup sg = viewport.getSelectionGroup();
2957     if (!toggleSeqs && !toggleCols)
2958     {
2959       // Hide everything by the current selection - this is a hack - we do the
2960       // invert and then hide
2961       // first check that there will be visible columns after the invert.
2962       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2963               && sg.getStartRes() <= sg.getEndRes()))
2964       {
2965         // now invert the sequence set, if required - empty selection implies
2966         // that no hiding is required.
2967         if (sg != null)
2968         {
2969           invertSequenceMenuItem_actionPerformed(null);
2970           sg = viewport.getSelectionGroup();
2971           toggleSeqs = true;
2972
2973         }
2974         viewport.expandColSelection(sg, true);
2975         // finally invert the column selection and get the new sequence
2976         // selection.
2977         invertColSel_actionPerformed(null);
2978         toggleCols = true;
2979       }
2980     }
2981
2982     if (toggleSeqs)
2983     {
2984       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2985       {
2986         hideSelSequences_actionPerformed(null);
2987         hide = true;
2988       }
2989       else if (!(toggleCols && viewport.hasSelectedColumns()))
2990       {
2991         showAllSeqs_actionPerformed(null);
2992       }
2993     }
2994
2995     if (toggleCols)
2996     {
2997       if (viewport.hasSelectedColumns())
2998       {
2999         hideSelColumns_actionPerformed(null);
3000         if (!toggleSeqs)
3001         {
3002           viewport.setSelectionGroup(sg);
3003         }
3004       }
3005       else if (!hide)
3006       {
3007         showAllColumns_actionPerformed(null);
3008       }
3009     }
3010   }
3011
3012   /*
3013    * (non-Javadoc)
3014    *
3015    * @see
3016    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3017    * event.ActionEvent)
3018    */
3019   @Override
3020   public void hideAllButSelection_actionPerformed(ActionEvent e)
3021   {
3022     toggleHiddenRegions(false, false);
3023     viewport.sendSelection();
3024   }
3025
3026   /*
3027    * (non-Javadoc)
3028    *
3029    * @see
3030    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3031    * .ActionEvent)
3032    */
3033   @Override
3034   public void hideAllSelection_actionPerformed(ActionEvent e)
3035   {
3036     SequenceGroup sg = viewport.getSelectionGroup();
3037     viewport.expandColSelection(sg, false);
3038     viewport.hideAllSelectedSeqs();
3039     viewport.hideSelectedColumns();
3040     alignPanel.paintAlignment(true, true);
3041     viewport.sendSelection();
3042   }
3043
3044   /*
3045    * (non-Javadoc)
3046    *
3047    * @see
3048    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3049    * ActionEvent)
3050    */
3051   @Override
3052   public void showAllhidden_actionPerformed(ActionEvent e)
3053   {
3054     viewport.showAllHiddenColumns();
3055     viewport.showAllHiddenSeqs();
3056     alignPanel.paintAlignment(true, true);
3057     viewport.sendSelection();
3058   }
3059
3060   @Override
3061   public void hideSelColumns_actionPerformed(ActionEvent e)
3062   {
3063     viewport.hideSelectedColumns();
3064     alignPanel.paintAlignment(true, true);
3065     viewport.sendSelection();
3066   }
3067
3068   @Override
3069   public void hiddenMarkers_actionPerformed(ActionEvent e)
3070   {
3071     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3072     repaint();
3073   }
3074
3075   /**
3076    * DOCUMENT ME!
3077    *
3078    * @param e
3079    *          DOCUMENT ME!
3080    */
3081   @Override
3082   protected void scaleAbove_actionPerformed(ActionEvent e)
3083   {
3084     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3085     // TODO: do we actually need to update overview for scale above change ?
3086     alignPanel.paintAlignment(true, false);
3087   }
3088
3089   /**
3090    * DOCUMENT ME!
3091    *
3092    * @param e
3093    *          DOCUMENT ME!
3094    */
3095   @Override
3096   protected void scaleLeft_actionPerformed(ActionEvent e)
3097   {
3098     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3099     alignPanel.paintAlignment(true, false);
3100   }
3101
3102   /**
3103    * DOCUMENT ME!
3104    *
3105    * @param e
3106    *          DOCUMENT ME!
3107    */
3108   @Override
3109   protected void scaleRight_actionPerformed(ActionEvent e)
3110   {
3111     viewport.setScaleRightWrapped(scaleRight.isSelected());
3112     alignPanel.paintAlignment(true, false);
3113   }
3114
3115   /**
3116    * DOCUMENT ME!
3117    *
3118    * @param e
3119    *          DOCUMENT ME!
3120    */
3121   @Override
3122   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3123   {
3124     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3125     alignPanel.paintAlignment(false, false);
3126   }
3127
3128   /**
3129    * DOCUMENT ME!
3130    *
3131    * @param e
3132    *          DOCUMENT ME!
3133    */
3134   @Override
3135   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3136   {
3137     viewport.setShowText(viewTextMenuItem.isSelected());
3138     alignPanel.paintAlignment(false, false);
3139   }
3140
3141   /**
3142    * DOCUMENT ME!
3143    *
3144    * @param e
3145    *          DOCUMENT ME!
3146    */
3147   @Override
3148   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3149   {
3150     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3151     alignPanel.paintAlignment(false, false);
3152   }
3153
3154   public FeatureSettings featureSettings;
3155
3156   @Override
3157   public FeatureSettingsControllerI getFeatureSettingsUI()
3158   {
3159     return featureSettings;
3160   }
3161
3162   @Override
3163   public void featureSettings_actionPerformed(ActionEvent e)
3164   {
3165     if (featureSettings != null)
3166     {
3167       featureSettings.close();
3168       featureSettings = null;
3169     }
3170     if (!showSeqFeatures.isSelected())
3171     {
3172       // make sure features are actually displayed
3173       showSeqFeatures.setSelected(true);
3174       showSeqFeatures_actionPerformed(null);
3175     }
3176     featureSettings = new FeatureSettings(this);
3177   }
3178
3179   /**
3180    * Set or clear 'Show Sequence Features'
3181    *
3182    * @param evt
3183    *          DOCUMENT ME!
3184    */
3185   @Override
3186   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3187   {
3188     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3189     alignPanel.paintAlignment(true, true);
3190   }
3191
3192   /**
3193    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3194    * the annotations panel as a whole.
3195    *
3196    * The options to show/hide all annotations should be enabled when the panel
3197    * is shown, and disabled when the panel is hidden.
3198    *
3199    * @param e
3200    */
3201   @Override
3202   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3203   {
3204     final boolean setVisible = annotationPanelMenuItem.isSelected();
3205     viewport.setShowAnnotation(setVisible);
3206     this.showAllSeqAnnotations.setEnabled(setVisible);
3207     this.hideAllSeqAnnotations.setEnabled(setVisible);
3208     this.showAllAlAnnotations.setEnabled(setVisible);
3209     this.hideAllAlAnnotations.setEnabled(setVisible);
3210     alignPanel.updateLayout();
3211   }
3212
3213   @Override
3214   public void alignmentProperties()
3215   {
3216     JEditorPane editPane = new JEditorPane("text/html", "");
3217     editPane.setEditable(false);
3218     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3219             .formatAsHtml();
3220     editPane.setText(
3221             MessageManager.formatMessage("label.html_content", new Object[]
3222             { contents.toString() }));
3223     JInternalFrame frame = new JInternalFrame();
3224     frame.getContentPane().add(new JScrollPane(editPane));
3225
3226     Desktop.addInternalFrame(frame, MessageManager
3227             .formatMessage("label.alignment_properties", new Object[]
3228             { getTitle() }), 500, 400);
3229   }
3230
3231   /**
3232    * DOCUMENT ME!
3233    *
3234    * @param e
3235    *          DOCUMENT ME!
3236    */
3237   @Override
3238   public void overviewMenuItem_actionPerformed(ActionEvent e)
3239   {
3240     if (alignPanel.overviewPanel != null)
3241     {
3242       return;
3243     }
3244
3245     JInternalFrame frame = new JInternalFrame();
3246     final OverviewPanel overview = new OverviewPanel(alignPanel);
3247     frame.setContentPane(overview);
3248     Desktop.addInternalFrame(frame, MessageManager
3249             .formatMessage("label.overview_params", new Object[]
3250             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3251             true, true);
3252     frame.pack();
3253     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3254     frame.addInternalFrameListener(
3255             new javax.swing.event.InternalFrameAdapter()
3256             {
3257               @Override
3258               public void internalFrameClosed(
3259                       javax.swing.event.InternalFrameEvent evt)
3260               {
3261                 overview.dispose();
3262                 alignPanel.setOverviewPanel(null);
3263               };
3264             });
3265     if (getKeyListeners().length > 0)
3266     {
3267       frame.addKeyListener(getKeyListeners()[0]);
3268     }
3269
3270     alignPanel.setOverviewPanel(overview);
3271   }
3272
3273   @Override
3274   public void textColour_actionPerformed()
3275   {
3276     new TextColourChooser().chooseColour(alignPanel, null);
3277   }
3278
3279   /*
3280    * public void covariationColour_actionPerformed() {
3281    * changeColour(new
3282    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3283    * ()[0])); }
3284    */
3285   @Override
3286   public void annotationColour_actionPerformed()
3287   {
3288     new AnnotationColourChooser(viewport, alignPanel);
3289   }
3290
3291   @Override
3292   public void annotationColumn_actionPerformed(ActionEvent e)
3293   {
3294     new AnnotationColumnChooser(viewport, alignPanel);
3295   }
3296
3297   /**
3298    * Action on the user checking or unchecking the option to apply the selected
3299    * colour scheme to all groups. If unchecked, groups may have their own
3300    * independent colour schemes.
