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.jbgui.GAlignFrame;
  85 import jalview.schemes.ColourSchemeI;
  86 import jalview.schemes.ColourSchemes;
  87 import jalview.schemes.ResidueColourScheme;
  88 import jalview.schemes.TCoffeeColourScheme;
  89 import jalview.util.MessageManager;
  90 import jalview.viewmodel.AlignmentViewport;
  91 import jalview.viewmodel.ViewportRanges;
  92 import jalview.ws.DBRefFetcher;
  93 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  94 import jalview.ws.jws1.Discoverer;
  95 import jalview.ws.jws2.Jws2Discoverer;
  96 import jalview.ws.jws2.jabaws2.Jws2Instance;
  97 import jalview.ws.seqfetcher.DbSourceProxy;
  98
  99 import java.awt.BorderLayout;
 100 import java.awt.Component;
 101 import java.awt.Rectangle;
 102 import java.awt.Toolkit;
 103 import java.awt.datatransfer.Clipboard;
 104 import java.awt.datatransfer.DataFlavor;
 105 import java.awt.datatransfer.StringSelection;
 106 import java.awt.datatransfer.Transferable;
 107 import java.awt.dnd.DnDConstants;
 108 import java.awt.dnd.DropTargetDragEvent;
 109 import java.awt.dnd.DropTargetDropEvent;
 110 import java.awt.dnd.DropTargetEvent;
 111 import java.awt.dnd.DropTargetListener;
 112 import java.awt.event.ActionEvent;
 113 import java.awt.event.ActionListener;
 114 import java.awt.event.FocusAdapter;
 115 import java.awt.event.FocusEvent;
 116 import java.awt.event.ItemEvent;
 117 import java.awt.event.ItemListener;
 118 import java.awt.event.KeyAdapter;
 119 import java.awt.event.KeyEvent;
 120 import java.awt.event.MouseEvent;
 121 import java.awt.print.PageFormat;
 122 import java.awt.print.PrinterJob;
 123 import java.beans.PropertyChangeEvent;
 124 import java.io.File;
 125 import java.io.FileWriter;
 126 import java.io.PrintWriter;
 127 import java.net.URL;
 128 import java.util.ArrayList;
 129 import java.util.Arrays;
 130 import java.util.Deque;
 131 import java.util.Enumeration;
 132 import java.util.Hashtable;
 133 import java.util.List;
 134 import java.util.Vector;
 135
 136 import javax.swing.JCheckBoxMenuItem;
 137 import javax.swing.JEditorPane;
 138 import javax.swing.JInternalFrame;
 139 import javax.swing.JLayeredPane;
 140 import javax.swing.JMenu;
 141 import javax.swing.JMenuItem;
 142 import javax.swing.JScrollPane;
 143 import javax.swing.SwingUtilities;
 144
 145 /**
 146  * DOCUMENT ME!
 147  *
 148  * @author $author$
 149  * @version $Revision$
 150  */
 151 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 152         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 153 {
 154
 155   public static final int DEFAULT_WIDTH = 700;
 156
 157   public static final int DEFAULT_HEIGHT = 500;
 158
 159   /*
 160    * The currently displayed panel (selected tabbed view if more than one)
 161    */
 162   public AlignmentPanel alignPanel;
 163
 164   AlignViewport viewport;
 165
 166   public AlignViewControllerI avc;
 167
 168   List<AlignmentPanel> alignPanels = new ArrayList<>();
 169
 170   /**
 171    * Last format used to load or save alignments in this window
 172    */
 173   FileFormatI currentFileFormat = null;
 174
 175   /**
 176    * Current filename for this alignment
 177    */
 178   String fileName = null;
 179
 180   /**
 181    * Creates a new AlignFrame object with specific width and height.
 182    *
 183    * @param al
 184    * @param width
 185    * @param height
 186    */
 187   public AlignFrame(AlignmentI al, int width, int height)
 188   {
 189     this(al, null, width, height);
 190   }
 191
 192   /**
 193    * Creates a new AlignFrame object with specific width, height and
 194    * sequenceSetId
 195    *
 196    * @param al
 197    * @param width
 198    * @param height
 199    * @param sequenceSetId
 200    */
 201   public AlignFrame(AlignmentI al, int width, int height,
 202           String sequenceSetId)
 203   {
 204     this(al, null, width, height, sequenceSetId);
 205   }
 206
 207   /**
 208    * Creates a new AlignFrame object with specific width, height and
 209    * sequenceSetId
 210    *
 211    * @param al
 212    * @param width
 213    * @param height
 214    * @param sequenceSetId
 215    * @param viewId
 216    */
 217   public AlignFrame(AlignmentI al, int width, int height,
 218           String sequenceSetId, String viewId)
 219   {
 220     this(al, null, width, height, sequenceSetId, viewId);
 221   }
 222
 223   /**
 224    * new alignment window with hidden columns
 225    *
 226    * @param al
 227    *          AlignmentI
 228    * @param hiddenColumns
 229    *          ColumnSelection or null
 230    * @param width
 231    *          Width of alignment frame
 232    * @param height
 233    *          height of frame.
 234    */
 235   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 236           int height)
 237   {
 238     this(al, hiddenColumns, width, height, null);
 239   }
 240
 241   /**
 242    * Create alignment frame for al with hiddenColumns, a specific width and
 243    * height, and specific sequenceId
 244    *
 245    * @param al
 246    * @param hiddenColumns
 247    * @param width
 248    * @param height
 249    * @param sequenceSetId
 250    *          (may be null)
 251    */
 252   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 253           int height, String sequenceSetId)
 254   {
 255     this(al, hiddenColumns, width, height, sequenceSetId, null);
 256   }
 257
 258   /**
 259    * Create alignment frame for al with hiddenColumns, a specific width and
 260    * height, and specific sequenceId
 261    *
 262    * @param al
 263    * @param hiddenColumns
 264    * @param width
 265    * @param height
 266    * @param sequenceSetId
 267    *          (may be null)
 268    * @param viewId
 269    *          (may be null)
 270    */
 271   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 272           int height, String sequenceSetId, String viewId)
 273   {
 274     setSize(width, height);
 275
 276     if (al.getDataset() == null)
 277     {
 278       al.setDataset(null);
 279     }
 280
 281     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 282
 283     alignPanel = new AlignmentPanel(this, viewport);
 284
 285     addAlignmentPanel(alignPanel, true);
 286     init();
 287   }
 288
 289   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 290           HiddenColumns hiddenColumns, int width, int height)
 291   {
 292     setSize(width, height);
 293
 294     if (al.getDataset() == null)
 295     {
 296       al.setDataset(null);
 297     }
 298
 299     viewport = new AlignViewport(al, hiddenColumns);
 300
 301     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 302     {
 303       viewport.hideSequence(hiddenSeqs);
 304     }
 305     alignPanel = new AlignmentPanel(this, viewport);
 306     addAlignmentPanel(alignPanel, true);
 307     init();
 308   }
 309
 310   /**
 311    * Make a new AlignFrame from existing alignmentPanels
 312    *
 313    * @param ap
 314    *          AlignmentPanel
 315    * @param av
 316    *          AlignViewport
 317    */
 318   public AlignFrame(AlignmentPanel ap)
 319   {
 320     viewport = ap.av;
 321     alignPanel = ap;
 322     addAlignmentPanel(ap, false);
 323     init();
 324   }
 325
 326   /**
 327    * initalise the alignframe from the underlying viewport data and the
 328    * configurations
 329    */
 330   void init()
 331   {
 332     if (!Jalview.isHeadlessMode())
 333     {
 334       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 335     }
 336
 337     avc = new jalview.controller.AlignViewController(this, viewport,
 338             alignPanel);
 339     if (viewport.getAlignmentConservationAnnotation() == null)
 340     {
 341       // BLOSUM62Colour.setEnabled(false);
 342       conservationMenuItem.setEnabled(false);
 343       modifyConservation.setEnabled(false);
 344       // PIDColour.setEnabled(false);
 345       // abovePIDThreshold.setEnabled(false);
 346       // modifyPID.setEnabled(false);
 347     }
 348
 349     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 350             "No sort");
 351
 352     if (sortby.equals("Id"))
 353     {
 354       sortIDMenuItem_actionPerformed(null);
 355     }
 356     else if (sortby.equals("Pairwise Identity"))
 357     {
 358       sortPairwiseMenuItem_actionPerformed(null);
 359     }
 360
 361     this.alignPanel.av
 362             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 363
 364     setMenusFromViewport(viewport);
 365     buildSortByAnnotationScoresMenu();
 366     calculateTree.addActionListener(new ActionListener()
 367     {
 368
 369       @Override
 370       public void actionPerformed(ActionEvent e)
 371       {
 372         openTreePcaDialog();
 373       }
 374     });
 375     buildColourMenu();
 376
 377     if (Desktop.desktop != null)
 378     {
 379       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 380       addServiceListeners();
 381       setGUINucleotide();
 382     }
 383
 384     if (viewport.getWrapAlignment())
 385     {
 386       wrapMenuItem_actionPerformed(null);
 387     }
 388
 389     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 390     {
 391       this.overviewMenuItem_actionPerformed(null);
 392     }
 393
 394     addKeyListener();
 395
 396     final List<AlignmentPanel> selviews = new ArrayList<>();
 397     final List<AlignmentPanel> origview = new ArrayList<>();
 398     final String menuLabel = MessageManager
 399             .getString("label.copy_format_from");
 400     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 401             new ViewSetProvider()
 402             {
 403
 404               @Override
 405               public AlignmentPanel[] getAllAlignmentPanels()
 406               {
 407                 origview.clear();
 408                 origview.add(alignPanel);
 409                 // make an array of all alignment panels except for this one
 410                 List<AlignmentPanel> aps = new ArrayList<>(
 411                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 412                 aps.remove(AlignFrame.this.alignPanel);
 413                 return aps.toArray(new AlignmentPanel[aps.size()]);
 414               }
 415             }, selviews, new ItemListener()
 416             {
 417
 418               @Override
 419               public void itemStateChanged(ItemEvent e)
 420               {
 421                 if (origview.size() > 0)
 422                 {
 423                   final AlignmentPanel ap = origview.get(0);
 424
 425                   /*
 426                    * Copy the ViewStyle of the selected panel to 'this one'.
 427                    * Don't change value of 'scaleProteinAsCdna' unless copying
 428                    * from a SplitFrame.
 429                    */
 430                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 431                           .getViewStyle();
 432                   boolean fromSplitFrame = selviews.get(0)
 433                           .getAlignViewport().getCodingComplement() != null;
 434                   if (!fromSplitFrame)
 435                   {
 436                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 437                             .getViewStyle().isScaleProteinAsCdna());
 438                   }
 439                   ap.getAlignViewport().setViewStyle(vs);
 440
 441                   /*
 442                    * Also rescale ViewStyle of SplitFrame complement if there is
 443                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 444                    * the whole ViewStyle (allow cDNA protein to have different
 445                    * fonts)
 446                    */
 447                   AlignViewportI complement = ap.getAlignViewport()
 448                           .getCodingComplement();
 449                   if (complement != null && vs.isScaleProteinAsCdna())
 450                   {
 451                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 452                     ((SplitFrame) af.getSplitViewContainer())
 453                             .adjustLayout();
 454                     af.setMenusForViewport();
 455                   }
 456
 457                   ap.updateLayout();
 458                   ap.setSelected(true);
 459                   ap.alignFrame.setMenusForViewport();
 460
 461                 }
 462               }
 463             });
 464     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 465             .indexOf("devel") > -1
 466             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 467                     .indexOf("test") > -1)
 468     {
 469       formatMenu.add(vsel);
 470     }
 471     addFocusListener(new FocusAdapter()
 472     {
 473       @Override
 474       public void focusGained(FocusEvent e)
 475       {
 476         Jalview.setCurrentAlignFrame(AlignFrame.this);
 477       }
 478     });
 479
 480   }
 481
 482   /**
 483    * Change the filename and format for the alignment, and enable the 'reload'
 484    * button functionality.
 485    *
 486    * @param file
 487    *          valid filename
 488    * @param format
 489    *          format of file
 490    */
 491   public void setFileName(String file, FileFormatI format)
 492   {
 493     fileName = file;
 494     setFileFormat(format);
 495     reload.setEnabled(true);
 496   }
 497
 498   /**
 499    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 500    * events
 501    */
 502   void addKeyListener()
 503   {
 504     addKeyListener(new KeyAdapter()
 505     {
 506       @Override
 507       public void keyPressed(KeyEvent evt)
 508       {
 509         if (viewport.cursorMode
 510                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 511                         && evt.getKeyCode() <= KeyEvent.VK_9)
 512                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 513                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 514                 && Character.isDigit(evt.getKeyChar()))
 515         {
 516           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 517         }
 518
 519         switch (evt.getKeyCode())
 520         {
 521
 522         case 27: // escape key
 523           deselectAllSequenceMenuItem_actionPerformed(null);
 524
 525           break;
 526
 527         case KeyEvent.VK_DOWN:
 528           if (evt.isAltDown() || !viewport.cursorMode)
 529           {
 530             moveSelectedSequences(false);
 531           }
 532           if (viewport.cursorMode)
 533           {
 534             alignPanel.getSeqPanel().moveCursor(0, 1);
 535           }
 536           break;
 537
 538         case KeyEvent.VK_UP:
 539           if (evt.isAltDown() || !viewport.cursorMode)
 540           {
 541             moveSelectedSequences(true);
 542           }
 543           if (viewport.cursorMode)
 544           {
 545             alignPanel.getSeqPanel().moveCursor(0, -1);
 546           }
 547
 548           break;
 549
 550         case KeyEvent.VK_LEFT:
 551           if (evt.isAltDown() || !viewport.cursorMode)
 552           {
 553             slideSequences(false,
 554                     alignPanel.getSeqPanel().getKeyboardNo1());
 555           }
 556           else
 557           {
 558             alignPanel.getSeqPanel().moveCursor(-1, 0);
 559           }
 560
 561           break;
 562
 563         case KeyEvent.VK_RIGHT:
 564           if (evt.isAltDown() || !viewport.cursorMode)
 565           {
 566             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 567           }
 568           else
 569           {
 570             alignPanel.getSeqPanel().moveCursor(1, 0);
 571           }
 572           break;
 573
 574         case KeyEvent.VK_SPACE:
 575           if (viewport.cursorMode)
 576           {
 577             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 578                     || evt.isShiftDown() || evt.isAltDown());
 579           }
 580           break;
 581
 582         // case KeyEvent.VK_A:
 583         // if (viewport.cursorMode)
 584         // {
 585         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 586         // //System.out.println("A");
 587         // }
 588         // break;
 589         /*
 590          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 591          * System.out.println("closing bracket"); } break;
 592          */
 593         case KeyEvent.VK_DELETE:
 594         case KeyEvent.VK_BACK_SPACE:
 595           if (!viewport.cursorMode)
 596           {
 597             cut_actionPerformed(null);
 598           }
 599           else
 600           {
 601             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 602                     || evt.isShiftDown() || evt.isAltDown());
 603           }
 604
 605           break;
 606
 607         case KeyEvent.VK_S:
 608           if (viewport.cursorMode)
 609           {
 610             alignPanel.getSeqPanel().setCursorRow();
 611           }
 612           break;
 613         case KeyEvent.VK_C:
 614           if (viewport.cursorMode && !evt.isControlDown())
 615           {
 616             alignPanel.getSeqPanel().setCursorColumn();
 617           }
 618           break;
 619         case KeyEvent.VK_P:
 620           if (viewport.cursorMode)
 621           {
 622             alignPanel.getSeqPanel().setCursorPosition();
 623           }
 624           break;
 625
 626         case KeyEvent.VK_ENTER:
 627         case KeyEvent.VK_COMMA:
 628           if (viewport.cursorMode)
 629           {
 630             alignPanel.getSeqPanel().setCursorRowAndColumn();
 631           }
 632           break;
 633
 634         case KeyEvent.VK_Q:
 635           if (viewport.cursorMode)
 636           {
 637             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 638           }
 639           break;
 640         case KeyEvent.VK_M:
 641           if (viewport.cursorMode)
 642           {
 643             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 644           }
 645           break;
 646
 647         case KeyEvent.VK_F2:
 648           viewport.cursorMode = !viewport.cursorMode;
 649           statusBar.setText(MessageManager
 650                   .formatMessage("label.keyboard_editing_mode", new String[]
 651                   { (viewport.cursorMode ? "on" : "off") }));
 652           if (viewport.cursorMode)
 653           {
 654             ViewportRanges ranges = viewport.getRanges();
 655             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 656                     .getStartRes();
 657             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 658                     .getStartSeq();
 659           }
 660           alignPanel.getSeqPanel().seqCanvas.repaint();
 661           break;
 662
 663         case KeyEvent.VK_F1:
 664           try
 665           {
 666             Help.showHelpWindow();
 667           } catch (Exception ex)
 668           {
 669             ex.printStackTrace();
 670           }
 671           break;
 672         case KeyEvent.VK_H:
 673         {
 674           boolean toggleSeqs = !evt.isControlDown();
 675           boolean toggleCols = !evt.isShiftDown();
 676           toggleHiddenRegions(toggleSeqs, toggleCols);
 677           break;
 678         }
 679         case KeyEvent.VK_B:
 680         {
 681           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 682           boolean modifyExisting = true; // always modify, don't clear
 683                                          // evt.isShiftDown();
 684           boolean invertHighlighted = evt.isAltDown();
 685           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 686                   toggleSel);
 687           break;
 688         }
 689         case KeyEvent.VK_PAGE_UP:
 690           viewport.getRanges().pageUp();
 691           break;
 692         case KeyEvent.VK_PAGE_DOWN:
 693           viewport.getRanges().pageDown();
 694           break;
 695         }
 696       }
 697
 698       @Override
 699       public void keyReleased(KeyEvent evt)
 700       {
 701         switch (evt.getKeyCode())
 702         {
 703         case KeyEvent.VK_LEFT:
 704           if (evt.isAltDown() || !viewport.cursorMode)
 705           {
 706             viewport.firePropertyChange("alignment", null,
 707                     viewport.getAlignment().getSequences());
 708           }
 709           break;
 710
 711         case KeyEvent.VK_RIGHT:
 712           if (evt.isAltDown() || !viewport.cursorMode)
 713           {
 714             viewport.firePropertyChange("alignment", null,
 715                     viewport.getAlignment().getSequences());
 716           }
 717           break;
 718         }
 719       }
 720     });
 721   }
 722
 723   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 724   {
 725     ap.alignFrame = this;
 726     avc = new jalview.controller.AlignViewController(this, viewport,
 727             alignPanel);
 728
 729     alignPanels.add(ap);
 730
 731     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 732
 733     int aSize = alignPanels.size();
 734
 735     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 736
 737     if (aSize == 1 && ap.av.viewName == null)
 738     {
 739       this.getContentPane().add(ap, BorderLayout.CENTER);
 740     }
 741     else
 742     {
 743       if (aSize == 2)
 744       {
 745         setInitialTabVisible();
 746       }
 747
 748       expandViews.setEnabled(true);
 749       gatherViews.setEnabled(true);
 750       tabbedPane.addTab(ap.av.viewName, ap);
 751
 752       ap.setVisible(false);
 753     }
 754
 755     if (newPanel)
 756     {
 757       if (ap.av.isPadGaps())
 758       {
 759         ap.av.getAlignment().padGaps();
 760       }
 761       ap.av.updateConservation(ap);
 762       ap.av.updateConsensus(ap);
 763       ap.av.updateStrucConsensus(ap);
 764     }
 765   }
 766
 767   public void setInitialTabVisible()
 768   {
 769     expandViews.setEnabled(true);
 770     gatherViews.setEnabled(true);
 771     tabbedPane.setVisible(true);
 772     AlignmentPanel first = alignPanels.get(0);
 773     tabbedPane.addTab(first.av.viewName, first);
 774     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 775   }
 776
 777   public AlignViewport getViewport()
 778   {
 779     return viewport;
 780   }
 781
 782   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 783   private void addServiceListeners()
 784   {
 785     final java.beans.PropertyChangeListener thisListener;
 786     Desktop.instance.addJalviewPropertyChangeListener("services",
 787             thisListener = new java.beans.PropertyChangeListener()
 788             {
 789               @Override
 790               public void propertyChange(PropertyChangeEvent evt)
 791               {
 792                 // // System.out.println("Discoverer property change.");
 793                 // if (evt.getPropertyName().equals("services"))
 794                 {
 795                   SwingUtilities.invokeLater(new Runnable()
 796                   {
 797
 798                     @Override
 799                     public void run()
 800                     {
 801                       System.err.println(
 802                               "Rebuild WS Menu for service change");
 803                       BuildWebServiceMenu();
 804                     }
 805
 806                   });
 807                 }
 808               }
 809             });
 810     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 811     {
 812       @Override
 813       public void internalFrameClosed(
 814               javax.swing.event.InternalFrameEvent evt)
 815       {
 816         // System.out.println("deregistering discoverer listener");
 817         Desktop.instance.removeJalviewPropertyChangeListener("services",
 818                 thisListener);
 819         closeMenuItem_actionPerformed(true);
 820       };
 821     });
 822     // Finally, build the menu once to get current service state
 823     new Thread(new Runnable()
 824     {
 825       @Override
 826       public void run()
 827       {
 828         BuildWebServiceMenu();
 829       }
 830     }).start();
 831   }
 832
 833   /**
 834    * Configure menu items that vary according to whether the alignment is
 835    * nucleotide or protein
 836    */
 837   public void setGUINucleotide()
 838   {
 839     AlignmentI al = getViewport().getAlignment();
 840     boolean nucleotide = al.isNucleotide();
 841
 842     showTranslation.setVisible(nucleotide);
 843     showReverse.setVisible(nucleotide);
 844     showReverseComplement.setVisible(nucleotide);
 845     conservationMenuItem.setEnabled(!nucleotide);
 846     modifyConservation
 847             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 848     showGroupConservation.setEnabled(!nucleotide);
 849
 850     showComplementMenuItem
 851             .setText(nucleotide ? MessageManager.getString("label.protein")
 852                     : MessageManager.getString("label.nucleotide"));
 853   }
 854
 855   /**
 856    * set up menus for the current viewport. This may be called after any
 857    * operation that affects the data in the current view (selection changed,
 858    * etc) to update the menus to reflect the new state.
