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           PrintWriter out = new PrintWriter(new FileWriter(file), true);
1194
1195           // TESTING code here
1196           boolean TESTING = true;
1197           if (TESTING)
1198           {
1199             out.print("; TESTSTART\n");
1200             int count = 20;
1201             for (int i = 0; i < count; i++)
1202             {
1203               // Thread.sleep(1000);
1204               out.println("; TEST: " + (count - 1 - i));
1205             }
1206           }
1207           out.print(output);
1208           if (TESTING)
1209           {
1210             out.print("; TESTEND\n");
1211           }
1212           out.close();
1213           this.setTitle(file);
1214           statusBar.setText(MessageManager.formatMessage(
1215                   "label.successfully_saved_to_file_in_format", new Object[]
1216                   { fileName, format.getName() }));
1217         } catch (Exception ex)
1218         {
1219           success = false;
1220           ex.printStackTrace();
1221         }
1222       }
1223     }
1224
1225     if (!success)
1226     {
1227       JvOptionPane.showInternalMessageDialog(this, MessageManager
1228               .formatMessage("label.couldnt_save_file", new Object[]
1229               { fileName }),
1230               MessageManager.getString("label.error_saving_file"),
1231               JvOptionPane.WARNING_MESSAGE);
1232     }
1233
1234     return success;
1235   }
1236
1237   private void warningMessage(String warning, String title)
1238   {
1239     if (new jalview.util.Platform().isHeadless())
1240     {
1241       System.err.println("Warning: " + title + "\nWarning: " + warning);
1242
1243     }
1244     else
1245     {
1246       JvOptionPane.showInternalMessageDialog(this, warning, title,
1247               JvOptionPane.WARNING_MESSAGE);
1248     }
1249     return;
1250   }
1251
1252   /**
1253    * DOCUMENT ME!
1254    *
1255    * @param e
1256    *          DOCUMENT ME!
1257    */
1258   @Override
1259   protected void outputText_actionPerformed(ActionEvent e)
1260   {
1261     FileFormatI fileFormat = FileFormats.getInstance()
1262             .forName(e.getActionCommand());
1263     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1264             viewport, null);
1265     if (exportData.getSettings().isCancelled())
1266     {
1267       return;
1268     }
1269     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1270     cap.setForInput(null);
1271     try
1272     {
1273       FileFormatI format = fileFormat;
1274       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1275               .formatSequences(format, exportData.getAlignment(),
1276                       exportData.getOmitHidden(),
1277                       exportData.getStartEndPostions(),
1278                       viewport.getAlignment().getHiddenColumns()));
1279       Desktop.addInternalFrame(cap, MessageManager
1280               .formatMessage("label.alignment_output_command", new Object[]
1281               { e.getActionCommand() }), 600, 500);
1282     } catch (OutOfMemoryError oom)
1283     {
1284       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1285               oom);
1286       cap.dispose();
1287     }
1288
1289   }
1290
1291   public static AlignmentExportData getAlignmentForExport(
1292           FileFormatI format, AlignViewportI viewport,
1293           AlignExportSettingI exportSettings)
1294   {
1295     AlignmentI alignmentToExport = null;
1296     AlignExportSettingI settings = exportSettings;
1297     String[] omitHidden = null;
1298
1299     HiddenSequences hiddenSeqs = viewport.getAlignment()
1300             .getHiddenSequences();
1301
1302     alignmentToExport = viewport.getAlignment();
1303
1304     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1305     if (settings == null)
1306     {
1307       settings = new AlignExportSettings(hasHiddenSeqs,
1308               viewport.hasHiddenColumns(), format);
1309     }
1310     // settings.isExportAnnotations();
1311
1312     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1313     {
1314       omitHidden = viewport.getViewAsString(false,
1315               settings.isExportHiddenSequences());
1316     }
1317
1318     int[] alignmentStartEnd = new int[2];
1319     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1320     {
1321       alignmentToExport = hiddenSeqs.getFullAlignment();
1322     }
1323     else
1324     {
1325       alignmentToExport = viewport.getAlignment();
1326     }
1327     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1328             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1329     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1330             omitHidden, alignmentStartEnd, settings);
1331     return ed;
1332   }
1333
1334   /**
1335    * DOCUMENT ME!
1336    *
1337    * @param e
1338    *          DOCUMENT ME!
1339    */
1340   @Override
1341   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1342   {
1343     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1344     htmlSVG.exportHTML(null);
1345   }
1346
1347   @Override
1348   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1349   {
1350     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1351     bjs.exportHTML(null);
1352   }
1353
1354   public void createImageMap(File file, String image)
1355   {
1356     alignPanel.makePNGImageMap(file, image);
1357   }
1358
1359   /**
1360    * DOCUMENT ME!
1361    *
1362    * @param e
1363    *          DOCUMENT ME!
1364    */
1365   @Override
1366   public void createPNG(File f)
1367   {
1368     alignPanel.makePNG(f);
1369   }
1370
1371   /**
1372    * DOCUMENT ME!
1373    *
1374    * @param e
1375    *          DOCUMENT ME!
1376    */
1377   @Override
1378   public void createEPS(File f)
1379   {
1380     alignPanel.makeEPS(f);
1381   }
1382
1383   @Override
1384   public void createSVG(File f)
1385   {
1386     alignPanel.makeSVG(f);
1387   }
1388
1389   @Override
1390   public void pageSetup_actionPerformed(ActionEvent e)
1391   {
1392     PrinterJob printJob = PrinterJob.getPrinterJob();
1393     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1394   }
1395
1396   /**
1397    * DOCUMENT ME!
1398    *
1399    * @param e
1400    *          DOCUMENT ME!
1401    */
1402   @Override
1403   public void printMenuItem_actionPerformed(ActionEvent e)
1404   {
1405     // Putting in a thread avoids Swing painting problems
1406     PrintThread thread = new PrintThread(alignPanel);
1407     thread.start();
1408   }
1409
1410   @Override
1411   public void exportFeatures_actionPerformed(ActionEvent e)
1412   {
1413     new AnnotationExporter(alignPanel).exportFeatures();
1414   }
1415
1416   @Override
1417   public void exportAnnotations_actionPerformed(ActionEvent e)
1418   {
1419     new AnnotationExporter(alignPanel).exportAnnotations();
1420   }
1421
1422   @Override
1423   public void associatedData_actionPerformed(ActionEvent e)
1424   {
1425     // Pick the tree file
1426     JalviewFileChooser chooser = new JalviewFileChooser(
1427             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1428     chooser.setFileView(new JalviewFileView());
1429     chooser.setDialogTitle(
1430             MessageManager.getString("label.load_jalview_annotations"));
1431     chooser.setToolTipText(
1432             MessageManager.getString("label.load_jalview_annotations"));
1433
1434     int value = chooser.showOpenDialog(null);
1435
1436     if (value == JalviewFileChooser.APPROVE_OPTION)
1437     {
1438       String choice = chooser.getSelectedFile().getPath();
1439       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1440       loadJalviewDataFile(choice, null, null, null);
1441     }
1442
1443   }
1444
1445   /**
1446    * Close the current view or all views in the alignment frame. If the frame
1447    * only contains one view then the alignment will be removed from memory.
1448    *
1449    * @param closeAllTabs
1450    */
1451   @Override
1452   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1453   {
1454     if (alignPanels != null && alignPanels.size() < 2)
1455     {
1456       closeAllTabs = true;
1457     }
1458
1459     try
1460     {
1461       if (alignPanels != null)
1462       {
1463         if (closeAllTabs)
1464         {
1465           if (this.isClosed())
1466           {
1467             // really close all the windows - otherwise wait till
1468             // setClosed(true) is called
1469             for (int i = 0; i < alignPanels.size(); i++)
1470             {
1471               AlignmentPanel ap = alignPanels.get(i);
1472               ap.closePanel();
1473             }
1474           }
1475         }
1476         else
1477         {
1478           closeView(alignPanel);
1479         }
1480       }
1481
1482       if (closeAllTabs)
1483       {
1484         /*
1485          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1486          * be called recursively, with the frame now in 'closed' state
1487          */
1488         this.setClosed(true);
1489       }
1490     } catch (Exception ex)
1491     {
1492       ex.printStackTrace();
1493     }
1494   }
1495
1496   /**
1497    * Close the specified panel and close up tabs appropriately.
1498    *
1499    * @param panelToClose
1500    */
1501   public void closeView(AlignmentPanel panelToClose)
1502   {
1503     int index = tabbedPane.getSelectedIndex();
1504     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1505     alignPanels.remove(panelToClose);
1506     panelToClose.closePanel();
1507     panelToClose = null;
1508
1509     tabbedPane.removeTabAt(closedindex);
1510     tabbedPane.validate();
1511
1512     if (index > closedindex || index == tabbedPane.getTabCount())
1513     {
1514       // modify currently selected tab index if necessary.
1515       index--;
1516     }
1517
1518     this.tabSelectionChanged(index);
1519   }
1520
1521   /**
1522    * DOCUMENT ME!
1523    */
1524   void updateEditMenuBar()
1525   {
1526
1527     if (viewport.getHistoryList().size() > 0)
1528     {
1529       undoMenuItem.setEnabled(true);
1530       CommandI command = viewport.getHistoryList().peek();
1531       undoMenuItem.setText(MessageManager
1532               .formatMessage("label.undo_command", new Object[]
1533               { command.getDescription() }));
1534     }
1535     else
1536     {
1537       undoMenuItem.setEnabled(false);
1538       undoMenuItem.setText(MessageManager.getString("action.undo"));
1539     }
1540
1541     if (viewport.getRedoList().size() > 0)
1542     {
1543       redoMenuItem.setEnabled(true);
1544
1545       CommandI command = viewport.getRedoList().peek();
1546       redoMenuItem.setText(MessageManager
1547               .formatMessage("label.redo_command", new Object[]
1548               { command.getDescription() }));
1549     }
1550     else
1551     {
1552       redoMenuItem.setEnabled(false);
1553       redoMenuItem.setText(MessageManager.getString("action.redo"));
1554     }
1555   }
1556
1557   @Override
1558   public void addHistoryItem(CommandI command)
1559   {
1560     if (command.getSize() > 0)
1561     {
1562       viewport.addToHistoryList(command);
1563       viewport.clearRedoList();
1564       updateEditMenuBar();
1565       viewport.updateHiddenColumns();
1566       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1567       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1568       // viewport.getColumnSelection()
1569       // .getHiddenColumns().size() > 0);
1570     }
1571   }
1572
1573   /**
1574    *
1575    * @return alignment objects for all views
1576    */
1577   AlignmentI[] getViewAlignments()
1578   {
1579     if (alignPanels != null)
1580     {
1581       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1582       int i = 0;
1583       for (AlignmentPanel ap : alignPanels)
1584       {
1585         als[i++] = ap.av.getAlignment();
1586       }
1587       return als;
1588     }
1589     if (viewport != null)
1590     {
1591       return new AlignmentI[] { viewport.getAlignment() };
1592     }
1593     return null;
1594   }
1595
1596   /**
1597    * DOCUMENT ME!
1598    *
1599    * @param e
1600    *          DOCUMENT ME!
1601    */
1602   @Override
1603   protected void undoMenuItem_actionPerformed(ActionEvent e)
1604   {
1605     if (viewport.getHistoryList().isEmpty())
1606     {
1607       return;
1608     }
1609     CommandI command = viewport.getHistoryList().pop();
1610     viewport.addToRedoList(command);
1611     command.undoCommand(getViewAlignments());
1612
1613     AlignmentViewport originalSource = getOriginatingSource(command);
1614     updateEditMenuBar();
1615
1616     if (originalSource != null)
1617     {
1618       if (originalSource != viewport)
1619       {
1620         Cache.log.warn(
1621                 "Implementation worry: mismatch of viewport origin for undo");
1622       }
1623       originalSource.updateHiddenColumns();
1624       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1625       // null
1626       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1627       // viewport.getColumnSelection()
1628       // .getHiddenColumns().size() > 0);
1629       originalSource.firePropertyChange("alignment", null,
1630               originalSource.getAlignment().getSequences());
1631     }
1632   }
1633
1634   /**
1635    * DOCUMENT ME!
1636    *
1637    * @param e
1638    *          DOCUMENT ME!
1639    */
1640   @Override
1641   protected void redoMenuItem_actionPerformed(ActionEvent e)
1642   {
1643     if (viewport.getRedoList().size() < 1)
1644     {
1645       return;
1646     }
1647
1648     CommandI command = viewport.getRedoList().pop();
1649     viewport.addToHistoryList(command);
1650     command.doCommand(getViewAlignments());
1651
1652     AlignmentViewport originalSource = getOriginatingSource(command);
1653     updateEditMenuBar();
1654
1655     if (originalSource != null)
1656     {
1657
1658       if (originalSource != viewport)
1659       {
1660         Cache.log.warn(
1661                 "Implementation worry: mismatch of viewport origin for redo");
1662       }
1663       originalSource.updateHiddenColumns();
1664       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1665       // null
1666       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1667       // viewport.getColumnSelection()
1668       // .getHiddenColumns().size() > 0);
1669       originalSource.firePropertyChange("alignment", null,
1670               originalSource.getAlignment().getSequences());
1671     }
1672   }
1673
1674   AlignmentViewport getOriginatingSource(CommandI command)
1675   {
1676     AlignmentViewport originalSource = null;
1677     // For sequence removal and addition, we need to fire
1678     // the property change event FROM the viewport where the
1679     // original alignment was altered
1680     AlignmentI al = null;
1681     if (command instanceof EditCommand)
1682     {
1683       EditCommand editCommand = (EditCommand) command;
1684       al = editCommand.getAlignment();
1685       List<Component> comps = PaintRefresher.components
1686               .get(viewport.getSequenceSetId());
1687
1688       for (Component comp : comps)
1689       {
1690         if (comp instanceof AlignmentPanel)
1691         {
1692           if (al == ((AlignmentPanel) comp).av.getAlignment())
1693           {
1694             originalSource = ((AlignmentPanel) comp).av;
1695             break;
1696           }
1697         }
1698       }
1699     }
1700
1701     if (originalSource == null)
1702     {
1703       // The original view is closed, we must validate
1704       // the current view against the closed view first
1705       if (al != null)
1706       {
1707         PaintRefresher.validateSequences(al, viewport.getAlignment());
1708       }
1709
1710       originalSource = viewport;
1711     }
1712
1713     return originalSource;
1714   }
1715
1716   /**
1717    * DOCUMENT ME!
1718    *
1719    * @param up
1720    *          DOCUMENT ME!