3301    *
3302    * @param selected
3303    */
3304   @Override
3305   public void applyToAllGroups_actionPerformed(boolean selected)
3306   {
3307     viewport.setColourAppliesToAllGroups(selected);
3308   }
3309
3310   /**
3311    * Action on user selecting a colour from the colour menu
3312    *
3313    * @param name
3314    *          the name (not the menu item label!) of the colour scheme
3315    */
3316   @Override
3317   public void changeColour_actionPerformed(String name)
3318   {
3319     /*
3320      * 'User Defined' opens a panel to configure or load a
3321      * user-defined colour scheme
3322      */
3323     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3324     {
3325       new UserDefinedColours(alignPanel);
3326       return;
3327     }
3328
3329     /*
3330      * otherwise set the chosen colour scheme (or null for 'None')
3331      */
3332     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3333             viewport.getAlignment(), viewport.getHiddenRepSequences());
3334     changeColour(cs);
3335   }
3336
3337   /**
3338    * Actions on setting or changing the alignment colour scheme
3339    *
3340    * @param cs
3341    */
3342   @Override
3343   public void changeColour(ColourSchemeI cs)
3344   {
3345     // TODO: pull up to controller method
3346     ColourMenuHelper.setColourSelected(colourMenu, cs);
3347
3348     viewport.setGlobalColourScheme(cs);
3349
3350     alignPanel.paintAlignment(true, true);
3351   }
3352
3353   /**
3354    * Show the PID threshold slider panel
3355    */
3356   @Override
3357   protected void modifyPID_actionPerformed()
3358   {
3359     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3360             alignPanel.getViewName());
3361     SliderPanel.showPIDSlider();
3362   }
3363
3364   /**
3365    * Show the Conservation slider panel
3366    */
3367   @Override
3368   protected void modifyConservation_actionPerformed()
3369   {
3370     SliderPanel.setConservationSlider(alignPanel,
3371             viewport.getResidueShading(), alignPanel.getViewName());
3372     SliderPanel.showConservationSlider();
3373   }
3374
3375   /**
3376    * Action on selecting or deselecting (Colour) By Conservation
3377    */
3378   @Override
3379   public void conservationMenuItem_actionPerformed(boolean selected)
3380   {
3381     modifyConservation.setEnabled(selected);
3382     viewport.setConservationSelected(selected);
3383     viewport.getResidueShading().setConservationApplied(selected);
3384
3385     changeColour(viewport.getGlobalColourScheme());
3386     if (selected)
3387     {
3388       modifyConservation_actionPerformed();
3389     }
3390     else
3391     {
3392       SliderPanel.hideConservationSlider();
3393     }
3394   }
3395
3396   /**
3397    * Action on selecting or deselecting (Colour) Above PID Threshold
3398    */
3399   @Override
3400   public void abovePIDThreshold_actionPerformed(boolean selected)
3401   {
3402     modifyPID.setEnabled(selected);
3403     viewport.setAbovePIDThreshold(selected);
3404     if (!selected)
3405     {
3406       viewport.getResidueShading().setThreshold(0,
3407               viewport.isIgnoreGapsConsensus());
3408     }
3409
3410     changeColour(viewport.getGlobalColourScheme());
3411     if (selected)
3412     {
3413       modifyPID_actionPerformed();
3414     }
3415     else
3416     {
3417       SliderPanel.hidePIDSlider();
3418     }
3419   }
3420
3421   /**
3422    * DOCUMENT ME!
3423    *
3424    * @param e
3425    *          DOCUMENT ME!
3426    */
3427   @Override
3428   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3429   {
3430     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3431     AlignmentSorter.sortByPID(viewport.getAlignment(),
3432             viewport.getAlignment().getSequenceAt(0));
3433     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3434             viewport.getAlignment()));
3435     alignPanel.paintAlignment(true, false);
3436   }
3437
3438   /**
3439    * DOCUMENT ME!
3440    *
3441    * @param e
3442    *          DOCUMENT ME!
3443    */
3444   @Override
3445   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3446   {
3447     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3448     AlignmentSorter.sortByID(viewport.getAlignment());
3449     addHistoryItem(
3450             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3451     alignPanel.paintAlignment(true, false);
3452   }
3453
3454   /**
3455    * DOCUMENT ME!
3456    *
3457    * @param e
3458    *          DOCUMENT ME!
3459    */
3460   @Override
3461   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3462   {
3463     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3464     AlignmentSorter.sortByLength(viewport.getAlignment());
3465     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3466             viewport.getAlignment()));
3467     alignPanel.paintAlignment(true, false);
3468   }
3469
3470   /**
3471    * DOCUMENT ME!
3472    *
3473    * @param e
3474    *          DOCUMENT ME!
3475    */
3476   @Override
3477   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3478   {
3479     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3480     AlignmentSorter.sortByGroup(viewport.getAlignment());
3481     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3482             viewport.getAlignment()));
3483
3484     alignPanel.paintAlignment(true, false);
3485   }
3486
3487   /**
3488    * DOCUMENT ME!
3489    *
3490    * @param e
3491    *          DOCUMENT ME!
3492    */
3493   @Override
3494   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3495   {
3496     new RedundancyPanel(alignPanel, this);
3497   }
3498
3499   /**
3500    * DOCUMENT ME!
3501    *
3502    * @param e
3503    *          DOCUMENT ME!
3504    */
3505   @Override
3506   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3507   {
3508     if ((viewport.getSelectionGroup() == null)
3509             || (viewport.getSelectionGroup().getSize() < 2))
3510     {
3511       JvOptionPane.showInternalMessageDialog(this,
3512               MessageManager.getString(
3513                       "label.you_must_select_least_two_sequences"),
3514               MessageManager.getString("label.invalid_selection"),
3515               JvOptionPane.WARNING_MESSAGE);
3516     }
3517     else
3518     {
3519       JInternalFrame frame = new JInternalFrame();
3520       frame.setContentPane(new PairwiseAlignPanel(viewport));
3521       Desktop.addInternalFrame(frame,
3522               MessageManager.getString("action.pairwise_alignment"), 600,
3523               500);
3524     }
3525   }
3526
3527   @Override
3528   public void autoCalculate_actionPerformed(ActionEvent e)
3529   {
3530     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3531     if (viewport.autoCalculateConsensus)
3532     {
3533       viewport.firePropertyChange("alignment", null,
3534               viewport.getAlignment().getSequences());
3535     }
3536   }
3537
3538   @Override
3539   public void sortByTreeOption_actionPerformed(ActionEvent e)
3540   {
3541     viewport.sortByTree = sortByTree.isSelected();
3542   }
3543
3544   @Override
3545   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3546   {
3547     viewport.followSelection = listenToViewSelections.isSelected();
3548   }
3549
3550   /**
3551    * Constructs a tree panel and adds it to the desktop
3552    *
3553    * @param type
3554    *          tree type (NJ or AV)
3555    * @param modelName
3556    *          name of score model used to compute the tree
3557    * @param options
3558    *          parameters for the distance or similarity calculation
3559    */
3560   void newTreePanel(String type, String modelName,
3561           SimilarityParamsI options)
3562   {
3563     String frameTitle = "";
3564     TreePanel tp;
3565
3566     boolean onSelection = false;
3567     if (viewport.getSelectionGroup() != null
3568             && viewport.getSelectionGroup().getSize() > 0)
3569     {
3570       SequenceGroup sg = viewport.getSelectionGroup();
3571
3572       /* Decide if the selection is a column region */
3573       for (SequenceI _s : sg.getSequences())
3574       {
3575         if (_s.getLength() < sg.getEndRes())
3576         {
3577           JvOptionPane.showMessageDialog(Desktop.desktop,
3578                   MessageManager.getString(
3579                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3580                   MessageManager.getString(
3581                           "label.sequences_selection_not_aligned"),
3582                   JvOptionPane.WARNING_MESSAGE);
3583
3584           return;
3585         }
3586       }
3587       onSelection = true;
3588     }
3589     else
3590     {
3591       if (viewport.getAlignment().getHeight() < 2)
3592       {
3593         return;
3594       }
3595     }
3596
3597     tp = new TreePanel(alignPanel, type, modelName, options);
3598     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3599
3600     frameTitle += " from ";
3601
3602     if (viewport.getViewName() != null)
3603     {
3604       frameTitle += viewport.getViewName() + " of ";
3605     }
3606
3607     frameTitle += this.title;
3608
3609     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3610   }
3611
3612   /**
3613    * DOCUMENT ME!
3614    *
3615    * @param title
3616    *          DOCUMENT ME!
3617    * @param order
3618    *          DOCUMENT ME!
3619    */
3620   public void addSortByOrderMenuItem(String title,
3621           final AlignmentOrder order)
3622   {
3623     final JMenuItem item = new JMenuItem(MessageManager
3624             .formatMessage("action.by_title_param", new Object[]
3625             { title }));
3626     sort.add(item);
3627     item.addActionListener(new java.awt.event.ActionListener()
3628     {
3629       @Override
3630       public void actionPerformed(ActionEvent e)
3631       {
3632         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3633
3634         // TODO: JBPNote - have to map order entries to curent SequenceI
3635         // pointers
3636         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3637
3638         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3639                 viewport.getAlignment()));
3640
3641         alignPanel.paintAlignment(true, false);
3642       }
3643     });
3644   }
3645
3646   /**
3647    * Add a new sort by annotation score menu item
3648    *
3649    * @param sort
3650    *          the menu to add the option to
3651    * @param scoreLabel
3652    *          the label used to retrieve scores for each sequence on the
3653    *          alignment
3654    */
3655   public void addSortByAnnotScoreMenuItem(JMenu sort,
3656           final String scoreLabel)
3657   {
3658     final JMenuItem item = new JMenuItem(scoreLabel);
3659     sort.add(item);
3660     item.addActionListener(new java.awt.event.ActionListener()
3661     {
3662       @Override
3663       public void actionPerformed(ActionEvent e)
3664       {
3665         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3666         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3667                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3668         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3669                 viewport.getAlignment()));
3670         alignPanel.paintAlignment(true, false);
3671       }
3672     });
3673   }
3674
3675   /**
3676    * last hash for alignment's annotation array - used to minimise cost of
3677    * rebuild.