 859    */
 860   @Override
 861   public void setMenusForViewport()
 862   {
 863     setMenusFromViewport(viewport);
 864   }
 865
 866   /**
 867    * Need to call this method when tabs are selected for multiple views, or when
 868    * loading from Jalview2XML.java
 869    *
 870    * @param av
 871    *          AlignViewport
 872    */
 873   void setMenusFromViewport(AlignViewport av)
 874   {
 875     padGapsMenuitem.setSelected(av.isPadGaps());
 876     colourTextMenuItem.setSelected(av.isShowColourText());
 877     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 878     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 879     conservationMenuItem.setSelected(av.getConservationSelected());
 880     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 881     seqLimits.setSelected(av.getShowJVSuffix());
 882     idRightAlign.setSelected(av.isRightAlignIds());
 883     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 884     renderGapsMenuItem.setSelected(av.isRenderGaps());
 885     wrapMenuItem.setSelected(av.getWrapAlignment());
 886     scaleAbove.setVisible(av.getWrapAlignment());
 887     scaleLeft.setVisible(av.getWrapAlignment());
 888     scaleRight.setVisible(av.getWrapAlignment());
 889     annotationPanelMenuItem.setState(av.isShowAnnotation());
 890     /*
 891      * Show/hide annotations only enabled if annotation panel is shown
 892      */
 893     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 894     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 895     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 896     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 897     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 898     viewTextMenuItem.setSelected(av.getShowText());
 899     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 900     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 901     showGroupConservation.setSelected(av.isShowGroupConservation());
 902     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 903     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 904     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 905
 906     ColourMenuHelper.setColourSelected(colourMenu,
 907             av.getGlobalColourScheme());
 908
 909     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 910     hiddenMarkers.setState(av.getShowHiddenMarkers());
 911     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 912     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 913     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 914     autoCalculate.setSelected(av.autoCalculateConsensus);
 915     sortByTree.setSelected(av.sortByTree);
 916     listenToViewSelections.setSelected(av.followSelection);
 917
 918     showProducts.setEnabled(canShowProducts());
 919     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 920
 921     updateEditMenuBar();
 922   }
 923
 924   /**
 925    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 926    *
 927    * @param b
 928    */
 929   public void setGroovyEnabled(boolean b)
 930   {
 931     runGroovy.setEnabled(b);
 932   }
 933
 934   private IProgressIndicator progressBar;
 935
 936   /*
 937    * (non-Javadoc)
 938    *
 939    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 940    */
 941   @Override
 942   public void setProgressBar(String message, long id)
 943   {
 944     progressBar.setProgressBar(message, id);
 945   }
 946
 947   @Override
 948   public void registerHandler(final long id,
 949           final IProgressIndicatorHandler handler)
 950   {
 951     progressBar.registerHandler(id, handler);
 952   }
 953
 954   /**
 955    *
 956    * @return true if any progress bars are still active
 957    */
 958   @Override
 959   public boolean operationInProgress()
 960   {
 961     return progressBar.operationInProgress();
 962   }
 963
 964   @Override
 965   public void setStatus(String text)
 966   {
 967     statusBar.setText(text);
 968   }
 969
 970   /*
 971    * Added so Castor Mapping file can obtain Jalview Version
 972    */
 973   public String getVersion()
 974   {
 975     return jalview.bin.Cache.getProperty("VERSION");
 976   }
 977
 978   public FeatureRenderer getFeatureRenderer()
 979   {
 980     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 981   }
 982
 983   @Override
 984   public void fetchSequence_actionPerformed(ActionEvent e)
 985   {
 986     new jalview.gui.SequenceFetcher(this);
 987   }
 988
 989   @Override
 990   public void addFromFile_actionPerformed(ActionEvent e)
 991   {
 992     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 993   }
 994
 995   @Override
 996   public void reload_actionPerformed(ActionEvent e)
 997   {
 998     if (fileName != null)
 999     {
1000       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1001       // originating file's format
1002       // TODO: work out how to recover feature settings for correct view(s) when
1003       // file is reloaded.
1004       if (FileFormat.Jalview.equals(currentFileFormat))
1005       {
1006         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1007         for (int i = 0; i < frames.length; i++)
1008         {
1009           if (frames[i] instanceof AlignFrame && frames[i] != this
1010                   && ((AlignFrame) frames[i]).fileName != null
1011                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1012           {
1013             try
1014             {
1015               frames[i].setSelected(true);
1016               Desktop.instance.closeAssociatedWindows();
1017             } catch (java.beans.PropertyVetoException ex)
1018             {
1019             }
1020           }
1021
1022         }
1023         Desktop.instance.closeAssociatedWindows();
1024
1025         FileLoader loader = new FileLoader();
1026         DataSourceType protocol = fileName.startsWith("http:")
1027                 ? DataSourceType.URL
1028                 : DataSourceType.FILE;
1029         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1030       }
1031       else
1032       {
1033         Rectangle bounds = this.getBounds();
1034
1035         FileLoader loader = new FileLoader();
1036         DataSourceType protocol = fileName.startsWith("http:")
1037                 ? DataSourceType.URL
1038                 : DataSourceType.FILE;
1039         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1040                 protocol, currentFileFormat);
1041
1042         newframe.setBounds(bounds);
1043         if (featureSettings != null && featureSettings.isShowing())
1044         {
1045           final Rectangle fspos = featureSettings.frame.getBounds();
1046           // TODO: need a 'show feature settings' function that takes bounds -
1047           // need to refactor Desktop.addFrame
1048           newframe.featureSettings_actionPerformed(null);
1049           final FeatureSettings nfs = newframe.featureSettings;
1050           SwingUtilities.invokeLater(new Runnable()
1051           {
1052             @Override
1053             public void run()
1054             {
1055               nfs.frame.setBounds(fspos);
1056             }
1057           });
1058           this.featureSettings.close();
1059           this.featureSettings = null;
1060         }
1061         this.closeMenuItem_actionPerformed(true);
1062       }
1063     }
1064   }
1065
1066   @Override
1067   public void addFromText_actionPerformed(ActionEvent e)
1068   {
1069     Desktop.instance
1070             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1071   }
1072
1073   @Override
1074   public void addFromURL_actionPerformed(ActionEvent e)
1075   {
1076     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1077   }
1078
1079   @Override
1080   public void save_actionPerformed(ActionEvent e)
1081   {
1082     if (fileName == null || (currentFileFormat == null)
1083             || fileName.startsWith("http"))
1084     {
1085       saveAs_actionPerformed(null);
1086     }
1087     else
1088     {
1089       saveAlignment(fileName, currentFileFormat);
1090     }
1091   }
1092
1093   /**
1094    * DOCUMENT ME!
1095    *
1096    * @param e
1097    *          DOCUMENT ME!
1098    */
1099   @Override
1100   public void saveAs_actionPerformed(ActionEvent e)
1101   {
1102     String format = currentFileFormat == null ? null
1103             : currentFileFormat.getName();
1104     JalviewFileChooser chooser = JalviewFileChooser
1105             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1106
1107     chooser.setFileView(new JalviewFileView());
1108     chooser.setDialogTitle(
1109             MessageManager.getString("label.save_alignment_to_file"));
1110     chooser.setToolTipText(MessageManager.getString("action.save"));
1111
1112     int value = chooser.showSaveDialog(this);
1113
1114     if (value == JalviewFileChooser.APPROVE_OPTION)
1115     {
1116       currentFileFormat = chooser.getSelectedFormat();
1117       while (currentFileFormat == null)
1118       {
1119         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1120                 MessageManager.getString(
1121                         "label.select_file_format_before_saving"),
1122                 MessageManager.getString("label.file_format_not_specified"),
1123                 JvOptionPane.WARNING_MESSAGE);
1124         currentFileFormat = chooser.getSelectedFormat();
1125         value = chooser.showSaveDialog(this);
1126         if (value != JalviewFileChooser.APPROVE_OPTION)
1127         {
1128           return;
1129         }
1130       }
1131
1132       fileName = chooser.getSelectedFile().getPath();
1133
1134       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1135
1136       Cache.setProperty("LAST_DIRECTORY", fileName);
1137       saveAlignment(fileName, currentFileFormat);
1138     }
1139   }
1140
1141   public boolean saveAlignment(String file, FileFormatI format)
1142   {
1143     boolean success = true;
1144
1145     if (FileFormat.Jalview.equals(format))
1146     {
1147       String shortName = title;
1148
1149       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1150       {
1151         shortName = shortName.substring(
1152                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1153       }
1154
1155       success = new Jalview2XML().saveAlignment(this, file, shortName);
1156
1157       statusBar.setText(MessageManager.formatMessage(
1158               "label.successfully_saved_to_file_in_format", new Object[]
1159               { fileName, format }));
1160
1161     }
1162     else
1163     {
1164       AlignmentExportData exportData = getAlignmentForExport(format,
1165               viewport, null);
1166       if (exportData.getSettings().isCancelled())
1167       {
1168         return false;
1169       }
1170       FormatAdapter f = new FormatAdapter(alignPanel,
1171               exportData.getSettings());
1172       String output = f.formatSequences(format, exportData.getAlignment(), // class
1173                                                                            // cast
1174                                                                            // exceptions
1175                                                                            // will
1176               // occur in the distant future
1177               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1178               f.getCacheSuffixDefault(format),
1179               viewport.getAlignment().getHiddenColumns());
1180
1181       if (output == null)
1182       {
1183         success = false;
1184       }
1185       else
1186       {
1187         try
1188         {
1189           PrintWriter out = new PrintWriter(new FileWriter(file));
1190
1191           out.print(output);
1192           out.close();
1193           this.setTitle(file);
1194           statusBar.setText(MessageManager.formatMessage(
1195                   "label.successfully_saved_to_file_in_format", new Object[]
1196                   { fileName, format.getName() }));
1197         } catch (Exception ex)
1198         {
1199           success = false;
1200           ex.printStackTrace();
1201         }
1202       }
1203     }
1204
1205     if (!success)
1206     {
1207       JvOptionPane.showInternalMessageDialog(this, MessageManager
1208               .formatMessage("label.couldnt_save_file", new Object[]
1209               { fileName }),
1210               MessageManager.getString("label.error_saving_file"),
1211               JvOptionPane.WARNING_MESSAGE);
1212     }
1213
1214     return success;
1215   }
1216
1217   private void warningMessage(String warning, String title)
1218   {
1219     if (new jalview.util.Platform().isHeadless())
1220     {
1221       System.err.println("Warning: " + title + "\nWarning: " + warning);
1222
1223     }
1224     else
1225     {
1226       JvOptionPane.showInternalMessageDialog(this, warning, title,
1227               JvOptionPane.WARNING_MESSAGE);
1228     }
1229     return;
1230   }
1231
1232   /**
1233    * DOCUMENT ME!
1234    *
1235    * @param e
1236    *          DOCUMENT ME!
1237    */
1238   @Override
1239   protected void outputText_actionPerformed(ActionEvent e)
1240   {
1241     FileFormatI fileFormat = FileFormats.getInstance()
1242             .forName(e.getActionCommand());
1243     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1244             viewport, null);
1245     if (exportData.getSettings().isCancelled())
1246     {
1247       return;
1248     }
1249     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1250     cap.setForInput(null);
1251     try
1252     {
1253       FileFormatI format = fileFormat;
1254       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1255               .formatSequences(format, exportData.getAlignment(),
1256                       exportData.getOmitHidden(),
1257                       exportData.getStartEndPostions(),
1258                       viewport.getAlignment().getHiddenColumns()));
1259       Desktop.addInternalFrame(cap, MessageManager
1260               .formatMessage("label.alignment_output_command", new Object[]
1261               { e.getActionCommand() }), 600, 500);
1262     } catch (OutOfMemoryError oom)
1263     {
1264       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1265               oom);
1266       cap.dispose();
1267     }
1268
1269   }
1270
1271   public static AlignmentExportData getAlignmentForExport(
1272           FileFormatI format, AlignViewportI viewport,
1273           AlignExportSettingI exportSettings)
1274   {
1275     AlignmentI alignmentToExport = null;
1276     AlignExportSettingI settings = exportSettings;
1277     String[] omitHidden = null;
1278
1279     HiddenSequences hiddenSeqs = viewport.getAlignment()
1280             .getHiddenSequences();
1281
1282     alignmentToExport = viewport.getAlignment();
1283
1284     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1285     if (settings == null)
1286     {
1287       settings = new AlignExportSettings(hasHiddenSeqs,
1288               viewport.hasHiddenColumns(), format);
1289     }
1290     // settings.isExportAnnotations();
1291
1292     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1293     {
1294       omitHidden = viewport.getViewAsString(false,
1295               settings.isExportHiddenSequences());
1296     }
1297
1298     int[] alignmentStartEnd = new int[2];
1299     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1300     {
1301       alignmentToExport = hiddenSeqs.getFullAlignment();
1302     }
1303     else
1304     {
1305       alignmentToExport = viewport.getAlignment();
1306     }
1307     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1308             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1309     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1310             omitHidden, alignmentStartEnd, settings);
1311     return ed;
1312   }
1313
1314   /**
1315    * DOCUMENT ME!
1316    *
1317    * @param e
1318    *          DOCUMENT ME!
1319    */
1320   @Override
1321   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1322   {
1323     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1324     htmlSVG.exportHTML(null);
1325   }
1326
1327   @Override
1328   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1329   {
1330     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1331     bjs.exportHTML(null);
1332   }
1333
1334   public void createImageMap(File file, String image)
1335   {
1336     alignPanel.makePNGImageMap(file, image);
1337   }
1338
1339   /**
1340    * DOCUMENT ME!
1341    *
1342    * @param e
1343    *          DOCUMENT ME!
1344    */
1345   @Override
1346   public void createPNG(File f)
1347   {
1348     alignPanel.makePNG(f);
1349   }
1350
1351   /**
1352    * DOCUMENT ME!
1353    *
1354    * @param e
1355    *          DOCUMENT ME!
1356    */
1357   @Override
1358   public void createEPS(File f)
1359   {
1360     alignPanel.makeEPS(f);
1361   }
1362
1363   @Override
1364   public void createSVG(File f)
1365   {
1366     alignPanel.makeSVG(f);
1367   }
1368
1369   @Override
1370   public void pageSetup_actionPerformed(ActionEvent e)
1371   {
1372     PrinterJob printJob = PrinterJob.getPrinterJob();
1373     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1374   }
1375
1376   /**
1377    * DOCUMENT ME!
1378    *
1379    * @param e
1380    *          DOCUMENT ME!
1381    */
1382   @Override
1383   public void printMenuItem_actionPerformed(ActionEvent e)
1384   {
1385     // Putting in a thread avoids Swing painting problems
1386     PrintThread thread = new PrintThread(alignPanel);
1387     thread.start();
1388   }
1389
1390   @Override
1391   public void exportFeatures_actionPerformed(ActionEvent e)
1392   {
1393     new AnnotationExporter().exportFeatures(alignPanel);
1394   }
1395
1396   @Override
1397   public void exportAnnotations_actionPerformed(ActionEvent e)
1398   {
1399     new AnnotationExporter().exportAnnotations(alignPanel);
1400   }
1401
1402   @Override
1403   public void associatedData_actionPerformed(ActionEvent e)
1404   {
1405     // Pick the tree file
1406     JalviewFileChooser chooser = new JalviewFileChooser(
1407             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1408     chooser.setFileView(new JalviewFileView());
1409     chooser.setDialogTitle(
1410             MessageManager.getString("label.load_jalview_annotations"));
1411     chooser.setToolTipText(
1412             MessageManager.getString("label.load_jalview_annotations"));
1413
1414     int value = chooser.showOpenDialog(null);
1415
1416     if (value == JalviewFileChooser.APPROVE_OPTION)
1417     {
1418       String choice = chooser.getSelectedFile().getPath();
1419       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1420       loadJalviewDataFile(choice, null, null, null);
1421     }
1422
1423   }
1424
1425   /**
1426    * Close the current view or all views in the alignment frame. If the frame
1427    * only contains one view then the alignment will be removed from memory.
1428    *
1429    * @param closeAllTabs
1430    */
1431   @Override
1432   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1433   {
1434     if (alignPanels != null && alignPanels.size() < 2)
1435     {
1436       closeAllTabs = true;
1437     }
1438
1439     try
1440     {
1441       if (alignPanels != null)
1442       {
1443         if (closeAllTabs)
1444         {
1445           if (this.isClosed())
1446           {
1447             // really close all the windows - otherwise wait till
1448             // setClosed(true) is called
1449             for (int i = 0; i < alignPanels.size(); i++)
1450             {
1451               AlignmentPanel ap = alignPanels.get(i);
1452               ap.closePanel();
1453             }
1454           }
1455         }
1456         else
1457         {
1458           closeView(alignPanel);
1459         }
1460       }
1461
1462       if (closeAllTabs)
1463       {
1464         /*
1465          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1466          * be called recursively, with the frame now in 'closed' state
1467          */
1468         this.setClosed(true);
1469       }
1470     } catch (Exception ex)
1471     {
1472       ex.printStackTrace();
1473     }
1474   }
1475
1476   /**
1477    * Close the specified panel and close up tabs appropriately.