1721    */
1722   public void moveSelectedSequences(boolean up)
1723   {
1724     SequenceGroup sg = viewport.getSelectionGroup();
1725
1726     if (sg == null)
1727     {
1728       return;
1729     }
1730     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1731             viewport.getHiddenRepSequences(), up);
1732     alignPanel.paintAlignment(true, false);
1733   }
1734
1735   synchronized void slideSequences(boolean right, int size)
1736   {
1737     List<SequenceI> sg = new ArrayList<>();
1738     if (viewport.cursorMode)
1739     {
1740       sg.add(viewport.getAlignment()
1741               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1742     }
1743     else if (viewport.getSelectionGroup() != null
1744             && viewport.getSelectionGroup().getSize() != viewport
1745                     .getAlignment().getHeight())
1746     {
1747       sg = viewport.getSelectionGroup()
1748               .getSequences(viewport.getHiddenRepSequences());
1749     }
1750
1751     if (sg.size() < 1)
1752     {
1753       return;
1754     }
1755
1756     List<SequenceI> invertGroup = new ArrayList<>();
1757
1758     for (SequenceI seq : viewport.getAlignment().getSequences())
1759     {
1760       if (!sg.contains(seq))
1761       {
1762         invertGroup.add(seq);
1763       }
1764     }
1765
1766     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1767
1768     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1769     for (int i = 0; i < invertGroup.size(); i++)
1770     {
1771       seqs2[i] = invertGroup.get(i);
1772     }
1773
1774     SlideSequencesCommand ssc;
1775     if (right)
1776     {
1777       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1778               viewport.getGapCharacter());
1779     }
1780     else
1781     {
1782       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1783               viewport.getGapCharacter());
1784     }
1785
1786     int groupAdjustment = 0;
1787     if (ssc.getGapsInsertedBegin() && right)
1788     {
1789       if (viewport.cursorMode)
1790       {
1791         alignPanel.getSeqPanel().moveCursor(size, 0);
1792       }
1793       else
1794       {
1795         groupAdjustment = size;
1796       }
1797     }
1798     else if (!ssc.getGapsInsertedBegin() && !right)
1799     {
1800       if (viewport.cursorMode)
1801       {
1802         alignPanel.getSeqPanel().moveCursor(-size, 0);
1803       }
1804       else
1805       {
1806         groupAdjustment = -size;
1807       }
1808     }
1809
1810     if (groupAdjustment != 0)
1811     {
1812       viewport.getSelectionGroup().setStartRes(
1813               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1814       viewport.getSelectionGroup().setEndRes(
1815               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1816     }
1817
1818     /*
1819      * just extend the last slide command if compatible; but not if in
1820      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1821      */
1822     boolean appendHistoryItem = false;
1823     Deque<CommandI> historyList = viewport.getHistoryList();
1824     boolean inSplitFrame = getSplitViewContainer() != null;
1825     if (!inSplitFrame && historyList != null && historyList.size() > 0
1826             && historyList.peek() instanceof SlideSequencesCommand)
1827     {
1828       appendHistoryItem = ssc.appendSlideCommand(
1829               (SlideSequencesCommand) historyList.peek());
1830     }
1831
1832     if (!appendHistoryItem)
1833     {
1834       addHistoryItem(ssc);
1835     }
1836
1837     repaint();
1838   }
1839
1840   /**
1841    * DOCUMENT ME!
1842    *
1843    * @param e
1844    *          DOCUMENT ME!
1845    */
1846   @Override
1847   protected void copy_actionPerformed(ActionEvent e)
1848   {
1849     if (viewport.getSelectionGroup() == null)
1850     {
1851       return;
1852     }
1853     // TODO: preserve the ordering of displayed alignment annotation in any
1854     // internal paste (particularly sequence associated annotation)
1855     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1856     String[] omitHidden = null;
1857
1858     if (viewport.hasHiddenColumns())
1859     {
1860       omitHidden = viewport.getViewAsString(true);
1861     }
1862
1863     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1864             seqs, omitHidden, null);
1865
1866     StringSelection ss = new StringSelection(output);
1867
1868     try
1869     {
1870       jalview.gui.Desktop.internalCopy = true;
1871       // Its really worth setting the clipboard contents
1872       // to empty before setting the large StringSelection!!
1873       Toolkit.getDefaultToolkit().getSystemClipboard()
1874               .setContents(new StringSelection(""), null);
1875
1876       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1877               Desktop.instance);
1878     } catch (OutOfMemoryError er)
1879     {
1880       new OOMWarning("copying region", er);
1881       return;
1882     }
1883
1884     HiddenColumns hiddenColumns = null;
1885     if (viewport.hasHiddenColumns())
1886     {
1887       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1888       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1889
1890       // create new HiddenColumns object with copy of hidden regions
1891       // between startRes and endRes, offset by startRes
1892       hiddenColumns = new HiddenColumns(
1893               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1894               hiddenCutoff, hiddenOffset);
1895     }
1896
1897     Desktop.jalviewClipboard = new Object[] { seqs,
1898         viewport.getAlignment().getDataset(), hiddenColumns };
1899     statusBar.setText(MessageManager.formatMessage(
1900             "label.copied_sequences_to_clipboard", new Object[]
1901             { Integer.valueOf(seqs.length).toString() }));
1902   }
1903
1904   /**
1905    * DOCUMENT ME!
1906    *
1907    * @param e
1908    *          DOCUMENT ME!
1909    */
1910   @Override
1911   protected void pasteNew_actionPerformed(ActionEvent e)
1912   {
1913     paste(true);
1914   }
1915
1916   /**
1917    * DOCUMENT ME!
1918    *
1919    * @param e
1920    *          DOCUMENT ME!
1921    */
1922   @Override
1923   protected void pasteThis_actionPerformed(ActionEvent e)
1924   {
1925     paste(false);
1926   }
1927
1928   /**
1929    * Paste contents of Jalview clipboard
1930    *
1931    * @param newAlignment
1932    *          true to paste to a new alignment, otherwise add to this.
1933    */
1934   void paste(boolean newAlignment)
1935   {
1936     boolean externalPaste = true;
1937     try
1938     {
1939       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1940       Transferable contents = c.getContents(this);
1941
1942       if (contents == null)
1943       {
1944         return;
1945       }
1946
1947       String str;
1948       FileFormatI format;
1949       try
1950       {
1951         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1952         if (str.length() < 1)
1953         {
1954           return;
1955         }
1956
1957         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1958
1959       } catch (OutOfMemoryError er)
1960       {
1961         new OOMWarning("Out of memory pasting sequences!!", er);
1962         return;
1963       }
1964
1965       SequenceI[] sequences;
1966       boolean annotationAdded = false;
1967       AlignmentI alignment = null;
1968
1969       if (Desktop.jalviewClipboard != null)
1970       {
1971         // The clipboard was filled from within Jalview, we must use the
1972         // sequences
1973         // And dataset from the copied alignment
1974         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1975         // be doubly sure that we create *new* sequence objects.
1976         sequences = new SequenceI[newseq.length];
1977         for (int i = 0; i < newseq.length; i++)
1978         {
1979           sequences[i] = new Sequence(newseq[i]);
1980         }
1981         alignment = new Alignment(sequences);
1982         externalPaste = false;
1983       }
1984       else
1985       {
1986         // parse the clipboard as an alignment.
1987         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1988                 format);
1989         sequences = alignment.getSequencesArray();
1990       }
1991
1992       int alwidth = 0;
1993       ArrayList<Integer> newGraphGroups = new ArrayList<>();
1994       int fgroup = -1;
1995
1996       if (newAlignment)
1997       {
1998
1999         if (Desktop.jalviewClipboard != null)
2000         {
2001           // dataset is inherited
2002           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2003         }
2004         else
2005         {
2006           // new dataset is constructed
2007           alignment.setDataset(null);
2008         }
2009         alwidth = alignment.getWidth() + 1;
2010       }
2011       else
2012       {
2013         AlignmentI pastedal = alignment; // preserve pasted alignment object
2014         // Add pasted sequences and dataset into existing alignment.
2015         alignment = viewport.getAlignment();
2016         alwidth = alignment.getWidth() + 1;
2017         // decide if we need to import sequences from an existing dataset
2018         boolean importDs = Desktop.jalviewClipboard != null
2019                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2020         // importDs==true instructs us to copy over new dataset sequences from
2021         // an existing alignment
2022         Vector newDs = (importDs) ? new Vector() : null; // used to create
2023         // minimum dataset set
2024
2025         for (int i = 0; i < sequences.length; i++)
2026         {
2027           if (importDs)
2028           {
2029             newDs.addElement(null);
2030           }
2031           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2032           // paste
2033           if (importDs && ds != null)
2034           {
2035             if (!newDs.contains(ds))
2036             {
2037               newDs.setElementAt(ds, i);
2038               ds = new Sequence(ds);
2039               // update with new dataset sequence
2040               sequences[i].setDatasetSequence(ds);
2041             }
2042             else
2043             {
2044               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2045             }
2046           }
2047           else
2048           {
2049             // copy and derive new dataset sequence
2050             sequences[i] = sequences[i].deriveSequence();
2051             alignment.getDataset()
2052                     .addSequence(sequences[i].getDatasetSequence());
2053             // TODO: avoid creation of duplicate dataset sequences with a
2054             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2055           }
2056           alignment.addSequence(sequences[i]); // merges dataset
2057         }
2058         if (newDs != null)
2059         {
2060           newDs.clear(); // tidy up
2061         }
2062         if (alignment.getAlignmentAnnotation() != null)
2063         {
2064           for (AlignmentAnnotation alan : alignment
2065                   .getAlignmentAnnotation())
2066           {
2067             if (alan.graphGroup > fgroup)
2068             {
2069               fgroup = alan.graphGroup;
2070             }
2071           }
2072         }
2073         if (pastedal.getAlignmentAnnotation() != null)
2074         {
2075           // Add any annotation attached to alignment.
2076           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2077           for (int i = 0; i < alann.length; i++)
2078           {
2079             annotationAdded = true;
2080             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2081             {
2082               AlignmentAnnotation newann = new AlignmentAnnotation(
2083                       alann[i]);
2084               if (newann.graphGroup > -1)
2085               {
2086                 if (newGraphGroups.size() <= newann.graphGroup
2087                         || newGraphGroups.get(newann.graphGroup) == null)
2088                 {
2089                   for (int q = newGraphGroups
2090                           .size(); q <= newann.graphGroup; q++)
2091                   {
2092                     newGraphGroups.add(q, null);
2093                   }
2094                   newGraphGroups.set(newann.graphGroup,
2095                           new Integer(++fgroup));
2096                 }
2097                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2098                         .intValue();
2099               }
2100
2101               newann.padAnnotation(alwidth);
2102               alignment.addAnnotation(newann);
2103             }
2104           }
2105         }
2106       }
2107       if (!newAlignment)
2108       {
2109         // /////
2110         // ADD HISTORY ITEM
2111         //
2112         addHistoryItem(new EditCommand(
2113                 MessageManager.getString("label.add_sequences"),
2114                 Action.PASTE, sequences, 0, alignment.getWidth(),
2115                 alignment));
2116       }
2117       // Add any annotations attached to sequences
2118       for (int i = 0; i < sequences.length; i++)
2119       {
2120         if (sequences[i].getAnnotation() != null)
2121         {
2122           AlignmentAnnotation newann;
2123           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2124           {
2125             annotationAdded = true;
2126             newann = sequences[i].getAnnotation()[a];
2127             newann.adjustForAlignment();
2128             newann.padAnnotation(alwidth);
2129             if (newann.graphGroup > -1)
2130             {
2131               if (newann.graphGroup > -1)
2132               {
2133                 if (newGraphGroups.size() <= newann.graphGroup
2134                         || newGraphGroups.get(newann.graphGroup) == null)
2135                 {
2136                   for (int q = newGraphGroups
2137                           .size(); q <= newann.graphGroup; q++)
2138                   {
2139                     newGraphGroups.add(q, null);
2140                   }
2141                   newGraphGroups.set(newann.graphGroup,
2142                           new Integer(++fgroup));
2143                 }
2144                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2145                         .intValue();
2146               }
2147             }
2148             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2149             // was
2150             // duplicated
2151             // earlier
2152             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2153                     a);
2154           }
2155         }
2156       }
2157       if (!newAlignment)
2158       {
2159
2160         // propagate alignment changed.
2161         viewport.getRanges().setEndSeq(alignment.getHeight());
2162         if (annotationAdded)
2163         {
2164           // Duplicate sequence annotation in all views.
2165           AlignmentI[] alview = this.getViewAlignments();
2166           for (int i = 0; i < sequences.length; i++)
2167           {
2168             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2169             if (sann == null)
2170             {
2171               continue;
2172             }
2173             for (int avnum = 0; avnum < alview.length; avnum++)
2174             {
2175               if (alview[avnum] != alignment)
2176               {
2177                 // duplicate in a view other than the one with input focus
2178                 int avwidth = alview[avnum].getWidth() + 1;
2179                 // this relies on sann being preserved after we
2180                 // modify the sequence's annotation array for each duplication
2181                 for (int a = 0; a < sann.length; a++)
2182                 {
2183                   AlignmentAnnotation newann = new AlignmentAnnotation(
2184                           sann[a]);
2185                   sequences[i].addAlignmentAnnotation(newann);
2186                   newann.padAnnotation(avwidth);
2187                   alview[avnum].addAnnotation(newann); // annotation was
2188                   // duplicated earlier
2189                   // TODO JAL-1145 graphGroups are not updated for sequence
2190                   // annotation added to several views. This may cause
2191                   // strangeness
2192                   alview[avnum].setAnnotationIndex(newann, a);
2193                 }
2194               }
2195             }
2196           }
2197           buildSortByAnnotationScoresMenu();
2198         }
2199         viewport.firePropertyChange("alignment", null,
2200                 alignment.getSequences());
2201         if (alignPanels != null)
2202         {
2203           for (AlignmentPanel ap : alignPanels)
2204           {
2205             ap.validateAnnotationDimensions(false);
2206           }
2207         }
2208         else
2209         {
2210           alignPanel.validateAnnotationDimensions(false);
2211         }
2212
2213       }
2214       else
2215       {
2216         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2217                 DEFAULT_HEIGHT);
2218         String newtitle = new String("Copied sequences");
2219
2220         if (Desktop.jalviewClipboard != null
2221                 && Desktop.jalviewClipboard[2] != null)
2222         {
2223           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2224           af.viewport.setHiddenColumns(hc);
2225         }
2226
2227         // >>>This is a fix for the moment, until a better solution is
2228         // found!!<<<
2229         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2230                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2231                         .getFeatureRenderer());
2232
2233         // TODO: maintain provenance of an alignment, rather than just make the
2234         // title a concatenation of operations.
2235         if (!externalPaste)
2236         {
2237           if (title.startsWith("Copied sequences"))
2238           {
2239             newtitle = title;
2240           }
2241           else
2242           {
2243             newtitle = newtitle.concat("- from " + title);
2244           }
2245         }
2246         else
2247         {
2248           newtitle = new String("Pasted sequences");
2249         }
2250
2251         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2252                 DEFAULT_HEIGHT);
2253
2254       }
2255
2256     } catch (Exception ex)
2257     {
2258       ex.printStackTrace();
2259       System.out.println("Exception whilst pasting: " + ex);
2260       // could be anything being pasted in here
2261     }
2262
2263   }
2264
2265   @Override
2266   protected void expand_newalign(ActionEvent e)
2267   {
2268     try
2269     {
2270       AlignmentI alignment = AlignmentUtils
2271               .expandContext(getViewport().getAlignment(), -1);
2272       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2273               DEFAULT_HEIGHT);
2274       String newtitle = new String("Flanking alignment");
2275
2276       if (Desktop.jalviewClipboard != null
2277               && Desktop.jalviewClipboard[2] != null)
2278       {
2279         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2280         af.viewport.setHiddenColumns(hc);
2281       }
2282
2283       // >>>This is a fix for the moment, until a better solution is
2284       // found!!<<<
2285       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2286               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2287                       .getFeatureRenderer());
2288
2289       // TODO: maintain provenance of an alignment, rather than just make the
2290       // title a concatenation of operations.
2291       {
2292         if (title.startsWith("Copied sequences"))
2293         {
2294           newtitle = title;
2295         }
2296         else
2297         {
2298           newtitle = newtitle.concat("- from " + title);
2299         }
2300       }
2301
2302       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2303
2304     } catch (Exception ex)
2305     {
2306       ex.printStackTrace();
2307       System.out.println("Exception whilst pasting: " + ex);
2308       // could be anything being pasted in here
2309     } catch (OutOfMemoryError oom)
2310     {
2311       new OOMWarning("Viewing flanking region of alignment", oom);
2312     }
2313   }
2314
2315   /**
2316    * DOCUMENT ME!
2317    *
2318    * @param e
2319    *          DOCUMENT ME!
