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