1478    *
1479    * @param panelToClose
1480    */
1481   public void closeView(AlignmentPanel panelToClose)
1482   {
1483     int index = tabbedPane.getSelectedIndex();
1484     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1485     alignPanels.remove(panelToClose);
1486     panelToClose.closePanel();
1487     panelToClose = null;
1488
1489     tabbedPane.removeTabAt(closedindex);
1490     tabbedPane.validate();
1491
1492     if (index > closedindex || index == tabbedPane.getTabCount())
1493     {
1494       // modify currently selected tab index if necessary.
1495       index--;
1496     }
1497
1498     this.tabSelectionChanged(index);
1499   }
1500
1501   /**
1502    * DOCUMENT ME!
1503    */
1504   void updateEditMenuBar()
1505   {
1506
1507     if (viewport.getHistoryList().size() > 0)
1508     {
1509       undoMenuItem.setEnabled(true);
1510       CommandI command = viewport.getHistoryList().peek();
1511       undoMenuItem.setText(MessageManager
1512               .formatMessage("label.undo_command", new Object[]
1513               { command.getDescription() }));
1514     }
1515     else
1516     {
1517       undoMenuItem.setEnabled(false);
1518       undoMenuItem.setText(MessageManager.getString("action.undo"));
1519     }
1520
1521     if (viewport.getRedoList().size() > 0)
1522     {
1523       redoMenuItem.setEnabled(true);
1524
1525       CommandI command = viewport.getRedoList().peek();
1526       redoMenuItem.setText(MessageManager
1527               .formatMessage("label.redo_command", new Object[]
1528               { command.getDescription() }));
1529     }
1530     else
1531     {
1532       redoMenuItem.setEnabled(false);
1533       redoMenuItem.setText(MessageManager.getString("action.redo"));
1534     }
1535   }
1536
1537   @Override
1538   public void addHistoryItem(CommandI command)
1539   {
1540     if (command.getSize() > 0)
1541     {
1542       viewport.addToHistoryList(command);
1543       viewport.clearRedoList();
1544       updateEditMenuBar();
1545       viewport.updateHiddenColumns();
1546       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1547       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1548       // viewport.getColumnSelection()
1549       // .getHiddenColumns().size() > 0);
1550     }
1551   }
1552
1553   /**
1554    *
1555    * @return alignment objects for all views
1556    */
1557   AlignmentI[] getViewAlignments()
1558   {
1559     if (alignPanels != null)
1560     {
1561       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1562       int i = 0;
1563       for (AlignmentPanel ap : alignPanels)
1564       {
1565         als[i++] = ap.av.getAlignment();
1566       }
1567       return als;
1568     }
1569     if (viewport != null)
1570     {
1571       return new AlignmentI[] { viewport.getAlignment() };
1572     }
1573     return null;
1574   }
1575
1576   /**
1577    * DOCUMENT ME!
1578    *
1579    * @param e
1580    *          DOCUMENT ME!
1581    */
1582   @Override
1583   protected void undoMenuItem_actionPerformed(ActionEvent e)
1584   {
1585     if (viewport.getHistoryList().isEmpty())
1586     {
1587       return;
1588     }
1589     CommandI command = viewport.getHistoryList().pop();
1590     viewport.addToRedoList(command);
1591     command.undoCommand(getViewAlignments());
1592
1593     AlignmentViewport originalSource = getOriginatingSource(command);
1594     updateEditMenuBar();
1595
1596     if (originalSource != null)
1597     {
1598       if (originalSource != viewport)
1599       {
1600         Cache.log.warn(
1601                 "Implementation worry: mismatch of viewport origin for undo");
1602       }
1603       originalSource.updateHiddenColumns();
1604       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1605       // null
1606       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1607       // viewport.getColumnSelection()
1608       // .getHiddenColumns().size() > 0);
1609       originalSource.firePropertyChange("alignment", null,
1610               originalSource.getAlignment().getSequences());
1611     }
1612   }
1613
1614   /**
1615    * DOCUMENT ME!
1616    *
1617    * @param e
1618    *          DOCUMENT ME!
1619    */
1620   @Override
1621   protected void redoMenuItem_actionPerformed(ActionEvent e)
1622   {
1623     if (viewport.getRedoList().size() < 1)
1624     {
1625       return;
1626     }
1627
1628     CommandI command = viewport.getRedoList().pop();
1629     viewport.addToHistoryList(command);
1630     command.doCommand(getViewAlignments());
1631
1632     AlignmentViewport originalSource = getOriginatingSource(command);
1633     updateEditMenuBar();
1634
1635     if (originalSource != null)
1636     {
1637
1638       if (originalSource != viewport)
1639       {
1640         Cache.log.warn(
1641                 "Implementation worry: mismatch of viewport origin for redo");
1642       }
1643       originalSource.updateHiddenColumns();
1644       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1645       // null
1646       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1647       // viewport.getColumnSelection()
1648       // .getHiddenColumns().size() > 0);
1649       originalSource.firePropertyChange("alignment", null,
1650               originalSource.getAlignment().getSequences());
1651     }
1652   }
1653
1654   AlignmentViewport getOriginatingSource(CommandI command)
1655   {
1656     AlignmentViewport originalSource = null;
1657     // For sequence removal and addition, we need to fire
1658     // the property change event FROM the viewport where the
1659     // original alignment was altered
1660     AlignmentI al = null;
1661     if (command instanceof EditCommand)
1662     {
1663       EditCommand editCommand = (EditCommand) command;
1664       al = editCommand.getAlignment();
1665       List<Component> comps = PaintRefresher.components
1666               .get(viewport.getSequenceSetId());
1667
1668       for (Component comp : comps)
1669       {
1670         if (comp instanceof AlignmentPanel)
1671         {
1672           if (al == ((AlignmentPanel) comp).av.getAlignment())
1673           {
1674             originalSource = ((AlignmentPanel) comp).av;
1675             break;
1676           }
1677         }
1678       }
1679     }
1680
1681     if (originalSource == null)
1682     {
1683       // The original view is closed, we must validate
1684       // the current view against the closed view first
1685       if (al != null)
1686       {
1687         PaintRefresher.validateSequences(al, viewport.getAlignment());
1688       }
1689
1690       originalSource = viewport;
1691     }
1692
1693     return originalSource;
1694   }
1695
1696   /**
1697    * DOCUMENT ME!
1698    *
1699    * @param up
1700    *          DOCUMENT ME!
1701    */
1702   public void moveSelectedSequences(boolean up)
1703   {
1704     SequenceGroup sg = viewport.getSelectionGroup();
1705
1706     if (sg == null)
1707     {
1708       return;
1709     }
1710     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1711             viewport.getHiddenRepSequences(), up);
1712     alignPanel.paintAlignment(true, false);
1713   }
1714
1715   synchronized void slideSequences(boolean right, int size)
1716   {
1717     List<SequenceI> sg = new ArrayList<>();
1718     if (viewport.cursorMode)
1719     {
1720       sg.add(viewport.getAlignment()
1721               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1722     }
1723     else if (viewport.getSelectionGroup() != null
1724             && viewport.getSelectionGroup().getSize() != viewport
1725                     .getAlignment().getHeight())
1726     {
1727       sg = viewport.getSelectionGroup()
1728               .getSequences(viewport.getHiddenRepSequences());
1729     }
1730
1731     if (sg.size() < 1)
1732     {
1733       return;
1734     }
1735
1736     List<SequenceI> invertGroup = new ArrayList<>();
1737
1738     for (SequenceI seq : viewport.getAlignment().getSequences())
1739     {
1740       if (!sg.contains(seq))
1741       {
1742         invertGroup.add(seq);
1743       }
1744     }
1745
1746     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1747
1748     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1749     for (int i = 0; i < invertGroup.size(); i++)
1750     {
1751       seqs2[i] = invertGroup.get(i);
1752     }
1753
1754     SlideSequencesCommand ssc;
1755     if (right)
1756     {
1757       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1758               viewport.getGapCharacter());
1759     }
1760     else
1761     {
1762       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1763               viewport.getGapCharacter());
1764     }
1765
1766     int groupAdjustment = 0;
1767     if (ssc.getGapsInsertedBegin() && right)
1768     {
1769       if (viewport.cursorMode)
1770       {
1771         alignPanel.getSeqPanel().moveCursor(size, 0);
1772       }
1773       else
1774       {
1775         groupAdjustment = size;
1776       }
1777     }
1778     else if (!ssc.getGapsInsertedBegin() && !right)
1779     {
1780       if (viewport.cursorMode)
1781       {
1782         alignPanel.getSeqPanel().moveCursor(-size, 0);
1783       }
1784       else
1785       {
1786         groupAdjustment = -size;
1787       }
1788     }
1789
1790     if (groupAdjustment != 0)
1791     {
1792       viewport.getSelectionGroup().setStartRes(
1793               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1794       viewport.getSelectionGroup().setEndRes(
1795               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1796     }
1797
1798     /*
1799      * just extend the last slide command if compatible; but not if in
1800      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1801      */
1802     boolean appendHistoryItem = false;
1803     Deque<CommandI> historyList = viewport.getHistoryList();
1804     boolean inSplitFrame = getSplitViewContainer() != null;
1805     if (!inSplitFrame && historyList != null && historyList.size() > 0
1806             && historyList.peek() instanceof SlideSequencesCommand)
1807     {
1808       appendHistoryItem = ssc.appendSlideCommand(
1809               (SlideSequencesCommand) historyList.peek());
1810     }
1811
1812     if (!appendHistoryItem)
1813     {
1814       addHistoryItem(ssc);
1815     }
1816
1817     repaint();
1818   }
1819
1820   /**
1821    * DOCUMENT ME!
1822    *
1823    * @param e
1824    *          DOCUMENT ME!
1825    */
1826   @Override
1827   protected void copy_actionPerformed(ActionEvent e)
1828   {
1829     System.gc();
1830     if (viewport.getSelectionGroup() == null)
1831     {
1832       return;
1833     }
1834     // TODO: preserve the ordering of displayed alignment annotation in any
1835     // internal paste (particularly sequence associated annotation)
1836     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1837     String[] omitHidden = null;
1838
1839     if (viewport.hasHiddenColumns())
1840     {
1841       omitHidden = viewport.getViewAsString(true);
1842     }
1843
1844     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1845             seqs, omitHidden, null);
1846
1847     StringSelection ss = new StringSelection(output);
1848
1849     try
1850     {
1851       jalview.gui.Desktop.internalCopy = true;
1852       // Its really worth setting the clipboard contents
1853       // to empty before setting the large StringSelection!!
1854       Toolkit.getDefaultToolkit().getSystemClipboard()
1855               .setContents(new StringSelection(""), null);
1856
1857       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1858               Desktop.instance);
1859     } catch (OutOfMemoryError er)
1860     {
1861       new OOMWarning("copying region", er);
1862       return;
1863     }
1864
1865     HiddenColumns hiddenColumns = null;
1866     if (viewport.hasHiddenColumns())
1867     {
1868       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1869       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1870
1871       // create new HiddenColumns object with copy of hidden regions
1872       // between startRes and endRes, offset by startRes
1873       hiddenColumns = new HiddenColumns(
1874               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1875               hiddenCutoff, hiddenOffset);
1876     }
1877
1878     Desktop.jalviewClipboard = new Object[] { seqs,
1879         viewport.getAlignment().getDataset(), hiddenColumns };
1880     statusBar.setText(MessageManager.formatMessage(
1881             "label.copied_sequences_to_clipboard", new Object[]
1882             { Integer.valueOf(seqs.length).toString() }));
1883   }
1884
1885   /**
1886    * DOCUMENT ME!
1887    *
1888    * @param e
1889    *          DOCUMENT ME!
1890    */
1891   @Override
1892   protected void pasteNew_actionPerformed(ActionEvent e)
1893   {
1894     paste(true);
1895   }
1896
1897   /**
1898    * DOCUMENT ME!
1899    *
1900    * @param e
1901    *          DOCUMENT ME!
1902    */
1903   @Override
1904   protected void pasteThis_actionPerformed(ActionEvent e)
1905   {
1906     paste(false);
1907   }
1908
1909   /**
1910    * Paste contents of Jalview clipboard
1911    *
1912    * @param newAlignment
1913    *          true to paste to a new alignment, otherwise add to this.
1914    */
1915   void paste(boolean newAlignment)
1916   {
1917     boolean externalPaste = true;
1918     try
1919     {
1920       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1921       Transferable contents = c.getContents(this);
1922
1923       if (contents == null)
1924       {
1925         return;
1926       }
1927
1928       String str;
1929       FileFormatI format;
1930       try
1931       {
1932         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1933         if (str.length() < 1)
1934         {
1935           return;
1936         }
1937
1938         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1939
1940       } catch (OutOfMemoryError er)
1941       {
1942         new OOMWarning("Out of memory pasting sequences!!", er);
1943         return;
1944       }
1945
1946       SequenceI[] sequences;
1947       boolean annotationAdded = false;
1948       AlignmentI alignment = null;
1949
1950       if (Desktop.jalviewClipboard != null)
1951       {
1952         // The clipboard was filled from within Jalview, we must use the
1953         // sequences
1954         // And dataset from the copied alignment
1955         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1956         // be doubly sure that we create *new* sequence objects.
1957         sequences = new SequenceI[newseq.length];
1958         for (int i = 0; i < newseq.length; i++)
1959         {
1960           sequences[i] = new Sequence(newseq[i]);
1961         }
1962         alignment = new Alignment(sequences);
1963         externalPaste = false;
1964       }
1965       else
1966       {
1967         // parse the clipboard as an alignment.
1968         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1969                 format);
1970         sequences = alignment.getSequencesArray();
1971       }
1972
1973       int alwidth = 0;
1974       ArrayList<Integer> newGraphGroups = new ArrayList<>();
1975       int fgroup = -1;
1976
1977       if (newAlignment)
1978       {
1979
1980         if (Desktop.jalviewClipboard != null)
1981         {
1982           // dataset is inherited
1983           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1984         }
1985         else
1986         {
1987           // new dataset is constructed
1988           alignment.setDataset(null);
1989         }
1990         alwidth = alignment.getWidth() + 1;
1991       }
1992       else
1993       {
1994         AlignmentI pastedal = alignment; // preserve pasted alignment object
1995         // Add pasted sequences and dataset into existing alignment.
1996         alignment = viewport.getAlignment();
1997         alwidth = alignment.getWidth() + 1;
1998         // decide if we need to import sequences from an existing dataset
1999         boolean importDs = Desktop.jalviewClipboard != null
2000                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2001         // importDs==true instructs us to copy over new dataset sequences from
2002         // an existing alignment
2003         Vector newDs = (importDs) ? new Vector() : null; // used to create
2004         // minimum dataset set
2005
2006         for (int i = 0; i < sequences.length; i++)
2007         {
2008           if (importDs)
2009           {
2010             newDs.addElement(null);
2011           }
2012           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2013           // paste
2014           if (importDs && ds != null)
2015           {
2016             if (!newDs.contains(ds))
2017             {
2018               newDs.setElementAt(ds, i);
2019               ds = new Sequence(ds);
2020               // update with new dataset sequence
2021               sequences[i].setDatasetSequence(ds);
2022             }
2023             else
2024             {
2025               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2026             }
2027           }
2028           else
2029           {
2030             // copy and derive new dataset sequence
2031             sequences[i] = sequences[i].deriveSequence();
2032             alignment.getDataset()
2033                     .addSequence(sequences[i].getDatasetSequence());
2034             // TODO: avoid creation of duplicate dataset sequences with a
2035             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2036           }
2037           alignment.addSequence(sequences[i]); // merges dataset
2038         }
2039         if (newDs != null)
2040         {
2041           newDs.clear(); // tidy up
2042         }
2043         if (alignment.getAlignmentAnnotation() != null)
2044         {
2045           for (AlignmentAnnotation alan : alignment
2046                   .getAlignmentAnnotation())
2047           {
2048             if (alan.graphGroup > fgroup)
2049             {
2050               fgroup = alan.graphGroup;
2051             }
2052           }
2053         }
2054         if (pastedal.getAlignmentAnnotation() != null)
2055         {
2056           // Add any annotation attached to alignment.
2057           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2058           for (int i = 0; i < alann.length; i++)
2059           {
2060             annotationAdded = true;
2061             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2062             {
2063               AlignmentAnnotation newann = new AlignmentAnnotation(
2064                       alann[i]);
2065               if (newann.graphGroup > -1)
2066               {
2067                 if (newGraphGroups.size() <= newann.graphGroup
2068                         || newGraphGroups.get(newann.graphGroup) == null)
2069                 {
2070                   for (int q = newGraphGroups
2071                           .size(); q <= newann.graphGroup; q++)
2072                   {
2073                     newGraphGroups.add(q, null);
2074                   }
2075                   newGraphGroups.set(newann.graphGroup,
2076                           new Integer(++fgroup));
2077                 }
2078                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2079                         .intValue();
2080               }
2081
2082               newann.padAnnotation(alwidth);
2083               alignment.addAnnotation(newann);
2084             }
2085           }
2086         }
2087       }
2088       if (!newAlignment)
2089       {
2090         // /////
2091         // ADD HISTORY ITEM
2092         //
2093         addHistoryItem(new EditCommand(
2094                 MessageManager.getString("label.add_sequences"),
2095                 Action.PASTE, sequences, 0, alignment.getWidth(),
2096                 alignment));
2097       }
2098       // Add any annotations attached to sequences
2099       for (int i = 0; i < sequences.length; i++)
2100       {
2101         if (sequences[i].getAnnotation() != null)
2102         {
2103           AlignmentAnnotation newann;
2104           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2105           {
2106             annotationAdded = true;
2107             newann = sequences[i].getAnnotation()[a];
2108             newann.adjustForAlignment();
2109             newann.padAnnotation(alwidth);
2110             if (newann.graphGroup > -1)
2111             {
2112               if (newann.graphGroup > -1)
2113               {
2114                 if (newGraphGroups.size() <= newann.graphGroup
2115                         || newGraphGroups.get(newann.graphGroup) == null)
2116                 {
2117                   for (int q = newGraphGroups
2118                           .size(); q <= newann.graphGroup; q++)
2119                   {
2120                     newGraphGroups.add(q, null);
2121                   }
2122                   newGraphGroups.set(newann.graphGroup,
2123                           new Integer(++fgroup));
2124                 }
2125                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2126                         .intValue();
2127               }
2128             }
2129             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2130             // was
2131             // duplicated
2132             // earlier
2133             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2134                     a);
2135           }
2136         }
2137       }
2138       if (!newAlignment)
2139       {
2140
2141         // propagate alignment changed.
2142         viewport.getRanges().setEndSeq(alignment.getHeight());
2143         if (annotationAdded)
2144         {
2145           // Duplicate sequence annotation in all views.
