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