src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.SimilarityParamsI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignedCodonFrame;
  49 import jalview.datamodel.Alignment;
  50 import jalview.datamodel.AlignmentAnnotation;
  51 import jalview.datamodel.AlignmentExportData;
  52 import jalview.datamodel.AlignmentI;
  53 import jalview.datamodel.AlignmentOrder;
  54 import jalview.datamodel.AlignmentView;
  55 import jalview.datamodel.ColumnSelection;
  56 import jalview.datamodel.HiddenColumns;
  57 import jalview.datamodel.HiddenSequences;
  58 import jalview.datamodel.PDBEntry;
  59 import jalview.datamodel.SeqCigar;
  60 import jalview.datamodel.Sequence;
  61 import jalview.datamodel.SequenceGroup;
  62 import jalview.datamodel.SequenceI;
  63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  65 import jalview.io.AlignmentProperties;
  66 import jalview.io.AnnotationFile;
  67 import jalview.io.BioJsHTMLOutput;
  68 import jalview.io.DataSourceType;
  69 import jalview.io.FileFormat;
  70 import jalview.io.FileFormatI;
  71 import jalview.io.FileFormats;
  72 import jalview.io.FileLoader;
  73 import jalview.io.FileParse;
  74 import jalview.io.FormatAdapter;
  75 import jalview.io.HtmlSvgOutput;
  76 import jalview.io.IdentifyFile;
  77 import jalview.io.JPredFile;
  78 import jalview.io.JalviewFileChooser;
  79 import jalview.io.JalviewFileView;
  80 import jalview.io.JnetAnnotationMaker;
  81 import jalview.io.NewickFile;
  82 import jalview.io.ScoreMatrixFile;
  83 import jalview.io.TCoffeeScoreFile;
  84 import jalview.io.vcf.VCFLoader;
  85 import jalview.jbgui.GAlignFrame;
  86 import jalview.schemes.ColourSchemeI;
  87 import jalview.schemes.ColourSchemes;
  88 import jalview.schemes.ResidueColourScheme;
  89 import jalview.schemes.TCoffeeColourScheme;
  90 import jalview.util.MessageManager;
  91 import jalview.viewmodel.AlignmentViewport;
  92 import jalview.viewmodel.ViewportRanges;
  93 import jalview.ws.DBRefFetcher;
  94 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  95 import jalview.ws.jws1.Discoverer;
  96 import jalview.ws.jws2.Jws2Discoverer;
  97 import jalview.ws.jws2.jabaws2.Jws2Instance;
  98 import jalview.ws.seqfetcher.DbSourceProxy;
  99
 100 import java.awt.BorderLayout;
 101 import java.awt.Component;
 102 import java.awt.Rectangle;
 103 import java.awt.Toolkit;
 104 import java.awt.datatransfer.Clipboard;
 105 import java.awt.datatransfer.DataFlavor;
 106 import java.awt.datatransfer.StringSelection;
 107 import java.awt.datatransfer.Transferable;
 108 import java.awt.dnd.DnDConstants;
 109 import java.awt.dnd.DropTargetDragEvent;
 110 import java.awt.dnd.DropTargetDropEvent;
 111 import java.awt.dnd.DropTargetEvent;
 112 import java.awt.dnd.DropTargetListener;
 113 import java.awt.event.ActionEvent;
 114 import java.awt.event.ActionListener;
 115 import java.awt.event.FocusAdapter;
 116 import java.awt.event.FocusEvent;
 117 import java.awt.event.ItemEvent;
 118 import java.awt.event.ItemListener;
 119 import java.awt.event.KeyAdapter;
 120 import java.awt.event.KeyEvent;
 121 import java.awt.event.MouseEvent;
 122 import java.awt.print.PageFormat;
 123 import java.awt.print.PrinterJob;
 124 import java.beans.PropertyChangeEvent;
 125 import java.io.File;
 126 import java.io.FileWriter;
 127 import java.io.PrintWriter;
 128 import java.net.URL;
 129 import java.util.ArrayList;
 130 import java.util.Arrays;
 131 import java.util.Deque;
 132 import java.util.Enumeration;
 133 import java.util.Hashtable;
 134 import java.util.List;
 135 import java.util.Vector;
 136
 137 import javax.swing.JCheckBoxMenuItem;
 138 import javax.swing.JEditorPane;
 139 import javax.swing.JInternalFrame;
 140 import javax.swing.JLayeredPane;
 141 import javax.swing.JMenu;
 142 import javax.swing.JMenuItem;
 143 import javax.swing.JScrollPane;
 144 import javax.swing.SwingUtilities;
 145
 146 /**
 147  * DOCUMENT ME!
 148  *
 149  * @author $author$
 150  * @version $Revision$
 151  */
 152 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 153         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 154 {
 155
 156   public static final int DEFAULT_WIDTH = 700;
 157
 158   public static final int DEFAULT_HEIGHT = 500;
 159
 160   /*
 161    * The currently displayed panel (selected tabbed view if more than one)
 162    */
 163   public AlignmentPanel alignPanel;
 164
 165   AlignViewport viewport;
 166
 167   public AlignViewControllerI avc;
 168
 169   List<AlignmentPanel> alignPanels = new ArrayList<>();
 170
 171   /**
 172    * Last format used to load or save alignments in this window
 173    */
 174   FileFormatI currentFileFormat = null;
 175
 176   /**
 177    * Current filename for this alignment
 178    */
 179   String fileName = null;
 180
 181   /**
 182    * Creates a new AlignFrame object with specific width and height.
 183    *
 184    * @param al
 185    * @param width
 186    * @param height
 187    */
 188   public AlignFrame(AlignmentI al, int width, int height)
 189   {
 190     this(al, null, width, height);
 191   }
 192
 193   /**
 194    * Creates a new AlignFrame object with specific width, height and
 195    * sequenceSetId
 196    *
 197    * @param al
 198    * @param width
 199    * @param height
 200    * @param sequenceSetId
 201    */
 202   public AlignFrame(AlignmentI al, int width, int height,
 203           String sequenceSetId)
 204   {
 205     this(al, null, width, height, sequenceSetId);
 206   }
 207
 208   /**
 209    * Creates a new AlignFrame object with specific width, height and
 210    * sequenceSetId
 211    *
 212    * @param al
 213    * @param width
 214    * @param height
 215    * @param sequenceSetId
 216    * @param viewId
 217    */
 218   public AlignFrame(AlignmentI al, int width, int height,
 219           String sequenceSetId, String viewId)
 220   {
 221     this(al, null, width, height, sequenceSetId, viewId);
 222   }
 223
 224   /**
 225    * new alignment window with hidden columns
 226    *
 227    * @param al
 228    *          AlignmentI
 229    * @param hiddenColumns
 230    *          ColumnSelection or null
 231    * @param width
 232    *          Width of alignment frame
 233    * @param height
 234    *          height of frame.
 235    */
 236   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 237           int height)
 238   {
 239     this(al, hiddenColumns, width, height, null);
 240   }
 241
 242   /**
 243    * Create alignment frame for al with hiddenColumns, a specific width and
 244    * height, and specific sequenceId
 245    *
 246    * @param al
 247    * @param hiddenColumns
 248    * @param width
 249    * @param height
 250    * @param sequenceSetId
 251    *          (may be null)
 252    */
 253   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 254           int height, String sequenceSetId)
 255   {
 256     this(al, hiddenColumns, width, height, sequenceSetId, null);
 257   }
 258
 259   /**
 260    * Create alignment frame for al with hiddenColumns, a specific width and
 261    * height, and specific sequenceId
 262    *
 263    * @param al
 264    * @param hiddenColumns
 265    * @param width
 266    * @param height
 267    * @param sequenceSetId
 268    *          (may be null)
 269    * @param viewId
 270    *          (may be null)
 271    */
 272   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 273           int height, String sequenceSetId, String viewId)
 274   {
 275     setSize(width, height);
 276
 277     if (al.getDataset() == null)
 278     {
 279       al.setDataset(null);
 280     }
 281
 282     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 283
 284     alignPanel = new AlignmentPanel(this, viewport);
 285
 286     addAlignmentPanel(alignPanel, true);
 287     init();
 288   }
 289
 290   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 291           HiddenColumns hiddenColumns, int width, int height)
 292   {
 293     setSize(width, height);
 294
 295     if (al.getDataset() == null)
 296     {
 297       al.setDataset(null);
 298     }
 299
 300     viewport = new AlignViewport(al, hiddenColumns);
 301
 302     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 303     {
 304       viewport.hideSequence(hiddenSeqs);
 305     }
 306     alignPanel = new AlignmentPanel(this, viewport);
 307     addAlignmentPanel(alignPanel, true);
 308     init();
 309   }
 310
 311   /**
 312    * Make a new AlignFrame from existing alignmentPanels
 313    *
 314    * @param ap
 315    *          AlignmentPanel
 316    * @param av
 317    *          AlignViewport
 318    */
 319   public AlignFrame(AlignmentPanel ap)
 320   {
 321     viewport = ap.av;
 322     alignPanel = ap;
 323     addAlignmentPanel(ap, false);
 324     init();
 325   }
 326
 327   /**
 328    * initalise the alignframe from the underlying viewport data and the
 329    * configurations
 330    */
 331   void init()
 332   {
 333     if (!Jalview.isHeadlessMode())
 334     {
 335       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 336     }
 337
 338     avc = new jalview.controller.AlignViewController(this, viewport,
 339             alignPanel);
 340     if (viewport.getAlignmentConservationAnnotation() == null)
 341     {
 342       // BLOSUM62Colour.setEnabled(false);
 343       conservationMenuItem.setEnabled(false);
 344       modifyConservation.setEnabled(false);
 345       // PIDColour.setEnabled(false);
 346       // abovePIDThreshold.setEnabled(false);
 347       // modifyPID.setEnabled(false);
 348     }
 349
 350     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 351             "No sort");
 352
 353     if (sortby.equals("Id"))
 354     {
 355       sortIDMenuItem_actionPerformed(null);
 356     }
 357     else if (sortby.equals("Pairwise Identity"))
 358     {
 359       sortPairwiseMenuItem_actionPerformed(null);
 360     }
 361
 362     this.alignPanel.av
 363             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 364
 365     setMenusFromViewport(viewport);
 366     buildSortByAnnotationScoresMenu();
 367     calculateTree.addActionListener(new ActionListener()
 368     {
 369
 370       @Override
 371       public void actionPerformed(ActionEvent e)
 372       {
 373         openTreePcaDialog();
 374       }
 375     });
 376     buildColourMenu();
 377
 378     if (Desktop.desktop != null)
 379     {
 380       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 381       addServiceListeners();
 382       setGUINucleotide();
 383     }
 384
 385     if (viewport.getWrapAlignment())
 386     {
 387       wrapMenuItem_actionPerformed(null);
 388     }
 389
 390     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 391     {
 392       this.overviewMenuItem_actionPerformed(null);
 393     }
 394
 395     addKeyListener();
 396
 397     final List<AlignmentPanel> selviews = new ArrayList<>();
 398     final List<AlignmentPanel> origview = new ArrayList<>();
 399     final String menuLabel = MessageManager
 400             .getString("label.copy_format_from");
 401     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 402             new ViewSetProvider()
 403             {
 404
 405               @Override
 406               public AlignmentPanel[] getAllAlignmentPanels()
 407               {
 408                 origview.clear();
 409                 origview.add(alignPanel);
 410                 // make an array of all alignment panels except for this one
 411                 List<AlignmentPanel> aps = new ArrayList<>(
 412                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 413                 aps.remove(AlignFrame.this.alignPanel);
 414                 return aps.toArray(new AlignmentPanel[aps.size()]);
 415               }
 416             }, selviews, new ItemListener()
 417             {
 418
 419               @Override
 420               public void itemStateChanged(ItemEvent e)
 421               {
 422                 if (origview.size() > 0)
 423                 {
 424                   final AlignmentPanel ap = origview.get(0);
 425
 426                   /*
 427                    * Copy the ViewStyle of the selected panel to 'this one'.
 428                    * Don't change value of 'scaleProteinAsCdna' unless copying
 429                    * from a SplitFrame.
 430                    */
 431                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 432                           .getViewStyle();
 433                   boolean fromSplitFrame = selviews.get(0)
 434                           .getAlignViewport().getCodingComplement() != null;
 435                   if (!fromSplitFrame)
 436                   {
 437                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 438                             .getViewStyle().isScaleProteinAsCdna());
 439                   }
 440                   ap.getAlignViewport().setViewStyle(vs);
 441
 442                   /*
 443                    * Also rescale ViewStyle of SplitFrame complement if there is
 444                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 445                    * the whole ViewStyle (allow cDNA protein to have different
 446                    * fonts)
 447                    */
 448                   AlignViewportI complement = ap.getAlignViewport()
 449                           .getCodingComplement();
 450                   if (complement != null && vs.isScaleProteinAsCdna())
 451                   {
 452                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 453                     ((SplitFrame) af.getSplitViewContainer())
 454                             .adjustLayout();
 455                     af.setMenusForViewport();
 456                   }
 457
 458                   ap.updateLayout();
 459                   ap.setSelected(true);
 460                   ap.alignFrame.setMenusForViewport();
 461
 462                 }
 463               }
 464             });
 465     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 466             .indexOf("devel") > -1
 467             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 468                     .indexOf("test") > -1)
 469     {
 470       formatMenu.add(vsel);
 471     }
 472     addFocusListener(new FocusAdapter()
 473     {
 474       @Override
 475       public void focusGained(FocusEvent e)
 476       {
 477         Jalview.setCurrentAlignFrame(AlignFrame.this);
 478       }
 479     });
 480
 481   }
 482
 483   /**
 484    * Change the filename and format for the alignment, and enable the 'reload'
 485    * button functionality.
 486    *
 487    * @param file
 488    *          valid filename
 489    * @param format
 490    *          format of file
 491    */
 492   public void setFileName(String file, FileFormatI format)
 493   {
 494     fileName = file;
 495     setFileFormat(format);
 496     reload.setEnabled(true);
 497   }
 498
 499   /**
 500    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 501    * events
 502    */
 503   void addKeyListener()
 504   {
 505     addKeyListener(new KeyAdapter()
 506     {
 507       @Override
 508       public void keyPressed(KeyEvent evt)
 509       {
 510         if (viewport.cursorMode
 511                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 512                         && evt.getKeyCode() <= KeyEvent.VK_9)
 513                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 514                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 515                 && Character.isDigit(evt.getKeyChar()))
 516         {
 517           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 518         }
 519
 520         switch (evt.getKeyCode())
 521         {
 522
 523         case 27: // escape key
 524           deselectAllSequenceMenuItem_actionPerformed(null);
 525
 526           break;
 527
 528         case KeyEvent.VK_DOWN:
 529           if (evt.isAltDown() || !viewport.cursorMode)
 530           {
 531             moveSelectedSequences(false);
 532           }
 533           if (viewport.cursorMode)
 534           {
 535             alignPanel.getSeqPanel().moveCursor(0, 1);
 536           }
 537           break;
 538
 539         case KeyEvent.VK_UP:
 540           if (evt.isAltDown() || !viewport.cursorMode)
 541           {
 542             moveSelectedSequences(true);
 543           }
 544           if (viewport.cursorMode)
 545           {
 546             alignPanel.getSeqPanel().moveCursor(0, -1);
 547           }
 548
 549           break;
 550
 551         case KeyEvent.VK_LEFT:
 552           if (evt.isAltDown() || !viewport.cursorMode)
 553           {
 554             slideSequences(false,
 555                     alignPanel.getSeqPanel().getKeyboardNo1());
 556           }
 557           else
 558           {
 559             alignPanel.getSeqPanel().moveCursor(-1, 0);
 560           }
 561
 562           break;
 563
 564         case KeyEvent.VK_RIGHT:
 565           if (evt.isAltDown() || !viewport.cursorMode)
 566           {
 567             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 568           }
 569           else
 570           {
 571             alignPanel.getSeqPanel().moveCursor(1, 0);
 572           }
 573           break;
 574
 575         case KeyEvent.VK_SPACE:
 576           if (viewport.cursorMode)
 577           {
 578             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 579                     || evt.isShiftDown() || evt.isAltDown());
 580           }
 581           break;
 582
 583         // case KeyEvent.VK_A:
 584         // if (viewport.cursorMode)
 585         // {
 586         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 587         // //System.out.println("A");
 588         // }
 589         // break;
 590         /*
 591          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 592          * System.out.println("closing bracket"); } break;
 593          */
 594         case KeyEvent.VK_DELETE:
 595         case KeyEvent.VK_BACK_SPACE:
 596           if (!viewport.cursorMode)
 597           {
 598             cut_actionPerformed(null);
 599           }
 600           else
 601           {
 602             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 603                     || evt.isShiftDown() || evt.isAltDown());
 604           }
 605
 606           break;
 607
 608         case KeyEvent.VK_S:
 609           if (viewport.cursorMode)
 610           {
 611             alignPanel.getSeqPanel().setCursorRow();
 612           }
 613           break;
 614         case KeyEvent.VK_C:
 615           if (viewport.cursorMode && !evt.isControlDown())
 616           {
 617             alignPanel.getSeqPanel().setCursorColumn();
 618           }
 619           break;
 620         case KeyEvent.VK_P:
 621           if (viewport.cursorMode)
 622           {
 623             alignPanel.getSeqPanel().setCursorPosition();
 624           }
 625           break;
 626
 627         case KeyEvent.VK_ENTER:
 628         case KeyEvent.VK_COMMA:
 629           if (viewport.cursorMode)
 630           {
 631             alignPanel.getSeqPanel().setCursorRowAndColumn();
 632           }
 633           break;
 634
 635         case KeyEvent.VK_Q:
 636           if (viewport.cursorMode)
 637           {
 638             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 639           }
 640           break;
 641         case KeyEvent.VK_M:
 642           if (viewport.cursorMode)
 643           {
 644             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 645           }
 646           break;
 647
 648         case KeyEvent.VK_F2:
 649           viewport.cursorMode = !viewport.cursorMode;
 650           statusBar.setText(MessageManager
 651                   .formatMessage("label.keyboard_editing_mode", new String[]
 652                   { (viewport.cursorMode ? "on" : "off") }));
 653           if (viewport.cursorMode)
 654           {
 655             ViewportRanges ranges = viewport.getRanges();
 656             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 657                     .getStartRes();
 658             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 659                     .getStartSeq();
 660           }
 661           alignPanel.getSeqPanel().seqCanvas.repaint();
 662           break;
 663
 664         case KeyEvent.VK_F1:
 665           try
 666           {
 667             Help.showHelpWindow();
 668           } catch (Exception ex)
 669           {
 670             ex.printStackTrace();
 671           }
 672           break;
 673         case KeyEvent.VK_H:
 674         {
 675           boolean toggleSeqs = !evt.isControlDown();
 676           boolean toggleCols = !evt.isShiftDown();
 677           toggleHiddenRegions(toggleSeqs, toggleCols);
 678           break;
 679         }
 680         case KeyEvent.VK_B:
 681         {
 682           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 683           boolean modifyExisting = true; // always modify, don't clear
 684                                          // evt.isShiftDown();
 685           boolean invertHighlighted = evt.isAltDown();
 686           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 687                   toggleSel);
 688           break;
 689         }
 690         case KeyEvent.VK_PAGE_UP:
 691           viewport.getRanges().pageUp();
 692           break;
 693         case KeyEvent.VK_PAGE_DOWN:
 694           viewport.getRanges().pageDown();
 695           break;
 696         }
 697       }
 698
 699       @Override
 700       public void keyReleased(KeyEvent evt)
 701       {
 702         switch (evt.getKeyCode())
 703         {
 704         case KeyEvent.VK_LEFT:
 705           if (evt.isAltDown() || !viewport.cursorMode)
 706           {
 707             viewport.firePropertyChange("alignment", null,
 708                     viewport.getAlignment().getSequences());
 709           }
 710           break;
 711
 712         case KeyEvent.VK_RIGHT:
 713           if (evt.isAltDown() || !viewport.cursorMode)
 714           {
 715             viewport.firePropertyChange("alignment", null,
 716                     viewport.getAlignment().getSequences());
 717           }
 718           break;
 719         }
 720       }
 721     });
 722   }
 723
 724   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 725   {
 726     ap.alignFrame = this;
 727     avc = new jalview.controller.AlignViewController(this, viewport,
 728             alignPanel);
 729
 730     alignPanels.add(ap);
 731
 732     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 733
 734     int aSize = alignPanels.size();
 735
 736     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 737
 738     if (aSize == 1 && ap.av.getViewName() == null)
 739     {
 740       this.getContentPane().add(ap, BorderLayout.CENTER);
 741     }
 742     else
 743     {
 744       if (aSize == 2)
 745       {
 746         setInitialTabVisible();
 747       }
 748
 749       expandViews.setEnabled(true);
 750       gatherViews.setEnabled(true);
 751       tabbedPane.addTab(ap.av.getViewName(), ap);
 752
 753       ap.setVisible(false);
 754     }
 755
 756     if (newPanel)
 757     {
 758       if (ap.av.isPadGaps())
 759       {
 760         ap.av.getAlignment().padGaps();
 761       }
 762       ap.av.updateConservation(ap);
 763       ap.av.updateConsensus(ap);
 764       ap.av.updateStrucConsensus(ap);
 765     }
 766   }
 767
 768   public void setInitialTabVisible()
 769   {
 770     expandViews.setEnabled(true);
 771     gatherViews.setEnabled(true);
 772     tabbedPane.setVisible(true);
 773     AlignmentPanel first = alignPanels.get(0);
 774     tabbedPane.addTab(first.av.getViewName(), first);
 775     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 776   }
 777
 778   public AlignViewport getViewport()
 779   {
 780     return viewport;
 781   }
 782
 783   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 784   private void addServiceListeners()
 785   {
 786     final java.beans.PropertyChangeListener thisListener;
 787     Desktop.instance.addJalviewPropertyChangeListener("services",
 788             thisListener = new java.beans.PropertyChangeListener()
 789             {
 790               @Override
 791               public void propertyChange(PropertyChangeEvent evt)
 792               {
 793                 // // System.out.println("Discoverer property change.");
 794                 // if (evt.getPropertyName().equals("services"))
 795                 {
 796                   SwingUtilities.invokeLater(new Runnable()
 797                   {
 798
 799                     @Override
 800                     public void run()
 801                     {
 802                       System.err.println(
 803                               "Rebuild WS Menu for service change");
 804                       BuildWebServiceMenu();
 805                     }
 806
 807                   });
 808                 }
 809               }
 810             });
 811     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 812     {
 813       @Override
 814       public void internalFrameClosed(
 815               javax.swing.event.InternalFrameEvent evt)
 816       {
 817         // System.out.println("deregistering discoverer listener");
 818         Desktop.instance.removeJalviewPropertyChangeListener("services",
 819                 thisListener);
 820         closeMenuItem_actionPerformed(true);
 821       };
 822     });
 823     // Finally, build the menu once to get current service state
 824     new Thread(new Runnable()
 825     {
 826       @Override
 827       public void run()
 828       {
 829         BuildWebServiceMenu();
 830       }
 831     }).start();
 832   }
 833
 834   /**
 835    * Configure menu items that vary according to whether the alignment is
 836    * nucleotide or protein
 837    */
 838   public void setGUINucleotide()
 839   {
 840     AlignmentI al = getViewport().getAlignment();
 841     boolean nucleotide = al.isNucleotide();
 842
 843     loadVcf.setVisible(nucleotide);
 844     showTranslation.setVisible(nucleotide);
 845     showReverse.setVisible(nucleotide);
 846     showReverseComplement.setVisible(nucleotide);
 847     conservationMenuItem.setEnabled(!nucleotide);
 848     modifyConservation
 849             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 850     showGroupConservation.setEnabled(!nucleotide);
 851
 852     showComplementMenuItem
 853             .setText(nucleotide ? MessageManager.getString("label.protein")
 854                     : MessageManager.getString("label.nucleotide"));
 855   }
 856
 857   /**
 858    * set up menus for the current viewport. This may be called after any
 859    * operation that affects the data in the current view (selection changed,
 860    * etc) to update the menus to reflect the new state.