2320    */
2321   @Override
2322   protected void cut_actionPerformed(ActionEvent e)
2323   {
2324     copy_actionPerformed(null);
2325     delete_actionPerformed(null);
2326   }
2327
2328   /**
2329    * DOCUMENT ME!
2330    *
2331    * @param e
2332    *          DOCUMENT ME!
2333    */
2334   @Override
2335   protected void delete_actionPerformed(ActionEvent evt)
2336   {
2337
2338     SequenceGroup sg = viewport.getSelectionGroup();
2339     if (sg == null)
2340     {
2341       return;
2342     }
2343
2344     /*
2345      * If the cut affects all sequences, warn, remove highlighted columns
2346      */
2347     if (sg.getSize() == viewport.getAlignment().getHeight())
2348     {
2349       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2350               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2351       if (isEntireAlignWidth)
2352       {
2353         int confirm = JvOptionPane.showConfirmDialog(this,
2354                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2355                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2356                 JvOptionPane.OK_CANCEL_OPTION);
2357
2358         if (confirm == JvOptionPane.CANCEL_OPTION
2359                 || confirm == JvOptionPane.CLOSED_OPTION)
2360         {
2361           return;
2362         }
2363       }
2364       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2365               sg.getEndRes() + 1);
2366     }
2367     SequenceI[] cut = sg.getSequences()
2368             .toArray(new SequenceI[sg.getSize()]);
2369
2370     addHistoryItem(new EditCommand(
2371             MessageManager.getString("label.cut_sequences"), Action.CUT,
2372             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2373             viewport.getAlignment()));
2374
2375     viewport.setSelectionGroup(null);
2376     viewport.sendSelection();
2377     viewport.getAlignment().deleteGroup(sg);
2378
2379     viewport.firePropertyChange("alignment", null,
2380             viewport.getAlignment().getSequences());
2381     if (viewport.getAlignment().getHeight() < 1)
2382     {
2383       try
2384       {
2385         this.setClosed(true);
2386       } catch (Exception ex)
2387       {
2388       }
2389     }
2390   }
2391
2392   /**
2393    * DOCUMENT ME!
2394    *
2395    * @param e
2396    *          DOCUMENT ME!
2397    */
2398   @Override
2399   protected void deleteGroups_actionPerformed(ActionEvent e)
2400   {
2401     if (avc.deleteGroups())
2402     {
2403       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2404       alignPanel.updateAnnotation();
2405       alignPanel.paintAlignment(true, true);
2406     }
2407   }
2408
2409   /**
2410    * DOCUMENT ME!
2411    *
2412    * @param e
2413    *          DOCUMENT ME!
2414    */
2415   @Override
2416   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2417   {
2418     SequenceGroup sg = new SequenceGroup();
2419
2420     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2421     {
2422       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2423     }
2424
2425     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2426     viewport.setSelectionGroup(sg);
2427     viewport.sendSelection();
2428     // JAL-2034 - should delegate to
2429     // alignPanel to decide if overview needs
2430     // updating.
2431     alignPanel.paintAlignment(false, false);
2432     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2433   }
2434
2435   /**
2436    * DOCUMENT ME!
2437    *
2438    * @param e
2439    *          DOCUMENT ME!
2440    */
2441   @Override
2442   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2443   {
2444     if (viewport.cursorMode)
2445     {
2446       alignPanel.getSeqPanel().keyboardNo1 = null;
2447       alignPanel.getSeqPanel().keyboardNo2 = null;
2448     }
2449     viewport.setSelectionGroup(null);
2450     viewport.getColumnSelection().clear();
2451     viewport.setSelectionGroup(null);
2452     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2453     // JAL-2034 - should delegate to
2454     // alignPanel to decide if overview needs
2455     // updating.
2456     alignPanel.paintAlignment(false, false);
2457     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2458     viewport.sendSelection();
2459   }
2460
2461   /**
2462    * DOCUMENT ME!
2463    *
2464    * @param e
2465    *          DOCUMENT ME!
2466    */
2467   @Override
2468   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2469   {
2470     SequenceGroup sg = viewport.getSelectionGroup();
2471
2472     if (sg == null)
2473     {
2474       selectAllSequenceMenuItem_actionPerformed(null);
2475
2476       return;
2477     }
2478
2479     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2480     {
2481       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2482     }
2483     // JAL-2034 - should delegate to
2484     // alignPanel to decide if overview needs
2485     // updating.
2486
2487     alignPanel.paintAlignment(true, false);
2488     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2489     viewport.sendSelection();
2490   }
2491
2492   @Override
2493   public void invertColSel_actionPerformed(ActionEvent e)
2494   {
2495     viewport.invertColumnSelection();
2496     alignPanel.paintAlignment(true, false);
2497     viewport.sendSelection();
2498   }
2499
2500   /**
2501    * DOCUMENT ME!
2502    *
2503    * @param e
2504    *          DOCUMENT ME!
2505    */
2506   @Override
2507   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2508   {
2509     trimAlignment(true);
2510   }
2511
2512   /**
2513    * DOCUMENT ME!
2514    *
2515    * @param e
2516    *          DOCUMENT ME!
2517    */
2518   @Override
2519   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2520   {
2521     trimAlignment(false);
2522   }
2523
2524   void trimAlignment(boolean trimLeft)
2525   {
2526     ColumnSelection colSel = viewport.getColumnSelection();
2527     int column;
2528
2529     if (!colSel.isEmpty())
2530     {
2531       if (trimLeft)
2532       {
2533         column = colSel.getMin();
2534       }
2535       else
2536       {
2537         column = colSel.getMax();
2538       }
2539
2540       SequenceI[] seqs;
2541       if (viewport.getSelectionGroup() != null)
2542       {
2543         seqs = viewport.getSelectionGroup()
2544                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2545       }
2546       else
2547       {
2548         seqs = viewport.getAlignment().getSequencesArray();
2549       }
2550
2551       TrimRegionCommand trimRegion;
2552       if (trimLeft)
2553       {
2554         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2555                 column, viewport.getAlignment());
2556         viewport.getRanges().setStartRes(0);
2557       }
2558       else
2559       {
2560         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2561                 column, viewport.getAlignment());
2562       }
2563
2564       statusBar.setText(MessageManager
2565               .formatMessage("label.removed_columns", new String[]
2566               { Integer.valueOf(trimRegion.getSize()).toString() }));
2567
2568       addHistoryItem(trimRegion);
2569
2570       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2571       {
2572         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2573                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2574         {
2575           viewport.getAlignment().deleteGroup(sg);
2576         }
2577       }
2578
2579       viewport.firePropertyChange("alignment", null,
2580               viewport.getAlignment().getSequences());
2581     }
2582   }
2583
2584   /**
2585    * DOCUMENT ME!
2586    *
2587    * @param e
2588    *          DOCUMENT ME!
2589    */
2590   @Override
2591   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2592   {
2593     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2594
2595     SequenceI[] seqs;
2596     if (viewport.getSelectionGroup() != null)
2597     {
2598       seqs = viewport.getSelectionGroup()
2599               .getSequencesAsArray(viewport.getHiddenRepSequences());
2600       start = viewport.getSelectionGroup().getStartRes();
2601       end = viewport.getSelectionGroup().getEndRes();
2602     }
2603     else
2604     {
2605       seqs = viewport.getAlignment().getSequencesArray();
2606     }
2607
2608     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2609             "Remove Gapped Columns", seqs, start, end,
2610             viewport.getAlignment());
2611
2612     addHistoryItem(removeGapCols);
2613
2614     statusBar.setText(MessageManager
2615             .formatMessage("label.removed_empty_columns", new Object[]
2616             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2617
2618     // This is to maintain viewport position on first residue
2619     // of first sequence
2620     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2621     ViewportRanges ranges = viewport.getRanges();
2622     int startRes = seq.findPosition(ranges.getStartRes());
2623     // ShiftList shifts;
2624     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2625     // edit.alColumnChanges=shifts.getInverse();
2626     // if (viewport.hasHiddenColumns)
2627     // viewport.getColumnSelection().compensateForEdits(shifts);
2628     ranges.setStartRes(seq.findIndex(startRes) - 1);
2629     viewport.firePropertyChange("alignment", null,
2630             viewport.getAlignment().getSequences());
2631
2632   }
2633
2634   /**
2635    * DOCUMENT ME!
2636    *
2637    * @param e
2638    *          DOCUMENT ME!
2639    */
2640   @Override
2641   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2642   {
2643     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2644
2645     SequenceI[] seqs;
2646     if (viewport.getSelectionGroup() != null)
2647     {
2648       seqs = viewport.getSelectionGroup()
2649               .getSequencesAsArray(viewport.getHiddenRepSequences());
2650       start = viewport.getSelectionGroup().getStartRes();
2651       end = viewport.getSelectionGroup().getEndRes();
2652     }
2653     else
2654     {
2655       seqs = viewport.getAlignment().getSequencesArray();
2656     }
2657
2658     // This is to maintain viewport position on first residue
2659     // of first sequence
2660     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2661     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2662
2663     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2664             viewport.getAlignment()));
2665
2666     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2667
2668     viewport.firePropertyChange("alignment", null,
2669             viewport.getAlignment().getSequences());
2670
2671   }
2672
2673   /**
2674    * DOCUMENT ME!
2675    *
2676    * @param e
2677    *          DOCUMENT ME!
2678    */
2679   @Override
2680   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2681   {
2682     viewport.setPadGaps(padGapsMenuitem.isSelected());
2683     viewport.firePropertyChange("alignment", null,
2684             viewport.getAlignment().getSequences());
2685   }
2686
2687   /**
2688    * DOCUMENT ME!
2689    *
2690    * @param e
2691    *          DOCUMENT ME!
2692    */
2693   @Override
2694   public void findMenuItem_actionPerformed(ActionEvent e)
2695   {
2696     new Finder();
2697   }
2698
2699   /**
2700    * Create a new view of the current alignment.
2701    */
2702   @Override
2703   public void newView_actionPerformed(ActionEvent e)
2704   {
2705     newView(null, true);
2706   }
2707
2708   /**
2709    * Creates and shows a new view of the current alignment.
2710    *
2711    * @param viewTitle
2712    *          title of newly created view; if null, one will be generated
2713    * @param copyAnnotation
2714    *          if true then duplicate all annnotation, groups and settings
2715    * @return new alignment panel, already displayed.
2716    */
2717   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2718   {
2719     /*
2720      * Create a new AlignmentPanel (with its own, new Viewport)
2721      */
2722     AlignmentPanel newap = new jalview.project.Jalview2XML()
2723             .copyAlignPanel(alignPanel);
2724     if (!copyAnnotation)
2725     {
2726       /*
2727        * remove all groups and annotation except for the automatic stuff
2728        */
2729       newap.av.getAlignment().deleteAllGroups();
2730       newap.av.getAlignment().deleteAllAnnotations(false);
2731     }
2732
2733     newap.av.setGatherViewsHere(false);
2734
2735     if (viewport.getViewName() == null)
2736     {
2737       viewport.setViewName(
2738               MessageManager.getString("label.view_name_original"));
2739     }
2740
2741     /*
2742      * Views share the same edits undo and redo stacks
2743      */
2744     newap.av.setHistoryList(viewport.getHistoryList());
2745     newap.av.setRedoList(viewport.getRedoList());
2746
2747     /*
2748      * Views share the same mappings; need to deregister any new mappings
2749      * created by copyAlignPanel, and register the new reference to the shared
2750      * mappings
2751      */
2752     newap.av.replaceMappings(viewport.getAlignment());
2753
2754     /*
2755      * start up cDNA consensus (if applicable) now mappings are in place
2756      */
2757     if (newap.av.initComplementConsensus())
2758     {
2759       newap.refresh(true); // adjust layout of annotations
2760     }
2761
2762     newap.av.setViewName(getNewViewName(viewTitle));
2763
2764     addAlignmentPanel(newap, true);
2765     newap.alignmentChanged();
2766
2767     if (alignPanels.size() == 2)
2768     {
2769       viewport.setGatherViewsHere(true);
2770     }
2771     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2772     return newap;
2773   }
2774
2775   /**
2776    * Make a new name for the view, ensuring it is unique within the current
2777    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2778    * these now use viewId. Unique view names are still desirable for usability.)
2779    *
2780    * @param viewTitle
2781    * @return
2782    */
2783   protected String getNewViewName(String viewTitle)
2784   {
2785     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2786     boolean addFirstIndex = false;
2787     if (viewTitle == null || viewTitle.trim().length() == 0)
2788     {
2789       viewTitle = MessageManager.getString("action.view");
2790       addFirstIndex = true;
2791     }
2792     else
2793     {
2794       index = 1;// we count from 1 if given a specific name
2795     }
2796     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2797
2798     List<Component> comps = PaintRefresher.components
2799             .get(viewport.getSequenceSetId());
2800
2801     List<String> existingNames = getExistingViewNames(comps);
2802
2803     while (existingNames.contains(newViewName))
2804     {
2805       newViewName = viewTitle + " " + (++index);
2806     }
2807     return newViewName;
2808   }
2809
2810   /**
2811    * Returns a list of distinct view names found in the given list of
2812    * components. View names are held on the viewport of an AlignmentPanel.
2813    *
2814    * @param comps
2815    * @return
2816    */
2817   protected List<String> getExistingViewNames(List<Component> comps)
2818   {
2819     List<String> existingNames = new ArrayList<>();
2820     for (Component comp : comps)
2821     {
2822       if (comp instanceof AlignmentPanel)
2823       {
2824         AlignmentPanel ap = (AlignmentPanel) comp;
2825         if (!existingNames.contains(ap.av.getViewName()))
2826         {
2827           existingNames.add(ap.av.getViewName());
2828         }
2829       }
2830     }
2831     return existingNames;
2832   }
2833
2834   /**
2835    * Explode tabbed views into separate windows.
2836    */
2837   @Override
2838   public void expandViews_actionPerformed(ActionEvent e)
2839   {
2840     Desktop.explodeViews(this);
2841   }
2842
2843   /**
2844    * Gather views in separate windows back into a tabbed presentation.
2845    */
2846   @Override
2847   public void gatherViews_actionPerformed(ActionEvent e)
2848   {
2849     Desktop.instance.gatherViews(this);
2850   }
2851
2852   /**
2853    * DOCUMENT ME!
2854    *
2855    * @param e
2856    *          DOCUMENT ME!
2857    */
2858   @Override
2859   public void font_actionPerformed(ActionEvent e)
2860   {
2861     new FontChooser(alignPanel);
2862   }
2863
2864   /**
2865    * DOCUMENT ME!
2866    *
2867    * @param e
2868    *          DOCUMENT ME!
2869    */
2870   @Override
2871   protected void seqLimit_actionPerformed(ActionEvent e)
2872   {
2873     viewport.setShowJVSuffix(seqLimits.isSelected());
2874
2875     alignPanel.getIdPanel().getIdCanvas()
2876             .setPreferredSize(alignPanel.calculateIdWidth());
2877     alignPanel.paintAlignment(true, false);
2878   }
2879
2880   @Override
2881   public void idRightAlign_actionPerformed(ActionEvent e)
2882   {
2883     viewport.setRightAlignIds(idRightAlign.isSelected());
2884     alignPanel.paintAlignment(false, false);
2885   }
2886
2887   @Override
2888   public void centreColumnLabels_actionPerformed(ActionEvent e)
2889   {
2890     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2891     alignPanel.paintAlignment(false, false);
2892   }
2893
2894   /*
2895    * (non-Javadoc)
2896    *
2897    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2898    */
2899   @Override
2900   protected void followHighlight_actionPerformed()
2901   {
2902     /*
2903      * Set the 'follow' flag on the Viewport (and scroll to position if now
2904      * true).