2146           AlignmentI[] alview = this.getViewAlignments();
2147           for (int i = 0; i < sequences.length; i++)
2148           {
2149             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2150             if (sann == null)
2151             {
2152               continue;
2153             }
2154             for (int avnum = 0; avnum < alview.length; avnum++)
2155             {
2156               if (alview[avnum] != alignment)
2157               {
2158                 // duplicate in a view other than the one with input focus
2159                 int avwidth = alview[avnum].getWidth() + 1;
2160                 // this relies on sann being preserved after we
2161                 // modify the sequence's annotation array for each duplication
2162                 for (int a = 0; a < sann.length; a++)
2163                 {
2164                   AlignmentAnnotation newann = new AlignmentAnnotation(
2165                           sann[a]);
2166                   sequences[i].addAlignmentAnnotation(newann);
2167                   newann.padAnnotation(avwidth);
2168                   alview[avnum].addAnnotation(newann); // annotation was
2169                   // duplicated earlier
2170                   // TODO JAL-1145 graphGroups are not updated for sequence
2171                   // annotation added to several views. This may cause
2172                   // strangeness
2173                   alview[avnum].setAnnotationIndex(newann, a);
2174                 }
2175               }
2176             }
2177           }
2178           buildSortByAnnotationScoresMenu();
2179         }
2180         viewport.firePropertyChange("alignment", null,
2181                 alignment.getSequences());
2182         if (alignPanels != null)
2183         {
2184           for (AlignmentPanel ap : alignPanels)
2185           {
2186             ap.validateAnnotationDimensions(false);
2187           }
2188         }
2189         else
2190         {
2191           alignPanel.validateAnnotationDimensions(false);
2192         }
2193
2194       }
2195       else
2196       {
2197         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2198                 DEFAULT_HEIGHT);
2199         String newtitle = new String("Copied sequences");
2200
2201         if (Desktop.jalviewClipboard != null
2202                 && Desktop.jalviewClipboard[2] != null)
2203         {
2204           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2205           af.viewport.setHiddenColumns(hc);
2206         }
2207
2208         // >>>This is a fix for the moment, until a better solution is
2209         // found!!<<<
2210         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2211                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2212                         .getFeatureRenderer());
2213
2214         // TODO: maintain provenance of an alignment, rather than just make the
2215         // title a concatenation of operations.
2216         if (!externalPaste)
2217         {
2218           if (title.startsWith("Copied sequences"))
2219           {
2220             newtitle = title;
2221           }
2222           else
2223           {
2224             newtitle = newtitle.concat("- from " + title);
2225           }
2226         }
2227         else
2228         {
2229           newtitle = new String("Pasted sequences");
2230         }
2231
2232         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2233                 DEFAULT_HEIGHT);
2234
2235       }
2236
2237     } catch (Exception ex)
2238     {
2239       ex.printStackTrace();
2240       System.out.println("Exception whilst pasting: " + ex);
2241       // could be anything being pasted in here
2242     }
2243
2244   }
2245
2246   @Override
2247   protected void expand_newalign(ActionEvent e)
2248   {
2249     try
2250     {
2251       AlignmentI alignment = AlignmentUtils
2252               .expandContext(getViewport().getAlignment(), -1);
2253       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2254               DEFAULT_HEIGHT);
2255       String newtitle = new String("Flanking alignment");
2256
2257       if (Desktop.jalviewClipboard != null
2258               && Desktop.jalviewClipboard[2] != null)
2259       {
2260         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2261         af.viewport.setHiddenColumns(hc);
2262       }
2263
2264       // >>>This is a fix for the moment, until a better solution is
2265       // found!!<<<
2266       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2267               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2268                       .getFeatureRenderer());
2269
2270       // TODO: maintain provenance of an alignment, rather than just make the
2271       // title a concatenation of operations.
2272       {
2273         if (title.startsWith("Copied sequences"))
2274         {
2275           newtitle = title;
2276         }
2277         else
2278         {
2279           newtitle = newtitle.concat("- from " + title);
2280         }
2281       }
2282
2283       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2284
2285     } catch (Exception ex)
2286     {
2287       ex.printStackTrace();
2288       System.out.println("Exception whilst pasting: " + ex);
2289       // could be anything being pasted in here
2290     } catch (OutOfMemoryError oom)
2291     {
2292       new OOMWarning("Viewing flanking region of alignment", oom);
2293     }
2294   }
2295
2296   /**
2297    * DOCUMENT ME!
2298    *
2299    * @param e
2300    *          DOCUMENT ME!
2301    */
2302   @Override
2303   protected void cut_actionPerformed(ActionEvent e)
2304   {
2305     copy_actionPerformed(null);
2306     delete_actionPerformed(null);
2307   }
2308
2309   /**
2310    * DOCUMENT ME!
2311    *
2312    * @param e
2313    *          DOCUMENT ME!
2314    */
2315   @Override
2316   protected void delete_actionPerformed(ActionEvent evt)
2317   {
2318
2319     SequenceGroup sg = viewport.getSelectionGroup();
2320     if (sg == null)
2321     {
2322       return;
2323     }
2324
2325     /*
2326      * If the cut affects all sequences, warn, remove highlighted columns
2327      */
2328     if (sg.getSize() == viewport.getAlignment().getHeight())
2329     {
2330       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2331               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2332       if (isEntireAlignWidth)
2333       {
2334         int confirm = JvOptionPane.showConfirmDialog(this,
2335                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2336                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2337                 JvOptionPane.OK_CANCEL_OPTION);
2338
2339         if (confirm == JvOptionPane.CANCEL_OPTION
2340                 || confirm == JvOptionPane.CLOSED_OPTION)
2341         {
2342           return;
2343         }
2344       }
2345       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2346               sg.getEndRes() + 1);
2347     }
2348     SequenceI[] cut = sg.getSequences()
2349             .toArray(new SequenceI[sg.getSize()]);
2350
2351     addHistoryItem(new EditCommand(
2352             MessageManager.getString("label.cut_sequences"), Action.CUT,
2353             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2354             viewport.getAlignment()));
2355
2356     viewport.setSelectionGroup(null);
2357     viewport.sendSelection();
2358     viewport.getAlignment().deleteGroup(sg);
2359
2360     viewport.firePropertyChange("alignment", null,
2361             viewport.getAlignment().getSequences());
2362     if (viewport.getAlignment().getHeight() < 1)
2363     {
2364       try
2365       {
2366         this.setClosed(true);
2367       } catch (Exception ex)
2368       {
2369       }
2370     }
2371   }
2372
2373   /**
2374    * DOCUMENT ME!
2375    *
2376    * @param e
2377    *          DOCUMENT ME!
2378    */
2379   @Override
2380   protected void deleteGroups_actionPerformed(ActionEvent e)
2381   {
2382     if (avc.deleteGroups())
2383     {
2384       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2385       alignPanel.updateAnnotation();
2386       alignPanel.paintAlignment(true, true);
2387     }
2388   }
2389
2390   /**
2391    * DOCUMENT ME!
2392    *
2393    * @param e
2394    *          DOCUMENT ME!
2395    */
2396   @Override
2397   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2398   {
2399     SequenceGroup sg = new SequenceGroup();
2400
2401     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2402     {
2403       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2404     }
2405
2406     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2407     viewport.setSelectionGroup(sg);
2408     viewport.sendSelection();
2409     // JAL-2034 - should delegate to
2410     // alignPanel to decide if overview needs
2411     // updating.
2412     alignPanel.paintAlignment(false, false);
2413     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2414   }
2415
2416   /**
2417    * DOCUMENT ME!
2418    *
2419    * @param e
2420    *          DOCUMENT ME!
2421    */
2422   @Override
2423   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2424   {
2425     if (viewport.cursorMode)
2426     {
2427       alignPanel.getSeqPanel().keyboardNo1 = null;
2428       alignPanel.getSeqPanel().keyboardNo2 = null;
2429     }
2430     viewport.setSelectionGroup(null);
2431     viewport.getColumnSelection().clear();
2432     viewport.setSelectionGroup(null);
2433     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2434     // JAL-2034 - should delegate to
2435     // alignPanel to decide if overview needs
2436     // updating.
2437     alignPanel.paintAlignment(false, false);
2438     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2439     viewport.sendSelection();
2440   }
2441
2442   /**
2443    * DOCUMENT ME!
2444    *
2445    * @param e
2446    *          DOCUMENT ME!
2447    */
2448   @Override
2449   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2450   {
2451     SequenceGroup sg = viewport.getSelectionGroup();
2452
2453     if (sg == null)
2454     {
2455       selectAllSequenceMenuItem_actionPerformed(null);
2456
2457       return;
2458     }
2459
2460     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2461     {
2462       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2463     }
2464     // JAL-2034 - should delegate to
2465     // alignPanel to decide if overview needs
2466     // updating.
2467
2468     alignPanel.paintAlignment(true, false);
2469     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2470     viewport.sendSelection();
2471   }
2472
2473   @Override
2474   public void invertColSel_actionPerformed(ActionEvent e)
2475   {
2476     viewport.invertColumnSelection();
2477     alignPanel.paintAlignment(true, false);
2478     viewport.sendSelection();
2479   }
2480
2481   /**
2482    * DOCUMENT ME!
2483    *
2484    * @param e
2485    *          DOCUMENT ME!
2486    */
2487   @Override
2488   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2489   {
2490     trimAlignment(true);
2491   }
2492
2493   /**
2494    * DOCUMENT ME!
2495    *
2496    * @param e
2497    *          DOCUMENT ME!
2498    */
2499   @Override
2500   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2501   {
2502     trimAlignment(false);
2503   }
2504
2505   void trimAlignment(boolean trimLeft)
2506   {
2507     ColumnSelection colSel = viewport.getColumnSelection();
2508     int column;
2509
2510     if (!colSel.isEmpty())
2511     {
2512       if (trimLeft)
2513       {
2514         column = colSel.getMin();
2515       }
2516       else
2517       {
2518         column = colSel.getMax();
2519       }
2520
2521       SequenceI[] seqs;
2522       if (viewport.getSelectionGroup() != null)
2523       {
2524         seqs = viewport.getSelectionGroup()
2525                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2526       }
2527       else
2528       {
2529         seqs = viewport.getAlignment().getSequencesArray();
2530       }
2531
2532       TrimRegionCommand trimRegion;
2533       if (trimLeft)
2534       {
2535         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2536                 column, viewport.getAlignment());
2537         viewport.getRanges().setStartRes(0);
2538       }
2539       else
2540       {
2541         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2542                 column, viewport.getAlignment());
2543       }
2544
2545       statusBar.setText(MessageManager
2546               .formatMessage("label.removed_columns", new String[]
2547               { Integer.valueOf(trimRegion.getSize()).toString() }));
2548
2549       addHistoryItem(trimRegion);
2550
2551       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2552       {
2553         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2554                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2555         {
2556           viewport.getAlignment().deleteGroup(sg);
2557         }
2558       }
2559
2560       viewport.firePropertyChange("alignment", null,
2561               viewport.getAlignment().getSequences());
2562     }
2563   }
2564
2565   /**
2566    * DOCUMENT ME!
2567    *
2568    * @param e
2569    *          DOCUMENT ME!
2570    */
2571   @Override
2572   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2573   {
2574     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2575
2576     SequenceI[] seqs;
2577     if (viewport.getSelectionGroup() != null)
2578     {
2579       seqs = viewport.getSelectionGroup()
2580               .getSequencesAsArray(viewport.getHiddenRepSequences());
2581       start = viewport.getSelectionGroup().getStartRes();
2582       end = viewport.getSelectionGroup().getEndRes();
2583     }
2584     else
2585     {
2586       seqs = viewport.getAlignment().getSequencesArray();
2587     }
2588
2589     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2590             "Remove Gapped Columns", seqs, start, end,
2591             viewport.getAlignment());
2592
2593     addHistoryItem(removeGapCols);
2594
2595     statusBar.setText(MessageManager
2596             .formatMessage("label.removed_empty_columns", new Object[]
2597             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2598
2599     // This is to maintain viewport position on first residue
2600     // of first sequence
2601     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2602     ViewportRanges ranges = viewport.getRanges();
2603     int startRes = seq.findPosition(ranges.getStartRes());
2604     // ShiftList shifts;
2605     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2606     // edit.alColumnChanges=shifts.getInverse();
2607     // if (viewport.hasHiddenColumns)
2608     // viewport.getColumnSelection().compensateForEdits(shifts);
2609     ranges.setStartRes(seq.findIndex(startRes) - 1);
2610     viewport.firePropertyChange("alignment", null,
2611             viewport.getAlignment().getSequences());
2612
2613   }
2614
2615   /**
2616    * DOCUMENT ME!
2617    *
2618    * @param e
2619    *          DOCUMENT ME!
2620    */
2621   @Override
2622   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2623   {
2624     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2625
2626     SequenceI[] seqs;
2627     if (viewport.getSelectionGroup() != null)
2628     {
2629       seqs = viewport.getSelectionGroup()
2630               .getSequencesAsArray(viewport.getHiddenRepSequences());
2631       start = viewport.getSelectionGroup().getStartRes();
2632       end = viewport.getSelectionGroup().getEndRes();
2633     }
2634     else
2635     {
2636       seqs = viewport.getAlignment().getSequencesArray();
2637     }
2638
2639     // This is to maintain viewport position on first residue
2640     // of first sequence
2641     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2642     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2643
2644     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2645             viewport.getAlignment()));
2646
2647     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2648
2649     viewport.firePropertyChange("alignment", null,
2650             viewport.getAlignment().getSequences());
2651
2652   }
2653
2654   /**
2655    * DOCUMENT ME!
2656    *
2657    * @param e
2658    *          DOCUMENT ME!
2659    */
2660   @Override
2661   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2662   {
2663     viewport.setPadGaps(padGapsMenuitem.isSelected());
2664     viewport.firePropertyChange("alignment", null,
2665             viewport.getAlignment().getSequences());
2666   }
2667
2668   /**
2669    * DOCUMENT ME!
2670    *
2671    * @param e
2672    *          DOCUMENT ME!
2673    */
2674   @Override
2675   public void findMenuItem_actionPerformed(ActionEvent e)
2676   {
2677     new Finder();
2678   }
2679
2680   /**
2681    * Create a new view of the current alignment.
2682    */
2683   @Override
2684   public void newView_actionPerformed(ActionEvent e)
2685   {
2686     newView(null, true);
2687   }
2688
2689   /**
2690    * Creates and shows a new view of the current alignment.
2691    *
2692    * @param viewTitle
2693    *          title of newly created view; if null, one will be generated
2694    * @param copyAnnotation
2695    *          if true then duplicate all annnotation, groups and settings
2696    * @return new alignment panel, already displayed.
2697    */
2698   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2699   {
2700     /*
2701      * Create a new AlignmentPanel (with its own, new Viewport)
2702      */
2703     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2704     if (!copyAnnotation)
2705     {
2706       /*
2707        * remove all groups and annotation except for the automatic stuff
2708        */
2709       newap.av.getAlignment().deleteAllGroups();
2710       newap.av.getAlignment().deleteAllAnnotations(false);
2711     }
2712
2713     newap.av.setGatherViewsHere(false);
2714
2715     if (viewport.viewName == null)
2716     {
2717       viewport.viewName = MessageManager
2718               .getString("label.view_name_original");
2719     }
2720
2721     /*
2722      * Views share the same edits undo and redo stacks
2723      */
2724     newap.av.setHistoryList(viewport.getHistoryList());
2725     newap.av.setRedoList(viewport.getRedoList());
2726
2727     /*
2728      * Views share the same mappings; need to deregister any new mappings
2729      * created by copyAlignPanel, and register the new reference to the shared
2730      * mappings
2731      */
2732     newap.av.replaceMappings(viewport.getAlignment());
2733
2734     /*
2735      * start up cDNA consensus (if applicable) now mappings are in place
2736      */
2737     if (newap.av.initComplementConsensus())
2738     {
2739       newap.refresh(true); // adjust layout of annotations
2740     }
2741
2742     newap.av.viewName = getNewViewName(viewTitle);
2743
2744     addAlignmentPanel(newap, true);
2745     newap.alignmentChanged();
2746
2747     if (alignPanels.size() == 2)
2748     {
2749       viewport.setGatherViewsHere(true);
2750     }
2751     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2752     return newap;
2753   }
2754
2755   /**
2756    * Make a new name for the view, ensuring it is unique within the current
2757    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2758    * these now use viewId. Unique view names are still desirable for usability.)
2759    *
2760    * @param viewTitle
2761    * @return
2762    */
2763   protected String getNewViewName(String viewTitle)
2764   {
2765     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2766     boolean addFirstIndex = false;
2767     if (viewTitle == null || viewTitle.trim().length() == 0)
2768     {
2769       viewTitle = MessageManager.getString("action.view");
2770       addFirstIndex = true;
2771     }
2772     else
2773     {
2774       index = 1;// we count from 1 if given a specific name
2775     }
2776     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2777
2778     List<Component> comps = PaintRefresher.components
2779             .get(viewport.getSequenceSetId());
2780
2781     List<String> existingNames = getExistingViewNames(comps);
2782
2783     while (existingNames.contains(newViewName))
2784     {
2785       newViewName = viewTitle + " " + (++index);
2786     }
2787     return newViewName;
2788   }
2789
2790   /**
2791    * Returns a list of distinct view names found in the given list of
2792    * components. View names are held on the viewport of an AlignmentPanel.
2793    *
2794    * @param comps
2795    * @return
2796    */
2797   protected List<String> getExistingViewNames(List<Component> comps)
2798   {
2799     List<String> existingNames = new ArrayList<>();
2800     for (Component comp : comps)
2801     {
2802       if (comp instanceof AlignmentPanel)
2803       {
2804         AlignmentPanel ap = (AlignmentPanel) comp;
2805         if (!existingNames.contains(ap.av.viewName))
2806         {
2807           existingNames.add(ap.av.viewName);
2808         }
2809       }
2810     }
2811     return existingNames;
2812   }
2813
2814   /**
2815    * Explode tabbed views into separate windows.
2816    */
2817   @Override
2818   public void expandViews_actionPerformed(ActionEvent e)
2819   {
2820     Desktop.explodeViews(this);
2821   }
2822
2823   /**
2824    * Gather views in separate windows back into a tabbed presentation.
2825    */
2826   @Override
2827   public void gatherViews_actionPerformed(ActionEvent e)
2828   {
2829     Desktop.instance.gatherViews(this);
2830   }
2831
2832   /**
2833    * DOCUMENT ME!
2834    *
2835    * @param e
2836    *          DOCUMENT ME!
2837    */
2838   @Override
2839   public void font_actionPerformed(ActionEvent e)
2840   {
2841     new FontChooser(alignPanel);
2842   }
2843
2844   /**
2845    * DOCUMENT ME!
2846    *
2847    * @param e
2848    *          DOCUMENT ME!
2849    */
2850   @Override
2851   protected void seqLimit_actionPerformed(ActionEvent e)
2852   {
2853     viewport.setShowJVSuffix(seqLimits.isSelected());
2854
2855     alignPanel.getIdPanel().getIdCanvas()
2856             .setPreferredSize(alignPanel.calculateIdWidth());
2857     alignPanel.paintAlignment(true, false);
2858   }
2859
2860   @Override
2861   public void idRightAlign_actionPerformed(ActionEvent e)
2862   {
2863     viewport.setRightAlignIds(idRightAlign.isSelected());
2864     alignPanel.paintAlignment(false, false);
2865   }
2866
2867   @Override
2868   public void centreColumnLabels_actionPerformed(ActionEvent e)
2869   {
2870     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2871     alignPanel.paintAlignment(false, false);
2872   }
2873
2874   /*
2875    * (non-Javadoc)
2876    *
2877    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2878    */
2879   @Override
2880   protected void followHighlight_actionPerformed()
2881   {
2882     /*
2883      * Set the 'follow' flag on the Viewport (and scroll to position if now
2884      * true).