 861    */
 862   @Override
 863   public void setMenusForViewport()
 864   {
 865     setMenusFromViewport(viewport);
 866   }
 867
 868   /**
 869    * Need to call this method when tabs are selected for multiple views, or when
 870    * loading from Jalview2XML.java
 871    *
 872    * @param av
 873    *          AlignViewport
 874    */
 875   public void setMenusFromViewport(AlignViewport av)
 876   {
 877     padGapsMenuitem.setSelected(av.isPadGaps());
 878     colourTextMenuItem.setSelected(av.isShowColourText());
 879     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 880     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 881     conservationMenuItem.setSelected(av.getConservationSelected());
 882     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 883     seqLimits.setSelected(av.getShowJVSuffix());
 884     idRightAlign.setSelected(av.isRightAlignIds());
 885     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 886     renderGapsMenuItem.setSelected(av.isRenderGaps());
 887     wrapMenuItem.setSelected(av.getWrapAlignment());
 888     scaleAbove.setVisible(av.getWrapAlignment());
 889     scaleLeft.setVisible(av.getWrapAlignment());
 890     scaleRight.setVisible(av.getWrapAlignment());
 891     annotationPanelMenuItem.setState(av.isShowAnnotation());
 892     /*
 893      * Show/hide annotations only enabled if annotation panel is shown
 894      */
 895     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 896     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 897     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 898     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 899     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 900     viewTextMenuItem.setSelected(av.getShowText());
 901     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 902     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 903     showGroupConservation.setSelected(av.isShowGroupConservation());
 904     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 905     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 906     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 907
 908     ColourMenuHelper.setColourSelected(colourMenu,
 909             av.getGlobalColourScheme());
 910
 911     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 912     hiddenMarkers.setState(av.getShowHiddenMarkers());
 913     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 914     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 915     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 916     autoCalculate.setSelected(av.autoCalculateConsensus);
 917     sortByTree.setSelected(av.sortByTree);
 918     listenToViewSelections.setSelected(av.followSelection);
 919
 920     showProducts.setEnabled(canShowProducts());
 921     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 922
 923     updateEditMenuBar();
 924   }
 925
 926   /**
 927    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 928    *
 929    * @param b
 930    */
 931   public void setGroovyEnabled(boolean b)
 932   {
 933     runGroovy.setEnabled(b);
 934   }
 935
 936   private IProgressIndicator progressBar;
 937
 938   /*
 939    * (non-Javadoc)
 940    *
 941    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 942    */
 943   @Override
 944   public void setProgressBar(String message, long id)
 945   {
 946     progressBar.setProgressBar(message, id);
 947   }
 948
 949   @Override
 950   public void registerHandler(final long id,
 951           final IProgressIndicatorHandler handler)
 952   {
 953     progressBar.registerHandler(id, handler);
 954   }
 955
 956   /**
 957    *
 958    * @return true if any progress bars are still active
 959    */
 960   @Override
 961   public boolean operationInProgress()
 962   {
 963     return progressBar.operationInProgress();
 964   }
 965
 966   @Override
 967   public void setStatus(String text)
 968   {
 969     statusBar.setText(text);
 970   }
 971
 972   /*
 973    * Added so Castor Mapping file can obtain Jalview Version
 974    */
 975   public String getVersion()
 976   {
 977     return jalview.bin.Cache.getProperty("VERSION");
 978   }
 979
 980   public FeatureRenderer getFeatureRenderer()
 981   {
 982     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
 983   }
 984
 985   @Override
 986   public void fetchSequence_actionPerformed(ActionEvent e)
 987   {
 988     new jalview.gui.SequenceFetcher(this);
 989   }
 990
 991   @Override
 992   public void addFromFile_actionPerformed(ActionEvent e)
 993   {
 994     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 995   }
 996
 997   @Override
 998   public void reload_actionPerformed(ActionEvent e)
 999   {
1000     if (fileName != null)
1001     {
1002       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1003       // originating file's format
1004       // TODO: work out how to recover feature settings for correct view(s) when
1005       // file is reloaded.
1006       if (FileFormat.Jalview.equals(currentFileFormat))
1007       {
1008         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1009         for (int i = 0; i < frames.length; i++)
1010         {
1011           if (frames[i] instanceof AlignFrame && frames[i] != this
1012                   && ((AlignFrame) frames[i]).fileName != null
1013                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1014           {
1015             try
1016             {
1017               frames[i].setSelected(true);
1018               Desktop.instance.closeAssociatedWindows();
1019             } catch (java.beans.PropertyVetoException ex)
1020             {
1021             }
1022           }
1023
1024         }
1025         Desktop.instance.closeAssociatedWindows();
1026
1027         FileLoader loader = new FileLoader();
1028         DataSourceType protocol = fileName.startsWith("http:")
1029                 ? DataSourceType.URL
1030                 : DataSourceType.FILE;
1031         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1032       }
1033       else
1034       {
1035         Rectangle bounds = this.getBounds();
1036
1037         FileLoader loader = new FileLoader();
1038         DataSourceType protocol = fileName.startsWith("http:")
1039                 ? DataSourceType.URL
1040                 : DataSourceType.FILE;
1041         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
1042                 protocol, currentFileFormat);
1043
1044         newframe.setBounds(bounds);
1045         if (featureSettings != null && featureSettings.isShowing())
1046         {
1047           final Rectangle fspos = featureSettings.frame.getBounds();
1048           // TODO: need a 'show feature settings' function that takes bounds -
1049           // need to refactor Desktop.addFrame
1050           newframe.featureSettings_actionPerformed(null);
1051           final FeatureSettings nfs = newframe.featureSettings;
1052           SwingUtilities.invokeLater(new Runnable()
1053           {
1054             @Override
1055             public void run()
1056             {
1057               nfs.frame.setBounds(fspos);
1058             }
1059           });
1060           this.featureSettings.close();
1061           this.featureSettings = null;
1062         }
1063         this.closeMenuItem_actionPerformed(true);
1064       }
1065     }
1066   }
1067
1068   @Override
1069   public void addFromText_actionPerformed(ActionEvent e)
1070   {
1071     Desktop.instance
1072             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1073   }
1074
1075   @Override
1076   public void addFromURL_actionPerformed(ActionEvent e)
1077   {
1078     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1079   }
1080
1081   @Override
1082   public void save_actionPerformed(ActionEvent e)
1083   {
1084     if (fileName == null || (currentFileFormat == null)
1085             || fileName.startsWith("http"))
1086     {
1087       saveAs_actionPerformed(null);
1088     }
1089     else
1090     {
1091       saveAlignment(fileName, currentFileFormat);
1092     }
1093   }
1094
1095   /**
1096    * DOCUMENT ME!
1097    *
1098    * @param e
1099    *          DOCUMENT ME!
1100    */
1101   @Override
1102   public void saveAs_actionPerformed(ActionEvent e)
1103   {
1104     String format = currentFileFormat == null ? null
1105             : currentFileFormat.getName();
1106     JalviewFileChooser chooser = JalviewFileChooser
1107             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1108
1109     chooser.setFileView(new JalviewFileView());
1110     chooser.setDialogTitle(
1111             MessageManager.getString("label.save_alignment_to_file"));
1112     chooser.setToolTipText(MessageManager.getString("action.save"));
1113
1114     int value = chooser.showSaveDialog(this);
1115
1116     if (value == JalviewFileChooser.APPROVE_OPTION)
1117     {
1118       currentFileFormat = chooser.getSelectedFormat();
1119       while (currentFileFormat == null)
1120       {
1121         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1122                 MessageManager.getString(
1123                         "label.select_file_format_before_saving"),
1124                 MessageManager.getString("label.file_format_not_specified"),
1125                 JvOptionPane.WARNING_MESSAGE);
1126         currentFileFormat = chooser.getSelectedFormat();
1127         value = chooser.showSaveDialog(this);
1128         if (value != JalviewFileChooser.APPROVE_OPTION)
1129         {
1130           return;
1131         }
1132       }
1133
1134       fileName = chooser.getSelectedFile().getPath();
1135
1136       Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1137
1138       Cache.setProperty("LAST_DIRECTORY", fileName);
1139       saveAlignment(fileName, currentFileFormat);
1140     }
1141   }
1142
1143   public boolean saveAlignment(String file, FileFormatI format)
1144   {
1145     boolean success = true;
1146
1147     if (FileFormat.Jalview.equals(format))
1148     {
1149       String shortName = title;
1150
1151       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1152       {
1153         shortName = shortName.substring(
1154                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
1155       }
1156
1157       success = new Jalview2XML().saveAlignment(this, file, shortName);
1158
1159       statusBar.setText(MessageManager.formatMessage(
1160               "label.successfully_saved_to_file_in_format", new Object[]
1161               { fileName, format }));
1162
1163     }
1164     else
1165     {
1166       AlignmentExportData exportData = getAlignmentForExport(format,
1167               viewport, null);
1168       if (exportData.getSettings().isCancelled())
1169       {
1170         return false;
1171       }
1172       FormatAdapter f = new FormatAdapter(alignPanel,
1173               exportData.getSettings());
1174       String output = f.formatSequences(format, exportData.getAlignment(), // class
1175                                                                            // cast
1176                                                                            // exceptions
1177                                                                            // will
1178               // occur in the distant future
1179               exportData.getOmitHidden(), exportData.getStartEndPostions(),
1180               f.getCacheSuffixDefault(format),
1181               viewport.getAlignment().getHiddenColumns());
1182
1183       if (output == null)
1184       {
1185         success = false;
1186       }
1187       else
1188       {
1189         try
1190         {
1191           PrintWriter out = new PrintWriter(new FileWriter(file));
1192
1193           out.print(output);
1194           out.close();
1195           this.setTitle(file);
1196           statusBar.setText(MessageManager.formatMessage(
1197                   "label.successfully_saved_to_file_in_format", new Object[]
1198                   { fileName, format.getName() }));
1199         } catch (Exception ex)
1200         {
1201           success = false;
1202           ex.printStackTrace();
1203         }
1204       }
1205     }
1206
1207     if (!success)
1208     {
1209       JvOptionPane.showInternalMessageDialog(this, MessageManager
1210               .formatMessage("label.couldnt_save_file", new Object[]
1211               { fileName }),
1212               MessageManager.getString("label.error_saving_file"),
1213               JvOptionPane.WARNING_MESSAGE);
1214     }
1215
1216     return success;
1217   }
1218
1219   private void warningMessage(String warning, String title)
1220   {
1221     if (new jalview.util.Platform().isHeadless())
1222     {
1223       System.err.println("Warning: " + title + "\nWarning: " + warning);
1224
1225     }
1226     else
1227     {
1228       JvOptionPane.showInternalMessageDialog(this, warning, title,
1229               JvOptionPane.WARNING_MESSAGE);
1230     }
1231     return;
1232   }
1233
1234   /**
1235    * DOCUMENT ME!
1236    *
1237    * @param e
1238    *          DOCUMENT ME!
1239    */
1240   @Override
1241   protected void outputText_actionPerformed(ActionEvent e)
1242   {
1243     FileFormatI fileFormat = FileFormats.getInstance()
1244             .forName(e.getActionCommand());
1245     AlignmentExportData exportData = getAlignmentForExport(fileFormat,
1246             viewport, null);
1247     if (exportData.getSettings().isCancelled())
1248     {
1249       return;
1250     }
1251     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1252     cap.setForInput(null);
1253     try
1254     {
1255       FileFormatI format = fileFormat;
1256       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
1257               .formatSequences(format, exportData.getAlignment(),
1258                       exportData.getOmitHidden(),
1259                       exportData.getStartEndPostions(),
1260                       viewport.getAlignment().getHiddenColumns()));
1261       Desktop.addInternalFrame(cap, MessageManager
1262               .formatMessage("label.alignment_output_command", new Object[]
1263               { e.getActionCommand() }), 600, 500);
1264     } catch (OutOfMemoryError oom)
1265     {
1266       new OOMWarning("Outputting alignment as " + e.getActionCommand(),
1267               oom);
1268       cap.dispose();
1269     }
1270
1271   }
1272
1273   public static AlignmentExportData getAlignmentForExport(
1274           FileFormatI format, AlignViewportI viewport,
1275           AlignExportSettingI exportSettings)
1276   {
1277     AlignmentI alignmentToExport = null;
1278     AlignExportSettingI settings = exportSettings;
1279     String[] omitHidden = null;
1280
1281     HiddenSequences hiddenSeqs = viewport.getAlignment()
1282             .getHiddenSequences();
1283
1284     alignmentToExport = viewport.getAlignment();
1285
1286     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
1287     if (settings == null)
1288     {
1289       settings = new AlignExportSettings(hasHiddenSeqs,
1290               viewport.hasHiddenColumns(), format);
1291     }
1292     // settings.isExportAnnotations();
1293
1294     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
1295     {
1296       omitHidden = viewport.getViewAsString(false,
1297               settings.isExportHiddenSequences());
1298     }
1299
1300     int[] alignmentStartEnd = new int[2];
1301     if (hasHiddenSeqs && settings.isExportHiddenSequences())
1302     {
1303       alignmentToExport = hiddenSeqs.getFullAlignment();
1304     }
1305     else
1306     {
1307       alignmentToExport = viewport.getAlignment();
1308     }
1309     alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
1310             .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
1311     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
1312             omitHidden, alignmentStartEnd, settings);
1313     return ed;
1314   }
1315
1316   /**
1317    * DOCUMENT ME!
1318    *
1319    * @param e
1320    *          DOCUMENT ME!
1321    */
1322   @Override
1323   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1324   {
1325     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1326     htmlSVG.exportHTML(null);
1327   }
1328
1329   @Override
1330   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1331   {
1332     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1333     bjs.exportHTML(null);
1334   }
1335
1336   public void createImageMap(File file, String image)
1337   {
1338     alignPanel.makePNGImageMap(file, image);
1339   }
1340
1341   /**
1342    * DOCUMENT ME!
1343    *
1344    * @param e
1345    *          DOCUMENT ME!
1346    */
1347   @Override
1348   public void createPNG(File f)
1349   {
1350     alignPanel.makePNG(f);
1351   }
1352
1353   /**
1354    * DOCUMENT ME!
1355    *
1356    * @param e
1357    *          DOCUMENT ME!
1358    */
1359   @Override
1360   public void createEPS(File f)
1361   {
1362     alignPanel.makeEPS(f);
1363   }
1364
1365   @Override
1366   public void createSVG(File f)
1367   {
1368     alignPanel.makeSVG(f);
1369   }
1370
1371   @Override
1372   public void pageSetup_actionPerformed(ActionEvent e)
1373   {
1374     PrinterJob printJob = PrinterJob.getPrinterJob();
1375     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1376   }
1377
1378   /**
1379    * DOCUMENT ME!
1380    *
1381    * @param e
1382    *          DOCUMENT ME!
1383    */
1384   @Override
1385   public void printMenuItem_actionPerformed(ActionEvent e)
1386   {
1387     // Putting in a thread avoids Swing painting problems
1388     PrintThread thread = new PrintThread(alignPanel);
1389     thread.start();
1390   }
1391
1392   @Override
1393   public void exportFeatures_actionPerformed(ActionEvent e)
1394   {
1395     new AnnotationExporter(alignPanel).exportFeatures();
1396   }
1397
1398   @Override
1399   public void exportAnnotations_actionPerformed(ActionEvent e)
1400   {
1401     new AnnotationExporter(alignPanel).exportAnnotations();
1402   }
1403
1404   @Override
1405   public void associatedData_actionPerformed(ActionEvent e)
1406   {
1407     // Pick the tree file
1408     JalviewFileChooser chooser = new JalviewFileChooser(
1409             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1410     chooser.setFileView(new JalviewFileView());
1411     chooser.setDialogTitle(
1412             MessageManager.getString("label.load_jalview_annotations"));
1413     chooser.setToolTipText(
1414             MessageManager.getString("label.load_jalview_annotations"));
1415
1416     int value = chooser.showOpenDialog(null);
1417
1418     if (value == JalviewFileChooser.APPROVE_OPTION)
1419     {
1420       String choice = chooser.getSelectedFile().getPath();
1421       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1422       loadJalviewDataFile(choice, null, null, null);
1423     }
1424
1425   }
1426
1427   /**
1428    * Close the current view or all views in the alignment frame. If the frame
1429    * only contains one view then the alignment will be removed from memory.