2905      */
2906     final boolean state = this.followHighlightMenuItem.getState();
2907     viewport.setFollowHighlight(state);
2908     if (state)
2909     {
2910       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2911     }
2912   }
2913
2914   /**
2915    * DOCUMENT ME!
2916    *
2917    * @param e
2918    *          DOCUMENT ME!
2919    */
2920   @Override
2921   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2922   {
2923     viewport.setColourText(colourTextMenuItem.isSelected());
2924     alignPanel.paintAlignment(false, false);
2925   }
2926
2927   /**
2928    * DOCUMENT ME!
2929    *
2930    * @param e
2931    *          DOCUMENT ME!
2932    */
2933   @Override
2934   public void wrapMenuItem_actionPerformed(ActionEvent e)
2935   {
2936     scaleAbove.setVisible(wrapMenuItem.isSelected());
2937     scaleLeft.setVisible(wrapMenuItem.isSelected());
2938     scaleRight.setVisible(wrapMenuItem.isSelected());
2939     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2940     alignPanel.updateLayout();
2941   }
2942
2943   @Override
2944   public void showAllSeqs_actionPerformed(ActionEvent e)
2945   {
2946     viewport.showAllHiddenSeqs();
2947   }
2948
2949   @Override
2950   public void showAllColumns_actionPerformed(ActionEvent e)
2951   {
2952     viewport.showAllHiddenColumns();
2953     alignPanel.paintAlignment(true, true);
2954     viewport.sendSelection();
2955   }
2956
2957   @Override
2958   public void hideSelSequences_actionPerformed(ActionEvent e)
2959   {
2960     viewport.hideAllSelectedSeqs();
2961   }
2962
2963   /**
2964    * called by key handler and the hide all/show all menu items
2965    *
2966    * @param toggleSeqs
2967    * @param toggleCols
2968    */
2969   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2970   {
2971
2972     boolean hide = false;
2973     SequenceGroup sg = viewport.getSelectionGroup();
2974     if (!toggleSeqs && !toggleCols)
2975     {
2976       // Hide everything by the current selection - this is a hack - we do the
2977       // invert and then hide
2978       // first check that there will be visible columns after the invert.
2979       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2980               && sg.getStartRes() <= sg.getEndRes()))
2981       {
2982         // now invert the sequence set, if required - empty selection implies
2983         // that no hiding is required.
2984         if (sg != null)
2985         {
2986           invertSequenceMenuItem_actionPerformed(null);
2987           sg = viewport.getSelectionGroup();
2988           toggleSeqs = true;
2989
2990         }
2991         viewport.expandColSelection(sg, true);
2992         // finally invert the column selection and get the new sequence
2993         // selection.
2994         invertColSel_actionPerformed(null);
2995         toggleCols = true;
2996       }
2997     }
2998
2999     if (toggleSeqs)
3000     {
3001       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3002       {
3003         hideSelSequences_actionPerformed(null);
3004         hide = true;
3005       }
3006       else if (!(toggleCols && viewport.hasSelectedColumns()))
3007       {
3008         showAllSeqs_actionPerformed(null);
3009       }
3010     }
3011
3012     if (toggleCols)
3013     {
3014       if (viewport.hasSelectedColumns())
3015       {
3016         hideSelColumns_actionPerformed(null);
3017         if (!toggleSeqs)
3018         {
3019           viewport.setSelectionGroup(sg);
3020         }
3021       }
3022       else if (!hide)
3023       {
3024         showAllColumns_actionPerformed(null);
3025       }
3026     }
3027   }
3028
3029   /*
3030    * (non-Javadoc)
3031    *
3032    * @see
3033    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3034    * event.ActionEvent)
3035    */
3036   @Override
3037   public void hideAllButSelection_actionPerformed(ActionEvent e)
3038   {
3039     toggleHiddenRegions(false, false);
3040     viewport.sendSelection();
3041   }
3042
3043   /*
3044    * (non-Javadoc)
3045    *
3046    * @see
3047    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3048    * .ActionEvent)
3049    */
3050   @Override
3051   public void hideAllSelection_actionPerformed(ActionEvent e)
3052   {
3053     SequenceGroup sg = viewport.getSelectionGroup();
3054     viewport.expandColSelection(sg, false);
3055     viewport.hideAllSelectedSeqs();
3056     viewport.hideSelectedColumns();
3057     alignPanel.paintAlignment(true, true);
3058     viewport.sendSelection();
3059   }
3060
3061   /*
3062    * (non-Javadoc)
3063    *
3064    * @see
3065    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3066    * ActionEvent)
3067    */
3068   @Override
3069   public void showAllhidden_actionPerformed(ActionEvent e)
3070   {
3071     viewport.showAllHiddenColumns();
3072     viewport.showAllHiddenSeqs();
3073     alignPanel.paintAlignment(true, true);
3074     viewport.sendSelection();
3075   }
3076
3077   @Override
3078   public void hideSelColumns_actionPerformed(ActionEvent e)
3079   {
3080     viewport.hideSelectedColumns();
3081     alignPanel.paintAlignment(true, true);
3082     viewport.sendSelection();
3083   }
3084
3085   @Override
3086   public void hiddenMarkers_actionPerformed(ActionEvent e)
3087   {
3088     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3089     repaint();
3090   }
3091
3092   /**
3093    * DOCUMENT ME!
3094    *
3095    * @param e
3096    *          DOCUMENT ME!
3097    */
3098   @Override
3099   protected void scaleAbove_actionPerformed(ActionEvent e)
3100   {
3101     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3102     // TODO: do we actually need to update overview for scale above change ?
3103     alignPanel.paintAlignment(true, false);
3104   }
3105
3106   /**
3107    * DOCUMENT ME!
3108    *
3109    * @param e
3110    *          DOCUMENT ME!
3111    */
3112   @Override
3113   protected void scaleLeft_actionPerformed(ActionEvent e)
3114   {
3115     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3116     alignPanel.paintAlignment(true, false);
3117   }
3118
3119   /**
3120    * DOCUMENT ME!
3121    *
3122    * @param e
3123    *          DOCUMENT ME!
3124    */
3125   @Override
3126   protected void scaleRight_actionPerformed(ActionEvent e)
3127   {
3128     viewport.setScaleRightWrapped(scaleRight.isSelected());
3129     alignPanel.paintAlignment(true, false);
3130   }
3131
3132   /**
3133    * DOCUMENT ME!
3134    *
3135    * @param e
3136    *          DOCUMENT ME!
3137    */
3138   @Override
3139   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3140   {
3141     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3142     alignPanel.paintAlignment(false, false);
3143   }
3144
3145   /**
3146    * DOCUMENT ME!
3147    *
3148    * @param e
3149    *          DOCUMENT ME!
3150    */
3151   @Override
3152   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3153   {
3154     viewport.setShowText(viewTextMenuItem.isSelected());
3155     alignPanel.paintAlignment(false, false);
3156   }
3157
3158   /**
3159    * DOCUMENT ME!
3160    *
3161    * @param e
3162    *          DOCUMENT ME!
3163    */
3164   @Override
3165   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3166   {
3167     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3168     alignPanel.paintAlignment(false, false);
3169   }
3170
3171   public FeatureSettings featureSettings;
3172
3173   @Override
3174   public FeatureSettingsControllerI getFeatureSettingsUI()
3175   {
3176     return featureSettings;
3177   }
3178
3179   @Override
3180   public void featureSettings_actionPerformed(ActionEvent e)
3181   {
3182     if (featureSettings != null)
3183     {
3184       featureSettings.close();
3185       featureSettings = null;
3186     }
3187     if (!showSeqFeatures.isSelected())
3188     {
3189       // make sure features are actually displayed
3190       showSeqFeatures.setSelected(true);
3191       showSeqFeatures_actionPerformed(null);
3192     }
3193     featureSettings = new FeatureSettings(this);
3194   }
3195
3196   /**
3197    * Set or clear 'Show Sequence Features'
3198    *
3199    * @param evt
3200    *          DOCUMENT ME!
3201    */
3202   @Override
3203   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3204   {
3205     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3206     alignPanel.paintAlignment(true, true);
3207   }
3208
3209   /**
3210    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3211    * the annotations panel as a whole.
3212    *
3213    * The options to show/hide all annotations should be enabled when the panel
3214    * is shown, and disabled when the panel is hidden.
3215    *
3216    * @param e
3217    */
3218   @Override
3219   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3220   {
3221     final boolean setVisible = annotationPanelMenuItem.isSelected();
3222     viewport.setShowAnnotation(setVisible);
3223     this.showAllSeqAnnotations.setEnabled(setVisible);
3224     this.hideAllSeqAnnotations.setEnabled(setVisible);
3225     this.showAllAlAnnotations.setEnabled(setVisible);
3226     this.hideAllAlAnnotations.setEnabled(setVisible);
3227     alignPanel.updateLayout();
3228   }
3229
3230   @Override
3231   public void alignmentProperties()
3232   {
3233     JEditorPane editPane = new JEditorPane("text/html", "");
3234     editPane.setEditable(false);
3235     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3236             .formatAsHtml();
3237     editPane.setText(
3238             MessageManager.formatMessage("label.html_content", new Object[]
3239             { contents.toString() }));
3240     JInternalFrame frame = new JInternalFrame();
3241     frame.getContentPane().add(new JScrollPane(editPane));
3242
3243     Desktop.addInternalFrame(frame, MessageManager
3244             .formatMessage("label.alignment_properties", new Object[]
3245             { getTitle() }), 500, 400);
3246   }
3247
3248   /**
3249    * DOCUMENT ME!
3250    *
3251    * @param e
3252    *          DOCUMENT ME!
3253    */
3254   @Override
3255   public void overviewMenuItem_actionPerformed(ActionEvent e)
3256   {
3257     if (alignPanel.overviewPanel != null)
3258     {
3259       return;
3260     }
3261
3262     JInternalFrame frame = new JInternalFrame();
3263     final OverviewPanel overview = new OverviewPanel(alignPanel);
3264     frame.setContentPane(overview);
3265     Desktop.addInternalFrame(frame, MessageManager
3266             .formatMessage("label.overview_params", new Object[]
3267             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3268             true, true);
3269     frame.pack();
3270     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3271     frame.addInternalFrameListener(
3272             new javax.swing.event.InternalFrameAdapter()
3273             {
3274               @Override
3275               public void internalFrameClosed(
3276                       javax.swing.event.InternalFrameEvent evt)
3277               {
3278                 overview.dispose();
3279                 alignPanel.setOverviewPanel(null);
3280               };
3281             });
3282     if (getKeyListeners().length > 0)
3283     {
3284       frame.addKeyListener(getKeyListeners()[0]);
3285     }
3286
3287     alignPanel.setOverviewPanel(overview);
3288   }
3289
3290   @Override
3291   public void textColour_actionPerformed()
3292   {
3293     new TextColourChooser().chooseColour(alignPanel, null);
3294   }
3295
3296   /*
3297    * public void covariationColour_actionPerformed() {
3298    * changeColour(new
3299    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3300    * ()[0])); }
3301    */
3302   @Override
3303   public void annotationColour_actionPerformed()
3304   {
3305     new AnnotationColourChooser(viewport, alignPanel);
3306   }
3307
3308   @Override
3309   public void annotationColumn_actionPerformed(ActionEvent e)
3310   {
3311     new AnnotationColumnChooser(viewport, alignPanel);
3312   }
3313
3314   /**
3315    * Action on the user checking or unchecking the option to apply the selected
3316    * colour scheme to all groups. If unchecked, groups may have their own
3317    * independent colour schemes.
3318    *
3319    * @param selected
3320    */
3321   @Override
3322   public void applyToAllGroups_actionPerformed(boolean selected)
3323   {
3324     viewport.setColourAppliesToAllGroups(selected);
3325   }
3326
3327   /**
3328    * Action on user selecting a colour from the colour menu
3329    *
3330    * @param name
3331    *          the name (not the menu item label!) of the colour scheme
3332    */
3333   @Override
3334   public void changeColour_actionPerformed(String name)
3335   {
3336     /*
3337      * 'User Defined' opens a panel to configure or load a
3338      * user-defined colour scheme
3339      */
3340     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3341     {
3342       new UserDefinedColours(alignPanel);
3343       return;
3344     }
3345
3346     /*
3347      * otherwise set the chosen colour scheme (or null for 'None')
3348      */
3349     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3350             viewport.getAlignment(), viewport.getHiddenRepSequences());
3351     changeColour(cs);
3352   }
3353
3354   /**
3355    * Actions on setting or changing the alignment colour scheme
3356    *
3357    * @param cs
3358    */
3359   @Override
3360   public void changeColour(ColourSchemeI cs)
3361   {
3362     // TODO: pull up to controller method
3363     ColourMenuHelper.setColourSelected(colourMenu, cs);
3364
3365     viewport.setGlobalColourScheme(cs);
3366
3367     alignPanel.paintAlignment(true, true);
3368   }
3369
3370   /**
3371    * Show the PID threshold slider panel
3372    */
3373   @Override
3374   protected void modifyPID_actionPerformed()
3375   {
3376     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3377             alignPanel.getViewName());
3378     SliderPanel.showPIDSlider();
3379   }
3380
3381   /**
3382    * Show the Conservation slider panel
3383    */
3384   @Override
3385   protected void modifyConservation_actionPerformed()
3386   {
3387     SliderPanel.setConservationSlider(alignPanel,
3388             viewport.getResidueShading(), alignPanel.getViewName());
3389     SliderPanel.showConservationSlider();
3390   }
3391
3392   /**
3393    * Action on selecting or deselecting (Colour) By Conservation
3394    */
3395   @Override
3396   public void conservationMenuItem_actionPerformed(boolean selected)
3397   {
3398     modifyConservation.setEnabled(selected);
3399     viewport.setConservationSelected(selected);
3400     viewport.getResidueShading().setConservationApplied(selected);
3401
3402     changeColour(viewport.getGlobalColourScheme());
3403     if (selected)
3404     {
3405       modifyConservation_actionPerformed();
3406     }
3407     else
3408     {
3409       SliderPanel.hideConservationSlider();
3410     }
3411   }
3412
3413   /**
3414    * Action on selecting or deselecting (Colour) Above PID Threshold
3415    */
3416   @Override
3417   public void abovePIDThreshold_actionPerformed(boolean selected)
3418   {
3419     modifyPID.setEnabled(selected);
3420     viewport.setAbovePIDThreshold(selected);
3421     if (!selected)
3422     {
3423       viewport.getResidueShading().setThreshold(0,
3424               viewport.isIgnoreGapsConsensus());
3425     }
3426
3427     changeColour(viewport.getGlobalColourScheme());
3428     if (selected)
3429     {
3430       modifyPID_actionPerformed();
3431     }
3432     else
3433     {
3434       SliderPanel.hidePIDSlider();
3435     }
3436   }
3437
3438   /**
3439    * DOCUMENT ME!
3440    *
3441    * @param e
3442    *          DOCUMENT ME!
3443    */
3444   @Override
3445   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3446   {
3447     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3448     AlignmentSorter.sortByPID(viewport.getAlignment(),
3449             viewport.getAlignment().getSequenceAt(0));
3450     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3451             viewport.getAlignment()));
3452     alignPanel.paintAlignment(true, false);
3453   }
3454
3455   /**
3456    * DOCUMENT ME!
3457    *
3458    * @param e
3459    *          DOCUMENT ME!
3460    */
3461   @Override
3462   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3463   {
3464     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3465     AlignmentSorter.sortByID(viewport.getAlignment());
3466     addHistoryItem(
3467             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3468     alignPanel.paintAlignment(true, false);
3469   }
3470
3471   /**
3472    * DOCUMENT ME!
3473    *
3474    * @param e
3475    *          DOCUMENT ME!