2885      */
2886     final boolean state = this.followHighlightMenuItem.getState();
2887     viewport.setFollowHighlight(state);
2888     if (state)
2889     {
2890       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2891     }
2892   }
2893
2894   /**
2895    * DOCUMENT ME!
2896    *
2897    * @param e
2898    *          DOCUMENT ME!
2899    */
2900   @Override
2901   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2902   {
2903     viewport.setColourText(colourTextMenuItem.isSelected());
2904     alignPanel.paintAlignment(false, false);
2905   }
2906
2907   /**
2908    * DOCUMENT ME!
2909    *
2910    * @param e
2911    *          DOCUMENT ME!
2912    */
2913   @Override
2914   public void wrapMenuItem_actionPerformed(ActionEvent e)
2915   {
2916     scaleAbove.setVisible(wrapMenuItem.isSelected());
2917     scaleLeft.setVisible(wrapMenuItem.isSelected());
2918     scaleRight.setVisible(wrapMenuItem.isSelected());
2919     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2920     alignPanel.updateLayout();
2921   }
2922
2923   @Override
2924   public void showAllSeqs_actionPerformed(ActionEvent e)
2925   {
2926     viewport.showAllHiddenSeqs();
2927   }
2928
2929   @Override
2930   public void showAllColumns_actionPerformed(ActionEvent e)
2931   {
2932     viewport.showAllHiddenColumns();
2933     alignPanel.paintAlignment(true, true);
2934     viewport.sendSelection();
2935   }
2936
2937   @Override
2938   public void hideSelSequences_actionPerformed(ActionEvent e)
2939   {
2940     viewport.hideAllSelectedSeqs();
2941   }
2942
2943   /**
2944    * called by key handler and the hide all/show all menu items
2945    *
2946    * @param toggleSeqs
2947    * @param toggleCols
2948    */
2949   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2950   {
2951
2952     boolean hide = false;
2953     SequenceGroup sg = viewport.getSelectionGroup();
2954     if (!toggleSeqs && !toggleCols)
2955     {
2956       // Hide everything by the current selection - this is a hack - we do the
2957       // invert and then hide
2958       // first check that there will be visible columns after the invert.
2959       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2960               && sg.getStartRes() <= sg.getEndRes()))
2961       {
2962         // now invert the sequence set, if required - empty selection implies
2963         // that no hiding is required.
2964         if (sg != null)
2965         {
2966           invertSequenceMenuItem_actionPerformed(null);
2967           sg = viewport.getSelectionGroup();
2968           toggleSeqs = true;
2969
2970         }
2971         viewport.expandColSelection(sg, true);
2972         // finally invert the column selection and get the new sequence
2973         // selection.
2974         invertColSel_actionPerformed(null);
2975         toggleCols = true;
2976       }
2977     }
2978
2979     if (toggleSeqs)
2980     {
2981       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2982       {
2983         hideSelSequences_actionPerformed(null);
2984         hide = true;
2985       }
2986       else if (!(toggleCols && viewport.hasSelectedColumns()))
2987       {
2988         showAllSeqs_actionPerformed(null);
2989       }
2990     }
2991
2992     if (toggleCols)
2993     {
2994       if (viewport.hasSelectedColumns())
2995       {
2996         hideSelColumns_actionPerformed(null);
2997         if (!toggleSeqs)
2998         {
2999           viewport.setSelectionGroup(sg);
3000         }
3001       }
3002       else if (!hide)
3003       {
3004         showAllColumns_actionPerformed(null);
3005       }
3006     }
3007   }
3008
3009   /*
3010    * (non-Javadoc)
3011    *
3012    * @see
3013    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3014    * event.ActionEvent)
3015    */
3016   @Override
3017   public void hideAllButSelection_actionPerformed(ActionEvent e)
3018   {
3019     toggleHiddenRegions(false, false);
3020     viewport.sendSelection();
3021   }
3022
3023   /*
3024    * (non-Javadoc)
3025    *
3026    * @see
3027    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3028    * .ActionEvent)
3029    */
3030   @Override
3031   public void hideAllSelection_actionPerformed(ActionEvent e)
3032   {
3033     SequenceGroup sg = viewport.getSelectionGroup();
3034     viewport.expandColSelection(sg, false);
3035     viewport.hideAllSelectedSeqs();
3036     viewport.hideSelectedColumns();
3037     alignPanel.paintAlignment(true, true);
3038     viewport.sendSelection();
3039   }
3040
3041   /*
3042    * (non-Javadoc)
3043    *
3044    * @see
3045    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3046    * ActionEvent)
3047    */
3048   @Override
3049   public void showAllhidden_actionPerformed(ActionEvent e)
3050   {
3051     viewport.showAllHiddenColumns();
3052     viewport.showAllHiddenSeqs();
3053     alignPanel.paintAlignment(true, true);
3054     viewport.sendSelection();
3055   }
3056
3057   @Override
3058   public void hideSelColumns_actionPerformed(ActionEvent e)
3059   {
3060     viewport.hideSelectedColumns();
3061     alignPanel.paintAlignment(true, true);
3062     viewport.sendSelection();
3063   }
3064
3065   @Override
3066   public void hiddenMarkers_actionPerformed(ActionEvent e)
3067   {
3068     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3069     repaint();
3070   }
3071
3072   /**
3073    * DOCUMENT ME!
3074    *
3075    * @param e
3076    *          DOCUMENT ME!
3077    */
3078   @Override
3079   protected void scaleAbove_actionPerformed(ActionEvent e)
3080   {
3081     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3082     // TODO: do we actually need to update overview for scale above change ?
3083     alignPanel.paintAlignment(true, false);
3084   }
3085
3086   /**
3087    * DOCUMENT ME!
3088    *
3089    * @param e
3090    *          DOCUMENT ME!
3091    */
3092   @Override
3093   protected void scaleLeft_actionPerformed(ActionEvent e)
3094   {
3095     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3096     alignPanel.paintAlignment(true, false);
3097   }
3098
3099   /**
3100    * DOCUMENT ME!
3101    *
3102    * @param e
3103    *          DOCUMENT ME!
3104    */
3105   @Override
3106   protected void scaleRight_actionPerformed(ActionEvent e)
3107   {
3108     viewport.setScaleRightWrapped(scaleRight.isSelected());
3109     alignPanel.paintAlignment(true, false);
3110   }
3111
3112   /**
3113    * DOCUMENT ME!
3114    *
3115    * @param e
3116    *          DOCUMENT ME!
3117    */
3118   @Override
3119   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3120   {
3121     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3122     alignPanel.paintAlignment(false, false);
3123   }
3124
3125   /**
3126    * DOCUMENT ME!
3127    *
3128    * @param e
3129    *          DOCUMENT ME!
3130    */
3131   @Override
3132   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3133   {
3134     viewport.setShowText(viewTextMenuItem.isSelected());
3135     alignPanel.paintAlignment(false, false);
3136   }
3137
3138   /**
3139    * DOCUMENT ME!
3140    *
3141    * @param e
3142    *          DOCUMENT ME!
3143    */
3144   @Override
3145   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3146   {
3147     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3148     alignPanel.paintAlignment(false, false);
3149   }
3150
3151   public FeatureSettings featureSettings;
3152
3153   @Override
3154   public FeatureSettingsControllerI getFeatureSettingsUI()
3155   {
3156     return featureSettings;
3157   }
3158
3159   @Override
3160   public void featureSettings_actionPerformed(ActionEvent e)
3161   {
3162     if (featureSettings != null)
3163     {
3164       featureSettings.close();
3165       featureSettings = null;
3166     }
3167     if (!showSeqFeatures.isSelected())
3168     {
3169       // make sure features are actually displayed
3170       showSeqFeatures.setSelected(true);
3171       showSeqFeatures_actionPerformed(null);
3172     }
3173     featureSettings = new FeatureSettings(this);
3174   }
3175
3176   /**
3177    * Set or clear 'Show Sequence Features'
3178    *
3179    * @param evt
3180    *          DOCUMENT ME!
3181    */
3182   @Override
3183   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3184   {
3185     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3186     alignPanel.paintAlignment(true, true);
3187   }
3188
3189   /**
3190    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3191    * the annotations panel as a whole.
3192    *
3193    * The options to show/hide all annotations should be enabled when the panel
3194    * is shown, and disabled when the panel is hidden.
3195    *
3196    * @param e
3197    */
3198   @Override
3199   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3200   {
3201     final boolean setVisible = annotationPanelMenuItem.isSelected();
3202     viewport.setShowAnnotation(setVisible);
3203     this.showAllSeqAnnotations.setEnabled(setVisible);
3204     this.hideAllSeqAnnotations.setEnabled(setVisible);
3205     this.showAllAlAnnotations.setEnabled(setVisible);
3206     this.hideAllAlAnnotations.setEnabled(setVisible);
3207     alignPanel.updateLayout();
3208   }
3209
3210   @Override
3211   public void alignmentProperties()
3212   {
3213     JEditorPane editPane = new JEditorPane("text/html", "");
3214     editPane.setEditable(false);
3215     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3216             .formatAsHtml();
3217     editPane.setText(
3218             MessageManager.formatMessage("label.html_content", new Object[]
3219             { contents.toString() }));
3220     JInternalFrame frame = new JInternalFrame();
3221     frame.getContentPane().add(new JScrollPane(editPane));
3222
3223     Desktop.addInternalFrame(frame, MessageManager
3224             .formatMessage("label.alignment_properties", new Object[]
3225             { getTitle() }), 500, 400);
3226   }
3227
3228   /**
3229    * DOCUMENT ME!
3230    *
3231    * @param e
3232    *          DOCUMENT ME!
3233    */
3234   @Override
3235   public void overviewMenuItem_actionPerformed(ActionEvent e)
3236   {
3237     if (alignPanel.overviewPanel != null)
3238     {
3239       return;
3240     }
3241
3242     JInternalFrame frame = new JInternalFrame();
3243     final OverviewPanel overview = new OverviewPanel(alignPanel);
3244     frame.setContentPane(overview);
3245     Desktop.addInternalFrame(frame, MessageManager
3246             .formatMessage("label.overview_params", new Object[]
3247             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3248             true, true);
3249     frame.pack();
3250     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3251     frame.addInternalFrameListener(
3252             new javax.swing.event.InternalFrameAdapter()
3253             {
3254               @Override
3255               public void internalFrameClosed(
3256                       javax.swing.event.InternalFrameEvent evt)
3257               {
3258                 overview.dispose();
3259                 alignPanel.setOverviewPanel(null);
3260               };
3261             });
3262     if (getKeyListeners().length > 0)
3263     {
3264       frame.addKeyListener(getKeyListeners()[0]);
3265     }
3266
3267     alignPanel.setOverviewPanel(overview);
3268   }
3269
3270   @Override
3271   public void textColour_actionPerformed()
3272   {
3273     new TextColourChooser().chooseColour(alignPanel, null);
3274   }
3275
3276   /*
3277    * public void covariationColour_actionPerformed() {
3278    * changeColour(new
3279    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3280    * ()[0])); }
3281    */
3282   @Override
3283   public void annotationColour_actionPerformed()
3284   {
3285     new AnnotationColourChooser(viewport, alignPanel);
3286   }
3287
3288   @Override
3289   public void annotationColumn_actionPerformed(ActionEvent e)
3290   {
3291     new AnnotationColumnChooser(viewport, alignPanel);
3292   }
3293
3294   /**
3295    * Action on the user checking or unchecking the option to apply the selected
3296    * colour scheme to all groups. If unchecked, groups may have their own
3297    * independent colour schemes.
3298    *
3299    * @param selected
3300    */
3301   @Override
3302   public void applyToAllGroups_actionPerformed(boolean selected)
3303   {
3304     viewport.setColourAppliesToAllGroups(selected);
3305   }
3306
3307   /**
3308    * Action on user selecting a colour from the colour menu
3309    *
3310    * @param name
3311    *          the name (not the menu item label!) of the colour scheme
3312    */
3313   @Override
3314   public void changeColour_actionPerformed(String name)
3315   {
3316     /*
3317      * 'User Defined' opens a panel to configure or load a
3318      * user-defined colour scheme
3319      */
3320     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3321     {
3322       new UserDefinedColours(alignPanel);
3323       return;
3324     }
3325
3326     /*
3327      * otherwise set the chosen colour scheme (or null for 'None')
3328      */
3329     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3330             viewport.getAlignment(), viewport.getHiddenRepSequences());
3331     changeColour(cs);
3332   }
3333
3334   /**
3335    * Actions on setting or changing the alignment colour scheme
3336    *
3337    * @param cs
3338    */
3339   @Override
3340   public void changeColour(ColourSchemeI cs)
3341   {
3342     // TODO: pull up to controller method
3343     ColourMenuHelper.setColourSelected(colourMenu, cs);
3344
3345     viewport.setGlobalColourScheme(cs);
3346
3347     alignPanel.paintAlignment(true, true);
3348   }
3349
3350   /**
3351    * Show the PID threshold slider panel
3352    */
3353   @Override
3354   protected void modifyPID_actionPerformed()
3355   {
3356     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3357             alignPanel.getViewName());
3358     SliderPanel.showPIDSlider();
3359   }
3360
3361   /**
3362    * Show the Conservation slider panel
3363    */
3364   @Override
3365   protected void modifyConservation_actionPerformed()
3366   {
3367     SliderPanel.setConservationSlider(alignPanel,
3368             viewport.getResidueShading(), alignPanel.getViewName());
3369     SliderPanel.showConservationSlider();
3370   }
3371
3372   /**
3373    * Action on selecting or deselecting (Colour) By Conservation
3374    */
3375   @Override
3376   public void conservationMenuItem_actionPerformed(boolean selected)
3377   {
3378     modifyConservation.setEnabled(selected);
3379     viewport.setConservationSelected(selected);
3380     viewport.getResidueShading().setConservationApplied(selected);
3381
3382     changeColour(viewport.getGlobalColourScheme());
3383     if (selected)
3384     {
3385       modifyConservation_actionPerformed();
3386     }
3387     else
3388     {
3389       SliderPanel.hideConservationSlider();
3390     }
3391   }
3392
3393   /**
3394    * Action on selecting or deselecting (Colour) Above PID Threshold
3395    */
3396   @Override
3397   public void abovePIDThreshold_actionPerformed(boolean selected)
3398   {
3399     modifyPID.setEnabled(selected);
3400     viewport.setAbovePIDThreshold(selected);
3401     if (!selected)
3402     {
3403       viewport.getResidueShading().setThreshold(0,
3404               viewport.isIgnoreGapsConsensus());
3405     }
3406
3407     changeColour(viewport.getGlobalColourScheme());
3408     if (selected)
3409     {
3410       modifyPID_actionPerformed();
3411     }
3412     else
3413     {
3414       SliderPanel.hidePIDSlider();
3415     }
3416   }
3417
3418   /**
3419    * DOCUMENT ME!
3420    *
3421    * @param e
3422    *          DOCUMENT ME!
3423    */
3424   @Override
3425   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3426   {
3427     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3428     AlignmentSorter.sortByPID(viewport.getAlignment(),
3429             viewport.getAlignment().getSequenceAt(0));
3430     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3431             viewport.getAlignment()));
3432     alignPanel.paintAlignment(true, false);
3433   }
3434
3435   /**
3436    * DOCUMENT ME!
3437    *
3438    * @param e
3439    *          DOCUMENT ME!
3440    */
3441   @Override
3442   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3443   {
3444     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3445     AlignmentSorter.sortByID(viewport.getAlignment());
3446     addHistoryItem(
3447             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3448     alignPanel.paintAlignment(true, false);
3449   }
3450
3451   /**
3452    * DOCUMENT ME!
3453    *
3454    * @param e
3455    *          DOCUMENT ME!
3456    */
3457   @Override
3458   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3459   {
3460     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3461     AlignmentSorter.sortByLength(viewport.getAlignment());
3462     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3463             viewport.getAlignment()));
3464     alignPanel.paintAlignment(true, false);
3465   }
3466
3467   /**
3468    * DOCUMENT ME!
3469    *
3470    * @param e
3471    *          DOCUMENT ME!
3472    */
3473   @Override
3474   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3475   {
3476     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3477     AlignmentSorter.sortByGroup(viewport.getAlignment());
3478     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3479             viewport.getAlignment()));
3480
3481     alignPanel.paintAlignment(true, false);
3482   }
3483
3484   /**
3485    * DOCUMENT ME!
3486    *
3487    * @param e
3488    *          DOCUMENT ME!
3489    */
3490   @Override
3491   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3492   {
3493     new RedundancyPanel(alignPanel, this);
3494   }
3495
3496   /**
3497    * DOCUMENT ME!
3498    *
3499    * @param e
3500    *          DOCUMENT ME!
3501    */
3502   @Override
3503   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3504   {
3505     if ((viewport.getSelectionGroup() == null)
3506             || (viewport.getSelectionGroup().getSize() < 2))
3507     {
3508       JvOptionPane.showInternalMessageDialog(this,
3509               MessageManager.getString(
3510                       "label.you_must_select_least_two_sequences"),
3511               MessageManager.getString("label.invalid_selection"),
3512               JvOptionPane.WARNING_MESSAGE);
3513     }
3514     else
3515     {
3516       JInternalFrame frame = new JInternalFrame();
3517       frame.setContentPane(new PairwiseAlignPanel(viewport));
3518       Desktop.addInternalFrame(frame,
3519               MessageManager.getString("action.pairwise_alignment"), 600,
3520               500);
3521     }
3522   }
3523
3524   @Override
3525   public void autoCalculate_actionPerformed(ActionEvent e)
3526   {
3527     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3528     if (viewport.autoCalculateConsensus)
3529     {
3530       viewport.firePropertyChange("alignment", null,
3531               viewport.getAlignment().getSequences());
3532     }
3533   }
3534
3535   @Override
3536   public void sortByTreeOption_actionPerformed(ActionEvent e)
3537   {
3538     viewport.sortByTree = sortByTree.isSelected();
3539   }
3540
3541   @Override
3542   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3543   {
3544     viewport.followSelection = listenToViewSelections.isSelected();
3545   }
3546
3547   /**
3548    * Constructs a tree panel and adds it to the desktop
3549    *
3550    * @param type
3551    *          tree type (NJ or AV)
3552    * @param modelName
3553    *          name of score model used to compute the tree
3554    * @param options
3555    *          parameters for the distance or similarity calculation
3556    */
3557   void newTreePanel(String type, String modelName,
3558           SimilarityParamsI options)
3559   {
3560     String frameTitle = "";
3561     TreePanel tp;
3562
3563     boolean onSelection = false;
3564     if (viewport.getSelectionGroup() != null
3565             && viewport.getSelectionGroup().getSize() > 0)
3566     {
3567       SequenceGroup sg = viewport.getSelectionGroup();
3568
3569       /* Decide if the selection is a column region */
3570       for (SequenceI _s : sg.getSequences())
3571       {
3572         if (_s.getLength() < sg.getEndRes())
3573         {
3574           JvOptionPane.showMessageDialog(Desktop.desktop,
3575                   MessageManager.getString(
3576                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3577                   MessageManager.getString(
3578                           "label.sequences_selection_not_aligned"),
3579                   JvOptionPane.WARNING_MESSAGE);
3580
3581           return;
3582         }
3583       }
3584       onSelection = true;
3585     }
3586     else
3587     {
3588       if (viewport.getAlignment().getHeight() < 2)
3589       {
3590         return;
3591       }
3592     }
3593
3594     tp = new TreePanel(alignPanel, type, modelName, options);
3595     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3596
3597     frameTitle += " from ";
3598
3599     if (viewport.viewName != null)
3600     {
3601       frameTitle += viewport.viewName + " of ";
3602     }
3603
3604     frameTitle += this.title;
3605
3606     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3607   }
3608
3609   /**
3610    * DOCUMENT ME!