3678    */
3679   protected int _annotationScoreVectorHash;
3680
3681   /**
3682    * search the alignment and rebuild the sort by annotation score submenu the
3683    * last alignment annotation vector hash is stored to minimize cost of
3684    * rebuilding in subsequence calls.
3685    *
3686    */
3687   @Override
3688   public void buildSortByAnnotationScoresMenu()
3689   {
3690     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3691     {
3692       return;
3693     }
3694
3695     if (viewport.getAlignment().getAlignmentAnnotation()
3696             .hashCode() != _annotationScoreVectorHash)
3697     {
3698       sortByAnnotScore.removeAll();
3699       // almost certainly a quicker way to do this - but we keep it simple
3700       Hashtable scoreSorts = new Hashtable();
3701       AlignmentAnnotation aann[];
3702       for (SequenceI sqa : viewport.getAlignment().getSequences())
3703       {
3704         aann = sqa.getAnnotation();
3705         for (int i = 0; aann != null && i < aann.length; i++)
3706         {
3707           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3708           {
3709             scoreSorts.put(aann[i].label, aann[i].label);
3710           }
3711         }
3712       }
3713       Enumeration labels = scoreSorts.keys();
3714       while (labels.hasMoreElements())
3715       {
3716         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3717                 (String) labels.nextElement());
3718       }
3719       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3720       scoreSorts.clear();
3721
3722       _annotationScoreVectorHash = viewport.getAlignment()
3723               .getAlignmentAnnotation().hashCode();
3724     }
3725   }
3726
3727   /**
3728    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3729    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3730    * call. Listeners are added to remove the menu item when the treePanel is
3731    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3732    * modified.
3733    */
3734   @Override
3735   public void buildTreeSortMenu()
3736   {
3737     sortByTreeMenu.removeAll();
3738
3739     List<Component> comps = PaintRefresher.components
3740             .get(viewport.getSequenceSetId());
3741     List<TreePanel> treePanels = new ArrayList<>();
3742     for (Component comp : comps)
3743     {
3744       if (comp instanceof TreePanel)
3745       {
3746         treePanels.add((TreePanel) comp);
3747       }
3748     }
3749
3750     if (treePanels.size() < 1)
3751     {
3752       sortByTreeMenu.setVisible(false);
3753       return;
3754     }
3755
3756     sortByTreeMenu.setVisible(true);
3757
3758     for (final TreePanel tp : treePanels)
3759     {
3760       final JMenuItem item = new JMenuItem(tp.getTitle());
3761       item.addActionListener(new java.awt.event.ActionListener()
3762       {
3763         @Override
3764         public void actionPerformed(ActionEvent e)
3765         {
3766           tp.sortByTree_actionPerformed();
3767           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3768
3769         }
3770       });
3771
3772       sortByTreeMenu.add(item);
3773     }
3774   }
3775
3776   public boolean sortBy(AlignmentOrder alorder, String undoname)
3777   {
3778     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3779     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3780     if (undoname != null)
3781     {
3782       addHistoryItem(new OrderCommand(undoname, oldOrder,
3783               viewport.getAlignment()));
3784     }
3785     alignPanel.paintAlignment(true, false);
3786     return true;
3787   }
3788
3789   /**
3790    * Work out whether the whole set of sequences or just the selected set will
3791    * be submitted for multiple alignment.
3792    *
3793    */
3794   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3795   {
3796     // Now, check we have enough sequences
3797     AlignmentView msa = null;
3798
3799     if ((viewport.getSelectionGroup() != null)
3800             && (viewport.getSelectionGroup().getSize() > 1))
3801     {
3802       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3803       // some common interface!
3804       /*
3805        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3806        * SequenceI[sz = seqs.getSize(false)];
3807        *
3808        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3809        * seqs.getSequenceAt(i); }
3810        */
3811       msa = viewport.getAlignmentView(true);
3812     }
3813     else if (viewport.getSelectionGroup() != null
3814             && viewport.getSelectionGroup().getSize() == 1)
3815     {
3816       int option = JvOptionPane.showConfirmDialog(this,
3817               MessageManager.getString("warn.oneseq_msainput_selection"),
3818               MessageManager.getString("label.invalid_selection"),
3819               JvOptionPane.OK_CANCEL_OPTION);
3820       if (option == JvOptionPane.OK_OPTION)
3821       {
3822         msa = viewport.getAlignmentView(false);
3823       }
3824     }
3825     else
3826     {
3827       msa = viewport.getAlignmentView(false);
3828     }
3829     return msa;
3830   }
3831
3832   /**
3833    * Decides what is submitted to a secondary structure prediction service: the
3834    * first sequence in the alignment, or in the current selection, or, if the
3835    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3836    * region or the whole alignment. (where the first sequence in the set is the
3837    * one that the prediction will be for).
3838    */
3839   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3840   {
3841     AlignmentView seqs = null;
3842
3843     if ((viewport.getSelectionGroup() != null)
3844             && (viewport.getSelectionGroup().getSize() > 0))
3845     {
3846       seqs = viewport.getAlignmentView(true);
3847     }
3848     else
3849     {
3850       seqs = viewport.getAlignmentView(false);
3851     }
3852     // limit sequences - JBPNote in future - could spawn multiple prediction
3853     // jobs
3854     // TODO: viewport.getAlignment().isAligned is a global state - the local
3855     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3856     if (!viewport.getAlignment().isAligned(false))
3857     {
3858       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3859       // TODO: if seqs.getSequences().length>1 then should really have warned
3860       // user!
3861
3862     }
3863     return seqs;
3864   }
3865
3866   /**
3867    * DOCUMENT ME!
3868    *
3869    * @param e
3870    *          DOCUMENT ME!
3871    */
3872   @Override
3873   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3874   {
3875     // Pick the tree file
3876     JalviewFileChooser chooser = new JalviewFileChooser(
3877             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3878     chooser.setFileView(new JalviewFileView());
3879     chooser.setDialogTitle(
3880             MessageManager.getString("label.select_newick_like_tree_file"));
3881     chooser.setToolTipText(
3882             MessageManager.getString("label.load_tree_file"));
3883
3884     int value = chooser.showOpenDialog(null);
3885
3886     if (value == JalviewFileChooser.APPROVE_OPTION)
3887     {
3888       String filePath = chooser.getSelectedFile().getPath();
3889       Cache.setProperty("LAST_DIRECTORY", filePath);
3890       NewickFile fin = null;
3891       try
3892       {
3893         fin = new NewickFile(filePath, DataSourceType.FILE);
3894         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3895       } catch (Exception ex)
3896       {
3897         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3898                 MessageManager.getString("label.problem_reading_tree_file"),
3899                 JvOptionPane.WARNING_MESSAGE);
3900         ex.printStackTrace();
3901       }
3902       if (fin != null && fin.hasWarningMessage())
3903       {
3904         JvOptionPane.showMessageDialog(Desktop.desktop,
3905                 fin.getWarningMessage(),
3906                 MessageManager
3907                         .getString("label.possible_problem_with_tree_file"),
3908                 JvOptionPane.WARNING_MESSAGE);
3909       }
3910     }
3911   }
3912
3913   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3914   {
3915     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3916   }
3917
3918   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3919           int h, int x, int y)
3920   {
3921     return showNewickTree(nf, treeTitle, null, w, h, x, y);
3922   }
3923
3924   /**
3925    * Add a treeviewer for the tree extracted from a Newick file object to the
3926    * current alignment view
3927    *
3928    * @param nf
3929    *          the tree
3930    * @param title
3931    *          tree viewer title
3932    * @param input
3933    *          Associated alignment input data (or null)
3934    * @param w
3935    *          width
3936    * @param h
3937    *          height
3938    * @param x
3939    *          position
3940    * @param y
3941    *          position
3942    * @return TreePanel handle
3943    */
3944   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3945           AlignmentView input, int w, int h, int x, int y)
3946   {
3947     TreePanel tp = null;
3948
3949     try
3950     {
3951       nf.parse();
3952
3953       if (nf.getTree() != null)
3954       {
3955         tp = new TreePanel(alignPanel, nf, treeTitle, input);
3956
3957         tp.setSize(w, h);
3958
3959         if (x > 0 && y > 0)
3960         {
3961           tp.setLocation(x, y);
3962         }
3963
3964         Desktop.addInternalFrame(tp, treeTitle, w, h);
3965       }
3966     } catch (Exception ex)
3967     {
3968       ex.printStackTrace();
3969     }
3970
3971     return tp;
3972   }
3973
3974   private boolean buildingMenu = false;
3975
3976   /**
3977    * Generates menu items and listener event actions for web service clients
3978    *
3979    */
3980   public void BuildWebServiceMenu()
3981   {
3982     while (buildingMenu)
3983     {
3984       try
3985       {
3986         System.err.println("Waiting for building menu to finish.");
3987         Thread.sleep(10);
3988       } catch (Exception e)
3989       {
3990       }
3991     }
3992     final AlignFrame me = this;
3993     buildingMenu = true;
3994     new Thread(new Runnable()
3995     {
3996       @Override
3997       public void run()
3998       {
3999         final List<JMenuItem> legacyItems = new ArrayList<>();
4000         try
4001         {
4002           // System.err.println("Building ws menu again "
4003           // + Thread.currentThread());
4004           // TODO: add support for context dependent disabling of services based
4005           // on
4006           // alignment and current selection
4007           // TODO: add additional serviceHandle parameter to specify abstract
4008           // handler
4009           // class independently of AbstractName
4010           // TODO: add in rediscovery GUI function to restart discoverer
4011           // TODO: group services by location as well as function and/or
4012           // introduce
4013           // object broker mechanism.