3476    */
3477   @Override
3478   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3479   {
3480     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3481     AlignmentSorter.sortByLength(viewport.getAlignment());
3482     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3483             viewport.getAlignment()));
3484     alignPanel.paintAlignment(true, false);
3485   }
3486
3487   /**
3488    * DOCUMENT ME!
3489    *
3490    * @param e
3491    *          DOCUMENT ME!
3492    */
3493   @Override
3494   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3495   {
3496     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3497     AlignmentSorter.sortByGroup(viewport.getAlignment());
3498     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3499             viewport.getAlignment()));
3500
3501     alignPanel.paintAlignment(true, false);
3502   }
3503
3504   /**
3505    * DOCUMENT ME!
3506    *
3507    * @param e
3508    *          DOCUMENT ME!
3509    */
3510   @Override
3511   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3512   {
3513     new RedundancyPanel(alignPanel, this);
3514   }
3515
3516   /**
3517    * DOCUMENT ME!
3518    *
3519    * @param e
3520    *          DOCUMENT ME!
3521    */
3522   @Override
3523   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3524   {
3525     if ((viewport.getSelectionGroup() == null)
3526             || (viewport.getSelectionGroup().getSize() < 2))
3527     {
3528       JvOptionPane.showInternalMessageDialog(this,
3529               MessageManager.getString(
3530                       "label.you_must_select_least_two_sequences"),
3531               MessageManager.getString("label.invalid_selection"),
3532               JvOptionPane.WARNING_MESSAGE);
3533     }
3534     else
3535     {
3536       JInternalFrame frame = new JInternalFrame();
3537       frame.setContentPane(new PairwiseAlignPanel(viewport));
3538       Desktop.addInternalFrame(frame,
3539               MessageManager.getString("action.pairwise_alignment"), 600,
3540               500);
3541     }
3542   }
3543
3544   @Override
3545   public void autoCalculate_actionPerformed(ActionEvent e)
3546   {
3547     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3548     if (viewport.autoCalculateConsensus)
3549     {
3550       viewport.firePropertyChange("alignment", null,
3551               viewport.getAlignment().getSequences());
3552     }
3553   }
3554
3555   @Override
3556   public void sortByTreeOption_actionPerformed(ActionEvent e)
3557   {
3558     viewport.sortByTree = sortByTree.isSelected();
3559   }
3560
3561   @Override
3562   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3563   {
3564     viewport.followSelection = listenToViewSelections.isSelected();
3565   }
3566
3567   /**
3568    * Constructs a tree panel and adds it to the desktop
3569    *
3570    * @param type
3571    *          tree type (NJ or AV)
3572    * @param modelName
3573    *          name of score model used to compute the tree
3574    * @param options
3575    *          parameters for the distance or similarity calculation
3576    */
3577   void newTreePanel(String type, String modelName,
3578           SimilarityParamsI options)
3579   {
3580     String frameTitle = "";
3581     TreePanel tp;
3582
3583     boolean onSelection = false;
3584     if (viewport.getSelectionGroup() != null
3585             && viewport.getSelectionGroup().getSize() > 0)
3586     {
3587       SequenceGroup sg = viewport.getSelectionGroup();
3588
3589       /* Decide if the selection is a column region */
3590       for (SequenceI _s : sg.getSequences())
3591       {
3592         if (_s.getLength() < sg.getEndRes())
3593         {
3594           JvOptionPane.showMessageDialog(Desktop.desktop,
3595                   MessageManager.getString(
3596                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3597                   MessageManager.getString(
3598                           "label.sequences_selection_not_aligned"),
3599                   JvOptionPane.WARNING_MESSAGE);
3600
3601           return;
3602         }
3603       }
3604       onSelection = true;
3605     }
3606     else
3607     {
3608       if (viewport.getAlignment().getHeight() < 2)
3609       {
3610         return;
3611       }
3612     }
3613
3614     tp = new TreePanel(alignPanel, type, modelName, options);
3615     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3616
3617     frameTitle += " from ";
3618
3619     if (viewport.getViewName() != null)
3620     {
3621       frameTitle += viewport.getViewName() + " of ";
3622     }
3623
3624     frameTitle += this.title;
3625
3626     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3627   }
3628
3629   /**
3630    * DOCUMENT ME!
3631    *
3632    * @param title
3633    *          DOCUMENT ME!
3634    * @param order
3635    *          DOCUMENT ME!
3636    */
3637   public void addSortByOrderMenuItem(String title,
3638           final AlignmentOrder order)
3639   {
3640     final JMenuItem item = new JMenuItem(MessageManager
3641             .formatMessage("action.by_title_param", new Object[]
3642             { title }));
3643     sort.add(item);
3644     item.addActionListener(new java.awt.event.ActionListener()
3645     {
3646       @Override
3647       public void actionPerformed(ActionEvent e)
3648       {
3649         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3650
3651         // TODO: JBPNote - have to map order entries to curent SequenceI
3652         // pointers
3653         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3654
3655         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3656                 viewport.getAlignment()));
3657
3658         alignPanel.paintAlignment(true, false);
3659       }
3660     });
3661   }
3662
3663   /**
3664    * Add a new sort by annotation score menu item
3665    *
3666    * @param sort
3667    *          the menu to add the option to
3668    * @param scoreLabel
3669    *          the label used to retrieve scores for each sequence on the
3670    *          alignment
3671    */
3672   public void addSortByAnnotScoreMenuItem(JMenu sort,
3673           final String scoreLabel)
3674   {
3675     final JMenuItem item = new JMenuItem(scoreLabel);
3676     sort.add(item);
3677     item.addActionListener(new java.awt.event.ActionListener()
3678     {
3679       @Override
3680       public void actionPerformed(ActionEvent e)
3681       {
3682         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3683         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3684                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3685         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3686                 viewport.getAlignment()));
3687         alignPanel.paintAlignment(true, false);
3688       }
3689     });
3690   }
3691
3692   /**
3693    * last hash for alignment's annotation array - used to minimise cost of
3694    * rebuild.
3695    */
3696   protected int _annotationScoreVectorHash;
3697
3698   /**
3699    * search the alignment and rebuild the sort by annotation score submenu the
3700    * last alignment annotation vector hash is stored to minimize cost of
3701    * rebuilding in subsequence calls.
3702    *
3703    */
3704   @Override
3705   public void buildSortByAnnotationScoresMenu()
3706   {
3707     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3708     {
3709       return;
3710     }
3711
3712     if (viewport.getAlignment().getAlignmentAnnotation()
3713             .hashCode() != _annotationScoreVectorHash)
3714     {
3715       sortByAnnotScore.removeAll();
3716       // almost certainly a quicker way to do this - but we keep it simple
3717       Hashtable scoreSorts = new Hashtable();
3718       AlignmentAnnotation aann[];
3719       for (SequenceI sqa : viewport.getAlignment().getSequences())
3720       {
3721         aann = sqa.getAnnotation();
3722         for (int i = 0; aann != null && i < aann.length; i++)
3723         {
3724           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3725           {
3726             scoreSorts.put(aann[i].label, aann[i].label);
3727           }
3728         }
3729       }
3730       Enumeration labels = scoreSorts.keys();
3731       while (labels.hasMoreElements())
3732       {
3733         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3734                 (String) labels.nextElement());
3735       }
3736       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3737       scoreSorts.clear();
3738
3739       _annotationScoreVectorHash = viewport.getAlignment()
3740               .getAlignmentAnnotation().hashCode();
3741     }
3742   }
3743
3744   /**
3745    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3746    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3747    * call. Listeners are added to remove the menu item when the treePanel is
3748    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3749    * modified.
3750    */
3751   @Override
3752   public void buildTreeSortMenu()
3753   {
3754     sortByTreeMenu.removeAll();
3755
3756     List<Component> comps = PaintRefresher.components
3757             .get(viewport.getSequenceSetId());
3758     List<TreePanel> treePanels = new ArrayList<>();
3759     for (Component comp : comps)
3760     {
3761       if (comp instanceof TreePanel)
3762       {
3763         treePanels.add((TreePanel) comp);
3764       }
3765     }
3766
3767     if (treePanels.size() < 1)
3768     {
3769       sortByTreeMenu.setVisible(false);
3770       return;
3771     }
3772
3773     sortByTreeMenu.setVisible(true);
3774
3775     for (final TreePanel tp : treePanels)
3776     {
3777       final JMenuItem item = new JMenuItem(tp.getTitle());
3778       item.addActionListener(new java.awt.event.ActionListener()
3779       {
3780         @Override
3781         public void actionPerformed(ActionEvent e)
3782         {
3783           tp.sortByTree_actionPerformed();
3784           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3785
3786         }
3787       });
3788
3789       sortByTreeMenu.add(item);
3790     }
3791   }
3792
3793   public boolean sortBy(AlignmentOrder alorder, String undoname)
3794   {
3795     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3796     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3797     if (undoname != null)
3798     {
3799       addHistoryItem(new OrderCommand(undoname, oldOrder,
3800               viewport.getAlignment()));
3801     }
3802     alignPanel.paintAlignment(true, false);
3803     return true;
3804   }
3805
3806   /**
3807    * Work out whether the whole set of sequences or just the selected set will
3808    * be submitted for multiple alignment.
3809    *
3810    */
3811   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3812   {
3813     // Now, check we have enough sequences
3814     AlignmentView msa = null;
3815
3816     if ((viewport.getSelectionGroup() != null)
3817             && (viewport.getSelectionGroup().getSize() > 1))
3818     {
3819       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3820       // some common interface!
3821       /*
3822        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3823        * SequenceI[sz = seqs.getSize(false)];
3824        *
3825        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3826        * seqs.getSequenceAt(i); }
3827        */
3828       msa = viewport.getAlignmentView(true);
3829     }
3830     else if (viewport.getSelectionGroup() != null
3831             && viewport.getSelectionGroup().getSize() == 1)
3832     {
3833       int option = JvOptionPane.showConfirmDialog(this,
3834               MessageManager.getString("warn.oneseq_msainput_selection"),
3835               MessageManager.getString("label.invalid_selection"),
3836               JvOptionPane.OK_CANCEL_OPTION);
3837       if (option == JvOptionPane.OK_OPTION)
3838       {
3839         msa = viewport.getAlignmentView(false);
3840       }
3841     }
3842     else
3843     {
3844       msa = viewport.getAlignmentView(false);
3845     }
3846     return msa;
3847   }
3848
3849   /**
3850    * Decides what is submitted to a secondary structure prediction service: the
3851    * first sequence in the alignment, or in the current selection, or, if the
3852    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3853    * region or the whole alignment. (where the first sequence in the set is the
3854    * one that the prediction will be for).
3855    */
3856   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3857   {
3858     AlignmentView seqs = null;
3859
3860     if ((viewport.getSelectionGroup() != null)
3861             && (viewport.getSelectionGroup().getSize() > 0))
3862     {
3863       seqs = viewport.getAlignmentView(true);
3864     }
3865     else
3866     {
3867       seqs = viewport.getAlignmentView(false);
3868     }
3869     // limit sequences - JBPNote in future - could spawn multiple prediction
3870     // jobs
3871     // TODO: viewport.getAlignment().isAligned is a global state - the local
3872     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3873     if (!viewport.getAlignment().isAligned(false))
3874     {
3875       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3876       // TODO: if seqs.getSequences().length>1 then should really have warned
3877       // user!
3878
3879     }
3880     return seqs;
3881   }
3882
3883   /**
3884    * DOCUMENT ME!
3885    *
3886    * @param e
3887    *          DOCUMENT ME!
3888    */
3889   @Override
3890   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3891   {
3892     // Pick the tree file
3893     JalviewFileChooser chooser = new JalviewFileChooser(
3894             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3895     chooser.setFileView(new JalviewFileView());
3896     chooser.setDialogTitle(
3897             MessageManager.getString("label.select_newick_like_tree_file"));
3898     chooser.setToolTipText(
3899             MessageManager.getString("label.load_tree_file"));
3900
3901     int value = chooser.showOpenDialog(null);
3902
3903     if (value == JalviewFileChooser.APPROVE_OPTION)
3904     {
3905       String filePath = chooser.getSelectedFile().getPath();
3906       Cache.setProperty("LAST_DIRECTORY", filePath);
3907       NewickFile fin = null;
3908       try
3909       {
3910         fin = new NewickFile(filePath, DataSourceType.FILE);
3911         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3912       } catch (Exception ex)
3913       {
3914         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3915                 MessageManager.getString("label.problem_reading_tree_file"),
3916                 JvOptionPane.WARNING_MESSAGE);
3917         ex.printStackTrace();
3918       }
3919       if (fin != null && fin.hasWarningMessage())
3920       {
3921         JvOptionPane.showMessageDialog(Desktop.desktop,
3922                 fin.getWarningMessage(),
3923                 MessageManager
3924                         .getString("label.possible_problem_with_tree_file"),
3925                 JvOptionPane.WARNING_MESSAGE);
3926       }
3927     }
3928   }
3929
3930   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3931   {
3932     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3933   }
3934
3935   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3936           int h, int x, int y)
3937   {
3938     return showNewickTree(nf, treeTitle, null, w, h, x, y);
3939   }
3940
3941   /**
3942    * Add a treeviewer for the tree extracted from a Newick file object to the
3943    * current alignment view
3944    *
3945    * @param nf
3946    *          the tree
3947    * @param title
3948    *          tree viewer title
3949    * @param input
3950    *          Associated alignment input data (or null)
3951    * @param w
3952    *          width
3953    * @param h
3954    *          height
3955    * @param x
3956    *          position
3957    * @param y
3958    *          position
3959    * @return TreePanel handle
3960    */
3961   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3962           AlignmentView input, int w, int h, int x, int y)
3963   {
3964     TreePanel tp = null;
3965
3966     try
3967     {
3968       nf.parse();
3969
3970       if (nf.getTree() != null)
3971       {
3972         tp = new TreePanel(alignPanel, nf, treeTitle, input);
3973
3974         tp.setSize(w, h);
3975
3976         if (x > 0 && y > 0)
3977         {
3978           tp.setLocation(x, y);
3979         }
3980
3981         Desktop.addInternalFrame(tp, treeTitle, w, h);
3982       }
3983     } catch (Exception ex)
3984     {
3985       ex.printStackTrace();
3986     }
3987
3988     return tp;
3989   }
3990
3991   private boolean buildingMenu = false;
3992
3993   /**
3994    * Generates menu items and listener event actions for web service clients
3995    *
3996    */
3997   public void BuildWebServiceMenu()
3998   {
3999     while (buildingMenu)
4000     {
4001       try
4002       {
4003         System.err.println("Waiting for building menu to finish.");
4004         Thread.sleep(10);
4005       } catch (Exception e)
4006       {
4007       }
4008     }
4009     final AlignFrame me = this;
4010     buildingMenu = true;
4011     new Thread(new Runnable()
4012     {
4013       @Override
4014       public void run()
4015       {
4016         final List<JMenuItem> legacyItems = new ArrayList<>();
4017         try
4018         {
4019           // System.err.println("Building ws menu again "
4020           // + Thread.currentThread());
4021           // TODO: add support for context dependent disabling of services based
4022           // on
4023           // alignment and current selection
4024           // TODO: add additional serviceHandle parameter to specify abstract
4025           // handler
4026           // class independently of AbstractName
4027           // TODO: add in rediscovery GUI function to restart discoverer
4028           // TODO: group services by location as well as function and/or
4029           // introduce
4030           // object broker mechanism.