3611    *
3612    * @param title
3613    *          DOCUMENT ME!
3614    * @param order
3615    *          DOCUMENT ME!
3616    */
3617   public void addSortByOrderMenuItem(String title,
3618           final AlignmentOrder order)
3619   {
3620     final JMenuItem item = new JMenuItem(MessageManager
3621             .formatMessage("action.by_title_param", new Object[]
3622             { title }));
3623     sort.add(item);
3624     item.addActionListener(new java.awt.event.ActionListener()
3625     {
3626       @Override
3627       public void actionPerformed(ActionEvent e)
3628       {
3629         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3630
3631         // TODO: JBPNote - have to map order entries to curent SequenceI
3632         // pointers
3633         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3634
3635         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3636                 viewport.getAlignment()));
3637
3638         alignPanel.paintAlignment(true, false);
3639       }
3640     });
3641   }
3642
3643   /**
3644    * Add a new sort by annotation score menu item
3645    *
3646    * @param sort
3647    *          the menu to add the option to
3648    * @param scoreLabel
3649    *          the label used to retrieve scores for each sequence on the
3650    *          alignment
3651    */
3652   public void addSortByAnnotScoreMenuItem(JMenu sort,
3653           final String scoreLabel)
3654   {
3655     final JMenuItem item = new JMenuItem(scoreLabel);
3656     sort.add(item);
3657     item.addActionListener(new java.awt.event.ActionListener()
3658     {
3659       @Override
3660       public void actionPerformed(ActionEvent e)
3661       {
3662         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3663         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3664                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3665         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3666                 viewport.getAlignment()));
3667         alignPanel.paintAlignment(true, false);
3668       }
3669     });
3670   }
3671
3672   /**
3673    * last hash for alignment's annotation array - used to minimise cost of
3674    * rebuild.
3675    */
3676   protected int _annotationScoreVectorHash;
3677
3678   /**
3679    * search the alignment and rebuild the sort by annotation score submenu the
3680    * last alignment annotation vector hash is stored to minimize cost of
3681    * rebuilding in subsequence calls.
3682    *
3683    */
3684   @Override
3685   public void buildSortByAnnotationScoresMenu()
3686   {
3687     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3688     {
3689       return;
3690     }
3691
3692     if (viewport.getAlignment().getAlignmentAnnotation()
3693             .hashCode() != _annotationScoreVectorHash)
3694     {
3695       sortByAnnotScore.removeAll();
3696       // almost certainly a quicker way to do this - but we keep it simple
3697       Hashtable scoreSorts = new Hashtable();
3698       AlignmentAnnotation aann[];
3699       for (SequenceI sqa : viewport.getAlignment().getSequences())
3700       {
3701         aann = sqa.getAnnotation();
3702         for (int i = 0; aann != null && i < aann.length; i++)
3703         {
3704           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3705           {
3706             scoreSorts.put(aann[i].label, aann[i].label);
3707           }
3708         }
3709       }
3710       Enumeration labels = scoreSorts.keys();
3711       while (labels.hasMoreElements())
3712       {
3713         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3714                 (String) labels.nextElement());
3715       }
3716       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3717       scoreSorts.clear();
3718
3719       _annotationScoreVectorHash = viewport.getAlignment()
3720               .getAlignmentAnnotation().hashCode();
3721     }
3722   }
3723
3724   /**
3725    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3726    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3727    * call. Listeners are added to remove the menu item when the treePanel is
3728    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3729    * modified.
3730    */
3731   @Override
3732   public void buildTreeSortMenu()
3733   {
3734     sortByTreeMenu.removeAll();
3735
3736     List<Component> comps = PaintRefresher.components
3737             .get(viewport.getSequenceSetId());
3738     List<TreePanel> treePanels = new ArrayList<>();
3739     for (Component comp : comps)
3740     {
3741       if (comp instanceof TreePanel)
3742       {
3743         treePanels.add((TreePanel) comp);
3744       }
3745     }
3746
3747     if (treePanels.size() < 1)
3748     {
3749       sortByTreeMenu.setVisible(false);
3750       return;
3751     }
3752
3753     sortByTreeMenu.setVisible(true);
3754
3755     for (final TreePanel tp : treePanels)
3756     {
3757       final JMenuItem item = new JMenuItem(tp.getTitle());
3758       item.addActionListener(new java.awt.event.ActionListener()
3759       {
3760         @Override
3761         public void actionPerformed(ActionEvent e)
3762         {
3763           tp.sortByTree_actionPerformed();
3764           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3765
3766         }
3767       });
3768
3769       sortByTreeMenu.add(item);
3770     }
3771   }
3772
3773   public boolean sortBy(AlignmentOrder alorder, String undoname)
3774   {
3775     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3776     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3777     if (undoname != null)
3778     {
3779       addHistoryItem(new OrderCommand(undoname, oldOrder,
3780               viewport.getAlignment()));
3781     }
3782     alignPanel.paintAlignment(true, false);
3783     return true;
3784   }
3785
3786   /**
3787    * Work out whether the whole set of sequences or just the selected set will
3788    * be submitted for multiple alignment.
3789    *
3790    */
3791   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3792   {
3793     // Now, check we have enough sequences
3794     AlignmentView msa = null;
3795
3796     if ((viewport.getSelectionGroup() != null)
3797             && (viewport.getSelectionGroup().getSize() > 1))
3798     {
3799       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3800       // some common interface!
3801       /*
3802        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3803        * SequenceI[sz = seqs.getSize(false)];
3804        *
3805        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3806        * seqs.getSequenceAt(i); }
3807        */
3808       msa = viewport.getAlignmentView(true);
3809     }
3810     else if (viewport.getSelectionGroup() != null
3811             && viewport.getSelectionGroup().getSize() == 1)
3812     {
3813       int option = JvOptionPane.showConfirmDialog(this,
3814               MessageManager.getString("warn.oneseq_msainput_selection"),
3815               MessageManager.getString("label.invalid_selection"),
3816               JvOptionPane.OK_CANCEL_OPTION);
3817       if (option == JvOptionPane.OK_OPTION)
3818       {
3819         msa = viewport.getAlignmentView(false);
3820       }
3821     }
3822     else
3823     {
3824       msa = viewport.getAlignmentView(false);
3825     }
3826     return msa;
3827   }
3828
3829   /**
3830    * Decides what is submitted to a secondary structure prediction service: the
3831    * first sequence in the alignment, or in the current selection, or, if the
3832    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3833    * region or the whole alignment. (where the first sequence in the set is the
3834    * one that the prediction will be for).
3835    */
3836   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3837   {
3838     AlignmentView seqs = null;
3839
3840     if ((viewport.getSelectionGroup() != null)
3841             && (viewport.getSelectionGroup().getSize() > 0))
3842     {
3843       seqs = viewport.getAlignmentView(true);
3844     }
3845     else
3846     {
3847       seqs = viewport.getAlignmentView(false);
3848     }
3849     // limit sequences - JBPNote in future - could spawn multiple prediction
3850     // jobs
3851     // TODO: viewport.getAlignment().isAligned is a global state - the local
3852     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3853     if (!viewport.getAlignment().isAligned(false))
3854     {
3855       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3856       // TODO: if seqs.getSequences().length>1 then should really have warned
3857       // user!
3858
3859     }
3860     return seqs;
3861   }
3862
3863   /**
3864    * DOCUMENT ME!
3865    *
3866    * @param e
3867    *          DOCUMENT ME!
3868    */
3869   @Override
3870   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3871   {
3872     // Pick the tree file
3873     JalviewFileChooser chooser = new JalviewFileChooser(
3874             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3875     chooser.setFileView(new JalviewFileView());
3876     chooser.setDialogTitle(
3877             MessageManager.getString("label.select_newick_like_tree_file"));
3878     chooser.setToolTipText(
3879             MessageManager.getString("label.load_tree_file"));
3880
3881     int value = chooser.showOpenDialog(null);
3882
3883     if (value == JalviewFileChooser.APPROVE_OPTION)
3884     {
3885       String filePath = chooser.getSelectedFile().getPath();
3886       Cache.setProperty("LAST_DIRECTORY", filePath);
3887       NewickFile fin = null;
3888       try
3889       {
3890         fin = new NewickFile(filePath, DataSourceType.FILE);
3891         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3892       } catch (Exception ex)
3893       {
3894         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3895                 MessageManager.getString("label.problem_reading_tree_file"),
3896                 JvOptionPane.WARNING_MESSAGE);
3897         ex.printStackTrace();
3898       }
3899       if (fin != null && fin.hasWarningMessage())
3900       {
3901         JvOptionPane.showMessageDialog(Desktop.desktop,
3902                 fin.getWarningMessage(),
3903                 MessageManager
3904                         .getString("label.possible_problem_with_tree_file"),
3905                 JvOptionPane.WARNING_MESSAGE);
3906       }
3907     }
3908   }
3909
3910   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3911   {
3912     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3913   }
3914
3915   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3916           int h, int x, int y)
3917   {
3918     return showNewickTree(nf, treeTitle, null, w, h, x, y);
3919   }
3920
3921   /**
3922    * Add a treeviewer for the tree extracted from a Newick file object to the
3923    * current alignment view
3924    *
3925    * @param nf
3926    *          the tree
3927    * @param title
3928    *          tree viewer title
3929    * @param input
3930    *          Associated alignment input data (or null)
3931    * @param w
3932    *          width
3933    * @param h
3934    *          height
3935    * @param x
3936    *          position
3937    * @param y
3938    *          position
3939    * @return TreePanel handle
3940    */
3941   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3942           AlignmentView input, int w, int h, int x, int y)
3943   {
3944     TreePanel tp = null;
3945
3946     try
3947     {
3948       nf.parse();
3949
3950       if (nf.getTree() != null)
3951       {
3952         tp = new TreePanel(alignPanel, nf, treeTitle, input);
3953
3954         tp.setSize(w, h);
3955
3956         if (x > 0 && y > 0)
3957         {
3958           tp.setLocation(x, y);
3959         }
3960
3961         Desktop.addInternalFrame(tp, treeTitle, w, h);
3962       }
3963     } catch (Exception ex)
3964     {
3965       ex.printStackTrace();
3966     }
3967
3968     return tp;
3969   }
3970
3971   private boolean buildingMenu = false;
3972
3973   /**
3974    * Generates menu items and listener event actions for web service clients
3975    *
3976    */
3977   public void BuildWebServiceMenu()
3978   {
3979     while (buildingMenu)
3980     {
3981       try
3982       {
3983         System.err.println("Waiting for building menu to finish.");
3984         Thread.sleep(10);
3985       } catch (Exception e)
3986       {
3987       }
3988     }
3989     final AlignFrame me = this;
3990     buildingMenu = true;
3991     new Thread(new Runnable()
3992     {
3993       @Override
3994       public void run()
3995       {
3996         final List<JMenuItem> legacyItems = new ArrayList<>();
3997         try
3998         {
3999           // System.err.println("Building ws menu again "
4000           // + Thread.currentThread());
4001           // TODO: add support for context dependent disabling of services based
4002           // on
4003           // alignment and current selection
4004           // TODO: add additional serviceHandle parameter to specify abstract
4005           // handler
4006           // class independently of AbstractName
4007           // TODO: add in rediscovery GUI function to restart discoverer
4008           // TODO: group services by location as well as function and/or
4009           // introduce
4010           // object broker mechanism.
4011           final Vector<JMenu> wsmenu = new Vector<>();
4012           final IProgressIndicator af = me;
4013
4014           /*
4015            * do not i18n these strings - they are hard-coded in class
4016            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4017            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4018            */
4019           final JMenu msawsmenu = new JMenu("Alignment");
4020           final JMenu secstrmenu = new JMenu(
4021                   "Secondary Structure Prediction");
4022           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4023           final JMenu analymenu = new JMenu("Analysis");
4024           final JMenu dismenu = new JMenu("Protein Disorder");
4025           // JAL-940 - only show secondary structure prediction services from
4026           // the legacy server
4027           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4028               // &&
4029           Discoverer.services != null && (Discoverer.services.size() > 0))
4030           {
4031             // TODO: refactor to allow list of AbstractName/Handler bindings to
4032             // be
4033             // stored or retrieved from elsewhere
4034             // No MSAWS used any more:
4035             // Vector msaws = null; // (Vector)
4036             // Discoverer.services.get("MsaWS");
4037             Vector secstrpr = (Vector) Discoverer.services
4038                     .get("SecStrPred");
4039             if (secstrpr != null)
4040             {
4041               // Add any secondary structure prediction services
4042               for (int i = 0, j = secstrpr.size(); i < j; i++)
4043               {
4044                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4045                         .get(i);
4046                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4047                         .getServiceClient(sh);
4048                 int p = secstrmenu.getItemCount();
4049                 impl.attachWSMenuEntry(secstrmenu, me);
4050                 int q = secstrmenu.getItemCount();
4051                 for (int litm = p; litm < q; litm++)
4052                 {
4053                   legacyItems.add(secstrmenu.getItem(litm));
4054                 }
4055               }
4056             }
4057           }
4058
4059           // Add all submenus in the order they should appear on the web
4060           // services menu
4061           wsmenu.add(msawsmenu);
4062           wsmenu.add(secstrmenu);
4063           wsmenu.add(dismenu);
4064           wsmenu.add(analymenu);
4065           // No search services yet
4066           // wsmenu.add(seqsrchmenu);
4067
4068           javax.swing.SwingUtilities.invokeLater(new Runnable()
4069           {
4070             @Override
4071             public void run()
4072             {
4073               try
4074               {
4075                 webService.removeAll();
4076                 // first, add discovered services onto the webservices menu
4077                 if (wsmenu.size() > 0)
4078                 {
4079                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4080                   {
4081                     webService.add(wsmenu.get(i));
4082                   }
4083                 }
4084                 else
4085                 {
4086                   webService.add(me.webServiceNoServices);
4087                 }
4088                 // TODO: move into separate menu builder class.
4089                 boolean new_sspred = false;
4090                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4091                 {
4092                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4093                   if (jws2servs != null)
4094                   {
4095                     if (jws2servs.hasServices())
4096                     {
4097                       jws2servs.attachWSMenuEntry(webService, me);
4098                       for (Jws2Instance sv : jws2servs.getServices())
4099                       {
4100                         if (sv.description.toLowerCase().contains("jpred"))
4101                         {
4102                           for (JMenuItem jmi : legacyItems)
4103                           {
4104                             jmi.setVisible(false);
4105                           }
4106                         }
4107                       }
4108
4109                     }
4110                     if (jws2servs.isRunning())
4111                     {
4112                       JMenuItem tm = new JMenuItem(
4113                               "Still discovering JABA Services");
4114                       tm.setEnabled(false);
4115                       webService.add(tm);
4116                     }
4117                   }
4118                 }
4119                 build_urlServiceMenu(me.webService);
4120                 build_fetchdbmenu(webService);
4121                 for (JMenu item : wsmenu)
4122                 {
4123                   if (item.getItemCount() == 0)
4124                   {
4125                     item.setEnabled(false);
4126                   }
4127                   else
4128                   {
4129                     item.setEnabled(true);
4130                   }
4131                 }
4132               } catch (Exception e)
4133               {
4134                 Cache.log.debug(
4135                         "Exception during web service menu building process.",
4136                         e);
4137               }
4138             }
4139           });
4140         } catch (Exception e)
4141         {
4142         }
4143         buildingMenu = false;
4144       }
4145     }).start();
4146
4147   }
4148
4149   /**
4150    * construct any groupURL type service menu entries.
4151    *
4152    * @param webService
4153    */
4154   private void build_urlServiceMenu(JMenu webService)
4155   {
4156     // TODO: remove this code when 2.7 is released
4157     // DEBUG - alignmentView
4158     /*
4159      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4160      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4161      *
4162      * @Override public void actionPerformed(ActionEvent e) {
4163      * jalview.datamodel.AlignmentView
4164      * .testSelectionViews(af.viewport.getAlignment(),
4165      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4166      *
4167      * }); webService.add(testAlView);
4168      */
4169     // TODO: refactor to RestClient discoverer and merge menu entries for
4170     // rest-style services with other types of analysis/calculation service
4171     // SHmmr test client - still being implemented.
4172     // DEBUG - alignmentView
4173
4174     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4175             .getRestClients())
4176     {
4177       client.attachWSMenuEntry(
4178               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4179               this);
4180     }
4181   }
4182
4183   /**
4184    * Searches the alignment sequences for xRefs and builds the Show
4185    * Cross-References menu (formerly called Show Products), with database
4186    * sources for which cross-references are found (protein sources for a
4187    * nucleotide alignment and vice versa)
4188    *
4189    * @return true if Show Cross-references menu should be enabled
4190    */
4191   public boolean canShowProducts()
4192   {
4193     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4194     AlignmentI dataset = viewport.getAlignment().getDataset();
4195
4196     showProducts.removeAll();
4197     final boolean dna = viewport.getAlignment().isNucleotide();
4198
4199     if (seqs == null || seqs.length == 0)
4200     {
4201       // nothing to see here.
4202       return false;
4203     }
4204
4205     boolean showp = false;
4206     try
4207     {
4208       List<String> ptypes = new CrossRef(seqs, dataset)
4209               .findXrefSourcesForSequences(dna);
4210
4211       for (final String source : ptypes)
4212       {
4213         showp = true;
4214         final AlignFrame af = this;
4215         JMenuItem xtype = new JMenuItem(source);
4216         xtype.addActionListener(new ActionListener()
4217         {
4218           @Override
4219           public void actionPerformed(ActionEvent e)
4220           {
4221             showProductsFor(af.viewport.getSequenceSelection(), dna,
4222                     source);
4223           }
4224         });
4225         showProducts.add(xtype);
4226       }
4227       showProducts.setVisible(showp);
4228       showProducts.setEnabled(showp);
4229     } catch (Exception e)
4230     {
4231       Cache.log.warn(
4232               "canShowProducts threw an exception - please report to help@jalview.org",
4233               e);
4234       return false;
4235     }
4236     return showp;
4237   }
4238
4239   /**
4240    * Finds and displays cross-references for the selected sequences (protein
4241    * products for nucleotide sequences, dna coding sequences for peptides).