1430    *
1431    * @param closeAllTabs
1432    */
1433   @Override
1434   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1435   {
1436     if (alignPanels != null && alignPanels.size() < 2)
1437     {
1438       closeAllTabs = true;
1439     }
1440
1441     try
1442     {
1443       if (alignPanels != null)
1444       {
1445         if (closeAllTabs)
1446         {
1447           if (this.isClosed())
1448           {
1449             // really close all the windows - otherwise wait till
1450             // setClosed(true) is called
1451             for (int i = 0; i < alignPanels.size(); i++)
1452             {
1453               AlignmentPanel ap = alignPanels.get(i);
1454               ap.closePanel();
1455             }
1456           }
1457         }
1458         else
1459         {
1460           closeView(alignPanel);
1461         }
1462       }
1463
1464       if (closeAllTabs)
1465       {
1466         /*
1467          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1468          * be called recursively, with the frame now in 'closed' state
1469          */
1470         this.setClosed(true);
1471       }
1472     } catch (Exception ex)
1473     {
1474       ex.printStackTrace();
1475     }
1476   }
1477
1478   /**
1479    * Close the specified panel and close up tabs appropriately.
1480    *
1481    * @param panelToClose
1482    */
1483   public void closeView(AlignmentPanel panelToClose)
1484   {
1485     int index = tabbedPane.getSelectedIndex();
1486     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1487     alignPanels.remove(panelToClose);
1488     panelToClose.closePanel();
1489     panelToClose = null;
1490
1491     tabbedPane.removeTabAt(closedindex);
1492     tabbedPane.validate();
1493
1494     if (index > closedindex || index == tabbedPane.getTabCount())
1495     {
1496       // modify currently selected tab index if necessary.
1497       index--;
1498     }
1499
1500     this.tabSelectionChanged(index);
1501   }
1502
1503   /**
1504    * DOCUMENT ME!
1505    */
1506   void updateEditMenuBar()
1507   {
1508
1509     if (viewport.getHistoryList().size() > 0)
1510     {
1511       undoMenuItem.setEnabled(true);
1512       CommandI command = viewport.getHistoryList().peek();
1513       undoMenuItem.setText(MessageManager
1514               .formatMessage("label.undo_command", new Object[]
1515               { command.getDescription() }));
1516     }
1517     else
1518     {
1519       undoMenuItem.setEnabled(false);
1520       undoMenuItem.setText(MessageManager.getString("action.undo"));
1521     }
1522
1523     if (viewport.getRedoList().size() > 0)
1524     {
1525       redoMenuItem.setEnabled(true);
1526
1527       CommandI command = viewport.getRedoList().peek();
1528       redoMenuItem.setText(MessageManager
1529               .formatMessage("label.redo_command", new Object[]
1530               { command.getDescription() }));
1531     }
1532     else
1533     {
1534       redoMenuItem.setEnabled(false);
1535       redoMenuItem.setText(MessageManager.getString("action.redo"));
1536     }
1537   }
1538
1539   @Override
1540   public void addHistoryItem(CommandI command)
1541   {
1542     if (command.getSize() > 0)
1543     {
1544       viewport.addToHistoryList(command);
1545       viewport.clearRedoList();
1546       updateEditMenuBar();
1547       viewport.updateHiddenColumns();
1548       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1549       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1550       // viewport.getColumnSelection()
1551       // .getHiddenColumns().size() > 0);
1552     }
1553   }
1554
1555   /**
1556    *
1557    * @return alignment objects for all views
1558    */
1559   AlignmentI[] getViewAlignments()
1560   {
1561     if (alignPanels != null)
1562     {
1563       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1564       int i = 0;
1565       for (AlignmentPanel ap : alignPanels)
1566       {
1567         als[i++] = ap.av.getAlignment();
1568       }
1569       return als;
1570     }
1571     if (viewport != null)
1572     {
1573       return new AlignmentI[] { viewport.getAlignment() };
1574     }
1575     return null;
1576   }
1577
1578   /**
1579    * DOCUMENT ME!
1580    *
1581    * @param e
1582    *          DOCUMENT ME!
1583    */
1584   @Override
1585   protected void undoMenuItem_actionPerformed(ActionEvent e)
1586   {
1587     if (viewport.getHistoryList().isEmpty())
1588     {
1589       return;
1590     }
1591     CommandI command = viewport.getHistoryList().pop();
1592     viewport.addToRedoList(command);
1593     command.undoCommand(getViewAlignments());
1594
1595     AlignmentViewport originalSource = getOriginatingSource(command);
1596     updateEditMenuBar();
1597
1598     if (originalSource != null)
1599     {
1600       if (originalSource != viewport)
1601       {
1602         Cache.log.warn(
1603                 "Implementation worry: mismatch of viewport origin for undo");
1604       }
1605       originalSource.updateHiddenColumns();
1606       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1607       // null
1608       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1609       // viewport.getColumnSelection()
1610       // .getHiddenColumns().size() > 0);
1611       originalSource.firePropertyChange("alignment", null,
1612               originalSource.getAlignment().getSequences());
1613     }
1614   }
1615
1616   /**
1617    * DOCUMENT ME!
1618    *
1619    * @param e
1620    *          DOCUMENT ME!
1621    */
1622   @Override
1623   protected void redoMenuItem_actionPerformed(ActionEvent e)
1624   {
1625     if (viewport.getRedoList().size() < 1)
1626     {
1627       return;
1628     }
1629
1630     CommandI command = viewport.getRedoList().pop();
1631     viewport.addToHistoryList(command);
1632     command.doCommand(getViewAlignments());
1633
1634     AlignmentViewport originalSource = getOriginatingSource(command);
1635     updateEditMenuBar();
1636
1637     if (originalSource != null)
1638     {
1639
1640       if (originalSource != viewport)
1641       {
1642         Cache.log.warn(
1643                 "Implementation worry: mismatch of viewport origin for redo");
1644       }
1645       originalSource.updateHiddenColumns();
1646       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1647       // null
1648       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1649       // viewport.getColumnSelection()
1650       // .getHiddenColumns().size() > 0);
1651       originalSource.firePropertyChange("alignment", null,
1652               originalSource.getAlignment().getSequences());
1653     }
1654   }
1655
1656   AlignmentViewport getOriginatingSource(CommandI command)
1657   {
1658     AlignmentViewport originalSource = null;
1659     // For sequence removal and addition, we need to fire
1660     // the property change event FROM the viewport where the
1661     // original alignment was altered
1662     AlignmentI al = null;
1663     if (command instanceof EditCommand)
1664     {
1665       EditCommand editCommand = (EditCommand) command;
1666       al = editCommand.getAlignment();
1667       List<Component> comps = PaintRefresher.components
1668               .get(viewport.getSequenceSetId());
1669
1670       for (Component comp : comps)
1671       {
1672         if (comp instanceof AlignmentPanel)
1673         {
1674           if (al == ((AlignmentPanel) comp).av.getAlignment())
1675           {
1676             originalSource = ((AlignmentPanel) comp).av;
1677             break;
1678           }
1679         }
1680       }
1681     }
1682
1683     if (originalSource == null)
1684     {
1685       // The original view is closed, we must validate
1686       // the current view against the closed view first
1687       if (al != null)
1688       {
1689         PaintRefresher.validateSequences(al, viewport.getAlignment());
1690       }
1691
1692       originalSource = viewport;
1693     }
1694
1695     return originalSource;
1696   }
1697
1698   /**
1699    * DOCUMENT ME!
1700    *
1701    * @param up
1702    *          DOCUMENT ME!
1703    */
1704   public void moveSelectedSequences(boolean up)
1705   {
1706     SequenceGroup sg = viewport.getSelectionGroup();
1707
1708     if (sg == null)
1709     {
1710       return;
1711     }
1712     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1713             viewport.getHiddenRepSequences(), up);
1714     alignPanel.paintAlignment(true, false);
1715   }
1716
1717   synchronized void slideSequences(boolean right, int size)
1718   {
1719     List<SequenceI> sg = new ArrayList<>();
1720     if (viewport.cursorMode)
1721     {
1722       sg.add(viewport.getAlignment()
1723               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1724     }
1725     else if (viewport.getSelectionGroup() != null
1726             && viewport.getSelectionGroup().getSize() != viewport
1727                     .getAlignment().getHeight())
1728     {
1729       sg = viewport.getSelectionGroup()
1730               .getSequences(viewport.getHiddenRepSequences());
1731     }
1732
1733     if (sg.size() < 1)
1734     {
1735       return;
1736     }
1737
1738     List<SequenceI> invertGroup = new ArrayList<>();
1739
1740     for (SequenceI seq : viewport.getAlignment().getSequences())
1741     {
1742       if (!sg.contains(seq))
1743       {
1744         invertGroup.add(seq);
1745       }
1746     }
1747
1748     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1749
1750     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1751     for (int i = 0; i < invertGroup.size(); i++)
1752     {
1753       seqs2[i] = invertGroup.get(i);
1754     }
1755
1756     SlideSequencesCommand ssc;
1757     if (right)
1758     {
1759       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1760               viewport.getGapCharacter());
1761     }
1762     else
1763     {
1764       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1765               viewport.getGapCharacter());
1766     }
1767
1768     int groupAdjustment = 0;
1769     if (ssc.getGapsInsertedBegin() && right)
1770     {
1771       if (viewport.cursorMode)
1772       {
1773         alignPanel.getSeqPanel().moveCursor(size, 0);
1774       }
1775       else
1776       {
1777         groupAdjustment = size;
1778       }
1779     }
1780     else if (!ssc.getGapsInsertedBegin() && !right)
1781     {
1782       if (viewport.cursorMode)
1783       {
1784         alignPanel.getSeqPanel().moveCursor(-size, 0);
1785       }
1786       else
1787       {
1788         groupAdjustment = -size;
1789       }
1790     }
1791
1792     if (groupAdjustment != 0)
1793     {
1794       viewport.getSelectionGroup().setStartRes(
1795               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1796       viewport.getSelectionGroup().setEndRes(
1797               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1798     }
1799
1800     /*
1801      * just extend the last slide command if compatible; but not if in
1802      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1803      */
1804     boolean appendHistoryItem = false;
1805     Deque<CommandI> historyList = viewport.getHistoryList();
1806     boolean inSplitFrame = getSplitViewContainer() != null;
1807     if (!inSplitFrame && historyList != null && historyList.size() > 0
1808             && historyList.peek() instanceof SlideSequencesCommand)
1809     {
1810       appendHistoryItem = ssc.appendSlideCommand(
1811               (SlideSequencesCommand) historyList.peek());
1812     }
1813
1814     if (!appendHistoryItem)
1815     {
1816       addHistoryItem(ssc);
1817     }
1818
1819     repaint();
1820   }
1821
1822   /**
1823    * DOCUMENT ME!
1824    *
1825    * @param e
1826    *          DOCUMENT ME!
1827    */
1828   @Override
1829   protected void copy_actionPerformed(ActionEvent e)
1830   {
1831     if (viewport.getSelectionGroup() == null)
1832     {
1833       return;
1834     }
1835     // TODO: preserve the ordering of displayed alignment annotation in any
1836     // internal paste (particularly sequence associated annotation)
1837     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1838     String[] omitHidden = null;
1839
1840     if (viewport.hasHiddenColumns())
1841     {
1842       omitHidden = viewport.getViewAsString(true);
1843     }
1844
1845     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1846             seqs, omitHidden, null);
1847
1848     StringSelection ss = new StringSelection(output);
1849
1850     try
1851     {
1852       jalview.gui.Desktop.internalCopy = true;
1853       // Its really worth setting the clipboard contents
1854       // to empty before setting the large StringSelection!!
1855       Toolkit.getDefaultToolkit().getSystemClipboard()
1856               .setContents(new StringSelection(""), null);
1857
1858       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1859               Desktop.instance);
1860     } catch (OutOfMemoryError er)
1861     {
1862       new OOMWarning("copying region", er);
1863       return;
1864     }
1865
1866     HiddenColumns hiddenColumns = null;
1867     if (viewport.hasHiddenColumns())
1868     {
1869       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1870       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1871
1872       // create new HiddenColumns object with copy of hidden regions
1873       // between startRes and endRes, offset by startRes
1874       hiddenColumns = new HiddenColumns(
1875               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1876               hiddenCutoff, hiddenOffset);
1877     }
1878
1879     Desktop.jalviewClipboard = new Object[] { seqs,
1880         viewport.getAlignment().getDataset(), hiddenColumns };
1881     statusBar.setText(MessageManager.formatMessage(
1882             "label.copied_sequences_to_clipboard", new Object[]
1883             { Integer.valueOf(seqs.length).toString() }));
1884   }
1885
1886   /**
1887    * DOCUMENT ME!
1888    *
1889    * @param e
1890    *          DOCUMENT ME!
1891    */
1892   @Override
1893   protected void pasteNew_actionPerformed(ActionEvent e)
1894   {
1895     paste(true);
1896   }
1897
1898   /**
1899    * DOCUMENT ME!
1900    *
1901    * @param e
1902    *          DOCUMENT ME!
1903    */
1904   @Override
1905   protected void pasteThis_actionPerformed(ActionEvent e)
1906   {
1907     paste(false);
1908   }
1909
1910   /**
1911    * Paste contents of Jalview clipboard
1912    *
1913    * @param newAlignment
1914    *          true to paste to a new alignment, otherwise add to this.
1915    */
1916   void paste(boolean newAlignment)
1917   {
1918     boolean externalPaste = true;
1919     try
1920     {
1921       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1922       Transferable contents = c.getContents(this);
1923
1924       if (contents == null)
1925       {
1926         return;
1927       }
1928
1929       String str;
1930       FileFormatI format;
1931       try
1932       {
1933         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1934         if (str.length() < 1)
1935         {
1936           return;
1937         }
1938
1939         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
1940
1941       } catch (OutOfMemoryError er)
1942       {
1943         new OOMWarning("Out of memory pasting sequences!!", er);
1944         return;
1945       }
1946
1947       SequenceI[] sequences;
1948       boolean annotationAdded = false;
1949       AlignmentI alignment = null;
1950
1951       if (Desktop.jalviewClipboard != null)
1952       {
1953         // The clipboard was filled from within Jalview, we must use the
1954         // sequences
1955         // And dataset from the copied alignment
1956         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1957         // be doubly sure that we create *new* sequence objects.
1958         sequences = new SequenceI[newseq.length];
1959         for (int i = 0; i < newseq.length; i++)
1960         {
1961           sequences[i] = new Sequence(newseq[i]);
1962         }
1963         alignment = new Alignment(sequences);
1964         externalPaste = false;
1965       }
1966       else
1967       {
1968         // parse the clipboard as an alignment.
1969         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
1970                 format);
1971         sequences = alignment.getSequencesArray();
1972       }
1973
1974       int alwidth = 0;
1975       ArrayList<Integer> newGraphGroups = new ArrayList<>();
1976       int fgroup = -1;
1977
1978       if (newAlignment)
1979       {
1980
1981         if (Desktop.jalviewClipboard != null)
1982         {
1983           // dataset is inherited
1984           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1985         }
1986         else
1987         {
1988           // new dataset is constructed
1989           alignment.setDataset(null);
1990         }
1991         alwidth = alignment.getWidth() + 1;
1992       }
1993       else
1994       {
1995         AlignmentI pastedal = alignment; // preserve pasted alignment object
1996         // Add pasted sequences and dataset into existing alignment.
1997         alignment = viewport.getAlignment();
1998         alwidth = alignment.getWidth() + 1;
1999         // decide if we need to import sequences from an existing dataset
2000         boolean importDs = Desktop.jalviewClipboard != null
2001                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2002         // importDs==true instructs us to copy over new dataset sequences from
2003         // an existing alignment
2004         Vector newDs = (importDs) ? new Vector() : null; // used to create
2005         // minimum dataset set
2006
2007         for (int i = 0; i < sequences.length; i++)
2008         {
2009           if (importDs)
2010           {
2011             newDs.addElement(null);
2012           }
2013           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2014           // paste
2015           if (importDs && ds != null)
2016           {
2017             if (!newDs.contains(ds))
2018             {
2019               newDs.setElementAt(ds, i);
2020               ds = new Sequence(ds);
2021               // update with new dataset sequence
2022               sequences[i].setDatasetSequence(ds);
2023             }
2024             else
2025             {
2026               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2027             }
2028           }
2029           else
2030           {
2031             // copy and derive new dataset sequence
2032             sequences[i] = sequences[i].deriveSequence();
2033             alignment.getDataset()
2034                     .addSequence(sequences[i].getDatasetSequence());
2035             // TODO: avoid creation of duplicate dataset sequences with a
2036             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2037           }
2038           alignment.addSequence(sequences[i]); // merges dataset
2039         }
2040         if (newDs != null)
2041         {
2042           newDs.clear(); // tidy up
2043         }
2044         if (alignment.getAlignmentAnnotation() != null)
2045         {
2046           for (AlignmentAnnotation alan : alignment
2047                   .getAlignmentAnnotation())
2048           {
2049             if (alan.graphGroup > fgroup)
2050             {
2051               fgroup = alan.graphGroup;
2052             }
2053           }
2054         }
2055         if (pastedal.getAlignmentAnnotation() != null)
2056         {
2057           // Add any annotation attached to alignment.
2058           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2059           for (int i = 0; i < alann.length; i++)
2060           {
2061             annotationAdded = true;
2062             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2063             {
2064               AlignmentAnnotation newann = new AlignmentAnnotation(
2065                       alann[i]);
2066               if (newann.graphGroup > -1)
2067               {
2068                 if (newGraphGroups.size() <= newann.graphGroup
2069                         || newGraphGroups.get(newann.graphGroup) == null)
2070                 {
2071                   for (int q = newGraphGroups
2072                           .size(); q <= newann.graphGroup; q++)
2073                   {
2074                     newGraphGroups.add(q, null);
2075                   }
2076                   newGraphGroups.set(newann.graphGroup,
2077                           new Integer(++fgroup));
2078                 }
2079                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2080                         .intValue();
2081               }
2082
2083               newann.padAnnotation(alwidth);
2084               alignment.addAnnotation(newann);
2085             }
2086           }
2087         }
2088       }
2089       if (!newAlignment)
2090       {
2091         // /////
2092         // ADD HISTORY ITEM
2093         //
2094         addHistoryItem(new EditCommand(
2095                 MessageManager.getString("label.add_sequences"),
2096                 Action.PASTE, sequences, 0, alignment.getWidth(),
2097                 alignment));
2098       }
2099       // Add any annotations attached to sequences
2100       for (int i = 0; i < sequences.length; i++)
2101       {
2102         if (sequences[i].getAnnotation() != null)
2103         {
2104           AlignmentAnnotation newann;
2105           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2106           {
2107             annotationAdded = true;
2108             newann = sequences[i].getAnnotation()[a];
2109             newann.adjustForAlignment();
2110             newann.padAnnotation(alwidth);
2111             if (newann.graphGroup > -1)
2112             {
2113               if (newann.graphGroup > -1)
2114               {
2115                 if (newGraphGroups.size() <= newann.graphGroup
2116                         || newGraphGroups.get(newann.graphGroup) == null)
2117                 {
2118                   for (int q = newGraphGroups
2119                           .size(); q <= newann.graphGroup; q++)
2120                   {
2121                     newGraphGroups.add(q, null);
2122                   }
2123                   newGraphGroups.set(newann.graphGroup,
2124                           new Integer(++fgroup));
2125                 }
2126                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2127                         .intValue();
2128               }
2129             }
2130             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2131             // was
2132             // duplicated
2133             // earlier
2134             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2135                     a);
2136           }
2137         }
2138       }
2139       if (!newAlignment)
2140       {
2141
2142         // propagate alignment changed.