4014           final Vector<JMenu> wsmenu = new Vector<>();
4015           final IProgressIndicator af = me;
4016
4017           /*
4018            * do not i18n these strings - they are hard-coded in class
4019            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4020            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4021            */
4022           final JMenu msawsmenu = new JMenu("Alignment");
4023           final JMenu secstrmenu = new JMenu(
4024                   "Secondary Structure Prediction");
4025           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4026           final JMenu analymenu = new JMenu("Analysis");
4027           final JMenu dismenu = new JMenu("Protein Disorder");
4028           // JAL-940 - only show secondary structure prediction services from
4029           // the legacy server
4030           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4031               // &&
4032           Discoverer.services != null && (Discoverer.services.size() > 0))
4033           {
4034             // TODO: refactor to allow list of AbstractName/Handler bindings to
4035             // be
4036             // stored or retrieved from elsewhere
4037             // No MSAWS used any more:
4038             // Vector msaws = null; // (Vector)
4039             // Discoverer.services.get("MsaWS");
4040             Vector secstrpr = (Vector) Discoverer.services
4041                     .get("SecStrPred");
4042             if (secstrpr != null)
4043             {
4044               // Add any secondary structure prediction services
4045               for (int i = 0, j = secstrpr.size(); i < j; i++)
4046               {
4047                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4048                         .get(i);
4049                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4050                         .getServiceClient(sh);
4051                 int p = secstrmenu.getItemCount();
4052                 impl.attachWSMenuEntry(secstrmenu, me);
4053                 int q = secstrmenu.getItemCount();
4054                 for (int litm = p; litm < q; litm++)
4055                 {
4056                   legacyItems.add(secstrmenu.getItem(litm));
4057                 }
4058               }
4059             }
4060           }
4061
4062           // Add all submenus in the order they should appear on the web
4063           // services menu
4064           wsmenu.add(msawsmenu);
4065           wsmenu.add(secstrmenu);
4066           wsmenu.add(dismenu);
4067           wsmenu.add(analymenu);
4068           // No search services yet
4069           // wsmenu.add(seqsrchmenu);
4070
4071           javax.swing.SwingUtilities.invokeLater(new Runnable()
4072           {
4073             @Override
4074             public void run()
4075             {
4076               try
4077               {
4078                 webService.removeAll();
4079                 // first, add discovered services onto the webservices menu
4080                 if (wsmenu.size() > 0)
4081                 {
4082                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4083                   {
4084                     webService.add(wsmenu.get(i));
4085                   }
4086                 }
4087                 else
4088                 {
4089                   webService.add(me.webServiceNoServices);
4090                 }
4091                 // TODO: move into separate menu builder class.
4092                 boolean new_sspred = false;
4093                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4094                 {
4095                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4096                   if (jws2servs != null)
4097                   {
4098                     if (jws2servs.hasServices())
4099                     {
4100                       jws2servs.attachWSMenuEntry(webService, me);
4101                       for (Jws2Instance sv : jws2servs.getServices())
4102                       {
4103                         if (sv.description.toLowerCase().contains("jpred"))
4104                         {
4105                           for (JMenuItem jmi : legacyItems)
4106                           {
4107                             jmi.setVisible(false);
4108                           }
4109                         }
4110                       }
4111
4112                     }
4113                     if (jws2servs.isRunning())
4114                     {
4115                       JMenuItem tm = new JMenuItem(
4116                               "Still discovering JABA Services");
4117                       tm.setEnabled(false);
4118                       webService.add(tm);
4119                     }
4120                   }
4121                 }
4122                 build_urlServiceMenu(me.webService);
4123                 build_fetchdbmenu(webService);
4124                 for (JMenu item : wsmenu)
4125                 {
4126                   if (item.getItemCount() == 0)
4127                   {
4128                     item.setEnabled(false);
4129                   }
4130                   else
4131                   {
4132                     item.setEnabled(true);
4133                   }
4134                 }
4135               } catch (Exception e)
4136               {
4137                 Cache.log.debug(
4138                         "Exception during web service menu building process.",
4139                         e);
4140               }
4141             }
4142           });
4143         } catch (Exception e)
4144         {
4145         }
4146         buildingMenu = false;
4147       }
4148     }).start();
4149
4150   }
4151
4152   /**
4153    * construct any groupURL type service menu entries.
4154    *
4155    * @param webService
4156    */
4157   private void build_urlServiceMenu(JMenu webService)
4158   {
4159     // TODO: remove this code when 2.7 is released
4160     // DEBUG - alignmentView
4161     /*
4162      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4163      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4164      *
4165      * @Override public void actionPerformed(ActionEvent e) {
4166      * jalview.datamodel.AlignmentView
4167      * .testSelectionViews(af.viewport.getAlignment(),
4168      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4169      *
4170      * }); webService.add(testAlView);
4171      */
4172     // TODO: refactor to RestClient discoverer and merge menu entries for
4173     // rest-style services with other types of analysis/calculation service
4174     // SHmmr test client - still being implemented.
4175     // DEBUG - alignmentView
4176
4177     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4178             .getRestClients())
4179     {
4180       client.attachWSMenuEntry(
4181               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4182               this);
4183     }
4184   }
4185
4186   /**
4187    * Searches the alignment sequences for xRefs and builds the Show
4188    * Cross-References menu (formerly called Show Products), with database
4189    * sources for which cross-references are found (protein sources for a
4190    * nucleotide alignment and vice versa)
4191    *
4192    * @return true if Show Cross-references menu should be enabled
4193    */
4194   public boolean canShowProducts()
4195   {
4196     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4197     AlignmentI dataset = viewport.getAlignment().getDataset();
4198
4199     showProducts.removeAll();
4200     final boolean dna = viewport.getAlignment().isNucleotide();
4201
4202     if (seqs == null || seqs.length == 0)
4203     {
4204       // nothing to see here.
4205       return false;
4206     }
4207
4208     boolean showp = false;
4209     try
4210     {
4211       List<String> ptypes = new CrossRef(seqs, dataset)
4212               .findXrefSourcesForSequences(dna);
4213
4214       for (final String source : ptypes)
4215       {
4216         showp = true;
4217         final AlignFrame af = this;
4218         JMenuItem xtype = new JMenuItem(source);
4219         xtype.addActionListener(new ActionListener()
4220         {
4221           @Override
4222           public void actionPerformed(ActionEvent e)
4223           {
4224             showProductsFor(af.viewport.getSequenceSelection(), dna,
4225                     source);
4226           }
4227         });
4228         showProducts.add(xtype);
4229       }
4230       showProducts.setVisible(showp);
4231       showProducts.setEnabled(showp);
4232     } catch (Exception e)
4233     {
4234       Cache.log.warn(
4235               "canShowProducts threw an exception - please report to help@jalview.org",
4236               e);
4237       return false;
4238     }
4239     return showp;
4240   }
4241
4242   /**
4243    * Finds and displays cross-references for the selected sequences (protein
4244    * products for nucleotide sequences, dna coding sequences for peptides).
4245    *
4246    * @param sel
4247    *          the sequences to show cross-references for
4248    * @param dna
4249    *          true if from a nucleotide alignment (so showing proteins)
4250    * @param source
4251    *          the database to show cross-references for
4252    */
4253   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4254           final String source)
4255   {
4256     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4257             .start();
4258   }
4259
4260   /**
4261    * Construct and display a new frame containing the translation of this
4262    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4263    */
4264   @Override
4265   public void showTranslation_actionPerformed(ActionEvent e)
4266   {
4267     AlignmentI al = null;
4268     try
4269     {
4270       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4271
4272       al = dna.translateCdna();
4273     } catch (Exception ex)
4274     {
4275       jalview.bin.Cache.log.error(
4276               "Exception during translation. Please report this !", ex);
4277       final String msg = MessageManager.getString(
4278               "label.error_when_translating_sequences_submit_bug_report");
4279       final String errorTitle = MessageManager
4280               .getString("label.implementation_error")
4281               + MessageManager.getString("label.translation_failed");
4282       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4283               JvOptionPane.ERROR_MESSAGE);
4284       return;
4285     }
4286     if (al == null || al.getHeight() == 0)
4287     {
4288       final String msg = MessageManager.getString(
4289               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4290       final String errorTitle = MessageManager
4291               .getString("label.translation_failed");
4292       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4293               JvOptionPane.WARNING_MESSAGE);
4294     }
4295     else
4296     {
4297       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4298       af.setFileFormat(this.currentFileFormat);
4299       final String newTitle = MessageManager
4300               .formatMessage("label.translation_of_params", new Object[]
4301               { this.getTitle() });
4302       af.setTitle(newTitle);
4303       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4304       {
4305         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4306         viewport.openSplitFrame(af, new Alignment(seqs));
4307       }
4308       else
4309       {
4310         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4311                 DEFAULT_HEIGHT);
4312       }
4313     }
4314   }
4315
4316   /**
4317    * Set the file format
4318    *
4319    * @param format
4320    */
4321   public void setFileFormat(FileFormatI format)
4322   {
4323     this.currentFileFormat = format;
4324   }
4325
4326   /**
4327    * Try to load a features file onto the alignment.
4328    *
4329    * @param file
4330    *          contents or path to retrieve file
4331    * @param sourceType
4332    *          access mode of file (see jalview.io.AlignFile)
4333    * @return true if features file was parsed correctly.