4242    *
4243    * @param sel
4244    *          the sequences to show cross-references for
4245    * @param dna
4246    *          true if from a nucleotide alignment (so showing proteins)
4247    * @param source
4248    *          the database to show cross-references for
4249    */
4250   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4251           final String source)
4252   {
4253     new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
4254             .start();
4255   }
4256
4257   /**
4258    * Construct and display a new frame containing the translation of this
4259    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4260    */
4261   @Override
4262   public void showTranslation_actionPerformed(ActionEvent e)
4263   {
4264     AlignmentI al = null;
4265     try
4266     {
4267       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4268
4269       al = dna.translateCdna();
4270     } catch (Exception ex)
4271     {
4272       jalview.bin.Cache.log.error(
4273               "Exception during translation. Please report this !", ex);
4274       final String msg = MessageManager.getString(
4275               "label.error_when_translating_sequences_submit_bug_report");
4276       final String errorTitle = MessageManager
4277               .getString("label.implementation_error")
4278               + MessageManager.getString("label.translation_failed");
4279       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4280               JvOptionPane.ERROR_MESSAGE);
4281       return;
4282     }
4283     if (al == null || al.getHeight() == 0)
4284     {
4285       final String msg = MessageManager.getString(
4286               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4287       final String errorTitle = MessageManager
4288               .getString("label.translation_failed");
4289       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4290               JvOptionPane.WARNING_MESSAGE);
4291     }
4292     else
4293     {
4294       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4295       af.setFileFormat(this.currentFileFormat);
4296       final String newTitle = MessageManager
4297               .formatMessage("label.translation_of_params", new Object[]
4298               { this.getTitle() });
4299       af.setTitle(newTitle);
4300       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4301       {
4302         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4303         viewport.openSplitFrame(af, new Alignment(seqs));
4304       }
4305       else
4306       {
4307         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4308                 DEFAULT_HEIGHT);
4309       }
4310     }
4311   }
4312
4313   /**
4314    * Set the file format
4315    *
4316    * @param format
4317    */
4318   public void setFileFormat(FileFormatI format)
4319   {
4320     this.currentFileFormat = format;
4321   }
4322
4323   /**
4324    * Try to load a features file onto the alignment.
4325    *
4326    * @param file
4327    *          contents or path to retrieve file
4328    * @param sourceType
4329    *          access mode of file (see jalview.io.AlignFile)
4330    * @return true if features file was parsed correctly.
4331    */
4332   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4333   {
4334     return avc.parseFeaturesFile(file, sourceType,
4335             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4336
4337   }
4338
4339   @Override
4340   public void refreshFeatureUI(boolean enableIfNecessary)
4341   {
4342     // note - currently this is only still here rather than in the controller
4343     // because of the featureSettings hard reference that is yet to be
4344     // abstracted
4345     if (enableIfNecessary)
4346     {
4347       viewport.setShowSequenceFeatures(true);
4348       showSeqFeatures.setSelected(true);
4349     }
4350
4351   }
4352
4353   @Override
4354   public void dragEnter(DropTargetDragEvent evt)
4355   {
4356   }
4357
4358   @Override
4359   public void dragExit(DropTargetEvent evt)
4360   {
4361   }
4362
4363   @Override
4364   public void dragOver(DropTargetDragEvent evt)
4365   {
4366   }
4367
4368   @Override
4369   public void dropActionChanged(DropTargetDragEvent evt)
4370   {
4371   }
4372
4373   @Override
4374   public void drop(DropTargetDropEvent evt)
4375   {
4376     // JAL-1552 - acceptDrop required before getTransferable call for
4377     // Java's Transferable for native dnd
4378     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4379     Transferable t = evt.getTransferable();
4380     final AlignFrame thisaf = this;
4381     final List<String> files = new ArrayList<>();
4382     List<DataSourceType> protocols = new ArrayList<>();
4383
4384     try
4385     {
4386       Desktop.transferFromDropTarget(files, protocols, evt, t);
4387     } catch (Exception e)
4388     {
4389       e.printStackTrace();
4390     }
4391     if (files != null)
4392     {
4393       new Thread(new Runnable()
4394       {
4395         @Override
4396         public void run()
4397         {
4398           try
4399           {
4400             // check to see if any of these files have names matching sequences
4401             // in
4402             // the alignment
4403             SequenceIdMatcher idm = new SequenceIdMatcher(
4404                     viewport.getAlignment().getSequencesArray());
4405             /**
4406              * Object[] { String,SequenceI}
4407              */
4408             ArrayList<Object[]> filesmatched = new ArrayList<>();
4409             ArrayList<String> filesnotmatched = new ArrayList<>();
4410             for (int i = 0; i < files.size(); i++)
4411             {
4412               String file = files.get(i).toString();
4413               String pdbfn = "";
4414               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4415               if (protocol == DataSourceType.FILE)
4416               {
4417                 File fl = new File(file);
4418                 pdbfn = fl.getName();
4419               }
4420               else if (protocol == DataSourceType.URL)
4421               {
4422                 URL url = new URL(file);
4423                 pdbfn = url.getFile();
4424               }
4425               if (pdbfn.length() > 0)
4426               {
4427                 // attempt to find a match in the alignment
4428                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4429                 int l = 0, c = pdbfn.indexOf(".");
4430                 while (mtch == null && c != -1)
4431                 {
4432                   do
4433                   {
4434                     l = c;
4435                   } while ((c = pdbfn.indexOf(".", l)) > l);
4436                   if (l > -1)
4437                   {
4438                     pdbfn = pdbfn.substring(0, l);
4439                   }
4440                   mtch = idm.findAllIdMatches(pdbfn);
4441                 }
4442                 if (mtch != null)
4443                 {
4444                   FileFormatI type = null;
4445                   try
4446                   {
4447                     type = new IdentifyFile().identify(file, protocol);
4448                   } catch (Exception ex)
4449                   {
4450                     type = null;
4451                   }
4452                   if (type != null && type.isStructureFile())
4453                   {
4454                     filesmatched.add(new Object[] { file, protocol, mtch });
4455                     continue;
4456                   }
4457                 }
4458                 // File wasn't named like one of the sequences or wasn't a PDB
4459                 // file.
4460                 filesnotmatched.add(file);
4461               }
4462             }
4463             int assocfiles = 0;
4464             if (filesmatched.size() > 0)
4465             {
4466               boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4467               if (!autoAssociate)
4468               {
4469                 String msg = MessageManager.formatMessage(
4470                         "label.automatically_associate_structure_files_with_sequences_same_name",
4471                         new Object[]
4472                         { Integer.valueOf(filesmatched.size())
4473                                 .toString() });
4474                 String ttl = MessageManager.getString(
4475                         "label.automatically_associate_structure_files_by_name");
4476                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4477                         ttl, JvOptionPane.YES_NO_OPTION);
4478                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4479               }
4480               if (autoAssociate)
4481               {
4482                 for (Object[] fm : filesmatched)
4483                 {
4484                   // try and associate
4485                   // TODO: may want to set a standard ID naming formalism for
4486                   // associating PDB files which have no IDs.
4487                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4488                   {
4489                     PDBEntry pe = new AssociatePdbFileWithSeq()
4490                             .associatePdbWithSeq((String) fm[0],
4491                                     (DataSourceType) fm[1], toassoc, false,
4492                                     Desktop.instance);
4493                     if (pe != null)
4494                     {
4495                       System.err.println("Associated file : "
4496                               + ((String) fm[0]) + " with "
4497                               + toassoc.getDisplayId(true));
4498                       assocfiles++;
4499                     }
4500                   }
4501                   // TODO: do we need to update overview ? only if features are
4502                   // shown I guess
4503                   alignPanel.paintAlignment(true, false);
4504                 }
4505               }
4506               else
4507               {
4508                 /*
4509                  * add declined structures as sequences
4510                  */
4511                 for (Object[] o : filesmatched)
4512                 {
4513                   filesnotmatched.add((String) o[0]);
4514                 }
4515               }
4516             }
4517             if (filesnotmatched.size() > 0)
4518             {
4519               if (assocfiles > 0 && (Cache.getDefault(
4520                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4521                       || JvOptionPane.showConfirmDialog(thisaf,
4522                               "<html>" + MessageManager.formatMessage(
4523                                       "label.ignore_unmatched_dropped_files_info",
4524                                       new Object[]
4525                                       { Integer.valueOf(
4526                                               filesnotmatched.size())
4527                                               .toString() })
4528                                       + "</html>",
4529                               MessageManager.getString(
4530                                       "label.ignore_unmatched_dropped_files"),
4531                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4532               {
4533                 return;
4534               }
4535               for (String fn : filesnotmatched)
4536               {
4537                 loadJalviewDataFile(fn, null, null, null);
4538               }
4539
4540             }
4541           } catch (Exception ex)
4542           {
4543             ex.printStackTrace();
4544           }
4545         }
4546       }).start();
4547     }
4548   }
4549
4550   /**
4551    * Attempt to load a "dropped" file or URL string, by testing in turn for
4552    * <ul>
4553    * <li>an Annotation file</li>
4554    * <li>a JNet file</li>
4555    * <li>a features file</li>
4556    * <li>else try to interpret as an alignment file</li>
4557    * </ul>
4558    *
4559    * @param file
4560    *          either a filename or a URL string.
4561    */
4562   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4563           FileFormatI format, SequenceI assocSeq)
4564   {
4565     try
4566     {
4567       if (sourceType == null)
4568       {
4569         sourceType = FormatAdapter.checkProtocol(file);
4570       }
4571       // if the file isn't identified, or not positively identified as some
4572       // other filetype (PFAM is default unidentified alignment file type) then
4573       // try to parse as annotation.
4574       boolean isAnnotation = (format == null
4575               || FileFormat.Pfam.equals(format))
4576                       ? new AnnotationFile().annotateAlignmentView(viewport,
4577                               file, sourceType)
4578                       : false;
4579
4580       if (!isAnnotation)
4581       {
4582         // first see if its a T-COFFEE score file
4583         TCoffeeScoreFile tcf = null;
4584         try
4585         {
4586           tcf = new TCoffeeScoreFile(file, sourceType);
4587           if (tcf.isValid())
4588           {
4589             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4590             {
4591               buildColourMenu();
4592               changeColour(
4593                       new TCoffeeColourScheme(viewport.getAlignment()));
4594               isAnnotation = true;
4595               statusBar.setText(MessageManager.getString(
4596                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4597             }
4598             else
4599             {
4600               // some problem - if no warning its probable that the ID matching
4601               // process didn't work
4602               JvOptionPane.showMessageDialog(Desktop.desktop,
4603                       tcf.getWarningMessage() == null
4604                               ? MessageManager.getString(
4605                                       "label.check_file_matches_sequence_ids_alignment")
4606                               : tcf.getWarningMessage(),
4607                       MessageManager.getString(
4608                               "label.problem_reading_tcoffee_score_file"),
4609                       JvOptionPane.WARNING_MESSAGE);
4610             }
4611           }
4612           else
4613           {
4614             tcf = null;
4615           }
4616         } catch (Exception x)
4617         {
4618           Cache.log.debug(
4619                   "Exception when processing data source as T-COFFEE score file",
4620                   x);
4621           tcf = null;
4622         }
4623         if (tcf == null)
4624         {
4625           // try to see if its a JNet 'concise' style annotation file *before*
4626           // we
4627           // try to parse it as a features file
4628           if (format == null)
4629           {
4630             format = new IdentifyFile().identify(file, sourceType);
4631           }
4632           if (FileFormat.ScoreMatrix == format)
4633           {
4634             ScoreMatrixFile sm = new ScoreMatrixFile(
4635                     new FileParse(file, sourceType));
4636             sm.parse();
4637             // todo: i18n this message
4638             statusBar.setText(MessageManager.formatMessage(
4639                     "label.successfully_loaded_matrix",
4640                     sm.getMatrixName()));
4641           }
4642           else if (FileFormat.Jnet.equals(format))
4643           {
4644             JPredFile predictions = new JPredFile(file, sourceType);
4645             new JnetAnnotationMaker();
4646             JnetAnnotationMaker.add_annotation(predictions,
4647                     viewport.getAlignment(), 0, false);
4648             viewport.getAlignment().setupJPredAlignment();
4649             isAnnotation = true;
4650           }
4651           // else if (IdentifyFile.FeaturesFile.equals(format))
4652           else if (FileFormat.Features.equals(format))
4653           {
4654             if (parseFeaturesFile(file, sourceType))
4655             {
4656               alignPanel.paintAlignment(true, true);
4657             }
4658           }
4659           else
4660           {
4661             new FileLoader().LoadFile(viewport, file, sourceType, format);
4662           }
4663         }
4664       }
4665       if (isAnnotation)
4666       {
4667
4668         alignPanel.adjustAnnotationHeight();
4669         viewport.updateSequenceIdColours();
4670         buildSortByAnnotationScoresMenu();
4671         alignPanel.paintAlignment(true, true);
4672       }
4673     } catch (Exception ex)
4674     {
4675       ex.printStackTrace();
4676     } catch (OutOfMemoryError oom)
4677     {
4678       try
4679       {
4680         System.gc();
4681       } catch (Exception x)
4682       {
4683       }
4684       new OOMWarning(
4685               "loading data "
4686                       + (sourceType != null
4687                               ? (sourceType == DataSourceType.PASTE
4688                                       ? "from clipboard."
4689                                       : "using " + sourceType + " from "
4690                                               + file)
4691                               : ".")
4692                       + (format != null
4693                               ? "(parsing as '" + format + "' file)"
4694                               : ""),
4695               oom, Desktop.desktop);
4696     }
4697   }
4698
4699   /**
4700    * Method invoked by the ChangeListener on the tabbed pane, in other words
4701    * when a different tabbed pane is selected by the user or programmatically.
4702    */
4703   @Override
4704   public void tabSelectionChanged(int index)
4705   {
4706     if (index > -1)
4707     {
4708       alignPanel = alignPanels.get(index);
4709       viewport = alignPanel.av;
4710       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4711       setMenusFromViewport(viewport);
4712     }
4713
4714     /*
4715      * 'focus' any colour slider that is open to the selected viewport
4716      */
4717     if (viewport.getConservationSelected())
4718     {
4719       SliderPanel.setConservationSlider(alignPanel,
4720               viewport.getResidueShading(), alignPanel.getViewName());
4721     }
4722     else
4723     {
4724       SliderPanel.hideConservationSlider();
4725     }
4726     if (viewport.getAbovePIDThreshold())
4727     {
4728       SliderPanel.setPIDSliderSource(alignPanel,
4729               viewport.getResidueShading(), alignPanel.getViewName());
4730     }
4731     else
4732     {
4733       SliderPanel.hidePIDSlider();
4734     }
4735
4736     /*
4737      * If there is a frame linked to this one in a SplitPane, switch it to the
4738      * same view tab index. No infinite recursion of calls should happen, since
4739      * tabSelectionChanged() should not get invoked on setting the selected
4740      * index to an unchanged value. Guard against setting an invalid index
4741      * before the new view peer tab has been created.
4742      */
4743     final AlignViewportI peer = viewport.getCodingComplement();
4744     if (peer != null)
4745     {
4746       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4747               .getAlignPanel().alignFrame;
4748       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4749       {
4750         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4751       }
4752     }
4753   }
4754
4755   /**
4756    * On right mouse click on view tab, prompt for and set new view name.
4757    */
4758   @Override
4759   public void tabbedPane_mousePressed(MouseEvent e)
4760   {
4761     if (e.isPopupTrigger())
4762     {
4763       String msg = MessageManager.getString("label.enter_view_name");
4764       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4765               JvOptionPane.QUESTION_MESSAGE);
4766
4767       if (reply != null)
4768       {
4769         viewport.viewName = reply;
4770         // TODO warn if reply is in getExistingViewNames()?
4771         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4772       }
4773     }
4774   }
4775
4776   public AlignViewport getCurrentView()
4777   {
4778     return viewport;
4779   }
4780
4781   /**
4782    * Open the dialog for regex description parsing.
4783    */
4784   @Override
4785   protected void extractScores_actionPerformed(ActionEvent e)
4786   {
4787     ParseProperties pp = new jalview.analysis.ParseProperties(
4788             viewport.getAlignment());
4789     // TODO: verify regex and introduce GUI dialog for version 2.5
4790     // if (pp.getScoresFromDescription("col", "score column ",
4791     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4792     // true)>0)
4793     if (pp.getScoresFromDescription("description column",
4794             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4795     {
4796       buildSortByAnnotationScoresMenu();
4797     }
4798   }
4799
4800   /*
4801    * (non-Javadoc)
4802    *
4803    * @see
4804    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4805    * )
4806    */
4807   @Override
4808   protected void showDbRefs_actionPerformed(ActionEvent e)
4809   {
4810     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4811   }
4812
4813   /*
4814    * (non-Javadoc)
4815    *
4816    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4817    * ActionEvent)
4818    */
4819   @Override
4820   protected void showNpFeats_actionPerformed(ActionEvent e)
4821   {
4822     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4823   }
4824
4825   /**
4826    * find the viewport amongst the tabs in this alignment frame and close that
4827    * tab
4828    *
4829    * @param av
4830    */
4831   public boolean closeView(AlignViewportI av)
4832   {
4833     if (viewport == av)
4834     {
4835       this.closeMenuItem_actionPerformed(false);
4836       return true;
4837     }
4838     Component[] comp = tabbedPane.getComponents();
4839     for (int i = 0; comp != null && i < comp.length; i++)
4840     {
4841       if (comp[i] instanceof AlignmentPanel)
4842       {
4843         if (((AlignmentPanel) comp[i]).av == av)
4844         {
4845           // close the view.
4846           closeView((AlignmentPanel) comp[i]);
4847           return true;
4848         }
4849       }
4850     }
4851     return false;
4852   }
4853
4854   protected void build_fetchdbmenu(JMenu webService)
4855   {
4856     // Temporary hack - DBRef Fetcher always top level ws entry.