2143         viewport.getRanges().setEndSeq(alignment.getHeight());
2144         if (annotationAdded)
2145         {
2146           // Duplicate sequence annotation in all views.
2147           AlignmentI[] alview = this.getViewAlignments();
2148           for (int i = 0; i < sequences.length; i++)
2149           {
2150             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2151             if (sann == null)
2152             {
2153               continue;
2154             }
2155             for (int avnum = 0; avnum < alview.length; avnum++)
2156             {
2157               if (alview[avnum] != alignment)
2158               {
2159                 // duplicate in a view other than the one with input focus
2160                 int avwidth = alview[avnum].getWidth() + 1;
2161                 // this relies on sann being preserved after we
2162                 // modify the sequence's annotation array for each duplication
2163                 for (int a = 0; a < sann.length; a++)
2164                 {
2165                   AlignmentAnnotation newann = new AlignmentAnnotation(
2166                           sann[a]);
2167                   sequences[i].addAlignmentAnnotation(newann);
2168                   newann.padAnnotation(avwidth);
2169                   alview[avnum].addAnnotation(newann); // annotation was
2170                   // duplicated earlier
2171                   // TODO JAL-1145 graphGroups are not updated for sequence
2172                   // annotation added to several views. This may cause
2173                   // strangeness
2174                   alview[avnum].setAnnotationIndex(newann, a);
2175                 }
2176               }
2177             }
2178           }
2179           buildSortByAnnotationScoresMenu();
2180         }
2181         viewport.firePropertyChange("alignment", null,
2182                 alignment.getSequences());
2183         if (alignPanels != null)
2184         {
2185           for (AlignmentPanel ap : alignPanels)
2186           {
2187             ap.validateAnnotationDimensions(false);
2188           }
2189         }
2190         else
2191         {
2192           alignPanel.validateAnnotationDimensions(false);
2193         }
2194
2195       }
2196       else
2197       {
2198         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2199                 DEFAULT_HEIGHT);
2200         String newtitle = new String("Copied sequences");
2201
2202         if (Desktop.jalviewClipboard != null
2203                 && Desktop.jalviewClipboard[2] != null)
2204         {
2205           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2206           af.viewport.setHiddenColumns(hc);
2207         }
2208
2209         // >>>This is a fix for the moment, until a better solution is
2210         // found!!<<<
2211         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2212                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2213                         .getFeatureRenderer());
2214
2215         // TODO: maintain provenance of an alignment, rather than just make the
2216         // title a concatenation of operations.
2217         if (!externalPaste)
2218         {
2219           if (title.startsWith("Copied sequences"))
2220           {
2221             newtitle = title;
2222           }
2223           else
2224           {
2225             newtitle = newtitle.concat("- from " + title);
2226           }
2227         }
2228         else
2229         {
2230           newtitle = new String("Pasted sequences");
2231         }
2232
2233         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2234                 DEFAULT_HEIGHT);
2235
2236       }
2237
2238     } catch (Exception ex)
2239     {
2240       ex.printStackTrace();
2241       System.out.println("Exception whilst pasting: " + ex);
2242       // could be anything being pasted in here
2243     }
2244
2245   }
2246
2247   @Override
2248   protected void expand_newalign(ActionEvent e)
2249   {
2250     try
2251     {
2252       AlignmentI alignment = AlignmentUtils
2253               .expandContext(getViewport().getAlignment(), -1);
2254       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2255               DEFAULT_HEIGHT);
2256       String newtitle = new String("Flanking alignment");
2257
2258       if (Desktop.jalviewClipboard != null
2259               && Desktop.jalviewClipboard[2] != null)
2260       {
2261         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2262         af.viewport.setHiddenColumns(hc);
2263       }
2264
2265       // >>>This is a fix for the moment, until a better solution is
2266       // found!!<<<
2267       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2268               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2269                       .getFeatureRenderer());
2270
2271       // TODO: maintain provenance of an alignment, rather than just make the
2272       // title a concatenation of operations.
2273       {
2274         if (title.startsWith("Copied sequences"))
2275         {
2276           newtitle = title;
2277         }
2278         else
2279         {
2280           newtitle = newtitle.concat("- from " + title);
2281         }
2282       }
2283
2284       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2285
2286     } catch (Exception ex)
2287     {
2288       ex.printStackTrace();
2289       System.out.println("Exception whilst pasting: " + ex);
2290       // could be anything being pasted in here
2291     } catch (OutOfMemoryError oom)
2292     {
2293       new OOMWarning("Viewing flanking region of alignment", oom);
2294     }
2295   }
2296
2297   /**
2298    * DOCUMENT ME!
2299    *
2300    * @param e
2301    *          DOCUMENT ME!
2302    */
2303   @Override
2304   protected void cut_actionPerformed(ActionEvent e)
2305   {
2306     copy_actionPerformed(null);
2307     delete_actionPerformed(null);
2308   }
2309
2310   /**
2311    * DOCUMENT ME!
2312    *
2313    * @param e
2314    *          DOCUMENT ME!
2315    */
2316   @Override
2317   protected void delete_actionPerformed(ActionEvent evt)
2318   {
2319
2320     SequenceGroup sg = viewport.getSelectionGroup();
2321     if (sg == null)
2322     {
2323       return;
2324     }
2325
2326     /*
2327      * If the cut affects all sequences, warn, remove highlighted columns
2328      */
2329     if (sg.getSize() == viewport.getAlignment().getHeight())
2330     {
2331       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2332               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2333       if (isEntireAlignWidth)
2334       {
2335         int confirm = JvOptionPane.showConfirmDialog(this,
2336                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2337                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2338                 JvOptionPane.OK_CANCEL_OPTION);
2339
2340         if (confirm == JvOptionPane.CANCEL_OPTION
2341                 || confirm == JvOptionPane.CLOSED_OPTION)
2342         {
2343           return;
2344         }
2345       }
2346       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2347               sg.getEndRes() + 1);
2348     }
2349     SequenceI[] cut = sg.getSequences()
2350             .toArray(new SequenceI[sg.getSize()]);
2351
2352     addHistoryItem(new EditCommand(
2353             MessageManager.getString("label.cut_sequences"), Action.CUT,
2354             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2355             viewport.getAlignment()));
2356
2357     viewport.setSelectionGroup(null);
2358     viewport.sendSelection();
2359     viewport.getAlignment().deleteGroup(sg);
2360
2361     viewport.firePropertyChange("alignment", null,
2362             viewport.getAlignment().getSequences());
2363     if (viewport.getAlignment().getHeight() < 1)
2364     {
2365       try
2366       {
2367         this.setClosed(true);
2368       } catch (Exception ex)
2369       {
2370       }
2371     }
2372   }
2373
2374   /**
2375    * DOCUMENT ME!
2376    *
2377    * @param e
2378    *          DOCUMENT ME!
2379    */
2380   @Override
2381   protected void deleteGroups_actionPerformed(ActionEvent e)
2382   {
2383     if (avc.deleteGroups())
2384     {
2385       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2386       alignPanel.updateAnnotation();
2387       alignPanel.paintAlignment(true, true);
2388     }
2389   }
2390
2391   /**
2392    * DOCUMENT ME!
2393    *
2394    * @param e
2395    *          DOCUMENT ME!
2396    */
2397   @Override
2398   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2399   {
2400     SequenceGroup sg = new SequenceGroup();
2401
2402     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2403     {
2404       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2405     }
2406
2407     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2408     viewport.setSelectionGroup(sg);
2409     viewport.sendSelection();
2410     // JAL-2034 - should delegate to
2411     // alignPanel to decide if overview needs
2412     // updating.
2413     alignPanel.paintAlignment(false, false);
2414     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2415   }
2416
2417   /**
2418    * DOCUMENT ME!
2419    *
2420    * @param e
2421    *          DOCUMENT ME!
2422    */
2423   @Override
2424   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2425   {
2426     if (viewport.cursorMode)
2427     {
2428       alignPanel.getSeqPanel().keyboardNo1 = null;
2429       alignPanel.getSeqPanel().keyboardNo2 = null;
2430     }
2431     viewport.setSelectionGroup(null);
2432     viewport.getColumnSelection().clear();
2433     viewport.setSelectionGroup(null);
2434     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2435     // JAL-2034 - should delegate to
2436     // alignPanel to decide if overview needs
2437     // updating.
2438     alignPanel.paintAlignment(false, false);
2439     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2440     viewport.sendSelection();
2441   }
2442
2443   /**
2444    * DOCUMENT ME!
2445    *
2446    * @param e
2447    *          DOCUMENT ME!
2448    */
2449   @Override
2450   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2451   {
2452     SequenceGroup sg = viewport.getSelectionGroup();
2453
2454     if (sg == null)
2455     {
2456       selectAllSequenceMenuItem_actionPerformed(null);
2457
2458       return;
2459     }
2460
2461     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2462     {
2463       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2464     }
2465     // JAL-2034 - should delegate to
2466     // alignPanel to decide if overview needs
2467     // updating.
2468
2469     alignPanel.paintAlignment(true, false);
2470     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2471     viewport.sendSelection();
2472   }
2473
2474   @Override
2475   public void invertColSel_actionPerformed(ActionEvent e)
2476   {
2477     viewport.invertColumnSelection();
2478     alignPanel.paintAlignment(true, false);
2479     viewport.sendSelection();
2480   }
2481
2482   /**
2483    * DOCUMENT ME!
2484    *
2485    * @param e
2486    *          DOCUMENT ME!
2487    */
2488   @Override
2489   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2490   {
2491     trimAlignment(true);
2492   }
2493
2494   /**
2495    * DOCUMENT ME!
2496    *
2497    * @param e
2498    *          DOCUMENT ME!
2499    */
2500   @Override
2501   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2502   {
2503     trimAlignment(false);
2504   }
2505
2506   void trimAlignment(boolean trimLeft)
2507   {
2508     ColumnSelection colSel = viewport.getColumnSelection();
2509     int column;
2510
2511     if (!colSel.isEmpty())
2512     {
2513       if (trimLeft)
2514       {
2515         column = colSel.getMin();
2516       }
2517       else
2518       {
2519         column = colSel.getMax();
2520       }
2521
2522       SequenceI[] seqs;
2523       if (viewport.getSelectionGroup() != null)
2524       {
2525         seqs = viewport.getSelectionGroup()
2526                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2527       }
2528       else
2529       {
2530         seqs = viewport.getAlignment().getSequencesArray();
2531       }
2532
2533       TrimRegionCommand trimRegion;
2534       if (trimLeft)
2535       {
2536         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2537                 column, viewport.getAlignment());
2538         viewport.getRanges().setStartRes(0);
2539       }
2540       else
2541       {
2542         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2543                 column, viewport.getAlignment());
2544       }
2545
2546       statusBar.setText(MessageManager
2547               .formatMessage("label.removed_columns", new String[]
2548               { Integer.valueOf(trimRegion.getSize()).toString() }));
2549
2550       addHistoryItem(trimRegion);
2551
2552       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2553       {
2554         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2555                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2556         {
2557           viewport.getAlignment().deleteGroup(sg);
2558         }
2559       }
2560
2561       viewport.firePropertyChange("alignment", null,
2562               viewport.getAlignment().getSequences());
2563     }
2564   }
2565
2566   /**
2567    * DOCUMENT ME!
2568    *
2569    * @param e
2570    *          DOCUMENT ME!
2571    */
2572   @Override
2573   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2574   {
2575     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2576
2577     SequenceI[] seqs;
2578     if (viewport.getSelectionGroup() != null)
2579     {
2580       seqs = viewport.getSelectionGroup()
2581               .getSequencesAsArray(viewport.getHiddenRepSequences());
2582       start = viewport.getSelectionGroup().getStartRes();
2583       end = viewport.getSelectionGroup().getEndRes();
2584     }
2585     else
2586     {
2587       seqs = viewport.getAlignment().getSequencesArray();
2588     }
2589
2590     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2591             "Remove Gapped Columns", seqs, start, end,
2592             viewport.getAlignment());
2593
2594     addHistoryItem(removeGapCols);
2595
2596     statusBar.setText(MessageManager
2597             .formatMessage("label.removed_empty_columns", new Object[]
2598             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2599
2600     // This is to maintain viewport position on first residue
2601     // of first sequence
2602     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2603     ViewportRanges ranges = viewport.getRanges();
2604     int startRes = seq.findPosition(ranges.getStartRes());
2605     // ShiftList shifts;
2606     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2607     // edit.alColumnChanges=shifts.getInverse();
2608     // if (viewport.hasHiddenColumns)
2609     // viewport.getColumnSelection().compensateForEdits(shifts);
2610     ranges.setStartRes(seq.findIndex(startRes) - 1);
2611     viewport.firePropertyChange("alignment", null,
2612             viewport.getAlignment().getSequences());
2613
2614   }
2615
2616   /**
2617    * DOCUMENT ME!
2618    *
2619    * @param e
2620    *          DOCUMENT ME!
2621    */
2622   @Override
2623   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2624   {
2625     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2626
2627     SequenceI[] seqs;
2628     if (viewport.getSelectionGroup() != null)
2629     {
2630       seqs = viewport.getSelectionGroup()
2631               .getSequencesAsArray(viewport.getHiddenRepSequences());
2632       start = viewport.getSelectionGroup().getStartRes();
2633       end = viewport.getSelectionGroup().getEndRes();
2634     }
2635     else
2636     {
2637       seqs = viewport.getAlignment().getSequencesArray();
2638     }
2639
2640     // This is to maintain viewport position on first residue
2641     // of first sequence
2642     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2643     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2644
2645     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2646             viewport.getAlignment()));
2647
2648     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2649
2650     viewport.firePropertyChange("alignment", null,
2651             viewport.getAlignment().getSequences());
2652
2653   }
2654
2655   /**
2656    * DOCUMENT ME!
2657    *
2658    * @param e
2659    *          DOCUMENT ME!
2660    */
2661   @Override
2662   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2663   {
2664     viewport.setPadGaps(padGapsMenuitem.isSelected());
2665     viewport.firePropertyChange("alignment", null,
2666             viewport.getAlignment().getSequences());
2667   }
2668
2669   /**
2670    * DOCUMENT ME!
2671    *
2672    * @param e
2673    *          DOCUMENT ME!
2674    */
2675   @Override
2676   public void findMenuItem_actionPerformed(ActionEvent e)
2677   {
2678     new Finder();
2679   }
2680
2681   /**
2682    * Create a new view of the current alignment.
2683    */
2684   @Override
2685   public void newView_actionPerformed(ActionEvent e)
2686   {
2687     newView(null, true);
2688   }
2689
2690   /**
2691    * Creates and shows a new view of the current alignment.
2692    *
2693    * @param viewTitle
2694    *          title of newly created view; if null, one will be generated
2695    * @param copyAnnotation
2696    *          if true then duplicate all annnotation, groups and settings
2697    * @return new alignment panel, already displayed.
2698    */
2699   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2700   {
2701     /*
2702      * Create a new AlignmentPanel (with its own, new Viewport)
2703      */
2704     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
2705     if (!copyAnnotation)
2706     {
2707       /*
2708        * remove all groups and annotation except for the automatic stuff
2709        */
2710       newap.av.getAlignment().deleteAllGroups();
2711       newap.av.getAlignment().deleteAllAnnotations(false);
2712     }
2713
2714     newap.av.setGatherViewsHere(false);
2715
2716     if (viewport.getViewName() == null)
2717     {
2718       viewport.setViewName(MessageManager
2719               .getString("label.view_name_original"));
2720     }
2721
2722     /*
2723      * Views share the same edits undo and redo stacks
2724      */
2725     newap.av.setHistoryList(viewport.getHistoryList());
2726     newap.av.setRedoList(viewport.getRedoList());
2727
2728     /*
2729      * Views share the same mappings; need to deregister any new mappings
2730      * created by copyAlignPanel, and register the new reference to the shared
2731      * mappings
2732      */
2733     newap.av.replaceMappings(viewport.getAlignment());
2734
2735     /*
2736      * start up cDNA consensus (if applicable) now mappings are in place
2737      */
2738     if (newap.av.initComplementConsensus())
2739     {
2740       newap.refresh(true); // adjust layout of annotations
2741     }
2742
2743     newap.av.setViewName(getNewViewName(viewTitle));
2744
2745     addAlignmentPanel(newap, true);
2746     newap.alignmentChanged();
2747
2748     if (alignPanels.size() == 2)
2749     {
2750       viewport.setGatherViewsHere(true);
2751     }
2752     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2753     return newap;
2754   }
2755
2756   /**
2757    * Make a new name for the view, ensuring it is unique within the current
2758    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2759    * these now use viewId. Unique view names are still desirable for usability.)
2760    *
2761    * @param viewTitle
2762    * @return
2763    */
2764   protected String getNewViewName(String viewTitle)
2765   {
2766     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2767     boolean addFirstIndex = false;
2768     if (viewTitle == null || viewTitle.trim().length() == 0)
2769     {
2770       viewTitle = MessageManager.getString("action.view");
2771       addFirstIndex = true;
2772     }
2773     else
2774     {
2775       index = 1;// we count from 1 if given a specific name
2776     }
2777     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2778
2779     List<Component> comps = PaintRefresher.components
2780             .get(viewport.getSequenceSetId());
2781
2782     List<String> existingNames = getExistingViewNames(comps);
2783
2784     while (existingNames.contains(newViewName))
2785     {
2786       newViewName = viewTitle + " " + (++index);
2787     }
2788     return newViewName;
2789   }
2790
2791   /**
2792    * Returns a list of distinct view names found in the given list of
2793    * components. View names are held on the viewport of an AlignmentPanel.
2794    *
2795    * @param comps
2796    * @return
2797    */
2798   protected List<String> getExistingViewNames(List<Component> comps)
2799   {
2800     List<String> existingNames = new ArrayList<>();
2801     for (Component comp : comps)
2802     {
2803       if (comp instanceof AlignmentPanel)
2804       {
2805         AlignmentPanel ap = (AlignmentPanel) comp;
2806         if (!existingNames.contains(ap.av.getViewName()))
2807         {
2808           existingNames.add(ap.av.getViewName());
2809         }
2810       }
2811     }
2812     return existingNames;
2813   }
2814
2815   /**
2816    * Explode tabbed views into separate windows.
2817    */
2818   @Override
2819   public void expandViews_actionPerformed(ActionEvent e)
2820   {
2821     Desktop.explodeViews(this);
2822   }
2823
2824   /**
2825    * Gather views in separate windows back into a tabbed presentation.
2826    */
2827   @Override
2828   public void gatherViews_actionPerformed(ActionEvent e)
2829   {
2830     Desktop.instance.gatherViews(this);
2831   }
2832
2833   /**
2834    * DOCUMENT ME!
2835    *
2836    * @param e
2837    *          DOCUMENT ME!
2838    */
2839   @Override
2840   public void font_actionPerformed(ActionEvent e)
2841   {
2842     new FontChooser(alignPanel);
2843   }
2844
2845   /**
2846    * DOCUMENT ME!
2847    *
2848    * @param e
2849    *          DOCUMENT ME!