4031           final Vector<JMenu> wsmenu = new Vector<>();
4032           final IProgressIndicator af = me;
4033
4034           /*
4035            * do not i18n these strings - they are hard-coded in class
4036            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4037            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4038            */
4039           final JMenu msawsmenu = new JMenu("Alignment");
4040           final JMenu secstrmenu = new JMenu(
4041                   "Secondary Structure Prediction");
4042           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4043           final JMenu analymenu = new JMenu("Analysis");
4044           final JMenu dismenu = new JMenu("Protein Disorder");
4045           // JAL-940 - only show secondary structure prediction services from
4046           // the legacy server
4047           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4048               // &&
4049           Discoverer.services != null && (Discoverer.services.size() > 0))
4050           {
4051             // TODO: refactor to allow list of AbstractName/Handler bindings to
4052             // be
4053             // stored or retrieved from elsewhere
4054             // No MSAWS used any more:
4055             // Vector msaws = null; // (Vector)
4056             // Discoverer.services.get("MsaWS");
4057             Vector secstrpr = (Vector) Discoverer.services
4058                     .get("SecStrPred");
4059             if (secstrpr != null)
4060             {
4061               // Add any secondary structure prediction services
4062               for (int i = 0, j = secstrpr.size(); i < j; i++)
4063               {
4064                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4065                         .get(i);
4066                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4067                         .getServiceClient(sh);
4068                 int p = secstrmenu.getItemCount();
4069                 impl.attachWSMenuEntry(secstrmenu, me);
4070                 int q = secstrmenu.getItemCount();
4071                 for (int litm = p; litm < q; litm++)
4072                 {
4073                   legacyItems.add(secstrmenu.getItem(litm));
4074                 }
4075               }
4076             }
4077           }
4078
4079           // Add all submenus in the order they should appear on the web
4080           // services menu
4081           wsmenu.add(msawsmenu);
4082           wsmenu.add(secstrmenu);
4083           wsmenu.add(dismenu);
4084           wsmenu.add(analymenu);
4085           // No search services yet
4086           // wsmenu.add(seqsrchmenu);
4087
4088           javax.swing.SwingUtilities.invokeLater(new Runnable()
4089           {
4090             @Override
4091             public void run()
4092             {
4093               try
4094               {
4095                 webService.removeAll();
4096                 // first, add discovered services onto the webservices menu
4097                 if (wsmenu.size() > 0)
4098                 {
4099                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4100                   {
4101                     webService.add(wsmenu.get(i));
4102                   }
4103                 }
4104                 else
4105                 {
4106                   webService.add(me.webServiceNoServices);
4107                 }
4108                 // TODO: move into separate menu builder class.
4109                 boolean new_sspred = false;
4110                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4111                 {
4112                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4113                   if (jws2servs != null)
4114                   {
4115                     if (jws2servs.hasServices())
4116                     {
4117                       jws2servs.attachWSMenuEntry(webService, me);
4118                       for (Jws2Instance sv : jws2servs.getServices())
4119                       {
4120                         if (sv.description.toLowerCase().contains("jpred"))
4121                         {
4122                           for (JMenuItem jmi : legacyItems)
4123                           {
4124                             jmi.setVisible(false);
4125                           }
4126                         }
4127                       }
4128
4129                     }
4130                     if (jws2servs.isRunning())
4131                     {
4132                       JMenuItem tm = new JMenuItem(
4133                               "Still discovering JABA Services");
4134                       tm.setEnabled(false);
4135                       webService.add(tm);
4136                     }
4137                   }
4138                 }
4139                 build_urlServiceMenu(me.webService);
4140                 build_fetchdbmenu(webService);
4141                 for (JMenu item : wsmenu)
4142                 {
4143                   if (item.getItemCount() == 0)
4144                   {
4145                     item.setEnabled(false);
4146                   }
4147                   else
4148                   {
4149                     item.setEnabled(true);
4150                   }
4151                 }
4152               } catch (Exception e)
4153               {
4154                 Cache.log.debug(
4155                         "Exception during web service menu building process.",
4156                         e);
4157               }
4158             }
4159           });
4160         } catch (Exception e)
4161         {
4162         }
4163         buildingMenu = false;
4164       }
4165     }).start();
4166
4167   }
4168
4169   /**
4170    * construct any groupURL type service menu entries.
4171    *
4172    * @param webService
4173    */
4174   private void build_urlServiceMenu(JMenu webService)
4175   {
4176     // TODO: remove this code when 2.7 is released
4177     // DEBUG - alignmentView
4178     /*
4179      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4180      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4181      *
4182      * @Override public void actionPerformed(ActionEvent e) {
4183      * jalview.datamodel.AlignmentView
4184      * .testSelectionViews(af.viewport.getAlignment(),
4185      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4186      *
4187      * }); webService.add(testAlView);
4188      */
4189     // TODO: refactor to RestClient discoverer and merge menu entries for
4190     // rest-style services with other types of analysis/calculation service
4191     // SHmmr test client - still being implemented.
4192     // DEBUG - alignmentView
4193
4194     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4195             .getRestClients())
4196     {
4197       client.attachWSMenuEntry(
4198               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4199               this);
4200     }
4201   }
4202
4203   /**
4204    * Searches the alignment sequences for xRefs and builds the Show
4205    * Cross-References menu (formerly called Show Products), with database
4206    * sources for which cross-references are found (protein sources for a
4207    * nucleotide alignment and vice versa)
4208    *
4209    * @return true if Show Cross-references menu should be enabled
4210    */
4211   public boolean canShowProducts()
4212   {
4213     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4214     AlignmentI dataset = viewport.getAlignment().getDataset();
4215
4216     showProducts.removeAll();
4217     final boolean dna = viewport.getAlignment().isNucleotide();
4218
4219     if (seqs == null || seqs.length == 0)
4220     {
4221       // nothing to see here.
4222       return false;
4223     }
4224
4225     boolean showp = false;
4226     try
4227     {
4228       List<String> ptypes = new CrossRef(seqs, dataset)
4229               .findXrefSourcesForSequences(dna);
4230
4231       for (final String source : ptypes)
4232       {
4233         showp = true;
4234         final AlignFrame af = this;
4235         JMenuItem xtype = new JMenuItem(source);
4236         xtype.addActionListener(new ActionListener()
4237         {
4238           @Override
4239           public void actionPerformed(ActionEvent e)
4240           {
4241             showProductsFor(af.viewport.getSequenceSelection(), dna,
4242                     source);
4243           }
4244         });
4245         showProducts.add(xtype);
4246       }
4247       showProducts.setVisible(showp);
4248       showProducts.setEnabled(showp);
4249     } catch (Exception e)
4250     {
4251       Cache.log.warn(
4252               "canShowProducts threw an exception - please report to help@jalview.org",
4253               e);
4254       return false;
4255     }
4256     return showp;
4257   }
4258
4259   /**
4260    * Finds and displays cross-references for the selected sequences (protein
4261    * products for nucleotide sequences, dna coding sequences for peptides).
4262    *
4263    * @param sel
4264    *          the sequences to show cross-references for
4265    * @param dna
4266    *          true if from a nucleotide alignment (so showing proteins)
4267    * @param source
4268    *          the database to show cross-references for
4269    */
4270   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4271           final String source)
4272   {
4273     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4274             .start();
4275   }
4276
4277   /**
4278    * Construct and display a new frame containing the translation of this
4279    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4280    */
4281   @Override
4282   public void showTranslation_actionPerformed(ActionEvent e)
4283   {
4284     AlignmentI al = null;
4285     try
4286     {
4287       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4288
4289       al = dna.translateCdna();
4290     } catch (Exception ex)
4291     {
4292       jalview.bin.Cache.log.error(
4293               "Exception during translation. Please report this !", ex);
4294       final String msg = MessageManager.getString(
4295               "label.error_when_translating_sequences_submit_bug_report");
4296       final String errorTitle = MessageManager
4297               .getString("label.implementation_error")
4298               + MessageManager.getString("label.translation_failed");
4299       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4300               JvOptionPane.ERROR_MESSAGE);
4301       return;
4302     }
4303     if (al == null || al.getHeight() == 0)
4304     {
4305       final String msg = MessageManager.getString(
4306               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4307       final String errorTitle = MessageManager
4308               .getString("label.translation_failed");
4309       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4310               JvOptionPane.WARNING_MESSAGE);
4311     }
4312     else
4313     {
4314       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4315       af.setFileFormat(this.currentFileFormat);
4316       final String newTitle = MessageManager
4317               .formatMessage("label.translation_of_params", new Object[]
4318               { this.getTitle() });
4319       af.setTitle(newTitle);
4320       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4321       {
4322         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4323         viewport.openSplitFrame(af, new Alignment(seqs));
4324       }
4325       else
4326       {
4327         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4328                 DEFAULT_HEIGHT);
4329       }
4330     }
4331   }
4332
4333   /**
4334    * Set the file format
4335    *
4336    * @param format
4337    */
4338   public void setFileFormat(FileFormatI format)
4339   {
4340     this.currentFileFormat = format;
4341   }
4342
4343   /**
4344    * Try to load a features file onto the alignment.
4345    *
4346    * @param file
4347    *          contents or path to retrieve file
4348    * @param sourceType
4349    *          access mode of file (see jalview.io.AlignFile)
4350    * @return true if features file was parsed correctly.
4351    */
4352   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4353   {
4354     return avc.parseFeaturesFile(file, sourceType,
4355             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4356
4357   }
4358
4359   @Override
4360   public void refreshFeatureUI(boolean enableIfNecessary)
4361   {
4362     // note - currently this is only still here rather than in the controller
4363     // because of the featureSettings hard reference that is yet to be
4364     // abstracted
4365     if (enableIfNecessary)
4366     {
4367       viewport.setShowSequenceFeatures(true);
4368       showSeqFeatures.setSelected(true);
4369     }
4370
4371   }
4372
4373   @Override
4374   public void dragEnter(DropTargetDragEvent evt)
4375   {
4376   }
4377
4378   @Override
4379   public void dragExit(DropTargetEvent evt)
4380   {
4381   }
4382
4383   @Override
4384   public void dragOver(DropTargetDragEvent evt)
4385   {
4386   }
4387
4388   @Override
4389   public void dropActionChanged(DropTargetDragEvent evt)
4390   {
4391   }
4392
4393   @Override
4394   public void drop(DropTargetDropEvent evt)
4395   {
4396     // JAL-1552 - acceptDrop required before getTransferable call for
4397     // Java's Transferable for native dnd
4398     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4399     Transferable t = evt.getTransferable();
4400     final AlignFrame thisaf = this;
4401     final List<String> files = new ArrayList<>();
4402     List<DataSourceType> protocols = new ArrayList<>();
4403
4404     try
4405     {
4406       Desktop.transferFromDropTarget(files, protocols, evt, t);
4407     } catch (Exception e)
4408     {
4409       e.printStackTrace();
4410     }
4411     if (files != null)
4412     {
4413       new Thread(new Runnable()
4414       {
4415         @Override
4416         public void run()
4417         {
4418           try
4419           {
4420             // check to see if any of these files have names matching sequences
4421             // in
4422             // the alignment
4423             SequenceIdMatcher idm = new SequenceIdMatcher(
4424                     viewport.getAlignment().getSequencesArray());
4425             /**
4426              * Object[] { String,SequenceI}
4427              */
4428             ArrayList<Object[]> filesmatched = new ArrayList<>();
4429             ArrayList<String> filesnotmatched = new ArrayList<>();
4430             for (int i = 0; i < files.size(); i++)
4431             {
4432               String file = files.get(i).toString();
4433               String pdbfn = "";
4434               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4435               if (protocol == DataSourceType.FILE)
4436               {
4437                 File fl = new File(file);
4438                 pdbfn = fl.getName();
4439               }
4440               else if (protocol == DataSourceType.URL)
4441               {
4442                 URL url = new URL(file);
4443                 pdbfn = url.getFile();
4444               }
4445               if (pdbfn.length() > 0)
4446               {
4447                 // attempt to find a match in the alignment
4448                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4449                 int l = 0, c = pdbfn.indexOf(".");
4450                 while (mtch == null && c != -1)
4451                 {
4452                   do
4453                   {
4454                     l = c;
4455                   } while ((c = pdbfn.indexOf(".", l)) > l);
4456                   if (l > -1)
4457                   {
4458                     pdbfn = pdbfn.substring(0, l);
4459                   }
4460                   mtch = idm.findAllIdMatches(pdbfn);
4461                 }
4462                 if (mtch != null)
4463                 {
4464                   FileFormatI type = null;
4465                   try
4466                   {
4467                     type = new IdentifyFile().identify(file, protocol);
4468                   } catch (Exception ex)
4469                   {
4470                     type = null;
4471                   }
4472                   if (type != null && type.isStructureFile())
4473                   {
4474                     filesmatched.add(new Object[] { file, protocol, mtch });
4475                     continue;
4476                   }
4477                 }
4478                 // File wasn't named like one of the sequences or wasn't a PDB
4479                 // file.
4480                 filesnotmatched.add(file);
4481               }
4482             }
4483             int assocfiles = 0;
4484             if (filesmatched.size() > 0)
4485             {
4486               boolean autoAssociate = Cache
4487                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4488               if (!autoAssociate)
4489               {
4490                 String msg = MessageManager.formatMessage(
4491                         "label.automatically_associate_structure_files_with_sequences_same_name",
4492                         new Object[]
4493                         { Integer.valueOf(filesmatched.size())
4494                                 .toString() });
4495                 String ttl = MessageManager.getString(
4496                         "label.automatically_associate_structure_files_by_name");
4497                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4498                         ttl, JvOptionPane.YES_NO_OPTION);
4499                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4500               }
4501               if (autoAssociate)
4502               {
4503                 for (Object[] fm : filesmatched)
4504                 {
4505                   // try and associate
4506                   // TODO: may want to set a standard ID naming formalism for
4507                   // associating PDB files which have no IDs.
4508                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4509                   {
4510                     PDBEntry pe = new AssociatePdbFileWithSeq()
4511                             .associatePdbWithSeq((String) fm[0],
4512                                     (DataSourceType) fm[1], toassoc, false,
4513                                     Desktop.instance);
4514                     if (pe != null)
4515                     {
4516                       System.err.println("Associated file : "
4517                               + ((String) fm[0]) + " with "
4518                               + toassoc.getDisplayId(true));
4519                       assocfiles++;
4520                     }
4521                   }
4522                   // TODO: do we need to update overview ? only if features are
4523                   // shown I guess
4524                   alignPanel.paintAlignment(true, false);
4525                 }
4526               }
4527               else
4528               {
4529                 /*
4530                  * add declined structures as sequences
4531                  */
4532                 for (Object[] o : filesmatched)
4533                 {
4534                   filesnotmatched.add((String) o[0]);
4535                 }
4536               }
4537             }
4538             if (filesnotmatched.size() > 0)
4539             {
4540               if (assocfiles > 0 && (Cache.getDefault(
4541                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4542                       || JvOptionPane.showConfirmDialog(thisaf,
4543                               "<html>" + MessageManager.formatMessage(
4544                                       "label.ignore_unmatched_dropped_files_info",
4545                                       new Object[]
4546                                       { Integer.valueOf(
4547                                               filesnotmatched.size())
4548                                               .toString() })
4549                                       + "</html>",
4550                               MessageManager.getString(
4551                                       "label.ignore_unmatched_dropped_files"),
4552                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4553               {
4554                 return;
4555               }
4556               for (String fn : filesnotmatched)
4557               {
4558                 loadJalviewDataFile(fn, null, null, null);
4559               }
4560
4561             }
4562           } catch (Exception ex)
4563           {
4564             ex.printStackTrace();
4565           }
4566         }
4567       }).start();
4568     }
4569   }
4570
4571   /**
4572    * Attempt to load a "dropped" file or URL string, by testing in turn for
4573    * <ul>
4574    * <li>an Annotation file</li>
4575    * <li>a JNet file</li>
4576    * <li>a features file</li>
4577    * <li>else try to interpret as an alignment file</li>
4578    * </ul>
4579    *
4580    * @param file
4581    *          either a filename or a URL string.