4857     // TODO We probably want to store a sequence database checklist in
4858     // preferences and have checkboxes.. rather than individual sources selected
4859     // here
4860     final JMenu rfetch = new JMenu(
4861             MessageManager.getString("action.fetch_db_references"));
4862     rfetch.setToolTipText(MessageManager.getString(
4863             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4864     webService.add(rfetch);
4865
4866     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4867             MessageManager.getString("option.trim_retrieved_seqs"));
4868     trimrs.setToolTipText(
4869             MessageManager.getString("label.trim_retrieved_sequences"));
4870     trimrs.setSelected(
4871             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4872     trimrs.addActionListener(new ActionListener()
4873     {
4874       @Override
4875       public void actionPerformed(ActionEvent e)
4876       {
4877         trimrs.setSelected(trimrs.isSelected());
4878         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4879                 Boolean.valueOf(trimrs.isSelected()).toString());
4880       };
4881     });
4882     rfetch.add(trimrs);
4883     JMenuItem fetchr = new JMenuItem(
4884             MessageManager.getString("label.standard_databases"));
4885     fetchr.setToolTipText(
4886             MessageManager.getString("label.fetch_embl_uniprot"));
4887     fetchr.addActionListener(new ActionListener()
4888     {
4889
4890       @Override
4891       public void actionPerformed(ActionEvent e)
4892       {
4893         new Thread(new Runnable()
4894         {
4895           @Override
4896           public void run()
4897           {
4898             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4899                     .getAlignment().isNucleotide();
4900             DBRefFetcher dbRefFetcher = new DBRefFetcher(
4901                     alignPanel.av.getSequenceSelection(),
4902                     alignPanel.alignFrame, null,
4903                     alignPanel.alignFrame.featureSettings, isNucleotide);
4904             dbRefFetcher.addListener(new FetchFinishedListenerI()
4905             {
4906               @Override
4907               public void finished()
4908               {
4909                 AlignFrame.this.setMenusForViewport();
4910               }
4911             });
4912             dbRefFetcher.fetchDBRefs(false);
4913           }
4914         }).start();
4915
4916       }
4917
4918     });
4919     rfetch.add(fetchr);
4920     final AlignFrame me = this;
4921     new Thread(new Runnable()
4922     {
4923       @Override
4924       public void run()
4925       {
4926         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4927                 .getSequenceFetcherSingleton(me);
4928         javax.swing.SwingUtilities.invokeLater(new Runnable()
4929         {
4930           @Override
4931           public void run()
4932           {
4933             String[] dbclasses = sf.getOrderedSupportedSources();
4934             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4935             // jalview.util.QuickSort.sort(otherdb, otherdb);
4936             List<DbSourceProxy> otherdb;
4937             JMenu dfetch = new JMenu();
4938             JMenu ifetch = new JMenu();
4939             JMenuItem fetchr = null;
4940             int comp = 0, icomp = 0, mcomp = 15;
4941             String mname = null;
4942             int dbi = 0;
4943             for (String dbclass : dbclasses)
4944             {
4945               otherdb = sf.getSourceProxy(dbclass);
4946               // add a single entry for this class, or submenu allowing 'fetch
4947               // all' or pick one
4948               if (otherdb == null || otherdb.size() < 1)
4949               {
4950                 continue;
4951               }
4952               // List<DbSourceProxy> dbs=otherdb;
4953               // otherdb=new ArrayList<DbSourceProxy>();
4954               // for (DbSourceProxy db:dbs)
4955               // {
4956               // if (!db.isA(DBRefSource.ALIGNMENTDB)
4957               // }
4958               if (mname == null)
4959               {
4960                 mname = "From " + dbclass;
4961               }
4962               if (otherdb.size() == 1)
4963               {
4964                 final DbSourceProxy[] dassource = otherdb
4965                         .toArray(new DbSourceProxy[0]);
4966                 DbSourceProxy src = otherdb.get(0);
4967                 fetchr = new JMenuItem(src.getDbSource());
4968                 fetchr.addActionListener(new ActionListener()
4969                 {
4970
4971                   @Override
4972                   public void actionPerformed(ActionEvent e)
4973                   {
4974                     new Thread(new Runnable()
4975                     {
4976
4977                       @Override
4978                       public void run()
4979                       {
4980                         boolean isNucleotide = alignPanel.alignFrame
4981                                 .getViewport().getAlignment()
4982                                 .isNucleotide();
4983                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
4984                                 alignPanel.av.getSequenceSelection(),
4985                                 alignPanel.alignFrame, dassource,
4986                                 alignPanel.alignFrame.featureSettings,
4987                                 isNucleotide);
4988                         dbRefFetcher
4989                                 .addListener(new FetchFinishedListenerI()
4990                                 {
4991                                   @Override
4992                                   public void finished()
4993                                   {
4994                                     AlignFrame.this.setMenusForViewport();
4995                                   }
4996                                 });
4997                         dbRefFetcher.fetchDBRefs(false);
4998                       }
4999                     }).start();
5000                   }
5001
5002                 });
5003                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5004                         MessageManager.formatMessage(
5005                                 "label.fetch_retrieve_from", new Object[]
5006                                 { src.getDbName() })));
5007                 dfetch.add(fetchr);
5008                 comp++;
5009               }
5010               else
5011               {
5012                 final DbSourceProxy[] dassource = otherdb
5013                         .toArray(new DbSourceProxy[0]);
5014                 // fetch all entry
5015                 DbSourceProxy src = otherdb.get(0);
5016                 fetchr = new JMenuItem(MessageManager
5017                         .formatMessage("label.fetch_all_param", new Object[]
5018                         { src.getDbSource() }));
5019                 fetchr.addActionListener(new ActionListener()
5020                 {
5021                   @Override
5022                   public void actionPerformed(ActionEvent e)
5023                   {
5024                     new Thread(new Runnable()
5025                     {
5026
5027                       @Override
5028                       public void run()
5029                       {
5030                         boolean isNucleotide = alignPanel.alignFrame
5031                                 .getViewport().getAlignment()
5032                                 .isNucleotide();
5033                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5034                                 alignPanel.av.getSequenceSelection(),
5035                                 alignPanel.alignFrame, dassource,
5036                                 alignPanel.alignFrame.featureSettings,
5037                                 isNucleotide);
5038                         dbRefFetcher
5039                                 .addListener(new FetchFinishedListenerI()
5040                                 {
5041                                   @Override
5042                                   public void finished()
5043                                   {
5044                                     AlignFrame.this.setMenusForViewport();
5045                                   }
5046                                 });
5047                         dbRefFetcher.fetchDBRefs(false);
5048                       }
5049                     }).start();
5050                   }
5051                 });
5052
5053                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5054                         MessageManager.formatMessage(
5055                                 "label.fetch_retrieve_from_all_sources",
5056                                 new Object[]
5057                                 { Integer.valueOf(otherdb.size())
5058                                         .toString(),
5059                                     src.getDbSource(), src.getDbName() })));
5060                 dfetch.add(fetchr);
5061                 comp++;
5062                 // and then build the rest of the individual menus
5063                 ifetch = new JMenu(MessageManager.formatMessage(
5064                         "label.source_from_db_source", new Object[]
5065                         { src.getDbSource() }));
5066                 icomp = 0;
5067                 String imname = null;
5068                 int i = 0;
5069                 for (DbSourceProxy sproxy : otherdb)
5070                 {
5071                   String dbname = sproxy.getDbName();
5072                   String sname = dbname.length() > 5
5073                           ? dbname.substring(0, 5) + "..."
5074                           : dbname;
5075                   String msname = dbname.length() > 10
5076                           ? dbname.substring(0, 10) + "..."
5077                           : dbname;
5078                   if (imname == null)
5079                   {
5080                     imname = MessageManager
5081                             .formatMessage("label.from_msname", new Object[]
5082                             { sname });
5083                   }
5084                   fetchr = new JMenuItem(msname);
5085                   final DbSourceProxy[] dassrc = { sproxy };
5086                   fetchr.addActionListener(new ActionListener()
5087                   {
5088
5089                     @Override
5090                     public void actionPerformed(ActionEvent e)
5091                     {
5092                       new Thread(new Runnable()
5093                       {
5094
5095                         @Override
5096                         public void run()
5097                         {
5098                           boolean isNucleotide = alignPanel.alignFrame
5099                                   .getViewport().getAlignment()
5100                                   .isNucleotide();
5101                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5102                                   alignPanel.av.getSequenceSelection(),
5103                                   alignPanel.alignFrame, dassrc,
5104                                   alignPanel.alignFrame.featureSettings,
5105                                   isNucleotide);
5106                           dbRefFetcher
5107                                   .addListener(new FetchFinishedListenerI()
5108                                   {
5109                                     @Override
5110                                     public void finished()
5111                                     {
5112                                       AlignFrame.this.setMenusForViewport();
5113                                     }
5114                                   });
5115                           dbRefFetcher.fetchDBRefs(false);
5116                         }
5117                       }).start();
5118                     }
5119
5120                   });
5121                   fetchr.setToolTipText(
5122                           "<html>" + MessageManager.formatMessage(
5123                                   "label.fetch_retrieve_from", new Object[]
5124                                   { dbname }));
5125                   ifetch.add(fetchr);
5126                   ++i;
5127                   if (++icomp >= mcomp || i == (otherdb.size()))
5128                   {
5129                     ifetch.setText(MessageManager.formatMessage(
5130                             "label.source_to_target", imname, sname));
5131                     dfetch.add(ifetch);
5132                     ifetch = new JMenu();
5133                     imname = null;
5134                     icomp = 0;
5135                     comp++;
5136                   }
5137                 }
5138               }
5139               ++dbi;
5140               if (comp >= mcomp || dbi >= (dbclasses.length))
5141               {
5142                 dfetch.setText(MessageManager.formatMessage(
5143                         "label.source_to_target", mname, dbclass));
5144                 rfetch.add(dfetch);
5145                 dfetch = new JMenu();
5146                 mname = null;
5147                 comp = 0;
5148               }
5149             }
5150           }
5151         });
5152       }
5153     }).start();
5154
5155   }
5156
5157   /**
5158    * Left justify the whole alignment.
5159    */
5160   @Override
5161   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5162   {
5163     AlignmentI al = viewport.getAlignment();
5164     al.justify(false);
5165     viewport.firePropertyChange("alignment", null, al);
5166   }
5167
5168   /**
5169    * Right justify the whole alignment.
5170    */
5171   @Override
5172   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5173   {
5174     AlignmentI al = viewport.getAlignment();
5175     al.justify(true);
5176     viewport.firePropertyChange("alignment", null, al);
5177   }
5178
5179   @Override
5180   public void setShowSeqFeatures(boolean b)
5181   {
5182     showSeqFeatures.setSelected(b);
5183     viewport.setShowSequenceFeatures(b);
5184   }
5185
5186   /*
5187    * (non-Javadoc)
5188    *
5189    * @see
5190    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5191    * awt.event.ActionEvent)
5192    */
5193   @Override
5194   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5195   {
5196     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5197     alignPanel.paintAlignment(false, false);
5198   }
5199
5200   /*
5201    * (non-Javadoc)
5202    *
5203    * @see
5204    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5205    * .ActionEvent)
5206    */
5207   @Override
5208   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5209   {
5210     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5211     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5212
5213   }
5214
5215   /*
5216    * (non-Javadoc)
5217    *
5218    * @see
5219    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5220    * .event.ActionEvent)
5221    */
5222   @Override
5223   protected void showGroupConservation_actionPerformed(ActionEvent e)
5224   {
5225     viewport.setShowGroupConservation(showGroupConservation.getState());
5226     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5227   }
5228
5229   /*
5230    * (non-Javadoc)
5231    *
5232    * @see
5233    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5234    * .event.ActionEvent)
5235    */
5236   @Override
5237   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5238   {
5239     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5240     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5241   }
5242
5243   /*
5244    * (non-Javadoc)
5245    *
5246    * @see
5247    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5248    * .event.ActionEvent)
5249    */
5250   @Override
5251   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5252   {
5253     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5254     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5255   }
5256
5257   @Override
5258   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5259   {
5260     showSequenceLogo.setState(true);
5261     viewport.setShowSequenceLogo(true);
5262     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5263     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5264   }
5265
5266   @Override
5267   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5268   {
5269     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5270   }
5271
5272   /*
5273    * (non-Javadoc)
5274    *
5275    * @see
5276    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5277    * .event.ActionEvent)
5278    */
5279   @Override
5280   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5281   {
5282     if (avc.makeGroupsFromSelection())
5283     {
5284       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5285       alignPanel.updateAnnotation();
5286       alignPanel.paintAlignment(true, true);
5287     }
5288   }
5289
5290   public void clearAlignmentSeqRep()
5291   {
5292     // TODO refactor alignmentseqrep to controller
5293     if (viewport.getAlignment().hasSeqrep())
5294     {
5295       viewport.getAlignment().setSeqrep(null);
5296       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5297       alignPanel.updateAnnotation();
5298       alignPanel.paintAlignment(true, true);
5299     }
5300   }
5301
5302   @Override
5303   protected void createGroup_actionPerformed(ActionEvent e)
5304   {
5305     if (avc.createGroup())
5306     {
5307       alignPanel.alignmentChanged();
5308     }
5309   }
5310
5311   @Override
5312   protected void unGroup_actionPerformed(ActionEvent e)
5313   {
5314     if (avc.unGroup())
5315     {
5316       alignPanel.alignmentChanged();
5317     }
5318   }
5319
5320   /**
5321    * make the given alignmentPanel the currently selected tab
5322    *
5323    * @param alignmentPanel
5324    */
5325   public void setDisplayedView(AlignmentPanel alignmentPanel)
5326   {
5327     if (!viewport.getSequenceSetId()
5328             .equals(alignmentPanel.av.getSequenceSetId()))
5329     {
5330       throw new Error(MessageManager.getString(
5331               "error.implementation_error_cannot_show_view_alignment_frame"));
5332     }
5333     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5334             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5335     {
5336       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5337     }
5338   }
5339
5340   /**
5341    * Action on selection of menu options to Show or Hide annotations.
5342    *
5343    * @param visible
5344    * @param forSequences
5345    *          update sequence-related annotations
5346    * @param forAlignment
5347    *          update non-sequence-related annotations
5348    */
5349   @Override
5350   protected void setAnnotationsVisibility(boolean visible,
5351           boolean forSequences, boolean forAlignment)
5352   {
5353     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5354             .getAlignmentAnnotation();
5355     if (anns == null)
5356     {
5357       return;
5358     }
5359     for (AlignmentAnnotation aa : anns)
5360     {
5361       /*
5362        * don't display non-positional annotations on an alignment
5363        */
5364       if (aa.annotations == null)
5365       {
5366         continue;
5367       }
5368       boolean apply = (aa.sequenceRef == null && forAlignment)
5369               || (aa.sequenceRef != null && forSequences);
5370       if (apply)
5371       {
5372         aa.visible = visible;
5373       }
5374     }
5375     alignPanel.validateAnnotationDimensions(true);
5376     alignPanel.alignmentChanged();
5377   }
5378
5379   /**
5380    * Store selected annotation sort order for the view and repaint.
5381    */
5382   @Override
5383   protected void sortAnnotations_actionPerformed()
5384   {
5385     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5386     this.alignPanel.av
5387             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5388     alignPanel.paintAlignment(false, false);
5389   }
5390
5391   /**
5392    *
5393    * @return alignment panels in this alignment frame
5394    */
5395   public List<? extends AlignmentViewPanel> getAlignPanels()
5396   {
5397     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5398   }
5399
5400   /**
5401    * Open a new alignment window, with the cDNA associated with this (protein)
5402    * alignment, aligned as is the protein.
5403    */
5404   protected void viewAsCdna_actionPerformed()
5405   {
5406     // TODO no longer a menu action - refactor as required
5407     final AlignmentI alignment = getViewport().getAlignment();
5408     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5409     if (mappings == null)
5410     {
5411       return;
5412     }
5413     List<SequenceI> cdnaSeqs = new ArrayList<>();
5414     for (SequenceI aaSeq : alignment.getSequences())
5415     {
5416       for (AlignedCodonFrame acf : mappings)
5417       {
5418         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5419         if (dnaSeq != null)
5420         {
5421           /*
5422            * There is a cDNA mapping for this protein sequence - add to new
5423            * alignment. It will share the same dataset sequence as other mapped
5424            * cDNA (no new mappings need to be created).
5425            */
5426           final Sequence newSeq = new Sequence(dnaSeq);
5427           newSeq.setDatasetSequence(dnaSeq);
5428           cdnaSeqs.add(newSeq);
5429         }
5430       }
5431     }
5432     if (cdnaSeqs.size() == 0)
5433     {
5434       // show a warning dialog no mapped cDNA
5435       return;
5436     }
5437     AlignmentI cdna = new Alignment(
5438             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5439     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5440             AlignFrame.DEFAULT_HEIGHT);
5441     cdna.alignAs(alignment);
5442     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5443             + this.title;
5444     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5445             AlignFrame.DEFAULT_HEIGHT);
5446   }
5447
5448   /**
5449    * Set visibility of dna/protein complement view (available when shown in a
5450    * split frame).
5451    *
5452    * @param show
5453    */
5454   @Override
5455   protected void showComplement_actionPerformed(boolean show)
5456   {
5457     SplitContainerI sf = getSplitViewContainer();
5458     if (sf != null)
5459     {
5460       sf.setComplementVisible(this, show);
5461     }
5462   }
5463
5464   /**
5465    * Generate the reverse (optionally complemented) of the selected sequences,
5466    * and add them to the alignment
5467    */
5468   @Override
5469   protected void showReverse_actionPerformed(boolean complement)
5470   {
5471     AlignmentI al = null;
5472     try
5473     {
5474       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5475       al = dna.reverseCdna(complement);
5476       viewport.addAlignment(al, "");
5477       addHistoryItem(new EditCommand(
5478               MessageManager.getString("label.add_sequences"), Action.PASTE,
5479               al.getSequencesArray(), 0, al.getWidth(),
5480               viewport.getAlignment()));
5481     } catch (Exception ex)
5482     {
5483       System.err.println(ex.getMessage());
5484       return;
5485     }
5486   }
5487
5488   /**
5489    * Try to run a script in the Groovy console, having first ensured that this
5490    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5491    * be targeted at this alignment.
5492    */
5493   @Override
5494   protected void runGroovy_actionPerformed()
5495   {
5496     Jalview.setCurrentAlignFrame(this);
5497     groovy.ui.Console console = Desktop.getGroovyConsole();
5498     if (console != null)
5499     {
5500       try
5501       {
5502         console.runScript();
5503       } catch (Exception ex)
5504       {
5505         System.err.println((ex.toString()));
5506         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5507                 MessageManager.getString("label.couldnt_run_groovy_script"),
5508                 MessageManager.getString("label.groovy_support_failed"),
5509                 JvOptionPane.ERROR_MESSAGE);
5510       }
5511     }
5512     else
5513     {
5514       System.err.println("Can't run Groovy script as console not found");
5515     }
5516   }
5517
5518   /**
5519    * Hides columns containing (or not containing) a specified feature, provided
5520    * that would not leave all columns hidden
5521    *
5522    * @param featureType
5523    * @param columnsContaining
5524    * @return
5525    */
5526   public boolean hideFeatureColumns(String featureType,
5527           boolean columnsContaining)
5528   {
5529     boolean notForHiding = avc.markColumnsContainingFeatures(
5530             columnsContaining, false, false, featureType);
5531     if (notForHiding)
5532     {
5533       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5534               false, featureType))
5535       {
5536         getViewport().hideSelectedColumns();
5537         return true;
5538       }
5539     }
5540     return false;
5541   }
5542
5543   @Override
5544   protected void selectHighlightedColumns_actionPerformed(
5545           ActionEvent actionEvent)
5546   {
5547     // include key modifier check in case user selects from menu
5548     avc.markHighlightedColumns(
5549             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5550             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5551                     | ActionEvent.CTRL_MASK)) != 0);
5552   }
5553
5554   /**
5555    * Rebuilds the Colour menu, including any user-defined colours which have
5556    * been loaded either on startup or during the session
5557    */
5558   public void buildColourMenu()
5559   {
5560     colourMenu.removeAll();
5561
5562     colourMenu.add(applyToAllGroups);
5563     colourMenu.add(textColour);
5564     colourMenu.addSeparator();
5565
5566     ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5567             false);
5568
5569     colourMenu.addSeparator();
5570     colourMenu.add(conservationMenuItem);
5571     colourMenu.add(modifyConservation);
5572     colourMenu.add(abovePIDThreshold);
5573     colourMenu.add(modifyPID);
5574     colourMenu.add(annotationColour);
5575
5576     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5577     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5578   }
5579
5580   /**
5581    * Open a dialog (if not already open) that allows the user to select and
5582    * calculate PCA or Tree analysis
5583    */
5584   protected void openTreePcaDialog()
5585   {
5586     if (alignPanel.getCalculationDialog() == null)
5587     {
5588       new CalculationChooser(AlignFrame.this);
5589     }
5590   }
5591 }
5592
5593 class PrintThread extends Thread
5594 {
5595   AlignmentPanel ap;
5596
5597   public PrintThread(AlignmentPanel ap)
5598   {
5599     this.ap = ap;
5600   }
5601
5602   static PageFormat pf;
5603
5604   @Override
5605   public void run()
5606   {
5607     PrinterJob printJob = PrinterJob.getPrinterJob();
5608
5609     if (pf != null)
5610     {
5611       printJob.setPrintable(ap, pf);
5612     }
5613     else
5614     {
5615       printJob.setPrintable(ap);
5616     }
5617
5618     if (printJob.printDialog())
5619     {
5620       try
5621       {
5622         printJob.print();
5623       } catch (Exception PrintException)
5624       {
5625         PrintException.printStackTrace();
5626       }
5627     }
5628   }
5629 }