2850    */
2851   @Override
2852   protected void seqLimit_actionPerformed(ActionEvent e)
2853   {
2854     viewport.setShowJVSuffix(seqLimits.isSelected());
2855
2856     alignPanel.getIdPanel().getIdCanvas()
2857             .setPreferredSize(alignPanel.calculateIdWidth());
2858     alignPanel.paintAlignment(true, false);
2859   }
2860
2861   @Override
2862   public void idRightAlign_actionPerformed(ActionEvent e)
2863   {
2864     viewport.setRightAlignIds(idRightAlign.isSelected());
2865     alignPanel.paintAlignment(false, false);
2866   }
2867
2868   @Override
2869   public void centreColumnLabels_actionPerformed(ActionEvent e)
2870   {
2871     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2872     alignPanel.paintAlignment(false, false);
2873   }
2874
2875   /*
2876    * (non-Javadoc)
2877    *
2878    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2879    */
2880   @Override
2881   protected void followHighlight_actionPerformed()
2882   {
2883     /*
2884      * Set the 'follow' flag on the Viewport (and scroll to position if now
2885      * true).
2886      */
2887     final boolean state = this.followHighlightMenuItem.getState();
2888     viewport.setFollowHighlight(state);
2889     if (state)
2890     {
2891       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2892     }
2893   }
2894
2895   /**
2896    * DOCUMENT ME!
2897    *
2898    * @param e
2899    *          DOCUMENT ME!
2900    */
2901   @Override
2902   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2903   {
2904     viewport.setColourText(colourTextMenuItem.isSelected());
2905     alignPanel.paintAlignment(false, false);
2906   }
2907
2908   /**
2909    * DOCUMENT ME!
2910    *
2911    * @param e
2912    *          DOCUMENT ME!
2913    */
2914   @Override
2915   public void wrapMenuItem_actionPerformed(ActionEvent e)
2916   {
2917     scaleAbove.setVisible(wrapMenuItem.isSelected());
2918     scaleLeft.setVisible(wrapMenuItem.isSelected());
2919     scaleRight.setVisible(wrapMenuItem.isSelected());
2920     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2921     alignPanel.updateLayout();
2922   }
2923
2924   @Override
2925   public void showAllSeqs_actionPerformed(ActionEvent e)
2926   {
2927     viewport.showAllHiddenSeqs();
2928   }
2929
2930   @Override
2931   public void showAllColumns_actionPerformed(ActionEvent e)
2932   {
2933     viewport.showAllHiddenColumns();
2934     alignPanel.paintAlignment(true, true);
2935     viewport.sendSelection();
2936   }
2937
2938   @Override
2939   public void hideSelSequences_actionPerformed(ActionEvent e)
2940   {
2941     viewport.hideAllSelectedSeqs();
2942   }
2943
2944   /**
2945    * called by key handler and the hide all/show all menu items
2946    *
2947    * @param toggleSeqs
2948    * @param toggleCols
2949    */
2950   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2951   {
2952
2953     boolean hide = false;
2954     SequenceGroup sg = viewport.getSelectionGroup();
2955     if (!toggleSeqs && !toggleCols)
2956     {
2957       // Hide everything by the current selection - this is a hack - we do the
2958       // invert and then hide
2959       // first check that there will be visible columns after the invert.
2960       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
2961               && sg.getStartRes() <= sg.getEndRes()))
2962       {
2963         // now invert the sequence set, if required - empty selection implies
2964         // that no hiding is required.
2965         if (sg != null)
2966         {
2967           invertSequenceMenuItem_actionPerformed(null);
2968           sg = viewport.getSelectionGroup();
2969           toggleSeqs = true;
2970
2971         }
2972         viewport.expandColSelection(sg, true);
2973         // finally invert the column selection and get the new sequence
2974         // selection.
2975         invertColSel_actionPerformed(null);
2976         toggleCols = true;
2977       }
2978     }
2979
2980     if (toggleSeqs)
2981     {
2982       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2983       {
2984         hideSelSequences_actionPerformed(null);
2985         hide = true;
2986       }
2987       else if (!(toggleCols && viewport.hasSelectedColumns()))
2988       {
2989         showAllSeqs_actionPerformed(null);
2990       }
2991     }
2992
2993     if (toggleCols)
2994     {
2995       if (viewport.hasSelectedColumns())
2996       {
2997         hideSelColumns_actionPerformed(null);
2998         if (!toggleSeqs)
2999         {
3000           viewport.setSelectionGroup(sg);
3001         }
3002       }
3003       else if (!hide)
3004       {
3005         showAllColumns_actionPerformed(null);
3006       }
3007     }
3008   }
3009
3010   /*
3011    * (non-Javadoc)
3012    *
3013    * @see
3014    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3015    * event.ActionEvent)
3016    */
3017   @Override
3018   public void hideAllButSelection_actionPerformed(ActionEvent e)
3019   {
3020     toggleHiddenRegions(false, false);
3021     viewport.sendSelection();
3022   }
3023
3024   /*
3025    * (non-Javadoc)
3026    *
3027    * @see
3028    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3029    * .ActionEvent)
3030    */
3031   @Override
3032   public void hideAllSelection_actionPerformed(ActionEvent e)
3033   {
3034     SequenceGroup sg = viewport.getSelectionGroup();
3035     viewport.expandColSelection(sg, false);
3036     viewport.hideAllSelectedSeqs();
3037     viewport.hideSelectedColumns();
3038     alignPanel.paintAlignment(true, true);
3039     viewport.sendSelection();
3040   }
3041
3042   /*
3043    * (non-Javadoc)
3044    *
3045    * @see
3046    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3047    * ActionEvent)
3048    */
3049   @Override
3050   public void showAllhidden_actionPerformed(ActionEvent e)
3051   {
3052     viewport.showAllHiddenColumns();
3053     viewport.showAllHiddenSeqs();
3054     alignPanel.paintAlignment(true, true);
3055     viewport.sendSelection();
3056   }
3057
3058   @Override
3059   public void hideSelColumns_actionPerformed(ActionEvent e)
3060   {
3061     viewport.hideSelectedColumns();
3062     alignPanel.paintAlignment(true, true);
3063     viewport.sendSelection();
3064   }
3065
3066   @Override
3067   public void hiddenMarkers_actionPerformed(ActionEvent e)
3068   {
3069     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3070     repaint();
3071   }
3072
3073   /**
3074    * DOCUMENT ME!
3075    *
3076    * @param e
3077    *          DOCUMENT ME!
3078    */
3079   @Override
3080   protected void scaleAbove_actionPerformed(ActionEvent e)
3081   {
3082     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3083     // TODO: do we actually need to update overview for scale above change ?
3084     alignPanel.paintAlignment(true, false);
3085   }
3086
3087   /**
3088    * DOCUMENT ME!
3089    *
3090    * @param e
3091    *          DOCUMENT ME!
3092    */
3093   @Override
3094   protected void scaleLeft_actionPerformed(ActionEvent e)
3095   {
3096     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3097     alignPanel.paintAlignment(true, false);
3098   }
3099
3100   /**
3101    * DOCUMENT ME!
3102    *
3103    * @param e
3104    *          DOCUMENT ME!
3105    */
3106   @Override
3107   protected void scaleRight_actionPerformed(ActionEvent e)
3108   {
3109     viewport.setScaleRightWrapped(scaleRight.isSelected());
3110     alignPanel.paintAlignment(true, false);
3111   }
3112
3113   /**
3114    * DOCUMENT ME!
3115    *
3116    * @param e
3117    *          DOCUMENT ME!
3118    */
3119   @Override
3120   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3121   {
3122     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3123     alignPanel.paintAlignment(false, false);
3124   }
3125
3126   /**
3127    * DOCUMENT ME!
3128    *
3129    * @param e
3130    *          DOCUMENT ME!
3131    */
3132   @Override
3133   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3134   {
3135     viewport.setShowText(viewTextMenuItem.isSelected());
3136     alignPanel.paintAlignment(false, false);
3137   }
3138
3139   /**
3140    * DOCUMENT ME!
3141    *
3142    * @param e
3143    *          DOCUMENT ME!
3144    */
3145   @Override
3146   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3147   {
3148     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3149     alignPanel.paintAlignment(false, false);
3150   }
3151
3152   public FeatureSettings featureSettings;
3153
3154   @Override
3155   public FeatureSettingsControllerI getFeatureSettingsUI()
3156   {
3157     return featureSettings;
3158   }
3159
3160   @Override
3161   public void featureSettings_actionPerformed(ActionEvent e)
3162   {
3163     if (featureSettings != null)
3164     {
3165       featureSettings.close();
3166       featureSettings = null;
3167     }
3168     if (!showSeqFeatures.isSelected())
3169     {
3170       // make sure features are actually displayed
3171       showSeqFeatures.setSelected(true);
3172       showSeqFeatures_actionPerformed(null);
3173     }
3174     featureSettings = new FeatureSettings(this);
3175   }
3176
3177   /**
3178    * Set or clear 'Show Sequence Features'
3179    *
3180    * @param evt
3181    *          DOCUMENT ME!
3182    */
3183   @Override
3184   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3185   {
3186     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3187     alignPanel.paintAlignment(true, true);
3188   }
3189
3190   /**
3191    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3192    * the annotations panel as a whole.
3193    *
3194    * The options to show/hide all annotations should be enabled when the panel
3195    * is shown, and disabled when the panel is hidden.
3196    *
3197    * @param e
3198    */
3199   @Override
3200   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3201   {
3202     final boolean setVisible = annotationPanelMenuItem.isSelected();
3203     viewport.setShowAnnotation(setVisible);
3204     this.showAllSeqAnnotations.setEnabled(setVisible);
3205     this.hideAllSeqAnnotations.setEnabled(setVisible);
3206     this.showAllAlAnnotations.setEnabled(setVisible);
3207     this.hideAllAlAnnotations.setEnabled(setVisible);
3208     alignPanel.updateLayout();
3209   }
3210
3211   @Override
3212   public void alignmentProperties()
3213   {
3214     JEditorPane editPane = new JEditorPane("text/html", "");
3215     editPane.setEditable(false);
3216     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3217             .formatAsHtml();
3218     editPane.setText(
3219             MessageManager.formatMessage("label.html_content", new Object[]
3220             { contents.toString() }));
3221     JInternalFrame frame = new JInternalFrame();
3222     frame.getContentPane().add(new JScrollPane(editPane));
3223
3224     Desktop.addInternalFrame(frame, MessageManager
3225             .formatMessage("label.alignment_properties", new Object[]
3226             { getTitle() }), 500, 400);
3227   }
3228
3229   /**
3230    * DOCUMENT ME!
3231    *
3232    * @param e
3233    *          DOCUMENT ME!
3234    */
3235   @Override
3236   public void overviewMenuItem_actionPerformed(ActionEvent e)
3237   {
3238     if (alignPanel.overviewPanel != null)
3239     {
3240       return;
3241     }
3242
3243     JInternalFrame frame = new JInternalFrame();
3244     final OverviewPanel overview = new OverviewPanel(alignPanel);
3245     frame.setContentPane(overview);
3246     Desktop.addInternalFrame(frame, MessageManager
3247             .formatMessage("label.overview_params", new Object[]
3248             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3249             true, true);
3250     frame.pack();
3251     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3252     frame.addInternalFrameListener(
3253             new javax.swing.event.InternalFrameAdapter()
3254             {
3255               @Override
3256               public void internalFrameClosed(
3257                       javax.swing.event.InternalFrameEvent evt)
3258               {
3259                 overview.dispose();
3260                 alignPanel.setOverviewPanel(null);
3261               };
3262             });
3263     if (getKeyListeners().length > 0)
3264     {
3265       frame.addKeyListener(getKeyListeners()[0]);
3266     }
3267
3268     alignPanel.setOverviewPanel(overview);
3269   }
3270
3271   @Override
3272   public void textColour_actionPerformed()
3273   {
3274     new TextColourChooser().chooseColour(alignPanel, null);
3275   }
3276
3277   /*
3278    * public void covariationColour_actionPerformed() {
3279    * changeColour(new
3280    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3281    * ()[0])); }
3282    */
3283   @Override
3284   public void annotationColour_actionPerformed()
3285   {
3286     new AnnotationColourChooser(viewport, alignPanel);
3287   }
3288
3289   @Override
3290   public void annotationColumn_actionPerformed(ActionEvent e)
3291   {
3292     new AnnotationColumnChooser(viewport, alignPanel);
3293   }
3294
3295   /**
3296    * Action on the user checking or unchecking the option to apply the selected
3297    * colour scheme to all groups. If unchecked, groups may have their own
3298    * independent colour schemes.
3299    *
3300    * @param selected
3301    */
3302   @Override
3303   public void applyToAllGroups_actionPerformed(boolean selected)
3304   {
3305     viewport.setColourAppliesToAllGroups(selected);
3306   }
3307
3308   /**
3309    * Action on user selecting a colour from the colour menu
3310    *
3311    * @param name
3312    *          the name (not the menu item label!) of the colour scheme
3313    */
3314   @Override
3315   public void changeColour_actionPerformed(String name)
3316   {
3317     /*
3318      * 'User Defined' opens a panel to configure or load a
3319      * user-defined colour scheme
3320      */
3321     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3322     {
3323       new UserDefinedColours(alignPanel);
3324       return;
3325     }
3326
3327     /*
3328      * otherwise set the chosen colour scheme (or null for 'None')
3329      */
3330     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3331             viewport.getAlignment(), viewport.getHiddenRepSequences());
3332     changeColour(cs);
3333   }
3334
3335   /**
3336    * Actions on setting or changing the alignment colour scheme
3337    *
3338    * @param cs
3339    */
3340   @Override
3341   public void changeColour(ColourSchemeI cs)
3342   {
3343     // TODO: pull up to controller method
3344     ColourMenuHelper.setColourSelected(colourMenu, cs);
3345
3346     viewport.setGlobalColourScheme(cs);
3347
3348     alignPanel.paintAlignment(true, true);
3349   }
3350
3351   /**
3352    * Show the PID threshold slider panel
3353    */
3354   @Override
3355   protected void modifyPID_actionPerformed()
3356   {
3357     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3358             alignPanel.getViewName());
3359     SliderPanel.showPIDSlider();
3360   }
3361
3362   /**
3363    * Show the Conservation slider panel
3364    */
3365   @Override
3366   protected void modifyConservation_actionPerformed()
3367   {
3368     SliderPanel.setConservationSlider(alignPanel,
3369             viewport.getResidueShading(), alignPanel.getViewName());
3370     SliderPanel.showConservationSlider();
3371   }
3372
3373   /**
3374    * Action on selecting or deselecting (Colour) By Conservation
3375    */
3376   @Override
3377   public void conservationMenuItem_actionPerformed(boolean selected)
3378   {
3379     modifyConservation.setEnabled(selected);
3380     viewport.setConservationSelected(selected);
3381     viewport.getResidueShading().setConservationApplied(selected);
3382
3383     changeColour(viewport.getGlobalColourScheme());
3384     if (selected)
3385     {
3386       modifyConservation_actionPerformed();
3387     }
3388     else
3389     {
3390       SliderPanel.hideConservationSlider();
3391     }
3392   }
3393
3394   /**
3395    * Action on selecting or deselecting (Colour) Above PID Threshold
3396    */
3397   @Override
3398   public void abovePIDThreshold_actionPerformed(boolean selected)
3399   {
3400     modifyPID.setEnabled(selected);
3401     viewport.setAbovePIDThreshold(selected);
3402     if (!selected)
3403     {
3404       viewport.getResidueShading().setThreshold(0,
3405               viewport.isIgnoreGapsConsensus());
3406     }
3407
3408     changeColour(viewport.getGlobalColourScheme());
3409     if (selected)
3410     {
3411       modifyPID_actionPerformed();
3412     }
3413     else
3414     {
3415       SliderPanel.hidePIDSlider();
3416     }
3417   }
3418
3419   /**
3420    * DOCUMENT ME!
3421    *
3422    * @param e
3423    *          DOCUMENT ME!
3424    */
3425   @Override
3426   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3427   {
3428     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3429     AlignmentSorter.sortByPID(viewport.getAlignment(),
3430             viewport.getAlignment().getSequenceAt(0));
3431     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3432             viewport.getAlignment()));
3433     alignPanel.paintAlignment(true, false);
3434   }
3435
3436   /**
3437    * DOCUMENT ME!
3438    *
3439    * @param e
3440    *          DOCUMENT ME!
3441    */
3442   @Override
3443   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3444   {
3445     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3446     AlignmentSorter.sortByID(viewport.getAlignment());
3447     addHistoryItem(
3448             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3449     alignPanel.paintAlignment(true, false);
3450   }
3451
3452   /**
3453    * DOCUMENT ME!
3454    *
3455    * @param e
3456    *          DOCUMENT ME!
3457    */
3458   @Override
3459   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3460   {
3461     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3462     AlignmentSorter.sortByLength(viewport.getAlignment());
3463     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3464             viewport.getAlignment()));
3465     alignPanel.paintAlignment(true, false);
3466   }
3467
3468   /**
3469    * DOCUMENT ME!
3470    *
3471    * @param e
3472    *          DOCUMENT ME!
3473    */
3474   @Override
3475   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3476   {
3477     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3478     AlignmentSorter.sortByGroup(viewport.getAlignment());
3479     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3480             viewport.getAlignment()));
3481
3482     alignPanel.paintAlignment(true, false);
3483   }
3484
3485   /**
3486    * DOCUMENT ME!
3487    *
3488    * @param e
3489    *          DOCUMENT ME!
3490    */
3491   @Override
3492   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3493   {
3494     new RedundancyPanel(alignPanel, this);
3495   }
3496
3497   /**
3498    * DOCUMENT ME!
3499    *
3500    * @param e
3501    *          DOCUMENT ME!
3502    */
3503   @Override
3504   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3505   {
3506     if ((viewport.getSelectionGroup() == null)
3507             || (viewport.getSelectionGroup().getSize() < 2))
3508     {
3509       JvOptionPane.showInternalMessageDialog(this,
3510               MessageManager.getString(
3511                       "label.you_must_select_least_two_sequences"),
3512               MessageManager.getString("label.invalid_selection"),
3513               JvOptionPane.WARNING_MESSAGE);
3514     }
3515     else
3516     {
3517       JInternalFrame frame = new JInternalFrame();
3518       frame.setContentPane(new PairwiseAlignPanel(viewport));
3519       Desktop.addInternalFrame(frame,
3520               MessageManager.getString("action.pairwise_alignment"), 600,
3521               500);
3522     }
3523   }
3524
3525   @Override
3526   public void autoCalculate_actionPerformed(ActionEvent e)
3527   {
3528     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3529     if (viewport.autoCalculateConsensus)
3530     {
3531       viewport.firePropertyChange("alignment", null,
3532               viewport.getAlignment().getSequences());
3533     }
3534   }
3535
3536   @Override
3537   public void sortByTreeOption_actionPerformed(ActionEvent e)
3538   {
3539     viewport.sortByTree = sortByTree.isSelected();
3540   }
3541
3542   @Override
3543   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3544   {
3545     viewport.followSelection = listenToViewSelections.isSelected();
3546   }
3547
3548   /**
3549    * Constructs a tree panel and adds it to the desktop
3550    *
3551    * @param type
3552    *          tree type (NJ or AV)
3553    * @param modelName
3554    *          name of score model used to compute the tree
3555    * @param options
3556    *          parameters for the distance or similarity calculation
3557    */
3558   void newTreePanel(String type, String modelName,
3559           SimilarityParamsI options)
3560   {
3561     String frameTitle = "";
3562     TreePanel tp;
3563
3564     boolean onSelection = false;
3565     if (viewport.getSelectionGroup() != null
3566             && viewport.getSelectionGroup().getSize() > 0)
3567     {
3568       SequenceGroup sg = viewport.getSelectionGroup();
3569
3570       /* Decide if the selection is a column region */
3571       for (SequenceI _s : sg.getSequences())
3572       {
3573         if (_s.getLength() < sg.getEndRes())
3574         {
3575           JvOptionPane.showMessageDialog(Desktop.desktop,
3576                   MessageManager.getString(
3577                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3578                   MessageManager.getString(
3579                           "label.sequences_selection_not_aligned"),
3580                   JvOptionPane.WARNING_MESSAGE);
3581
3582           return;
3583         }
3584       }
3585       onSelection = true;
3586     }
3587     else
3588     {
3589       if (viewport.getAlignment().getHeight() < 2)
3590       {
3591         return;
3592       }
3593     }
3594
3595     tp = new TreePanel(alignPanel, type, modelName, options);
3596     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3597
3598     frameTitle += " from ";
3599
3600     if (viewport.getViewName() != null)
3601     {
3602       frameTitle += viewport.getViewName() + " of ";
3603     }
3604
3605     frameTitle += this.title;
3606
3607     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3608   }
3609
3610   /**
3611    * DOCUMENT ME!