4334    */
4335   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4336   {
4337     return avc.parseFeaturesFile(file, sourceType,
4338             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4339
4340   }
4341
4342   @Override
4343   public void refreshFeatureUI(boolean enableIfNecessary)
4344   {
4345     // note - currently this is only still here rather than in the controller
4346     // because of the featureSettings hard reference that is yet to be
4347     // abstracted
4348     if (enableIfNecessary)
4349     {
4350       viewport.setShowSequenceFeatures(true);
4351       showSeqFeatures.setSelected(true);
4352     }
4353
4354   }
4355
4356   @Override
4357   public void dragEnter(DropTargetDragEvent evt)
4358   {
4359   }
4360
4361   @Override
4362   public void dragExit(DropTargetEvent evt)
4363   {
4364   }
4365
4366   @Override
4367   public void dragOver(DropTargetDragEvent evt)
4368   {
4369   }
4370
4371   @Override
4372   public void dropActionChanged(DropTargetDragEvent evt)
4373   {
4374   }
4375
4376   @Override
4377   public void drop(DropTargetDropEvent evt)
4378   {
4379     // JAL-1552 - acceptDrop required before getTransferable call for
4380     // Java's Transferable for native dnd
4381     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4382     Transferable t = evt.getTransferable();
4383     final AlignFrame thisaf = this;
4384     final List<String> files = new ArrayList<>();
4385     List<DataSourceType> protocols = new ArrayList<>();
4386
4387     try
4388     {
4389       Desktop.transferFromDropTarget(files, protocols, evt, t);
4390     } catch (Exception e)
4391     {
4392       e.printStackTrace();
4393     }
4394     if (files != null)
4395     {
4396       new Thread(new Runnable()
4397       {
4398         @Override
4399         public void run()
4400         {
4401           try
4402           {
4403             // check to see if any of these files have names matching sequences
4404             // in
4405             // the alignment
4406             SequenceIdMatcher idm = new SequenceIdMatcher(
4407                     viewport.getAlignment().getSequencesArray());
4408             /**
4409              * Object[] { String,SequenceI}
4410              */
4411             ArrayList<Object[]> filesmatched = new ArrayList<>();
4412             ArrayList<String> filesnotmatched = new ArrayList<>();
4413             for (int i = 0; i < files.size(); i++)
4414             {
4415               String file = files.get(i).toString();
4416               String pdbfn = "";
4417               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4418               if (protocol == DataSourceType.FILE)
4419               {
4420                 File fl = new File(file);
4421                 pdbfn = fl.getName();
4422               }
4423               else if (protocol == DataSourceType.URL)
4424               {
4425                 URL url = new URL(file);
4426                 pdbfn = url.getFile();
4427               }
4428               if (pdbfn.length() > 0)
4429               {
4430                 // attempt to find a match in the alignment
4431                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4432                 int l = 0, c = pdbfn.indexOf(".");
4433                 while (mtch == null && c != -1)
4434                 {
4435                   do
4436                   {
4437                     l = c;
4438                   } while ((c = pdbfn.indexOf(".", l)) > l);
4439                   if (l > -1)
4440                   {
4441                     pdbfn = pdbfn.substring(0, l);
4442                   }
4443                   mtch = idm.findAllIdMatches(pdbfn);
4444                 }
4445                 if (mtch != null)
4446                 {
4447                   FileFormatI type = null;
4448                   try
4449                   {
4450                     type = new IdentifyFile().identify(file, protocol);
4451                   } catch (Exception ex)
4452                   {
4453                     type = null;
4454                   }
4455                   if (type != null && type.isStructureFile())
4456                   {
4457                     filesmatched.add(new Object[] { file, protocol, mtch });
4458                     continue;
4459                   }
4460                 }
4461                 // File wasn't named like one of the sequences or wasn't a PDB
4462                 // file.
4463                 filesnotmatched.add(file);
4464               }
4465             }
4466             int assocfiles = 0;
4467             if (filesmatched.size() > 0)
4468             {
4469               boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4470               if (!autoAssociate)
4471               {
4472                 String msg = MessageManager.formatMessage(
4473                         "label.automatically_associate_structure_files_with_sequences_same_name",
4474                         new Object[]
4475                         { Integer.valueOf(filesmatched.size())
4476                                 .toString() });
4477                 String ttl = MessageManager.getString(
4478                         "label.automatically_associate_structure_files_by_name");
4479                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4480                         ttl, JvOptionPane.YES_NO_OPTION);
4481                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4482               }
4483               if (autoAssociate)
4484               {
4485                 for (Object[] fm : filesmatched)
4486                 {
4487                   // try and associate
4488                   // TODO: may want to set a standard ID naming formalism for
4489                   // associating PDB files which have no IDs.
4490                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4491                   {
4492                     PDBEntry pe = new AssociatePdbFileWithSeq()
4493                             .associatePdbWithSeq((String) fm[0],
4494                                     (DataSourceType) fm[1], toassoc, false,
4495                                     Desktop.instance);
4496                     if (pe != null)
4497                     {
4498                       System.err.println("Associated file : "
4499                               + ((String) fm[0]) + " with "
4500                               + toassoc.getDisplayId(true));
4501                       assocfiles++;
4502                     }
4503                   }
4504                   // TODO: do we need to update overview ? only if features are
4505                   // shown I guess
4506                   alignPanel.paintAlignment(true, false);
4507                 }
4508               }
4509               else
4510               {
4511                 /*
4512                  * add declined structures as sequences
4513                  */
4514                 for (Object[] o : filesmatched)
4515                 {
4516                   filesnotmatched.add((String) o[0]);
4517                 }
4518               }
4519             }
4520             if (filesnotmatched.size() > 0)
4521             {
4522               if (assocfiles > 0 && (Cache.getDefault(
4523                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4524                       || JvOptionPane.showConfirmDialog(thisaf,
4525                               "<html>" + MessageManager.formatMessage(
4526                                       "label.ignore_unmatched_dropped_files_info",
4527                                       new Object[]
4528                                       { Integer.valueOf(
4529                                               filesnotmatched.size())
4530                                               .toString() })
4531                                       + "</html>",
4532                               MessageManager.getString(
4533                                       "label.ignore_unmatched_dropped_files"),
4534                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4535               {
4536                 return;
4537               }
4538               for (String fn : filesnotmatched)
4539               {
4540                 loadJalviewDataFile(fn, null, null, null);
4541               }
4542
4543             }
4544           } catch (Exception ex)
4545           {
4546             ex.printStackTrace();
4547           }
4548         }
4549       }).start();
4550     }
4551   }
4552
4553   /**
4554    * Attempt to load a "dropped" file or URL string, by testing in turn for
4555    * <ul>
4556    * <li>an Annotation file</li>
4557    * <li>a JNet file</li>
4558    * <li>a features file</li>
4559    * <li>else try to interpret as an alignment file</li>
4560    * </ul>
4561    *
4562    * @param file
4563    *          either a filename or a URL string.
4564    */
4565   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4566           FileFormatI format, SequenceI assocSeq)
4567   {
4568     try
4569     {
4570       if (sourceType == null)
4571       {
4572         sourceType = FormatAdapter.checkProtocol(file);
4573       }
4574       // if the file isn't identified, or not positively identified as some
4575       // other filetype (PFAM is default unidentified alignment file type) then
4576       // try to parse as annotation.
4577       boolean isAnnotation = (format == null
4578               || FileFormat.Pfam.equals(format))
4579                       ? new AnnotationFile().annotateAlignmentView(viewport,
4580                               file, sourceType)
4581                       : false;
4582
4583       if (!isAnnotation)
4584       {
4585         // first see if its a T-COFFEE score file
4586         TCoffeeScoreFile tcf = null;
4587         try
4588         {
4589           tcf = new TCoffeeScoreFile(file, sourceType);
4590           if (tcf.isValid())
4591           {
4592             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4593             {
4594               buildColourMenu();
4595               changeColour(
4596                       new TCoffeeColourScheme(viewport.getAlignment()));
4597               isAnnotation = true;
4598               statusBar.setText(MessageManager.getString(
4599                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4600             }
4601             else
4602             {
4603               // some problem - if no warning its probable that the ID matching
4604               // process didn't work
4605               JvOptionPane.showMessageDialog(Desktop.desktop,
4606                       tcf.getWarningMessage() == null
4607                               ? MessageManager.getString(
4608                                       "label.check_file_matches_sequence_ids_alignment")
4609                               : tcf.getWarningMessage(),
4610                       MessageManager.getString(
4611                               "label.problem_reading_tcoffee_score_file"),
4612                       JvOptionPane.WARNING_MESSAGE);
4613             }
4614           }
4615           else
4616           {
4617             tcf = null;
4618           }
4619         } catch (Exception x)
4620         {
4621           Cache.log.debug(
4622                   "Exception when processing data source as T-COFFEE score file",
4623                   x);
4624           tcf = null;
4625         }
4626         if (tcf == null)
4627         {
4628           // try to see if its a JNet 'concise' style annotation file *before*
4629           // we
4630           // try to parse it as a features file
4631           if (format == null)
4632           {
4633             format = new IdentifyFile().identify(file, sourceType);
4634           }
4635           if (FileFormat.ScoreMatrix == format)
4636           {
4637             ScoreMatrixFile sm = new ScoreMatrixFile(
4638                     new FileParse(file, sourceType));
4639             sm.parse();
4640             // todo: i18n this message
4641             statusBar.setText(MessageManager.formatMessage(
4642                     "label.successfully_loaded_matrix",
4643                     sm.getMatrixName()));
4644           }
4645           else if (FileFormat.Jnet.equals(format))
4646           {
4647             JPredFile predictions = new JPredFile(file, sourceType);
4648             new JnetAnnotationMaker();
4649             JnetAnnotationMaker.add_annotation(predictions,
4650                     viewport.getAlignment(), 0, false);
4651             viewport.getAlignment().setupJPredAlignment();
4652             isAnnotation = true;
4653           }
4654           // else if (IdentifyFile.FeaturesFile.equals(format))
4655           else if (FileFormat.Features.equals(format))
4656           {
4657             if (parseFeaturesFile(file, sourceType))
4658             {
4659               alignPanel.paintAlignment(true, true);
4660             }
4661           }
4662           else
4663           {
4664             new FileLoader().LoadFile(viewport, file, sourceType, format);
4665           }
4666         }
4667       }
4668       if (isAnnotation)
4669       {
4670
4671         alignPanel.adjustAnnotationHeight();
4672         viewport.updateSequenceIdColours();
4673         buildSortByAnnotationScoresMenu();
4674         alignPanel.paintAlignment(true, true);
4675       }
4676     } catch (Exception ex)
4677     {
4678       ex.printStackTrace();
4679     } catch (OutOfMemoryError oom)
4680     {
4681       try
4682       {
4683         System.gc();
4684       } catch (Exception x)
4685       {
4686       }
4687       new OOMWarning(
4688               "loading data "
4689                       + (sourceType != null
4690                               ? (sourceType == DataSourceType.PASTE
4691                                       ? "from clipboard."