4582    */
4583   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4584           FileFormatI format, SequenceI assocSeq)
4585   {
4586     try
4587     {
4588       if (sourceType == null)
4589       {
4590         sourceType = FormatAdapter.checkProtocol(file);
4591       }
4592       // if the file isn't identified, or not positively identified as some
4593       // other filetype (PFAM is default unidentified alignment file type) then
4594       // try to parse as annotation.
4595       boolean isAnnotation = (format == null
4596               || FileFormat.Pfam.equals(format))
4597                       ? new AnnotationFile().annotateAlignmentView(viewport,
4598                               file, sourceType)
4599                       : false;
4600
4601       if (!isAnnotation)
4602       {
4603         // first see if its a T-COFFEE score file
4604         TCoffeeScoreFile tcf = null;
4605         try
4606         {
4607           tcf = new TCoffeeScoreFile(file, sourceType);
4608           if (tcf.isValid())
4609           {
4610             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4611             {
4612               buildColourMenu();
4613               changeColour(
4614                       new TCoffeeColourScheme(viewport.getAlignment()));
4615               isAnnotation = true;
4616               statusBar.setText(MessageManager.getString(
4617                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4618             }
4619             else
4620             {
4621               // some problem - if no warning its probable that the ID matching
4622               // process didn't work
4623               JvOptionPane.showMessageDialog(Desktop.desktop,
4624                       tcf.getWarningMessage() == null
4625                               ? MessageManager.getString(
4626                                       "label.check_file_matches_sequence_ids_alignment")
4627                               : tcf.getWarningMessage(),
4628                       MessageManager.getString(
4629                               "label.problem_reading_tcoffee_score_file"),
4630                       JvOptionPane.WARNING_MESSAGE);
4631             }
4632           }
4633           else
4634           {
4635             tcf = null;
4636           }
4637         } catch (Exception x)
4638         {
4639           Cache.log.debug(
4640                   "Exception when processing data source as T-COFFEE score file",
4641                   x);
4642           tcf = null;
4643         }
4644         if (tcf == null)
4645         {
4646           // try to see if its a JNet 'concise' style annotation file *before*
4647           // we
4648           // try to parse it as a features file
4649           if (format == null)
4650           {
4651             format = new IdentifyFile().identify(file, sourceType);
4652           }
4653           if (FileFormat.ScoreMatrix == format)
4654           {
4655             ScoreMatrixFile sm = new ScoreMatrixFile(
4656                     new FileParse(file, sourceType));
4657             sm.parse();
4658             // todo: i18n this message
4659             statusBar.setText(MessageManager.formatMessage(
4660                     "label.successfully_loaded_matrix",
4661                     sm.getMatrixName()));
4662           }
4663           else if (FileFormat.Jnet.equals(format))
4664           {
4665             JPredFile predictions = new JPredFile(file, sourceType);
4666             new JnetAnnotationMaker();
4667             JnetAnnotationMaker.add_annotation(predictions,
4668                     viewport.getAlignment(), 0, false);
4669             viewport.getAlignment().setupJPredAlignment();
4670             isAnnotation = true;
4671           }
4672           // else if (IdentifyFile.FeaturesFile.equals(format))
4673           else if (FileFormat.Features.equals(format))
4674           {
4675             if (parseFeaturesFile(file, sourceType))
4676             {
4677               alignPanel.paintAlignment(true, true);
4678             }
4679           }
4680           else
4681           {
4682             new FileLoader().LoadFile(viewport, file, sourceType, format);
4683           }
4684         }
4685       }
4686       if (isAnnotation)
4687       {
4688
4689         alignPanel.adjustAnnotationHeight();
4690         viewport.updateSequenceIdColours();
4691         buildSortByAnnotationScoresMenu();
4692         alignPanel.paintAlignment(true, true);
4693       }
4694     } catch (Exception ex)
4695     {
4696       ex.printStackTrace();
4697     } catch (OutOfMemoryError oom)
4698     {
4699       try
4700       {
4701         System.gc();
4702       } catch (Exception x)
4703       {
4704       }
4705       new OOMWarning(
4706               "loading data "
4707                       + (sourceType != null
4708                               ? (sourceType == DataSourceType.PASTE
4709                                       ? "from clipboard."
4710                                       : "using " + sourceType + " from "
4711                                               + file)
4712                               : ".")
4713                       + (format != null
4714                               ? "(parsing as '" + format + "' file)"
4715                               : ""),
4716               oom, Desktop.desktop);
4717     }
4718   }
4719
4720   /**
4721    * Method invoked by the ChangeListener on the tabbed pane, in other words
4722    * when a different tabbed pane is selected by the user or programmatically.
4723    */
4724   @Override
4725   public void tabSelectionChanged(int index)
4726   {
4727     if (index > -1)
4728     {
4729       alignPanel = alignPanels.get(index);
4730       viewport = alignPanel.av;
4731       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4732       setMenusFromViewport(viewport);
4733     }
4734
4735     /*
4736      * 'focus' any colour slider that is open to the selected viewport
4737      */
4738     if (viewport.getConservationSelected())
4739     {
4740       SliderPanel.setConservationSlider(alignPanel,
4741               viewport.getResidueShading(), alignPanel.getViewName());
4742     }
4743     else
4744     {
4745       SliderPanel.hideConservationSlider();
4746     }
4747     if (viewport.getAbovePIDThreshold())
4748     {
4749       SliderPanel.setPIDSliderSource(alignPanel,
4750               viewport.getResidueShading(), alignPanel.getViewName());
4751     }
4752     else
4753     {
4754       SliderPanel.hidePIDSlider();
4755     }
4756
4757     /*
4758      * If there is a frame linked to this one in a SplitPane, switch it to the
4759      * same view tab index. No infinite recursion of calls should happen, since
4760      * tabSelectionChanged() should not get invoked on setting the selected
4761      * index to an unchanged value. Guard against setting an invalid index
4762      * before the new view peer tab has been created.
4763      */
4764     final AlignViewportI peer = viewport.getCodingComplement();
4765     if (peer != null)
4766     {
4767       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4768               .getAlignPanel().alignFrame;
4769       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4770       {
4771         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4772       }
4773     }
4774   }
4775
4776   /**
4777    * On right mouse click on view tab, prompt for and set new view name.
4778    */
4779   @Override
4780   public void tabbedPane_mousePressed(MouseEvent e)
4781   {
4782     if (e.isPopupTrigger())
4783     {
4784       String msg = MessageManager.getString("label.enter_view_name");
4785       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4786               JvOptionPane.QUESTION_MESSAGE);
4787
4788       if (reply != null)
4789       {
4790         viewport.setViewName(reply);
4791         // TODO warn if reply is in getExistingViewNames()?
4792         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4793       }
4794     }
4795   }
4796
4797   public AlignViewport getCurrentView()
4798   {
4799     return viewport;
4800   }
4801
4802   /**
4803    * Open the dialog for regex description parsing.
4804    */
4805   @Override
4806   protected void extractScores_actionPerformed(ActionEvent e)
4807   {
4808     ParseProperties pp = new jalview.analysis.ParseProperties(
4809             viewport.getAlignment());
4810     // TODO: verify regex and introduce GUI dialog for version 2.5
4811     // if (pp.getScoresFromDescription("col", "score column ",
4812     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4813     // true)>0)
4814     if (pp.getScoresFromDescription("description column",
4815             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4816     {
4817       buildSortByAnnotationScoresMenu();
4818     }
4819   }
4820
4821   /*
4822    * (non-Javadoc)
4823    *
4824    * @see
4825    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4826    * )
4827    */
4828   @Override
4829   protected void showDbRefs_actionPerformed(ActionEvent e)
4830   {
4831     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4832   }
4833
4834   /*
4835    * (non-Javadoc)
4836    *
4837    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4838    * ActionEvent)
4839    */
4840   @Override
4841   protected void showNpFeats_actionPerformed(ActionEvent e)
4842   {
4843     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4844   }
4845
4846   /**
4847    * find the viewport amongst the tabs in this alignment frame and close that
4848    * tab
4849    *
4850    * @param av
4851    */
4852   public boolean closeView(AlignViewportI av)
4853   {
4854     if (viewport == av)
4855     {
4856       this.closeMenuItem_actionPerformed(false);
4857       return true;
4858     }
4859     Component[] comp = tabbedPane.getComponents();
4860     for (int i = 0; comp != null && i < comp.length; i++)
4861     {
4862       if (comp[i] instanceof AlignmentPanel)
4863       {
4864         if (((AlignmentPanel) comp[i]).av == av)
4865         {
4866           // close the view.
4867           closeView((AlignmentPanel) comp[i]);
4868           return true;
4869         }
4870       }
4871     }
4872     return false;
4873   }
4874
4875   protected void build_fetchdbmenu(JMenu webService)
4876   {
4877     // Temporary hack - DBRef Fetcher always top level ws entry.
4878     // TODO We probably want to store a sequence database checklist in
4879     // preferences and have checkboxes.. rather than individual sources selected
4880     // here
4881     final JMenu rfetch = new JMenu(
4882             MessageManager.getString("action.fetch_db_references"));
4883     rfetch.setToolTipText(MessageManager.getString(
4884             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4885     webService.add(rfetch);
4886
4887     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4888             MessageManager.getString("option.trim_retrieved_seqs"));
4889     trimrs.setToolTipText(
4890             MessageManager.getString("label.trim_retrieved_sequences"));
4891     trimrs.setSelected(
4892             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4893     trimrs.addActionListener(new ActionListener()
4894     {
4895       @Override
4896       public void actionPerformed(ActionEvent e)
4897       {
4898         trimrs.setSelected(trimrs.isSelected());
4899         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4900                 Boolean.valueOf(trimrs.isSelected()).toString());
4901       };
4902     });
4903     rfetch.add(trimrs);
4904     JMenuItem fetchr = new JMenuItem(
4905             MessageManager.getString("label.standard_databases"));
4906     fetchr.setToolTipText(
4907             MessageManager.getString("label.fetch_embl_uniprot"));
4908     fetchr.addActionListener(new ActionListener()
4909     {
4910
4911       @Override
4912       public void actionPerformed(ActionEvent e)
4913       {
4914         new Thread(new Runnable()
4915         {
4916           @Override
4917           public void run()
4918           {
4919             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4920                     .getAlignment().isNucleotide();
4921             DBRefFetcher dbRefFetcher = new DBRefFetcher(
4922                     alignPanel.av.getSequenceSelection(),
4923                     alignPanel.alignFrame, null,
4924                     alignPanel.alignFrame.featureSettings, isNucleotide);
4925             dbRefFetcher.addListener(new FetchFinishedListenerI()
4926             {
4927               @Override
4928               public void finished()
4929               {
4930                 AlignFrame.this.setMenusForViewport();
4931               }
4932             });
4933             dbRefFetcher.fetchDBRefs(false);
4934           }
4935         }).start();
4936
4937       }
4938
4939     });
4940     rfetch.add(fetchr);
4941     final AlignFrame me = this;
4942     new Thread(new Runnable()
4943     {
4944       @Override
4945       public void run()
4946       {
4947         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4948                 .getSequenceFetcherSingleton(me);
4949         javax.swing.SwingUtilities.invokeLater(new Runnable()
4950         {
4951           @Override
4952           public void run()
4953           {
4954             String[] dbclasses = sf.getOrderedSupportedSources();
4955             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4956             // jalview.util.QuickSort.sort(otherdb, otherdb);
4957             List<DbSourceProxy> otherdb;
4958             JMenu dfetch = new JMenu();
4959             JMenu ifetch = new JMenu();
4960             JMenuItem fetchr = null;
4961             int comp = 0, icomp = 0, mcomp = 15;
4962             String mname = null;
4963             int dbi = 0;
4964             for (String dbclass : dbclasses)
4965             {
4966               otherdb = sf.getSourceProxy(dbclass);
4967               // add a single entry for this class, or submenu allowing 'fetch
4968               // all' or pick one
4969               if (otherdb == null || otherdb.size() < 1)
4970               {
4971                 continue;
4972               }
4973               // List<DbSourceProxy> dbs=otherdb;
4974               // otherdb=new ArrayList<DbSourceProxy>();
4975               // for (DbSourceProxy db:dbs)
4976               // {
4977               // if (!db.isA(DBRefSource.ALIGNMENTDB)
4978               // }
4979               if (mname == null)
4980               {
4981                 mname = "From " + dbclass;
4982               }
4983               if (otherdb.size() == 1)
4984               {
4985                 final DbSourceProxy[] dassource = otherdb
4986                         .toArray(new DbSourceProxy[0]);
4987                 DbSourceProxy src = otherdb.get(0);
4988                 fetchr = new JMenuItem(src.getDbSource());
4989                 fetchr.addActionListener(new ActionListener()
4990                 {
4991
4992                   @Override
4993                   public void actionPerformed(ActionEvent e)
4994                   {
4995                     new Thread(new Runnable()
4996                     {
4997
4998                       @Override
4999                       public void run()
5000                       {
5001                         boolean isNucleotide = alignPanel.alignFrame
5002                                 .getViewport().getAlignment()
5003                                 .isNucleotide();
5004                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5005                                 alignPanel.av.getSequenceSelection(),
5006                                 alignPanel.alignFrame, dassource,
5007                                 alignPanel.alignFrame.featureSettings,
5008                                 isNucleotide);
5009                         dbRefFetcher
5010                                 .addListener(new FetchFinishedListenerI()
5011                                 {
5012                                   @Override
5013                                   public void finished()
5014                                   {
5015                                     AlignFrame.this.setMenusForViewport();
5016                                   }
5017                                 });
5018                         dbRefFetcher.fetchDBRefs(false);
5019                       }
5020                     }).start();
5021                   }
5022
5023                 });
5024                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5025                         MessageManager.formatMessage(
5026                                 "label.fetch_retrieve_from", new Object[]
5027                                 { src.getDbName() })));
5028                 dfetch.add(fetchr);
5029                 comp++;
5030               }
5031               else
5032               {
5033                 final DbSourceProxy[] dassource = otherdb
5034                         .toArray(new DbSourceProxy[0]);
5035                 // fetch all entry
5036                 DbSourceProxy src = otherdb.get(0);
5037                 fetchr = new JMenuItem(MessageManager
5038                         .formatMessage("label.fetch_all_param", new Object[]
5039                         { src.getDbSource() }));
5040                 fetchr.addActionListener(new ActionListener()
5041                 {
5042                   @Override
5043                   public void actionPerformed(ActionEvent e)
5044                   {
5045                     new Thread(new Runnable()
5046                     {
5047
5048                       @Override
5049                       public void run()
5050                       {
5051                         boolean isNucleotide = alignPanel.alignFrame
5052                                 .getViewport().getAlignment()
5053                                 .isNucleotide();
5054                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5055                                 alignPanel.av.getSequenceSelection(),
5056                                 alignPanel.alignFrame, dassource,
5057                                 alignPanel.alignFrame.featureSettings,
5058                                 isNucleotide);
5059                         dbRefFetcher
5060                                 .addListener(new FetchFinishedListenerI()
5061                                 {
5062                                   @Override
5063                                   public void finished()
5064                                   {
5065                                     AlignFrame.this.setMenusForViewport();
5066                                   }
5067                                 });
5068                         dbRefFetcher.fetchDBRefs(false);
5069                       }
5070                     }).start();
5071                   }
5072                 });
5073
5074                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5075                         MessageManager.formatMessage(
5076                                 "label.fetch_retrieve_from_all_sources",
5077                                 new Object[]
5078                                 { Integer.valueOf(otherdb.size())
5079                                         .toString(),
5080                                     src.getDbSource(), src.getDbName() })));
5081                 dfetch.add(fetchr);
5082                 comp++;
5083                 // and then build the rest of the individual menus
5084                 ifetch = new JMenu(MessageManager.formatMessage(
5085                         "label.source_from_db_source", new Object[]
5086                         { src.getDbSource() }));
5087                 icomp = 0;
5088                 String imname = null;
5089                 int i = 0;
5090                 for (DbSourceProxy sproxy : otherdb)
5091                 {
5092                   String dbname = sproxy.getDbName();
5093                   String sname = dbname.length() > 5
5094                           ? dbname.substring(0, 5) + "..."