3612    *
3613    * @param title
3614    *          DOCUMENT ME!
3615    * @param order
3616    *          DOCUMENT ME!
3617    */
3618   public void addSortByOrderMenuItem(String title,
3619           final AlignmentOrder order)
3620   {
3621     final JMenuItem item = new JMenuItem(MessageManager
3622             .formatMessage("action.by_title_param", new Object[]
3623             { title }));
3624     sort.add(item);
3625     item.addActionListener(new java.awt.event.ActionListener()
3626     {
3627       @Override
3628       public void actionPerformed(ActionEvent e)
3629       {
3630         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3631
3632         // TODO: JBPNote - have to map order entries to curent SequenceI
3633         // pointers
3634         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3635
3636         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3637                 viewport.getAlignment()));
3638
3639         alignPanel.paintAlignment(true, false);
3640       }
3641     });
3642   }
3643
3644   /**
3645    * Add a new sort by annotation score menu item
3646    *
3647    * @param sort
3648    *          the menu to add the option to
3649    * @param scoreLabel
3650    *          the label used to retrieve scores for each sequence on the
3651    *          alignment
3652    */
3653   public void addSortByAnnotScoreMenuItem(JMenu sort,
3654           final String scoreLabel)
3655   {
3656     final JMenuItem item = new JMenuItem(scoreLabel);
3657     sort.add(item);
3658     item.addActionListener(new java.awt.event.ActionListener()
3659     {
3660       @Override
3661       public void actionPerformed(ActionEvent e)
3662       {
3663         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3664         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3665                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3666         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3667                 viewport.getAlignment()));
3668         alignPanel.paintAlignment(true, false);
3669       }
3670     });
3671   }
3672
3673   /**
3674    * last hash for alignment's annotation array - used to minimise cost of
3675    * rebuild.
3676    */
3677   protected int _annotationScoreVectorHash;
3678
3679   /**
3680    * search the alignment and rebuild the sort by annotation score submenu the
3681    * last alignment annotation vector hash is stored to minimize cost of
3682    * rebuilding in subsequence calls.
3683    *
3684    */
3685   @Override
3686   public void buildSortByAnnotationScoresMenu()
3687   {
3688     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3689     {
3690       return;
3691     }
3692
3693     if (viewport.getAlignment().getAlignmentAnnotation()
3694             .hashCode() != _annotationScoreVectorHash)
3695     {
3696       sortByAnnotScore.removeAll();
3697       // almost certainly a quicker way to do this - but we keep it simple
3698       Hashtable scoreSorts = new Hashtable();
3699       AlignmentAnnotation aann[];
3700       for (SequenceI sqa : viewport.getAlignment().getSequences())
3701       {
3702         aann = sqa.getAnnotation();
3703         for (int i = 0; aann != null && i < aann.length; i++)
3704         {
3705           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3706           {
3707             scoreSorts.put(aann[i].label, aann[i].label);
3708           }
3709         }
3710       }
3711       Enumeration labels = scoreSorts.keys();
3712       while (labels.hasMoreElements())
3713       {
3714         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3715                 (String) labels.nextElement());
3716       }
3717       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3718       scoreSorts.clear();
3719
3720       _annotationScoreVectorHash = viewport.getAlignment()
3721               .getAlignmentAnnotation().hashCode();
3722     }
3723   }
3724
3725   /**
3726    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3727    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3728    * call. Listeners are added to remove the menu item when the treePanel is
3729    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3730    * modified.
3731    */
3732   @Override
3733   public void buildTreeSortMenu()
3734   {
3735     sortByTreeMenu.removeAll();
3736
3737     List<Component> comps = PaintRefresher.components
3738             .get(viewport.getSequenceSetId());
3739     List<TreePanel> treePanels = new ArrayList<>();
3740     for (Component comp : comps)
3741     {
3742       if (comp instanceof TreePanel)
3743       {
3744         treePanels.add((TreePanel) comp);
3745       }
3746     }
3747
3748     if (treePanels.size() < 1)
3749     {
3750       sortByTreeMenu.setVisible(false);
3751       return;
3752     }
3753
3754     sortByTreeMenu.setVisible(true);
3755
3756     for (final TreePanel tp : treePanels)
3757     {
3758       final JMenuItem item = new JMenuItem(tp.getTitle());
3759       item.addActionListener(new java.awt.event.ActionListener()
3760       {
3761         @Override
3762         public void actionPerformed(ActionEvent e)
3763         {
3764           tp.sortByTree_actionPerformed();
3765           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3766
3767         }
3768       });
3769
3770       sortByTreeMenu.add(item);
3771     }
3772   }
3773
3774   public boolean sortBy(AlignmentOrder alorder, String undoname)
3775   {
3776     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3777     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3778     if (undoname != null)
3779     {
3780       addHistoryItem(new OrderCommand(undoname, oldOrder,
3781               viewport.getAlignment()));
3782     }
3783     alignPanel.paintAlignment(true, false);
3784     return true;
3785   }
3786
3787   /**
3788    * Work out whether the whole set of sequences or just the selected set will
3789    * be submitted for multiple alignment.
3790    *
3791    */
3792   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3793   {
3794     // Now, check we have enough sequences
3795     AlignmentView msa = null;
3796
3797     if ((viewport.getSelectionGroup() != null)
3798             && (viewport.getSelectionGroup().getSize() > 1))
3799     {
3800       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3801       // some common interface!
3802       /*
3803        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3804        * SequenceI[sz = seqs.getSize(false)];
3805        *
3806        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3807        * seqs.getSequenceAt(i); }
3808        */
3809       msa = viewport.getAlignmentView(true);
3810     }
3811     else if (viewport.getSelectionGroup() != null
3812             && viewport.getSelectionGroup().getSize() == 1)
3813     {
3814       int option = JvOptionPane.showConfirmDialog(this,
3815               MessageManager.getString("warn.oneseq_msainput_selection"),
3816               MessageManager.getString("label.invalid_selection"),
3817               JvOptionPane.OK_CANCEL_OPTION);
3818       if (option == JvOptionPane.OK_OPTION)
3819       {
3820         msa = viewport.getAlignmentView(false);
3821       }
3822     }
3823     else
3824     {
3825       msa = viewport.getAlignmentView(false);
3826     }
3827     return msa;
3828   }
3829
3830   /**
3831    * Decides what is submitted to a secondary structure prediction service: the
3832    * first sequence in the alignment, or in the current selection, or, if the
3833    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3834    * region or the whole alignment. (where the first sequence in the set is the
3835    * one that the prediction will be for).
3836    */
3837   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3838   {
3839     AlignmentView seqs = null;
3840
3841     if ((viewport.getSelectionGroup() != null)
3842             && (viewport.getSelectionGroup().getSize() > 0))
3843     {
3844       seqs = viewport.getAlignmentView(true);
3845     }
3846     else
3847     {
3848       seqs = viewport.getAlignmentView(false);
3849     }
3850     // limit sequences - JBPNote in future - could spawn multiple prediction
3851     // jobs
3852     // TODO: viewport.getAlignment().isAligned is a global state - the local
3853     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3854     if (!viewport.getAlignment().isAligned(false))
3855     {
3856       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3857       // TODO: if seqs.getSequences().length>1 then should really have warned
3858       // user!
3859
3860     }
3861     return seqs;
3862   }
3863
3864   /**
3865    * DOCUMENT ME!
3866    *
3867    * @param e
3868    *          DOCUMENT ME!
3869    */
3870   @Override
3871   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3872   {
3873     // Pick the tree file
3874     JalviewFileChooser chooser = new JalviewFileChooser(
3875             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3876     chooser.setFileView(new JalviewFileView());
3877     chooser.setDialogTitle(
3878             MessageManager.getString("label.select_newick_like_tree_file"));
3879     chooser.setToolTipText(
3880             MessageManager.getString("label.load_tree_file"));
3881
3882     int value = chooser.showOpenDialog(null);
3883
3884     if (value == JalviewFileChooser.APPROVE_OPTION)
3885     {
3886       String filePath = chooser.getSelectedFile().getPath();
3887       Cache.setProperty("LAST_DIRECTORY", filePath);
3888       NewickFile fin = null;
3889       try
3890       {
3891         fin = new NewickFile(filePath, DataSourceType.FILE);
3892         viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3893       } catch (Exception ex)
3894       {
3895         JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3896                 MessageManager.getString("label.problem_reading_tree_file"),
3897                 JvOptionPane.WARNING_MESSAGE);
3898         ex.printStackTrace();
3899       }
3900       if (fin != null && fin.hasWarningMessage())
3901       {
3902         JvOptionPane.showMessageDialog(Desktop.desktop,
3903                 fin.getWarningMessage(),
3904                 MessageManager
3905                         .getString("label.possible_problem_with_tree_file"),
3906                 JvOptionPane.WARNING_MESSAGE);
3907       }
3908     }
3909   }
3910
3911   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
3912   {
3913     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
3914   }
3915
3916   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
3917           int h, int x, int y)
3918   {
3919     return showNewickTree(nf, treeTitle, null, w, h, x, y);
3920   }
3921
3922   /**
3923    * Add a treeviewer for the tree extracted from a Newick file object to the
3924    * current alignment view
3925    *
3926    * @param nf
3927    *          the tree
3928    * @param title
3929    *          tree viewer title
3930    * @param input
3931    *          Associated alignment input data (or null)
3932    * @param w
3933    *          width
3934    * @param h
3935    *          height
3936    * @param x
3937    *          position
3938    * @param y
3939    *          position
3940    * @return TreePanel handle
3941    */
3942   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
3943           AlignmentView input, int w, int h, int x, int y)
3944   {
3945     TreePanel tp = null;
3946
3947     try
3948     {
3949       nf.parse();
3950
3951       if (nf.getTree() != null)
3952       {
3953         tp = new TreePanel(alignPanel, nf, treeTitle, input);
3954
3955         tp.setSize(w, h);
3956
3957         if (x > 0 && y > 0)
3958         {
3959           tp.setLocation(x, y);
3960         }
3961
3962         Desktop.addInternalFrame(tp, treeTitle, w, h);
3963       }
3964     } catch (Exception ex)
3965     {
3966       ex.printStackTrace();
3967     }
3968
3969     return tp;
3970   }
3971
3972   private boolean buildingMenu = false;
3973
3974   /**
3975    * Generates menu items and listener event actions for web service clients
3976    *
3977    */
3978   public void BuildWebServiceMenu()
3979   {
3980     while (buildingMenu)
3981     {
3982       try
3983       {
3984         System.err.println("Waiting for building menu to finish.");
3985         Thread.sleep(10);
3986       } catch (Exception e)
3987       {
3988       }
3989     }
3990     final AlignFrame me = this;
3991     buildingMenu = true;
3992     new Thread(new Runnable()
3993     {
3994       @Override
3995       public void run()
3996       {
3997         final List<JMenuItem> legacyItems = new ArrayList<>();
3998         try
3999         {
4000           // System.err.println("Building ws menu again "
4001           // + Thread.currentThread());
4002           // TODO: add support for context dependent disabling of services based
4003           // on
4004           // alignment and current selection
4005           // TODO: add additional serviceHandle parameter to specify abstract
4006           // handler
4007           // class independently of AbstractName
4008           // TODO: add in rediscovery GUI function to restart discoverer
4009           // TODO: group services by location as well as function and/or
4010           // introduce
4011           // object broker mechanism.
4012           final Vector<JMenu> wsmenu = new Vector<>();
4013           final IProgressIndicator af = me;
4014
4015           /*
4016            * do not i18n these strings - they are hard-coded in class
4017            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4018            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4019            */
4020           final JMenu msawsmenu = new JMenu("Alignment");
4021           final JMenu secstrmenu = new JMenu(
4022                   "Secondary Structure Prediction");
4023           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4024           final JMenu analymenu = new JMenu("Analysis");
4025           final JMenu dismenu = new JMenu("Protein Disorder");
4026           // JAL-940 - only show secondary structure prediction services from
4027           // the legacy server
4028           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4029               // &&
4030           Discoverer.services != null && (Discoverer.services.size() > 0))
4031           {
4032             // TODO: refactor to allow list of AbstractName/Handler bindings to
4033             // be
4034             // stored or retrieved from elsewhere
4035             // No MSAWS used any more:
4036             // Vector msaws = null; // (Vector)
4037             // Discoverer.services.get("MsaWS");
4038             Vector secstrpr = (Vector) Discoverer.services
4039                     .get("SecStrPred");
4040             if (secstrpr != null)
4041             {
4042               // Add any secondary structure prediction services
4043               for (int i = 0, j = secstrpr.size(); i < j; i++)
4044               {
4045                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4046                         .get(i);
4047                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4048                         .getServiceClient(sh);
4049                 int p = secstrmenu.getItemCount();
4050                 impl.attachWSMenuEntry(secstrmenu, me);
4051                 int q = secstrmenu.getItemCount();
4052                 for (int litm = p; litm < q; litm++)
4053                 {
4054                   legacyItems.add(secstrmenu.getItem(litm));
4055                 }
4056               }
4057             }
4058           }
4059
4060           // Add all submenus in the order they should appear on the web
4061           // services menu
4062           wsmenu.add(msawsmenu);
4063           wsmenu.add(secstrmenu);
4064           wsmenu.add(dismenu);
4065           wsmenu.add(analymenu);
4066           // No search services yet
4067           // wsmenu.add(seqsrchmenu);
4068
4069           javax.swing.SwingUtilities.invokeLater(new Runnable()
4070           {
4071             @Override
4072             public void run()
4073             {
4074               try
4075               {
4076                 webService.removeAll();
4077                 // first, add discovered services onto the webservices menu
4078                 if (wsmenu.size() > 0)
4079                 {
4080                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4081                   {
4082                     webService.add(wsmenu.get(i));
4083                   }
4084                 }
4085                 else
4086                 {
4087                   webService.add(me.webServiceNoServices);
4088                 }
4089                 // TODO: move into separate menu builder class.
4090                 boolean new_sspred = false;
4091                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4092                 {
4093                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4094                   if (jws2servs != null)
4095                   {
4096                     if (jws2servs.hasServices())
4097                     {
4098                       jws2servs.attachWSMenuEntry(webService, me);
4099                       for (Jws2Instance sv : jws2servs.getServices())
4100                       {
4101                         if (sv.description.toLowerCase().contains("jpred"))
4102                         {
4103                           for (JMenuItem jmi : legacyItems)
4104                           {
4105                             jmi.setVisible(false);
4106                           }
4107                         }
4108                       }
4109
4110                     }
4111                     if (jws2servs.isRunning())
4112                     {
4113                       JMenuItem tm = new JMenuItem(
4114                               "Still discovering JABA Services");
4115                       tm.setEnabled(false);
4116                       webService.add(tm);
4117                     }
4118                   }
4119                 }
4120                 build_urlServiceMenu(me.webService);
4121                 build_fetchdbmenu(webService);
4122                 for (JMenu item : wsmenu)
4123                 {
4124                   if (item.getItemCount() == 0)
4125                   {
4126                     item.setEnabled(false);
4127                   }
4128                   else
4129                   {
4130                     item.setEnabled(true);
4131                   }
4132                 }
4133               } catch (Exception e)
4134               {
4135                 Cache.log.debug(
4136                         "Exception during web service menu building process.",
4137                         e);
4138               }
4139             }
4140           });
4141         } catch (Exception e)
4142         {
4143         }
4144         buildingMenu = false;
4145       }
4146     }).start();
4147
4148   }
4149
4150   /**
4151    * construct any groupURL type service menu entries.
4152    *
4153    * @param webService
4154    */
4155   private void build_urlServiceMenu(JMenu webService)
4156   {
4157     // TODO: remove this code when 2.7 is released
4158     // DEBUG - alignmentView
4159     /*
4160      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4161      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4162      *
4163      * @Override public void actionPerformed(ActionEvent e) {
4164      * jalview.datamodel.AlignmentView
4165      * .testSelectionViews(af.viewport.getAlignment(),
4166      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4167      *
4168      * }); webService.add(testAlView);
4169      */
4170     // TODO: refactor to RestClient discoverer and merge menu entries for
4171     // rest-style services with other types of analysis/calculation service
4172     // SHmmr test client - still being implemented.
4173     // DEBUG - alignmentView
4174
4175     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4176             .getRestClients())
4177     {
4178       client.attachWSMenuEntry(
4179               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4180               this);
4181     }
4182   }
4183
4184   /**
4185    * Searches the alignment sequences for xRefs and builds the Show
4186    * Cross-References menu (formerly called Show Products), with database
4187    * sources for which cross-references are found (protein sources for a
4188    * nucleotide alignment and vice versa)
4189    *
4190    * @return true if Show Cross-references menu should be enabled
4191    */
4192   public boolean canShowProducts()
4193   {
4194     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4195     AlignmentI dataset = viewport.getAlignment().getDataset();
4196
4197     showProducts.removeAll();
4198     final boolean dna = viewport.getAlignment().isNucleotide();
4199
4200     if (seqs == null || seqs.length == 0)
4201     {
4202       // nothing to see here.
4203       return false;
4204     }
4205
4206     boolean showp = false;
4207     try
4208     {
4209       List<String> ptypes = new CrossRef(seqs, dataset)
4210               .findXrefSourcesForSequences(dna);
4211
4212       for (final String source : ptypes)
4213       {
4214         showp = true;
4215         final AlignFrame af = this;
4216         JMenuItem xtype = new JMenuItem(source);
4217         xtype.addActionListener(new ActionListener()
4218         {
4219           @Override
4220           public void actionPerformed(ActionEvent e)
4221           {
4222             showProductsFor(af.viewport.getSequenceSelection(), dna,
4223                     source);
4224           }
4225         });
4226         showProducts.add(xtype);
4227       }
4228       showProducts.setVisible(showp);
4229       showProducts.setEnabled(showp);
4230     } catch (Exception e)
4231     {
4232       Cache.log.warn(
4233               "canShowProducts threw an exception - please report to help@jalview.org",
4234               e);
4235       return false;
4236     }
4237     return showp;
4238   }
4239
4240   /**
4241    * Finds and displays cross-references for the selected sequences (protein
4242    * products for nucleotide sequences, dna coding sequences for peptides).
4243    *
4244    * @param sel
4245    *          the sequences to show cross-references for
4246    * @param dna
4247    *          true if from a nucleotide alignment (so showing proteins)
4248    * @param source
4249    *          the database to show cross-references for
4250    */
4251   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4252           final String source)
4253   {
4254     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4255             .start();
4256   }
4257
4258   /**
4259    * Construct and display a new frame containing the translation of this
4260    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4261    */
4262   @Override
4263   public void showTranslation_actionPerformed(ActionEvent e)
4264   {
4265     AlignmentI al = null;
4266     try
4267     {
4268       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4269
4270       al = dna.translateCdna();
4271     } catch (Exception ex)
4272     {
4273       jalview.bin.Cache.log.error(
4274               "Exception during translation. Please report this !", ex);
4275       final String msg = MessageManager.getString(
4276               "label.error_when_translating_sequences_submit_bug_report");
4277       final String errorTitle = MessageManager
4278               .getString("label.implementation_error")
4279               + MessageManager.getString("label.translation_failed");
4280       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4281               JvOptionPane.ERROR_MESSAGE);
4282       return;
4283     }
4284     if (al == null || al.getHeight() == 0)
4285     {
4286       final String msg = MessageManager.getString(
4287               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4288       final String errorTitle = MessageManager
4289               .getString("label.translation_failed");
4290       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4291               JvOptionPane.WARNING_MESSAGE);
4292     }
4293     else
4294     {
4295       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4296       af.setFileFormat(this.currentFileFormat);
4297       final String newTitle = MessageManager
4298               .formatMessage("label.translation_of_params", new Object[]
4299               { this.getTitle() });
4300       af.setTitle(newTitle);
4301       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4302       {
4303         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4304         viewport.openSplitFrame(af, new Alignment(seqs));
4305       }
4306       else
4307       {
4308         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4309                 DEFAULT_HEIGHT);
4310       }
4311     }
4312   }
4313
4314   /**
4315    * Set the file format
4316    *
4317    * @param format
4318    */
4319   public void setFileFormat(FileFormatI format)
4320   {
4321     this.currentFileFormat = format;
4322   }
4323
4324   /**
4325    * Try to load a features file onto the alignment.