4692                                       : "using " + sourceType + " from "
4693                                               + file)
4694                               : ".")
4695                       + (format != null
4696                               ? "(parsing as '" + format + "' file)"
4697                               : ""),
4698               oom, Desktop.desktop);
4699     }
4700   }
4701
4702   /**
4703    * Method invoked by the ChangeListener on the tabbed pane, in other words
4704    * when a different tabbed pane is selected by the user or programmatically.
4705    */
4706   @Override
4707   public void tabSelectionChanged(int index)
4708   {
4709     if (index > -1)
4710     {
4711       alignPanel = alignPanels.get(index);
4712       viewport = alignPanel.av;
4713       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4714       setMenusFromViewport(viewport);
4715     }
4716
4717     /*
4718      * 'focus' any colour slider that is open to the selected viewport
4719      */
4720     if (viewport.getConservationSelected())
4721     {
4722       SliderPanel.setConservationSlider(alignPanel,
4723               viewport.getResidueShading(), alignPanel.getViewName());
4724     }
4725     else
4726     {
4727       SliderPanel.hideConservationSlider();
4728     }
4729     if (viewport.getAbovePIDThreshold())
4730     {
4731       SliderPanel.setPIDSliderSource(alignPanel,
4732               viewport.getResidueShading(), alignPanel.getViewName());
4733     }
4734     else
4735     {
4736       SliderPanel.hidePIDSlider();
4737     }
4738
4739     /*
4740      * If there is a frame linked to this one in a SplitPane, switch it to the
4741      * same view tab index. No infinite recursion of calls should happen, since
4742      * tabSelectionChanged() should not get invoked on setting the selected
4743      * index to an unchanged value. Guard against setting an invalid index
4744      * before the new view peer tab has been created.
4745      */
4746     final AlignViewportI peer = viewport.getCodingComplement();
4747     if (peer != null)
4748     {
4749       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4750               .getAlignPanel().alignFrame;
4751       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4752       {
4753         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4754       }
4755     }
4756   }
4757
4758   /**
4759    * On right mouse click on view tab, prompt for and set new view name.
4760    */
4761   @Override
4762   public void tabbedPane_mousePressed(MouseEvent e)
4763   {
4764     if (e.isPopupTrigger())
4765     {
4766       String msg = MessageManager.getString("label.enter_view_name");
4767       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4768               JvOptionPane.QUESTION_MESSAGE);
4769
4770       if (reply != null)
4771       {
4772         viewport.setViewName(reply);
4773         // TODO warn if reply is in getExistingViewNames()?
4774         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4775       }
4776     }
4777   }
4778
4779   public AlignViewport getCurrentView()
4780   {
4781     return viewport;
4782   }
4783
4784   /**
4785    * Open the dialog for regex description parsing.
4786    */
4787   @Override
4788   protected void extractScores_actionPerformed(ActionEvent e)
4789   {
4790     ParseProperties pp = new jalview.analysis.ParseProperties(
4791             viewport.getAlignment());
4792     // TODO: verify regex and introduce GUI dialog for version 2.5
4793     // if (pp.getScoresFromDescription("col", "score column ",
4794     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4795     // true)>0)
4796     if (pp.getScoresFromDescription("description column",
4797             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4798     {
4799       buildSortByAnnotationScoresMenu();
4800     }
4801   }
4802
4803   /*
4804    * (non-Javadoc)
4805    *
4806    * @see
4807    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4808    * )
4809    */
4810   @Override
4811   protected void showDbRefs_actionPerformed(ActionEvent e)
4812   {
4813     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4814   }
4815
4816   /*
4817    * (non-Javadoc)
4818    *
4819    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4820    * ActionEvent)
4821    */
4822   @Override
4823   protected void showNpFeats_actionPerformed(ActionEvent e)
4824   {
4825     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4826   }
4827
4828   /**
4829    * find the viewport amongst the tabs in this alignment frame and close that
4830    * tab
4831    *
4832    * @param av
4833    */
4834   public boolean closeView(AlignViewportI av)
4835   {
4836     if (viewport == av)
4837     {
4838       this.closeMenuItem_actionPerformed(false);
4839       return true;
4840     }
4841     Component[] comp = tabbedPane.getComponents();
4842     for (int i = 0; comp != null && i < comp.length; i++)
4843     {
4844       if (comp[i] instanceof AlignmentPanel)
4845       {
4846         if (((AlignmentPanel) comp[i]).av == av)
4847         {
4848           // close the view.
4849           closeView((AlignmentPanel) comp[i]);
4850           return true;
4851         }
4852       }
4853     }
4854     return false;
4855   }
4856
4857   protected void build_fetchdbmenu(JMenu webService)
4858   {
4859     // Temporary hack - DBRef Fetcher always top level ws entry.
4860     // TODO We probably want to store a sequence database checklist in
4861     // preferences and have checkboxes.. rather than individual sources selected
4862     // here
4863     final JMenu rfetch = new JMenu(
4864             MessageManager.getString("action.fetch_db_references"));
4865     rfetch.setToolTipText(MessageManager.getString(
4866             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4867     webService.add(rfetch);
4868
4869     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4870             MessageManager.getString("option.trim_retrieved_seqs"));
4871     trimrs.setToolTipText(
4872             MessageManager.getString("label.trim_retrieved_sequences"));
4873     trimrs.setSelected(
4874             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4875     trimrs.addActionListener(new ActionListener()
4876     {
4877       @Override
4878       public void actionPerformed(ActionEvent e)
4879       {
4880         trimrs.setSelected(trimrs.isSelected());
4881         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4882                 Boolean.valueOf(trimrs.isSelected()).toString());
4883       };
4884     });
4885     rfetch.add(trimrs);
4886     JMenuItem fetchr = new JMenuItem(
4887             MessageManager.getString("label.standard_databases"));
4888     fetchr.setToolTipText(
4889             MessageManager.getString("label.fetch_embl_uniprot"));
4890     fetchr.addActionListener(new ActionListener()
4891     {
4892
4893       @Override
4894       public void actionPerformed(ActionEvent e)
4895       {
4896         new Thread(new Runnable()
4897         {
4898           @Override
4899           public void run()
4900           {
4901             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4902                     .getAlignment().isNucleotide();
4903             DBRefFetcher dbRefFetcher = new DBRefFetcher(
4904                     alignPanel.av.getSequenceSelection(),
4905                     alignPanel.alignFrame, null,
4906                     alignPanel.alignFrame.featureSettings, isNucleotide);
4907             dbRefFetcher.addListener(new FetchFinishedListenerI()
4908             {
4909               @Override
4910               public void finished()
4911               {
4912                 AlignFrame.this.setMenusForViewport();
4913               }
4914             });
4915             dbRefFetcher.fetchDBRefs(false);
4916           }
4917         }).start();
4918
4919       }
4920
4921     });
4922     rfetch.add(fetchr);
4923     final AlignFrame me = this;
4924     new Thread(new Runnable()
4925     {
4926       @Override
4927       public void run()
4928       {
4929         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4930                 .getSequenceFetcherSingleton(me);
4931         javax.swing.SwingUtilities.invokeLater(new Runnable()
4932         {
4933           @Override
4934           public void run()
4935           {
4936             String[] dbclasses = sf.getOrderedSupportedSources();
4937             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4938             // jalview.util.QuickSort.sort(otherdb, otherdb);
4939             List<DbSourceProxy> otherdb;
4940             JMenu dfetch = new JMenu();
4941             JMenu ifetch = new JMenu();
4942             JMenuItem fetchr = null;
4943             int comp = 0, icomp = 0, mcomp = 15;
4944             String mname = null;
4945             int dbi = 0;
4946             for (String dbclass : dbclasses)
4947             {
4948               otherdb = sf.getSourceProxy(dbclass);
4949               // add a single entry for this class, or submenu allowing 'fetch
4950               // all' or pick one
4951               if (otherdb == null || otherdb.size() < 1)
4952               {
4953                 continue;
4954               }
4955               // List<DbSourceProxy> dbs=otherdb;
4956               // otherdb=new ArrayList<DbSourceProxy>();
4957               // for (DbSourceProxy db:dbs)
4958               // {
4959               // if (!db.isA(DBRefSource.ALIGNMENTDB)
4960               // }
4961               if (mname == null)
4962               {
4963                 mname = "From " + dbclass;
4964               }
4965               if (otherdb.size() == 1)
4966               {
4967                 final DbSourceProxy[] dassource = otherdb
4968                         .toArray(new DbSourceProxy[0]);
4969                 DbSourceProxy src = otherdb.get(0);
4970                 fetchr = new JMenuItem(src.getDbSource());
4971                 fetchr.addActionListener(new ActionListener()
4972                 {
4973
4974                   @Override
4975                   public void actionPerformed(ActionEvent e)
4976                   {
4977                     new Thread(new Runnable()
4978                     {
4979
4980                       @Override
4981                       public void run()
4982                       {
4983                         boolean isNucleotide = alignPanel.alignFrame
4984                                 .getViewport().getAlignment()
4985                                 .isNucleotide();
4986                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
4987                                 alignPanel.av.getSequenceSelection(),
4988                                 alignPanel.alignFrame, dassource,
4989                                 alignPanel.alignFrame.featureSettings,
4990                                 isNucleotide);
4991                         dbRefFetcher
4992                                 .addListener(new FetchFinishedListenerI()
4993                                 {
4994                                   @Override
4995                                   public void finished()
4996                                   {
4997                                     AlignFrame.this.setMenusForViewport();
4998                                   }
4999                                 });
5000                         dbRefFetcher.fetchDBRefs(false);
5001                       }
5002                     }).start();
5003                   }
5004
5005                 });
5006                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5007                         MessageManager.formatMessage(
5008                                 "label.fetch_retrieve_from", new Object[]
5009                                 { src.getDbName() })));
5010                 dfetch.add(fetchr);
5011                 comp++;
5012               }
5013               else
5014               {
5015                 final DbSourceProxy[] dassource = otherdb
5016                         .toArray(new DbSourceProxy[0]);