5095                           : dbname;
5096                   String msname = dbname.length() > 10
5097                           ? dbname.substring(0, 10) + "..."
5098                           : dbname;
5099                   if (imname == null)
5100                   {
5101                     imname = MessageManager
5102                             .formatMessage("label.from_msname", new Object[]
5103                             { sname });
5104                   }
5105                   fetchr = new JMenuItem(msname);
5106                   final DbSourceProxy[] dassrc = { sproxy };
5107                   fetchr.addActionListener(new ActionListener()
5108                   {
5109
5110                     @Override
5111                     public void actionPerformed(ActionEvent e)
5112                     {
5113                       new Thread(new Runnable()
5114                       {
5115
5116                         @Override
5117                         public void run()
5118                         {
5119                           boolean isNucleotide = alignPanel.alignFrame
5120                                   .getViewport().getAlignment()
5121                                   .isNucleotide();
5122                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5123                                   alignPanel.av.getSequenceSelection(),
5124                                   alignPanel.alignFrame, dassrc,
5125                                   alignPanel.alignFrame.featureSettings,
5126                                   isNucleotide);
5127                           dbRefFetcher
5128                                   .addListener(new FetchFinishedListenerI()
5129                                   {
5130                                     @Override
5131                                     public void finished()
5132                                     {
5133                                       AlignFrame.this.setMenusForViewport();
5134                                     }
5135                                   });
5136                           dbRefFetcher.fetchDBRefs(false);
5137                         }
5138                       }).start();
5139                     }
5140
5141                   });
5142                   fetchr.setToolTipText(
5143                           "<html>" + MessageManager.formatMessage(
5144                                   "label.fetch_retrieve_from", new Object[]
5145                                   { dbname }));
5146                   ifetch.add(fetchr);
5147                   ++i;
5148                   if (++icomp >= mcomp || i == (otherdb.size()))
5149                   {
5150                     ifetch.setText(MessageManager.formatMessage(
5151                             "label.source_to_target", imname, sname));
5152                     dfetch.add(ifetch);
5153                     ifetch = new JMenu();
5154                     imname = null;
5155                     icomp = 0;
5156                     comp++;
5157                   }
5158                 }
5159               }
5160               ++dbi;
5161               if (comp >= mcomp || dbi >= (dbclasses.length))
5162               {
5163                 dfetch.setText(MessageManager.formatMessage(
5164                         "label.source_to_target", mname, dbclass));
5165                 rfetch.add(dfetch);
5166                 dfetch = new JMenu();
5167                 mname = null;
5168                 comp = 0;
5169               }
5170             }
5171           }
5172         });
5173       }
5174     }).start();
5175
5176   }
5177
5178   /**
5179    * Left justify the whole alignment.
5180    */
5181   @Override
5182   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5183   {
5184     AlignmentI al = viewport.getAlignment();
5185     al.justify(false);
5186     viewport.firePropertyChange("alignment", null, al);
5187   }
5188
5189   /**
5190    * Right justify the whole alignment.
5191    */
5192   @Override
5193   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5194   {
5195     AlignmentI al = viewport.getAlignment();
5196     al.justify(true);
5197     viewport.firePropertyChange("alignment", null, al);
5198   }
5199
5200   @Override
5201   public void setShowSeqFeatures(boolean b)
5202   {
5203     showSeqFeatures.setSelected(b);
5204     viewport.setShowSequenceFeatures(b);
5205   }
5206
5207   /*
5208    * (non-Javadoc)
5209    *
5210    * @see
5211    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5212    * awt.event.ActionEvent)
5213    */
5214   @Override
5215   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5216   {
5217     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5218     alignPanel.paintAlignment(false, false);
5219   }
5220
5221   /*
5222    * (non-Javadoc)
5223    *
5224    * @see
5225    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5226    * .ActionEvent)
5227    */
5228   @Override
5229   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5230   {
5231     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5232     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5233
5234   }
5235
5236   /*
5237    * (non-Javadoc)
5238    *
5239    * @see
5240    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5241    * .event.ActionEvent)
5242    */
5243   @Override
5244   protected void showGroupConservation_actionPerformed(ActionEvent e)
5245   {
5246     viewport.setShowGroupConservation(showGroupConservation.getState());
5247     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5248   }
5249
5250   /*
5251    * (non-Javadoc)
5252    *
5253    * @see
5254    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5255    * .event.ActionEvent)
5256    */
5257   @Override
5258   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5259   {
5260     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5261     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5262   }
5263
5264   /*
5265    * (non-Javadoc)
5266    *
5267    * @see
5268    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5269    * .event.ActionEvent)
5270    */
5271   @Override
5272   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5273   {
5274     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5275     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5276   }
5277
5278   @Override
5279   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5280   {
5281     showSequenceLogo.setState(true);
5282     viewport.setShowSequenceLogo(true);
5283     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5284     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5285   }
5286
5287   @Override
5288   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5289   {
5290     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5291   }
5292
5293   /*
5294    * (non-Javadoc)
5295    *
5296    * @see
5297    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5298    * .event.ActionEvent)
5299    */
5300   @Override
5301   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5302   {
5303     if (avc.makeGroupsFromSelection())
5304     {
5305       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5306       alignPanel.updateAnnotation();
5307       alignPanel.paintAlignment(true, true);
5308     }
5309   }
5310
5311   public void clearAlignmentSeqRep()
5312   {
5313     // TODO refactor alignmentseqrep to controller
5314     if (viewport.getAlignment().hasSeqrep())
5315     {
5316       viewport.getAlignment().setSeqrep(null);
5317       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5318       alignPanel.updateAnnotation();
5319       alignPanel.paintAlignment(true, true);
5320     }
5321   }
5322
5323   @Override
5324   protected void createGroup_actionPerformed(ActionEvent e)
5325   {
5326     if (avc.createGroup())
5327     {
5328       if (applyAutoAnnotationSettings.isSelected())
5329       {
5330         alignPanel.updateAnnotation(true, false);
5331       }
5332       alignPanel.alignmentChanged();
5333     }
5334   }
5335
5336   @Override
5337   protected void unGroup_actionPerformed(ActionEvent e)
5338   {
5339     if (avc.unGroup())
5340     {
5341       alignPanel.alignmentChanged();
5342     }
5343   }
5344
5345   /**
5346    * make the given alignmentPanel the currently selected tab
5347    *
5348    * @param alignmentPanel
5349    */
5350   public void setDisplayedView(AlignmentPanel alignmentPanel)
5351   {
5352     if (!viewport.getSequenceSetId()
5353             .equals(alignmentPanel.av.getSequenceSetId()))
5354     {
5355       throw new Error(MessageManager.getString(
5356               "error.implementation_error_cannot_show_view_alignment_frame"));
5357     }
5358     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5359             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5360     {
5361       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5362     }
5363   }
5364
5365   /**
5366    * Action on selection of menu options to Show or Hide annotations.
5367    *
5368    * @param visible
5369    * @param forSequences
5370    *          update sequence-related annotations
5371    * @param forAlignment
5372    *          update non-sequence-related annotations
5373    */
5374   @Override
5375   protected void setAnnotationsVisibility(boolean visible,
5376           boolean forSequences, boolean forAlignment)
5377   {
5378     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5379             .getAlignmentAnnotation();
5380     if (anns == null)
5381     {
5382       return;
5383     }
5384     for (AlignmentAnnotation aa : anns)
5385     {
5386       /*
5387        * don't display non-positional annotations on an alignment
5388        */
5389       if (aa.annotations == null)
5390       {
5391         continue;
5392       }
5393       boolean apply = (aa.sequenceRef == null && forAlignment)
5394               || (aa.sequenceRef != null && forSequences);
5395       if (apply)
5396       {
5397         aa.visible = visible;
5398       }
5399     }
5400     alignPanel.validateAnnotationDimensions(true);
5401     alignPanel.alignmentChanged();
5402   }
5403
5404   /**
5405    * Store selected annotation sort order for the view and repaint.
5406    */
5407   @Override
5408   protected void sortAnnotations_actionPerformed()
5409   {
5410     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5411     this.alignPanel.av
5412             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5413     alignPanel.paintAlignment(false, false);
5414   }
5415
5416   /**
5417    *
5418    * @return alignment panels in this alignment frame
5419    */
5420   public List<? extends AlignmentViewPanel> getAlignPanels()
5421   {
5422     // alignPanels is never null
5423     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5424     return alignPanels;
5425   }
5426
5427   /**
5428    * Open a new alignment window, with the cDNA associated with this (protein)
5429    * alignment, aligned as is the protein.
5430    */
5431   protected void viewAsCdna_actionPerformed()
5432   {
5433     // TODO no longer a menu action - refactor as required
5434     final AlignmentI alignment = getViewport().getAlignment();
5435     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5436     if (mappings == null)
5437     {
5438       return;
5439     }
5440     List<SequenceI> cdnaSeqs = new ArrayList<>();
5441     for (SequenceI aaSeq : alignment.getSequences())
5442     {
5443       for (AlignedCodonFrame acf : mappings)
5444       {
5445         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5446         if (dnaSeq != null)
5447         {
5448           /*
5449            * There is a cDNA mapping for this protein sequence - add to new
5450            * alignment. It will share the same dataset sequence as other mapped
5451            * cDNA (no new mappings need to be created).
5452            */
5453           final Sequence newSeq = new Sequence(dnaSeq);
5454           newSeq.setDatasetSequence(dnaSeq);
5455           cdnaSeqs.add(newSeq);
5456         }
5457       }
5458     }
5459     if (cdnaSeqs.size() == 0)
5460     {
5461       // show a warning dialog no mapped cDNA
5462       return;
5463     }
5464     AlignmentI cdna = new Alignment(
5465             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5466     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5467             AlignFrame.DEFAULT_HEIGHT);
5468     cdna.alignAs(alignment);
5469     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5470             + this.title;
5471     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5472             AlignFrame.DEFAULT_HEIGHT);
5473   }
5474
5475   /**
5476    * Set visibility of dna/protein complement view (available when shown in a
5477    * split frame).
5478    *
5479    * @param show
5480    */
5481   @Override
5482   protected void showComplement_actionPerformed(boolean show)
5483   {
5484     SplitContainerI sf = getSplitViewContainer();
5485     if (sf != null)
5486     {
5487       sf.setComplementVisible(this, show);
5488     }
5489   }
5490
5491   /**
5492    * Generate the reverse (optionally complemented) of the selected sequences,
5493    * and add them to the alignment
5494    */
5495   @Override
5496   protected void showReverse_actionPerformed(boolean complement)
5497   {
5498     AlignmentI al = null;
5499     try
5500     {
5501       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5502       al = dna.reverseCdna(complement);
5503       viewport.addAlignment(al, "");
5504       addHistoryItem(new EditCommand(
5505               MessageManager.getString("label.add_sequences"), Action.PASTE,
5506               al.getSequencesArray(), 0, al.getWidth(),
5507               viewport.getAlignment()));
5508     } catch (Exception ex)
5509     {
5510       System.err.println(ex.getMessage());
5511       return;
5512     }
5513   }
5514
5515   /**
5516    * Try to run a script in the Groovy console, having first ensured that this
5517    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5518    * be targeted at this alignment.
5519    */
5520   @Override
5521   protected void runGroovy_actionPerformed()
5522   {
5523     Jalview.setCurrentAlignFrame(this);
5524     groovy.ui.Console console = Desktop.getGroovyConsole();
5525     if (console != null)
5526     {
5527       try
5528       {
5529         console.runScript();
5530       } catch (Exception ex)
5531       {
5532         System.err.println((ex.toString()));
5533         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5534                 MessageManager.getString("label.couldnt_run_groovy_script"),
5535                 MessageManager.getString("label.groovy_support_failed"),
5536                 JvOptionPane.ERROR_MESSAGE);
5537       }
5538     }
5539     else
5540     {
5541       System.err.println("Can't run Groovy script as console not found");
5542     }
5543   }
5544
5545   /**
5546    * Hides columns containing (or not containing) a specified feature, provided
5547    * that would not leave all columns hidden
5548    *
5549    * @param featureType
5550    * @param columnsContaining
5551    * @return
5552    */
5553   public boolean hideFeatureColumns(String featureType,
5554           boolean columnsContaining)
5555   {
5556     boolean notForHiding = avc.markColumnsContainingFeatures(
5557             columnsContaining, false, false, featureType);
5558     if (notForHiding)
5559     {
5560       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5561               false, featureType))
5562       {
5563         getViewport().hideSelectedColumns();
5564         return true;
5565       }
5566     }
5567     return false;
5568   }
5569
5570   @Override
5571   protected void selectHighlightedColumns_actionPerformed(
5572           ActionEvent actionEvent)
5573   {
5574     // include key modifier check in case user selects from menu
5575     avc.markHighlightedColumns(
5576             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5577             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5578                     | ActionEvent.CTRL_MASK)) != 0);
5579   }
5580
5581   /**
5582    * Rebuilds the Colour menu, including any user-defined colours which have
5583    * been loaded either on startup or during the session
5584    */
5585   public void buildColourMenu()
5586   {
5587     colourMenu.removeAll();
5588
5589     colourMenu.add(applyToAllGroups);
5590     colourMenu.add(textColour);
5591     colourMenu.addSeparator();
5592
5593     ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5594             false);
5595
5596     colourMenu.addSeparator();
5597     colourMenu.add(conservationMenuItem);
5598     colourMenu.add(modifyConservation);
5599     colourMenu.add(abovePIDThreshold);
5600     colourMenu.add(modifyPID);
5601     colourMenu.add(annotationColour);
5602
5603     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5604     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5605   }
5606
5607   /**
5608    * Open a dialog (if not already open) that allows the user to select and
5609    * calculate PCA or Tree analysis
5610    */
5611   protected void openTreePcaDialog()
5612   {
5613     if (alignPanel.getCalculationDialog() == null)
5614     {
5615       new CalculationChooser(AlignFrame.this);
5616     }
5617   }
5618
5619   @Override
5620   protected void loadVcf_actionPerformed()
5621   {
5622     JalviewFileChooser chooser = new JalviewFileChooser(
5623             Cache.getProperty("LAST_DIRECTORY"));
5624     chooser.setFileView(new JalviewFileView());
5625     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5626     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5627
5628     int value = chooser.showOpenDialog(null);
5629
5630     if (value == JalviewFileChooser.APPROVE_OPTION)
5631     {
5632       String choice = chooser.getSelectedFile().getPath();
5633       Cache.setProperty("LAST_DIRECTORY", choice);
5634       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5635       new VCFLoader(choice).loadVCF(seqs, this);
5636     }
5637
5638   }
5639 }
5640
5641 class PrintThread extends Thread
5642 {
5643   AlignmentPanel ap;
5644
5645   public PrintThread(AlignmentPanel ap)
5646   {
5647     this.ap = ap;
5648   }
5649
5650   static PageFormat pf;
5651
5652   @Override
5653   public void run()
5654   {
5655     PrinterJob printJob = PrinterJob.getPrinterJob();
5656
5657     if (pf != null)
5658     {
5659       printJob.setPrintable(ap, pf);
5660     }
5661     else
5662     {
5663       printJob.setPrintable(ap);
5664     }
5665
5666     if (printJob.printDialog())
5667     {
5668       try
5669       {
5670         printJob.print();
5671       } catch (Exception PrintException)
5672       {
5673         PrintException.printStackTrace();
5674       }
5675     }
5676   }
5677 }