4326    *
4327    * @param file
4328    *          contents or path to retrieve file
4329    * @param sourceType
4330    *          access mode of file (see jalview.io.AlignFile)
4331    * @return true if features file was parsed correctly.
4332    */
4333   public boolean parseFeaturesFile(String file, DataSourceType sourceType)
4334   {
4335     return avc.parseFeaturesFile(file, sourceType,
4336             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4337
4338   }
4339
4340   @Override
4341   public void refreshFeatureUI(boolean enableIfNecessary)
4342   {
4343     // note - currently this is only still here rather than in the controller
4344     // because of the featureSettings hard reference that is yet to be
4345     // abstracted
4346     if (enableIfNecessary)
4347     {
4348       viewport.setShowSequenceFeatures(true);
4349       showSeqFeatures.setSelected(true);
4350     }
4351
4352   }
4353
4354   @Override
4355   public void dragEnter(DropTargetDragEvent evt)
4356   {
4357   }
4358
4359   @Override
4360   public void dragExit(DropTargetEvent evt)
4361   {
4362   }
4363
4364   @Override
4365   public void dragOver(DropTargetDragEvent evt)
4366   {
4367   }
4368
4369   @Override
4370   public void dropActionChanged(DropTargetDragEvent evt)
4371   {
4372   }
4373
4374   @Override
4375   public void drop(DropTargetDropEvent evt)
4376   {
4377     // JAL-1552 - acceptDrop required before getTransferable call for
4378     // Java's Transferable for native dnd
4379     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4380     Transferable t = evt.getTransferable();
4381     final AlignFrame thisaf = this;
4382     final List<String> files = new ArrayList<>();
4383     List<DataSourceType> protocols = new ArrayList<>();
4384
4385     try
4386     {
4387       Desktop.transferFromDropTarget(files, protocols, evt, t);
4388     } catch (Exception e)
4389     {
4390       e.printStackTrace();
4391     }
4392     if (files != null)
4393     {
4394       new Thread(new Runnable()
4395       {
4396         @Override
4397         public void run()
4398         {
4399           try
4400           {
4401             // check to see if any of these files have names matching sequences
4402             // in
4403             // the alignment
4404             SequenceIdMatcher idm = new SequenceIdMatcher(
4405                     viewport.getAlignment().getSequencesArray());
4406             /**
4407              * Object[] { String,SequenceI}
4408              */
4409             ArrayList<Object[]> filesmatched = new ArrayList<>();
4410             ArrayList<String> filesnotmatched = new ArrayList<>();
4411             for (int i = 0; i < files.size(); i++)
4412             {
4413               String file = files.get(i).toString();
4414               String pdbfn = "";
4415               DataSourceType protocol = FormatAdapter.checkProtocol(file);
4416               if (protocol == DataSourceType.FILE)
4417               {
4418                 File fl = new File(file);
4419                 pdbfn = fl.getName();
4420               }
4421               else if (protocol == DataSourceType.URL)
4422               {
4423                 URL url = new URL(file);
4424                 pdbfn = url.getFile();
4425               }
4426               if (pdbfn.length() > 0)
4427               {
4428                 // attempt to find a match in the alignment
4429                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4430                 int l = 0, c = pdbfn.indexOf(".");
4431                 while (mtch == null && c != -1)
4432                 {
4433                   do
4434                   {
4435                     l = c;
4436                   } while ((c = pdbfn.indexOf(".", l)) > l);
4437                   if (l > -1)
4438                   {
4439                     pdbfn = pdbfn.substring(0, l);
4440                   }
4441                   mtch = idm.findAllIdMatches(pdbfn);
4442                 }
4443                 if (mtch != null)
4444                 {
4445                   FileFormatI type = null;
4446                   try
4447                   {
4448                     type = new IdentifyFile().identify(file, protocol);
4449                   } catch (Exception ex)
4450                   {
4451                     type = null;
4452                   }
4453                   if (type != null && type.isStructureFile())
4454                   {
4455                     filesmatched.add(new Object[] { file, protocol, mtch });
4456                     continue;
4457                   }
4458                 }
4459                 // File wasn't named like one of the sequences or wasn't a PDB
4460                 // file.
4461                 filesnotmatched.add(file);
4462               }
4463             }
4464             int assocfiles = 0;
4465             if (filesmatched.size() > 0)
4466             {
4467               boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4468               if (!autoAssociate)
4469               {
4470                 String msg = MessageManager.formatMessage(
4471                         "label.automatically_associate_structure_files_with_sequences_same_name",
4472                         new Object[]
4473                         { Integer.valueOf(filesmatched.size())
4474                                 .toString() });
4475                 String ttl = MessageManager.getString(
4476                         "label.automatically_associate_structure_files_by_name");
4477                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4478                         ttl, JvOptionPane.YES_NO_OPTION);
4479                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4480               }
4481               if (autoAssociate)
4482               {
4483                 for (Object[] fm : filesmatched)
4484                 {
4485                   // try and associate
4486                   // TODO: may want to set a standard ID naming formalism for
4487                   // associating PDB files which have no IDs.
4488                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4489                   {
4490                     PDBEntry pe = new AssociatePdbFileWithSeq()
4491                             .associatePdbWithSeq((String) fm[0],
4492                                     (DataSourceType) fm[1], toassoc, false,
4493                                     Desktop.instance);
4494                     if (pe != null)
4495                     {
4496                       System.err.println("Associated file : "
4497                               + ((String) fm[0]) + " with "
4498                               + toassoc.getDisplayId(true));
4499                       assocfiles++;
4500                     }
4501                   }
4502                   // TODO: do we need to update overview ? only if features are
4503                   // shown I guess
4504                   alignPanel.paintAlignment(true, false);
4505                 }
4506               }
4507               else
4508               {
4509                 /*
4510                  * add declined structures as sequences
4511                  */
4512                 for (Object[] o : filesmatched)
4513                 {
4514                   filesnotmatched.add((String) o[0]);
4515                 }
4516               }
4517             }
4518             if (filesnotmatched.size() > 0)
4519             {
4520               if (assocfiles > 0 && (Cache.getDefault(
4521                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4522                       || JvOptionPane.showConfirmDialog(thisaf,
4523                               "<html>" + MessageManager.formatMessage(
4524                                       "label.ignore_unmatched_dropped_files_info",
4525                                       new Object[]
4526                                       { Integer.valueOf(
4527                                               filesnotmatched.size())
4528                                               .toString() })
4529                                       + "</html>",
4530                               MessageManager.getString(
4531                                       "label.ignore_unmatched_dropped_files"),
4532                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4533               {
4534                 return;
4535               }
4536               for (String fn : filesnotmatched)
4537               {
4538                 loadJalviewDataFile(fn, null, null, null);
4539               }
4540
4541             }
4542           } catch (Exception ex)
4543           {
4544             ex.printStackTrace();
4545           }
4546         }
4547       }).start();
4548     }
4549   }
4550
4551   /**
4552    * Attempt to load a "dropped" file or URL string, by testing in turn for
4553    * <ul>
4554    * <li>an Annotation file</li>
4555    * <li>a JNet file</li>
4556    * <li>a features file</li>
4557    * <li>else try to interpret as an alignment file</li>
4558    * </ul>
4559    *
4560    * @param file
4561    *          either a filename or a URL string.
4562    */
4563   public void loadJalviewDataFile(String file, DataSourceType sourceType,
4564           FileFormatI format, SequenceI assocSeq)
4565   {
4566     try
4567     {
4568       if (sourceType == null)
4569       {
4570         sourceType = FormatAdapter.checkProtocol(file);
4571       }
4572       // if the file isn't identified, or not positively identified as some
4573       // other filetype (PFAM is default unidentified alignment file type) then
4574       // try to parse as annotation.
4575       boolean isAnnotation = (format == null
4576               || FileFormat.Pfam.equals(format))
4577                       ? new AnnotationFile().annotateAlignmentView(viewport,
4578                               file, sourceType)
4579                       : false;
4580
4581       if (!isAnnotation)
4582       {
4583         // first see if its a T-COFFEE score file
4584         TCoffeeScoreFile tcf = null;
4585         try
4586         {
4587           tcf = new TCoffeeScoreFile(file, sourceType);
4588           if (tcf.isValid())
4589           {
4590             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4591             {
4592               buildColourMenu();
4593               changeColour(
4594                       new TCoffeeColourScheme(viewport.getAlignment()));
4595               isAnnotation = true;
4596               statusBar.setText(MessageManager.getString(
4597                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4598             }
4599             else
4600             {
4601               // some problem - if no warning its probable that the ID matching
4602               // process didn't work
4603               JvOptionPane.showMessageDialog(Desktop.desktop,
4604                       tcf.getWarningMessage() == null
4605                               ? MessageManager.getString(
4606                                       "label.check_file_matches_sequence_ids_alignment")
4607                               : tcf.getWarningMessage(),
4608                       MessageManager.getString(
4609                               "label.problem_reading_tcoffee_score_file"),
4610                       JvOptionPane.WARNING_MESSAGE);
4611             }
4612           }
4613           else
4614           {
4615             tcf = null;
4616           }
4617         } catch (Exception x)
4618         {
4619           Cache.log.debug(
4620                   "Exception when processing data source as T-COFFEE score file",
4621                   x);
4622           tcf = null;
4623         }
4624         if (tcf == null)
4625         {
4626           // try to see if its a JNet 'concise' style annotation file *before*
4627           // we
4628           // try to parse it as a features file
4629           if (format == null)
4630           {
4631             format = new IdentifyFile().identify(file, sourceType);
4632           }
4633           if (FileFormat.ScoreMatrix == format)
4634           {
4635             ScoreMatrixFile sm = new ScoreMatrixFile(
4636                     new FileParse(file, sourceType));
4637             sm.parse();
4638             // todo: i18n this message
4639             statusBar.setText(MessageManager.formatMessage(
4640                     "label.successfully_loaded_matrix",
4641                     sm.getMatrixName()));
4642           }
4643           else if (FileFormat.Jnet.equals(format))
4644           {
4645             JPredFile predictions = new JPredFile(file, sourceType);
4646             new JnetAnnotationMaker();
4647             JnetAnnotationMaker.add_annotation(predictions,
4648                     viewport.getAlignment(), 0, false);
4649             viewport.getAlignment().setupJPredAlignment();
4650             isAnnotation = true;
4651           }
4652           // else if (IdentifyFile.FeaturesFile.equals(format))
4653           else if (FileFormat.Features.equals(format))
4654           {
4655             if (parseFeaturesFile(file, sourceType))
4656             {
4657               alignPanel.paintAlignment(true, true);
4658             }
4659           }
4660           else
4661           {
4662             new FileLoader().LoadFile(viewport, file, sourceType, format);
4663           }
4664         }
4665       }
4666       if (isAnnotation)
4667       {
4668
4669         alignPanel.adjustAnnotationHeight();
4670         viewport.updateSequenceIdColours();
4671         buildSortByAnnotationScoresMenu();
4672         alignPanel.paintAlignment(true, true);
4673       }
4674     } catch (Exception ex)
4675     {
4676       ex.printStackTrace();
4677     } catch (OutOfMemoryError oom)
4678     {
4679       try
4680       {
4681         System.gc();
4682       } catch (Exception x)
4683       {
4684       }
4685       new OOMWarning(
4686               "loading data "
4687                       + (sourceType != null
4688                               ? (sourceType == DataSourceType.PASTE
4689                                       ? "from clipboard."
4690                                       : "using " + sourceType + " from "
4691                                               + file)
4692                               : ".")
4693                       + (format != null
4694                               ? "(parsing as '" + format + "' file)"
4695                               : ""),
4696               oom, Desktop.desktop);
4697     }
4698   }
4699
4700   /**
4701    * Method invoked by the ChangeListener on the tabbed pane, in other words
4702    * when a different tabbed pane is selected by the user or programmatically.
4703    */
4704   @Override
4705   public void tabSelectionChanged(int index)
4706   {
4707     if (index > -1)
4708     {
4709       alignPanel = alignPanels.get(index);
4710       viewport = alignPanel.av;
4711       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4712       setMenusFromViewport(viewport);
4713     }
4714
4715     /*
4716      * 'focus' any colour slider that is open to the selected viewport
4717      */
4718     if (viewport.getConservationSelected())
4719     {
4720       SliderPanel.setConservationSlider(alignPanel,
4721               viewport.getResidueShading(), alignPanel.getViewName());
4722     }
4723     else
4724     {
4725       SliderPanel.hideConservationSlider();
4726     }
4727     if (viewport.getAbovePIDThreshold())
4728     {
4729       SliderPanel.setPIDSliderSource(alignPanel,
4730               viewport.getResidueShading(), alignPanel.getViewName());
4731     }
4732     else
4733     {
4734       SliderPanel.hidePIDSlider();
4735     }
4736
4737     /*
4738      * If there is a frame linked to this one in a SplitPane, switch it to the
4739      * same view tab index. No infinite recursion of calls should happen, since
4740      * tabSelectionChanged() should not get invoked on setting the selected
4741      * index to an unchanged value. Guard against setting an invalid index
4742      * before the new view peer tab has been created.
4743      */
4744     final AlignViewportI peer = viewport.getCodingComplement();
4745     if (peer != null)
4746     {
4747       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4748               .getAlignPanel().alignFrame;
4749       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4750       {
4751         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4752       }
4753     }
4754   }
4755
4756   /**
4757    * On right mouse click on view tab, prompt for and set new view name.
4758    */
4759   @Override
4760   public void tabbedPane_mousePressed(MouseEvent e)
4761   {
4762     if (e.isPopupTrigger())
4763     {
4764       String msg = MessageManager.getString("label.enter_view_name");
4765       String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
4766               JvOptionPane.QUESTION_MESSAGE);
4767
4768       if (reply != null)
4769       {
4770         viewport.setViewName(reply);
4771         // TODO warn if reply is in getExistingViewNames()?
4772         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4773       }
4774     }
4775   }
4776
4777   public AlignViewport getCurrentView()
4778   {
4779     return viewport;
4780   }
4781
4782   /**
4783    * Open the dialog for regex description parsing.
4784    */
4785   @Override
4786   protected void extractScores_actionPerformed(ActionEvent e)
4787   {
4788     ParseProperties pp = new jalview.analysis.ParseProperties(
4789             viewport.getAlignment());
4790     // TODO: verify regex and introduce GUI dialog for version 2.5
4791     // if (pp.getScoresFromDescription("col", "score column ",
4792     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4793     // true)>0)
4794     if (pp.getScoresFromDescription("description column",
4795             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4796     {
4797       buildSortByAnnotationScoresMenu();
4798     }
4799   }
4800
4801   /*
4802    * (non-Javadoc)
4803    *
4804    * @see
4805    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4806    * )
4807    */
4808   @Override
4809   protected void showDbRefs_actionPerformed(ActionEvent e)
4810   {
4811     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4812   }
4813
4814   /*
4815    * (non-Javadoc)
4816    *
4817    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4818    * ActionEvent)
4819    */
4820   @Override
4821   protected void showNpFeats_actionPerformed(ActionEvent e)
4822   {
4823     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4824   }
4825
4826   /**
4827    * find the viewport amongst the tabs in this alignment frame and close that
4828    * tab
4829    *
4830    * @param av
4831    */
4832   public boolean closeView(AlignViewportI av)
4833   {
4834     if (viewport == av)
4835     {
4836       this.closeMenuItem_actionPerformed(false);
4837       return true;
4838     }
4839     Component[] comp = tabbedPane.getComponents();
4840     for (int i = 0; comp != null && i < comp.length; i++)
4841     {
4842       if (comp[i] instanceof AlignmentPanel)
4843       {
4844         if (((AlignmentPanel) comp[i]).av == av)
4845         {
4846           // close the view.
4847           closeView((AlignmentPanel) comp[i]);
4848           return true;
4849         }
4850       }
4851     }
4852     return false;
4853   }
4854
4855   protected void build_fetchdbmenu(JMenu webService)
4856   {
4857     // Temporary hack - DBRef Fetcher always top level ws entry.