5017                 // fetch all entry
5018                 DbSourceProxy src = otherdb.get(0);
5019                 fetchr = new JMenuItem(MessageManager
5020                         .formatMessage("label.fetch_all_param", new Object[]
5021                         { src.getDbSource() }));
5022                 fetchr.addActionListener(new ActionListener()
5023                 {
5024                   @Override
5025                   public void actionPerformed(ActionEvent e)
5026                   {
5027                     new Thread(new Runnable()
5028                     {
5029
5030                       @Override
5031                       public void run()
5032                       {
5033                         boolean isNucleotide = alignPanel.alignFrame
5034                                 .getViewport().getAlignment()
5035                                 .isNucleotide();
5036                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5037                                 alignPanel.av.getSequenceSelection(),
5038                                 alignPanel.alignFrame, dassource,
5039                                 alignPanel.alignFrame.featureSettings,
5040                                 isNucleotide);
5041                         dbRefFetcher
5042                                 .addListener(new FetchFinishedListenerI()
5043                                 {
5044                                   @Override
5045                                   public void finished()
5046                                   {
5047                                     AlignFrame.this.setMenusForViewport();
5048                                   }
5049                                 });
5050                         dbRefFetcher.fetchDBRefs(false);
5051                       }
5052                     }).start();
5053                   }
5054                 });
5055
5056                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5057                         MessageManager.formatMessage(
5058                                 "label.fetch_retrieve_from_all_sources",
5059                                 new Object[]
5060                                 { Integer.valueOf(otherdb.size())
5061                                         .toString(),
5062                                     src.getDbSource(), src.getDbName() })));
5063                 dfetch.add(fetchr);
5064                 comp++;
5065                 // and then build the rest of the individual menus
5066                 ifetch = new JMenu(MessageManager.formatMessage(
5067                         "label.source_from_db_source", new Object[]
5068                         { src.getDbSource() }));
5069                 icomp = 0;
5070                 String imname = null;
5071                 int i = 0;
5072                 for (DbSourceProxy sproxy : otherdb)
5073                 {
5074                   String dbname = sproxy.getDbName();
5075                   String sname = dbname.length() > 5
5076                           ? dbname.substring(0, 5) + "..."
5077                           : dbname;
5078                   String msname = dbname.length() > 10
5079                           ? dbname.substring(0, 10) + "..."
5080                           : dbname;
5081                   if (imname == null)
5082                   {
5083                     imname = MessageManager
5084                             .formatMessage("label.from_msname", new Object[]
5085                             { sname });
5086                   }
5087                   fetchr = new JMenuItem(msname);
5088                   final DbSourceProxy[] dassrc = { sproxy };
5089                   fetchr.addActionListener(new ActionListener()
5090                   {
5091
5092                     @Override
5093                     public void actionPerformed(ActionEvent e)
5094                     {
5095                       new Thread(new Runnable()
5096                       {
5097
5098                         @Override
5099                         public void run()
5100                         {
5101                           boolean isNucleotide = alignPanel.alignFrame
5102                                   .getViewport().getAlignment()
5103                                   .isNucleotide();
5104                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5105                                   alignPanel.av.getSequenceSelection(),
5106                                   alignPanel.alignFrame, dassrc,
5107                                   alignPanel.alignFrame.featureSettings,
5108                                   isNucleotide);
5109                           dbRefFetcher
5110                                   .addListener(new FetchFinishedListenerI()
5111                                   {
5112                                     @Override
5113                                     public void finished()
5114                                     {
5115                                       AlignFrame.this.setMenusForViewport();
5116                                     }
5117                                   });
5118                           dbRefFetcher.fetchDBRefs(false);
5119                         }
5120                       }).start();
5121                     }
5122
5123                   });
5124                   fetchr.setToolTipText(
5125                           "<html>" + MessageManager.formatMessage(
5126                                   "label.fetch_retrieve_from", new Object[]
5127                                   { dbname }));
5128                   ifetch.add(fetchr);
5129                   ++i;
5130                   if (++icomp >= mcomp || i == (otherdb.size()))
5131                   {
5132                     ifetch.setText(MessageManager.formatMessage(
5133                             "label.source_to_target", imname, sname));
5134                     dfetch.add(ifetch);
5135                     ifetch = new JMenu();
5136                     imname = null;
5137                     icomp = 0;
5138                     comp++;
5139                   }
5140                 }
5141               }
5142               ++dbi;
5143               if (comp >= mcomp || dbi >= (dbclasses.length))
5144               {
5145                 dfetch.setText(MessageManager.formatMessage(
5146                         "label.source_to_target", mname, dbclass));
5147                 rfetch.add(dfetch);
5148                 dfetch = new JMenu();
5149                 mname = null;
5150                 comp = 0;
5151               }
5152             }
5153           }
5154         });
5155       }
5156     }).start();
5157
5158   }
5159
5160   /**
5161    * Left justify the whole alignment.
5162    */
5163   @Override
5164   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5165   {
5166     AlignmentI al = viewport.getAlignment();
5167     al.justify(false);
5168     viewport.firePropertyChange("alignment", null, al);
5169   }
5170
5171   /**
5172    * Right justify the whole alignment.
5173    */
5174   @Override
5175   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5176   {
5177     AlignmentI al = viewport.getAlignment();
5178     al.justify(true);
5179     viewport.firePropertyChange("alignment", null, al);
5180   }
5181
5182   @Override
5183   public void setShowSeqFeatures(boolean b)
5184   {
5185     showSeqFeatures.setSelected(b);
5186     viewport.setShowSequenceFeatures(b);
5187   }
5188
5189   /*
5190    * (non-Javadoc)
5191    *
5192    * @see
5193    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5194    * awt.event.ActionEvent)
5195    */
5196   @Override
5197   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5198   {
5199     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5200     alignPanel.paintAlignment(false, false);
5201   }
5202
5203   /*
5204    * (non-Javadoc)
5205    *
5206    * @see
5207    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5208    * .ActionEvent)
5209    */
5210   @Override
5211   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5212   {
5213     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5214     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5215
5216   }
5217
5218   /*
5219    * (non-Javadoc)
5220    *
5221    * @see
5222    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5223    * .event.ActionEvent)
5224    */
5225   @Override
5226   protected void showGroupConservation_actionPerformed(ActionEvent e)
5227   {
5228     viewport.setShowGroupConservation(showGroupConservation.getState());
5229     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5230   }
5231
5232   /*
5233    * (non-Javadoc)
5234    *
5235    * @see
5236    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5237    * .event.ActionEvent)
5238    */
5239   @Override
5240   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5241   {
5242     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5243     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5244   }
5245
5246   /*
5247    * (non-Javadoc)
5248    *
5249    * @see
5250    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5251    * .event.ActionEvent)
5252    */
5253   @Override
5254   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5255   {
5256     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5257     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5258   }
5259
5260   @Override
5261   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5262   {
5263     showSequenceLogo.setState(true);
5264     viewport.setShowSequenceLogo(true);
5265     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5266     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5267   }
5268
5269   @Override
5270   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5271   {
5272     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5273   }
5274
5275   /*
5276    * (non-Javadoc)
5277    *
5278    * @see
5279    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5280    * .event.ActionEvent)
5281    */
5282   @Override
5283   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5284   {
5285     if (avc.makeGroupsFromSelection())
5286     {
5287       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5288       alignPanel.updateAnnotation();
5289       alignPanel.paintAlignment(true, true);
5290     }
5291   }
5292
5293   public void clearAlignmentSeqRep()
5294   {
5295     // TODO refactor alignmentseqrep to controller
5296     if (viewport.getAlignment().hasSeqrep())
5297     {
5298       viewport.getAlignment().setSeqrep(null);
5299       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5300       alignPanel.updateAnnotation();
5301       alignPanel.paintAlignment(true, true);
5302     }
5303   }
5304
5305   @Override
5306   protected void createGroup_actionPerformed(ActionEvent e)
5307   {
5308     if (avc.createGroup())
5309     {
5310       if (applyAutoAnnotationSettings.isSelected())
5311       {
5312         alignPanel.updateAnnotation(true, false);
5313       }
5314       alignPanel.alignmentChanged();
5315     }
5316   }
5317
5318   @Override
5319   protected void unGroup_actionPerformed(ActionEvent e)
5320   {
5321     if (avc.unGroup())
5322     {
5323       alignPanel.alignmentChanged();
5324     }
5325   }
5326
5327   /**
5328    * make the given alignmentPanel the currently selected tab
5329    *
5330    * @param alignmentPanel
5331    */
5332   public void setDisplayedView(AlignmentPanel alignmentPanel)
5333   {
5334     if (!viewport.getSequenceSetId()
5335             .equals(alignmentPanel.av.getSequenceSetId()))
5336     {
5337       throw new Error(MessageManager.getString(
5338               "error.implementation_error_cannot_show_view_alignment_frame"));
5339     }
5340     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5341             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5342     {
5343       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5344     }
5345   }
5346
5347   /**
5348    * Action on selection of menu options to Show or Hide annotations.
5349    *
5350    * @param visible
5351    * @param forSequences
5352    *          update sequence-related annotations
5353    * @param forAlignment
5354    *          update non-sequence-related annotations
5355    */
5356   @Override
5357   protected void setAnnotationsVisibility(boolean visible,
5358           boolean forSequences, boolean forAlignment)
5359   {
5360     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5361             .getAlignmentAnnotation();
5362     if (anns == null)
5363     {
5364       return;
5365     }
5366     for (AlignmentAnnotation aa : anns)
5367     {
5368       /*
5369        * don't display non-positional annotations on an alignment
5370        */
5371       if (aa.annotations == null)
5372       {
5373         continue;
5374       }
5375       boolean apply = (aa.sequenceRef == null && forAlignment)
5376               || (aa.sequenceRef != null && forSequences);
5377       if (apply)
5378       {
5379         aa.visible = visible;
5380       }
5381     }
5382     alignPanel.validateAnnotationDimensions(true);
5383     alignPanel.alignmentChanged();
5384   }
5385
5386   /**
5387    * Store selected annotation sort order for the view and repaint.
5388    */
5389   @Override
5390   protected void sortAnnotations_actionPerformed()
5391   {
5392     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5393     this.alignPanel.av
5394             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5395     alignPanel.paintAlignment(false, false);
5396   }
5397
5398   /**
5399    *
5400    * @return alignment panels in this alignment frame
5401    */
5402   public List<? extends AlignmentViewPanel> getAlignPanels()
5403   {
5404     // alignPanels is never null
5405     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5406     return alignPanels;
5407   }
5408
5409   /**
5410    * Open a new alignment window, with the cDNA associated with this (protein)
5411    * alignment, aligned as is the protein.
5412    */
5413   protected void viewAsCdna_actionPerformed()
5414   {
5415     // TODO no longer a menu action - refactor as required
5416     final AlignmentI alignment = getViewport().getAlignment();
5417     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5418     if (mappings == null)
5419     {
5420       return;
5421     }
5422     List<SequenceI> cdnaSeqs = new ArrayList<>();
5423     for (SequenceI aaSeq : alignment.getSequences())
5424     {
5425       for (AlignedCodonFrame acf : mappings)
5426       {
5427         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5428         if (dnaSeq != null)
5429         {
5430           /*
5431            * There is a cDNA mapping for this protein sequence - add to new
5432            * alignment. It will share the same dataset sequence as other mapped
5433            * cDNA (no new mappings need to be created).
5434            */
5435           final Sequence newSeq = new Sequence(dnaSeq);
5436           newSeq.setDatasetSequence(dnaSeq);
5437           cdnaSeqs.add(newSeq);
5438         }
5439       }
5440     }
5441     if (cdnaSeqs.size() == 0)
5442     {
5443       // show a warning dialog no mapped cDNA
5444       return;
5445     }
5446     AlignmentI cdna = new Alignment(
5447             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5448     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5449             AlignFrame.DEFAULT_HEIGHT);
5450     cdna.alignAs(alignment);
5451     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5452             + this.title;
5453     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5454             AlignFrame.DEFAULT_HEIGHT);
5455   }
5456
5457   /**
5458    * Set visibility of dna/protein complement view (available when shown in a
5459    * split frame).
5460    *
5461    * @param show
5462    */
5463   @Override
5464   protected void showComplement_actionPerformed(boolean show)
5465   {
5466     SplitContainerI sf = getSplitViewContainer();
5467     if (sf != null)
5468     {
5469       sf.setComplementVisible(this, show);
5470     }
5471   }
5472
5473   /**
5474    * Generate the reverse (optionally complemented) of the selected sequences,
5475    * and add them to the alignment
5476    */
5477   @Override
5478   protected void showReverse_actionPerformed(boolean complement)
5479   {
5480     AlignmentI al = null;
5481     try
5482     {
5483       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5484       al = dna.reverseCdna(complement);
5485       viewport.addAlignment(al, "");
5486       addHistoryItem(new EditCommand(
5487               MessageManager.getString("label.add_sequences"), Action.PASTE,
5488               al.getSequencesArray(), 0, al.getWidth(),
5489               viewport.getAlignment()));
5490     } catch (Exception ex)
5491     {
5492       System.err.println(ex.getMessage());
5493       return;
5494     }
5495   }
5496
5497   /**
5498    * Try to run a script in the Groovy console, having first ensured that this
5499    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5500    * be targeted at this alignment.
5501    */
5502   @Override
5503   protected void runGroovy_actionPerformed()
5504   {
5505     Jalview.setCurrentAlignFrame(this);
5506     groovy.ui.Console console = Desktop.getGroovyConsole();
5507     if (console != null)
5508     {
5509       try
5510       {
5511         console.runScript();
5512       } catch (Exception ex)
5513       {
5514         System.err.println((ex.toString()));
5515         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5516                 MessageManager.getString("label.couldnt_run_groovy_script"),
5517                 MessageManager.getString("label.groovy_support_failed"),
5518                 JvOptionPane.ERROR_MESSAGE);
5519       }
5520     }
5521     else
5522     {
5523       System.err.println("Can't run Groovy script as console not found");
5524     }
5525   }
5526
5527   /**
5528    * Hides columns containing (or not containing) the specified feature(s),
5529    * provided that would not leave all columns hidden
5530    *
5531    * @param columnsContaining
5532    * @param featureTypes
5533    *
5534    * @return
5535    */
5536   public boolean hideFeatureColumns(boolean columnsContaining,
5537           String... featureTypes)
5538   {
5539     boolean notForHiding = avc.markColumnsContainingFeatures(
5540             columnsContaining, false, false, featureTypes);
5541     if (notForHiding)
5542     {
5543       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5544               false, featureTypes))
5545       {
5546         getViewport().hideSelectedColumns();
5547         return true;
5548       }
5549     }
5550     return false;
5551   }
5552
5553   @Override
5554   protected void selectHighlightedColumns_actionPerformed(
5555           ActionEvent actionEvent)
5556   {
5557     // include key modifier check in case user selects from menu
5558     avc.markHighlightedColumns(
5559             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5560             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5561                     | ActionEvent.CTRL_MASK)) != 0);
5562   }
5563
5564   /**
5565    * Rebuilds the Colour menu, including any user-defined colours which have
5566    * been loaded either on startup or during the session
5567    */
5568   public void buildColourMenu()
5569   {
5570     colourMenu.removeAll();
5571
5572     colourMenu.add(applyToAllGroups);
5573     colourMenu.add(textColour);
5574     colourMenu.addSeparator();
5575
5576     ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5577             false);
5578
5579     colourMenu.addSeparator();
5580     colourMenu.add(conservationMenuItem);
5581     colourMenu.add(modifyConservation);
5582     colourMenu.add(abovePIDThreshold);
5583     colourMenu.add(modifyPID);
5584     colourMenu.add(annotationColour);
5585
5586     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5587     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5588   }
5589
5590   /**
5591    * Open a dialog (if not already open) that allows the user to select and
5592    * calculate PCA or Tree analysis
5593    */
5594   protected void openTreePcaDialog()
5595   {
5596     if (alignPanel.getCalculationDialog() == null)
5597     {
5598       new CalculationChooser(AlignFrame.this);
5599     }
5600   }
5601
5602   @Override
5603   protected void loadVcf_actionPerformed()
5604   {
5605     JalviewFileChooser chooser = new JalviewFileChooser(
5606             Cache.getProperty("LAST_DIRECTORY"));
5607     chooser.setFileView(new JalviewFileView());
5608     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5609     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5610
5611     int value = chooser.showOpenDialog(null);
5612
5613     if (value == JalviewFileChooser.APPROVE_OPTION)
5614     {
5615       String choice = chooser.getSelectedFile().getPath();
5616       Cache.setProperty("LAST_DIRECTORY", choice);
5617       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5618       new VCFLoader(choice).loadVCF(seqs, this);
5619     }
5620
5621   }
5622 }
5623
5624 class PrintThread extends Thread
5625 {
5626   AlignmentPanel ap;
5627
5628   public PrintThread(AlignmentPanel ap)
5629   {
5630     this.ap = ap;
5631   }
5632
5633   static PageFormat pf;
5634
5635   @Override
5636   public void run()
5637   {
5638     PrinterJob printJob = PrinterJob.getPrinterJob();
5639
5640     if (pf != null)
5641     {
5642       printJob.setPrintable(ap, pf);
5643     }
5644     else
5645     {
5646       printJob.setPrintable(ap);
5647     }
5648
5649     if (printJob.printDialog())
5650     {
5651       try
5652       {
5653         printJob.print();
5654       } catch (Exception PrintException)
5655       {
5656         PrintException.printStackTrace();
5657       }
5658     }
5659   }
5660 }