4858     // TODO We probably want to store a sequence database checklist in
4859     // preferences and have checkboxes.. rather than individual sources selected
4860     // here
4861     final JMenu rfetch = new JMenu(
4862             MessageManager.getString("action.fetch_db_references"));
4863     rfetch.setToolTipText(MessageManager.getString(
4864             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4865     webService.add(rfetch);
4866
4867     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4868             MessageManager.getString("option.trim_retrieved_seqs"));
4869     trimrs.setToolTipText(
4870             MessageManager.getString("label.trim_retrieved_sequences"));
4871     trimrs.setSelected(
4872             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4873     trimrs.addActionListener(new ActionListener()
4874     {
4875       @Override
4876       public void actionPerformed(ActionEvent e)
4877       {
4878         trimrs.setSelected(trimrs.isSelected());
4879         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4880                 Boolean.valueOf(trimrs.isSelected()).toString());
4881       };
4882     });
4883     rfetch.add(trimrs);
4884     JMenuItem fetchr = new JMenuItem(
4885             MessageManager.getString("label.standard_databases"));
4886     fetchr.setToolTipText(
4887             MessageManager.getString("label.fetch_embl_uniprot"));
4888     fetchr.addActionListener(new ActionListener()
4889     {
4890
4891       @Override
4892       public void actionPerformed(ActionEvent e)
4893       {
4894         new Thread(new Runnable()
4895         {
4896           @Override
4897           public void run()
4898           {
4899             boolean isNucleotide = alignPanel.alignFrame.getViewport()
4900                     .getAlignment().isNucleotide();
4901             DBRefFetcher dbRefFetcher = new DBRefFetcher(
4902                     alignPanel.av.getSequenceSelection(),
4903                     alignPanel.alignFrame, null,
4904                     alignPanel.alignFrame.featureSettings, isNucleotide);
4905             dbRefFetcher.addListener(new FetchFinishedListenerI()
4906             {
4907               @Override
4908               public void finished()
4909               {
4910                 AlignFrame.this.setMenusForViewport();
4911               }
4912             });
4913             dbRefFetcher.fetchDBRefs(false);
4914           }
4915         }).start();
4916
4917       }
4918
4919     });
4920     rfetch.add(fetchr);
4921     final AlignFrame me = this;
4922     new Thread(new Runnable()
4923     {
4924       @Override
4925       public void run()
4926       {
4927         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
4928                 .getSequenceFetcherSingleton(me);
4929         javax.swing.SwingUtilities.invokeLater(new Runnable()
4930         {
4931           @Override
4932           public void run()
4933           {
4934             String[] dbclasses = sf.getOrderedSupportedSources();
4935             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
4936             // jalview.util.QuickSort.sort(otherdb, otherdb);
4937             List<DbSourceProxy> otherdb;
4938             JMenu dfetch = new JMenu();
4939             JMenu ifetch = new JMenu();
4940             JMenuItem fetchr = null;
4941             int comp = 0, icomp = 0, mcomp = 15;
4942             String mname = null;
4943             int dbi = 0;
4944             for (String dbclass : dbclasses)
4945             {
4946               otherdb = sf.getSourceProxy(dbclass);
4947               // add a single entry for this class, or submenu allowing 'fetch
4948               // all' or pick one
4949               if (otherdb == null || otherdb.size() < 1)
4950               {
4951                 continue;
4952               }
4953               // List<DbSourceProxy> dbs=otherdb;
4954               // otherdb=new ArrayList<DbSourceProxy>();
4955               // for (DbSourceProxy db:dbs)
4956               // {
4957               // if (!db.isA(DBRefSource.ALIGNMENTDB)
4958               // }
4959               if (mname == null)
4960               {
4961                 mname = "From " + dbclass;
4962               }
4963               if (otherdb.size() == 1)
4964               {
4965                 final DbSourceProxy[] dassource = otherdb
4966                         .toArray(new DbSourceProxy[0]);
4967                 DbSourceProxy src = otherdb.get(0);
4968                 fetchr = new JMenuItem(src.getDbSource());
4969                 fetchr.addActionListener(new ActionListener()
4970                 {
4971
4972                   @Override
4973                   public void actionPerformed(ActionEvent e)
4974                   {
4975                     new Thread(new Runnable()
4976                     {
4977
4978                       @Override
4979                       public void run()
4980                       {
4981                         boolean isNucleotide = alignPanel.alignFrame
4982                                 .getViewport().getAlignment()
4983                                 .isNucleotide();
4984                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
4985                                 alignPanel.av.getSequenceSelection(),
4986                                 alignPanel.alignFrame, dassource,
4987                                 alignPanel.alignFrame.featureSettings,
4988                                 isNucleotide);
4989                         dbRefFetcher
4990                                 .addListener(new FetchFinishedListenerI()
4991                                 {
4992                                   @Override
4993                                   public void finished()
4994                                   {
4995                                     AlignFrame.this.setMenusForViewport();
4996                                   }
4997                                 });
4998                         dbRefFetcher.fetchDBRefs(false);
4999                       }
5000                     }).start();
5001                   }
5002
5003                 });
5004                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5005                         MessageManager.formatMessage(
5006                                 "label.fetch_retrieve_from", new Object[]
5007                                 { src.getDbName() })));
5008                 dfetch.add(fetchr);
5009                 comp++;
5010               }
5011               else
5012               {
5013                 final DbSourceProxy[] dassource = otherdb
5014                         .toArray(new DbSourceProxy[0]);
5015                 // fetch all entry
5016                 DbSourceProxy src = otherdb.get(0);
5017                 fetchr = new JMenuItem(MessageManager
5018                         .formatMessage("label.fetch_all_param", new Object[]
5019                         { src.getDbSource() }));
5020                 fetchr.addActionListener(new ActionListener()
5021                 {
5022                   @Override
5023                   public void actionPerformed(ActionEvent e)
5024                   {
5025                     new Thread(new Runnable()
5026                     {
5027
5028                       @Override
5029                       public void run()
5030                       {
5031                         boolean isNucleotide = alignPanel.alignFrame
5032                                 .getViewport().getAlignment()
5033                                 .isNucleotide();
5034                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5035                                 alignPanel.av.getSequenceSelection(),
5036                                 alignPanel.alignFrame, dassource,
5037                                 alignPanel.alignFrame.featureSettings,
5038                                 isNucleotide);
5039                         dbRefFetcher
5040                                 .addListener(new FetchFinishedListenerI()
5041                                 {
5042                                   @Override
5043                                   public void finished()
5044                                   {
5045                                     AlignFrame.this.setMenusForViewport();
5046                                   }
5047                                 });
5048                         dbRefFetcher.fetchDBRefs(false);
5049                       }
5050                     }).start();
5051                   }
5052                 });
5053
5054                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5055                         MessageManager.formatMessage(
5056                                 "label.fetch_retrieve_from_all_sources",
5057                                 new Object[]
5058                                 { Integer.valueOf(otherdb.size())
5059                                         .toString(),
5060                                     src.getDbSource(), src.getDbName() })));
5061                 dfetch.add(fetchr);
5062                 comp++;
5063                 // and then build the rest of the individual menus
5064                 ifetch = new JMenu(MessageManager.formatMessage(
5065                         "label.source_from_db_source", new Object[]
5066                         { src.getDbSource() }));
5067                 icomp = 0;
5068                 String imname = null;
5069                 int i = 0;
5070                 for (DbSourceProxy sproxy : otherdb)
5071                 {
5072                   String dbname = sproxy.getDbName();
5073                   String sname = dbname.length() > 5
5074                           ? dbname.substring(0, 5) + "..."
5075                           : dbname;
5076                   String msname = dbname.length() > 10
5077                           ? dbname.substring(0, 10) + "..."
5078                           : dbname;
5079                   if (imname == null)
5080                   {
5081                     imname = MessageManager
5082                             .formatMessage("label.from_msname", new Object[]
5083                             { sname });
5084                   }
5085                   fetchr = new JMenuItem(msname);
5086                   final DbSourceProxy[] dassrc = { sproxy };
5087                   fetchr.addActionListener(new ActionListener()
5088                   {
5089
5090                     @Override
5091                     public void actionPerformed(ActionEvent e)
5092                     {
5093                       new Thread(new Runnable()
5094                       {
5095
5096                         @Override
5097                         public void run()
5098                         {
5099                           boolean isNucleotide = alignPanel.alignFrame
5100                                   .getViewport().getAlignment()
5101                                   .isNucleotide();
5102                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5103                                   alignPanel.av.getSequenceSelection(),
5104                                   alignPanel.alignFrame, dassrc,
5105                                   alignPanel.alignFrame.featureSettings,
5106                                   isNucleotide);
5107                           dbRefFetcher
5108                                   .addListener(new FetchFinishedListenerI()
5109                                   {
5110                                     @Override
5111                                     public void finished()
5112                                     {
5113                                       AlignFrame.this.setMenusForViewport();
5114                                     }
5115                                   });
5116                           dbRefFetcher.fetchDBRefs(false);
5117                         }
5118                       }).start();
5119                     }
5120
5121                   });
5122                   fetchr.setToolTipText(
5123                           "<html>" + MessageManager.formatMessage(
5124                                   "label.fetch_retrieve_from", new Object[]
5125                                   { dbname }));
5126                   ifetch.add(fetchr);
5127                   ++i;
5128                   if (++icomp >= mcomp || i == (otherdb.size()))
5129                   {
5130                     ifetch.setText(MessageManager.formatMessage(
5131                             "label.source_to_target", imname, sname));
5132                     dfetch.add(ifetch);
5133                     ifetch = new JMenu();
5134                     imname = null;
5135                     icomp = 0;
5136                     comp++;
5137                   }
5138                 }
5139               }
5140               ++dbi;
5141               if (comp >= mcomp || dbi >= (dbclasses.length))
5142               {
5143                 dfetch.setText(MessageManager.formatMessage(
5144                         "label.source_to_target", mname, dbclass));
5145                 rfetch.add(dfetch);
5146                 dfetch = new JMenu();
5147                 mname = null;
5148                 comp = 0;
5149               }
5150             }
5151           }
5152         });
5153       }
5154     }).start();
5155
5156   }
5157
5158   /**
5159    * Left justify the whole alignment.
5160    */
5161   @Override
5162   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5163   {
5164     AlignmentI al = viewport.getAlignment();
5165     al.justify(false);
5166     viewport.firePropertyChange("alignment", null, al);
5167   }
5168
5169   /**
5170    * Right justify the whole alignment.
5171    */
5172   @Override
5173   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5174   {
5175     AlignmentI al = viewport.getAlignment();
5176     al.justify(true);
5177     viewport.firePropertyChange("alignment", null, al);
5178   }
5179
5180   @Override
5181   public void setShowSeqFeatures(boolean b)
5182   {
5183     showSeqFeatures.setSelected(b);
5184     viewport.setShowSequenceFeatures(b);
5185   }
5186
5187   /*
5188    * (non-Javadoc)
5189    *
5190    * @see
5191    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5192    * awt.event.ActionEvent)
5193    */
5194   @Override
5195   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5196   {
5197     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5198     alignPanel.paintAlignment(false, false);
5199   }
5200
5201   /*
5202    * (non-Javadoc)
5203    *
5204    * @see
5205    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5206    * .ActionEvent)
5207    */
5208   @Override
5209   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5210   {
5211     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5212     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5213
5214   }
5215
5216   /*
5217    * (non-Javadoc)
5218    *
5219    * @see
5220    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5221    * .event.ActionEvent)
5222    */
5223   @Override
5224   protected void showGroupConservation_actionPerformed(ActionEvent e)
5225   {
5226     viewport.setShowGroupConservation(showGroupConservation.getState());
5227     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5228   }
5229
5230   /*
5231    * (non-Javadoc)
5232    *
5233    * @see
5234    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5235    * .event.ActionEvent)
5236    */
5237   @Override
5238   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5239   {
5240     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5241     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5242   }
5243
5244   /*
5245    * (non-Javadoc)
5246    *
5247    * @see
5248    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5249    * .event.ActionEvent)
5250    */
5251   @Override
5252   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5253   {
5254     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5255     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5256   }
5257
5258   @Override
5259   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5260   {
5261     showSequenceLogo.setState(true);
5262     viewport.setShowSequenceLogo(true);
5263     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5264     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5265   }
5266
5267   @Override
5268   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5269   {
5270     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5271   }
5272
5273   /*
5274    * (non-Javadoc)
5275    *
5276    * @see
5277    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5278    * .event.ActionEvent)
5279    */
5280   @Override
5281   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5282   {
5283     if (avc.makeGroupsFromSelection())
5284     {
5285       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5286       alignPanel.updateAnnotation();
5287       alignPanel.paintAlignment(true, true);
5288     }
5289   }
5290
5291   public void clearAlignmentSeqRep()
5292   {
5293     // TODO refactor alignmentseqrep to controller
5294     if (viewport.getAlignment().hasSeqrep())
5295     {
5296       viewport.getAlignment().setSeqrep(null);
5297       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5298       alignPanel.updateAnnotation();
5299       alignPanel.paintAlignment(true, true);
5300     }
5301   }
5302
5303   @Override
5304   protected void createGroup_actionPerformed(ActionEvent e)
5305   {
5306     if (avc.createGroup())
5307     {
5308       if (applyAutoAnnotationSettings.isSelected())
5309       {
5310         alignPanel.updateAnnotation(true, false);
5311       }
5312       alignPanel.alignmentChanged();
5313     }
5314   }
5315
5316   @Override
5317   protected void unGroup_actionPerformed(ActionEvent e)
5318   {
5319     if (avc.unGroup())
5320     {
5321       alignPanel.alignmentChanged();
5322     }
5323   }
5324
5325   /**
5326    * make the given alignmentPanel the currently selected tab
5327    *
5328    * @param alignmentPanel
5329    */
5330   public void setDisplayedView(AlignmentPanel alignmentPanel)
5331   {
5332     if (!viewport.getSequenceSetId()
5333             .equals(alignmentPanel.av.getSequenceSetId()))
5334     {
5335       throw new Error(MessageManager.getString(
5336               "error.implementation_error_cannot_show_view_alignment_frame"));
5337     }
5338     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5339             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5340     {
5341       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5342     }
5343   }
5344
5345   /**
5346    * Action on selection of menu options to Show or Hide annotations.
5347    *
5348    * @param visible
5349    * @param forSequences
5350    *          update sequence-related annotations
5351    * @param forAlignment
5352    *          update non-sequence-related annotations
5353    */
5354   @Override
5355   protected void setAnnotationsVisibility(boolean visible,
5356           boolean forSequences, boolean forAlignment)
5357   {
5358     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5359             .getAlignmentAnnotation();
5360     if (anns == null)
5361     {
5362       return;
5363     }
5364     for (AlignmentAnnotation aa : anns)
5365     {
5366       /*
5367        * don't display non-positional annotations on an alignment
5368        */
5369       if (aa.annotations == null)
5370       {
5371         continue;
5372       }
5373       boolean apply = (aa.sequenceRef == null && forAlignment)
5374               || (aa.sequenceRef != null && forSequences);
5375       if (apply)
5376       {
5377         aa.visible = visible;
5378       }
5379     }
5380     alignPanel.validateAnnotationDimensions(true);
5381     alignPanel.alignmentChanged();
5382   }
5383
5384   /**
5385    * Store selected annotation sort order for the view and repaint.
5386    */
5387   @Override
5388   protected void sortAnnotations_actionPerformed()
5389   {
5390     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5391     this.alignPanel.av
5392             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5393     alignPanel.paintAlignment(false, false);
5394   }
5395
5396   /**
5397    *
5398    * @return alignment panels in this alignment frame
5399    */
5400   public List<? extends AlignmentViewPanel> getAlignPanels()
5401   {
5402     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5403   }
5404
5405   /**
5406    * Open a new alignment window, with the cDNA associated with this (protein)
5407    * alignment, aligned as is the protein.
5408    */
5409   protected void viewAsCdna_actionPerformed()
5410   {
5411     // TODO no longer a menu action - refactor as required
5412     final AlignmentI alignment = getViewport().getAlignment();
5413     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5414     if (mappings == null)
5415     {
5416       return;
5417     }
5418     List<SequenceI> cdnaSeqs = new ArrayList<>();
5419     for (SequenceI aaSeq : alignment.getSequences())
5420     {
5421       for (AlignedCodonFrame acf : mappings)
5422       {
5423         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5424         if (dnaSeq != null)
5425         {
5426           /*
5427            * There is a cDNA mapping for this protein sequence - add to new
5428            * alignment. It will share the same dataset sequence as other mapped
5429            * cDNA (no new mappings need to be created).
5430            */
5431           final Sequence newSeq = new Sequence(dnaSeq);
5432           newSeq.setDatasetSequence(dnaSeq);
5433           cdnaSeqs.add(newSeq);
5434         }
5435       }
5436     }
5437     if (cdnaSeqs.size() == 0)
5438     {
5439       // show a warning dialog no mapped cDNA
5440       return;
5441     }
5442     AlignmentI cdna = new Alignment(
5443             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5444     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5445             AlignFrame.DEFAULT_HEIGHT);
5446     cdna.alignAs(alignment);
5447     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5448             + this.title;
5449     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5450             AlignFrame.DEFAULT_HEIGHT);
5451   }
5452
5453   /**
5454    * Set visibility of dna/protein complement view (available when shown in a
5455    * split frame).
5456    *
5457    * @param show
5458    */
5459   @Override
5460   protected void showComplement_actionPerformed(boolean show)
5461   {
5462     SplitContainerI sf = getSplitViewContainer();
5463     if (sf != null)
5464     {
5465       sf.setComplementVisible(this, show);
5466     }
5467   }
5468
5469   /**
5470    * Generate the reverse (optionally complemented) of the selected sequences,
5471    * and add them to the alignment
5472    */
5473   @Override
5474   protected void showReverse_actionPerformed(boolean complement)
5475   {
5476     AlignmentI al = null;
5477     try
5478     {
5479       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5480       al = dna.reverseCdna(complement);
5481       viewport.addAlignment(al, "");
5482       addHistoryItem(new EditCommand(
5483               MessageManager.getString("label.add_sequences"), Action.PASTE,
5484               al.getSequencesArray(), 0, al.getWidth(),
5485               viewport.getAlignment()));
5486     } catch (Exception ex)
5487     {
5488       System.err.println(ex.getMessage());
5489       return;
5490     }
5491   }
5492
5493   /**
5494    * Try to run a script in the Groovy console, having first ensured that this
5495    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5496    * be targeted at this alignment.
5497    */
5498   @Override
5499   protected void runGroovy_actionPerformed()
5500   {
5501     Jalview.setCurrentAlignFrame(this);
5502     groovy.ui.Console console = Desktop.getGroovyConsole();
5503     if (console != null)
5504     {
5505       try
5506       {
5507         console.runScript();
5508       } catch (Exception ex)
5509       {
5510         System.err.println((ex.toString()));
5511         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5512                 MessageManager.getString("label.couldnt_run_groovy_script"),
5513                 MessageManager.getString("label.groovy_support_failed"),
5514                 JvOptionPane.ERROR_MESSAGE);
5515       }
5516     }
5517     else
5518     {
5519       System.err.println("Can't run Groovy script as console not found");
5520     }
5521   }
5522
5523   /**
5524    * Hides columns containing (or not containing) a specified feature, provided
5525    * that would not leave all columns hidden
5526    *
5527    * @param featureType
5528    * @param columnsContaining
5529    * @return
5530    */
5531   public boolean hideFeatureColumns(String featureType,
5532           boolean columnsContaining)
5533   {
5534     boolean notForHiding = avc.markColumnsContainingFeatures(
5535             columnsContaining, false, false, featureType);
5536     if (notForHiding)
5537     {
5538       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5539               false, featureType))
5540       {
5541         getViewport().hideSelectedColumns();
5542         return true;
5543       }
5544     }
5545     return false;
5546   }
5547
5548   @Override
5549   protected void selectHighlightedColumns_actionPerformed(
5550           ActionEvent actionEvent)
5551   {
5552     // include key modifier check in case user selects from menu
5553     avc.markHighlightedColumns(
5554             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5555             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5556                     | ActionEvent.CTRL_MASK)) != 0);
5557   }
5558
5559   /**
5560    * Rebuilds the Colour menu, including any user-defined colours which have
5561    * been loaded either on startup or during the session
5562    */
5563   public void buildColourMenu()
5564   {
5565     colourMenu.removeAll();
5566
5567     colourMenu.add(applyToAllGroups);
5568     colourMenu.add(textColour);
5569     colourMenu.addSeparator();
5570
5571     ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5572             false);
5573
5574     colourMenu.addSeparator();
5575     colourMenu.add(conservationMenuItem);
5576     colourMenu.add(modifyConservation);
5577     colourMenu.add(abovePIDThreshold);
5578     colourMenu.add(modifyPID);
5579     colourMenu.add(annotationColour);
5580
5581     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5582     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5583   }
5584
5585   /**
5586    * Open a dialog (if not already open) that allows the user to select and
5587    * calculate PCA or Tree analysis
5588    */
5589   protected void openTreePcaDialog()
5590   {
5591     if (alignPanel.getCalculationDialog() == null)
5592     {
5593       new CalculationChooser(AlignFrame.this);
5594     }
5595   }
5596
5597   @Override
5598   protected void loadVcf_actionPerformed()
5599   {
5600     JalviewFileChooser chooser = new JalviewFileChooser(
5601             Cache.getProperty("LAST_DIRECTORY"));
5602     chooser.setFileView(new JalviewFileView());
5603     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5604     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5605
5606     int value = chooser.showOpenDialog(null);
5607
5608     if (value == JalviewFileChooser.APPROVE_OPTION)
5609     {
5610       String choice = chooser.getSelectedFile().getPath();
5611       Cache.setProperty("LAST_DIRECTORY", choice);
5612       SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5613       new VCFLoader(choice).loadVCF(seqs, this);
5614     }
5615
5616   }
5617 }
5618
5619 class PrintThread extends Thread
5620 {
5621   AlignmentPanel ap;
5622
5623   public PrintThread(AlignmentPanel ap)
5624   {
5625     this.ap = ap;
5626   }
5627
5628   static PageFormat pf;
5629
5630   @Override
5631   public void run()
5632   {
5633     PrinterJob printJob = PrinterJob.getPrinterJob();
5634
5635     if (pf != null)
5636     {
5637       printJob.setPrintable(ap, pf);
5638     }
5639     else
5640     {
5641       printJob.setPrintable(ap);
5642     }
5643
5644     if (printJob.printDialog())
5645     {
5646       try
5647       {
5648         printJob.print();
5649       } catch (Exception PrintException)
5650       {
5651         PrintException.printStackTrace();
5652       }
5653     }
5654   }
5655 }